From 993a81e80daea4aa40fbc42b2a3d5dadc7d23f84 Mon Sep 17 00:00:00 2001 From: Wild Me Date: Mon, 20 Apr 2026 06:59:40 -0700 Subject: [PATCH 1/7] Obscure Shepherd leaks --- src/main/java/org/ecocean/OpenSearch.java | 54 ++--- src/main/java/org/ecocean/api/BulkImport.java | 32 +-- .../java/org/ecocean/identity/IBEISIA.java | 208 +++++++++--------- .../java/org/ecocean/servlet/RestServlet.java | 12 + .../org/ecocean/shepherd/core/Shepherd.java | 28 ++- 5 files changed, 184 insertions(+), 150 deletions(-) diff --git a/src/main/java/org/ecocean/OpenSearch.java b/src/main/java/org/ecocean/OpenSearch.java index 25d2b4ced1..c0a0c24c50 100644 --- a/src/main/java/org/ecocean/OpenSearch.java +++ b/src/main/java/org/ecocean/OpenSearch.java @@ -167,27 +167,27 @@ public void run() { } private static void updatePermissionsIndex(String context) { - Shepherd myShepherd = new Shepherd(context); - - myShepherd.setAction("OpenSearch.backgroundPermissions"); + Shepherd myShepherd = null; try { + myShepherd = new Shepherd(context); + myShepherd.setAction("OpenSearch.backgroundPermissions"); myShepherd.beginDBTransaction(); System.out.println("OpenSearch background permissions running..."); Encounter.opensearchIndexPermissionsBackground(myShepherd); System.out.println("OpenSearch background permissions finished."); myShepherd.commitDBTransaction(); // need commit since we might have changed SystemValues - myShepherd.closeDBTransaction(); } catch (Exception ex) { ex.printStackTrace(); - myShepherd.rollbackAndClose(); + } finally { + if (myShepherd != null) myShepherd.rollbackAndClose(); } } public static void updateEncounterIndexes(String context) { - Shepherd myShepherd = new Shepherd(context); - - myShepherd.setAction("OpenSearch.backgroundIndexing"); + Shepherd myShepherd = null; try { + myShepherd = new Shepherd(context); + myShepherd.setAction("OpenSearch.backgroundIndexing"); myShepherd.beginDBTransaction(); System.out.println("OpenSearch background indexing running..."); Base.opensearchSyncIndex(myShepherd, Encounter.class, BACKGROUND_SLICE_SIZE); @@ -199,7 +199,7 @@ public static void updateEncounterIndexes(String context) { } catch (Exception ex) { ex.printStackTrace(); } finally { - myShepherd.rollbackAndClose(); + if (myShepherd != null) myShepherd.rollbackAndClose(); unsetActiveIndexingBackground(); } } @@ -663,17 +663,17 @@ public static void setPermissionsNeeded(Shepherd myShepherd, boolean value) { } public static void setPermissionsNeeded(boolean value) { - Shepherd myShepherd = new Shepherd("context0"); - - myShepherd.setAction("OpenSearch.setPermissionsNeeded"); - myShepherd.beginDBTransaction(); + Shepherd myShepherd = null; try { + myShepherd = new Shepherd("context0"); + myShepherd.setAction("OpenSearch.setPermissionsNeeded"); + myShepherd.beginDBTransaction(); setPermissionsNeeded(myShepherd, value); myShepherd.commitDBTransaction(); - myShepherd.closeDBTransaction(); } catch (Exception ex) { ex.printStackTrace(); - myShepherd.rollbackAndClose(); + } finally { + if (myShepherd != null) myShepherd.rollbackAndClose(); } } @@ -783,32 +783,32 @@ public static void unsetActiveIndexingBackground() { static void setActive(String type) { // we want our own shepherd as the main shepherd may not persist this til later - Shepherd myShepherd = new Shepherd("context0"); - - myShepherd.setAction("OpenSearch.setActive"); - myShepherd.beginDBTransaction(); + Shepherd myShepherd = null; try { + myShepherd = new Shepherd("context0"); + myShepherd.setAction("OpenSearch.setActive"); + myShepherd.beginDBTransaction(); SystemValue.set(myShepherd, type, true); myShepherd.commitDBTransaction(); - myShepherd.closeDBTransaction(); } catch (Exception ex) { ex.printStackTrace(); - myShepherd.rollbackAndClose(); + } finally { + if (myShepherd != null) myShepherd.rollbackAndClose(); } } static void unsetActive(String type) { - Shepherd myShepherd = new Shepherd("context0"); - - myShepherd.setAction("OpenSearch.unsetActive"); - myShepherd.beginDBTransaction(); + Shepherd myShepherd = null; try { + myShepherd = new Shepherd("context0"); + myShepherd.setAction("OpenSearch.unsetActive"); + myShepherd.beginDBTransaction(); SystemValue.set(myShepherd, type, false); myShepherd.commitDBTransaction(); - myShepherd.closeDBTransaction(); } catch (Exception ex) { ex.printStackTrace(); - myShepherd.rollbackAndClose(); + } finally { + if (myShepherd != null) myShepherd.rollbackAndClose(); } } diff --git a/src/main/java/org/ecocean/api/BulkImport.java b/src/main/java/org/ecocean/api/BulkImport.java index c371fd4df4..8b81e69f94 100644 --- a/src/main/java/org/ecocean/api/BulkImport.java +++ b/src/main/java/org/ecocean/api/BulkImport.java @@ -36,13 +36,13 @@ protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { String context = ServletUtilities.getContext(request); int statusCode = 500; - Shepherd myShepherd = new Shepherd(context); - - myShepherd.setAction("api.Bulk.doGet"); - myShepherd.beginDBTransaction(); JSONObject rtn = new JSONObject("{\"success\": false}"); + Shepherd myShepherd = null; try { + myShepherd = new Shepherd(context); + myShepherd.setAction("api.Bulk.doGet"); + myShepherd.beginDBTransaction(); User currentUser = myShepherd.getUser(request); if (currentUser == null) { response.setStatus(401); @@ -121,7 +121,7 @@ protected void doGet(HttpServletRequest request, HttpServletResponse response) } catch (Exception ex) { ex.printStackTrace(); } finally { - myShepherd.rollbackAndClose(); + if (myShepherd != null) myShepherd.rollbackAndClose(); } rtn.put("statusCode", statusCode); response.setStatus(statusCode); @@ -144,12 +144,13 @@ protected void doPost(HttpServletRequest request, HttpServletResponse response) JSONObject encAssets = null; String dupId = null; // gets set as bulkImporId to be used in finally block long startProcess = System.currentTimeMillis(); - Shepherd myShepherd = new Shepherd(context); + Shepherd myShepherd = null; - myShepherd.setAction("api.Bulk.doPost"); - myShepherd.beginDBTransaction(); long startTime = System.currentTimeMillis(); try { + myShepherd = new Shepherd(context); + myShepherd.setAction("api.Bulk.doPost"); + myShepherd.beginDBTransaction(); User currentUser = myShepherd.getUser(request); if (currentUser == null) { response.setStatus(401); @@ -416,10 +417,11 @@ protected void doPost(HttpServletRequest request, HttpServletResponse response) final boolean bgSkipDetection = skipDetection; final boolean bgSkipIdentification = skipIdentification; final String currentUsername = currentUser.getUsername(); + final String bgContext = myShepherd.getContext(); Runnable r = new Runnable() { public void run() { // make our background thread safely use our own Shepherd - Shepherd bgShepherd = new Shepherd(myShepherd.getContext()); + Shepherd bgShepherd = new Shepherd(bgContext); bgShepherd.setAction("api.Bulk.processBackground"); bgShepherd.beginDBTransaction(); @@ -618,12 +620,14 @@ public void run() { statusCode = 500; ex.printStackTrace(); } finally { - if ((statusCode == 200) && !validateOnly) { - myShepherd.commitDBTransaction(); - } else { - myShepherd.rollbackDBTransaction(); + if (myShepherd != null) { + if ((statusCode == 200) && !validateOnly) { + myShepherd.commitDBTransaction(); + } else { + myShepherd.rollbackDBTransaction(); + } + myShepherd.closeDBTransaction(); } - myShepherd.closeDBTransaction(); if ((statusCode == 200) && !skipDetection) initiateIA(dupId, skipIdentification, encAssets, matchingSetFilter); } diff --git a/src/main/java/org/ecocean/identity/IBEISIA.java b/src/main/java/org/ecocean/identity/IBEISIA.java index 43ae4650d8..6cd456c41c 100644 --- a/src/main/java/org/ecocean/identity/IBEISIA.java +++ b/src/main/java/org/ecocean/identity/IBEISIA.java @@ -1384,122 +1384,134 @@ public static JSONObject processCallback(String taskID, JSONObject resp, String JSONObject rtn = new JSONObject("{\"success\": false}"); rtn.put("taskId", taskID); if (taskID == null) return rtn; + + JSONObject newAnns = null; Shepherd myShepherd = new Shepherd(context); myShepherd.setAction("IBEISIA.processCallback"); myShepherd.beginDBTransaction(); - ArrayList logs = IdentityServiceLog.loadByTaskID(taskID, "IBEISIA", - myShepherd); - rtn.put("_logs", logs); - if ((logs == null) || (logs.size() < 1)) return rtn; - JSONObject newAnns = null; - String type = getTaskType(logs); - System.out.println("**** type ---------------> [" + type + "]"); - if ("detect".equals(type)) { - rtn.put("success", true); - JSONObject dres = processCallbackDetect(taskID, logs, resp, myShepherd, context, - rootDir); - rtn.put("processResult", dres); - /* - for detection, we have to check if we have generated any Annotations, which we then pass on to IA.intake() for identification ... BUT - * only after we commit* (below) !! since ident stuff is queue-based - */ - newAnns = dres.optJSONObject("annotations"); - } else if ("identify".equals(type)) { - rtn.put("success", true); - rtn.put("processResult", processCallbackIdentify(taskID, logs, resp, context, rootDir)); - } else { - rtn.put("error", "unknown task action type " + type); + try { + ArrayList logs = IdentityServiceLog.loadByTaskID(taskID, "IBEISIA", + myShepherd); + rtn.put("_logs", logs); + if ((logs == null) || (logs.size() < 1)) return rtn; + String type = getTaskType(logs); + System.out.println("**** type ---------------> [" + type + "]"); + if ("detect".equals(type)) { + rtn.put("success", true); + JSONObject dres = processCallbackDetect(taskID, logs, resp, myShepherd, context, + rootDir); + rtn.put("processResult", dres); + /* + for detection, we have to check if we have generated any Annotations, which we then pass on to IA.intake() for identification ... BUT + * only after we commit* (below) !! since ident stuff is queue-based + */ + newAnns = dres.optJSONObject("annotations"); + } else if ("identify".equals(type)) { + rtn.put("success", true); + rtn.put("processResult", processCallbackIdentify(taskID, logs, resp, context, + rootDir)); + } else { + rtn.put("error", "unknown task action type " + type); + } + myShepherd.commitDBTransaction(); + } finally { + // Always run rollbackAndClose: rollback is a no-op once commit has landed, and close + // must run on every path (including the early return when logs is empty) so the PM + // and its pooled connection are released. + myShepherd.rollbackAndClose(); } - myShepherd.commitDBTransaction(); - myShepherd.closeDBTransaction(); boolean skipIdent = Util.booleanNotFalse(IA.getProperty(context, "IBEISIADisableIdentification")); // now we pick up IA.intake(anns) from detection above (if applicable) // should we cluster these based on MediaAsset instead? send them in groups to IA.intake()? if (!skipIdent && (newAnns != null)) { - List needIdentifying = new ArrayList(); - Shepherd myShepherd2 = new Shepherd(context); - myShepherd2.setAction("IBEISIA.processCallback-IA.intake"); - myShepherd2.beginDBTransaction(); - Task parentTask = Task.load(taskID, myShepherd2); - // Task parametersSkipIdent looks at the parent task.. It works for non-ID Wildbooks. If you are sending multiple annotations from a - // single image, and some need - // ID, some don't, you need to check downstream. - if (taskParametersSkipIdent(parentTask)) { - System.out.println("NOTICE: IBEISIA.processCallback() " + parentTask + - " skipped identification"); - } else { - Iterator keys = newAnns.keys(); - while (keys.hasNext()) { - String maId = (String)keys.next(); - System.out.println("maId -> " + maId); - JSONArray annIds = newAnns.optJSONArray(maId); - if (annIds == null) continue; - System.out.println(" ---> " + annIds); - for (int i = 0; i < annIds.length(); i++) { - String aid = annIds.optString(i, null); - if (aid == null) continue; - Annotation ann = ((Annotation)(myShepherd2.getPM().getObjectById( - myShepherd2.getPM().newObjectIdInstance(Annotation.class, aid), true))); - if (ann != null && IBEISIA.validForIdentification(ann, - myShepherd2.getContext())) { - needIdentifying.add(ann); + Shepherd myShepherd2 = null; + try { + myShepherd2 = new Shepherd(context); + myShepherd2.setAction("IBEISIA.processCallback-IA.intake"); + myShepherd2.beginDBTransaction(); + List needIdentifying = new ArrayList(); + Task parentTask = Task.load(taskID, myShepherd2); + // Task parametersSkipIdent looks at the parent task.. It works for non-ID Wildbooks. If you are sending multiple annotations from a + // single image, and some need + // ID, some don't, you need to check downstream. + if (taskParametersSkipIdent(parentTask)) { + System.out.println("NOTICE: IBEISIA.processCallback() " + parentTask + + " skipped identification"); + } else { + Iterator keys = newAnns.keys(); + while (keys.hasNext()) { + String maId = (String)keys.next(); + System.out.println("maId -> " + maId); + JSONArray annIds = newAnns.optJSONArray(maId); + if (annIds == null) continue; + System.out.println(" ---> " + annIds); + for (int i = 0; i < annIds.length(); i++) { + String aid = annIds.optString(i, null); + if (aid == null) continue; + Annotation ann = ((Annotation)(myShepherd2.getPM().getObjectById( + myShepherd2.getPM().newObjectIdInstance(Annotation.class, aid), + true))); + if (ann != null && IBEISIA.validForIdentification(ann, + myShepherd2.getContext())) { + needIdentifying.add(ann); + } } } } - } - if (needIdentifying.size() > 0) { - // split the results into encounters - HashMap > needIdentifyingMap = new HashMap >(); - for (Annotation annot : needIdentifying) { - Encounter enc = annot.findEncounter(myShepherd2); - if (enc != null) { - if (needIdentifyingMap.containsKey(enc.getCatalogNumber())) { - ArrayList annots = needIdentifyingMap.get( - enc.getCatalogNumber()); - annots.add(annot); - needIdentifyingMap.put(enc.getCatalogNumber(), annots); - } else { - ArrayList annots = new ArrayList(); - annots.add(annot); - needIdentifyingMap.put(enc.getCatalogNumber(), annots); + if (needIdentifying.size() > 0) { + // split the results into encounters + HashMap > needIdentifyingMap = new HashMap >(); + for (Annotation annot : needIdentifying) { + Encounter enc = annot.findEncounter(myShepherd2); + if (enc != null) { + if (needIdentifyingMap.containsKey(enc.getCatalogNumber())) { + ArrayList annots = needIdentifyingMap.get( + enc.getCatalogNumber()); + annots.add(annot); + needIdentifyingMap.put(enc.getCatalogNumber(), annots); + } else { + ArrayList annots = new ArrayList(); + annots.add(annot); + needIdentifyingMap.put(enc.getCatalogNumber(), annots); + } } } - } - // send to ID by Encounter - for (String encUUID : needIdentifyingMap.keySet()) { - ArrayList annots = needIdentifyingMap.get(encUUID); - JSONObject taskParameters = new JSONObject(); - JSONObject mf = new JSONObject(); - Encounter enc = myShepherd2.getEncounter(encUUID); - if (enc != null && enc.getLocationID() != null) { - ArrayList locationIDs = new ArrayList(); - List matchTheseLocationIDs = LocationID.getIDForParentAndChildren( - enc.getLocationID(), locationIDs, null); - mf.put("locationIds", matchTheseLocationIDs); + // send to ID by Encounter + for (String encUUID : needIdentifyingMap.keySet()) { + ArrayList annots = needIdentifyingMap.get(encUUID); + JSONObject taskParameters = new JSONObject(); + JSONObject mf = new JSONObject(); + Encounter enc = myShepherd2.getEncounter(encUUID); + if (enc != null && enc.getLocationID() != null) { + ArrayList locationIDs = new ArrayList(); + List matchTheseLocationIDs = + LocationID.getIDForParentAndChildren(enc.getLocationID(), + locationIDs, null); + mf.put("locationIds", matchTheseLocationIDs); + } + taskParameters.put("matchingSetFilter", mf); + Task subParentTask = new Task(); + subParentTask.setParameters(taskParameters); + myShepherd2.storeNewTask(subParentTask); + myShepherd2.updateDBTransaction(); + + Task childTask = IA.intakeAnnotations(myShepherd2, annots, subParentTask, + false); + myShepherd2.storeNewTask(childTask); + myShepherd2.updateDBTransaction(); + subParentTask.addChild(childTask); + myShepherd2.updateDBTransaction(); } - taskParameters.put("matchingSetFilter", mf); - Task subParentTask = new Task(); - subParentTask.setParameters(taskParameters); - myShepherd2.storeNewTask(subParentTask); - myShepherd2.updateDBTransaction(); - - - Task childTask = IA.intakeAnnotations(myShepherd2, annots, subParentTask, - false); - myShepherd2.storeNewTask(childTask); - myShepherd2.updateDBTransaction(); - subParentTask.addChild(childTask); - myShepherd2.updateDBTransaction(); + } else { + System.out.println( + "[INFO]: No annotations were suitable for identification. Check resulting identification class(es)."); } - } else { - System.out.println( - "[INFO]: No annotations were suitable for identification. Check resulting identification class(es)."); - myShepherd2.rollbackDBTransaction(); + } finally { + if (myShepherd2 != null) myShepherd2.rollbackAndClose(); } - myShepherd2.rollbackAndClose(); } return rtn; } diff --git a/src/main/java/org/ecocean/servlet/RestServlet.java b/src/main/java/org/ecocean/servlet/RestServlet.java index 1f8f9ec0cf..81dd005cdf 100644 --- a/src/main/java/org/ecocean/servlet/RestServlet.java +++ b/src/main/java/org/ecocean/servlet/RestServlet.java @@ -422,6 +422,7 @@ protected void doPost(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException { resp.setHeader("Access-Control-Allow-Origin", "*"); String servletID = Util.generateUUID(); + try { getPMF(req, servletID); if (req.getContentLength() < 1) { resp.setContentLength(0); @@ -525,12 +526,16 @@ protected void doPost(HttpServletRequest req, HttpServletResponse resp) pm.close(); } resp.setStatus(201); // created + } finally { + ShepherdState.removeShepherdState("RestServlet.class" + "_" + servletID); + } } protected void doDelete(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException { String servletID = Util.generateUUID(); + try { getPMF(req, servletID); PersistenceManager pm = pmf.getPersistenceManager(); try { @@ -607,12 +612,16 @@ protected void doDelete(HttpServletRequest req, HttpServletResponse resp) } resp.setContentLength(0); resp.setStatus(204); // created + } finally { + ShepherdState.removeShepherdState("RestServlet.class" + "_" + servletID); + } } protected void doHead(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException { String servletID = Util.generateUUID(); + try { getPMF(req, servletID); String className = getNextTokenAfterSlash(req); ClassLoaderResolver clr = nucCtx.getClassLoaderResolver(RestServlet.class.getClassLoader()); @@ -677,6 +686,9 @@ protected void doHead(HttpServletRequest req, HttpServletResponse resp) } pm.close(); } + } finally { + ShepherdState.removeShepherdState("RestServlet.class" + "_" + servletID); + } } boolean restAccessCheck(Object obj, HttpServletRequest req, JSONObject jsonobj) { diff --git a/src/main/java/org/ecocean/shepherd/core/Shepherd.java b/src/main/java/org/ecocean/shepherd/core/Shepherd.java index a5c250703a..f1bb53f632 100644 --- a/src/main/java/org/ecocean/shepherd/core/Shepherd.java +++ b/src/main/java/org/ecocean/shepherd/core/Shepherd.java @@ -3301,22 +3301,26 @@ public void updateDBTransaction() { * Closes a PersistenceManager */ public void closeDBTransaction() { + boolean closed = false; try { if ((pm != null) && (!pm.isClosed())) { pm.close(); } - // ShepherdState.setShepherdState(action+"_"+shepherdID, "close"); - ShepherdState.removeShepherdState(action + "_" + shepherdID); - - // logger.info("A PersistenceManager has been successfully closed."); + closed = true; } catch (JDOUserException jdoe) { System.out.println("I hit an error trying to close a DBTransaction."); jdoe.printStackTrace(); - - // logger.error("I failed to close a PersistenceManager."+"\n"+jdoe.getStackTrace()); } catch (NullPointerException npe) { System.out.println("I hit a NullPointerException trying to close a DBTransaction."); npe.printStackTrace(); + } finally { + // Only clear the diagnostic state entry if the close actually succeeded. + // If it threw, leave evidence behind so dbconnections.jsp can surface the leak. + if (closed) { + ShepherdState.removeShepherdState(action + "_" + shepherdID); + } else { + ShepherdState.setShepherdState(action + "_" + shepherdID, "close-failed"); + } } } @@ -3324,21 +3328,23 @@ public void closeDBTransaction() { * Undoes any changes made to an open database. */ public void rollbackDBTransaction() { + boolean rolledBack = false; try { if ((pm != null) && (pm.currentTransaction().isActive())) { - // System.out.println(" Now rollingback a transaction with pm"+(String)pm.getUserObject()); pm.currentTransaction().rollback(); - // System.out.println("A transaction has been successfully committed."); - } else { - // System.out.println("You are trying to rollback an inactive transaction."); } - ShepherdState.setShepherdState(action + "_" + shepherdID, "rollback"); + rolledBack = true; } catch (JDOUserException jdoe) { jdoe.printStackTrace(); } catch (JDOFatalUserException fdoe) { fdoe.printStackTrace(); } catch (NullPointerException npe) { npe.printStackTrace(); + } finally { + // Always publish a terminal rollback state so leaked "begin" entries do not accumulate, + // but distinguish success from failure so close-follow-up can see the evidence. + ShepherdState.setShepherdState(action + "_" + shepherdID, + rolledBack ? "rollback" : "rollback-failed"); } } From 31cd46c65f50f500f0c17d8d9248f83e14a22dd6 Mon Sep 17 00:00:00 2001 From: JasonWildMe Date: Wed, 22 Apr 2026 13:35:10 -0700 Subject: [PATCH 2/7] Wrap scanEndApplet.jsp Shepherds in try/finally Both Shepherds in scanEndApplet.jsp previously had their close calls outside any try/finally. The `indShepherd` block (lines 603-786) was the source of accumulating `scanEndApplet.jsp_displayNames:begin` entries on Sharkbook dbconnections.jsp: any exception during `xmlReader.read(file)` on a partially-written scan XML, or any `getMarkedIndividual` failure, skipped the close, and the page auto-refreshes every 15s during active scans. Wraps both Shepherds with try { ... } finally { rollbackAndClose(); } matching the pattern used elsewhere in this branch. Co-Authored-By: Claude Opus 4.7 (1M context) --- src/main/webapp/encounters/scanEndApplet.jsp | 1646 +++++++++--------- 1 file changed, 824 insertions(+), 822 deletions(-) diff --git a/src/main/webapp/encounters/scanEndApplet.jsp b/src/main/webapp/encounters/scanEndApplet.jsp index 6b07cf5489..46eac65762 100755 --- a/src/main/webapp/encounters/scanEndApplet.jsp +++ b/src/main/webapp/encounters/scanEndApplet.jsp @@ -1,822 +1,824 @@ - - - -<%@ page contentType="text/html; charset=iso-8859-1" language="java" - import="org.ecocean.servlet.ServletUtilities,org.dom4j.Document, org.dom4j.Element,org.dom4j.io.SAXReader, org.ecocean.*, org.ecocean.grid.MatchComparator, org.ecocean.grid.MatchObject, org.ecocean.grid.GridManager, org.ecocean.grid.GridManagerFactory, java.io.File, java.util.Arrays, java.util.Iterator, java.util.List, -org.ecocean.grid.ScanTask, -java.util.ArrayList, -org.json.JSONArray, -java.text.MessageFormat, -java.util.Properties, -java.util.Vector" %> -<%@ page import="org.ecocean.shepherd.core.Shepherd" %> -<%@ page import="org.ecocean.shepherd.core.ShepherdProperties" %> - -<% - -String context="context0"; -context=ServletUtilities.getContext(request); - -//let's set up references to our file system components -String rootWebappPath = getServletContext().getRealPath("/"); -File webappsDir = new File(rootWebappPath).getParentFile(); -File shepherdDataDir = new File(webappsDir, CommonConfiguration.getDataDirectoryName(context)); -File encountersDir=new File(shepherdDataDir.getAbsolutePath()+"/encounters"); - - String num=""; - ArrayList locationIDs = new ArrayList(); - boolean scanInProgress = false; - boolean scanTaskExists = false; - int numComplete = 0; - int numTotal = 0; - long scanTaskStartTime = -1; - - if(request.getParameter("number")!=null){ - Shepherd myShepherd=new Shepherd(context); - myShepherd.setAction("scanEndApplet.jsp"); - myShepherd.beginDBTransaction(); - if(myShepherd.isEncounter(ServletUtilities.preventCrossSiteScriptingAttacks(request.getParameter("number")))){ - num = ServletUtilities.preventCrossSiteScriptingAttacks(request.getParameter("number")); - } - - //get any scantask locationID lists and check scan status - String taskID = request.getParameter("taskID"); - boolean isRightSide = (request.getParameter("rightSide") != null) && request.getParameter("rightSide").equals("true"); - if (taskID == null) taskID = "scan" + (isRightSide ? "R" : "L") + num; - if(taskID != null) { - ScanTask st=myShepherd.getScanTask(taskID); - if(st!=null){ - scanTaskExists = true; - if(st.getLocationIDFilters()!=null){ - locationIDs=st.getLocationIDFilters(); - } - if(!st.hasFinished()){ - scanInProgress = true; - scanTaskStartTime = st.getStartTime(); - // Check how much work is done via GridManager - GridManager gm = GridManagerFactory.getGridManager(); - numComplete = gm.getNumWorkItemsCompleteForTask(taskID); - numTotal = numComplete + gm.getNumWorkItemsIncompleteForTask(taskID); - } - } - } - myShepherd.rollbackDBTransaction(); - myShepherd.closeDBTransaction(); - } - String encSubdir = Encounter.subdir(num); - - String sessionId = session.getId(); - boolean xmlOK = false; - SAXReader xmlReader = new SAXReader(); - File file = new File("foo"); - String scanDate = ""; - String C = ""; - String R = ""; - String epsilon = ""; - String Sizelim = ""; - String maxTriangleRotation = ""; - String side2 = ""; - - // Determine the language for i18n - String langCode = "en"; - if (session.getAttribute("langCode") != null) langCode = (String) session.getAttribute("langCode"); - Properties i18n = ShepherdProperties.getProperties("commonConfigurationLabels.properties", langCode, context); -%> - - - - -<% -// If scan is in progress, add auto-refresh -if (scanInProgress) { -%> - -<% -} -%> - -
- -
    -
  • Encounter - <%=num%> -
    • - - - <% - String fileSider = ""; - File finalXMLFile; - File locationIDXMLFile; - if ((request.getParameter("rightSide") != null) && (request.getParameter("rightSide").equals("true"))) { - finalXMLFile = new File(encountersDir.getAbsolutePath()+"/"+ encSubdir + "/lastFullRightI3SScan.xml"); - locationIDXMLFile = new File(encountersDir.getAbsolutePath()+"/"+ encSubdir + "/lastFullRightLocationIDScan.xml"); - - - side2 = "right"; - fileSider = "&rightSide=true"; - } else { - finalXMLFile = new File(encountersDir.getAbsolutePath()+"/" + encSubdir + "/lastFullI3SScan.xml"); - locationIDXMLFile = new File(encountersDir.getAbsolutePath()+"/" + encSubdir + "/lastFullLocationIDScan.xml"); - } - - - if (locationIDXMLFile.exists()) { - %> - - <% - } - %> - -
  • Modified Groth (Full)
    • - <% - - if (finalXMLFile.exists()) { - %> - -
  • I3S -
    • - <% - } - - - %> - - -
- -<% - // ============================================================ - // SCAN IN PROGRESS: Show waiting message with progress - // ============================================================ - if (scanInProgress) { -%> - -
- -

<%=MessageFormat.format(i18n.getProperty("scanInProgress.title", "Scan in progress for encounter {0}"), num)%>

-

<%=i18n.getProperty("scanInProgress.message", "The pattern matching scan is running. Results will appear here when complete.")%>

- - <% - if (numTotal > 0) { - int pct = (int) ((numComplete * 100.0) / numTotal); - %> -
- <%=MessageFormat.format(i18n.getProperty("scanInProgress.progress", "{0} of {1} comparisons complete"), String.valueOf(numComplete), String.valueOf(numTotal))%> -
-
-
-
- <% - } else { - %> -

<%=i18n.getProperty("scanInProgress.queuing", "Preparing comparisons...")%>

- <% - } - %> -

<%=i18n.getProperty("scanInProgress.autoRefresh", "This page will automatically refresh every 15 seconds.")%>

-
- -<% - } else { - // ============================================================ - // SCAN COMPLETE or NO SCAN: Show results - // ============================================================ -%> - -<% - Vector initresults = new Vector(); - Document doc; - Element root; - String side = "left"; - - try { - if ((request.getParameter("rightSide") != null) && (request.getParameter("rightSide").equals("true"))) { - file = new File(encountersDir.getAbsolutePath()+"/" + encSubdir + "/lastFullRightScan.xml"); - side = "right"; - } else { - file = new File(encountersDir.getAbsolutePath()+"/" + encSubdir + "/lastFullScan.xml"); - } - doc = xmlReader.read(file); - root = doc.getRootElement(); - scanDate = root.attributeValue("scanDate"); - xmlOK = true; - R = root.attributeValue("R"); - C = root.attributeValue("C"); - maxTriangleRotation = root.attributeValue("maxTriangleRotation"); - Sizelim = root.attributeValue("Sizelim"); - epsilon = root.attributeValue("epsilon"); - } catch (Exception ioe) { - System.out.println("Error accessing the stored scan XML data for encounter: " + num); - ioe.printStackTrace(); - xmlOK = false; - } - - MatchObject[] matches = new MatchObject[0]; - if (!xmlOK) { - int resultsSize = initresults.size(); - System.out.println(resultsSize); - matches = new MatchObject[resultsSize]; - for (int a = 0; a < resultsSize; a++) { - matches[a] = (MatchObject) initresults.get(a); - } - R = request.getParameter("R"); - C = request.getParameter("C"); - maxTriangleRotation = request.getParameter("maxTriangleRotation"); - Sizelim = request.getParameter("Sizelim"); - epsilon = request.getParameter("epsilon"); - } -%> - -

- -<% - if (!xmlOK && !scanTaskExists) { - // No scan has ever been run and no XML exists -%> -

<%=i18n.getProperty("scanResults.noResults.title", "No Scan Results")%>

-

<%=i18n.getProperty("scanResults.noResults.message", "No pattern matching scan has been run for this encounter yet.")%>

-<% - } else if (!xmlOK && scanTaskExists) { - // Scan task finished but XML was not written (failed or partial write) -%> -

<%=i18n.getProperty("scanResults.failed.title", "Scan Failed")%>

-

<%=i18n.getProperty("scanResults.failed.message", "The scan task completed but results could not be written. Please try running the scan again.")%>

-<% - } else if (xmlOK) { - // We have results to display -%> -

Modified Groth Scan Results

-

-

The following encounter(s) received the highest - match values against a <%=side%>-side scan of encounter <%=num%>.

- - -<% - if (xmlOK) {%> -

 Saved - scan data may be old and invalid. Check the date below and run a fresh - scan for the latest results.

- -

Date of scan: <%=scanDate%> -

-<%}%> - -

See the table below for score breakdowns.

- - - - -<% - String feedURL = "//" + CommonConfiguration.getURLLocation(request) + "/TrackerFeed?number=" + num; - String baseURL = "/"+CommonConfiguration.getDataDirectoryName(context)+"/encounters/"; - - if (xmlOK) { - if ((request.getParameter("rightSide") != null) && (request.getParameter("rightSide").equals("true"))) { - feedURL = baseURL + encSubdir + "/lastFullRightScan.xml?"; - } else { - feedURL = baseURL + encSubdir + "/lastFullScan.xml?"; - } - } - String rightSA = ""; - if ((request.getParameter("rightSide") != null) && (request.getParameter("rightSide").equals("true"))) { - rightSA = "&filePrefix=extractRight"; - } - -java.util.Random rnd = new java.util.Random(); -%> -"); - %> - - - - - -
-
-
- -
-
-
-
-
- -
-
-
-
-
-
- - -
-
-
- - - -
-
- - -
-

- - - - - - - - - - - - - - - - - - - <% - Shepherd indShepherd = new Shepherd(context); - indShepherd.setAction("scanEndApplet.jsp_displayNames"); - indShepherd.beginDBTransaction(); - java.util.HashMap displayNameCache = new java.util.HashMap<>(); - - if (!xmlOK) { - - MatchObject[] results = new MatchObject[1]; - results = matches; - Arrays.sort(results, new MatchComparator()); - for (int p = 0; p < results.length; p++) { - if ((results[p].matchValue != 0) || (request.getAttribute("singleComparison") != null)) { - String indId_mo = results[p].getIndividualName(); - String displayName_mo = displayNameCache.get(indId_mo); - if (displayName_mo == null && indId_mo != null) { - MarkedIndividual ind_mo = indShepherd.getMarkedIndividual(indId_mo); - displayName_mo = (ind_mo != null) ? ind_mo.getDisplayName() : indId_mo; - displayNameCache.put(indId_mo, displayName_mo); - } - if (displayName_mo == null) displayName_mo = "Unknown"; - %> - - - <%if (results[p].encounterNumber.equals("N/A")) {%> - - <%} else {%> - - <% - } - String adjustedMatchValueString = (new Double(results[p].adjustedMatchValue)).toString(); - if (adjustedMatchValueString.length() > 5) { - adjustedMatchValueString = adjustedMatchValueString.substring(0, 5); - } - %> - - <% - String finalscore2 = (new Double(results[p].matchValue * results[p].adjustedMatchValue)).toString(); - - //trim the length of finalscore - if (finalscore2.length() > 7) { - finalscore2 = finalscore2.substring(0, 6); - } - %> - - - - - - - - <% - //end if matchValue!=0 loop - } - //end for loop - } - -//or use XML output here - } else { - doc = xmlReader.read(file); - root = doc.getRootElement(); - - Iterator matchsets = root.elementIterator("match"); - int ct = 0; - while (matchsets.hasNext()) { - Element match = (Element) matchsets.next(); - List encounters = match.elements("encounter"); - Element enc1 = (Element) encounters.get(0); - Element enc2 = (Element) encounters.get(1); - String indId_xml = enc1.attributeValue("assignedToShark"); - String displayName_xml = displayNameCache.get(indId_xml); - if (displayName_xml == null && indId_xml != null) { - MarkedIndividual ind_xml = indShepherd.getMarkedIndividual(indId_xml); - displayName_xml = (ind_xml != null) ? ind_xml.getDisplayName() : indId_xml; - displayNameCache.put(indId_xml, displayName_xml); - } - if (displayName_xml == null) displayName_xml = "Unknown"; - %> - - " - style="cursor: pointer;" onClick="spotDisplayPair(<%=ct%>);" title="jump to this match pair"> - - <%if (enc1.attributeValue("number").equals("N/A")) {%> - - <%} else {%> - - <% - } - String adjustedpoints = "No Adj."; - adjustedpoints = match.attributeValue("adjustedpoints"); - if (adjustedpoints == null) { - adjustedpoints = " "; - } - if (adjustedpoints.length() > 5) { - adjustedpoints = adjustedpoints.substring(0, 5); - } else { - adjustedpoints = adjustedpoints + "
"; - } - %> - - <% - String finalscore = " "; - try { - if (match.attributeValue("finalscore") != null) { - finalscore = match.attributeValue("finalscore"); - } - } catch (NullPointerException npe) { - } - - //trim the length of finalscore - if (finalscore.length() > 7) { - finalscore = finalscore.substring(0, 6); - } - - %> - - - - - <% - String evaluation = "No Adj."; - evaluation = match.attributeValue("evaluation"); - if (evaluation == null) { - evaluation = " "; - } - - %> - - - - - <% - - - ct++; - } - } - - %> - -
Individual ID EncounterFraction Matched Triangles Match Score logM std. dev.ConfidenceMatched Keywords
- <%=displayName_mo%> - - N/A<%=results[p].encounterNumber%> - <%=(adjustedMatchValueString)%>
- 		<%=finalscore2%> - <%=results[p].getLogMStdDev()%> - <%=results[p].getEvaluation()%> -
- - <%=displayName_xml%> - - N/A">Link - <%=adjustedpoints%> - <%=finalscore%> - <%=match.attributeValue("logMStdDev")%> - <%=evaluation%> - - <% - String keywords = ""; - for (Iterator i = match.elementIterator("keywords"); i.hasNext();) { - Element kws = (Element) i.next(); - // iterate the keywords themselves - for (Iterator j = kws.elementIterator("keyword"); j.hasNext();) { - Element kws2 = (Element) j.next(); - keywords = keywords + "
  • " + kws2.attributeValue("name") + "
    • "; - } - } - if (keywords.length() <= 1) { - keywords = " "; - } - %> -
      <%=keywords%> -
    -
    - - - - <% - indShepherd.rollbackDBTransaction(); - indShepherd.closeDBTransaction(); - - - - //myShepherd.closeDBTransaction(); - //myShepherd = null; - doc = null; - root = null; - initresults = null; - file = null; - xmlReader = null; - -if ((request.getParameter("epsilon") != null) && (request.getParameter("R") != null)) {%> -

    Custom Scan

    - <%} else {%> -

    Standard Scan

    - <%}%> -

    For this scan, the following variables were used:

    -
      - - -
    • epsilon (<%=epsilon%>)
      • -
    • R (<%=R%>)
      • -
    • Sizelim (<%=Sizelim%>)
      • -
    • C (<%=C%>)
      • -
    • Max. Triangle Rotation (<%=maxTriangleRotation%>)
      • - -
    -<% - } // end if xmlOK -%> -
    -<% - } // end else (not scanInProgress) -%> -
    - + + + +<%@ page contentType="text/html; charset=iso-8859-1" language="java" + import="org.ecocean.servlet.ServletUtilities,org.dom4j.Document, org.dom4j.Element,org.dom4j.io.SAXReader, org.ecocean.*, org.ecocean.grid.MatchComparator, org.ecocean.grid.MatchObject, org.ecocean.grid.GridManager, org.ecocean.grid.GridManagerFactory, java.io.File, java.util.Arrays, java.util.Iterator, java.util.List, +org.ecocean.grid.ScanTask, +java.util.ArrayList, +org.json.JSONArray, +java.text.MessageFormat, +java.util.Properties, +java.util.Vector" %> +<%@ page import="org.ecocean.shepherd.core.Shepherd" %> +<%@ page import="org.ecocean.shepherd.core.ShepherdProperties" %> + +<% + +String context="context0"; +context=ServletUtilities.getContext(request); + +//let's set up references to our file system components +String rootWebappPath = getServletContext().getRealPath("/"); +File webappsDir = new File(rootWebappPath).getParentFile(); +File shepherdDataDir = new File(webappsDir, CommonConfiguration.getDataDirectoryName(context)); +File encountersDir=new File(shepherdDataDir.getAbsolutePath()+"/encounters"); + + String num=""; + ArrayList locationIDs = new ArrayList(); + boolean scanInProgress = false; + boolean scanTaskExists = false; + int numComplete = 0; + int numTotal = 0; + long scanTaskStartTime = -1; + + if(request.getParameter("number")!=null){ + Shepherd myShepherd=new Shepherd(context); + myShepherd.setAction("scanEndApplet.jsp"); + myShepherd.beginDBTransaction(); + try { + if(myShepherd.isEncounter(ServletUtilities.preventCrossSiteScriptingAttacks(request.getParameter("number")))){ + num = ServletUtilities.preventCrossSiteScriptingAttacks(request.getParameter("number")); + } + + //get any scantask locationID lists and check scan status + String taskID = request.getParameter("taskID"); + boolean isRightSide = (request.getParameter("rightSide") != null) && request.getParameter("rightSide").equals("true"); + if (taskID == null) taskID = "scan" + (isRightSide ? "R" : "L") + num; + if(taskID != null) { + ScanTask st=myShepherd.getScanTask(taskID); + if(st!=null){ + scanTaskExists = true; + if(st.getLocationIDFilters()!=null){ + locationIDs=st.getLocationIDFilters(); + } + if(!st.hasFinished()){ + scanInProgress = true; + scanTaskStartTime = st.getStartTime(); + // Check how much work is done via GridManager + GridManager gm = GridManagerFactory.getGridManager(); + numComplete = gm.getNumWorkItemsCompleteForTask(taskID); + numTotal = numComplete + gm.getNumWorkItemsIncompleteForTask(taskID); + } + } + } + } finally { + myShepherd.rollbackAndClose(); + } + } + String encSubdir = Encounter.subdir(num); + + String sessionId = session.getId(); + boolean xmlOK = false; + SAXReader xmlReader = new SAXReader(); + File file = new File("foo"); + String scanDate = ""; + String C = ""; + String R = ""; + String epsilon = ""; + String Sizelim = ""; + String maxTriangleRotation = ""; + String side2 = ""; + + // Determine the language for i18n + String langCode = "en"; + if (session.getAttribute("langCode") != null) langCode = (String) session.getAttribute("langCode"); + Properties i18n = ShepherdProperties.getProperties("commonConfigurationLabels.properties", langCode, context); +%> + + + + +<% +// If scan is in progress, add auto-refresh +if (scanInProgress) { +%> + +<% +} +%> + +
    + +
      +
    • Encounter + <%=num%> +
      • + + + <% + String fileSider = ""; + File finalXMLFile; + File locationIDXMLFile; + if ((request.getParameter("rightSide") != null) && (request.getParameter("rightSide").equals("true"))) { + finalXMLFile = new File(encountersDir.getAbsolutePath()+"/"+ encSubdir + "/lastFullRightI3SScan.xml"); + locationIDXMLFile = new File(encountersDir.getAbsolutePath()+"/"+ encSubdir + "/lastFullRightLocationIDScan.xml"); + + + side2 = "right"; + fileSider = "&rightSide=true"; + } else { + finalXMLFile = new File(encountersDir.getAbsolutePath()+"/" + encSubdir + "/lastFullI3SScan.xml"); + locationIDXMLFile = new File(encountersDir.getAbsolutePath()+"/" + encSubdir + "/lastFullLocationIDScan.xml"); + } + + + if (locationIDXMLFile.exists()) { + %> + + <% + } + %> + +
    • Modified Groth (Full)
      • + <% + + if (finalXMLFile.exists()) { + %> + +
    • I3S +
      • + <% + } + + + %> + + +
    + +<% + // ============================================================ + // SCAN IN PROGRESS: Show waiting message with progress + // ============================================================ + if (scanInProgress) { +%> + +
    + +

    <%=MessageFormat.format(i18n.getProperty("scanInProgress.title", "Scan in progress for encounter {0}"), num)%>

    +

    <%=i18n.getProperty("scanInProgress.message", "The pattern matching scan is running. Results will appear here when complete.")%>

    + + <% + if (numTotal > 0) { + int pct = (int) ((numComplete * 100.0) / numTotal); + %> +
    + <%=MessageFormat.format(i18n.getProperty("scanInProgress.progress", "{0} of {1} comparisons complete"), String.valueOf(numComplete), String.valueOf(numTotal))%> +
    +
    +
    +
    + <% + } else { + %> +

    <%=i18n.getProperty("scanInProgress.queuing", "Preparing comparisons...")%>

    + <% + } + %> +

    <%=i18n.getProperty("scanInProgress.autoRefresh", "This page will automatically refresh every 15 seconds.")%>

    +
    + +<% + } else { + // ============================================================ + // SCAN COMPLETE or NO SCAN: Show results + // ============================================================ +%> + +<% + Vector initresults = new Vector(); + Document doc; + Element root; + String side = "left"; + + try { + if ((request.getParameter("rightSide") != null) && (request.getParameter("rightSide").equals("true"))) { + file = new File(encountersDir.getAbsolutePath()+"/" + encSubdir + "/lastFullRightScan.xml"); + side = "right"; + } else { + file = new File(encountersDir.getAbsolutePath()+"/" + encSubdir + "/lastFullScan.xml"); + } + doc = xmlReader.read(file); + root = doc.getRootElement(); + scanDate = root.attributeValue("scanDate"); + xmlOK = true; + R = root.attributeValue("R"); + C = root.attributeValue("C"); + maxTriangleRotation = root.attributeValue("maxTriangleRotation"); + Sizelim = root.attributeValue("Sizelim"); + epsilon = root.attributeValue("epsilon"); + } catch (Exception ioe) { + System.out.println("Error accessing the stored scan XML data for encounter: " + num); + ioe.printStackTrace(); + xmlOK = false; + } + + MatchObject[] matches = new MatchObject[0]; + if (!xmlOK) { + int resultsSize = initresults.size(); + System.out.println(resultsSize); + matches = new MatchObject[resultsSize]; + for (int a = 0; a < resultsSize; a++) { + matches[a] = (MatchObject) initresults.get(a); + } + R = request.getParameter("R"); + C = request.getParameter("C"); + maxTriangleRotation = request.getParameter("maxTriangleRotation"); + Sizelim = request.getParameter("Sizelim"); + epsilon = request.getParameter("epsilon"); + } +%> + +

    + +<% + if (!xmlOK && !scanTaskExists) { + // No scan has ever been run and no XML exists +%> +

    <%=i18n.getProperty("scanResults.noResults.title", "No Scan Results")%>

    +

    <%=i18n.getProperty("scanResults.noResults.message", "No pattern matching scan has been run for this encounter yet.")%>

    +<% + } else if (!xmlOK && scanTaskExists) { + // Scan task finished but XML was not written (failed or partial write) +%> +

    <%=i18n.getProperty("scanResults.failed.title", "Scan Failed")%>

    +

    <%=i18n.getProperty("scanResults.failed.message", "The scan task completed but results could not be written. Please try running the scan again.")%>

    +<% + } else if (xmlOK) { + // We have results to display +%> +

    Modified Groth Scan Results

    +

    +

    The following encounter(s) received the highest + match values against a <%=side%>-side scan of encounter <%=num%>.

    + + +<% + if (xmlOK) {%> +

     Saved + scan data may be old and invalid. Check the date below and run a fresh + scan for the latest results.

    + +

    Date of scan: <%=scanDate%> +

    +<%}%> + +

    See the table below for score breakdowns.

    + + + + +<% + String feedURL = "//" + CommonConfiguration.getURLLocation(request) + "/TrackerFeed?number=" + num; + String baseURL = "/"+CommonConfiguration.getDataDirectoryName(context)+"/encounters/"; + + if (xmlOK) { + if ((request.getParameter("rightSide") != null) && (request.getParameter("rightSide").equals("true"))) { + feedURL = baseURL + encSubdir + "/lastFullRightScan.xml?"; + } else { + feedURL = baseURL + encSubdir + "/lastFullScan.xml?"; + } + } + String rightSA = ""; + if ((request.getParameter("rightSide") != null) && (request.getParameter("rightSide").equals("true"))) { + rightSA = "&filePrefix=extractRight"; + } + +java.util.Random rnd = new java.util.Random(); +%> +"); + %> + + + + + +
    +
    +
    + +
    +
    +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + + + +
    +
    + + +
    +

    + + + + + + + + + + + + + + + + + + + <% + Shepherd indShepherd = new Shepherd(context); + indShepherd.setAction("scanEndApplet.jsp_displayNames"); + indShepherd.beginDBTransaction(); + try { + java.util.HashMap displayNameCache = new java.util.HashMap<>(); + + if (!xmlOK) { + + MatchObject[] results = new MatchObject[1]; + results = matches; + Arrays.sort(results, new MatchComparator()); + for (int p = 0; p < results.length; p++) { + if ((results[p].matchValue != 0) || (request.getAttribute("singleComparison") != null)) { + String indId_mo = results[p].getIndividualName(); + String displayName_mo = displayNameCache.get(indId_mo); + if (displayName_mo == null && indId_mo != null) { + MarkedIndividual ind_mo = indShepherd.getMarkedIndividual(indId_mo); + displayName_mo = (ind_mo != null) ? ind_mo.getDisplayName() : indId_mo; + displayNameCache.put(indId_mo, displayName_mo); + } + if (displayName_mo == null) displayName_mo = "Unknown"; + %> + + + <%if (results[p].encounterNumber.equals("N/A")) {%> + + <%} else {%> + + <% + } + String adjustedMatchValueString = (new Double(results[p].adjustedMatchValue)).toString(); + if (adjustedMatchValueString.length() > 5) { + adjustedMatchValueString = adjustedMatchValueString.substring(0, 5); + } + %> + + <% + String finalscore2 = (new Double(results[p].matchValue * results[p].adjustedMatchValue)).toString(); + + //trim the length of finalscore + if (finalscore2.length() > 7) { + finalscore2 = finalscore2.substring(0, 6); + } + %> + + + + + + + + <% + //end if matchValue!=0 loop + } + //end for loop + } + +//or use XML output here + } else { + doc = xmlReader.read(file); + root = doc.getRootElement(); + + Iterator matchsets = root.elementIterator("match"); + int ct = 0; + while (matchsets.hasNext()) { + Element match = (Element) matchsets.next(); + List encounters = match.elements("encounter"); + Element enc1 = (Element) encounters.get(0); + Element enc2 = (Element) encounters.get(1); + String indId_xml = enc1.attributeValue("assignedToShark"); + String displayName_xml = displayNameCache.get(indId_xml); + if (displayName_xml == null && indId_xml != null) { + MarkedIndividual ind_xml = indShepherd.getMarkedIndividual(indId_xml); + displayName_xml = (ind_xml != null) ? ind_xml.getDisplayName() : indId_xml; + displayNameCache.put(indId_xml, displayName_xml); + } + if (displayName_xml == null) displayName_xml = "Unknown"; + %> + + " + style="cursor: pointer;" onClick="spotDisplayPair(<%=ct%>);" title="jump to this match pair"> + + <%if (enc1.attributeValue("number").equals("N/A")) {%> + + <%} else {%> + + <% + } + String adjustedpoints = "No Adj."; + adjustedpoints = match.attributeValue("adjustedpoints"); + if (adjustedpoints == null) { + adjustedpoints = " "; + } + if (adjustedpoints.length() > 5) { + adjustedpoints = adjustedpoints.substring(0, 5); + } else { + adjustedpoints = adjustedpoints + "
    "; + } + %> + + <% + String finalscore = " "; + try { + if (match.attributeValue("finalscore") != null) { + finalscore = match.attributeValue("finalscore"); + } + } catch (NullPointerException npe) { + } + + //trim the length of finalscore + if (finalscore.length() > 7) { + finalscore = finalscore.substring(0, 6); + } + + %> + + + + + <% + String evaluation = "No Adj."; + evaluation = match.attributeValue("evaluation"); + if (evaluation == null) { + evaluation = " "; + } + + %> + + + + + <% + + + ct++; + } + } + + %> + +
    Individual ID EncounterFraction Matched Triangles Match Score logM std. dev.ConfidenceMatched Keywords
    + <%=displayName_mo%> + + N/A<%=results[p].encounterNumber%> + <%=(adjustedMatchValueString)%>
    +     		<%=finalscore2%> + <%=results[p].getLogMStdDev()%> + <%=results[p].getEvaluation()%> +
    + + <%=displayName_xml%> + + N/A">Link + <%=adjustedpoints%> + <%=finalscore%> + <%=match.attributeValue("logMStdDev")%> + <%=evaluation%> + + <% + String keywords = ""; + for (Iterator i = match.elementIterator("keywords"); i.hasNext();) { + Element kws = (Element) i.next(); + // iterate the keywords themselves + for (Iterator j = kws.elementIterator("keyword"); j.hasNext();) { + Element kws2 = (Element) j.next(); + keywords = keywords + "
  • " + kws2.attributeValue("name") + "
    • "; + } + } + if (keywords.length() <= 1) { + keywords = " "; + } + %> +
      <%=keywords%> +
    +
    + + + + <% + } finally { + indShepherd.rollbackAndClose(); + } + + //myShepherd.closeDBTransaction(); + //myShepherd = null; + doc = null; + root = null; + initresults = null; + file = null; + xmlReader = null; + +if ((request.getParameter("epsilon") != null) && (request.getParameter("R") != null)) {%> +

    Custom Scan

    + <%} else {%> +

    Standard Scan

    + <%}%> +

    For this scan, the following variables were used:

    +
      + + +
    • epsilon (<%=epsilon%>)
      • +
    • R (<%=R%>)
      • +
    • Sizelim (<%=Sizelim%>)
      • +
    • C (<%=C%>)
      • +
    • Max. Triangle Rotation (<%=maxTriangleRotation%>)
      • + +
    +<% + } // end if xmlOK +%> +
    +<% + } // end else (not scanInProgress) +%> +
    + From 90bf531a507996ddb7d28a72f69f743cf932247c Mon Sep 17 00:00:00 2001 From: JasonWildMe Date: Tue, 28 Apr 2026 14:16:13 -0700 Subject: [PATCH 3/7] Fix JDO connection pool starvation root-causing dbconnections leaks MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Most of the stuck "begin" entries on Sharkbook's dbconnections.jsp are not individual Shepherd leaks but symptoms of one upstream cause: threads waiting for a Postgres connection that is pinned by a long-running operation. Two fixes: 1. Encounter.opensearchIndexPermissions() — the periodic permissions sweep was holding a Postgres tx open for the entire duration of per-encounter OpenSearch HTTP updates. On installs with hundreds of thousands of encounters this pinned a connection for tens of minutes per run, starving every concurrent request behind it. Refactored into two phases: phase 1 loads users/collab maps and all eligible encounter rows into in-memory structures under a short-lived Shepherd, which is then closed; phase 2 iterates the in-memory rows and issues OpenSearch updates with no DB connection held. Same OpenSearch updates, same filter logic. 2. jdoconfig.properties — datanucleus.connectionPool.maxWait was -1 (wait forever). Threads blocked on the pool sat indefinitely and showed up as stuck "begin" entries. Set to 30000 ms so a request under contention fails fast with a clear error and pool slots free up. Co-Authored-By: Claude Opus 4.7 (1M context) --- src/main/java/org/ecocean/Encounter.java | 11316 ++++++++-------- .../resources/bundles/jdoconfig.properties | 129 +- 2 files changed, 5715 insertions(+), 5730 deletions(-) diff --git a/src/main/java/org/ecocean/Encounter.java b/src/main/java/org/ecocean/Encounter.java index b7c972c26b..c339e4d3b6 100644 --- a/src/main/java/org/ecocean/Encounter.java +++ b/src/main/java/org/ecocean/Encounter.java @@ -1,5667 +1,5649 @@ -package org.ecocean; - -import org.apache.commons.codec.digest.DigestUtils; - -import java.io.*; -import java.lang.Math; -import java.net.URI; -import java.net.URL; -import java.text.SimpleDateFormat; -import java.util.*; -import java.util.concurrent.Executors; -import java.util.concurrent.ExecutorService; -import java.util.concurrent.ThreadPoolExecutor; - -import javax.jdo.Query; - -import org.apache.commons.lang3.builder.ToStringBuilder; - -import com.fasterxml.jackson.core.JsonGenerator; -import com.fasterxml.jackson.core.JsonProcessingException; -import javax.servlet.http.HttpServletRequest; - -import org.ecocean.api.ApiException; -import org.ecocean.api.bulk.BulkImportUtil; -import org.ecocean.api.bulk.BulkValidatorException; -import org.ecocean.api.patch.EncounterPatchValidator; -import org.ecocean.genetics.*; -import org.ecocean.ia.IA; -import org.ecocean.ia.Task; -import org.ecocean.identity.IBEISIA; -import org.ecocean.media.*; -import org.ecocean.security.Collaboration; -import org.ecocean.servlet.importer.ImportTask; -import org.ecocean.shepherd.core.Shepherd; -import org.ecocean.shepherd.core.ShepherdProperties; -import org.ecocean.social.Membership; -import org.ecocean.social.SocialUnit; -import org.ecocean.tag.AcousticTag; -import org.ecocean.tag.DigitalArchiveTag; -import org.ecocean.tag.MetalTag; -import org.ecocean.tag.SatelliteTag; -import org.ecocean.Util.MeasurementDesc; -import org.joda.time.DateTime; -import org.joda.time.format.DateTimeFormat; -import org.joda.time.format.DateTimeFormatter; -import org.joda.time.LocalDateTime; - -import org.datanucleus.api.rest.orgjson.JSONArray; -import org.datanucleus.api.rest.orgjson.JSONException; -import org.datanucleus.api.rest.orgjson.JSONObject; - -/** - * An encounter object stores the complete data for a single sighting/capture report. - * Encounters are added to MarkedIndividual objects as multiple encounters are associated with known individuals. - *

    - * - * @author Jason Holmberg - * @version 2.0 - */ -public class Encounter extends Base implements java.io.Serializable { - static final long serialVersionUID = -146404246317385604L; - - public static final String STATE_MATCHING_ONLY = "matching_only"; - - @Override public String opensearchIndexName() { return "encounter"; } - - public static final double ENCOUNTER_AUTO_SOURCE_CONFIDENCE_CUTOFF = 0.7; - public static final String STATE_AUTO_SOURCED = "auto_sourced"; - - private String sex = null; - private String locationID = null; - private Double maximumDepthInMeters; - private Double maximumElevationInMeters; - private String catalogNumber = ""; - private MarkedIndividual individual; - private int day = 0; - private int month = -1; - private int year = 0; - private Double decimalLatitude; - private Double decimalLongitude; - - private Double endDecimalLatitude; - private Double endDecimalLongitude; - - private String verbatimLocality; - private String occurrenceRemarks = ""; - private String modified; - private String occurrenceID; - private String recordedBy; - private String otherCatalogNumbers; - private String behavior; - private String eventID; - private String measurementUnit; - private String verbatimEventDate; - private String dynamicProperties; - public String identificationRemarks = ""; - public String genus = ""; - public String specificEpithet; - public String lifeStage; - public String country; - public String zebraClass = ""; // via lewa: lactating female, territorial male, etc etc - - private String imageSet; - private String soil; - - private String reproductiveStage; - private Double bodyCondition; - private Double parasiteLoad; - private Double immunoglobin; - private Boolean sampleTakenForDiet; - private Boolean injured; - private boolean opensearchProcessPermissions = false; - - private ArrayList observations = new ArrayList(); - - public String getSoil() { return soil; } - public void setSoil(String soil) { this.soil = soil; } - - public String getReproductiveStage() { return reproductiveStage; } - public void setReproductiveStage(String reproductiveStage) { - this.reproductiveStage = reproductiveStage; - } - - public Double getBodyCondition() { return bodyCondition; } - public void setBodyCondition(Double bodyCondition) { this.bodyCondition = bodyCondition; } - - public Double getParasiteLoad() { return parasiteLoad; } - public void setParasiteLoad(Double parasiteLoad) { this.parasiteLoad = parasiteLoad; } - - public Double getImmunoglobin() { return immunoglobin; } - public void setImmunoglobin(Double immunoglobin) { this.immunoglobin = immunoglobin; } - - public Boolean getSampleTakenForDiet() { return sampleTakenForDiet; } - public void setSampleTakenForDiet(Boolean sampleTakenForDiet) { - this.sampleTakenForDiet = sampleTakenForDiet; - } - - public Boolean getInjured() { return injured; } - public void setInjured(Boolean injured) { this.injured = injured; } - - // for searchability - private String imageNames; - - private List submitters; - private List photographers; - private List informOthers; - - private static HashMap > _matchEncounterCache = new HashMap >(); - - // An URL to a thumbnail image representing the encounter. - private String dwcImageURL; - - // Defines whether the sighting represents a living or deceased individual. - // Currently supported values are: "alive" and "dead". - private String livingStatus; - - // observed age (if any) via IBEIS zebra projects - private Double age; - - // Date the encounter was added to the library. - private String dwcDateAdded; - private Long dwcDateAddedLong; - - // If Encounter spanned more than one day, date of release - private Date releaseDate; - - private Long releaseDateLong; - - // Size of the individual in meters - private Double size; - - // Additional comments added by library users - private String researcherComments = "None"; - - // username of the logged in researcher assigned to the encounter - // this String is matched to an org.ecocean.User object to obtain more information - private String submitterID; - - // name, email, phone, address of the encounter reporter - private String submitterEmail, submitterPhone, submitterAddress; - private String hashedSubmitterEmail; - private String hashedPhotographerEmail; - private String hashedInformOthers; - private String informothers; - - // name, email, phone, address of the encounter photographer - private String photographerName, photographerEmail, photographerPhone, photographerAddress; - - // a Vector of Strings defining the relative path to each photo. The path is relative to the servlet base directory - public Vector additionalImageNames = new Vector(); - - // a Vector of Strings of email addresses to notify when this encounter is modified - private Vector interestedResearchers = new Vector(); - - // time metrics of the report - private int hour = 0; - private String minutes = "00"; - - private String state = ""; - - // the globally unique identifier (GUID) for this Encounter - private String guid; - - private Long endDateInMilliseconds; - private Long dateInMilliseconds; - - // describes how the shark was measured - private String size_guess = "none provided"; - - // String reported GPS values for lat and long of the encounter - private String gpsLongitude = "", gpsLatitude = ""; - private String gpsEndLongitude = "", gpsEndLatitude = ""; - - // Indicates whether this record can be exposed via TapirLink - private boolean okExposeViaTapirLink = false; - - public String spotImageFileName = ""; - - // name of the stored file from which the right-side spots were extracted - public String rightSpotImageFileName = ""; - - // string descriptor of the most obvious scar (if any) as reported by the original submitter - // we also use keywords to be more specific - public String distinguishingScar = "None"; - // describes how this encounter was matched to an existing shark - by eye, by pattern recognition algorithm etc. - - // SPOTS - // an array of the extracted left-side superSpots - // private superSpot[] spots; - private ArrayList spots; - - // an array of the extracted right-side superSpots - // private superSpot[] rightSpots; - private ArrayList rightSpots; - - // an array of the three extracted left-side superSpots used for the affine transform of the I3S algorithm - // private superSpot[] leftReferenceSpots; - private ArrayList leftReferenceSpots; - - // an array of the three extracted right-side superSpots used for the affine transform of the I3S algorithm - // private superSpot[] rightReferenceSpots; - private ArrayList rightReferenceSpots; - - // an open ended string that allows a type of patterning to be identified. - // as an example, see the use of color codes at splashcatalog.org, allowing pre-defined fluke patterning types - // to be used to help narrow the search for a marked individual - private String patterningCode; - - // submitting organization and project further detail the scope of who submitted this project - private String submitterOrganization; - private String submitterProject; - private List submitterResearchers; - - // hold submittedData - // private List collectedData; - private List tissueSamples; - private List images; - // private ArrayList media; - private ArrayList annotations; - private List measurements; - private List metalTags; - private AcousticTag acousticTag; - private SatelliteTag satelliteTag; - private DigitalArchiveTag digitalArchiveTag; - - private Boolean mmaCompatible = false; - - // Variables used in the Survey, SurveyTrack, Path, Location model - - private String correspondingSurveyTrackID = null; - private String correspondingSurveyID = null; - - // This is the eventual replacement for the old decimal lat lon and other location data. - private PointLocation pointLocation; - - // This is the number used to cross reference with dates to find occurances. (Read Lab) - private String sightNo = ""; - - // This is what researchers eyeball is the individual's ID in the field - // it could be a name that only has meaning in the context of that day's work - // (not necessarily an individual name from the WB database) - private String fieldID; - - // This is a standard 1-5 color scale used by cetacean researchers - private Integer flukeType; - - // added by request for ASWN, this is the role an individual served in its occurrence - // (from a standard list like Escort Male) - private String groupRole; - - // identifies the import/dataset this came from for data provenance - private String dataSource; - - // start constructors - - /** - * empty constructor required by the JDO Enhancer - */ - public Encounter() {} - - public Encounter(boolean skipSetup) { - if (skipSetup) return; - this.catalogNumber = Util.generateUUID(); - this.setDWCDateAdded(); - this.setDWCDateLastModified(); - this.resetDateInMilliseconds(); - this.annotations = new ArrayList(); - } - - /** - * Use this constructor to add the minimum level of information for a new encounter The Vector additionalImages must be a Vector of - * Blob objects - * - * TODO: evaluate and remove if this is DEPRECATED cuz, SinglePhotoVideos? really? - */ - public Encounter(int day, int month, int year, int hour, String minutes, String size_guess, - String location) { - if (images != null) - System.out.println( - "WARNING: danger! deprecated SinglePhotoVideo-based Encounter constructor used!"); - this.verbatimLocality = location; - - this.images = images; - this.day = day; - this.month = month; - this.year = year; - this.hour = hour; - this.minutes = minutes; - this.size_guess = size_guess; - - this.setDWCDateAdded(); - this.setDWCDateLastModified(); - this.resetDateInMilliseconds(); - } - - public Encounter(Annotation ann) { - this(new ArrayList(Arrays.asList(ann))); - } - - public Encounter(ArrayList anns) { - this.catalogNumber = Util.generateUUID(); - this.annotations = anns; - if (!this.annotationsAreEmpty()) { - this.setDateFromAssets(); - this.setSpeciesFromAnnotations(); - this.setLatLonFromAssets(); - } - this.setDWCDateAdded(); - this.setDWCDateLastModified(); - this.resetDateInMilliseconds(); - } - private boolean annotationsAreEmpty() { - return (this.annotations == null || this.annotations.size() == 0 || - (this.annotations.size() == 1 && (this.annotations.get(0) == null))); - } - - // space saver since we're about to use this hundreds of times - private boolean shouldReplace(String str1, String str2) { - return Util.shouldReplace(str1, str2); - } - - // also returns true when str1 is a superstring of str2. - private boolean shouldReplaceSuperStr(String str1, String str2) { - return (shouldReplace(str1, str2) || (Util.stringExists(str1) && str1.contains(str2))); - } - - public void mergeAndDelete(Encounter enc2, Shepherd myShepherd) { - mergeDataFrom(enc2); - MarkedIndividual ind = myShepherd.getMarkedIndividual(enc2); - if (ind != null) { - ind.removeEncounter(enc2); - ind.addEncounter(this); // duplicate-safe - } - Occurrence occ = myShepherd.getOccurrence(enc2); - if (occ != null) { - occ.removeEncounter(enc2); - occ.addEncounter(this); // duplicate-safe - } - // Remove it from an ImportTask if needed - ImportTask task = myShepherd.getImportTaskForEncounter(enc2.getCatalogNumber()); - if (task != null) { - task.removeEncounter(enc2); - myShepherd.updateDBTransaction(); - } - // Remove from Project if needed - List projects = myShepherd.getProjectsForEncounter(enc2); - if (projects != null && !projects.isEmpty()) { - for (Project project : projects) { - project.removeEncounter(enc2); - myShepherd.updateDBTransaction(); - } - } - // remove tissue samples because of bogus foreign key constraint that prevents deletion - int numTissueSamples = 0; - if (enc2.getTissueSamples() != null) numTissueSamples = enc2.getTissueSamples().size(); - for (int i = 0; i < numTissueSamples; i++) { - enc2.removeTissueSample(0); - } - this.addComments("

    Merged in encounter " + enc2.getCatalogNumber() + "."); - - myShepherd.throwAwayEncounter(enc2); - } - - // copies otherEnc's data into thisEnc, not overwriting anything - public void mergeDataFrom(Encounter enc2) { - if (enc2.getIndividual() != null) setIndividual(enc2.getIndividual()); - // simple string fields - if (shouldReplace(enc2.getSex(), getSex())) setSex(enc2.getSex()); - if (shouldReplace(enc2.getLocationID(), getLocationID())) - setLocationID(enc2.getLocationID()); - if (shouldReplace(enc2.getVerbatimLocality(), getVerbatimLocality())) - setVerbatimLocality(enc2.getVerbatimLocality()); - if (shouldReplace(enc2.getOccurrenceID(), getOccurrenceID())) - setOccurrenceID(enc2.getOccurrenceID()); - if (shouldReplace(enc2.getRecordedBy(), getRecordedBy())) - setRecordedBy(enc2.getRecordedBy()); - if (shouldReplace(enc2.getEventID(), getEventID())) setEventID(enc2.getEventID()); - if (shouldReplace(enc2.getGenus(), getGenus())) setGenus(enc2.getGenus()); - if (shouldReplace(enc2.getSpecificEpithet(), getSpecificEpithet())) - setSpecificEpithet(enc2.getSpecificEpithet()); - if (shouldReplace(enc2.getLifeStage(), getLifeStage())) setLifeStage(enc2.getLifeStage()); - if (shouldReplace(enc2.getCountry(), getCountry())) setCountry(enc2.getCountry()); - if (shouldReplace(enc2.getZebraClass(), getZebraClass())) - setZebraClass(enc2.getZebraClass()); - if (shouldReplace(enc2.getSoil(), getSoil())) setSoil(enc2.getSoil()); - if (shouldReplace(enc2.getReproductiveStage(), getReproductiveStage())) - setReproductiveStage(enc2.getReproductiveStage()); - if (shouldReplace(enc2.getLivingStatus(), getLivingStatus())) - setLivingStatus(enc2.getLivingStatus()); - if (shouldReplace(enc2.getSubmitterEmail(), getSubmitterEmail())) - setSubmitterEmail(enc2.getSubmitterEmail()); - if (shouldReplace(enc2.getSubmitterPhone(), getSubmitterPhone())) - setSubmitterPhone(enc2.getSubmitterPhone()); - if (shouldReplace(enc2.getSubmitterAddress(), getSubmitterAddress())) - setSubmitterAddress(enc2.getSubmitterAddress()); - if (shouldReplace(enc2.getState(), getState())) setState(enc2.getState()); - if (shouldReplace(enc2.getGPSLongitude(), getGPSLongitude())) - setGPSLongitude(enc2.getGPSLongitude()); - if (shouldReplace(enc2.getGPSLatitude(), getGPSLatitude())) - setGPSLatitude(enc2.getGPSLatitude()); - if (shouldReplace(enc2.getPatterningCode(), getPatterningCode())) - setPatterningCode(enc2.getPatterningCode()); - if (shouldReplace(enc2.getSubmitterOrganization(), getSubmitterOrganization())) - setSubmitterOrganization(enc2.getSubmitterOrganization()); - if (shouldReplace(enc2.getSubmitterProject(), getSubmitterProject())) - setSubmitterProject(enc2.getSubmitterProject()); - if (shouldReplace(enc2.getFieldID(), getFieldID())) setFieldID(enc2.getFieldID()); - if (shouldReplace(enc2.getGroupRole(), getGroupRole())) setGroupRole(enc2.getGroupRole()); - // now string fields that might need to be combined rather than replaced - if (shouldReplaceSuperStr(enc2.getDynamicProperties(), getDynamicProperties())) { - setDynamicProperties(enc2.getDynamicProperties()); - } else if (Util.stringExists(enc2.getDynamicProperties())) { // shouldn't replace, should combine - addDynamicProperties(enc2.getDynamicProperties()); - } - if (shouldReplaceSuperStr(enc2.getOccurrenceRemarks(), getOccurrenceRemarks())) { - setOccurrenceRemarks(enc2.getOccurrenceRemarks()); - } else if (Util.stringExists(enc2.getOccurrenceRemarks())) { // shouldn't replace, should combine - setOccurrenceRemarks(getOccurrenceRemarks() + " " + enc2.getOccurrenceRemarks()); - } - // now combine list fields making sure not to add duplicate entries - setAnnotations(Util.combineArrayListsInPlace(getAnnotations(), enc2.getAnnotations())); - setObservationArrayList(Util.combineArrayListsInPlace(getObservationArrayList(), - enc2.getObservationArrayList())); - setSubmitterResearchers(Util.combineListsInPlace(getSubmitterResearchers(), - enc2.getSubmitterResearchers())); - // custom no-duplicate logic bc the same sampleID may have been added on both encounters, but this would create unique tissuesample objects - Set sampleIDs = getTissueSampleIDs(); - for (TissueSample samp : enc2.getTissueSamples()) { - if (!sampleIDs.contains(samp.getSampleID())) addTissueSample(samp); - } - setMeasurements(Util.combineListsInPlace(getMeasurements(), enc2.getMeasurements())); - setMetalTags(Util.combineListsInPlace(getMetalTags(), enc2.getMetalTags())); - - // spot lists - setSpots(Util.combineArrayListsInPlace(getSpots(), enc2.getSpots())); - setRightSpots(Util.combineArrayListsInPlace(getRightSpots(), enc2.getRightSpots())); - setLeftReferenceSpots(Util.combineArrayListsInPlace(getLeftReferenceSpots(), - enc2.getLeftReferenceSpots())); - setRightReferenceSpots(Util.combineArrayListsInPlace(getRightReferenceSpots(), - enc2.getRightReferenceSpots())); - // tags - if (enc2.getAcousticTag() != null && getAcousticTag() == null) - setAcousticTag(enc2.getAcousticTag()); - if (enc2.getSatelliteTag() != null && getSatelliteTag() == null) - setSatelliteTag(enc2.getSatelliteTag()); - if (enc2.getDTag() != null && getDTag() == null) setDTag(enc2.getDTag()); - // skip time stuff bc if the time is different we probably don't want to combine the encounters anyway. - } - - public String getZebraClass() { - return zebraClass; - } - - public void setZebraClass(String c) { - zebraClass = c; - } - - public String getImageNames() { - return imageNames; - } - - public void addImageName(String name) { - if (imageNames == null) imageNames = name; - else if (name != null) imageNames += (", " + name); - } - - public String addAllImageNamesFromAnnots(boolean overwrite) { - if (overwrite) imageNames = null; - return addAllImageNamesFromAnnots(); - } - - public String addAllImageNamesFromAnnots() { - for (Annotation ann : getAnnotations()) { - for (Feature feat : ann.getFeatures()) { - try { - MediaAsset ma = feat.getMediaAsset(); - addImageName(ma.getFilename()); - } catch (Exception e) { - System.out.println("exception parsing image name from feature " + feat); - } - } - } - return imageNames; - } - - /** - * Returns an array of all of the superSpots for this encounter. - * - * @return the array of superSpots, taken from the croppedImage, that make up the digital fingerprint for this encounter - */ - public ArrayList getSpots() { - return spots; - } - - public ArrayList getRightSpots() { - return rightSpots; - } - - /** - * Returns an array of all of the superSpots for this encounter. - * - * @return the array of superSpots, taken from the croppedImage, that make up the digital fingerprint for this encounter - */ -/* TODO: evaluate if this is deprecate and can be removed - these have gone away! dont be setting spots on Encounter any more .... NOT SO FAST... we regress for whaleshark.org... */ - public void setSpots(ArrayList newSpots) { - spots = newSpots; - } - - public void setRightSpots(ArrayList newSpots) { - rightSpots = newSpots; - } - - /** - * Removes any spot data - */ - public void removeSpots() { - spots = null; - } - - public void removeRightSpots() { - rightSpots = null; - } - - public Integer getFlukeType() { return this.flukeType; } - public void setFlukeType(Integer flukeType) { this.flukeType = flukeType; } - // this averages all the fluketypes - public void setFlukeTypeFromKeywords() { - int totalFlukeType = 0; - int numFlukes = 0; - - for (Annotation ann : getAnnotations()) { - Integer thisFlukeType = getFlukeTypeFromAnnotation(ann); - if (thisFlukeType != null) { - totalFlukeType += thisFlukeType; - numFlukes++; - } - } - if (numFlukes == 0) return; - setFlukeType(totalFlukeType / numFlukes); - } - - // assuming the list is of erroneously-duplicated encounters, returns the one we want to keep - public static Encounter chooseFromDupes(List encs) { - int maxAnns = -1; - int encWithMax = 0; - - for (int i = 0; i < encs.size(); i++) { - Encounter enc = encs.get(i); - if (enc.numAnnotations() > maxAnns) { - maxAnns = enc.numAnnotations(); - encWithMax = i; - } - } - return encs.get(encWithMax); - } - - public static Integer getFlukeTypeFromAnnotation(Annotation ann) { - return getFlukeTypeFromAnnotation(ann, 5); - } - - // int maxScore is used because some people store flukeType on a 5 point (most standard), some on a 9 point scale - public static Integer getFlukeTypeFromAnnotation(Annotation ann, int maxScore) { - MediaAsset ma = ann.getMediaAsset(); - - if (ma == null || !ma.hasKeywords()) return null; - String flukeTypeKwPrefix = "fluke" + maxScore + ":"; - for (Keyword kw : ma.getKeywords()) { - String kwName = kw.getReadableName(); - if (kwName.contains(flukeTypeKwPrefix)) { - String justScore = kwName.split(flukeTypeKwPrefix)[1]; - try { - Integer score = Integer.parseInt(justScore); - if (score != null) return score; - } catch (NumberFormatException nfe) { - System.out.println("NFE on getFlukeTypeFromAnnotation! For ann " + ann + - " and kwPrefix " + flukeTypeKwPrefix); - } - } - } - return null; - } - - // yes, there "should" be only one of each of these, but we be thorough! - public void removeLeftSpotMediaAssets(Shepherd myShepherd) { - ArrayList spotMAs = this.findAllMediaByLabel(myShepherd, "_spot"); - - for (MediaAsset ma : spotMAs) { - System.out.println("INFO: removeLeftSpotMediaAsset() detaching " + ma + - " from parent id=" + ma.getParentId()); - ma.setParentId(null); - } - } - - public void removeRightSpotMediaAssets(Shepherd myShepherd) { - ArrayList spotMAs = this.findAllMediaByLabel(myShepherd, "_spotRight"); - - for (MediaAsset ma : spotMAs) { - System.out.println("INFO: removeRightSpotMediaAsset() detaching " + ma + - " from parent id=" + ma.getParentId()); - ma.setParentId(null); - } - } - - public void nukeAllSpots() { - leftReferenceSpots = null; - rightReferenceSpots = null; - spots = null; - rightSpots = null; - } - - /** - * Returns the number of spots in the cropped image stored for this encounter. - * - * @return the number of superSpots that make up the digital fingerprint for this encounter - */ - public int getNumSpots() { - return (spots == null) ? 0 : spots.size(); - } - - public int getNumRightSpots() { - return (rightSpots == null) ? 0 : rightSpots.size(); - } - - public boolean hasLeftSpotImage() { - return (this.getNumSpots() > 0); - } - - public boolean hasRightSpotImage() { - return (this.getNumRightSpots() > 0); - } - - // Sets the recorded length of the shark for this encounter. - public void setSize(Double mysize) { - if (mysize != null) { size = mysize; } else { size = null; } - } - - // @return the length of the shark - public double getSize() { - return size.doubleValue(); - } - - public Double getSizeAsDouble() { - return size; - } - - // Sets the units of the recorded size and depth of the shark for this encounter. Acceptable entries are either "Feet" or "Meters" - public void setMeasureUnits(String measure) { - measurementUnit = measure; - } - - // @return the units of measure used by the recorded of this encounter, either "feet" or "meters" - public String getMeasureUnits() { - return measurementUnit; - } - - public String getMeasurementUnit() { - return measurementUnit; - } - - // @return the location of this encounter - public String getLocation() { - return verbatimLocality; - } - - public void setLocation(String location) { - this.verbatimLocality = location; - } - - // Sets the recorded sex of the shark in this encounter. Acceptable values are "Male" or "Female" - public void setSex(String thesex) { - if (thesex != null) { sex = thesex; } else { sex = null; } - } - - // @return the sex of the shark, either "male" or "female" - public String getSex() { - return sex; - } - - // @return any comments regarding observed scarring on the shark's body - public boolean getMmaCompatible() { - if (mmaCompatible == null) return false; - return mmaCompatible; - } - - public void setMmaCompatible(boolean b) { - mmaCompatible = b; - } - - // @return Occurrence Remarks String - @Override public String getComments() { - return occurrenceRemarks; - } - - // FIXME why is setComments() affecting occurrenceRemarks, and yet - // addComments() affecting researchComments !!!!!???? - // @param newComments Occurrence remarks to set - @Override public void setComments(String newComments) { - occurrenceRemarks = newComments; - } - - // @return any comments added by authroized researchers - public String getRComments() { - return researcherComments; - } - - // @param newComments any additional comments to be added to the encounter - @Override public void addComments(String newComments) { - if ((researcherComments != null) && (!(researcherComments.equals("None")))) { - researcherComments += newComments; - } else { - researcherComments = newComments; - } - } - - // @return the name of the person who submitted this encounter to the database - public String getSubmitterName() { - return recordedBy; - } - - public void setSubmitterName(String newname) { - if (newname == null) { - recordedBy = null; - } else { - recordedBy = newname; - } - } - - // @return the e-mail address of the person who submitted this encounter data - public String getSubmitterEmail() { - return submitterEmail; - } - - public void setSubmitterEmail(String newemail) { - if (newemail == null) { - submitterEmail = null; - this.hashedSubmitterEmail = null; - } else { - submitterEmail = newemail; - this.hashedSubmitterEmail = Encounter.getHashOfEmailString(newemail); - } - } - - // @return the phone number of the person who submitted this encounter data - public String getSubmitterPhone() { - return submitterPhone; - } - - // Sets the phone number of the person who submitted this encounter data. - public void setSubmitterPhone(String newphone) { - if (newphone == null) { - submitterPhone = null; - } else { - submitterPhone = newphone; - } - } - - // @return the mailing address of the person who submitted this encounter data - public String getSubmitterAddress() { - return submitterAddress; - } - - // Sets the mailing address of the person who submitted this encounter data. - public void setSubmitterAddress(String address) { - if (address == null) { - submitterAddress = null; - } else { - submitterAddress = address; - } - } - - // @return the name of the photographer who took the primary image for this encounter - public String getPhotographerName() { - return photographerName; - } - - // @return the name of the photographer who took the primary image for this encounter - public void setPhotographerName(String name) { - if (name == null) { - photographerName = null; - } else { - photographerName = name; - } - } - - // @return the e-mail address of the photographer who took the primary image for this encounter - public String getPhotographerEmail() { - return photographerEmail; - } - - // Sets the e-mail address of the person who took the primaryImage this encounter. - public void setPhotographerEmail(String email) { - if (email == null) { - photographerEmail = null; - this.hashedPhotographerEmail = null; - } else { - photographerEmail = email; - this.hashedPhotographerEmail = Encounter.getHashOfEmailString(email); - } - } - - // @return the phone number of the photographer who took the primary image for this encounter - public String getPhotographerPhone() { - return photographerPhone; - } - - // this is a cruddy "solution" to .submitterName and .submitters existing simultaneously - public Set getAllSubmitterIds(Shepherd myShepherd) { - Set all = new HashSet(); - User owner = this.getSubmitterUser(myShepherd); - - if (owner == null) { - all.add(this.submitterID); - all.add(this.submitterEmail); - } else { - all.add(owner.getUsername()); - all.add(owner.getFullName()); - all.add(owner.getId()); - all.add(owner.getEmailAddress()); - } - if (this.submitters != null) - for (User user : this.submitters) { - all.add(user.getUsername()); - all.add(user.getFullName()); - all.add(user.getId()); - all.add(user.getEmailAddress()); - } - all.remove(null); - all.remove(""); - return all; - } - - // similar to above - public Set getAllPhotographerIds() { - Set all = new HashSet(); - - all.add(this.photographerName); - if (this.photographers != null) - for (User user : this.photographers) { - all.add(user.getUsername()); - all.add(user.getFullName()); - all.add(user.getId()); - all.add(user.getEmailAddress()); - } - all.remove(null); - all.remove(""); - return all; - } - - public Set getAllInformOtherIds() { - Set all = new HashSet(); - - if (this.informOthers != null) - for (User user : this.informOthers) { - all.add(user.getUsername()); - all.add(user.getFullName()); - all.add(user.getId()); - all.add(user.getEmailAddress()); - } - all.remove(null); - all.remove(""); - return all; - } - - public String getWebUrl(HttpServletRequest req) { - return getWebUrl(this.getCatalogNumber(), req); - } - - public static String getWebUrl(String encId, HttpServletRequest req) { - return getWebUrl(encId, CommonConfiguration.getServerURL(req)); - } - - public static String getWebUrl(String encId, String serverUrl) { - return (serverUrl + "/encounters/encounter.jsp?number=" + encId); - } - - // Sets the phone number of the person who took the primaryImage this encounter. - public void setPhotographerPhone(String phone) { - if (phone == null) { - photographerPhone = null; - } else { - photographerPhone = phone; - } - } - - // @return the mailing address of the photographer who took the primary image for this encounter - public String getPhotographerAddress() { - return photographerAddress; - } - - // Sets the mailing address of the person who took the primaryImage this encounter. - public void setPhotographerAddress(String address) { - if (address == null) { - photographerAddress = null; - } else { - photographerAddress = address; - } - } - - // Sets the recorded depth of this encounter. - public void setDepth(Double myDepth) { - if (myDepth != null) { maximumDepthInMeters = myDepth; } else { - maximumDepthInMeters = null; - } - } - - // @return the recorded depth for this encounter - public double getDepth() { - return maximumDepthInMeters.doubleValue(); - } - - public Double getDepthAsDouble() { - return maximumDepthInMeters; - } - - // @return a vector of image name Strings - public Vector getAdditionalImageNames() { - Vector imageNamesOnly = new Vector(); - - if ((images != null) && (images.size() > 0)) { - int imagesSize = images.size(); - for (int i = 0; i < imagesSize; i++) { - SinglePhotoVideo dce = (SinglePhotoVideo)images.get(i); - imageNamesOnly.add(dce.getFilename()); - } - } - return imageNamesOnly; - } - - public String getFieldID() { - return this.fieldID; - } - - public void setFieldID(String fieldID) { - this.fieldID = fieldID; - } - - public String getGroupRole() { - return this.groupRole; - } - - public void setGroupRole(String role) { - this.groupRole = role; - } - - public String getDataSource() { - return dataSource; - } - - public void setDataSource(String dataSource) { - this.dataSource = dataSource; - } - - public String getImageOriginalName() { - MediaAsset ma = getPrimaryMediaAsset(); - - if (ma == null) return null; - return ma.getFilename(); - } - - // @return a unique integer String used to identify this encounter in the database - public String getEncounterNumber() { - return catalogNumber; - } - - public String generateEncounterNumber() { - return Util.generateUUID(); - } - - public String dir(String baseDir) { - return baseDir + File.separator + "encounters" + File.separator + this.subdir(); - } - - // like above, but class method so you pass the encID - public static String dir(String baseDir, String id) { - return baseDir + File.separator + "encounters" + File.separator + subdir(id); - } - - // like above, but can pass a File in for base - public static String dir(File baseDir, String id) { - return baseDir.getAbsolutePath() + File.separator + "encounters" + File.separator + - subdir(id); - } - - // subdir() is kind of a utility function, which can be called as enc.subdir() or Encounter.subdir(IDSTRING) as needed - public String subdir() { - return subdir(this.getEncounterNumber()); - } - - public static String subdir(String id) { - String d = id; // old-world - - if (Util.isUUID(id)) { // new-world - d = id.charAt(0) + File.separator + id.charAt(1) + File.separator + id; - } - return d; - } - - // @return a Date object - public String getDate() { - String date = ""; - String time = ""; - - if (year <= 0) { - return "Unknown"; - } else if (month == -1) { - return Integer.toString(year); - } - if (hour != -1) { - String localMinutes = minutes; - if (!Util.stringExists(localMinutes)) { - localMinutes = "00"; - } else if (localMinutes.length() == 1) { - localMinutes = "0" + localMinutes; - } - time = String.format("%02d:%s", hour, localMinutes); - } - if (day > 0) { - date = String.format("%04d-%02d-%02d %s", year, month, day, time); - } else if (month > 0) { - date = String.format("%04d-%02d %s", year, month, time); - } else { - date = String.format("%04d %s", year, time); - } - return date.trim(); - } - - public String getShortDate() { - String date = ""; - - if (year <= 0) { - return "Unknown"; - } else if (month == -1) { - return Integer.toString(year); - } - if (day > 0) { - date = String.format("%02d/%02d/%04d", day, month, year); - } else { - date = String.format("%02d/%04d", month, year); - } - return date; - } - - public org.json.JSONObject getDateValuesJson() { - org.json.JSONObject dv = new org.json.JSONObject(); - // in theory we *always* should have at least a year, but our data probably says otherwise - // sadly we just bail empty if we dont have a year - if (getYear() < 1900) return dv; - dv.put("year", getYear()); - // from here on out we only add things if the previous one existed; hence the short-circuit return - // e.g. we do not add a day if there was no month - if ((getMonth() < 1) || (getMonth() > 12)) return dv; - dv.put("month", getMonth()); - // sorry not checking actual days-per-month here - if ((getDay() < 1) || (getDay() > 31)) return dv; - dv.put("day", getDay()); - if ((getHour() < 0) || (getHour() > 23)) return dv; - dv.put("hour", getHour()); - // sigh, deal with string-based minutes... - Integer min = getMinutesInteger(); - if ((min != null) && (min >= 0) && (min < 60)) { - dv.put("minutes", min); - } else { - // choosing to do this because we *must* have hour value here, so dumb to leave null? - dv.put("minutes", 0); - } - return dv; - } - - // @return a String with text about how the size of this animal was estimated/measured - public String getSizeGuess() { - return size_guess; - } - - public void setDay(int day) { - this.day = day; - resetDateInMilliseconds(); - } - - public void setHour(int hour) { - this.hour = hour; - resetDateInMilliseconds(); - } - - public void setMinutes(String minutes) { - this.minutes = minutes; - resetDateInMilliseconds(); - } - - public String getMinutes() { - return minutes; - } - - public Integer getMinutesInteger() { - Integer min = null; - - try { min = Integer.parseInt(minutes); } catch (Exception e) {} - return min; - } - - public int getHour() { - return hour; - } - - public void setMonth(int month) { - this.month = month; - resetDateInMilliseconds(); - } - - public void setYear(int year) { - this.year = year; - resetDateInMilliseconds(); - } - - // this does not reset year/month/etc - public void setDateInMillisOnly(long ms) { - this.dateInMilliseconds = ms; - } - - public int getDay() { - return day; - } - - public int getMonth() { - return month; - } - - public int getYear() { - return year; - } - - public boolean wasInPeriod(DateTime start, DateTime end) { - Long thisTime = getDateInMilliseconds(); - - if (thisTime == null) return false; - long endOfDay = end.withTime(23, 59, 59, 999).getMillis(); - return (start.getMillis() <= thisTime && endOfDay >= thisTime); - } - - // @return the String holding specific location data used for searching - public String getLocationCode() { - return locationID; - } - - // TODO: Verify and remove if this is deprecated: A legacy method replaced by setLocationID(...). - public void setLocationCode(String newLoc) { - setLocationID(newLoc); - } - - // @return the String holding specific location data used for searching - public String getDistinguishingScar() { - return distinguishingScar; - } - - // Sets the String holding scarring information for the encounter - public void setDistinguishingScar(String scar) { - distinguishingScar = scar; - } - - // Sets the String documenting how the size of this animal was approximated. - public void setSizeGuess(String newGuess) { - size_guess = newGuess; - } - - public String getMatchedBy() { - if ((identificationRemarks == null) || (identificationRemarks.equals(""))) { - return "Unknown"; - } - return identificationRemarks; - } - - public void setMatchedBy(String matchType) { - identificationRemarks = matchType; - } - - public void setIdentificationRemarks(String matchType) { - identificationRemarks = matchType; - } - - /** - * Sets the unique encounter identifier to be usd with this encounter. Once this is set, it cannot be changed without possible impact to the - * database structure. - * - * @param num the unique integer to be used to uniquely identify this encoun ter in the database - */ - public void setEncounterNumber(String num) { - catalogNumber = num; - } - - public boolean hasMarkedIndividual() { - return (individual != null); - } - - public boolean hasMarkedIndividual(MarkedIndividual match) { - if (match == null) return false; - if (individual == null) return false; - return (match.getId().equals(individual.getId())); - } - - public void assignToMarkedIndividual(MarkedIndividual indiv) { - setIndividual(indiv); - } - - public void setIndividual(MarkedIndividual indiv) { - if (indiv == null) { this.individual = null; } else { this.individual = indiv; } - this.refreshAnnotationLiteIndividual(); - } - - public MarkedIndividual getIndividual() { - return individual; - } - - public String getDisplayName() { - return (individual == null) ? null : individual.getDisplayName(); - } - - public String getIndividualID() { - if (individual == null) return null; - return individual.getId(); - } - - public String getGPSLongitude() { - if (gpsLongitude == null) { - return ""; - } else { - return gpsLongitude; - } - } - - public void setGPSLongitude(String newLong) { - gpsLongitude = newLong; - } - - public String getGPSLatitude() { - if (gpsLatitude == null) { - return ""; - } else { - return gpsLatitude; - } - } - - public void setGPSLatitude(String newLat) { - gpsLatitude = newLat; - } - - public Encounter getClone() { - Encounter tempEnc = new Encounter(); - - try { - tempEnc = (Encounter)this.clone(); - } catch (java.lang.CloneNotSupportedException e) { - e.printStackTrace(); - } - return tempEnc; - } - - public String getSpotImageFileName() { - return spotImageFileName; - } - - public void setSpotImageFileName(String name) { - spotImageFileName = name; - } - - // ------------- - // for the right side spot image - - public String getRightSpotImageFileName() { - return rightSpotImageFileName; - } - - public void setRightSpotImageFileName(String name) { - rightSpotImageFileName = name; - } - - // ---------------- - - // TODO: evaluate and remove if this has been deprecated: really only intended to convert legacy SinglePhotoVideo to MediaAsset/Annotation world - public ArrayList generateAnnotations(String baseDir, Shepherd myShepherd) { - if ((annotations != null) && (annotations.size() > 0)) return annotations; - if ((images == null) || (images.size() < 1)) return null; // probably pointless, so... - if (annotations == null) annotations = new ArrayList(); - boolean thumbDone = false; - ArrayList haveMedia = new ArrayList(); // so we dont add duplicates! - for (SinglePhotoVideo spv : images) { - MediaAsset ma = spv.toMediaAsset(myShepherd); - if (ma == null) { - System.out.println( - "WARNING: Encounter.generateAnnotations() could not create MediaAsset from SinglePhotoVideo " - + spv.getDataCollectionEventID() + "; skipping"); - continue; - } - if (haveMedia.contains(ma)) { - System.out.println( - "WARNING: Encounter.generateAnnotations() found a duplicate MediaAsset in the SinglePhotoVideo images; skipping -- " - + ma); - continue; - } - // note: we need at least minimal metadata (w,h) in order to make annotation, so if this fails, we are no-go - try { - ma.updateMetadata(); - } catch (IOException ioe) { - System.out.println( - "WARNING: Encounter.generateAnnotations() failed to updateMetadata() on original MediaAsset " - + ma + " (skipping): " + ioe.toString()); - continue; - } - ma.addLabel("_original"); - haveMedia.add(ma); - - annotations.add(new Annotation(getTaxonomyString(), ma)); - File idir = new File(spv.getFullFileSystemPath()).getParentFile(); - - addMediaIfNeeded(myShepherd, new File(idir, spv.getDataCollectionEventID() + ".jpg"), - "spv/" + spv.getDataCollectionEventID() + "/" + spv.getDataCollectionEventID() + - ".jpg", ma, "_watermark"); - addMediaIfNeeded(myShepherd, - new File(idir, spv.getDataCollectionEventID() + "-mid.jpg"), - "spv/" + spv.getDataCollectionEventID() + "/" + spv.getDataCollectionEventID() + - "-mid.jpg", ma, "_mid"); - // note: we "assume" thumb was created from 0th spv, cuz we simply dont know but want it living somewhere - if (!thumbDone) - addMediaIfNeeded(myShepherd, new File(idir, "/thumb.jpg"), - "spv/" + spv.getDataCollectionEventID() + "/thumb.jpg", ma, "_thumb"); - thumbDone = true; - } - // we need to have the spot image as a child under *some* MediaAsset from above, but unfortunately we do not know its lineage. so we just - // pick one. :/ - MediaAsset sma = spotImageAsMediaAsset(((annotations.size() < - 1) ? null : annotations.get(0).getMediaAsset()), baseDir, myShepherd); - return annotations; - } - - // utility method for created MediaAssets - // note: also will check for existence of mpath and fail silently if doesnt exist - private MediaAsset addMediaIfNeeded(Shepherd myShepherd, File mpath, String key, - MediaAsset parentMA, String label) { - if ((mpath == null) || !mpath.exists()) return null; - AssetStore astore = AssetStore.getDefault(myShepherd); - org.json.JSONObject sp = astore.createParameters(mpath); - if (key != null) sp.put("key", key); // will use default from createParameters() (if there was one even) - MediaAsset ma = astore.find(sp, myShepherd); - if (ma != null) { - ma.addLabel(label); - if (parentMA != null) ma.setParentId(parentMA.getIdInt()); - return ma; - } - System.out.println("creating new MediaAsset for key=" + key); - try { - ma = astore.copyIn(mpath, sp); - } catch (IOException ioe) { - System.out.println("Could not create MediaAsset for key=" + key + ": " + - ioe.toString()); - return null; - } - if (parentMA != null) { - ma.setParentId(parentMA.getIdInt()); - ma.updateMinimalMetadata(); // for children (ostensibly derived?) MediaAssets, really only need minimal metadata or so i claim - } else { - try { - ma.updateMetadata(); // root images get the whole deal (guess this sh/could key off label=_original ?) - } catch (IOException ioe) { - // we dont care (well sorta) ... since IOException usually means we couldnt open file or some nonsense that we cant recover from - } - } - ma.addLabel(label); - MediaAssetFactory.save(ma, myShepherd); - return ma; - } - - // this makes assumption (for flukes) that both right and left image files are identical - public MediaAsset spotImageAsMediaAsset(MediaAsset parent, String baseDir, - Shepherd myShepherd) { - if ((spotImageFileName == null) || spotImageFileName.equals("")) return null; - File fullPath = new File(this.dir(baseDir) + "/" + spotImageFileName); -// System.out.println("**** * ***** looking for spot file " + fullPath.toString()); - if (!fullPath.exists()) return null; // note: this only technically matters if we are *creating* the MediaAsset - if (parent == null) { - System.out.println("seems like we do not have a parent MediaAsset on enc " + - this.getCatalogNumber() + ", so cannot add spot MediaAsset for " + - fullPath.toString()); - return null; - } - AssetStore astore = AssetStore.getDefault(myShepherd); - if (astore == null) { - System.out.println("No AssetStore in Encounter.spotImageAsMediaAsset()"); - return null; - } - System.out.println("trying spotImageAsMediaAsset with file=" + fullPath.toString()); - org.json.JSONObject sp = astore.createParameters(fullPath); - sp.put("key", this.subdir() + "/spotImage-" + spotImageFileName); - // others? - MediaAsset ma = astore.find(sp, myShepherd); - if (ma == null) { - System.out.println("did not find MediaAsset for params=" + sp + "; creating one?"); - try { - ma = astore.copyIn(fullPath, sp); - ma.addDerivationMethod("historicSpotImageConversion", true); - ma.updateMinimalMetadata(); -// System.out.println("params? " + ma.getParameters()); - ma.addLabel("_spot"); - ma.addLabel("_annotation"); - MediaAssetFactory.save(ma, myShepherd); -// System.out.println("params? " + ma.getParameters()); - } catch (java.io.IOException ex) { - System.out.println("spotImageAsMediaAsset threw IOException " + ex.toString()); - } - } - ma.setParentId(parent.getIdInt()); - return ma; - } - - public void setSubmitterID(String username) { - if (username != null) { submitterID = username; } else { submitterID = null; } - } - - // old method. use getAssignedUser() instead - public String getSubmitterID() { - return getAssignedUsername(); - } - - public String getAssignedUsername() { - return submitterID; - } - - public User getSubmitterUser(Shepherd myShepherd) { - return myShepherd.getUser(submitterID); - } - - public Vector getInterestedResearchers() { - return interestedResearchers; - } - - public void addInterestedResearcher(String email) { - interestedResearchers.add(email); - } - - public double getRightmostSpot() { - double rightest = 0; - ArrayList spots = getSpots(); - - for (int iter = 0; iter < spots.size(); iter++) { - if (spots.get(iter).getTheSpot().getCentroidX() > rightest) { - rightest = spots.get(iter).getTheSpot().getCentroidX(); - } - } - return rightest; - } - - public double getLeftmostSpot() { - double leftest = getRightmostSpot(); - ArrayList spots = getSpots(); - - for (int iter = 0; iter < spots.size(); iter++) { - if (spots.get(iter).getTheSpot().getCentroidX() < leftest) { - leftest = spots.get(iter).getTheSpot().getCentroidX(); - } - } - return leftest; - } - - public double getHighestSpot() { - double highest = getLowestSpot(); - ArrayList spots = getSpots(); - - for (int iter = 0; iter < spots.size(); iter++) { - if (spots.get(iter).getTheSpot().getCentroidY() < highest) { - highest = spots.get(iter).getTheSpot().getCentroidY(); - } - } - return highest; - } - - public double getLowestSpot() { - double lowest = 0; - ArrayList spots = getSpots(); - - for (int iter = 0; iter < spots.size(); iter++) { - if (spots.get(iter).getTheSpot().getCentroidY() > lowest) { - lowest = spots.get(iter).getTheSpot().getCentroidY(); - } - } - return lowest; - } - - public com.reijns.I3S.Point2D[] getThreeLeftFiducialPoints() { - com.reijns.I3S.Point2D[] Rray = new com.reijns.I3S.Point2D[3]; - if (getLeftReferenceSpots() != null) { - ArrayList refsLeft = getLeftReferenceSpots(); - - Rray[0] = new com.reijns.I3S.Point2D(refsLeft.get(0).getTheSpot().getCentroidX(), - refsLeft.get(0).getTheSpot().getCentroidY()); - Rray[1] = new com.reijns.I3S.Point2D(refsLeft.get(1).getTheSpot().getCentroidX(), - refsLeft.get(1).getTheSpot().getCentroidY()); - Rray[2] = new com.reijns.I3S.Point2D(refsLeft.get(2).getTheSpot().getCentroidX(), - refsLeft.get(2).getTheSpot().getCentroidY()); - System.out.println("\tI found three left reference points!"); - } else { - com.reijns.I3S.Point2D topLeft = new com.reijns.I3S.Point2D(getLeftmostSpot(), - getHighestSpot()); - com.reijns.I3S.Point2D bottomLeft = new com.reijns.I3S.Point2D(getLeftmostSpot(), - getLowestSpot()); - com.reijns.I3S.Point2D bottomRight = new com.reijns.I3S.Point2D(getRightmostSpot(), - getLowestSpot()); - Rray[0] = topLeft; - Rray[1] = bottomLeft; - Rray[2] = bottomRight; - } - return Rray; - } - - public com.reijns.I3S.Point2D[] getThreeRightFiducialPoints() { - com.reijns.I3S.Point2D[] Rray = new com.reijns.I3S.Point2D[3]; - if (getRightReferenceSpots() != null) { - ArrayList refsRight = getRightReferenceSpots(); - Rray[0] = new com.reijns.I3S.Point2D(refsRight.get(0).getTheSpot().getCentroidX(), - refsRight.get(0).getTheSpot().getCentroidY()); - Rray[1] = new com.reijns.I3S.Point2D(refsRight.get(1).getTheSpot().getCentroidX(), - refsRight.get(1).getTheSpot().getCentroidY()); - Rray[2] = new com.reijns.I3S.Point2D(refsRight.get(2).getTheSpot().getCentroidX(), - refsRight.get(2).getTheSpot().getCentroidY()); - } else { - com.reijns.I3S.Point2D topRight = new com.reijns.I3S.Point2D(getRightmostRightSpot(), - getHighestRightSpot()); - com.reijns.I3S.Point2D bottomRight = new com.reijns.I3S.Point2D(getRightmostRightSpot(), - getLowestRightSpot()); - com.reijns.I3S.Point2D bottomLeft = new com.reijns.I3S.Point2D(getLeftmostRightSpot(), - getLowestRightSpot()); - - Rray[0] = topRight; - Rray[1] = bottomRight; - Rray[2] = bottomLeft; - } - return Rray; - } - - public double getRightmostRightSpot() { - double rightest = 0; - ArrayList rightSpots = getRightSpots(); - - for (int iter = 0; iter < rightSpots.size(); iter++) { - if (rightSpots.get(iter).getTheSpot().getCentroidX() > rightest) { - rightest = rightSpots.get(iter).getTheSpot().getCentroidX(); - } - } - return rightest; - } - - public double getLeftmostRightSpot() { - double leftest = getRightmostRightSpot(); - ArrayList rightSpots = getRightSpots(); - - for (int iter = 0; iter < rightSpots.size(); iter++) { - if (rightSpots.get(iter).getTheSpot().getCentroidX() < leftest) { - leftest = rightSpots.get(iter).getTheSpot().getCentroidX(); - } - } - return leftest; - } - - public double getHighestRightSpot() { - double highest = getLowestRightSpot(); - ArrayList rightSpots = getRightSpots(); - - for (int iter = 0; iter < rightSpots.size(); iter++) { - if (rightSpots.get(iter).getTheSpot().getCentroidY() < highest) { - highest = rightSpots.get(iter).getTheSpot().getCentroidY(); - } - } - return highest; - } - - public double getLowestRightSpot() { - double lowest = 0; - ArrayList rightSpots = getRightSpots(); - - for (int iter = 0; iter < rightSpots.size(); iter++) { - if (rightSpots.get(iter).getTheSpot().getCentroidY() > lowest) { - lowest = rightSpots.get(iter).getTheSpot().getCentroidY(); - } - } - return lowest; - } - - public ArrayList getLeftReferenceSpots() { - // return HACKgetAnyReferenceSpots(); - return leftReferenceSpots; - } - - public ArrayList getRightReferenceSpots() { - // return HACKgetAnyReferenceSpots(); - return rightReferenceSpots; - } - -/* gone! no more setting spots on encounters! ... whoa there, yes there is for whaleshark.org */ - public void setLeftReferenceSpots(ArrayList leftReferenceSpots) { - this.leftReferenceSpots = leftReferenceSpots; - } - - public void setRightReferenceSpots(ArrayList rightReferenceSpots) { - this.rightReferenceSpots = rightReferenceSpots; - } - - // this is for jsonForApiGet() - public org.json.JSONObject spotMappingJsonForApiGet() { - org.json.JSONObject rtn = new org.json.JSONObject(); - boolean enabled = CommonConfiguration.useSpotPatternRecognition("context0"); - rtn.put("enabled", enabled); - if (!enabled) return rtn; - rtn.put("numberLeftSpots", getNumSpots()); - rtn.put("numberRightSpots", getNumRightSpots()); - rtn.put("hasLeftSpots", getNumSpots() > 0); - rtn.put("hasRightSpots", getNumRightSpots() > 0); - rtn.put("hasSpots", (getNumSpots() + getNumRightSpots()) > 0); - - // check where results xml is stored (per spotMappingAlgorith.jsp) - File ddir = Util.getDataDir(); - String encDir = dir(ddir.toString()); - rtn.put("resultsGrothLeft", new File(encDir, "lastFullScan.xml").exists()); - rtn.put("resultsGrothRight", new File(encDir, "lastFullRightScan.xml").exists()); - rtn.put("resultsI3SLeft", new File(encDir, "lastFullI3SScan.xml").exists()); - rtn.put("resultsI3SRight", new File(encDir, "lastFullRightI3SScan.xml").exists()); - return rtn; - } - - // @return the variance for population - public double variance(double[] population) { - long n = 0; - double mean = 0; - double s = 0.0; - - for (double x : population) { - n++; - double delta = x - mean; - mean += delta / n; - s += delta * (x - mean); - } - // if you want to calculate std deviation - // of a sample change this to (s/(n-1)) - // return (s / n); - return (s / (n - 1)); - } - - // @return the standard deviation for population - public double standard_deviation(double[] population) { - return Math.sqrt(variance(population)); - } - - public void setDWCGlobalUniqueIdentifier(String guid) { - this.guid = guid; - } - - public String getDWCGlobalUniqueIdentifier() { - return guid; - } - - public void setDWCImageURL(String link) { - dwcImageURL = link; - } - - // lmao, we have this capitalization of the getter for reflexivity purposes - public String getModified() { - return modified; - } - - public String getDWCDateLastModified() { - return modified; - } - - public void setDWCDateLastModified(String lastModified) { - modified = lastModified; - } - - public void setDWCDateLastModified() { - modified = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(new Date()); - } - - public String getDWCDateAdded() { - return dwcDateAdded; - } - - // lmao, we have this capitalization of the getter for reflexivity purposes - public String getDwcDateAdded() { - return dwcDateAdded; - } - - public Long getDWCDateAddedLong() { - return dwcDateAddedLong; - } - - public Long getDwcDateAddedLong() { - return dwcDateAddedLong; - } - - public void setDWCDateAdded(String m_dateAdded) { - dwcDateAdded = m_dateAdded; - } - - public void setDWCDateAdded() { - Date myDate = new Date(); - - dwcDateAddedLong = new Long(myDate.getTime()); - dwcDateAdded = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(myDate); - } - - public void setDWCDateAdded(Long m_dateAdded) { - dwcDateAddedLong = m_dateAdded; - } - - // TODO: evaluate and remove if deprecated - public Date getReleaseDateDONOTUSE() { - return releaseDate; - } - - public Date getReleaseDate() { - if ((releaseDateLong != null) && (releaseDateLong > 0)) { - Date mDate = new Date(releaseDateLong); - return mDate; - } - return null; - } - - public Long getReleaseDateLong() { return releaseDateLong; } - - public void setReleaseDate(Long releaseDate) { - this.releaseDateLong = releaseDate; - } - - // Survey ect associations... - - public void setSurveyTrackID(String id) { - if (id != null && !id.equals("")) { - this.correspondingSurveyTrackID = id; - } - } - - public String getSurveyTrackID() { - if (correspondingSurveyTrackID != null) { - return correspondingSurveyTrackID; - } - return null; - } - - public void setPointLocation(PointLocation loc) { - if (loc.getID() != null) { - this.pointLocation = loc; - } - } - - public PointLocation getPointLocation() { - if (pointLocation != null) { - return pointLocation; - } - return null; - } - - public String getSurveyID() { - if (correspondingSurveyID != null && !correspondingSurveyID.equals("")) { - return correspondingSurveyID; - } - return null; - } - - public void setSurveyID(String id) { - if (id != null && !id.equals("")) { - this.correspondingSurveyID = id; - } - } - - public void setSurvey() { - } - - // TODO: Get all this lat lon over to Locations - - public void setDWCDecimalLatitude(double lat) { - if (lat == -9999.0) { - decimalLatitude = null; - } else { - decimalLatitude = (new Double(lat)); - } - } - - public void setDWCDecimalLatitude(Double lat) { - if ((lat != null) && (lat <= 90) && (lat >= -90)) { - this.decimalLatitude = lat; - } else { this.decimalLatitude = null; } - } - - public String getDWCDecimalLatitude() { - if (decimalLatitude != null) { return Double.toString(decimalLatitude); } - return null; - } - - public void setDWCDecimalLongitude(double longit) { - if ((longit >= -180) && (longit <= 180)) { - this.decimalLongitude = longit; - } - } - - public String getDWCDecimalLongitude() { - if (decimalLongitude != null) { - return Double.toString(decimalLongitude); - } - return null; - } - - public boolean getOKExposeViaTapirLink() { - return okExposeViaTapirLink; - } - - public void setOKExposeViaTapirLink(boolean ok) { - okExposeViaTapirLink = ok; - } - - public void setAlternateID(String newID) { - this.otherCatalogNumbers = newID; - } - - public String getAlternateID() { - if (otherCatalogNumbers == null) { - return null; - } - return otherCatalogNumbers; - } - - public String getOLDInformOthersFORLEGACYCONVERSION() { - if (informothers == null) { - return ""; - } - return informothers; - } - - public String getLocationID() { - return locationID; - } - - public String getLocationName() { - if (locationID == null) return null; - return LocationID.getNameForLocationID(locationID, null); - } - - public void setLocationID(String newLocationID) { - if (newLocationID != null) { - this.locationID = newLocationID.trim(); - } else { - this.locationID = null; - } - } - - public Double getMaximumDepthInMeters() { - return maximumDepthInMeters; - } - - public void setMaximumDepthInMeters(Double newDepth) { - this.maximumDepthInMeters = newDepth; - } - - public Double getMaximumElevationInMeters() { - return maximumElevationInMeters; - } - - public void setMaximumElevationInMeters(Double newElev) { - this.maximumElevationInMeters = newElev; - } - - // @return Catalog Number String - @Override public String getId() { - return catalogNumber; - } - - // @param newNumber The Catalog Number to set. - @Override public void setId(String newNumber) { - this.catalogNumber = newNumber; - } - - // TODO: remove if actually deprecated and unused - // ##DEPRECATED #509 - Base class getId() method - public String getCatalogNumber() { - return catalogNumber; - } - - // TODO: remove if actually deprecated and unused - // ##DEPRECATED #509 - Base class setId() method - public void setCatalogNumber(String newNumber) { - this.catalogNumber = newNumber; - } - - // TODO: remove if actually deprecated and unused - // ##DEPRECATED #509 - Base class getId() method - public String getID() { - return catalogNumber; - } - - // TODO: remove if actually deprecated and unused - // ##DEPRECATED #509 - Base class setId() method - public void setID(String newNumber) { - this.catalogNumber = newNumber; - } - - public String getVerbatimLocality() { - return verbatimLocality; - } - - public void setVerbatimLocality(String vlcl) { - this.verbatimLocality = vlcl; - } - - public Double getDecimalLatitudeAsDouble() { - return (decimalLatitude == null) ? null : decimalLatitude.doubleValue(); - } - - public void setDecimalLatitude(Double lat) { - this.decimalLatitude = lat; - gpsLatitude = Util.decimalLatLonToString(lat); - } - - public Double getDecimalLongitudeAsDouble() { - return (decimalLongitude == null) ? null : decimalLongitude.doubleValue(); - } - - public void setDecimalLongitude(Double lon) { - this.decimalLongitude = lon; - gpsLongitude = Util.decimalLatLonToString(lon); - } - - public Double getEndDecimalLatitudeAsDouble() { - return (endDecimalLatitude == null) ? null : endDecimalLatitude.doubleValue(); - } - - public void setEndDecimalLatitude(Double lat) { - this.endDecimalLatitude = lat; - gpsEndLatitude = Util.decimalLatLonToString(lat); - } - - public Double getEndDecimalLongitudeAsDouble() { - return (endDecimalLongitude == null) ? null : endDecimalLongitude.doubleValue(); - } - - public void setEndDecimalLongitude(Double lon) { - this.endDecimalLongitude = lon; - gpsEndLongitude = Util.decimalLatLonToString(lon); - } - - public String getOccurrenceRemarks() { - return occurrenceRemarks; - } - - public void setOccurrenceRemarks(String remarks) { - this.occurrenceRemarks = remarks; - } - - public String getRecordedBy() { - return recordedBy; - } - - public void setRecordedBy(String submitterName) { - this.recordedBy = submitterName; - } - - public String getOtherCatalogNumbers() { - return otherCatalogNumbers; - } - - public void setOtherCatalogNumbers(String otherNums) { - this.otherCatalogNumbers = otherNums; - } - - public String getLivingStatus() { - return livingStatus; - } - - public void setLivingStatus(String status) { - this.livingStatus = status; - } - - public void setAge(Double a) { - age = a; - } - - public Double getAge() { - return age; - } - - public String getBehavior() { - return behavior; - } - - public void setBehavior(String beh) { - this.behavior = beh; - } - - public String getEventID() { - return eventID; - } - - public void setEventID(String id) { - this.eventID = id; - } - - public String getVerbatimEventDate() { - return verbatimEventDate; - } - - public void setVerbatimEventDate(String vet) { - if (vet != null) { this.verbatimEventDate = vet; } else { this.verbatimEventDate = null; } - } - - public String getDynamicProperties() { - return dynamicProperties; - } - - public org.json.JSONObject getDynamicPropertiesJSONObject() { - org.json.JSONObject dp = new org.json.JSONObject(); - if (dynamicProperties == null) return dp; - StringTokenizer st = new StringTokenizer(dynamicProperties, ";"); - while (st.hasMoreTokens()) { - String token = st.nextToken(); - int equalPlace = token.indexOf("="); - if (equalPlace > 0) - dp.put(token.substring(0, equalPlace), token.substring(equalPlace + 1)); - } - return dp; - } - - public void setDynamicProperties(String allDynamicProperties) { - this.dynamicProperties = allDynamicProperties; - } - - public void addDynamicProperties(String allDynamicProperties) { - this.dynamicProperties += allDynamicProperties; - } - - public void setDynamicProperty(String name, String value) { - name = name.replaceAll(";", "_").trim().replaceAll("%20", " "); - value = value.replaceAll(";", "_").trim(); - if (dynamicProperties == null) { dynamicProperties = name + "=" + value + ";"; } else { - // let's create a TreeMap of the properties - TreeMap tm = new TreeMap(); - StringTokenizer st = new StringTokenizer(dynamicProperties, ";"); - while (st.hasMoreTokens()) { - String token = st.nextToken(); - int equalPlace = token.indexOf("="); - try { - tm.put(token.substring(0, equalPlace), token.substring(equalPlace + 1)); - } catch (java.lang.StringIndexOutOfBoundsException soe) { - // this is a badly formatted pair that should be ignored - } - } - if (tm.containsKey(name)) { - tm.remove(name); - tm.put(name, value); - - // now let's recreate the dynamicProperties String - String newProps = tm.toString(); - int stringSize = newProps.length(); - dynamicProperties = newProps.substring(1, (stringSize - 1)).replaceAll(", ", - ";") + ";"; - } else { - dynamicProperties = dynamicProperties + name + "=" + value + ";"; - } - } - } - - public String getDynamicPropertyValue(String name) { - if (dynamicProperties != null) { - name = name.replaceAll("%20", " "); - // let's create a TreeMap of the properties - TreeMap tm = new TreeMap(); - StringTokenizer st = new StringTokenizer(dynamicProperties, ";"); - while (st.hasMoreTokens()) { - String token = st.nextToken(); - int equalPlace = token.indexOf("="); - tm.put(token.substring(0, equalPlace), token.substring(equalPlace + 1)); - } - if (tm.containsKey(name)) { - return tm.get(name); - } - } - return null; - } - - public boolean hasDynamicProperty(String name) { - return (this.getDynamicPropertyValue(name) != null); - } - - public void removeDynamicProperty(String name) { - name = name.replaceAll(";", "_").trim().replaceAll("%20", " "); - if (dynamicProperties != null) { - // let's create a TreeMap of the properties - TreeMap tm = new TreeMap(); - StringTokenizer st = new StringTokenizer(dynamicProperties, ";"); - while (st.hasMoreTokens()) { - String token = st.nextToken(); - int equalPlace = token.indexOf("="); - tm.put(token.substring(0, (equalPlace)), token.substring(equalPlace + 1)); - } - if (tm.containsKey(name)) { - tm.remove(name); - - // now let's recreate the dynamicProperties String - String newProps = tm.toString(); - int stringSize = newProps.length(); - dynamicProperties = newProps.substring(1, (stringSize - 1)).replaceAll(", ", - ";") + ";"; - } - } - } - - public String getIdentificationRemarks() { - return identificationRemarks; - } - - public String getHashedSubmitterEmail() { - return hashedSubmitterEmail; - } - - public String getHashedPhotographerEmail() { - return hashedPhotographerEmail; - } - - public String getHashedInformOthers() { - return hashedInformOthers; - } - - public static String getHashOfEmailString(String hashMe) { - if (hashMe == null) return null; - String returnString = ""; - StringTokenizer tokenizer = new StringTokenizer(hashMe, ","); - while (tokenizer.hasMoreTokens()) { - String emailAddress = tokenizer.nextToken().trim().toLowerCase(); - if (!emailAddress.equals("")) { - String md5 = DigestUtils.md5Hex(emailAddress); - if (returnString.equals("")) { - returnString += md5; - } else { - returnString += "," + md5; - } - } - } - return returnString; - } - - public String getGenus() { - return genus; - } - - public void setGenus(String newGenus) { - if (newGenus != null) { genus = newGenus; } else { genus = null; } - this.refreshAnnotationLiteTaxonomy(); - } - - // we need these methods because our side-effected setGenus will silently break an import (!!!!!) in an edge case I cannot identify - public void setGenusOnly(String genus) { - this.genus = genus; - this.refreshAnnotationLiteTaxonomy(); - } - - public void setSpeciesOnly(String species) { - setSpecificEpithet(species); - this.refreshAnnotationLiteTaxonomy(); - } - - public String getSpecificEpithet() { - return specificEpithet; - } - - public void setSpecificEpithet(String newEpithet) { - if (newEpithet != null) { specificEpithet = newEpithet.replaceAll("_", " "); } else { - specificEpithet = null; - } - this.refreshAnnotationLiteTaxonomy(); - } - - public String getTaxonomyString() { - return Util.taxonomyString(getGenus(), getSpecificEpithet()); - } - - // hacky (as generates new Taxonomy -- with random uuid) but still should work for tax1.equals(tax2); - // TODO: FIXME this should be superceded by the getter for Taxonomy property in the future.... - public Taxonomy getTaxonomy(Shepherd myShepherd) { - String sciname = this.getTaxonomyString(); - - if (sciname == null) return null; - return myShepherd.getOrCreateTaxonomy(sciname, false); // false means don't commit the taxonomy - } - - // right now this updates .genus and .specificEpithet ... but in some glorious future we will just store Taxonomy! - // note that "null" cases will leave *current values untouched* (does not reset them) - public void setTaxonomy(Taxonomy tax) { - if (tax == null) return; - String[] gs = tax.getGenusSpecificEpithet(); - if ((gs == null) || (gs.length < 1)) return; - if (gs.length == 1) { - this.genus = gs[0]; - this.specificEpithet = null; - } else { - this.genus = gs[0]; - this.specificEpithet = gs[1].replaceAll("_", " "); - } - this.refreshAnnotationLiteTaxonomy(); - } - - public void setTaxonomyFromString(String s) { // basically scientific name (will get split on space) - String[] gs = Util.stringToGenusSpecificEpithet(s); - - if ((gs == null) || (gs.length < 1)) return; - if (gs.length == 1) { - this.genus = gs[0]; - this.specificEpithet = null; - } else { - this.genus = gs[0]; - this.specificEpithet = gs[1].replaceAll("_", " "); - } - this.refreshAnnotationLiteTaxonomy(); - } - - public void setTaxonomyFromIAClass(String iaClass, Shepherd myShepherd) { - setTaxonomy(IBEISIA.iaClassToTaxonomy(iaClass, myShepherd)); - } - - public String getPatterningCode() { return patterningCode; } - public void setPatterningCode(String newCode) { this.patterningCode = newCode; } - - // crawls thru assets and sets date - public void setDateFromAssets() { - // FIXME if you dare. i can *promise you* there are some timezone problems here. ymmv. - if ((annotations == null) || (annotations.size() < 1)) return; - DateTime dt = null; - for (Annotation ann : annotations) { - MediaAsset ma = ann.getMediaAsset(); - if (ma == null) continue; - dt = ma.getDateTime(); - if (dt != null) break; // we just take the first one - } - if (dt != null) setDateInMilliseconds(dt.getMillis()); - } - - // this can(should?) fail in a lot of cases, since we may not know - public void setSpeciesFromAnnotations() { - if ((annotations == null) || (annotations.size() < 1)) return; - String[] sp = null; - for (Annotation ann : annotations) { - sp = IBEISIA.convertSpecies(annotations.get(0).getIAClass()); - if (sp != null) break; // use first one we get - } - // note: now we require (exactly) two parts ... please fix this, Taxonomy class! - if ((sp == null) || (sp.length != 2)) return; - this.setGenus(sp[0]); - this.setSpecificEpithet(sp[1]); - } - - // find the first one(s) we can - public void setLatLonFromAssets() { - if ((annotations == null) || (annotations.size() < 1)) return; - Double lat = null; - Double lon = null; - for (Annotation ann : annotations) { - MediaAsset ma = ann.getMediaAsset(); - if (ma == null) continue; - if (lat == null) lat = ma.getLatitude(); - if (lon == null) lon = ma.getLongitude(); - if ((lat != null) && (lon != null)) break; - } - if (lat != null) this.setDecimalLatitude(lat); - if (lon != null) this.setDecimalLongitude(lon); - } - - // sets date to the closes we have to "not set" :) - public void zeroOutDate() { - year = 0; - month = 0; - day = 0; - hour = -1; - minutes = "00"; - resetDateInMilliseconds(); // should set that to null as well - } - - public void resetDateInMilliseconds() { - dateInMilliseconds = computeDateInMilliseconds(); - } - - public Long computeDateInMilliseconds() { - if (year > 0) { - int localMonth = 0; - if (month > 0) { localMonth = month - 1; } - int localDay = 1; - if (day > 0) { localDay = day; } - int localHour = 0; - if (hour > -1) { localHour = hour; } - int myMinutes = 0; - try { myMinutes = Integer.parseInt(minutes); } catch (Exception e) {} - TimeZone tz = TimeZone.getTimeZone("UTC"); - Calendar calendar = Calendar.getInstance(tz); - calendar.set(year, localMonth, localDay, localHour, myMinutes); - return new Long(calendar.getTimeInMillis()); - } - return null; - } - - public java.lang.Long getDateInMilliseconds() { return dateInMilliseconds; } - - public Long getDateInMillisecondsFallback() { - if (dateInMilliseconds != null) return dateInMilliseconds; - return computeDateInMilliseconds(); - } - - // this will set all date stuff based on ms since epoch - public void setDateInMilliseconds(long ms) { - Calendar cal = Calendar.getInstance(TimeZone.getTimeZone("UTC")); - - cal.setTimeInMillis(ms); - this.year = cal.get(Calendar.YEAR); - this.month = cal.get(Calendar.MONTH) + 1; - this.day = cal.get(Calendar.DAY_OF_MONTH); - this.hour = cal.get(Calendar.HOUR); - this.minutes = Integer.toString(cal.get(Calendar.MINUTE)); - if (this.minutes.length() == 1) this.minutes = "0" + this.minutes; - this.dateInMilliseconds = ms; - } - - // also supports YYYY and YYYY-MM - // per issue 1489, cannot set a future date - public void setDateFromISO8601String(String iso8601) - throws ApiException { - if (!validISO8601String(iso8601)) return; - - // this is for potential ApiException - org.json.JSONObject error = new org.json.JSONObject(); - error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); - - if (iso8601.length() == 4) { // assume year - try { - this.year = Integer.parseInt(iso8601); - } catch (Exception ex) {} - - // got an int year, but lets see if it is valid - if (Util.dateIsInFuture(this.year, null, null)) { - error.put("fieldName", "year"); - error.put("value", this.year); - throw new ApiException("date is in the future", error); - } - resetDateInMilliseconds(); - return; - } - // this format should already be validated so we can trust it (flw) - if (iso8601.length() == 7) { - try { - this.year = Integer.parseInt(iso8601.substring(0, 4)); - this.month = Integer.parseInt(iso8601.substring(5, 7)); - } catch (Exception ex) {} - if (Util.dateIsInFuture(this.year, this.month, null)) { - // if we wanted to be super thorough we could do errors array of year & month - error.put("fieldName", "month"); - error.put("value", this.month); - throw new ApiException("date is in the future", error); - } - resetDateInMilliseconds(); - return; - } - try { - String adjusted = Util.getISO8601Date(iso8601); - DateTime dt = new DateTime(adjusted); - if (Util.dateIsInFuture(dt.getYear(), dt.getMonthOfYear(), dt.getDayOfMonth())) { - error.put("fieldName", "day"); - error.put("value", dt.getDayOfMonth()); - throw new ApiException("date is in the future", error); - } - this.setDateInMilliseconds(dt.getMillis()); - // pass this flavor out... - } catch (ApiException ex) { - throw ex; - // this catches failure of new DateTime() basically, so we make this an ApiException - } catch (Exception ex) { - System.out.println("setDateFromISO8601String(" + iso8601 + ") failed: " + ex); - throw new ApiException("date/time values are invalid"); - } - resetDateInMilliseconds(); - } - - // also supports YYYY and YYYY-MM - public static boolean validISO8601String(String iso8601) { - if (iso8601 == null) return false; - if (iso8601.length() == 4) { - Integer yr = null; - try { - yr = Integer.parseInt(iso8601); - } catch (Exception ex) {} - return (yr != null); - } - if (iso8601.length() == 7) { - Integer yr = null; - Integer mo = null; - try { - yr = Integer.parseInt(iso8601.substring(0, 4)); - mo = Integer.parseInt(iso8601.substring(5, 7)); - } catch (Exception ex) {} - if ((yr == null) || (mo == null)) return false; - if ((mo < 1) || (mo > 12)) return false; - return true; - } - long test = Util.getVersionFromModified(iso8601); - return (test > 0); - } - - public Long getEndDateInMilliseconds() { - return endDateInMilliseconds; - } - - public void setEndDateInMilliseconds(long ms) { - this.endDateInMilliseconds = ms; - } - - private String milliToMonthDayYear(Long millis) { - DateTime dt = new DateTime(millis); - DateTimeFormatter dtf = DateTimeFormat.forPattern("yyyy-MM-dd hh:mm a"); - - return dtf.print(dt); - } - - public String getStartDateTime() { - return milliToMonthDayYear(dateInMilliseconds); - } - - public String getEndDateTime() { - return milliToMonthDayYear(endDateInMilliseconds); - } - - public String getDecimalLatitude() { - if (decimalLatitude != null) { return Double.toString(decimalLatitude); } - return null; - } - - public String getDecimalLongitude() { - if (decimalLongitude != null) { return Double.toString(decimalLongitude); } - return null; - } - - public String getEndDecimalLongitude() { - if (endDecimalLongitude != null) { return Double.toString(endDecimalLongitude); } - return null; - } - - public String getEndDecimalLatitude() { - if (endDecimalLatitude != null) { return Double.toString(endDecimalLatitude); } - return null; - } - - public String getSubmitterProject() { - return submitterProject; - } - - public void setSubmitterProject(String newProject) { - if (newProject != null) { submitterProject = newProject; } else { submitterProject = null; } - } - - public String getSubmitterOrganization() { - return submitterOrganization; - } - - public void setSubmitterOrganization(String newOrg) { - if (newOrg != null) { submitterOrganization = newOrg; } else { - submitterOrganization = null; - } - } - - public List getSubmitterResearchers() { - return submitterResearchers; - } - - public void addSubmitterResearcher(String researcher) { - if (submitterResearchers == null) submitterResearchers = new ArrayList(); - submitterResearchers.add(researcher); - } - - public void setSubmitterResearchers(Collection researchers) { - if (researchers != null) this.submitterResearchers = new ArrayList(researchers); - } - - public List getProjects(Shepherd myShepherd) { - return myShepherd.getProjectsForEncounter(this); - } - - public void addTissueSample(TissueSample dce) { - if (tissueSamples == null) { tissueSamples = new ArrayList(); } - if (!tissueSamples.contains(dce)) { tissueSamples.add(dce); } - dce.setCorrespondingEncounterNumber(getCatalogNumber()); - } - - public void setTissueSamples(List samps) { - this.tissueSamples = samps; - } - - public void removeTissueSample(int num) { tissueSamples.remove(num); } - public List getTissueSamples() { return tissueSamples; } - public Set getTissueSampleIDs() { - Set ids = new HashSet(); - - if (tissueSamples != null) - for (TissueSample ts : tissueSamples) { - ids.add(ts.getSampleID()); - } - return ids; - } - - public void removeTissueSample(TissueSample num) { tissueSamples.remove(num); } - - public void addSinglePhotoVideo(SinglePhotoVideo dce) { - if (images == null) { images = new ArrayList(); } - if (!images.contains(dce)) { images.add(dce); } - } - - public void removeSinglePhotoVideo(int num) { images.remove(num); } - public List getSinglePhotoVideo() { return images; } - public void removeSinglePhotoVideo(SinglePhotoVideo num) { images.remove(num); } - - public void setMeasurements(List measurements) { - this.measurements = measurements; - } - - public void setMeasurement(Measurement measurement, Shepherd myShepherd) { - // if measurements are null, set the empty list - if (measurements == null) { measurements = new ArrayList(); } - // now start checking for existence of a previous measurement - // if we have it but the new value is null, remove the measurement - if ((this.hasMeasurement(measurement.getType())) && (measurement.getValue() == null)) { - Measurement m = this.getMeasurement(measurement.getType()); - measurements.remove(m); - myShepherd.getPM().deletePersistent(m); - myShepherd.commitDBTransaction(); - myShepherd.beginDBTransaction(); - } - // just add the measurement it if we did not have it before - else if (!this.hasMeasurement(measurement.getType())) { - measurements.add(measurement); - myShepherd.commitDBTransaction(); - myShepherd.beginDBTransaction(); - } - // if we had it before then just update the value - else if ((this.hasMeasurement(measurement.getType())) && (measurement != null)) { - Measurement m = this.getMeasurement(measurement.getType()); - m.setValue(measurement.getValue()); - m.setSamplingProtocol(measurement.getSamplingProtocol()); - myShepherd.commitDBTransaction(); - myShepherd.beginDBTransaction(); - } - } - - public Measurement removeMeasurementByType(String type) { - // findMeasurementOfType() seems to return even ones with value=null - // (versus getMeasurement())... so this seems the better choice? - Measurement m = findMeasurementOfType(type); - - if (m != null) measurements.remove(m); - return m; - } - - // will find the Measurement (by type) and modify it *or* make a new one - public Measurement getOrCreateMeasurement(org.json.JSONObject jdata) { - if (jdata == null) return null; - String type = jdata.optString("type", null); - if (type == null) return null; - Measurement m = findMeasurementOfType(type); - if (m == null) { - m = new Measurement(this.getId(), type, jdata.optDouble("value", 0.0D), - jdata.optString("units", null), jdata.optString("samplingProtocol", null)); - } else { - m.setValue(jdata.optDouble("value", 0.0D)); - m.setUnits(jdata.optString("units", null)); - m.setSamplingProtocol(jdata.optString("samplingProtocol", null)); - } - return m; - } - - // like above but way less persisty - public void setMeasurement(Measurement measurement) { - if (measurement == null) return; - if (measurements == null) measurements = new ArrayList(); - Measurement hasType = this.getMeasurement(measurement.getType()); - if (hasType == null) { - measurements.add(measurement); - } else if (measurement.getValue() == null) { - // i guess this means we remove it - measurements.remove(hasType); - } else { - // update existing - hasType.setValue(measurement.getValue()); - hasType.setSamplingProtocol(measurement.getSamplingProtocol()); - } - } - - // like above but less..... checky (trust the caller!) - public void addMeasurement(Measurement meas) { - if (meas == null) return; - if (measurements == null) measurements = new ArrayList(); - measurements.add(meas); - } - - public void removeMeasurement(int num) { measurements.remove(num); } - public List getMeasurements() { return measurements; } - public void removeMeasurement(Measurement num) { measurements.remove(num); } - // FIXME this seems suspiciously just like getMeasurement(type) - public Measurement findMeasurementOfType(String type) { - List measurements = getMeasurements(); - - if (measurements != null) { - for (Measurement measurement : measurements) { - if (type.equals(measurement.getType())) { - return measurement; - } - } - } - return null; - } - - public void addMetalTag(MetalTag metalTag) { - if (metalTags == null) { - metalTags = new ArrayList(); - } - metalTags.add(metalTag); - } - - // this does NOT validate values - public MetalTag addOrUpdateMetalTag(String location, String number) { - if ((location == null) || (number == null)) return null; - MetalTag tag = findMetalTagForLocation(location); - if (tag == null) { - tag = new MetalTag(number, location); - addMetalTag(tag); - } else { - tag.setTagNumber(number); - } - return tag; - } - - public void removeMetalTag(MetalTag metalTag) { - metalTags.remove(metalTag); - } - - // this will clear out ALL tags with this location, but i think we - // are supposed to only have [at most] one anyway! - public void removeMetalTag(String location) { - if ((location == null) || (metalTags == null)) return; - ListIterator it = metalTags.listIterator(); - while (it.hasNext()) { - MetalTag next = it.next(); - if (location.equals(next.getLocation())) it.remove(); - } - } - - public void setMetalTags(List metalTags) { - this.metalTags = metalTags; - } - - public List getMetalTags() { - return metalTags; - } - - public MetalTag findMetalTagForLocation(String location) { - List metalTags = getMetalTags(); - - if (metalTags != null) { - for (MetalTag metalTag : metalTags) { - if (location.equals(metalTag.getLocation())) { - return metalTag; - } - } - } - return null; - } - - public AcousticTag getAcousticTag() { - return acousticTag; - } - - public void setAcousticTag(AcousticTag acousticTag) { - this.acousticTag = acousticTag; - } - - public SatelliteTag getSatelliteTag() { - return satelliteTag; - } - - public void setSatelliteTag(SatelliteTag satelliteTag) { - this.satelliteTag = satelliteTag; - } - - public DigitalArchiveTag getDTag() { - return digitalArchiveTag; - } - - public void setDTag(DigitalArchiveTag dt) { - this.digitalArchiveTag = dt; - } - - public String getLifeStage() { return lifeStage; } - public void setLifeStage(String newStage) { - if (newStage != null) { lifeStage = newStage; } else { lifeStage = null; } - } - - // A convenience method that returns the first haplotype found in the TissueSamples for this Encounter. - public String getHaplotype() { - if (tissueSamples != null) { - int numTissueSamples = tissueSamples.size(); - if (numTissueSamples > 0) { - for (int j = 0; j < numTissueSamples; j++) { - TissueSample thisSample = tissueSamples.get(j); - int numAnalyses = thisSample.getNumAnalyses(); - if (numAnalyses > 0) { - List gAnalyses = thisSample.getGeneticAnalyses(); - for (int g = 0; g < numAnalyses; g++) { - GeneticAnalysis ga = gAnalyses.get(g); - if (ga.getAnalysisType().equals("MitochondrialDNA")) { - MitochondrialDNAAnalysis mito = (MitochondrialDNAAnalysis)ga; - if (mito.getHaplotype() != null) { return mito.getHaplotype(); } - } - } - } - } - } - } - return null; - } - - // A convenience method that returns the first genetic sex found in the TissueSamples for this Encounter. - public String getGeneticSex() { - if (tissueSamples != null) { - int numTissueSamples = tissueSamples.size(); - if (numTissueSamples > 0) { - for (int j = 0; j < numTissueSamples; j++) { - TissueSample thisSample = tissueSamples.get(j); - int numAnalyses = thisSample.getNumAnalyses(); - if (numAnalyses > 0) { - List gAnalyses = thisSample.getGeneticAnalyses(); - for (int g = 0; g < numAnalyses; g++) { - GeneticAnalysis ga = gAnalyses.get(g); - if (ga.getAnalysisType().equals("SexAnalysis")) { - SexAnalysis mito = (SexAnalysis)ga; - if (mito.getSex() != null) { return mito.getSex(); } - } - } - } - } - } - } - return null; - } - - public List getMicrosatelliteMarkers() { - List markers = - new ArrayList(); - - if (tissueSamples == null) return markers; - for (TissueSample tsamp : tissueSamples) { - for (GeneticAnalysis gan : tsamp.getGeneticAnalyses()) { - if (!"MicrosatelliteMarkers".equals(gan.getAnalysisType())) continue; - markers.add((MicrosatelliteMarkersAnalysis)gan); - } - } - return markers; - } - - public List getImages() { return images; } - - public boolean hasAnnotation(Annotation ann) { - return (annotations != null && annotations.contains(ann)); - } - - public boolean hasAnnotations() { - return (annotations != null && annotations.size() > 0); - } - - public int numAnnotations() { - if (annotations == null) return 0; - return annotations.size(); - } - - public int numNonTrivialAnnotations() { - if (annotations == null) return 0; - int ct = 0; - for (Annotation ann : annotations) { - if (!ann.isTrivial()) ct++; - } - return ct; - } - - public ArrayList getAnnotations() { - return annotations; - } - - public Annotation getAnnotation(String annId) { - if ((annId == null) || (annotations == null)) return null; - for (Annotation ann : annotations) { - if (annId.equals(ann.getId())) return ann; - } - return null; - } - - public Set getAnnotationViewpoints() { - Set vps = new HashSet(); - - if (!hasAnnotations()) return vps; - for (Annotation ann : annotations) { - if (ann.getViewpoint() != null) vps.add(ann.getViewpoint()); - } - return vps; - } - - public Set getAnnotationIAClasses() { - Set classes = new HashSet(); - - if (!hasAnnotations()) return classes; - for (Annotation ann : annotations) { - if (ann.getIAClass() != null) classes.add(ann.getIAClass()); - } - // TODO: we should find out how/where bunk iaClass values are getting set - // and stop the via isValidIAClass() or similar - // also should be considered for any data integrity/repair tools - classes.remove("____"); - return classes; - } - - // all an enc's annotations on a given asset (might be multiple if parts are involved) - public List getAnnotations(MediaAsset ma) { - List anns = new ArrayList(); - - for (Annotation ann : getAnnotations()) { - if (ann.getMediaAsset() == ma) anns.add(ann); - } - return anns; - } - - public void setAnnotations(ArrayList anns) { - annotations = anns; - } - - public void addAnnotations(List anns) { - if (annotations == null) annotations = new ArrayList(); - for (Annotation ann : anns) { - if (!annotations.contains(ann)) annotations.add(ann); - } - } - - public void addAnnotation(Annotation ann) { - if (annotations == null) annotations = new ArrayList(); - if (!annotations.contains(ann)) annotations.add(ann); - } - - public void useAnnotationsForMatching(boolean use) { - if (getAnnotations() != null && getAnnotations().size() >= 1) { - for (Annotation ann : getAnnotations()) { - ann.setMatchAgainst(use); - } - } - } - - public Annotation getAnnotationWithKeyword(String word) { - System.out.println("getAnnotationWithKeyword called for " + word); - System.out.println("getAnnotationWithKeyword called, annotations = " + annotations); - if (annotations == null) return null; - for (Annotation ann : annotations) { - if (ann == null) continue; - MediaAsset ma = ann.getMediaAsset(); - if (ma != null && ma.hasKeyword(word)) return ann; - } - return null; - } - - // pretty much only useful for frames pulled from video (after detection, to be made into encounters) - public static List collateFrameAnnotations(List anns, - Shepherd myShepherd) { - if ((anns == null) || (anns.size() < 1)) return null; - // Determine skipped frames before another encounter should be made. - int minGapSize = 4; - try { - String gapFromProperties = IA.getProperty(myShepherd.getContext(), - "newEncounterFrameGap"); - if (gapFromProperties != null) { - minGapSize = Integer.parseInt(gapFromProperties); - } - } catch (NumberFormatException nfe) {} - SortedMap > ordered = new TreeMap >(); - MediaAsset parentRoot = null; - for (Annotation ann : anns) { - System.out.println("========================== >>>>>> " + ann); - if (ann.getFeatures().get(0).isUnity()) continue; // makes big assumption there is one-and-only-one feature btw (detection should have - // bbox) - MediaAsset ma = ann.getMediaAsset(); - if (parentRoot == null) parentRoot = ma.getParentRoot(myShepherd); - System.out.println(" -->>> ma = " + ma); - if (!ma.hasLabel("_frame") || (ma.getParentId() == null)) continue; // nope thx - int offset = ma.getParameters().optInt("extractOffset", -1); - System.out.println(" -->>> offset = " + offset); - if (offset < 0) continue; - if (ordered.get(offset) == null) ordered.put(offset, new ArrayList()); - ordered.get(offset).add(ann); - } - if (ordered.size() < 1) return null; // none used! - - // now construct Encounters based upon spacing of frame-clusters - List newEncs = new ArrayList(); - int prevOffset = -1; - int groupsMade = 1; - ArrayList tmpAnns = new ArrayList(); - for (Integer i : ordered.keySet()) { - if ((prevOffset > -1) && ((i - prevOffset) >= minGapSize)) { - Encounter newEnc = __encForCollate(tmpAnns, parentRoot); - if (newEnc != null) { // null means none of the frames met minimum detection confidence - newEnc.setDynamicProperty("frameSplitNumber", Integer.toString(groupsMade + 1)); - newEncs.add(newEnc); - System.out.println(" cluster [" + (groupsMade) + "] -> " + newEnc); - groupsMade++; - tmpAnns = new ArrayList(); - } - } - prevOffset = i; - tmpAnns.addAll(ordered.get(i)); - } - // deal with dangling tmpAnns content - if (tmpAnns.size() > 0) { - Encounter newEnc = __encForCollate(tmpAnns, parentRoot); - if (newEnc != null) { - newEnc.setDynamicProperty("frameSplitNumber", Integer.toString(groupsMade + 1)); - newEncs.add(newEnc); - System.out.println(" (final)cluster [" + groupsMade + "] -> " + newEnc); - groupsMade++; - } - } - return newEncs; - } - - // this is really only for above method - private static Encounter __encForCollate(ArrayList tmpAnns, MediaAsset parentRoot) { - if ((tmpAnns == null) || (tmpAnns.size() < 1)) return null; - // make sure we even can use these annots first - double bestConfidence = 0.0; - for (Annotation ann : tmpAnns) { - if ((ann.getFeatures() == null) || (ann.getFeatures().size() < 1) || - (ann.getFeatures().get(0).getParameters() == null)) continue; - double conf = ann.getFeatures().get(0).getParameters().optDouble("detectionConfidence", - -1.0); - if (conf > bestConfidence) bestConfidence = conf; - } - if (bestConfidence < ENCOUNTER_AUTO_SOURCE_CONFIDENCE_CUTOFF) { - System.out.println("[INFO] bestConfidence=" + bestConfidence + - " below threshold; rejecting 1 enc from " + parentRoot); - return null; - } - Encounter newEnc = new Encounter(tmpAnns); - newEnc.setState(STATE_AUTO_SOURCED); - newEnc.zeroOutDate(); // do *not* want it using the video source date - newEnc.setDynamicProperty("bestDetectionConfidence", Double.toString(bestConfidence)); - if (parentRoot == null) { - newEnc.setSubmitterName("Unknown video source"); - newEnc.addComments("unable to determine video source - possibly YouTube error?"); - } else { - newEnc.addComments("

    YouTube ID: " + parentRoot.getParameters().optString("id") + - "

    "); - String consolidatedRemarks = - "

    Auto-sourced from YouTube Parent Video: " + - parentRoot.getParameters().optString("id") + "

    "; - // set the video ID as the EventID for distinct access later - newEnc.setEventID("youtube:" + parentRoot.getParameters().optString("id")); - if ((parentRoot.getMetadata() != null) && - (parentRoot.getMetadata().getData() != null)) { - if (parentRoot.getMetadata().getData().optJSONObject("basic") != null) { - newEnc.setSubmitterName(parentRoot.getMetadata().getData().getJSONObject( - "basic").optString("author_name", "[unknown]") + " (by way of YouTube)"); - consolidatedRemarks += "

    From YouTube video: " + - parentRoot.getMetadata().getData().getJSONObject("basic").optString("title", - "[unknown]") + "

    "; - newEnc.addComments(consolidatedRemarks); - - // add a dynamic property to make a quick link to the video - } - if (parentRoot.getMetadata().getData().optJSONObject("detailed") != null) { - String desc = "

    " + - parentRoot.getMetadata().getData().getJSONObject("detailed").optString( - "description", "[no description]") + "

    "; - if (parentRoot.getMetadata().getData().getJSONObject("detailed").optJSONArray( - "tags") != null) { - desc += "

    tags: " + - parentRoot.getMetadata().getData().getJSONObject( - "detailed").getJSONArray("tags").toString() + "

    "; - } - consolidatedRemarks += desc; - } - } - newEnc.setOccurrenceRemarks(consolidatedRemarks); - } - return newEnc; - } - - // convenience method - public ArrayList getMedia() { - ArrayList m = new ArrayList(); - - if ((annotations == null) || (annotations.size() < 1)) return m; - for (Annotation ann : annotations) { - if (ann == null) continue; // really weird that this happens sometimes - MediaAsset ma = ann.getMediaAsset(); - if (ma != null) m.add(ma); - } - return m; - } - - public MediaAsset getMediaAssetByFilename(String filename) { - if (!Util.stringExists(filename)) return null; - for (MediaAsset ma : getMedia()) { - if (Util.stringsEqualish(filename, ma.getFilename())) return ma; - } - return null; - } - - // only checks top-level MediaAssets, not children or resized images - public boolean hasTopLevelMediaAsset(int id) { - return (indexOfMediaAsset(id) >= 0); - } - - // finds the index of the MA we're looking for - public int indexOfMediaAsset(int id) { - if (annotations == null) return -1; - for (int i = 0; i < annotations.size(); i++) { - MediaAsset ma = annotations.get(i).getMediaAsset(); - if (ma == null) continue; - if (ma.getIdInt() == id) return i; - } - return -1; - } - - // creates a new annotation and attaches the asset - public void addMediaAsset(MediaAsset ma) { - Annotation ann = new Annotation(getTaxonomyString(), ma); - - if (annotations == null) annotations = new ArrayList(); - annotations.add(ann); - } - - public void removeAnnotation(Annotation ann) { - if (annotations == null) return; - annotations.remove(ann); - } - - public void removeAnnotation(int index) { - annotations.remove(index); - } - - // this removes an Annotation from Encounter (and from its MediaAsset!!) and replaces it with a new one - // please note: the oldAnn gets killed off (not orphaned) - public void replaceAnnotation(Annotation oldAnn, Annotation newAnn) { - oldAnn.detachFromMediaAsset(); - // note: newAnn should already attached to a MediaAsset - removeAnnotation(oldAnn); - addAnnotation(newAnn); - } - - public void removeMediaAsset(MediaAsset ma) { - removeAnnotation(indexOfMediaAsset(ma.getIdInt())); - } - - // this is a kinda hacky way to find media ... really used by encounter.jsp now but likely should go away? - public ArrayList findAllMediaByFeatureId(Shepherd myShepherd, String[] featureIds) { - ArrayList mas = new ArrayList(); - - for (MediaAsset ma : getMedia()) { - if (ma.hasFeatures(featureIds)) mas.add(ma); - ArrayList kids = ma.findChildren(myShepherd); // note: does not recurse, but... meh? - if ((kids == null) || (kids.size() < 1)) continue; - for (MediaAsset kma : kids) { - if (kma.hasFeatures(featureIds)) mas.add(kma); - } - } - return mas; - } - - // down-n-dirty with no myShepherd passed! :/ - public ArrayList findAllMediaByFeatureId(String[] featureIds) { - Shepherd myShepherd = new Shepherd("context0"); - - myShepherd.setAction("Encounter.class.findAllMediaByFeatureID"); - myShepherd.beginDBTransaction(); - ArrayList all = findAllMediaByFeatureId(myShepherd, featureIds); - myShepherd.rollbackDBTransaction(); - myShepherd.closeDBTransaction(); - return all; - } - - public ArrayList findAllMediaByLabel(Shepherd myShepherd, String label) { - return MediaAsset.findAllByLabel(getMedia(), myShepherd, label); - } - - public boolean hasKeyword(Keyword word) { - int imagesSize = images.size(); - - for (int i = 0; i < imagesSize; i++) { - SinglePhotoVideo image = images.get(i); - if (image.getKeywords().contains(word)) { return true; } - } - return false; - } - - public Set getMediaAssetKeywords() { - Set mak = new HashSet(); - - for (MediaAsset ma : this.getMedia()) { - ArrayList kws = ma.getKeywords(); - if (kws != null) mak.addAll(kws); - } - return mak; - } - - public String getState() { return state; } - - public void setState(String newState) { this.state = newState; } - - // DO NOT USE - LEGACY MIGRATION ONLY - /* - public boolean getApproved(){return approved;} - public boolean getUnidentifiable(){return unidentifiable;} - */ - public Vector getOldAdditionalImageNames() { return additionalImageNames; } - - public Double getLatitudeAsDouble() { return decimalLatitude; } - public Double getLongitudeAsDouble() { return decimalLongitude; } - - public boolean hasMeasurements() { - if ((measurements != null) && (measurements.size() > 0)) { - int numMeasurements = measurements.size(); - for (int i = 0; i < numMeasurements; i++) { - Measurement m = measurements.get(i); - if (m.getValue() != null) { return true; } - } - } - return false; - } - - public boolean hasMeasurement(String type) { - if ((measurements != null) && (measurements.size() > 0)) { - int numMeasurements = measurements.size(); - for (int i = 0; i < numMeasurements; i++) { - Measurement m = measurements.get(i); - if ((m.getValue() != null) && (m.getType().equals(type))) { return true; } - } - } - return false; - } - - public boolean hasBiologicalMeasurement(String type) { - if ((tissueSamples != null) && (tissueSamples.size() > 0)) { - int numTissueSamples = tissueSamples.size(); - for (int i = 0; i < numTissueSamples; i++) { - TissueSample ts = tissueSamples.get(i); - if (ts.getBiologicalMeasurement(type) != null) { - BiologicalMeasurement bm = ts.getBiologicalMeasurement(type); - if (bm.getValue() != null) { return true; } - } - } - } - return false; - } - - // Returns the first measurement of the specified type - public Measurement getMeasurement(String type) { - if ((measurements != null) && (measurements.size() > 0)) { - int numMeasurements = measurements.size(); - for (int i = 0; i < numMeasurements; i++) { - Measurement m = measurements.get(i); - if ((m.getValue() != null) && (m.getType().equals(type))) { return m; } - } - } - return null; - } - - public Map getBiologicalMeasurementsByType() { - Map meas = new HashMap(); - - for (MeasurementDesc mdesc : Util.findBiologicalMeasurementDescs("en", "context0")) { - BiologicalMeasurement bm = getBiologicalMeasurement(mdesc.getType()); - if (bm != null) meas.put(mdesc.getType(), bm); - } - return meas; - } - - public BiologicalMeasurement getBiologicalMeasurement(String type) { - if (tissueSamples != null) { - int numTissueSamples = tissueSamples.size(); - for (int y = 0; y < numTissueSamples; y++) { - TissueSample ts = tissueSamples.get(y); - if ((ts.getGeneticAnalyses() != null) && (ts.getGeneticAnalyses().size() > 0)) { - int numMeasurements = ts.getGeneticAnalyses().size(); - for (int i = 0; i < numMeasurements; i++) { - GeneticAnalysis m = ts.getGeneticAnalyses().get(i); - if (m.getAnalysisType().equals("BiologicalMeasurement")) { - BiologicalMeasurement f = (BiologicalMeasurement)m; - if ((f.getMeasurementType().equals(type)) && (f.getValue() != null)) { - return f; - } - } - } - } - } - } - return null; - } - - public String getCountry() { return country; } - - public void setCountry(String newCountry) { - if (newCountry != null) { country = newCountry; } else { country = null; } - } - - public void setOccurrenceID(String vet) { - if (vet != null) { this.occurrenceID = vet; } else { this.occurrenceID = null; } - } - - public String getOccurrenceID() { return occurrenceID; } - - public Occurrence getOccurrence(Shepherd myShepherd) { - return myShepherd.getOccurrence(this); - } - - public DateTime getOccurrenceDateTime(Shepherd myShepherd) { - Occurrence occ = this.getOccurrence(myShepherd); - - if (occ == null) return null; - return occ.getDateTime(); - } - - public boolean hasSinglePhotoVideoByFileName(String filename) { - int numImages = images.size(); - - for (int i = 0; i < numImages; i++) { - SinglePhotoVideo single = images.get(i); - if (single.getFilename().trim().toLowerCase().equals(filename.trim().toLowerCase())) { - return true; - } - } - return false; - } - - // convenience function to Collaboration permissions - public boolean canUserAccess(HttpServletRequest request) { - return Collaboration.canUserAccessEncounter(this, request); - } - - public boolean canUserAccess(User user, String context) { - if (user == null) return false; - // see comment below on canUserEdit(); substituting isUserOwner() now - // if (canUserEdit(user)) return true; - if (isUserOwner(user)) return true; - String username = user.getUsername(); - if (username == null) return false; - return Collaboration.canUserAccessEncounter(this, context, username); - } - - /* - this really is ugly cuz what is "view" vs "access", but i do NOT want to futz with canUserAccess() and - cause unintended consequences. so, for now, canUserView() is pretty much exclusively for search - */ - public boolean canUserView(User user, Shepherd myShepherd) { - return (user != null) && (user.isAdmin(myShepherd) || this.canUserAccess(user, - myShepherd.getContext())); - } - - // as part of 10.9, canUserEdit() was modified. it was not -/* - public boolean canUserEdit(User user) { - return isUserOwner(user); - } - */ - - // rewrite for 10.9 tries to actually do the right thing and (maybe) make sense - @Override public boolean canUserEdit(User user, Shepherd myShepherd) { - if (user == null) return false; - if (isUserOwner(user)) return true; - if (user.isAdmin(myShepherd)) return true; - if (Collaboration.canEditEncounter(this, user, myShepherd.getContext())) return true; - // TODO there seems to be some legacy stuff about roles based on location. is this real? - return false; - } - - public boolean isUserOwner(User user) { // the definition of this might change? - if (user == null) return false; - if ((submitters != null) && submitters.contains(user)) return true; - if ((submitterID != null) && submitterID.equals(user.getUsername())) return true; - return false; - } - - // new logic means we only need users who are in collab with submitting user - // and if public, we dont need to do this at all - public List userIdsWithViewAccess(Shepherd myShepherd) { - List ids = new ArrayList(); - - if (this.isPubliclyReadable()) return ids; - List collabs = Collaboration.collaborationsForUser(myShepherd, - this.getSubmitterID()); - for (Collaboration collab : collabs) { - User user = myShepherd.getUser(collab.getOtherUsername(this.getSubmitterID())); - if (user != null) ids.add(user.getId()); - } - return ids; - } - -/* - public List userIdsWithEditAccess(Shepherd myShepherd) { - List ids = new ArrayList(); - - for (User user : myShepherd.getUsersWithUsername()) { - if ((user.getId() != null) && this.canUserEdit(user)) ids.add(user.getId()); - } - return ids; - } - */ - public JSONObject sanitizeJson(HttpServletRequest request, JSONObject jobj) - throws JSONException { - boolean fullAccess = this.canUserAccess(request); - String useProjectContext = "false"; - - if (request.getParameter("useProjectContext") != null) { - useProjectContext = request.getParameter("useProjectContext"); - } - if (fullAccess) { - if (this.individual != null) { - jobj.put("individualID", this.individual.getIndividualID()); - if ("true".equals(useProjectContext)) { - jobj.put("displayName", this.individual.getDisplayName(request)); - } else { - jobj.put("displayName", this.individual.getDisplayName()); - } - } - return jobj; - } - jobj.remove("gpsLatitude"); - jobj.remove("location"); - jobj.remove("gpsLongitude"); - jobj.remove("verbatimLocality"); - jobj.remove("locationID"); - jobj.remove("gpsLongitude"); - jobj.remove("genus"); - jobj.remove("specificEpithet"); - jobj.put("_sanitized", true); - - return jobj; - } - - public JSONObject decorateJsonNoAnnots(HttpServletRequest request, JSONObject jobj) - throws JSONException { - jobj.put("location", this.getLocation()); - // these are for convenience, like .hasImages above (for use in table building e.g.) - if ((this.getTissueSamples() != null) && (this.getTissueSamples().size() > 0)) - jobj.put("hasTissueSamples", true); - if (this.hasMeasurements()) jobj.put("hasMeasurements", true); - return jobj; - } - - public JSONObject decorateJson(HttpServletRequest request, JSONObject jobj) - throws JSONException { - jobj = decorateJsonNoAnnots(request, jobj); - - jobj.put("_imagesNote", - ".images have been deprecated! long live MediaAssets! (see: .annotations)"); - - boolean fullAccess = this.canUserAccess(request); - if ((this.getAnnotations() != null) && (this.getAnnotations().size() > 0)) { - jobj.put("hasAnnotations", true); - JSONArray jarr = new JSONArray(); - for (Annotation ann : this.getAnnotations()) { - jarr.put(ann.sanitizeJson(request, fullAccess)); - } - jobj.put("annotations", jarr); - } - return jobj; - } - - public JSONObject uiJson(HttpServletRequest request) - throws JSONException { - JSONObject jobj = new JSONObject(); - - jobj.put("individualID", this.getIndividualID()); - jobj.put("url", this.getUrl(request)); - jobj.put("year", this.getYear()); - jobj.put("month", this.getMonth()); - jobj.put("day", this.getDay()); - jobj.put("gpsLatitude", this.getGPSLatitude()); - jobj.put("gpsLongitude", this.getGPSLongitude()); - jobj.put("location", this.getLocation()); - jobj.put("locationID", this.getLocationID()); - - jobj = sanitizeJson(request, jobj); - // we don't want annotations, which are added by sanitizeJson - jobj.remove("annotations"); - return jobj; - } - - public String getUrl(HttpServletRequest request) { - return request.getScheme() + "://" + CommonConfiguration.getURLLocation(request) + - "/encounters/encounter.jsp?number=" + this.getCatalogNumber(); - } - - /** - * returns an array of the MediaAsset sanitized JSON, because whenever UI queries our DB (regardless of class query), all they want in return are - * MediaAssets TODO: decorate with metadata - **/ - public org.datanucleus.api.rest.orgjson.JSONArray sanitizeMedia(HttpServletRequest request) - throws org.datanucleus.api.rest.orgjson.JSONException { - org.datanucleus.api.rest.orgjson.JSONArray jarr = - new org.datanucleus.api.rest.orgjson.JSONArray(); - boolean fullAccess = this.canUserAccess(request); - if ((this.getAnnotations() != null) && (this.getAnnotations().size() > 0)) { - for (Annotation ann : this.getAnnotations()) { - jarr.put(ann.sanitizeMedia(request, fullAccess)); - } - } - return jarr; - } - - // this simple version makes some assumptions: you already have list of collabs, and it is not visible - public String collaborationLockHtml(List collabs) { - Collaboration c = Collaboration.findCollaborationWithUser(this.getAssignedUsername(), - collabs); - String collabClass = "pending"; - - if ((c == null) || (c.getState() == null)) { - collabClass = "new"; - } else if (c.getState().equals(Collaboration.STATE_REJECTED)) { - collabClass = "blocked"; - } - return "
     
    "; - } - - // pass in a Vector of Encounters, get out a list that the user can NOT see - public static Vector blocked(Vector encs, HttpServletRequest request) { - Vector blk = new Vector(); - - for (int i = 0; i < encs.size(); i++) { - Encounter e = (Encounter)encs.get(i); - if (!e.canUserAccess(request)) blk.add(e); - } - return blk; - } - -/* - in short, this rebuilds (or builds for the first time) ALL *derived* images (etc?) for this encounter. - it is a baby step into the future of MediaAssets that hopefully will provide a smooth(er) transition to that. - right now its primary purpose is to create derived formats upon encounter creation; but that is obviously subject to change. - it should be considered an asyncronous action that happens in the background magickally - */ -/////other possiblity: only pass basedir??? do we need context if we do that? - - public boolean refreshAssetFormats(Shepherd myShepherd) { - ArrayList mas = this.getMedia(); - - if ((mas == null) || (mas.size() < 1)) return true; - for (MediaAsset ma : mas) { - ma.updateStandardChildren(myShepherd); - } - return true; - } - -/* - NOTE on "thumb.jpg" ... we only get one of these per encounter; and we do not have stored (i dont think?) which SPV it came from! - this is a problem, as we cant make a thumb in refreshAssetFormats(req, spv) since we dont know if that is the "right" spv. - thus, we have to treat it as a special case. - */ - // see also: future, MediaAssets - public String getThumbnailUrl(String context) { - MediaAsset ma = getPrimaryMediaAsset(); - - if (ma == null) return null; - String url = null; - Shepherd myShepherd = new Shepherd(context); - myShepherd.setAction("Encounter.class.getThumbnailUrl"); - myShepherd.beginDBTransaction(); - ArrayList kids = ma.findChildrenByLabel(myShepherd, "_thumb"); - if ((kids == null) || (kids.size() <= 0)) { - myShepherd.rollbackDBTransaction(); - myShepherd.closeDBTransaction(); - return null; - } - ma = kids.get(0); - if (ma.webURL() == null) { - myShepherd.rollbackDBTransaction(); - myShepherd.closeDBTransaction(); - return null; - } - url = ma.webURL().toString(); - myShepherd.rollbackDBTransaction(); - myShepherd.closeDBTransaction(); - return url; - } - - // this probably needs a better name and should allow for something more like an ordered list; that said, - // knowing we can always try to get THE ONE is probably useful too - public MediaAsset getPrimaryMediaAsset() { - ArrayList mas = getMedia(); - - if (mas.size() < 1) return null; - // here we could walk thru and find keywords, for example - return mas.get(0); - } - - public boolean restAccess(HttpServletRequest request, org.json.JSONObject jsonobj) - throws Exception { - ApiAccess access = new ApiAccess(); - - System.out.println("hello i am in restAccess() on Encounter"); - - String fail = access.checkRequest(this, request, jsonobj); - System.out.println("fail -----> " + fail); - if (fail != null) throw new Exception(fail); - return true; - } - -///////// this is bunk now: see fix for findAllByMediaAsset() if you need this - public static Encounter findByMediaAsset(MediaAsset ma, Shepherd myShepherd) { - String queryString = - "SELECT FROM org.ecocean.Encounter WHERE annotations.contains(ann) && ann.mediaAsset.id ==" - + ma.getId(); - Encounter returnEnc = null; - Query query = myShepherd.getPM().newQuery(queryString); - List results = (List)query.execute(); - - if ((results != null) && (results.size() >= 1)) { - returnEnc = (Encounter)results.get(0); - } - query.closeAll(); - return returnEnc; - } - - public static List findAllByMediaAsset(MediaAsset ma, Shepherd myShepherd) { - List returnEncs = new ArrayList(); - - try { - String queryString = - "SELECT FROM org.ecocean.Encounter WHERE annotations.contains(ann) && ann.features.contains(feat) && mediaAsset.features.contains(feat) && mediaAsset.id ==" - + ma.getId() + - " VARIABLES org.ecocean.media.MediaAsset mediaAsset; org.ecocean.Annotation ann; org.ecocean.media.Feature feat"; - Query query = myShepherd.getPM().newQuery(queryString); - Collection results = (Collection)query.execute(); - returnEncs = new ArrayList(results); - query.closeAll(); - } catch (Exception e) {} - return returnEncs; - } - - public String getPrefixForLocationID() { // convenience function - return LocationID.getPrefixForLocationID(this.getLocationID(), null); - } - - public int getPrefixDigitPaddingForLocationID() { // convenience function - return LocationID.getPrefixDigitPaddingForLocationID(this.getLocationID(), null); - } - - public static Encounter findByAnnotation(Annotation annot, Shepherd myShepherd) { - String queryString = - "SELECT FROM org.ecocean.Encounter WHERE annotations.contains(ann) && ann.id =='" + - annot.getId() + "'"; - Encounter returnEnc = null; - Query query = myShepherd.getPM().newQuery(queryString); - List results = (List)query.execute(); - - if ((results != null) && (results.size() >= 1)) { - if (results.size() > 1) - System.out.println("WARNING: Encounter.findByAnnotation() found " + results.size() + - " Encounters that contain Annotation " + annot.getId()); - returnEnc = (Encounter)results.get(0); - } - query.closeAll(); - return returnEnc; - } - - public static Encounter findByAnnotationId(String annid, Shepherd myShepherd) { - Annotation ann = ((Annotation)(myShepherd.getPM().getObjectById( - myShepherd.getPM().newObjectIdInstance(Annotation.class, annid), true))); - - if (ann == null) return null; - return findByAnnotation(ann, myShepherd); - } - - public static ArrayList getEncountersForMatching(String taxonomyString, - Shepherd myShepherd) { - if (_matchEncounterCache.get(taxonomyString) != null) - return _matchEncounterCache.get(taxonomyString); - ArrayList encs = new ArrayList(); - String queryString = "SELECT FROM org.ecocean.media.MediaAsset WHERE !features.isEmpty()"; - Query query = myShepherd.getPM().newQuery(queryString); - List results = (List)query.execute(); - for (int i = 0; i < results.size(); i++) { - MediaAsset ma = (MediaAsset)results.get(i); - MediaAsset top = ma.getParentRoot(myShepherd); - if (top == null) continue; - Encounter enc = Encounter.findByMediaAsset(top, myShepherd); - if (enc == null) System.out.println("could not find enc for ma " + ma); - if (enc == null) continue; - if (!enc.getTaxonomyString().equals(taxonomyString)) continue; - if (!encs.contains(enc)) encs.add(enc); - } - query.closeAll(); - _matchEncounterCache.put(taxonomyString, encs); - return encs; - } - -/* - this section are intentionally hacky backwards-compatible ways to get spots on an encounter in the new world of Features/Annotations/MediaAssets - ... do not use these, of course... and SOON we must weed out all the encounter-based-spot calls from everywhere and clean all this mess up! - */ - public ArrayList HACKgetSpots() { - return HACKgetAnySpots("spotsLeft"); - } - - public ArrayList HACKgetRightSpots() { - return HACKgetAnySpots("spotsRight"); - } - - public ArrayList HACKgetAnySpots(String which) { - ArrayList mas = findAllMediaByFeatureId( - new String[] { "org.ecocean.flukeEdge.edgeSpots", "org.ecocean.dorsalEdge.edgeSpots" }); - - if ((mas == null) || (mas.size() < 1)) return new ArrayList(); - for (Feature f : mas.get(0).getFeatures()) { - if (f.isType("org.ecocean.flukeEdge.edgeSpots") || - f.isType("org.ecocean.dorsalEdge.edgeSpots")) { - if (f.getParameters() != null) - return SuperSpot.listFromJSONArray(f.getParameters().optJSONArray(which)); - } - } - return new ArrayList(); - } - - // err, i think ref spots are the same right or left.... at least for flukes/dorsals. :/ good luck with mantas and whalesharks! - public ArrayList HACKgetAnyReferenceSpots() { - ArrayList mas = findAllMediaByFeatureId( - new String[] { "org.ecocean.flukeEdge.referenceSpots", - "org.ecocean.referenceEdge.edgeSpots" }); - - if ((mas == null) || (mas.size() < 1)) return new ArrayList(); - for (Feature f : mas.get(0).getFeatures()) { - if (f.isType("org.ecocean.flukeEdge.referenceSpots") || - f.isType("org.ecocean.dorsalEdge.referenceSpots")) { - if (f.getParameters() != null) - return SuperSpot.listFromJSONArray(f.getParameters().optJSONArray("spots")); - } - } - return new ArrayList(); - } - - // note this sets some things (e.g. species) which might (should!) need to be adjusted after, e.g. with setSpeciesFromAnnotations() - public Encounter cloneWithoutAnnotations(Shepherd myShepherd) { - Encounter enc = new Encounter(this.day, this.month, this.year, this.hour, this.minutes, - this.size_guess, this.verbatimLocality); - - enc.setCatalogNumber(Util.generateUUID()); - System.out.println("NOTE: cloneWithoutAnnotations(" + this.catalogNumber + ") -> " + - enc.getCatalogNumber()); - enc.setGenus(this.getGenus()); - enc.setSpecificEpithet(this.getSpecificEpithet()); - enc.setDecimalLatitude(this.getDecimalLatitudeAsDouble()); - enc.setDecimalLongitude(this.getDecimalLongitudeAsDouble()); - // just going to go ahead and go nuts here and copy most "logical"(?) things. reset on clone if needed - enc.setSubmitterID(this.getSubmitterID()); - enc.setSubmitters(this.submitters); - enc.setPhotographers(this.photographers); - enc.setSex(this.getSex()); - enc.setLocationID(this.getLocationID()); - enc.setVerbatimLocality(this.getVerbatimLocality()); - if (this.getCountry() != null && !"".equals(this.getCountry())) { - enc.setCountry(this.getCountry()); - } - Occurrence occ = myShepherd.getOccurrence(this); - if (occ != null) { - occ.addEncounter(enc); - enc.setOccurrenceID(occ.getOccurrenceID()); - } - // WB-1949: clone into same projects too - ArrayList projects = myShepherd.getAllProjectsForEncounter(this); - if (projects != null) { - for (Project proj : projects) { - proj.addEncounter(enc); - } - } - enc.setRecordedBy(this.getRecordedBy()); - enc.setState(this.getState()); // not too sure about this one? - - enc.setAlternateID(this.getAlternateID()); - enc.setOccurrenceRemarks(this.getOccurrenceRemarks()); - enc.addComments("NOTE: cloneWithoutAnnotations(" + this.catalogNumber + ") -> " + - enc.getCatalogNumber()); - - ImportTask itask = getImportTask(myShepherd); - if (itask != null) itask.addEncounter(enc); - return enc; - } - - // for convenience - public ImportTask getImportTask(Shepherd myShepherd) { - return myShepherd.getImportTaskForEncounter(this); - } - - // this is a special state only used now for match.jsp but basically means the data should be mostly hidden and soon deleted, roughly speaking??? - // TODO: figure out what this really means - public void setMatchingOnly() { - this.setState(STATE_MATCHING_ONLY); - } - - // ann is the Annotation that was created after IA detection. mostly this is just to notify... someone - // note: this is for singly-made encounters; see also Occurrence.fromDetection() - public void detectedAnnotation(Shepherd myShepherd, Annotation ann) { - System.out.println(">>>>> detectedAnnotation() on " + this); - } - - /* - note: these are baby steps into proper ownership of Encounters. a similar (but cleaner) attempt is done in MediaAssets... however, really this - probably should be upon some (mythical) BASE CLASS!!!! ... for now, this Encounter variation kinda fudges with existing "ownership" stuff, - namely, the submitterID - which maps (in theory!) to a User username. TODO: much much much ... incl call via constructor maybe ?? etc. - */ - // NOTE: not going to currently persist the AccessControl object yet, but create on the fly... clever? stupid? - public AccessControl getAccessControl() { - if ((submitterID == null) || submitterID.equals("")) return new AccessControl(); // not sure if we really have some "" but lets be safe - return new AccessControl(submitterID); - } - - public void setAccessControl(HttpServletRequest request) { // really just setting submitterID duh - this.submitterID = AccessControl.simpleUserString(request); // null if anon - } - - public String toString() { - return new ToStringBuilder(this) - .append("catalogNumber", catalogNumber) - .append("individualID", (hasMarkedIndividual() ? individual.getId() : null)) - .append("species", getTaxonomyString()) - .append("sex", getSex()) - .append("shortDate", getShortDate()) - .append("numAnnotations", ((annotations == null) ? 0 : annotations.size())) - .toString(); - } - - public boolean hasMediaFromAssetStoreType(AssetStoreType aType) { - System.out.println("Entering Encounter.hasMediaFromAssetStoreType"); - if (getMediaAssetsOfType(aType).size() > 0) { return true; } - return false; - } - - public ArrayList getMediaAssetsOfType(AssetStoreType aType) { - System.out.println("Entering Encounter.getMediaAssetsOfType"); - ArrayList results = new ArrayList(); - try { - ArrayList assets = getMedia(); - int numAssets = assets.size(); - for (int i = 0; i < numAssets; i++) { - MediaAsset ma = assets.get(i); - if (ma.getStore().getType() == aType) { results.add(ma); } - } - } catch (Exception e) { e.printStackTrace(); } - System.out.println("Exiting Encounter.getMediaAssetsOfType with this num results: " + - results.size()); - return results; - } - - public void setObservationArrayList(ArrayList obs) { - this.observations = obs; - } - - public ArrayList getObservationArrayList() { - return observations; - } - - public void addObservationArrayList(ArrayList arr) { - if (observations.isEmpty()) { - observations = arr; - } else { - observations.addAll(arr); - } - } - - public void addObservation(Observation obs) { - boolean found = false; - - // System.out.println("Adding Observation in Base Class... : "+obs.toString()); - if (observations != null && observations.size() > 0) { - for (Observation ob : observations) { - if (ob.getName() != null) { - if (ob.getName().toLowerCase().trim().equals( - obs.getName().toLowerCase().trim())) { - found = true; - break; - } - } - } - if (!found) { - observations.add(obs); - } - } else { - observations.add(obs); - } - } - - public Observation getObservationByName(String obName) { - if (observations != null && observations.size() > 0) { - for (Observation ob : observations) { - if (ob.getName() != null) { - if (ob.getName().toLowerCase().trim().equals(obName.toLowerCase().trim())) { - return ob; - } - } - } - } - return null; - } - - public Observation getObservationByID(String obId) { - if (observations != null && observations.size() > 0) { - for (Observation ob : observations) { - if (ob.getID() != null && ob.getID().equals(obId)) { - return ob; - } - } - } - return null; - } - - public void removeObservation(String name) { - int counter = 0; - - if (observations != null && observations.size() > 0) { - System.out.println("Looking for the Observation to delete..."); - for (Observation ob : observations) { - if (ob.getName() != null) { - if (ob.getName().toLowerCase().trim().equals(name.toLowerCase().trim())) { - System.out.println("Match! Trying to delete Observation " + name + - " at index " + counter); - observations.remove(counter); - break; - } - } - counter++; - } - } - } - - public List getSubmitters() { - return submitters; - } - - public List getInformOthers() { - return informOthers; - } - - public List getSubmitterEmails() { - ArrayList listy = new ArrayList(); - ArrayList subs = new ArrayList(); - - if (getSubmitters() != null) subs.addAll(getSubmitters()); - int numUsers = subs.size(); - for (int k = 0; k < numUsers; k++) { - User use = subs.get(k); - if ((use.getEmailAddress() != null) && (!use.getEmailAddress().trim().equals(""))) { - listy.add(use.getEmailAddress()); - } - } - return listy; - } - - public List getHashedSubmitterEmails() { - ArrayList listy = new ArrayList(); - ArrayList subs = new ArrayList(); - - if (getSubmitters() != null) subs.addAll(getSubmitters()); - int numUsers = subs.size(); - for (int k = 0; k < numUsers; k++) { - User use = subs.get(k); - if ((use.getHashedEmailAddress() != null) && - (!use.getHashedEmailAddress().trim().equals(""))) { - listy.add(use.getHashedEmailAddress()); - } - } - return listy; - } - - public List getPhotographers() { - return photographers; - } - - public List getPhotographerEmails() { - ArrayList listy = new ArrayList(); - ArrayList subs = new ArrayList(); - - if (getPhotographers() != null) subs.addAll(getPhotographers()); - int numUsers = subs.size(); - for (int k = 0; k < numUsers; k++) { - User use = subs.get(k); - if ((use.getEmailAddress() != null) && (!use.getEmailAddress().trim().equals(""))) { - listy.add(use.getEmailAddress()); - } - } - return listy; - } - - public List getInformOthersEmails() { - ArrayList listy = new ArrayList(); - ArrayList subs = new ArrayList(); - - if (getInformOthers() != null) subs.addAll(getInformOthers()); - int numUsers = subs.size(); - for (int k = 0; k < numUsers; k++) { - User use = subs.get(k); - if ((use.getEmailAddress() != null) && (!use.getEmailAddress().trim().equals(""))) { - listy.add(use.getEmailAddress()); - } - } - return listy; - } - - public List getHashedPhotographerEmails() { - ArrayList listy = new ArrayList(); - ArrayList subs = new ArrayList(); - - if (getPhotographers() != null) subs.addAll(getPhotographers()); - int numUsers = subs.size(); - for (int k = 0; k < numUsers; k++) { - User use = subs.get(k); - if ((use.getHashedEmailAddress() != null) && - (!use.getHashedEmailAddress().trim().equals(""))) { - listy.add(use.getHashedEmailAddress()); - } - } - return listy; - } - - public void addSubmitter(User user) { - if (user == null) return; - if (submitters == null) submitters = new ArrayList(); - if (!submitters.contains(user)) submitters.add(user); - } - - public void removeSubmitter(User user) { - if ((user == null) || (submitters == null)) return; - submitters.remove(user); - } - - public void addPhotographer(User user) { - if (user == null) return; - if (photographers == null) photographers = new ArrayList(); - if (!photographers.contains(user)) photographers.add(user); - } - - public void setSubmitters(List submitters) { - if (submitters == null) { this.submitters = null; } else { - this.submitters = submitters; - } - } - - public void setPhotographers(List photographers) { - if (photographers == null) { this.photographers = null; } else { - this.photographers = photographers; - } - } - - public void removePhotographer(User user) { - if ((user == null) || (photographers == null)) return; - photographers.remove(user); - } - - public void addInformOther(User user) { - if (user == null) return; - if (informOthers == null) informOthers = new ArrayList(); - if (!informOthers.contains(user)) informOthers.add(user); - } - - public void setInformOthers(List users) { - if (users == null) { this.informOthers = null; } else { - this.informOthers = users; - } - } - - public void removeInformOther(User user) { - if ((user == null) || (informOthers == null)) return; - informOthers.remove(user); - } - - public static List getIndividualIDs(Collection encs) { - Set idSet = new HashSet(); - - for (Encounter enc : encs) { - if (enc.hasMarkedIndividual()) idSet.add(enc.getIndividualID()); - } - return Util.asSortedList(idSet); - } - - public void refreshAnnotationLiteTaxonomy() { - if (!this.hasAnnotations()) return; - String tax = this.getTaxonomyString(); - for (Annotation ann : this.annotations) { - ann.refreshLiteTaxonomy(tax); - } - } - - public void refreshAnnotationLiteIndividual() { - if (!this.hasAnnotations()) return; - String indivId = "____"; - if (this.individual != null) indivId = this.individual.getIndividualID(); - for (Annotation ann : this.annotations) { - ann.refreshLiteIndividual(indivId); - } - } - - public int hashCode() { // we need this along with equals() for collections methods (contains etc) to work!! - if (this.getCatalogNumber() == null) return Util.generateUUID().hashCode(); // random(ish) so we dont get two identical for null values - return this.getCatalogNumber().hashCode(); - } - - // sadly, this mess needs to carry on the tradition set up in User.isUsernameAnonymous() - // thanks to the logic in Collaboration.canUserAccessOwnedObject() - public boolean isPubliclyReadable() { - if (!Collaboration.securityEnabled("context0")) return true; - return User.isUsernameAnonymous(this.submitterID); - } - - public boolean getOpensearchProcessPermissions() { - return opensearchProcessPermissions; - } - - public void setOpensearchProcessPermissions(boolean value) { - opensearchProcessPermissions = value; - } - - // wrapper for below, that checks if we really need to be run - public static void opensearchIndexPermissionsBackground(Shepherd myShepherd) { - boolean runIt = false; - Long lastRun = OpenSearch.getPermissionsTimestamp(myShepherd); - long now = System.currentTimeMillis(); - - if ((lastRun == null) || - ((now - lastRun) > OpenSearch.BACKGROUND_PERMISSIONS_MAX_FORCE_MINUTES * 60000)) { - System.out.println( - "opensearchIndexPermissionsBackground: forced run due to max time since previous"); - runIt = true; - } - boolean needed = OpenSearch.getPermissionsNeeded(myShepherd); - if (needed && !runIt) { - System.out.println("opensearchIndexPermissionsBackground: running due to needed=true"); - runIt = true; - } - if (!runIt) { - System.out.println("opensearchIndexPermissionsBackground: running not required; done"); - return; - } - // i think we should set these first... tho they may not get persisted til after? - OpenSearch.setPermissionsTimestamp(myShepherd); - OpenSearch.setPermissionsNeeded(myShepherd, false); - opensearchIndexPermissions(); - System.out.println("opensearchIndexPermissionsBackground: running completed"); - } - -/* note: there are a great deal of users with *no username* that seem to appear in enc.submitters array. - however, very few (2 out of 5600+) encounters with such .submitters have a blank submitterID value - therefore: submitterID will be assumed to be a required value on users which need to be - - this seems further validated by the facts that: - - canUserAccess(user) returns false if no username on user - - a user wihtout a username cant be logged in (and thus cant search) - - "admin" users are just ignored entirely, as they will be exempt from the viewUsers criteria during searching. - - other than "ownership" (via submitterID), a user can view if they have view or edit collab with - another user. so we frontload *approved* collabs for every user here too. - - in terms of "public" encounters, it seems that (based on Collaboration.canUserAccessEncounter()), - encounters with submitterID in (NULL, "public", "", "N/A" [ugh]) is readable by anyone; so we will - skip these from processing as they should be flagged with the boolean isPubliclyReadable in indexing - */ - public static void opensearchIndexPermissions() { - Util.mark("perm start"); - long startT = System.currentTimeMillis(); - System.out.println("opensearchIndexPermissions(): begin..."); - // no security => everything publiclyReadable - saves us work, no? - if (!Collaboration.securityEnabled("context0")) return; - OpenSearch os = new OpenSearch(); - Map > collab = new HashMap >(); - Map usernameToId = new HashMap(); - Shepherd myShepherd = new Shepherd("context0"); - myShepherd.setAction("Encounter.opensearchIndexPermissions"); - myShepherd.beginDBTransaction(); - // it seems as though user.uuid is *required* so we can trust that - try { - for (User user : myShepherd.getUsersWithUsername()) { - usernameToId.put(user.getUsername(), user.getId()); - List collabsFor = Collaboration.collaborationsForUser(myShepherd, - user.getUsername()); - if (Util.collectionIsEmptyOrNull(collabsFor)) continue; - for (Collaboration col : collabsFor) { - if (!col.isApproved() && !col.isEditApproved()) continue; - if (!collab.containsKey(user.getId())) - collab.put(user.getId(), new HashSet()); - collab.get(user.getId()).add(col.getOtherUsername(user.getUsername())); - } - } - } catch (Exception ex) { - ex.printStackTrace(); - } - Util.mark("perm: user build done", startT); - System.out.println("opensearchIndexPermissions(): " + usernameToId.size() + - " total users; " + collab.size() + " have active collab"); - // now iterated over (non-public) encounters - int encCount = 0; - org.json.JSONObject updateData = new org.json.JSONObject(); - // we do not need full Encounter objects here to update index docs, so lets do this via sql/fields - much faster - String sql = - "SELECT \"CATALOGNUMBER\", \"SUBMITTERID\" FROM \"ENCOUNTER\" WHERE \"SUBMITTERID\" IS NOT NULL AND \"SUBMITTERID\" != '' AND \"SUBMITTERID\" != 'N/A' AND \"SUBMITTERID\" != 'public'"; - Query q = null; - try { - q = myShepherd.getPM().newQuery("javax.jdo.query.SQL", sql); - List results = (List)q.execute(); - Util.mark("perm: start encs, size=" + results.size(), startT); - Iterator it = results.iterator(); - while (it.hasNext()) { - Object[] row = (Object[])it.next(); - String id = (String)row[0]; - String submitterId = (String)row[1]; - org.json.JSONArray viewUsers = new org.json.JSONArray(); - String uid = usernameToId.get(submitterId); - if (uid == null) { - // see issue 939 for example :( - System.out.println("opensearchIndexPermissions(): WARNING invalid username " + - submitterId + " on enc " + id); - continue; - } - encCount++; - if (encCount % 1000 == 0) Util.mark("enc[" + encCount + "]", startT); - // viewUsers.put(uid); // we no longer do this as we use submitterUserId from regular indexing in query filter - - // this first part asks the question: who is the owner of the Encounter collaborating with? - // Let those people see the encounter - // This ignores the one-way visibility of admins and orgAdmins - // the question is backwards: it asks: who can the owning user see? - // better to ask: who can see this Encounter by collaborating with its owner? - /* - if (collab.containsKey(uid)) { - for (String colUsername : collab.get(uid)) { - String colId = usernameToId.get(colUsername); - if (colId == null) { - System.out.println( - "opensearchIndexPermissions(): WARNING invalid username " + - colUsername + " in collaboration with userId=" + uid); - continue; - } - viewUsers.put(colId); - } - }*/ - - // better: ask the question, who else can see this encounter via collaboration? - // get the entry set for all collaborations - Set uids = collab.keySet(); - // iterate over the key set - Iterator uidsIter = uids.iterator(); - while (uidsIter.hasNext()) { - // get the uid for the user of this entry - String localUid = uidsIter.next(); - // get the list of usernames in this entry - Set localCollabs = collab.get(localUid); - // evaluate if the submitterId (a username) of this encounter is in this list - if (localCollabs.contains(submitterId)) { - // if the submitterId is in the list, put the uid of the user in viewUsers for OpenSearch - viewUsers.put(localUid); - } - } - if (viewUsers.length() > 0) { - updateData.put("viewUsers", viewUsers); - try { - os.indexUpdate("encounter", id, updateData); - } catch (Exception ex) { - // keeping this quiet cuz it can get noise while index builds - // System.out.println("opensearchIndexPermissions(): WARNING failed to update viewUsers on enc " + enc.getId() + "; likely has not been indexed yet: " + ex); - } - } - } - } catch (Exception ex) { - System.out.println("opensearchIndexPermissions(): failed during encounter loop: " + ex); - ex.printStackTrace(); - } finally { - if (q != null) q.closeAll(); - } - Util.mark("perm: done encs", startT); - myShepherd.rollbackAndClose(); - System.out.println("opensearchIndexPermissions(): ...end [" + encCount + " encs; " + - Math.round((System.currentTimeMillis() - startT) / 1000) + "sec]"); - } - - public static org.json.JSONObject opensearchQuery(final org.json.JSONObject query, int numFrom, - int pageSize, String sort, String sortOrder) - throws IOException { - return Base.opensearchQuery("encounter", query, numFrom, pageSize, sort, sortOrder); - } - - public void opensearchDocumentSerializer(JsonGenerator jgen) - throws IOException, JsonProcessingException { - Shepherd myShepherd = new Shepherd("context0"); - - myShepherd.setAction("Encounter.opensearchDocumentSerializer"); - myShepherd.beginDBTransaction(); - try { - opensearchDocumentSerializer(jgen, myShepherd); - } catch (Exception ex) { - ex.printStackTrace(); - } finally { - myShepherd.rollbackAndClose(); - } - } - - public void opensearchDocumentSerializer(JsonGenerator jgen, Shepherd myShepherd) - throws IOException, JsonProcessingException { - super.opensearchDocumentSerializer(jgen, myShepherd); - - jgen.writeStringField("locationId", this.getLocationID()); - jgen.writeStringField("locationName", this.getLocationName()); - Long dim = this.getDateInMillisecondsFallback(); - if (dim != null) jgen.writeNumberField("dateMillis", dim); - String date = Util.getISO8601Date(this.getDate()); - if (date != null) jgen.writeStringField("date", date); - date = Util.getISO8601Date(this.getDWCDateAdded()); - if (date != null) jgen.writeStringField("dateSubmitted", date); - jgen.writeStringField("verbatimEventDate", this.getVerbatimEventDate()); - jgen.writeStringField("sex", this.getSex()); - jgen.writeStringField("taxonomy", this.getTaxonomyString()); - jgen.writeStringField("lifeStage", this.getLifeStage()); - jgen.writeStringField("livingStatus", this.getLivingStatus()); - jgen.writeStringField("verbatimLocality", this.getVerbatimLocality()); - jgen.writeStringField("country", this.getCountry()); - jgen.writeStringField("behavior", this.getBehavior()); - jgen.writeStringField("patterningCode", this.getPatterningCode()); - jgen.writeStringField("state", this.getState()); - jgen.writeStringField("occurrenceRemarks", this.getOccurrenceRemarks()); - jgen.writeStringField("otherCatalogNumbers", this.getOtherCatalogNumbers()); - jgen.writeBooleanField("publiclyReadable", this.isPubliclyReadable()); - jgen.writeStringField("distinguishingScar", this.getDistinguishingScar()); - String featuredAssetId = null; - List mas = this.getMedia(); - jgen.writeNumberField("numberAnnotations", this.numNonTrivialAnnotations()); - jgen.writeNumberField("numberMediaAssets", mas.size()); - jgen.writeArrayFieldStart("mediaAssets"); - for (MediaAsset ma : mas) { - jgen.writeStartObject(); - jgen.writeNumberField("id", ma.getIdInt()); - jgen.writeStringField("uuid", ma.getUUID()); - jgen.writeNumberField("width", ma.getWidth()); - jgen.writeNumberField("height", ma.getHeight()); - jgen.writeStringField("mimeTypeMajor", ma.getMimeTypeMajor()); - jgen.writeStringField("mimeTypeMinor", ma.getMimeTypeMinor()); - try { - // historic data might throw IllegalArgumentException: Path not under given root - URL url = ma.safeURL(myShepherd, null, "master"); - if (url != null) jgen.writeStringField("url", url.toString()); - } catch (Exception ex) {} - // we (likely) dont need annotations to search on, but they are needed for - // many of the usages (export, gallery, etc) of search *results* - jgen.writeArrayFieldStart("annotations"); - if (ma.hasAnnotations()) - for (Annotation ann : ma.getAnnotations()) { - jgen.writeStartObject(); - jgen.writeStringField("id", ann.getId()); - jgen.writeStringField("iaClass", ann.getIAClass()); - jgen.writeStringField("viewpoint", ann.getViewpoint()); - jgen.writeBooleanField("isTrivial", ann.isTrivial()); - jgen.writeNumberField("theta", ann.getTheta()); - jgen.writeArrayFieldStart("boundingBox"); - Feature ft = ann.getFeature(); // attempt force loading features for getBbox() - int[] bbox = ann.getBbox(); - if (bbox != null) - for (int i : bbox) { - jgen.writeNumber(i); - } - jgen.writeEndArray(); - Encounter annEnc = ann.findEncounter(myShepherd); - if (annEnc != null) jgen.writeStringField("encounterId", annEnc.getId()); - jgen.writeEndObject(); - } - jgen.writeEndArray(); - jgen.writeEndObject(); - if (featuredAssetId == null) featuredAssetId = ma.getUUID(); - } - jgen.writeEndArray(); - if (featuredAssetId != null) jgen.writeStringField("featuredAssetUuid", featuredAssetId); - if (this.submitterID == null) { - jgen.writeNullField("assignedUsername"); - } else { - jgen.writeStringField("assignedUsername", this.submitterID); - User submitter = this.getSubmitterUser(myShepherd); - if (submitter != null) jgen.writeStringField("submitterUserId", submitter.getId()); - } - jgen.writeArrayFieldStart("submitters"); - for (String id : this.getAllSubmitterIds(myShepherd)) { - jgen.writeString(id); - } - jgen.writeEndArray(); - jgen.writeArrayFieldStart("photographers"); - for (String id : this.getAllPhotographerIds()) { - jgen.writeString(id); - } - jgen.writeEndArray(); - jgen.writeArrayFieldStart("informOthers"); - for (String id : this.getAllInformOtherIds()) { - jgen.writeString(id); - } - jgen.writeEndArray(); - - List kws = new ArrayList(); - Map lkws = new HashMap(); - for (Keyword kw : this.getMediaAssetKeywords()) { - if (kw instanceof LabeledKeyword) { - LabeledKeyword lkw = (LabeledKeyword)kw; - lkws.put(lkw.getLabel(), lkw.getValue()); - } else { - String name = kw.getDisplayName(); - if (!kws.contains(name)) kws.add(name); - } - } - jgen.writeArrayFieldStart("mediaAssetKeywords"); - for (String kw : kws) { - jgen.writeString(kw); - } - jgen.writeEndArray(); - jgen.writeObjectFieldStart("mediaAssetLabeledKeywords"); - for (String kwLabel : lkws.keySet()) { - jgen.writeStringField(kwLabel, lkws.get(kwLabel)); - } - jgen.writeEndObject(); - - List projs = this.getProjects(myShepherd); - jgen.writeArrayFieldStart("projects"); - if (projs != null) - for (Project proj : projs) { - jgen.writeString(proj.getId()); - } - jgen.writeEndArray(); - - ImportTask itask = this.getImportTask(myShepherd); - if (itask != null) { - jgen.writeStringField("importTaskId", itask.getId()); - if (itask.getCreator() != null) - jgen.writeStringField("importTaskCreatorId", itask.getCreator().getId()); - String sourceName = itask.getSourceName(); - if (sourceName != null) - jgen.writeStringField("importTaskSourceName", sourceName); - } - jgen.writeArrayFieldStart("annotationViewpoints"); - for (String vp : this.getAnnotationViewpoints()) { - jgen.writeString(vp); - } - jgen.writeEndArray(); - - jgen.writeArrayFieldStart("annotationIAClasses"); - for (String cls : this.getAnnotationIAClasses()) { - jgen.writeString(cls); - } - jgen.writeEndArray(); - - jgen.writeArrayFieldStart("measurements"); - if (this.measurements != null) - for (Measurement meas : this.measurements) { - if (meas.getValue() == null) continue; // no value means we should skip - jgen.writeStartObject(); - jgen.writeNumberField("value", meas.getValue()); - if (meas.getType() != null) jgen.writeStringField("type", meas.getType()); - if (meas.getUnits() != null) jgen.writeStringField("units", meas.getUnits()); - if (meas.getSamplingProtocol() != null) - jgen.writeStringField("samplingProtocol", meas.getSamplingProtocol()); - jgen.writeEndObject(); - } - jgen.writeEndArray(); - - jgen.writeArrayFieldStart("metalTags"); - if (this.getMetalTags() != null) - for (MetalTag tag : this.getMetalTags()) { - jgen.writeStartObject(); - jgen.writeStringField("number", tag.getTagNumber()); - jgen.writeStringField("location", tag.getLocation()); - jgen.writeEndObject(); - } - jgen.writeEndArray(); - if (this.getAcousticTag() != null) { - jgen.writeObjectFieldStart("acousticTag"); - jgen.writeStringField("idNumber", this.getAcousticTag().getIdNumber()); - jgen.writeStringField("serialNumber", this.getAcousticTag().getSerialNumber()); - jgen.writeEndObject(); - } - if (this.getSatelliteTag() != null) { - jgen.writeObjectFieldStart("satelliteTag"); - jgen.writeStringField("name", this.getSatelliteTag().getName()); - jgen.writeStringField("serialNumber", this.getSatelliteTag().getSerialNumber()); - jgen.writeStringField("argosPttNumber", this.getSatelliteTag().getArgosPttNumber()); - jgen.writeEndObject(); - } - if (this.getDTag() != null) { - jgen.writeObjectFieldStart("digitalArchiveTag"); - jgen.writeStringField("dTagID", this.getDTag().getDTagID()); - jgen.writeStringField("serialNumber", this.getDTag().getSerialNumber()); - jgen.writeEndObject(); - } - org.json.JSONObject dpj = this.getDynamicPropertiesJSONObject(); - jgen.writeObjectFieldStart("dynamicProperties"); - for (String key : (Set)dpj.keySet()) { - jgen.writeStringField(key, dpj.optString(key, null)); - } - jgen.writeEndObject(); - - Double dlat = this.getDecimalLatitudeAsDouble(); - Double dlon = this.getDecimalLongitudeAsDouble(); - if ((dlat == null) || !Util.isValidDecimalLatitude(dlat) || (dlon == null) || - !Util.isValidDecimalLongitude(dlon)) { - jgen.writeNullField("locationGeoPoint"); - } else { - jgen.writeObjectFieldStart("locationGeoPoint"); - jgen.writeNumberField("lat", dlat); - jgen.writeNumberField("lon", dlon); - jgen.writeEndObject(); - } - MarkedIndividual indiv = this.getIndividual(); - if (indiv == null) { - jgen.writeNullField("individualId"); - } else { - jgen.writeStringField("individualId", indiv.getId()); - jgen.writeStringField("individualSex", indiv.getSex()); - jgen.writeStringField("individualTaxonomy", indiv.getTaxonomyString()); - jgen.writeNumberField("individualNumberEncounters", indiv.getNumEncounters()); - jgen.writeStringField("individualDisplayName", indiv.getDisplayName()); - jgen.writeArrayFieldStart("individualNames"); - Set names = indiv.getAllNamesList(); - if (names != null) - for (String name : names) { - jgen.writeString(name); - } - jgen.writeEndArray(); - jgen.writeStringField("individualNickName", indiv.getNickName()); - if (indiv.getTimeOfBirth() > 0) { - String birthTime = Util.getISO8601Date(new DateTime( - indiv.getTimeOfBirth()).toString()); - jgen.writeStringField("individualTimeOfBirth", birthTime); - } - if (indiv.getTimeOfDeath() > 0) { - String deathTime = Util.getISO8601Date(new DateTime( - indiv.getTimeOfDeath()).toString()); - jgen.writeStringField("individualTimeOfDeath", deathTime); - } - Encounter[] encs = indiv.getDateSortedEncounters(true); - if ((encs != null) && (encs.length > 0)) { - String encDate = Util.getISO8601Date(encs[0].getDate()); - if (encDate != null) jgen.writeStringField("individualFirstEncounterDate", encDate); - encDate = Util.getISO8601Date(encs[encs.length - 1].getDate()); - if (encDate != null) jgen.writeStringField("individualLastEncounterDate", encDate); - } - jgen.writeArrayFieldStart("individualSocialUnits"); - for (SocialUnit su : myShepherd.getAllSocialUnitsForMarkedIndividual(indiv)) { - Membership mem = su.getMembershipForMarkedIndividual(indiv); - if (mem != null) jgen.writeString(su.getSocialUnitName()); - } - jgen.writeEndArray(); - - jgen.writeArrayFieldStart("individualRelationshipRoles"); - for (String relRole : myShepherd.getAllRoleNamesForMarkedIndividual(indiv.getId())) { - jgen.writeString(relRole); - } - jgen.writeEndArray(); - } - DateTime occdt = getOccurrenceDateTime(myShepherd); - if (occdt != null) jgen.writeStringField("occurrenceDate", occdt.toString()); - jgen.writeStringField("geneticSex", this.getGeneticSex()); - jgen.writeStringField("haplotype", this.getHaplotype()); - - jgen.writeArrayFieldStart("microsatelliteMarkers"); - for (MicrosatelliteMarkersAnalysis msm : getMicrosatelliteMarkers()) { - jgen.writeStartObject(); - jgen.writeStringField("analysisId", msm.getAnalysisID()); - jgen.writeObjectFieldStart("loci"); - if (msm.getLoci() != null) - for (Locus locus : msm.getLoci()) { - if (locus.getName() == null) continue; // snh - jgen.writeObjectFieldStart(locus.getName()); - for (int i = 0; i < 4; i++) { - Integer allele = locus.getAllele(i); - if (allele != null) jgen.writeNumberField("allele" + i, allele); - } - jgen.writeEndObject(); - } - jgen.writeEndObject(); - jgen.writeEndObject(); - } - jgen.writeEndArray(); - - Occurrence occ = this.getOccurrence(myShepherd); - if (occ == null) { - jgen.writeNullField("occurrenceId"); - } else { - jgen.writeStringField("occurrenceId", occ.getId()); - jgen.writeStringField("occurrenceGroupBehavior", occ.getGroupBehavior()); - jgen.writeStringField("occurrenceGroupComposition", occ.getGroupComposition()); - jgen.writeStringField("occurrenceComments", occ.getComments()); - if (occ.getVisibilityIndex() != null) - jgen.writeNumberField("occurrenceVisibilityIndex", occ.getVisibilityIndex()); - if (occ.getIndividualCount() != null) - jgen.writeNumberField("occurrenceIndividualCount", occ.getIndividualCount()); - if (occ.getMinGroupSizeEstimate() != null) - jgen.writeNumberField("occurrenceMinGroupSizeEstimate", - occ.getMinGroupSizeEstimate()); - if (occ.getMaxGroupSizeEstimate() != null) - jgen.writeNumberField("occurrenceMaxGroupSizeEstimate", - occ.getMaxGroupSizeEstimate()); - if (occ.getBestGroupSizeEstimate() != null) - jgen.writeNumberField("occurrenceBestGroupSizeEstimate", - occ.getBestGroupSizeEstimate()); - if (occ.getBearing() != null) - jgen.writeNumberField("occurrenceBearing", occ.getBearing()); - if (occ.getDistance() != null) - jgen.writeNumberField("occurrenceDistance", occ.getDistance()); - Double odlat = occ.getDecimalLatitude(); - Double odlon = occ.getDecimalLongitude(); - if ((odlat == null) || !Util.isValidDecimalLatitude(odlat) || (odlon == null) || - !Util.isValidDecimalLongitude(odlon)) { - jgen.writeNullField("occurrenceLocationGeoPoint"); - } else { - jgen.writeObjectFieldStart("occurrenceLocationGeoPoint"); - jgen.writeNumberField("lat", odlat); - jgen.writeNumberField("lon", odlon); - jgen.writeEndObject(); - } - } - jgen.writeArrayFieldStart("organizations"); - User owner = this.getSubmitterUser(myShepherd); - if ((owner != null) && (owner.getOrganizations() != null)) - for (Organization org : owner.getOrganizations()) { - jgen.writeString(org.getId()); - } - jgen.writeEndArray(); - - jgen.writeArrayFieldStart("tissueSampleIds"); - for (String id : this.getTissueSampleIDs()) { - jgen.writeString(id); - } - jgen.writeEndArray(); - - Map bmeas = this.getBiologicalMeasurementsByType(); - jgen.writeObjectFieldStart("biologicalMeasurements"); - for (String type : (Set)bmeas.keySet()) { - jgen.writeNumberField(type, bmeas.get(type).getValue()); - } - jgen.writeEndObject(); - // this gets set on specific single-encounter-only actions, when extra expense is okay - // otherwise this will be computed by permissions backgrounding - if (this.getOpensearchProcessPermissions()) { - System.out.println("opensearchProcessPermissions=true for " + this.getId() + - "; indexing permissions"); - jgen.writeFieldName("viewUsers"); - jgen.writeStartArray(); - for (String id : this.userIdsWithViewAccess(myShepherd)) { - System.out.println("opensearch whhhh: " + id); - jgen.writeString(id); - } - jgen.writeEndArray(); - } - } - - public void opensearchIndexDeep() - throws IOException { - this.opensearchIndex(); - - final String encId = this.getId(); - ExecutorService executor = Executors.newFixedThreadPool(4); - Runnable rn = new Runnable() { - public void run() { - Shepherd bgShepherd = new Shepherd("context0"); - bgShepherd.setAction("Encounter.opensearchIndexDeep_" + encId); - bgShepherd.beginDBTransaction(); - try { - Encounter enc = bgShepherd.getEncounter(encId); - if ((enc == null) || (!enc.hasMarkedIndividual() && !enc.hasAnnotations())) { - // bgShepherd.rollbackAndClose(); - executor.shutdown(); - return; - } - MarkedIndividual indiv = enc.getIndividual(); - if (indiv != null) { - System.out.println("opensearchIndexDeep() background indexing indiv " + - indiv.getId() + " via enc " + encId); - try { - indiv.opensearchIndex(); - } catch (Exception ex) { - System.out.println("opensearchIndexDeep() background indexing " + - indiv.getId() + " FAILED: " + ex.toString()); - ex.printStackTrace(); - } - } - Occurrence occ = enc.getOccurrence(bgShepherd); - if (occ != null) { - System.out.println("opensearchIndexDeep() background indexing occ " + - occ.getId() + " via enc " + encId); - try { - occ.opensearchIndex(); - } catch (Exception ex) { - System.out.println("opensearchIndexDeep() background indexing " + - occ.getId() + " FAILED: " + ex.toString()); - ex.printStackTrace(); - } - } - if (enc.hasAnnotations()) { - for (Annotation ann : enc.getAnnotations()) { - System.out.println("opensearchIndexDeep() background indexing annot " + - ann.getId() + " via enc " + encId); - try { - ann.opensearchIndex(); - } catch (Exception ex) { - System.out.println("opensearchIndexDeep() background indexing " + - ann.getId() + " FAILED: " + ex.toString()); - ex.printStackTrace(); - } - } - } - } catch (Exception e) { - System.out.println("opensearchIndexDeep() backgrounding Encounter " + encId + - " hit an exception."); - e.printStackTrace(); - } finally { - bgShepherd.rollbackAndClose(); - } - System.out.println("opensearchIndexDeep() backgrounding Encounter " + encId + - " finished."); - executor.shutdown(); - } - }; - System.out.println("opensearchIndexDeep() begin backgrounding for " + this); - executor.execute(rn); - System.out.println("opensearchIndexDeep() [foreground] finished for Encounter " + encId); - } - - // given a doc from opensearch, can user access it? - public static boolean opensearchAccess(org.json.JSONObject doc, User user, - Shepherd myShepherd) { - if ((doc == null) || (user == null)) return false; - if (doc.optBoolean("publiclyReadable", false)) return true; - if (doc.optString("submitterUserId", "__FAIL__").equals(user.getId())) return true; - if (user.isAdmin(myShepherd)) return true; - org.json.JSONArray viewUsers = doc.optJSONArray("viewUsers"); - if (viewUsers == null) return false; - for (int i = 0; i < viewUsers.length(); i++) { - if (viewUsers.optString(i, "__FAIL__").equals(user.getId())) return true; - } - return false; - } - - @Override public Base getById(Shepherd myShepherd, String id) { - return myShepherd.getEncounter(id); - } - - @Override public String getAllVersionsSql() { - return - "SELECT \"CATALOGNUMBER\", CAST(COALESCE(EXTRACT(EPOCH FROM CAST(\"MODIFIED\" AS TIMESTAMP))*1000,-1) AS BIGINT) AS version FROM \"ENCOUNTER\" ORDER BY version"; - } - - @Override public long getVersion() { - return Util.getVersionFromModified(modified); - } - - public org.json.JSONObject opensearchMapping() { - org.json.JSONObject map = super.opensearchMapping(); - org.json.JSONObject keywordType = new org.json.JSONObject("{\"type\": \"keyword\"}"); - org.json.JSONObject keywordNormalType = new org.json.JSONObject( - "{\"type\": \"keyword\", \"normalizer\": \"wildbook_keyword_normalizer\"}"); - map.put("date", new org.json.JSONObject("{\"type\": \"date\"}")); - map.put("dateSubmitted", new org.json.JSONObject("{\"type\": \"date\"}")); - map.put("verbatimEventDate", new org.json.JSONObject("{\"type\": \"text\"}")); - map.put("individualTimeOfBirth", new org.json.JSONObject("{\"type\": \"date\"}")); - map.put("individualTimeOfDeath", new org.json.JSONObject("{\"type\": \"date\"}")); - map.put("locationGeoPoint", new org.json.JSONObject("{\"type\": \"geo_point\"}")); - map.put("occurrenceLocationGeoPoint", new org.json.JSONObject("{\"type\": \"geo_point\"}")); - - // if we want to sort on it (and it is texty), it needs to be keyword - // (ints, dates, etc are all sortable) - // note: "id" is done in Base.java - map.put("taxonomy", keywordType); - map.put("occurrenceId", keywordType); - map.put("state", keywordType); - map.put("submitterUserId", keywordType); - map.put("individualTaxonomy", keywordType); - map.put("individualId", keywordType); - map.put("importTaskId", keywordType); - map.put("importTaskCreatorId", keywordType); - map.put("importTaskSourceName", keywordType); - - // all case-insensitive keyword-ish types - map.put("locationId", keywordNormalType); - map.put("locationName", keywordNormalType); - map.put("country", keywordNormalType); - map.put("assignedUsername", keywordNormalType); - map.put("projects", keywordNormalType); - map.put("behavior", keywordNormalType); - map.put("patterningCode", keywordNormalType); - map.put("annotationViewpoints", keywordNormalType); - map.put("mediaAssetKeywords", keywordNormalType); - map.put("annotationIAClasses", keywordNormalType); - map.put("haplotype", keywordNormalType); - map.put("individualSocialUnits", keywordNormalType); - map.put("individualRelationshipRoles", keywordNormalType); - map.put("individualDisplayName", keywordNormalType); - map.put("organizations", keywordNormalType); - map.put("otherCatalogNumbers", keywordNormalType); - map.put("lifeStage", keywordNormalType); - map.put("submitters", keywordNormalType); - map.put("photographers", keywordNormalType); - map.put("informOthers", keywordNormalType); - - // https://stackoverflow.com/questions/68760699/matching-documents-where-multiple-fields-match-in-an-array-of-objects - map.put("measurements", new org.json.JSONObject("{\"type\": \"nested\"}")); - map.put("metalTags", new org.json.JSONObject("{\"type\": \"nested\"}")); - return map; - } - - // for encounters, we allow null user to see *some* things - public org.json.JSONObject jsonForApiGet(Shepherd myShepherd, User user) - throws IOException { - org.json.JSONObject rtn = new org.json.JSONObject(); - boolean isPublic = isPubliclyReadable(); - // anon-user can only see public, so we 401 here - if ((user == null) && !isPublic) { - rtn.put("statusCode", 401); - rtn.put("success", false); - return rtn; - } - rtn = opensearchDocumentAsJSONObject(myShepherd); - rtn.put("success", true); - rtn.put("statusCode", 200); - rtn.put("access", "read"); - rtn.put("isPublic", isPublic); - - boolean hideUserEmail = true; - User submitter = getSubmitterUser(myShepherd); - if (submitter != null) - rtn.put("submitterInfo", - submitter.infoJSONObject(myShepherd, user != null, hideUserEmail)); - // check to see if logged-in-user is outright blocked - if (user != null) { - boolean blocked = true; - if (canUserEdit(user, myShepherd)) { - rtn.put("access", "write"); - blocked = false; - // we can allow email being shown when access=write - hideUserEmail = false; - if (submitter != null) - rtn.put("submitterInfo", - submitter.infoJSONObject(myShepherd, true, hideUserEmail)); - } else if (canUserView(user, myShepherd)) { - blocked = false; - } - if (blocked) { - // we keep this very minimal - org.json.JSONObject blockedRtn = new org.json.JSONObject(); - blockedRtn.put("success", true); - blockedRtn.put("statusCode", 200); - blockedRtn.put("access", "none"); - blockedRtn.put("id", rtn.get("id")); - // need this to know who to collab with - Collaboration col = Collaboration.collaborationBetweenUsers(user, submitter, - myShepherd.getContext()); - if (col != null) { - blockedRtn.put("collaborationState", col.getState()); - blockedRtn.put("collaborationCreated", col.getDateStringCreated()); - } - blockedRtn.put("assignedUsername", rtn.optString("assignedUsername", null)); - blockedRtn.put("submitterUserId", rtn.optString("submitterUserId", null)); - blockedRtn.put("submitterInfo", rtn.optJSONObject("submitterInfo")); - return blockedRtn; - } - } - // additional fields we want - rtn.put("dateValues", getDateValuesJson()); - rtn.put("researcherComments", getRComments()); - rtn.put("groupRole", getGroupRole()); - rtn.put("identificationRemarks", getIdentificationRemarks()); - rtn.put("spotMapping", spotMappingJsonForApiGet()); - - // the user-listy things - rtn.put("submitters", - userListJSONArray(myShepherd, this.submitters, user != null, hideUserEmail)); - rtn.put("photographers", - userListJSONArray(myShepherd, this.photographers, user != null, hideUserEmail)); - rtn.put("informOthers", - userListJSONArray(myShepherd, this.informOthers, user != null, hideUserEmail)); - // sanitize for non-logged-in users (hence, on public data) - if (user == null) { - rtn.put("access", "read"); - String[] blocked = { - "importTaskSourceName", "locationId", "locationName", "country", "verbatimLocality", - "microsatelliteMarkers", "locationGeoPoint", "occurrenceLocationGeoPoint", - "mediaAssetKeywords", "mediaAssetLabeledKeywords", "biologicalMeasurements", - "importTaskCreatorId", "annotationIAClasses", "annotationViewpoints", - "researcherComments", "informOthers", "photographers", "submitters", - "assignedUsername" - }; - for (String field : blocked) { - rtn.remove(field); - } - // we redo mediaAssets, with no annots and mid size - org.json.JSONArray mas = new org.json.JSONArray(); - for (MediaAsset ma : getMedia()) { - org.json.JSONObject maj = new org.json.JSONObject(); - maj.put("uuid", ma.getUUID()); - maj.put("mimeTypeMajor", ma.getMimeTypeMajor()); - maj.put("mimeTypeMinor", ma.getMimeTypeMinor()); - maj.put("rotationInfo", ma.getRotationInfo()); - try { - // historic data might throw IllegalArgumentException: Path not under given root - java.net.URL url = ma.safeURL(myShepherd, null, "mid"); - if (url != null) maj.put("url", url.toString()); - } catch (Exception ex) {} - mas.put(maj); - } - rtn.put("mediaAssets", mas); - } else { - // for real users we add some extras to assets and annotations - if (rtn.optJSONArray("mediaAssets") != null) { - for (int i = 0; i < rtn.getJSONArray("mediaAssets").length(); i++) { - if (rtn.getJSONArray("mediaAssets").optJSONObject(i) != null) { - MediaAsset ma = MediaAssetFactory.loadByUuid(rtn.getJSONArray( - "mediaAssets").getJSONObject(i).optString("uuid"), myShepherd); - if (ma != null) { - rtn.getJSONArray("mediaAssets").getJSONObject(i).put("keywords", - ma.getKeywordsJSONArray()); - rtn.getJSONArray("mediaAssets").getJSONObject(i).put("detectionStatus", - ma.getDetectionStatus()); - rtn.getJSONArray("mediaAssets").getJSONObject(i).put("userFilename", - ma.getUserFilename()); - rtn.getJSONArray("mediaAssets").getJSONObject(i).put("rotationInfo", - ma.getRotationInfo()); - } - // now we cram some stuff into each annotation as well - if (rtn.getJSONArray("mediaAssets").getJSONObject(i).optJSONArray( - "annotations") != null) { - for (int j = 0; - j < - rtn.getJSONArray("mediaAssets").getJSONObject(i).getJSONArray( - "annotations").length(); - j++) { - if (rtn.getJSONArray("mediaAssets").getJSONObject(i).getJSONArray( - "annotations").optJSONObject(j) == null) continue; - // this parsing of nested json really makes me miss perl - Annotation ann = myShepherd.getAnnotation(rtn.getJSONArray( - "mediaAssets").getJSONObject(i).getJSONArray( - "annotations").getJSONObject(j).optString("id", null)); - if (ann == null) continue; - rtn.getJSONArray("mediaAssets").getJSONObject(i).getJSONArray( - "annotations").getJSONObject(j).put("identificationStatus", - ann.getIdentificationStatus()); - // annTasks are in chron order so most recent will be at end - List annTasks = ann.getRootIATasks(myShepherd); - int ntasks = Util.collectionSize(annTasks); - if (ntasks > 0) { - rtn.getJSONArray("mediaAssets").getJSONObject(i).getJSONArray( - "annotations").getJSONObject(j).put("iaTaskId", - annTasks.get(ntasks - 1).getId()); - rtn.getJSONArray("mediaAssets").getJSONObject(i).getJSONArray( - "annotations").getJSONObject(j).put("iaTaskParameters", - annTasks.get(ntasks - 1).getParameters()); - } - } - } - } - } - } - } - return rtn; - } - - // internal utility function - private org.json.JSONArray userListJSONArray(Shepherd myShepherd, List users, - boolean includeSensitive, boolean hideEmail) { - org.json.JSONArray arr = new org.json.JSONArray(); - if (Util.collectionIsEmptyOrNull(users)) return arr; - for (User user : users) { - arr.put(user.infoJSONObject(myShepherd, includeSensitive, hideEmail)); - } - return arr; - } - - public static Base createFromApi(org.json.JSONObject payload, List files, - Shepherd myShepherd) - throws ApiException { - if (payload == null) throw new ApiException("empty payload"); - User user = (User)payload.opt("_currentUser"); - - // these need validation (will throw ApiException if fail) - String locationID = (String)validateFieldValue("locationId", payload); - String dateTime = (String)validateFieldValue("dateTime", payload); - String txStr = (String)validateFieldValue("taxonomy", payload); - String submitterEmail = (String)validateFieldValue("submitterEmail", payload); - String photographerEmail = (String)validateFieldValue("photographerEmail", payload); - Double decimalLatitude = (Double)validateFieldValue("decimalLatitude", payload); - Double decimalLongitude = (Double)validateFieldValue("decimalLongitude", payload); - if (((decimalLatitude == null) && (decimalLongitude != null)) || - ((decimalLatitude != null) && (decimalLongitude == null))) { - org.json.JSONObject error = new org.json.JSONObject(); - error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); - // i guess we pick one, since both are wrong - error.put("fieldName", "decimalLatitude"); - error.put("value", decimalLatitude); - throw new ApiException("cannot send just one of decimalLatitude and decimalLongitude", - error); - } - String additionalEmailsValue = payload.optString("additionalEmails", null); - String[] additionalEmails = null; - if (!Util.stringIsEmptyOrNull(additionalEmailsValue)) - additionalEmails = additionalEmailsValue.split("[,\\s]+"); - if (additionalEmails != null) { - org.json.JSONObject error = new org.json.JSONObject(); - error.put("fieldName", "additionalEmails"); - for (String email : additionalEmails) { - if (!Util.isValidEmailAddress(email)) { - error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); - error.put("value", email); - throw new ApiException("invalid email address", error); - } - } - } - Encounter enc = new Encounter(false); - if (Util.isUUID(payload.optString("_id"))) enc.setId(payload.getString("_id")); - enc.setLocationID(locationID); - enc.setDecimalLatitude(decimalLatitude); - enc.setDecimalLongitude(decimalLongitude); - enc.setDateFromISO8601String(dateTime); - enc.setTaxonomyFromString(txStr); - if (CommonConfiguration.getProperty("encounterState0", myShepherd.getContext()) != null) { - enc.setState(CommonConfiguration.getProperty("encounterState0", - myShepherd.getContext())); - } - enc.setComments(payload.optString("comments", null)); - if (user == null) { - enc.setSubmitterID("public"); // this seems to be what EncounterForm servlet does so... - } else { - enc.setSubmitterID(user.getUsername()); - enc.addSubmitter(user); - } - if (!Util.stringIsEmptyOrNull(submitterEmail)) { - User submitterUser = myShepherd.getOrCreateUserByEmailAddress(submitterEmail, - payload.optString("submitterName", null)); - // set this after the owner-submitter being set - enc.addSubmitter(submitterUser); - } - if (!Util.stringIsEmptyOrNull(photographerEmail)) { - User photographerUser = myShepherd.getOrCreateUserByEmailAddress(photographerEmail, - payload.optString("photographerName", null)); - enc.addPhotographer(photographerUser); - } - if (additionalEmails != null) { - for (String email : additionalEmails) { - User addlUser = myShepherd.getOrCreateUserByEmailAddress(email, null); - enc.addInformOther(addlUser); - } - } - // this will get/make an Occurrence no matter what - Occurrence occ = myShepherd.getOrCreateOccurrence(payload.optString("occurrenceId", null)); - occ.addEncounterAndUpdateIt(enc); - myShepherd.getPM().makePersistent(occ); - return enc; - } - - // user should already have been validated -- via obj.canUserEdit() -- in api/BaseObject, so this - // does not need to be tested here. however, more detailed checks may require user (e.g. can user - // also alter another object, such as Occurrence) - public org.json.JSONObject processPatch(org.json.JSONArray patchArr, User user, - Shepherd myShepherd) - throws ApiException { - if (patchArr == null) - throw new ApiException("null patch array", ApiException.ERROR_RETURN_CODE_REQUIRED); - this.setSkipAutoIndexing(true); - org.json.JSONArray resArr = new org.json.JSONArray(); - Set occNeedPruning = new HashSet(); - Set indivNeedPruning = new HashSet(); - for (int i = 0; i < patchArr.length(); i++) { - System.out.println("applied patch at [i=" + i + "]: " + patchArr.optJSONObject(i)); - org.json.JSONObject patchRes = EncounterPatchValidator.applyPatch(this, - patchArr.optJSONObject(i), user, myShepherd); - for (int j = 0; j < patchRes.getJSONArray("_mayNeedPruning").length(); j++) { - Object p = patchRes.getJSONArray("_mayNeedPruning").get(j); - if (p instanceof Occurrence) { - occNeedPruning.add((Occurrence)p); - } else if (p instanceof MarkedIndividual) { - indivNeedPruning.add((MarkedIndividual)p); - } - } - patchRes.remove("_mayNeedPruning"); - System.out.println("patch returned at [i=" + i + "]: " + patchRes); - resArr.put(patchRes); - } - org.json.JSONObject rtn = new org.json.JSONObject(); - rtn.put("patchResults", resArr); - // after applying each patch, make sure nothing is wrong - EncounterPatchValidator.finalValidation(this, myShepherd); - // now we need to look at modified objects which may be empty (and thus need pruning) - for (Occurrence occ : occNeedPruning) { - if (!occ.pruneIfNeeded(myShepherd)) { - occ.setSkipAutoIndexing(false); - } - } - for (MarkedIndividual indiv : indivNeedPruning) { - if (!indiv.pruneIfNeeded(myShepherd)) { - indiv.setSkipAutoIndexing(false); - } - } - // no exceptions means success - rtn.put("success", true); - rtn.put("statusCode", 200); - this.setDWCDateLastModified(); - this._log(resArr); - this.setSkipAutoIndexing(false); - return rtn; - } - - // see note on painful redundancy with bulk import and createFromApi on - // Base.applyPatchOp() - public Object applyPatchOp(String fieldName, Object value, String op) - throws ApiException { - System.out.println("[DEBUG] applyPatchOp(): " + op + " " + fieldName + "=>" + value + - " on: " + this); - if (op == null) - throw new ApiException("op is required", ApiException.ERROR_RETURN_CODE_REQUIRED); - // TODO future enhancement: op=remove path=annotations/ANNOT_ID should perform - // functionality of servlet/EncounterRemoveAnnotation.java - User user = null; // needed for some options below - switch (fieldName) { - case "decimalLatitude": - setDecimalLatitude((Double)value); - break; - case "decimalLongitude": - setDecimalLongitude((Double)value); - break; - case "alternateId": - // note: is same as otherCatalogNumbers - setAlternateID((String)value); - break; - case "behavior": - setBehavior((String)value); - break; - case "country": - setCountry((String)value); - break; - case "dateInMilliseconds": - if (value != null) setDateInMilliseconds((Long)value); - break; - case "year": - if (value == null) { - setYear(0); - } else { - setYear((Integer)value); - } - break; - case "month": - if (value == null) { - setMonth(0); - } else { - setMonth((Integer)value); - } - break; - case "day": - if (value == null) { - setDay(0); - } else { - setDay((Integer)value); - } - break; - case "hour": - if (value == null) { - setHour(-1); // grr - } else { - setHour((Integer)value); - } - break; - case "minutes": - if (value == null) { - setMinutes(null); - } else { - setMinutes(value.toString()); - } - break; - case "depth": - setDepth((Double)value); - break; - case "elevation": - setMaximumElevationInMeters((Double)value); - break; - case "genus": - setGenus((String)value); - break; - case "specificEpithet": - setSpecificEpithet((String)value); - break; - case "lifeStage": - setLifeStage((String)value); - break; - case "livingStatus": - setLivingStatus((String)value); - break; - case "locationId": - setLocationID((String)value); - break; - case "sex": - setSex((String)value); - break; - case "state": - setState((String)value); - break; - case "submitterID": - setSubmitterID((String)value); - break; - case "submitterName": - setSubmitterName((String)value); - break; - case "submitterOrganization": - setSubmitterOrganization((String)value); - break; - case "distinguishingScar": - setDistinguishingScar((String)value); - break; - case "groupRole": - setGroupRole((String)value); - break; - case "identificationRemarks": - setIdentificationRemarks((String)value); - break; - case "occurrenceRemarks": - case "sightingRemarks": - setOccurrenceRemarks((String)value); - break; - case "otherCatalogNumbers": - setOtherCatalogNumbers((String)value); - break; - case "patterningCode": - setPatterningCode((String)value); - break; - case "satelliteTag": - setSatelliteTag((SatelliteTag)value); - break; - case "acousticTag": - setAcousticTag((AcousticTag)value); - break; - case "metalTags": - // we only need location to remove - if ("remove".equals(op) && (value != null)) { - removeMetalTag(value.toString()); - } else if (("add".equals(op) || "replace".equals(op)) && - (value instanceof org.json.JSONObject)) { - // add or replace will update based on location if exists - org.json.JSONObject jval = (org.json.JSONObject)value; - addOrUpdateMetalTag(jval.optString("location", null), - jval.optString("number", null)); - } - break; - case "measurements": - if ("remove".equals(op) && (value != null)) { - removeMeasurementByType(value.toString()); - } else if (value instanceof Measurement) { - // for op=add or op=replace, if it has the measurement (i.e. by type), it means - // it should be changed in place already so dont do anything - Measurement meas = (Measurement)value; - if (findMeasurementOfType(meas.getType()) == null) addMeasurement(meas); - } - break; - case "annotations": - // for now we can only patch op=remove on path=annotations - // adding annots is done through legacy servlet - if ("remove".equals(op) && (value instanceof Annotation)) { - // enc.removeAnnotation and deletePersistent (from db/shepherd) done in EncounterPatchValidator - // so we only need to clean up some loose ends here - Annotation goneAnnot = (Annotation)value; - goneAnnot.setSkipAutoIndexing(true); - goneAnnot.opensearchUnindexQuiet(); - } - break; - // these we really only want to append to (i think??) - // so this should only happen when op=add/replace and - // value is non-null - case "researcherComments": - if (value != null) addComments((String)value); - break; - case "verbatimLocality": - setVerbatimLocality((String)value); - break; - case "verbatimEventDate": - setVerbatimEventDate((String)value); - break; - // we should get value as a MarkedIndividual here (or null) - case "individualId": - if ("remove".equals(op) || (value == null)) { - MarkedIndividual current = removeIndividual(); - if (current != null) { - System.out.println("enc.applyPatchOp() removed " + this + " from " + current); - } - } else { - // value should be an individual (new or existing) - MarkedIndividual indiv = (MarkedIndividual)value; - MarkedIndividual current = getIndividual(); - if (indiv.equals(current)) { - System.out.println( - "enc.applyPatchOp() ignoring adding existing individual to " + this); - break; - } - current = removeIndividual(); - if (current != null) { - current.setSkipAutoIndexing(false); - setIndividual(null); - System.out.println("enc.applyPatchOp() removed (prior to re-setting) " + this + - " from " + current); - } - indiv.addEncounter(this); - setIndividual(indiv); - // this will only set indiv taxonomy if NOT set - // so for new indiv and existing with no taxonomy - if (indiv.getTaxonomyString() == null) - indiv.setTaxonomyString(this.getTaxonomyString()); - // indiv.version will be updated by above calls - System.out.println("enc.applyPatchOp() added " + this + " to " + indiv); - } - break; - // value should be an Occurrence here (already validated and permission-checked) - case "occurrenceId": - // if EncounterPatchValidator let thru null value, we do nothing - if (value == null) break; - Occurrence occ = (Occurrence)value; - if ("remove".equals(op)) { - // in remove case, we are given occ to remove from - occ.removeEncounter(this); - this.occurrenceID = null; - } else { - // otherwise it is occ we add to - occ.addEncounterAndUpdateIt(this); - } - break; - case "assets": - if ("add".equals(op) && (value != null)) { - MediaAsset ma = (MediaAsset)value; - ma.setDetectionStatus("_new"); - addMediaAsset(ma); - } - break; - // value should be a user here - case "informOthers": - user = (User)value; - if (op.equals("remove")) { - removeInformOther(user); - } else { - addInformOther(user); - } - break; - case "submitters": - user = (User)value; - if (op.equals("remove")) { - removeSubmitter(user); - } else { - addSubmitter(user); - } - break; - case "photographers": - user = (User)value; - if (op.equals("remove")) { - removePhotographer(user); - } else { - addPhotographer(user); - } - break; - default: - throw new ApiException("unknown fieldName: " + fieldName, - ApiException.ERROR_RETURN_CODE_INVALID); - } - return value; - } - - public org.json.JSONObject afterPatch(Shepherd myShepherd) { - org.json.JSONObject res = new org.json.JSONObject(); - List needsIndexing = new ArrayList(); - org.json.JSONArray newAssetsArr = new org.json.JSONArray(); - // we update children here (not backgrounded) since we need them available - // once the api returns the results - for (MediaAsset ma : this.getMedia()) { - if ("_new".equals(ma.getDetectionStatus())) { - // _post_new is meant to be temporary, as it - // will get overwritten once put into IA pipeline - ma.setDetectionStatus("_post_new"); - ma.updateStandardChildren(myShepherd); - needsIndexing.add(ma); - org.json.JSONObject maj = new org.json.JSONObject(); - maj.put("id", ma.getIdInt()); - try { - URL url = ma.safeURL(myShepherd, null, "master"); - if (url != null) maj.put("url", url.toString()); - } catch (Exception ex) {} - newAssetsArr.put(maj); - } - } - if (newAssetsArr.length() > 0) res.put("newMediaAssets", newAssetsArr); - BulkImportUtil.bulkOpensearchIndex(needsIndexing); - return res; - } - - // this is allowed to have its own new thread since encounter is persisted - public org.json.JSONObject afterPatchTransaction(String context) { - List ids = new ArrayList(); - - // we use _post_new state to determine what needs to go to IA - // see: afterPatch() above - for (MediaAsset ma : this.getMedia()) { - if ("_post_new".equals(ma.getDetectionStatus())) { - ids.add(ma.getIdInt()); - } - } - if (ids.size() < 1) return null; - Task task = this.sendToIA(ids, context); - if (task == null) return null; - org.json.JSONObject rtn = new org.json.JSONObject(); - rtn.put("taskId", task.getId()); - return rtn; - } - - public MarkedIndividual removeIndividual() { - MarkedIndividual current = getIndividual(); - - if (current == null) return null; - // skip auto indexing cuz race conditions; must manually index later - current.setSkipAutoIndexing(true); - current.removeEncounter(this); - setIndividual(null); - return current; - } - - public static Object validateFieldValue(String fieldName, org.json.JSONObject data) - throws ApiException { - if (data == null) throw new ApiException("empty payload"); - org.json.JSONObject error = new org.json.JSONObject(); - error.put("fieldName", fieldName); - String exMessage = "invalid value for " + fieldName; - Object returnValue = null; - double UNSET_LATLON = 9999.99; - switch (fieldName) { - case "locationId": - returnValue = data.optString(fieldName, null); - if (returnValue == null) { - error.put("code", ApiException.ERROR_RETURN_CODE_REQUIRED); - throw new ApiException(exMessage, error); - } - if (!LocationID.isValidLocationID((String)returnValue)) { - error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); - error.put("value", returnValue); - throw new ApiException(exMessage, error); - } - break; - - case "dateTime": - returnValue = data.optString(fieldName, null); - if (returnValue == null) { - error.put("code", ApiException.ERROR_RETURN_CODE_REQUIRED); - throw new ApiException(exMessage, error); - } - if (!validISO8601String((String)returnValue)) { - error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); - error.put("value", returnValue); - throw new ApiException(exMessage, error); - } - break; - - case "taxonomy": - returnValue = data.optString(fieldName, null); - if (returnValue != null) { // null is allowed, but will not pass validity - // this is throwaway read-only shepherd - Shepherd myShepherd = new Shepherd("context0"); - myShepherd.setAction("Encounter.validateFieldValue"); - boolean validTaxonomy = false; - myShepherd.beginDBTransaction(); - try { - validTaxonomy = myShepherd.isValidTaxonomyName((String)returnValue); - } catch (Exception e) { e.printStackTrace(); } finally { - myShepherd.rollbackAndClose(); - } - if (!validTaxonomy) { - error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); - error.put("value", returnValue); - throw new ApiException(exMessage, error); - } - } - break; - - case "photographerEmail": - case "submitterEmail": - returnValue = data.optString(fieldName, null); - if ((returnValue != null) && !Util.isValidEmailAddress((String)returnValue)) { - error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); - error.put("value", returnValue); - throw new ApiException(exMessage, error); - } - break; - - case "decimalLatitude": - returnValue = data.optDouble(fieldName, UNSET_LATLON); - if ((double)returnValue == UNSET_LATLON) { - returnValue = null; - } else if (!Util.isValidDecimalLatitude((double)returnValue)) { - error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); - error.put("value", returnValue); - throw new ApiException(exMessage, error); - } - break; - - case "decimalLongitude": - returnValue = data.optDouble(fieldName, UNSET_LATLON); - if ((double)returnValue == UNSET_LATLON) { - returnValue = null; - } else if (!Util.isValidDecimalLongitude((double)returnValue)) { - error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); - error.put("value", returnValue); - throw new ApiException(exMessage, error); - } - break; - - default: - System.out.println("Encounter.validateFieldValue(): WARNING unsupported fieldName=" + - fieldName); - } - // must be okay! - return returnValue; - } - - // basically ripped from servlet/EncounterForm - public Task sendToIA(Shepherd myShepherd) { - Task task = null; - - try { - IAJsonProperties iaConfig = IAJsonProperties.iaConfig(); - if (iaConfig.hasIA(this, myShepherd)) { - for (MediaAsset ma : this.getMedia()) { - ma.setDetectionStatus(IBEISIA.STATUS_INITIATED); - } - Task parentTask = null; // this is *not* persisted, but only used so intakeMediaAssets will inherit its params - if (this.getLocationID() != null) { - parentTask = new Task(); - org.json.JSONObject tp = new org.json.JSONObject(); - org.json.JSONObject mf = new org.json.JSONObject(); - mf.put("locationId", this.getLocationID()); - tp.put("matchingSetFilter", mf); - parentTask.setParameters(tp); - } - task = IA.intakeMediaAssets(myShepherd, this.getMedia(), parentTask); - myShepherd.storeNewTask(task); - System.out.println("sendToIA() success on " + this + " => " + task); - } else { - System.out.println("sendToIA() skipped; no config for " + this); - } - } catch (Exception ex) { - System.out.println("sendToIA() failed on " + this + ": " + ex); - ex.printStackTrace(); - } - return task; - } - - // this is based on servlet/MediaAssetCreate and differs only slightly from - // above - mainly in that it can handle multiple assets and creates own shepherd - // (note: all assets assumed to be using *this encounter* - public Task sendToIA(List ids, String context) { - Task task = null; - Shepherd myShepherd = new Shepherd(context); - - myShepherd.setAction("Encounter.sendToIA()"); - myShepherd.beginDBTransaction(); - try { - IAJsonProperties iaConfig = IAJsonProperties.iaConfig(); - boolean hasConfig = iaConfig.hasIA(this, myShepherd); - List allMAs = new ArrayList(); - for (Integer id : ids) { - if (id < 0) continue; - MediaAsset ma = MediaAssetFactory.load(id, myShepherd); - if (ma != null) { - ma.setDetectionStatus(hasConfig ? IBEISIA.STATUS_INITIATED : IBEISIA.STATUS_COMPLETE); - allMAs.add(ma); - } - } - if (!hasConfig) { - System.out.println("sendToIA() skipped; no config for " + this); - } else if (allMAs.size() > 0) { - Task parentTask = null; // not persisted - if (this.getLocationID() != null) { - parentTask = new Task(); - org.json.JSONObject tp = new org.json.JSONObject(); - org.json.JSONObject mf = new org.json.JSONObject(); - mf.put("locationId", this.getLocationID()); - tp.put("matchingSetFilter", mf); - parentTask.setParameters(tp); - } - Taxonomy taxy = this.getTaxonomy(myShepherd); - if (taxy != null) { - task = IA.intakeMediaAssetsOneSpecies(myShepherd, allMAs, taxy, parentTask); - } else { - task = IA.intakeMediaAssets(myShepherd, allMAs); - } - myShepherd.storeNewTask(task); - System.out.println("sendToIA() created " + task + " for " + this); - } - // persist will catch change on asset detectionStatus regardless - myShepherd.commitDBTransaction(); - } catch (Exception ex) { - ex.printStackTrace(); - myShepherd.rollbackDBTransaction(); - } finally { - myShepherd.closeDBTransaction(); - } - return task; - } - - public Set getNotificationEmailAddresses() { - Set addrs = new HashSet(); - - addrs.addAll(Util.getUserEmailAddresses(this.getSubmitters())); - addrs.addAll(Util.getUserEmailAddresses(this.getPhotographers())); - addrs.addAll(Util.getUserEmailAddresses(this.getInformOthers())); - return addrs; - } - - // FIXME passing the langCode is dumb imho, but this is "standard practice" - // better would be that each recipient user's language preference would be used for their email - public void sendCreationEmails(Shepherd myShepherd, String langCode) { - String context = myShepherd.getContext(); - - if (!CommonConfiguration.sendEmailNotifications(context)) return; - myShepherd.beginDBTransaction(); - try { - URI uri = CommonConfiguration.getServerURI(myShepherd); - if (uri == null) throw new IOException("could not find server uri"); - ThreadPoolExecutor es = MailThreadExecutorService.getExecutorService(); - Properties submitProps = ShepherdProperties.getProperties("submit.properties", langCode, - context); - Map tagMap = NotificationMailer.createBasicTagMap(this); - tagMap.put(NotificationMailer.WILDBOOK_COMMUNITY_URL, - CommonConfiguration.getWildbookCommunityURL(context)); - List mailTo = NotificationMailer.splitEmails( - CommonConfiguration.getNewSubmissionEmail(context)); - String mailSubj = submitProps.getProperty("newEncounter") + this.getCatalogNumber(); - for (String emailTo : mailTo) { - NotificationMailer mailer = new NotificationMailer(context, emailTo, langCode, - "newSubmission-summary", tagMap); - mailer.setUrlScheme(uri.getScheme()); - es.execute(mailer); - } - // this will be empty if no locationID - Set locEmails = myShepherd.getAllUserEmailAddressesForLocationIDAsSet( - this.getLocationID(), context); - for (String emailTo : locEmails) { - NotificationMailer mailer = new NotificationMailer(context, langCode, emailTo, - "newSubmission-summary", tagMap); - mailer.setUrlScheme(uri.getScheme()); - es.execute(mailer); - } - // Add encounter dont-track tag for remaining notifications (still needs email-hash assigned). - tagMap.put(NotificationMailer.EMAIL_NOTRACK, "number=" + this.getCatalogNumber()); - // this is a mashup of: submitters, photographers, informOthers.... - for (String emailTo : this.getNotificationEmailAddresses()) { - tagMap.put(NotificationMailer.EMAIL_HASH_TAG, getHashOfEmailString(emailTo)); - NotificationMailer mailer = new NotificationMailer(context, langCode, emailTo, - "newSubmission", tagMap); - mailer.setUrlScheme(uri.getScheme()); - es.execute(mailer); - } - es.shutdown(); - } catch (Exception ex) { - System.out.println("sendCreationEmails() on " + this + " failed: " + ex); - ex.printStackTrace(); - } finally { - myShepherd.rollbackDBTransaction(); - } - } - -/* - in anticipation of 10.10.0, this is a sketchy of what logging might look like - for a change in an Encounter via PATCH. - - FIXME this should be fully replaced (or wrapped around) the more basic log functionality - that is yet to be written. this can serve as an idea of some things which might be - desirable to support in general logging. take with a grain of salt. - */ - public void _log(org.json.JSONArray arr) { - if ((arr == null) || (arr.length() == 0)) return; - String actionId = Util.generateUUID(); - for (int i = 0; i < arr.length(); i++) { - if (arr.optJSONObject(i) == null) continue; - org.json.JSONObject p = arr.getJSONObject(i).optJSONObject("_patch"); - if (p == null) continue; - String op = p.optString("op", "UNKNOWN_OP"); - String path = p.optString("path", "UNKNOWN_PATH"); - Object value = null; - if (p.has("value") && !p.isNull("value")) value = p.get("value"); - String logMessage = "modified by PATCH op=" + op + ", path " + path + " with value: " + - ((value == null) ? "NULL" : value.toString()); - _log2(null, null, null, "Encounter", this.getId(), actionId, logMessage); - // legacy "audit log" (aka some random comment) - // TODO really need to add the user/who part here - this.addComments("

    " + Util.prettyTimeStamp() + - " modified " + path + " with operation " + op + "" + ((value == - null) ? "" : " and value " + value.toString() + "") + "

    "); - } - } - - // one of many dilemmas: we need a request object to get user + ip address, but dont have - // it at this point. so we likely need to pass it all around somehow. maybe on a shepherd or - // some other more common object? FIXME TODO - public void _log2( - // "standard" levels (null should be some reasonable default???) - String logLevel, - // reference to who did it, could be multiple users etc. probably should be id _and_ username? - String user, - // pretty obvious? - String ip, - // class of object acted upon - String objectClass, - // primary key - String objectId, - // for groupin multiple logs into one "action" (e.g. a PATCH on object) - String actionId, - // message - String message) { - System.out.println(String.join("\t", "[TMPLOG]", - new Long(System.currentTimeMillis()).toString(), user, ip, objectClass, objectId, - actionId, message)); - } -} +package org.ecocean; + +import org.apache.commons.codec.digest.DigestUtils; + +import java.io.*; +import java.lang.Math; +import java.net.URI; +import java.net.URL; +import java.text.SimpleDateFormat; +import java.util.*; +import java.util.concurrent.Executors; +import java.util.concurrent.ExecutorService; +import java.util.concurrent.ThreadPoolExecutor; + +import javax.jdo.Query; + +import org.apache.commons.lang3.builder.ToStringBuilder; + +import com.fasterxml.jackson.core.JsonGenerator; +import com.fasterxml.jackson.core.JsonProcessingException; +import javax.servlet.http.HttpServletRequest; + +import org.ecocean.api.ApiException; +import org.ecocean.api.bulk.BulkImportUtil; +import org.ecocean.api.bulk.BulkValidatorException; +import org.ecocean.api.patch.EncounterPatchValidator; +import org.ecocean.genetics.*; +import org.ecocean.ia.IA; +import org.ecocean.ia.Task; +import org.ecocean.identity.IBEISIA; +import org.ecocean.media.*; +import org.ecocean.security.Collaboration; +import org.ecocean.servlet.importer.ImportTask; +import org.ecocean.shepherd.core.Shepherd; +import org.ecocean.shepherd.core.ShepherdProperties; +import org.ecocean.social.Membership; +import org.ecocean.social.SocialUnit; +import org.ecocean.tag.AcousticTag; +import org.ecocean.tag.DigitalArchiveTag; +import org.ecocean.tag.MetalTag; +import org.ecocean.tag.SatelliteTag; +import org.ecocean.Util.MeasurementDesc; +import org.joda.time.DateTime; +import org.joda.time.format.DateTimeFormat; +import org.joda.time.format.DateTimeFormatter; +import org.joda.time.LocalDateTime; + +import org.datanucleus.api.rest.orgjson.JSONArray; +import org.datanucleus.api.rest.orgjson.JSONException; +import org.datanucleus.api.rest.orgjson.JSONObject; + +/** + * An encounter object stores the complete data for a single sighting/capture report. + * Encounters are added to MarkedIndividual objects as multiple encounters are associated with known individuals. + *

    + * + * @author Jason Holmberg + * @version 2.0 + */ +public class Encounter extends Base implements java.io.Serializable { + static final long serialVersionUID = -146404246317385604L; + + public static final String STATE_MATCHING_ONLY = "matching_only"; + + @Override public String opensearchIndexName() { return "encounter"; } + + public static final double ENCOUNTER_AUTO_SOURCE_CONFIDENCE_CUTOFF = 0.7; + public static final String STATE_AUTO_SOURCED = "auto_sourced"; + + private String sex = null; + private String locationID = null; + private Double maximumDepthInMeters; + private Double maximumElevationInMeters; + private String catalogNumber = ""; + private MarkedIndividual individual; + private int day = 0; + private int month = -1; + private int year = 0; + private Double decimalLatitude; + private Double decimalLongitude; + + private Double endDecimalLatitude; + private Double endDecimalLongitude; + + private String verbatimLocality; + private String occurrenceRemarks = ""; + private String modified; + private String occurrenceID; + private String recordedBy; + private String otherCatalogNumbers; + private String behavior; + private String eventID; + private String measurementUnit; + private String verbatimEventDate; + private String dynamicProperties; + public String identificationRemarks = ""; + public String genus = ""; + public String specificEpithet; + public String lifeStage; + public String country; + public String zebraClass = ""; // via lewa: lactating female, territorial male, etc etc + + private String imageSet; + private String soil; + + private String reproductiveStage; + private Double bodyCondition; + private Double parasiteLoad; + private Double immunoglobin; + private Boolean sampleTakenForDiet; + private Boolean injured; + private boolean opensearchProcessPermissions = false; + + private ArrayList observations = new ArrayList(); + + public String getSoil() { return soil; } + public void setSoil(String soil) { this.soil = soil; } + + public String getReproductiveStage() { return reproductiveStage; } + public void setReproductiveStage(String reproductiveStage) { + this.reproductiveStage = reproductiveStage; + } + + public Double getBodyCondition() { return bodyCondition; } + public void setBodyCondition(Double bodyCondition) { this.bodyCondition = bodyCondition; } + + public Double getParasiteLoad() { return parasiteLoad; } + public void setParasiteLoad(Double parasiteLoad) { this.parasiteLoad = parasiteLoad; } + + public Double getImmunoglobin() { return immunoglobin; } + public void setImmunoglobin(Double immunoglobin) { this.immunoglobin = immunoglobin; } + + public Boolean getSampleTakenForDiet() { return sampleTakenForDiet; } + public void setSampleTakenForDiet(Boolean sampleTakenForDiet) { + this.sampleTakenForDiet = sampleTakenForDiet; + } + + public Boolean getInjured() { return injured; } + public void setInjured(Boolean injured) { this.injured = injured; } + + // for searchability + private String imageNames; + + private List submitters; + private List photographers; + private List informOthers; + + private static HashMap > _matchEncounterCache = new HashMap >(); + + // An URL to a thumbnail image representing the encounter. + private String dwcImageURL; + + // Defines whether the sighting represents a living or deceased individual. + // Currently supported values are: "alive" and "dead". + private String livingStatus; + + // observed age (if any) via IBEIS zebra projects + private Double age; + + // Date the encounter was added to the library. + private String dwcDateAdded; + private Long dwcDateAddedLong; + + // If Encounter spanned more than one day, date of release + private Date releaseDate; + + private Long releaseDateLong; + + // Size of the individual in meters + private Double size; + + // Additional comments added by library users + private String researcherComments = "None"; + + // username of the logged in researcher assigned to the encounter + // this String is matched to an org.ecocean.User object to obtain more information + private String submitterID; + + // name, email, phone, address of the encounter reporter + private String submitterEmail, submitterPhone, submitterAddress; + private String hashedSubmitterEmail; + private String hashedPhotographerEmail; + private String hashedInformOthers; + private String informothers; + + // name, email, phone, address of the encounter photographer + private String photographerName, photographerEmail, photographerPhone, photographerAddress; + + // a Vector of Strings defining the relative path to each photo. The path is relative to the servlet base directory + public Vector additionalImageNames = new Vector(); + + // a Vector of Strings of email addresses to notify when this encounter is modified + private Vector interestedResearchers = new Vector(); + + // time metrics of the report + private int hour = 0; + private String minutes = "00"; + + private String state = ""; + + // the globally unique identifier (GUID) for this Encounter + private String guid; + + private Long endDateInMilliseconds; + private Long dateInMilliseconds; + + // describes how the shark was measured + private String size_guess = "none provided"; + + // String reported GPS values for lat and long of the encounter + private String gpsLongitude = "", gpsLatitude = ""; + private String gpsEndLongitude = "", gpsEndLatitude = ""; + + // Indicates whether this record can be exposed via TapirLink + private boolean okExposeViaTapirLink = false; + + public String spotImageFileName = ""; + + // name of the stored file from which the right-side spots were extracted + public String rightSpotImageFileName = ""; + + // string descriptor of the most obvious scar (if any) as reported by the original submitter + // we also use keywords to be more specific + public String distinguishingScar = "None"; + // describes how this encounter was matched to an existing shark - by eye, by pattern recognition algorithm etc. + + // SPOTS + // an array of the extracted left-side superSpots + // private superSpot[] spots; + private ArrayList spots; + + // an array of the extracted right-side superSpots + // private superSpot[] rightSpots; + private ArrayList rightSpots; + + // an array of the three extracted left-side superSpots used for the affine transform of the I3S algorithm + // private superSpot[] leftReferenceSpots; + private ArrayList leftReferenceSpots; + + // an array of the three extracted right-side superSpots used for the affine transform of the I3S algorithm + // private superSpot[] rightReferenceSpots; + private ArrayList rightReferenceSpots; + + // an open ended string that allows a type of patterning to be identified. + // as an example, see the use of color codes at splashcatalog.org, allowing pre-defined fluke patterning types + // to be used to help narrow the search for a marked individual + private String patterningCode; + + // submitting organization and project further detail the scope of who submitted this project + private String submitterOrganization; + private String submitterProject; + private List submitterResearchers; + + // hold submittedData + // private List collectedData; + private List tissueSamples; + private List images; + // private ArrayList media; + private ArrayList annotations; + private List measurements; + private List metalTags; + private AcousticTag acousticTag; + private SatelliteTag satelliteTag; + private DigitalArchiveTag digitalArchiveTag; + + private Boolean mmaCompatible = false; + + // Variables used in the Survey, SurveyTrack, Path, Location model + + private String correspondingSurveyTrackID = null; + private String correspondingSurveyID = null; + + // This is the eventual replacement for the old decimal lat lon and other location data. + private PointLocation pointLocation; + + // This is the number used to cross reference with dates to find occurances. (Read Lab) + private String sightNo = ""; + + // This is what researchers eyeball is the individual's ID in the field + // it could be a name that only has meaning in the context of that day's work + // (not necessarily an individual name from the WB database) + private String fieldID; + + // This is a standard 1-5 color scale used by cetacean researchers + private Integer flukeType; + + // added by request for ASWN, this is the role an individual served in its occurrence + // (from a standard list like Escort Male) + private String groupRole; + + // identifies the import/dataset this came from for data provenance + private String dataSource; + + // start constructors + + /** + * empty constructor required by the JDO Enhancer + */ + public Encounter() {} + + public Encounter(boolean skipSetup) { + if (skipSetup) return; + this.catalogNumber = Util.generateUUID(); + this.setDWCDateAdded(); + this.setDWCDateLastModified(); + this.resetDateInMilliseconds(); + this.annotations = new ArrayList(); + } + + /** + * Use this constructor to add the minimum level of information for a new encounter The Vector additionalImages must be a Vector of + * Blob objects + * + * TODO: evaluate and remove if this is DEPRECATED cuz, SinglePhotoVideos? really? + */ + public Encounter(int day, int month, int year, int hour, String minutes, String size_guess, + String location) { + if (images != null) + System.out.println( + "WARNING: danger! deprecated SinglePhotoVideo-based Encounter constructor used!"); + this.verbatimLocality = location; + + this.images = images; + this.day = day; + this.month = month; + this.year = year; + this.hour = hour; + this.minutes = minutes; + this.size_guess = size_guess; + + this.setDWCDateAdded(); + this.setDWCDateLastModified(); + this.resetDateInMilliseconds(); + } + + public Encounter(Annotation ann) { + this(new ArrayList(Arrays.asList(ann))); + } + + public Encounter(ArrayList anns) { + this.catalogNumber = Util.generateUUID(); + this.annotations = anns; + if (!this.annotationsAreEmpty()) { + this.setDateFromAssets(); + this.setSpeciesFromAnnotations(); + this.setLatLonFromAssets(); + } + this.setDWCDateAdded(); + this.setDWCDateLastModified(); + this.resetDateInMilliseconds(); + } + private boolean annotationsAreEmpty() { + return (this.annotations == null || this.annotations.size() == 0 || + (this.annotations.size() == 1 && (this.annotations.get(0) == null))); + } + + // space saver since we're about to use this hundreds of times + private boolean shouldReplace(String str1, String str2) { + return Util.shouldReplace(str1, str2); + } + + // also returns true when str1 is a superstring of str2. + private boolean shouldReplaceSuperStr(String str1, String str2) { + return (shouldReplace(str1, str2) || (Util.stringExists(str1) && str1.contains(str2))); + } + + public void mergeAndDelete(Encounter enc2, Shepherd myShepherd) { + mergeDataFrom(enc2); + MarkedIndividual ind = myShepherd.getMarkedIndividual(enc2); + if (ind != null) { + ind.removeEncounter(enc2); + ind.addEncounter(this); // duplicate-safe + } + Occurrence occ = myShepherd.getOccurrence(enc2); + if (occ != null) { + occ.removeEncounter(enc2); + occ.addEncounter(this); // duplicate-safe + } + // Remove it from an ImportTask if needed + ImportTask task = myShepherd.getImportTaskForEncounter(enc2.getCatalogNumber()); + if (task != null) { + task.removeEncounter(enc2); + myShepherd.updateDBTransaction(); + } + // Remove from Project if needed + List projects = myShepherd.getProjectsForEncounter(enc2); + if (projects != null && !projects.isEmpty()) { + for (Project project : projects) { + project.removeEncounter(enc2); + myShepherd.updateDBTransaction(); + } + } + // remove tissue samples because of bogus foreign key constraint that prevents deletion + int numTissueSamples = 0; + if (enc2.getTissueSamples() != null) numTissueSamples = enc2.getTissueSamples().size(); + for (int i = 0; i < numTissueSamples; i++) { + enc2.removeTissueSample(0); + } + this.addComments("

    Merged in encounter " + enc2.getCatalogNumber() + "."); + + myShepherd.throwAwayEncounter(enc2); + } + + // copies otherEnc's data into thisEnc, not overwriting anything + public void mergeDataFrom(Encounter enc2) { + if (enc2.getIndividual() != null) setIndividual(enc2.getIndividual()); + // simple string fields + if (shouldReplace(enc2.getSex(), getSex())) setSex(enc2.getSex()); + if (shouldReplace(enc2.getLocationID(), getLocationID())) + setLocationID(enc2.getLocationID()); + if (shouldReplace(enc2.getVerbatimLocality(), getVerbatimLocality())) + setVerbatimLocality(enc2.getVerbatimLocality()); + if (shouldReplace(enc2.getOccurrenceID(), getOccurrenceID())) + setOccurrenceID(enc2.getOccurrenceID()); + if (shouldReplace(enc2.getRecordedBy(), getRecordedBy())) + setRecordedBy(enc2.getRecordedBy()); + if (shouldReplace(enc2.getEventID(), getEventID())) setEventID(enc2.getEventID()); + if (shouldReplace(enc2.getGenus(), getGenus())) setGenus(enc2.getGenus()); + if (shouldReplace(enc2.getSpecificEpithet(), getSpecificEpithet())) + setSpecificEpithet(enc2.getSpecificEpithet()); + if (shouldReplace(enc2.getLifeStage(), getLifeStage())) setLifeStage(enc2.getLifeStage()); + if (shouldReplace(enc2.getCountry(), getCountry())) setCountry(enc2.getCountry()); + if (shouldReplace(enc2.getZebraClass(), getZebraClass())) + setZebraClass(enc2.getZebraClass()); + if (shouldReplace(enc2.getSoil(), getSoil())) setSoil(enc2.getSoil()); + if (shouldReplace(enc2.getReproductiveStage(), getReproductiveStage())) + setReproductiveStage(enc2.getReproductiveStage()); + if (shouldReplace(enc2.getLivingStatus(), getLivingStatus())) + setLivingStatus(enc2.getLivingStatus()); + if (shouldReplace(enc2.getSubmitterEmail(), getSubmitterEmail())) + setSubmitterEmail(enc2.getSubmitterEmail()); + if (shouldReplace(enc2.getSubmitterPhone(), getSubmitterPhone())) + setSubmitterPhone(enc2.getSubmitterPhone()); + if (shouldReplace(enc2.getSubmitterAddress(), getSubmitterAddress())) + setSubmitterAddress(enc2.getSubmitterAddress()); + if (shouldReplace(enc2.getState(), getState())) setState(enc2.getState()); + if (shouldReplace(enc2.getGPSLongitude(), getGPSLongitude())) + setGPSLongitude(enc2.getGPSLongitude()); + if (shouldReplace(enc2.getGPSLatitude(), getGPSLatitude())) + setGPSLatitude(enc2.getGPSLatitude()); + if (shouldReplace(enc2.getPatterningCode(), getPatterningCode())) + setPatterningCode(enc2.getPatterningCode()); + if (shouldReplace(enc2.getSubmitterOrganization(), getSubmitterOrganization())) + setSubmitterOrganization(enc2.getSubmitterOrganization()); + if (shouldReplace(enc2.getSubmitterProject(), getSubmitterProject())) + setSubmitterProject(enc2.getSubmitterProject()); + if (shouldReplace(enc2.getFieldID(), getFieldID())) setFieldID(enc2.getFieldID()); + if (shouldReplace(enc2.getGroupRole(), getGroupRole())) setGroupRole(enc2.getGroupRole()); + // now string fields that might need to be combined rather than replaced + if (shouldReplaceSuperStr(enc2.getDynamicProperties(), getDynamicProperties())) { + setDynamicProperties(enc2.getDynamicProperties()); + } else if (Util.stringExists(enc2.getDynamicProperties())) { // shouldn't replace, should combine + addDynamicProperties(enc2.getDynamicProperties()); + } + if (shouldReplaceSuperStr(enc2.getOccurrenceRemarks(), getOccurrenceRemarks())) { + setOccurrenceRemarks(enc2.getOccurrenceRemarks()); + } else if (Util.stringExists(enc2.getOccurrenceRemarks())) { // shouldn't replace, should combine + setOccurrenceRemarks(getOccurrenceRemarks() + " " + enc2.getOccurrenceRemarks()); + } + // now combine list fields making sure not to add duplicate entries + setAnnotations(Util.combineArrayListsInPlace(getAnnotations(), enc2.getAnnotations())); + setObservationArrayList(Util.combineArrayListsInPlace(getObservationArrayList(), + enc2.getObservationArrayList())); + setSubmitterResearchers(Util.combineListsInPlace(getSubmitterResearchers(), + enc2.getSubmitterResearchers())); + // custom no-duplicate logic bc the same sampleID may have been added on both encounters, but this would create unique tissuesample objects + Set sampleIDs = getTissueSampleIDs(); + for (TissueSample samp : enc2.getTissueSamples()) { + if (!sampleIDs.contains(samp.getSampleID())) addTissueSample(samp); + } + setMeasurements(Util.combineListsInPlace(getMeasurements(), enc2.getMeasurements())); + setMetalTags(Util.combineListsInPlace(getMetalTags(), enc2.getMetalTags())); + + // spot lists + setSpots(Util.combineArrayListsInPlace(getSpots(), enc2.getSpots())); + setRightSpots(Util.combineArrayListsInPlace(getRightSpots(), enc2.getRightSpots())); + setLeftReferenceSpots(Util.combineArrayListsInPlace(getLeftReferenceSpots(), + enc2.getLeftReferenceSpots())); + setRightReferenceSpots(Util.combineArrayListsInPlace(getRightReferenceSpots(), + enc2.getRightReferenceSpots())); + // tags + if (enc2.getAcousticTag() != null && getAcousticTag() == null) + setAcousticTag(enc2.getAcousticTag()); + if (enc2.getSatelliteTag() != null && getSatelliteTag() == null) + setSatelliteTag(enc2.getSatelliteTag()); + if (enc2.getDTag() != null && getDTag() == null) setDTag(enc2.getDTag()); + // skip time stuff bc if the time is different we probably don't want to combine the encounters anyway. + } + + public String getZebraClass() { + return zebraClass; + } + + public void setZebraClass(String c) { + zebraClass = c; + } + + public String getImageNames() { + return imageNames; + } + + public void addImageName(String name) { + if (imageNames == null) imageNames = name; + else if (name != null) imageNames += (", " + name); + } + + public String addAllImageNamesFromAnnots(boolean overwrite) { + if (overwrite) imageNames = null; + return addAllImageNamesFromAnnots(); + } + + public String addAllImageNamesFromAnnots() { + for (Annotation ann : getAnnotations()) { + for (Feature feat : ann.getFeatures()) { + try { + MediaAsset ma = feat.getMediaAsset(); + addImageName(ma.getFilename()); + } catch (Exception e) { + System.out.println("exception parsing image name from feature " + feat); + } + } + } + return imageNames; + } + + /** + * Returns an array of all of the superSpots for this encounter. + * + * @return the array of superSpots, taken from the croppedImage, that make up the digital fingerprint for this encounter + */ + public ArrayList getSpots() { + return spots; + } + + public ArrayList getRightSpots() { + return rightSpots; + } + + /** + * Returns an array of all of the superSpots for this encounter. + * + * @return the array of superSpots, taken from the croppedImage, that make up the digital fingerprint for this encounter + */ +/* TODO: evaluate if this is deprecate and can be removed + these have gone away! dont be setting spots on Encounter any more .... NOT SO FAST... we regress for whaleshark.org... */ + public void setSpots(ArrayList newSpots) { + spots = newSpots; + } + + public void setRightSpots(ArrayList newSpots) { + rightSpots = newSpots; + } + + /** + * Removes any spot data + */ + public void removeSpots() { + spots = null; + } + + public void removeRightSpots() { + rightSpots = null; + } + + public Integer getFlukeType() { return this.flukeType; } + public void setFlukeType(Integer flukeType) { this.flukeType = flukeType; } + // this averages all the fluketypes + public void setFlukeTypeFromKeywords() { + int totalFlukeType = 0; + int numFlukes = 0; + + for (Annotation ann : getAnnotations()) { + Integer thisFlukeType = getFlukeTypeFromAnnotation(ann); + if (thisFlukeType != null) { + totalFlukeType += thisFlukeType; + numFlukes++; + } + } + if (numFlukes == 0) return; + setFlukeType(totalFlukeType / numFlukes); + } + + // assuming the list is of erroneously-duplicated encounters, returns the one we want to keep + public static Encounter chooseFromDupes(List encs) { + int maxAnns = -1; + int encWithMax = 0; + + for (int i = 0; i < encs.size(); i++) { + Encounter enc = encs.get(i); + if (enc.numAnnotations() > maxAnns) { + maxAnns = enc.numAnnotations(); + encWithMax = i; + } + } + return encs.get(encWithMax); + } + + public static Integer getFlukeTypeFromAnnotation(Annotation ann) { + return getFlukeTypeFromAnnotation(ann, 5); + } + + // int maxScore is used because some people store flukeType on a 5 point (most standard), some on a 9 point scale + public static Integer getFlukeTypeFromAnnotation(Annotation ann, int maxScore) { + MediaAsset ma = ann.getMediaAsset(); + + if (ma == null || !ma.hasKeywords()) return null; + String flukeTypeKwPrefix = "fluke" + maxScore + ":"; + for (Keyword kw : ma.getKeywords()) { + String kwName = kw.getReadableName(); + if (kwName.contains(flukeTypeKwPrefix)) { + String justScore = kwName.split(flukeTypeKwPrefix)[1]; + try { + Integer score = Integer.parseInt(justScore); + if (score != null) return score; + } catch (NumberFormatException nfe) { + System.out.println("NFE on getFlukeTypeFromAnnotation! For ann " + ann + + " and kwPrefix " + flukeTypeKwPrefix); + } + } + } + return null; + } + + // yes, there "should" be only one of each of these, but we be thorough! + public void removeLeftSpotMediaAssets(Shepherd myShepherd) { + ArrayList spotMAs = this.findAllMediaByLabel(myShepherd, "_spot"); + + for (MediaAsset ma : spotMAs) { + System.out.println("INFO: removeLeftSpotMediaAsset() detaching " + ma + + " from parent id=" + ma.getParentId()); + ma.setParentId(null); + } + } + + public void removeRightSpotMediaAssets(Shepherd myShepherd) { + ArrayList spotMAs = this.findAllMediaByLabel(myShepherd, "_spotRight"); + + for (MediaAsset ma : spotMAs) { + System.out.println("INFO: removeRightSpotMediaAsset() detaching " + ma + + " from parent id=" + ma.getParentId()); + ma.setParentId(null); + } + } + + public void nukeAllSpots() { + leftReferenceSpots = null; + rightReferenceSpots = null; + spots = null; + rightSpots = null; + } + + /** + * Returns the number of spots in the cropped image stored for this encounter. + * + * @return the number of superSpots that make up the digital fingerprint for this encounter + */ + public int getNumSpots() { + return (spots == null) ? 0 : spots.size(); + } + + public int getNumRightSpots() { + return (rightSpots == null) ? 0 : rightSpots.size(); + } + + public boolean hasLeftSpotImage() { + return (this.getNumSpots() > 0); + } + + public boolean hasRightSpotImage() { + return (this.getNumRightSpots() > 0); + } + + // Sets the recorded length of the shark for this encounter. + public void setSize(Double mysize) { + if (mysize != null) { size = mysize; } else { size = null; } + } + + // @return the length of the shark + public double getSize() { + return size.doubleValue(); + } + + public Double getSizeAsDouble() { + return size; + } + + // Sets the units of the recorded size and depth of the shark for this encounter. Acceptable entries are either "Feet" or "Meters" + public void setMeasureUnits(String measure) { + measurementUnit = measure; + } + + // @return the units of measure used by the recorded of this encounter, either "feet" or "meters" + public String getMeasureUnits() { + return measurementUnit; + } + + public String getMeasurementUnit() { + return measurementUnit; + } + + // @return the location of this encounter + public String getLocation() { + return verbatimLocality; + } + + public void setLocation(String location) { + this.verbatimLocality = location; + } + + // Sets the recorded sex of the shark in this encounter. Acceptable values are "Male" or "Female" + public void setSex(String thesex) { + if (thesex != null) { sex = thesex; } else { sex = null; } + } + + // @return the sex of the shark, either "male" or "female" + public String getSex() { + return sex; + } + + // @return any comments regarding observed scarring on the shark's body + public boolean getMmaCompatible() { + if (mmaCompatible == null) return false; + return mmaCompatible; + } + + public void setMmaCompatible(boolean b) { + mmaCompatible = b; + } + + // @return Occurrence Remarks String + @Override public String getComments() { + return occurrenceRemarks; + } + + // FIXME why is setComments() affecting occurrenceRemarks, and yet + // addComments() affecting researchComments !!!!!???? + // @param newComments Occurrence remarks to set + @Override public void setComments(String newComments) { + occurrenceRemarks = newComments; + } + + // @return any comments added by authroized researchers + public String getRComments() { + return researcherComments; + } + + // @param newComments any additional comments to be added to the encounter + @Override public void addComments(String newComments) { + if ((researcherComments != null) && (!(researcherComments.equals("None")))) { + researcherComments += newComments; + } else { + researcherComments = newComments; + } + } + + // @return the name of the person who submitted this encounter to the database + public String getSubmitterName() { + return recordedBy; + } + + public void setSubmitterName(String newname) { + if (newname == null) { + recordedBy = null; + } else { + recordedBy = newname; + } + } + + // @return the e-mail address of the person who submitted this encounter data + public String getSubmitterEmail() { + return submitterEmail; + } + + public void setSubmitterEmail(String newemail) { + if (newemail == null) { + submitterEmail = null; + this.hashedSubmitterEmail = null; + } else { + submitterEmail = newemail; + this.hashedSubmitterEmail = Encounter.getHashOfEmailString(newemail); + } + } + + // @return the phone number of the person who submitted this encounter data + public String getSubmitterPhone() { + return submitterPhone; + } + + // Sets the phone number of the person who submitted this encounter data. + public void setSubmitterPhone(String newphone) { + if (newphone == null) { + submitterPhone = null; + } else { + submitterPhone = newphone; + } + } + + // @return the mailing address of the person who submitted this encounter data + public String getSubmitterAddress() { + return submitterAddress; + } + + // Sets the mailing address of the person who submitted this encounter data. + public void setSubmitterAddress(String address) { + if (address == null) { + submitterAddress = null; + } else { + submitterAddress = address; + } + } + + // @return the name of the photographer who took the primary image for this encounter + public String getPhotographerName() { + return photographerName; + } + + // @return the name of the photographer who took the primary image for this encounter + public void setPhotographerName(String name) { + if (name == null) { + photographerName = null; + } else { + photographerName = name; + } + } + + // @return the e-mail address of the photographer who took the primary image for this encounter + public String getPhotographerEmail() { + return photographerEmail; + } + + // Sets the e-mail address of the person who took the primaryImage this encounter. + public void setPhotographerEmail(String email) { + if (email == null) { + photographerEmail = null; + this.hashedPhotographerEmail = null; + } else { + photographerEmail = email; + this.hashedPhotographerEmail = Encounter.getHashOfEmailString(email); + } + } + + // @return the phone number of the photographer who took the primary image for this encounter + public String getPhotographerPhone() { + return photographerPhone; + } + + // this is a cruddy "solution" to .submitterName and .submitters existing simultaneously + public Set getAllSubmitterIds(Shepherd myShepherd) { + Set all = new HashSet(); + User owner = this.getSubmitterUser(myShepherd); + + if (owner == null) { + all.add(this.submitterID); + all.add(this.submitterEmail); + } else { + all.add(owner.getUsername()); + all.add(owner.getFullName()); + all.add(owner.getId()); + all.add(owner.getEmailAddress()); + } + if (this.submitters != null) + for (User user : this.submitters) { + all.add(user.getUsername()); + all.add(user.getFullName()); + all.add(user.getId()); + all.add(user.getEmailAddress()); + } + all.remove(null); + all.remove(""); + return all; + } + + // similar to above + public Set getAllPhotographerIds() { + Set all = new HashSet(); + + all.add(this.photographerName); + if (this.photographers != null) + for (User user : this.photographers) { + all.add(user.getUsername()); + all.add(user.getFullName()); + all.add(user.getId()); + all.add(user.getEmailAddress()); + } + all.remove(null); + all.remove(""); + return all; + } + + public Set getAllInformOtherIds() { + Set all = new HashSet(); + + if (this.informOthers != null) + for (User user : this.informOthers) { + all.add(user.getUsername()); + all.add(user.getFullName()); + all.add(user.getId()); + all.add(user.getEmailAddress()); + } + all.remove(null); + all.remove(""); + return all; + } + + public String getWebUrl(HttpServletRequest req) { + return getWebUrl(this.getCatalogNumber(), req); + } + + public static String getWebUrl(String encId, HttpServletRequest req) { + return getWebUrl(encId, CommonConfiguration.getServerURL(req)); + } + + public static String getWebUrl(String encId, String serverUrl) { + return (serverUrl + "/encounters/encounter.jsp?number=" + encId); + } + + // Sets the phone number of the person who took the primaryImage this encounter. + public void setPhotographerPhone(String phone) { + if (phone == null) { + photographerPhone = null; + } else { + photographerPhone = phone; + } + } + + // @return the mailing address of the photographer who took the primary image for this encounter + public String getPhotographerAddress() { + return photographerAddress; + } + + // Sets the mailing address of the person who took the primaryImage this encounter. + public void setPhotographerAddress(String address) { + if (address == null) { + photographerAddress = null; + } else { + photographerAddress = address; + } + } + + // Sets the recorded depth of this encounter. + public void setDepth(Double myDepth) { + if (myDepth != null) { maximumDepthInMeters = myDepth; } else { + maximumDepthInMeters = null; + } + } + + // @return the recorded depth for this encounter + public double getDepth() { + return maximumDepthInMeters.doubleValue(); + } + + public Double getDepthAsDouble() { + return maximumDepthInMeters; + } + + // @return a vector of image name Strings + public Vector getAdditionalImageNames() { + Vector imageNamesOnly = new Vector(); + + if ((images != null) && (images.size() > 0)) { + int imagesSize = images.size(); + for (int i = 0; i < imagesSize; i++) { + SinglePhotoVideo dce = (SinglePhotoVideo)images.get(i); + imageNamesOnly.add(dce.getFilename()); + } + } + return imageNamesOnly; + } + + public String getFieldID() { + return this.fieldID; + } + + public void setFieldID(String fieldID) { + this.fieldID = fieldID; + } + + public String getGroupRole() { + return this.groupRole; + } + + public void setGroupRole(String role) { + this.groupRole = role; + } + + public String getDataSource() { + return dataSource; + } + + public void setDataSource(String dataSource) { + this.dataSource = dataSource; + } + + public String getImageOriginalName() { + MediaAsset ma = getPrimaryMediaAsset(); + + if (ma == null) return null; + return ma.getFilename(); + } + + // @return a unique integer String used to identify this encounter in the database + public String getEncounterNumber() { + return catalogNumber; + } + + public String generateEncounterNumber() { + return Util.generateUUID(); + } + + public String dir(String baseDir) { + return baseDir + File.separator + "encounters" + File.separator + this.subdir(); + } + + // like above, but class method so you pass the encID + public static String dir(String baseDir, String id) { + return baseDir + File.separator + "encounters" + File.separator + subdir(id); + } + + // like above, but can pass a File in for base + public static String dir(File baseDir, String id) { + return baseDir.getAbsolutePath() + File.separator + "encounters" + File.separator + + subdir(id); + } + + // subdir() is kind of a utility function, which can be called as enc.subdir() or Encounter.subdir(IDSTRING) as needed + public String subdir() { + return subdir(this.getEncounterNumber()); + } + + public static String subdir(String id) { + String d = id; // old-world + + if (Util.isUUID(id)) { // new-world + d = id.charAt(0) + File.separator + id.charAt(1) + File.separator + id; + } + return d; + } + + // @return a Date object + public String getDate() { + String date = ""; + String time = ""; + + if (year <= 0) { + return "Unknown"; + } else if (month == -1) { + return Integer.toString(year); + } + if (hour != -1) { + String localMinutes = minutes; + if (!Util.stringExists(localMinutes)) { + localMinutes = "00"; + } else if (localMinutes.length() == 1) { + localMinutes = "0" + localMinutes; + } + time = String.format("%02d:%s", hour, localMinutes); + } + if (day > 0) { + date = String.format("%04d-%02d-%02d %s", year, month, day, time); + } else if (month > 0) { + date = String.format("%04d-%02d %s", year, month, time); + } else { + date = String.format("%04d %s", year, time); + } + return date.trim(); + } + + public String getShortDate() { + String date = ""; + + if (year <= 0) { + return "Unknown"; + } else if (month == -1) { + return Integer.toString(year); + } + if (day > 0) { + date = String.format("%02d/%02d/%04d", day, month, year); + } else { + date = String.format("%02d/%04d", month, year); + } + return date; + } + + public org.json.JSONObject getDateValuesJson() { + org.json.JSONObject dv = new org.json.JSONObject(); + // in theory we *always* should have at least a year, but our data probably says otherwise + // sadly we just bail empty if we dont have a year + if (getYear() < 1900) return dv; + dv.put("year", getYear()); + // from here on out we only add things if the previous one existed; hence the short-circuit return + // e.g. we do not add a day if there was no month + if ((getMonth() < 1) || (getMonth() > 12)) return dv; + dv.put("month", getMonth()); + // sorry not checking actual days-per-month here + if ((getDay() < 1) || (getDay() > 31)) return dv; + dv.put("day", getDay()); + if ((getHour() < 0) || (getHour() > 23)) return dv; + dv.put("hour", getHour()); + // sigh, deal with string-based minutes... + Integer min = getMinutesInteger(); + if ((min != null) && (min >= 0) && (min < 60)) { + dv.put("minutes", min); + } else { + // choosing to do this because we *must* have hour value here, so dumb to leave null? + dv.put("minutes", 0); + } + return dv; + } + + // @return a String with text about how the size of this animal was estimated/measured + public String getSizeGuess() { + return size_guess; + } + + public void setDay(int day) { + this.day = day; + resetDateInMilliseconds(); + } + + public void setHour(int hour) { + this.hour = hour; + resetDateInMilliseconds(); + } + + public void setMinutes(String minutes) { + this.minutes = minutes; + resetDateInMilliseconds(); + } + + public String getMinutes() { + return minutes; + } + + public Integer getMinutesInteger() { + Integer min = null; + + try { min = Integer.parseInt(minutes); } catch (Exception e) {} + return min; + } + + public int getHour() { + return hour; + } + + public void setMonth(int month) { + this.month = month; + resetDateInMilliseconds(); + } + + public void setYear(int year) { + this.year = year; + resetDateInMilliseconds(); + } + + // this does not reset year/month/etc + public void setDateInMillisOnly(long ms) { + this.dateInMilliseconds = ms; + } + + public int getDay() { + return day; + } + + public int getMonth() { + return month; + } + + public int getYear() { + return year; + } + + public boolean wasInPeriod(DateTime start, DateTime end) { + Long thisTime = getDateInMilliseconds(); + + if (thisTime == null) return false; + long endOfDay = end.withTime(23, 59, 59, 999).getMillis(); + return (start.getMillis() <= thisTime && endOfDay >= thisTime); + } + + // @return the String holding specific location data used for searching + public String getLocationCode() { + return locationID; + } + + // TODO: Verify and remove if this is deprecated: A legacy method replaced by setLocationID(...). + public void setLocationCode(String newLoc) { + setLocationID(newLoc); + } + + // @return the String holding specific location data used for searching + public String getDistinguishingScar() { + return distinguishingScar; + } + + // Sets the String holding scarring information for the encounter + public void setDistinguishingScar(String scar) { + distinguishingScar = scar; + } + + // Sets the String documenting how the size of this animal was approximated. + public void setSizeGuess(String newGuess) { + size_guess = newGuess; + } + + public String getMatchedBy() { + if ((identificationRemarks == null) || (identificationRemarks.equals(""))) { + return "Unknown"; + } + return identificationRemarks; + } + + public void setMatchedBy(String matchType) { + identificationRemarks = matchType; + } + + public void setIdentificationRemarks(String matchType) { + identificationRemarks = matchType; + } + + /** + * Sets the unique encounter identifier to be usd with this encounter. Once this is set, it cannot be changed without possible impact to the + * database structure. + * + * @param num the unique integer to be used to uniquely identify this encoun ter in the database + */ + public void setEncounterNumber(String num) { + catalogNumber = num; + } + + public boolean hasMarkedIndividual() { + return (individual != null); + } + + public boolean hasMarkedIndividual(MarkedIndividual match) { + if (match == null) return false; + if (individual == null) return false; + return (match.getId().equals(individual.getId())); + } + + public void assignToMarkedIndividual(MarkedIndividual indiv) { + setIndividual(indiv); + } + + public void setIndividual(MarkedIndividual indiv) { + if (indiv == null) { this.individual = null; } else { this.individual = indiv; } + this.refreshAnnotationLiteIndividual(); + } + + public MarkedIndividual getIndividual() { + return individual; + } + + public String getDisplayName() { + return (individual == null) ? null : individual.getDisplayName(); + } + + public String getIndividualID() { + if (individual == null) return null; + return individual.getId(); + } + + public String getGPSLongitude() { + if (gpsLongitude == null) { + return ""; + } else { + return gpsLongitude; + } + } + + public void setGPSLongitude(String newLong) { + gpsLongitude = newLong; + } + + public String getGPSLatitude() { + if (gpsLatitude == null) { + return ""; + } else { + return gpsLatitude; + } + } + + public void setGPSLatitude(String newLat) { + gpsLatitude = newLat; + } + + public Encounter getClone() { + Encounter tempEnc = new Encounter(); + + try { + tempEnc = (Encounter)this.clone(); + } catch (java.lang.CloneNotSupportedException e) { + e.printStackTrace(); + } + return tempEnc; + } + + public String getSpotImageFileName() { + return spotImageFileName; + } + + public void setSpotImageFileName(String name) { + spotImageFileName = name; + } + + // ------------- + // for the right side spot image + + public String getRightSpotImageFileName() { + return rightSpotImageFileName; + } + + public void setRightSpotImageFileName(String name) { + rightSpotImageFileName = name; + } + + // ---------------- + + // TODO: evaluate and remove if this has been deprecated: really only intended to convert legacy SinglePhotoVideo to MediaAsset/Annotation world + public ArrayList generateAnnotations(String baseDir, Shepherd myShepherd) { + if ((annotations != null) && (annotations.size() > 0)) return annotations; + if ((images == null) || (images.size() < 1)) return null; // probably pointless, so... + if (annotations == null) annotations = new ArrayList(); + boolean thumbDone = false; + ArrayList haveMedia = new ArrayList(); // so we dont add duplicates! + for (SinglePhotoVideo spv : images) { + MediaAsset ma = spv.toMediaAsset(myShepherd); + if (ma == null) { + System.out.println( + "WARNING: Encounter.generateAnnotations() could not create MediaAsset from SinglePhotoVideo " + + spv.getDataCollectionEventID() + "; skipping"); + continue; + } + if (haveMedia.contains(ma)) { + System.out.println( + "WARNING: Encounter.generateAnnotations() found a duplicate MediaAsset in the SinglePhotoVideo images; skipping -- " + + ma); + continue; + } + // note: we need at least minimal metadata (w,h) in order to make annotation, so if this fails, we are no-go + try { + ma.updateMetadata(); + } catch (IOException ioe) { + System.out.println( + "WARNING: Encounter.generateAnnotations() failed to updateMetadata() on original MediaAsset " + + ma + " (skipping): " + ioe.toString()); + continue; + } + ma.addLabel("_original"); + haveMedia.add(ma); + + annotations.add(new Annotation(getTaxonomyString(), ma)); + File idir = new File(spv.getFullFileSystemPath()).getParentFile(); + + addMediaIfNeeded(myShepherd, new File(idir, spv.getDataCollectionEventID() + ".jpg"), + "spv/" + spv.getDataCollectionEventID() + "/" + spv.getDataCollectionEventID() + + ".jpg", ma, "_watermark"); + addMediaIfNeeded(myShepherd, + new File(idir, spv.getDataCollectionEventID() + "-mid.jpg"), + "spv/" + spv.getDataCollectionEventID() + "/" + spv.getDataCollectionEventID() + + "-mid.jpg", ma, "_mid"); + // note: we "assume" thumb was created from 0th spv, cuz we simply dont know but want it living somewhere + if (!thumbDone) + addMediaIfNeeded(myShepherd, new File(idir, "/thumb.jpg"), + "spv/" + spv.getDataCollectionEventID() + "/thumb.jpg", ma, "_thumb"); + thumbDone = true; + } + // we need to have the spot image as a child under *some* MediaAsset from above, but unfortunately we do not know its lineage. so we just + // pick one. :/ + MediaAsset sma = spotImageAsMediaAsset(((annotations.size() < + 1) ? null : annotations.get(0).getMediaAsset()), baseDir, myShepherd); + return annotations; + } + + // utility method for created MediaAssets + // note: also will check for existence of mpath and fail silently if doesnt exist + private MediaAsset addMediaIfNeeded(Shepherd myShepherd, File mpath, String key, + MediaAsset parentMA, String label) { + if ((mpath == null) || !mpath.exists()) return null; + AssetStore astore = AssetStore.getDefault(myShepherd); + org.json.JSONObject sp = astore.createParameters(mpath); + if (key != null) sp.put("key", key); // will use default from createParameters() (if there was one even) + MediaAsset ma = astore.find(sp, myShepherd); + if (ma != null) { + ma.addLabel(label); + if (parentMA != null) ma.setParentId(parentMA.getIdInt()); + return ma; + } + System.out.println("creating new MediaAsset for key=" + key); + try { + ma = astore.copyIn(mpath, sp); + } catch (IOException ioe) { + System.out.println("Could not create MediaAsset for key=" + key + ": " + + ioe.toString()); + return null; + } + if (parentMA != null) { + ma.setParentId(parentMA.getIdInt()); + ma.updateMinimalMetadata(); // for children (ostensibly derived?) MediaAssets, really only need minimal metadata or so i claim + } else { + try { + ma.updateMetadata(); // root images get the whole deal (guess this sh/could key off label=_original ?) + } catch (IOException ioe) { + // we dont care (well sorta) ... since IOException usually means we couldnt open file or some nonsense that we cant recover from + } + } + ma.addLabel(label); + MediaAssetFactory.save(ma, myShepherd); + return ma; + } + + // this makes assumption (for flukes) that both right and left image files are identical + public MediaAsset spotImageAsMediaAsset(MediaAsset parent, String baseDir, + Shepherd myShepherd) { + if ((spotImageFileName == null) || spotImageFileName.equals("")) return null; + File fullPath = new File(this.dir(baseDir) + "/" + spotImageFileName); +// System.out.println("**** * ***** looking for spot file " + fullPath.toString()); + if (!fullPath.exists()) return null; // note: this only technically matters if we are *creating* the MediaAsset + if (parent == null) { + System.out.println("seems like we do not have a parent MediaAsset on enc " + + this.getCatalogNumber() + ", so cannot add spot MediaAsset for " + + fullPath.toString()); + return null; + } + AssetStore astore = AssetStore.getDefault(myShepherd); + if (astore == null) { + System.out.println("No AssetStore in Encounter.spotImageAsMediaAsset()"); + return null; + } + System.out.println("trying spotImageAsMediaAsset with file=" + fullPath.toString()); + org.json.JSONObject sp = astore.createParameters(fullPath); + sp.put("key", this.subdir() + "/spotImage-" + spotImageFileName); + // others? + MediaAsset ma = astore.find(sp, myShepherd); + if (ma == null) { + System.out.println("did not find MediaAsset for params=" + sp + "; creating one?"); + try { + ma = astore.copyIn(fullPath, sp); + ma.addDerivationMethod("historicSpotImageConversion", true); + ma.updateMinimalMetadata(); +// System.out.println("params? " + ma.getParameters()); + ma.addLabel("_spot"); + ma.addLabel("_annotation"); + MediaAssetFactory.save(ma, myShepherd); +// System.out.println("params? " + ma.getParameters()); + } catch (java.io.IOException ex) { + System.out.println("spotImageAsMediaAsset threw IOException " + ex.toString()); + } + } + ma.setParentId(parent.getIdInt()); + return ma; + } + + public void setSubmitterID(String username) { + if (username != null) { submitterID = username; } else { submitterID = null; } + } + + // old method. use getAssignedUser() instead + public String getSubmitterID() { + return getAssignedUsername(); + } + + public String getAssignedUsername() { + return submitterID; + } + + public User getSubmitterUser(Shepherd myShepherd) { + return myShepherd.getUser(submitterID); + } + + public Vector getInterestedResearchers() { + return interestedResearchers; + } + + public void addInterestedResearcher(String email) { + interestedResearchers.add(email); + } + + public double getRightmostSpot() { + double rightest = 0; + ArrayList spots = getSpots(); + + for (int iter = 0; iter < spots.size(); iter++) { + if (spots.get(iter).getTheSpot().getCentroidX() > rightest) { + rightest = spots.get(iter).getTheSpot().getCentroidX(); + } + } + return rightest; + } + + public double getLeftmostSpot() { + double leftest = getRightmostSpot(); + ArrayList spots = getSpots(); + + for (int iter = 0; iter < spots.size(); iter++) { + if (spots.get(iter).getTheSpot().getCentroidX() < leftest) { + leftest = spots.get(iter).getTheSpot().getCentroidX(); + } + } + return leftest; + } + + public double getHighestSpot() { + double highest = getLowestSpot(); + ArrayList spots = getSpots(); + + for (int iter = 0; iter < spots.size(); iter++) { + if (spots.get(iter).getTheSpot().getCentroidY() < highest) { + highest = spots.get(iter).getTheSpot().getCentroidY(); + } + } + return highest; + } + + public double getLowestSpot() { + double lowest = 0; + ArrayList spots = getSpots(); + + for (int iter = 0; iter < spots.size(); iter++) { + if (spots.get(iter).getTheSpot().getCentroidY() > lowest) { + lowest = spots.get(iter).getTheSpot().getCentroidY(); + } + } + return lowest; + } + + public com.reijns.I3S.Point2D[] getThreeLeftFiducialPoints() { + com.reijns.I3S.Point2D[] Rray = new com.reijns.I3S.Point2D[3]; + if (getLeftReferenceSpots() != null) { + ArrayList refsLeft = getLeftReferenceSpots(); + + Rray[0] = new com.reijns.I3S.Point2D(refsLeft.get(0).getTheSpot().getCentroidX(), + refsLeft.get(0).getTheSpot().getCentroidY()); + Rray[1] = new com.reijns.I3S.Point2D(refsLeft.get(1).getTheSpot().getCentroidX(), + refsLeft.get(1).getTheSpot().getCentroidY()); + Rray[2] = new com.reijns.I3S.Point2D(refsLeft.get(2).getTheSpot().getCentroidX(), + refsLeft.get(2).getTheSpot().getCentroidY()); + System.out.println("\tI found three left reference points!"); + } else { + com.reijns.I3S.Point2D topLeft = new com.reijns.I3S.Point2D(getLeftmostSpot(), + getHighestSpot()); + com.reijns.I3S.Point2D bottomLeft = new com.reijns.I3S.Point2D(getLeftmostSpot(), + getLowestSpot()); + com.reijns.I3S.Point2D bottomRight = new com.reijns.I3S.Point2D(getRightmostSpot(), + getLowestSpot()); + Rray[0] = topLeft; + Rray[1] = bottomLeft; + Rray[2] = bottomRight; + } + return Rray; + } + + public com.reijns.I3S.Point2D[] getThreeRightFiducialPoints() { + com.reijns.I3S.Point2D[] Rray = new com.reijns.I3S.Point2D[3]; + if (getRightReferenceSpots() != null) { + ArrayList refsRight = getRightReferenceSpots(); + Rray[0] = new com.reijns.I3S.Point2D(refsRight.get(0).getTheSpot().getCentroidX(), + refsRight.get(0).getTheSpot().getCentroidY()); + Rray[1] = new com.reijns.I3S.Point2D(refsRight.get(1).getTheSpot().getCentroidX(), + refsRight.get(1).getTheSpot().getCentroidY()); + Rray[2] = new com.reijns.I3S.Point2D(refsRight.get(2).getTheSpot().getCentroidX(), + refsRight.get(2).getTheSpot().getCentroidY()); + } else { + com.reijns.I3S.Point2D topRight = new com.reijns.I3S.Point2D(getRightmostRightSpot(), + getHighestRightSpot()); + com.reijns.I3S.Point2D bottomRight = new com.reijns.I3S.Point2D(getRightmostRightSpot(), + getLowestRightSpot()); + com.reijns.I3S.Point2D bottomLeft = new com.reijns.I3S.Point2D(getLeftmostRightSpot(), + getLowestRightSpot()); + + Rray[0] = topRight; + Rray[1] = bottomRight; + Rray[2] = bottomLeft; + } + return Rray; + } + + public double getRightmostRightSpot() { + double rightest = 0; + ArrayList rightSpots = getRightSpots(); + + for (int iter = 0; iter < rightSpots.size(); iter++) { + if (rightSpots.get(iter).getTheSpot().getCentroidX() > rightest) { + rightest = rightSpots.get(iter).getTheSpot().getCentroidX(); + } + } + return rightest; + } + + public double getLeftmostRightSpot() { + double leftest = getRightmostRightSpot(); + ArrayList rightSpots = getRightSpots(); + + for (int iter = 0; iter < rightSpots.size(); iter++) { + if (rightSpots.get(iter).getTheSpot().getCentroidX() < leftest) { + leftest = rightSpots.get(iter).getTheSpot().getCentroidX(); + } + } + return leftest; + } + + public double getHighestRightSpot() { + double highest = getLowestRightSpot(); + ArrayList rightSpots = getRightSpots(); + + for (int iter = 0; iter < rightSpots.size(); iter++) { + if (rightSpots.get(iter).getTheSpot().getCentroidY() < highest) { + highest = rightSpots.get(iter).getTheSpot().getCentroidY(); + } + } + return highest; + } + + public double getLowestRightSpot() { + double lowest = 0; + ArrayList rightSpots = getRightSpots(); + + for (int iter = 0; iter < rightSpots.size(); iter++) { + if (rightSpots.get(iter).getTheSpot().getCentroidY() > lowest) { + lowest = rightSpots.get(iter).getTheSpot().getCentroidY(); + } + } + return lowest; + } + + public ArrayList getLeftReferenceSpots() { + // return HACKgetAnyReferenceSpots(); + return leftReferenceSpots; + } + + public ArrayList getRightReferenceSpots() { + // return HACKgetAnyReferenceSpots(); + return rightReferenceSpots; + } + +/* gone! no more setting spots on encounters! ... whoa there, yes there is for whaleshark.org */ + public void setLeftReferenceSpots(ArrayList leftReferenceSpots) { + this.leftReferenceSpots = leftReferenceSpots; + } + + public void setRightReferenceSpots(ArrayList rightReferenceSpots) { + this.rightReferenceSpots = rightReferenceSpots; + } + + // this is for jsonForApiGet() + public org.json.JSONObject spotMappingJsonForApiGet() { + org.json.JSONObject rtn = new org.json.JSONObject(); + boolean enabled = CommonConfiguration.useSpotPatternRecognition("context0"); + rtn.put("enabled", enabled); + if (!enabled) return rtn; + rtn.put("numberLeftSpots", getNumSpots()); + rtn.put("numberRightSpots", getNumRightSpots()); + rtn.put("hasLeftSpots", getNumSpots() > 0); + rtn.put("hasRightSpots", getNumRightSpots() > 0); + rtn.put("hasSpots", (getNumSpots() + getNumRightSpots()) > 0); + + // check where results xml is stored (per spotMappingAlgorith.jsp) + File ddir = Util.getDataDir(); + String encDir = dir(ddir.toString()); + rtn.put("resultsGrothLeft", new File(encDir, "lastFullScan.xml").exists()); + rtn.put("resultsGrothRight", new File(encDir, "lastFullRightScan.xml").exists()); + rtn.put("resultsI3SLeft", new File(encDir, "lastFullI3SScan.xml").exists()); + rtn.put("resultsI3SRight", new File(encDir, "lastFullRightI3SScan.xml").exists()); + return rtn; + } + + // @return the variance for population + public double variance(double[] population) { + long n = 0; + double mean = 0; + double s = 0.0; + + for (double x : population) { + n++; + double delta = x - mean; + mean += delta / n; + s += delta * (x - mean); + } + // if you want to calculate std deviation + // of a sample change this to (s/(n-1)) + // return (s / n); + return (s / (n - 1)); + } + + // @return the standard deviation for population + public double standard_deviation(double[] population) { + return Math.sqrt(variance(population)); + } + + public void setDWCGlobalUniqueIdentifier(String guid) { + this.guid = guid; + } + + public String getDWCGlobalUniqueIdentifier() { + return guid; + } + + public void setDWCImageURL(String link) { + dwcImageURL = link; + } + + // lmao, we have this capitalization of the getter for reflexivity purposes + public String getModified() { + return modified; + } + + public String getDWCDateLastModified() { + return modified; + } + + public void setDWCDateLastModified(String lastModified) { + modified = lastModified; + } + + public void setDWCDateLastModified() { + modified = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(new Date()); + } + + public String getDWCDateAdded() { + return dwcDateAdded; + } + + // lmao, we have this capitalization of the getter for reflexivity purposes + public String getDwcDateAdded() { + return dwcDateAdded; + } + + public Long getDWCDateAddedLong() { + return dwcDateAddedLong; + } + + public Long getDwcDateAddedLong() { + return dwcDateAddedLong; + } + + public void setDWCDateAdded(String m_dateAdded) { + dwcDateAdded = m_dateAdded; + } + + public void setDWCDateAdded() { + Date myDate = new Date(); + + dwcDateAddedLong = new Long(myDate.getTime()); + dwcDateAdded = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(myDate); + } + + public void setDWCDateAdded(Long m_dateAdded) { + dwcDateAddedLong = m_dateAdded; + } + + // TODO: evaluate and remove if deprecated + public Date getReleaseDateDONOTUSE() { + return releaseDate; + } + + public Date getReleaseDate() { + if ((releaseDateLong != null) && (releaseDateLong > 0)) { + Date mDate = new Date(releaseDateLong); + return mDate; + } + return null; + } + + public Long getReleaseDateLong() { return releaseDateLong; } + + public void setReleaseDate(Long releaseDate) { + this.releaseDateLong = releaseDate; + } + + // Survey ect associations... + + public void setSurveyTrackID(String id) { + if (id != null && !id.equals("")) { + this.correspondingSurveyTrackID = id; + } + } + + public String getSurveyTrackID() { + if (correspondingSurveyTrackID != null) { + return correspondingSurveyTrackID; + } + return null; + } + + public void setPointLocation(PointLocation loc) { + if (loc.getID() != null) { + this.pointLocation = loc; + } + } + + public PointLocation getPointLocation() { + if (pointLocation != null) { + return pointLocation; + } + return null; + } + + public String getSurveyID() { + if (correspondingSurveyID != null && !correspondingSurveyID.equals("")) { + return correspondingSurveyID; + } + return null; + } + + public void setSurveyID(String id) { + if (id != null && !id.equals("")) { + this.correspondingSurveyID = id; + } + } + + public void setSurvey() { + } + + // TODO: Get all this lat lon over to Locations + + public void setDWCDecimalLatitude(double lat) { + if (lat == -9999.0) { + decimalLatitude = null; + } else { + decimalLatitude = (new Double(lat)); + } + } + + public void setDWCDecimalLatitude(Double lat) { + if ((lat != null) && (lat <= 90) && (lat >= -90)) { + this.decimalLatitude = lat; + } else { this.decimalLatitude = null; } + } + + public String getDWCDecimalLatitude() { + if (decimalLatitude != null) { return Double.toString(decimalLatitude); } + return null; + } + + public void setDWCDecimalLongitude(double longit) { + if ((longit >= -180) && (longit <= 180)) { + this.decimalLongitude = longit; + } + } + + public String getDWCDecimalLongitude() { + if (decimalLongitude != null) { + return Double.toString(decimalLongitude); + } + return null; + } + + public boolean getOKExposeViaTapirLink() { + return okExposeViaTapirLink; + } + + public void setOKExposeViaTapirLink(boolean ok) { + okExposeViaTapirLink = ok; + } + + public void setAlternateID(String newID) { + this.otherCatalogNumbers = newID; + } + + public String getAlternateID() { + if (otherCatalogNumbers == null) { + return null; + } + return otherCatalogNumbers; + } + + public String getOLDInformOthersFORLEGACYCONVERSION() { + if (informothers == null) { + return ""; + } + return informothers; + } + + public String getLocationID() { + return locationID; + } + + public String getLocationName() { + if (locationID == null) return null; + return LocationID.getNameForLocationID(locationID, null); + } + + public void setLocationID(String newLocationID) { + if (newLocationID != null) { + this.locationID = newLocationID.trim(); + } else { + this.locationID = null; + } + } + + public Double getMaximumDepthInMeters() { + return maximumDepthInMeters; + } + + public void setMaximumDepthInMeters(Double newDepth) { + this.maximumDepthInMeters = newDepth; + } + + public Double getMaximumElevationInMeters() { + return maximumElevationInMeters; + } + + public void setMaximumElevationInMeters(Double newElev) { + this.maximumElevationInMeters = newElev; + } + + // @return Catalog Number String + @Override public String getId() { + return catalogNumber; + } + + // @param newNumber The Catalog Number to set. + @Override public void setId(String newNumber) { + this.catalogNumber = newNumber; + } + + // TODO: remove if actually deprecated and unused + // ##DEPRECATED #509 - Base class getId() method + public String getCatalogNumber() { + return catalogNumber; + } + + // TODO: remove if actually deprecated and unused + // ##DEPRECATED #509 - Base class setId() method + public void setCatalogNumber(String newNumber) { + this.catalogNumber = newNumber; + } + + // TODO: remove if actually deprecated and unused + // ##DEPRECATED #509 - Base class getId() method + public String getID() { + return catalogNumber; + } + + // TODO: remove if actually deprecated and unused + // ##DEPRECATED #509 - Base class setId() method + public void setID(String newNumber) { + this.catalogNumber = newNumber; + } + + public String getVerbatimLocality() { + return verbatimLocality; + } + + public void setVerbatimLocality(String vlcl) { + this.verbatimLocality = vlcl; + } + + public Double getDecimalLatitudeAsDouble() { + return (decimalLatitude == null) ? null : decimalLatitude.doubleValue(); + } + + public void setDecimalLatitude(Double lat) { + this.decimalLatitude = lat; + gpsLatitude = Util.decimalLatLonToString(lat); + } + + public Double getDecimalLongitudeAsDouble() { + return (decimalLongitude == null) ? null : decimalLongitude.doubleValue(); + } + + public void setDecimalLongitude(Double lon) { + this.decimalLongitude = lon; + gpsLongitude = Util.decimalLatLonToString(lon); + } + + public Double getEndDecimalLatitudeAsDouble() { + return (endDecimalLatitude == null) ? null : endDecimalLatitude.doubleValue(); + } + + public void setEndDecimalLatitude(Double lat) { + this.endDecimalLatitude = lat; + gpsEndLatitude = Util.decimalLatLonToString(lat); + } + + public Double getEndDecimalLongitudeAsDouble() { + return (endDecimalLongitude == null) ? null : endDecimalLongitude.doubleValue(); + } + + public void setEndDecimalLongitude(Double lon) { + this.endDecimalLongitude = lon; + gpsEndLongitude = Util.decimalLatLonToString(lon); + } + + public String getOccurrenceRemarks() { + return occurrenceRemarks; + } + + public void setOccurrenceRemarks(String remarks) { + this.occurrenceRemarks = remarks; + } + + public String getRecordedBy() { + return recordedBy; + } + + public void setRecordedBy(String submitterName) { + this.recordedBy = submitterName; + } + + public String getOtherCatalogNumbers() { + return otherCatalogNumbers; + } + + public void setOtherCatalogNumbers(String otherNums) { + this.otherCatalogNumbers = otherNums; + } + + public String getLivingStatus() { + return livingStatus; + } + + public void setLivingStatus(String status) { + this.livingStatus = status; + } + + public void setAge(Double a) { + age = a; + } + + public Double getAge() { + return age; + } + + public String getBehavior() { + return behavior; + } + + public void setBehavior(String beh) { + this.behavior = beh; + } + + public String getEventID() { + return eventID; + } + + public void setEventID(String id) { + this.eventID = id; + } + + public String getVerbatimEventDate() { + return verbatimEventDate; + } + + public void setVerbatimEventDate(String vet) { + if (vet != null) { this.verbatimEventDate = vet; } else { this.verbatimEventDate = null; } + } + + public String getDynamicProperties() { + return dynamicProperties; + } + + public org.json.JSONObject getDynamicPropertiesJSONObject() { + org.json.JSONObject dp = new org.json.JSONObject(); + if (dynamicProperties == null) return dp; + StringTokenizer st = new StringTokenizer(dynamicProperties, ";"); + while (st.hasMoreTokens()) { + String token = st.nextToken(); + int equalPlace = token.indexOf("="); + if (equalPlace > 0) + dp.put(token.substring(0, equalPlace), token.substring(equalPlace + 1)); + } + return dp; + } + + public void setDynamicProperties(String allDynamicProperties) { + this.dynamicProperties = allDynamicProperties; + } + + public void addDynamicProperties(String allDynamicProperties) { + this.dynamicProperties += allDynamicProperties; + } + + public void setDynamicProperty(String name, String value) { + name = name.replaceAll(";", "_").trim().replaceAll("%20", " "); + value = value.replaceAll(";", "_").trim(); + if (dynamicProperties == null) { dynamicProperties = name + "=" + value + ";"; } else { + // let's create a TreeMap of the properties + TreeMap tm = new TreeMap(); + StringTokenizer st = new StringTokenizer(dynamicProperties, ";"); + while (st.hasMoreTokens()) { + String token = st.nextToken(); + int equalPlace = token.indexOf("="); + try { + tm.put(token.substring(0, equalPlace), token.substring(equalPlace + 1)); + } catch (java.lang.StringIndexOutOfBoundsException soe) { + // this is a badly formatted pair that should be ignored + } + } + if (tm.containsKey(name)) { + tm.remove(name); + tm.put(name, value); + + // now let's recreate the dynamicProperties String + String newProps = tm.toString(); + int stringSize = newProps.length(); + dynamicProperties = newProps.substring(1, (stringSize - 1)).replaceAll(", ", + ";") + ";"; + } else { + dynamicProperties = dynamicProperties + name + "=" + value + ";"; + } + } + } + + public String getDynamicPropertyValue(String name) { + if (dynamicProperties != null) { + name = name.replaceAll("%20", " "); + // let's create a TreeMap of the properties + TreeMap tm = new TreeMap(); + StringTokenizer st = new StringTokenizer(dynamicProperties, ";"); + while (st.hasMoreTokens()) { + String token = st.nextToken(); + int equalPlace = token.indexOf("="); + tm.put(token.substring(0, equalPlace), token.substring(equalPlace + 1)); + } + if (tm.containsKey(name)) { + return tm.get(name); + } + } + return null; + } + + public boolean hasDynamicProperty(String name) { + return (this.getDynamicPropertyValue(name) != null); + } + + public void removeDynamicProperty(String name) { + name = name.replaceAll(";", "_").trim().replaceAll("%20", " "); + if (dynamicProperties != null) { + // let's create a TreeMap of the properties + TreeMap tm = new TreeMap(); + StringTokenizer st = new StringTokenizer(dynamicProperties, ";"); + while (st.hasMoreTokens()) { + String token = st.nextToken(); + int equalPlace = token.indexOf("="); + tm.put(token.substring(0, (equalPlace)), token.substring(equalPlace + 1)); + } + if (tm.containsKey(name)) { + tm.remove(name); + + // now let's recreate the dynamicProperties String + String newProps = tm.toString(); + int stringSize = newProps.length(); + dynamicProperties = newProps.substring(1, (stringSize - 1)).replaceAll(", ", + ";") + ";"; + } + } + } + + public String getIdentificationRemarks() { + return identificationRemarks; + } + + public String getHashedSubmitterEmail() { + return hashedSubmitterEmail; + } + + public String getHashedPhotographerEmail() { + return hashedPhotographerEmail; + } + + public String getHashedInformOthers() { + return hashedInformOthers; + } + + public static String getHashOfEmailString(String hashMe) { + if (hashMe == null) return null; + String returnString = ""; + StringTokenizer tokenizer = new StringTokenizer(hashMe, ","); + while (tokenizer.hasMoreTokens()) { + String emailAddress = tokenizer.nextToken().trim().toLowerCase(); + if (!emailAddress.equals("")) { + String md5 = DigestUtils.md5Hex(emailAddress); + if (returnString.equals("")) { + returnString += md5; + } else { + returnString += "," + md5; + } + } + } + return returnString; + } + + public String getGenus() { + return genus; + } + + public void setGenus(String newGenus) { + if (newGenus != null) { genus = newGenus; } else { genus = null; } + this.refreshAnnotationLiteTaxonomy(); + } + + // we need these methods because our side-effected setGenus will silently break an import (!!!!!) in an edge case I cannot identify + public void setGenusOnly(String genus) { + this.genus = genus; + this.refreshAnnotationLiteTaxonomy(); + } + + public void setSpeciesOnly(String species) { + setSpecificEpithet(species); + this.refreshAnnotationLiteTaxonomy(); + } + + public String getSpecificEpithet() { + return specificEpithet; + } + + public void setSpecificEpithet(String newEpithet) { + if (newEpithet != null) { specificEpithet = newEpithet.replaceAll("_", " "); } else { + specificEpithet = null; + } + this.refreshAnnotationLiteTaxonomy(); + } + + public String getTaxonomyString() { + return Util.taxonomyString(getGenus(), getSpecificEpithet()); + } + + // hacky (as generates new Taxonomy -- with random uuid) but still should work for tax1.equals(tax2); + // TODO: FIXME this should be superceded by the getter for Taxonomy property in the future.... + public Taxonomy getTaxonomy(Shepherd myShepherd) { + String sciname = this.getTaxonomyString(); + + if (sciname == null) return null; + return myShepherd.getOrCreateTaxonomy(sciname, false); // false means don't commit the taxonomy + } + + // right now this updates .genus and .specificEpithet ... but in some glorious future we will just store Taxonomy! + // note that "null" cases will leave *current values untouched* (does not reset them) + public void setTaxonomy(Taxonomy tax) { + if (tax == null) return; + String[] gs = tax.getGenusSpecificEpithet(); + if ((gs == null) || (gs.length < 1)) return; + if (gs.length == 1) { + this.genus = gs[0]; + this.specificEpithet = null; + } else { + this.genus = gs[0]; + this.specificEpithet = gs[1].replaceAll("_", " "); + } + this.refreshAnnotationLiteTaxonomy(); + } + + public void setTaxonomyFromString(String s) { // basically scientific name (will get split on space) + String[] gs = Util.stringToGenusSpecificEpithet(s); + + if ((gs == null) || (gs.length < 1)) return; + if (gs.length == 1) { + this.genus = gs[0]; + this.specificEpithet = null; + } else { + this.genus = gs[0]; + this.specificEpithet = gs[1].replaceAll("_", " "); + } + this.refreshAnnotationLiteTaxonomy(); + } + + public void setTaxonomyFromIAClass(String iaClass, Shepherd myShepherd) { + setTaxonomy(IBEISIA.iaClassToTaxonomy(iaClass, myShepherd)); + } + + public String getPatterningCode() { return patterningCode; } + public void setPatterningCode(String newCode) { this.patterningCode = newCode; } + + // crawls thru assets and sets date + public void setDateFromAssets() { + // FIXME if you dare. i can *promise you* there are some timezone problems here. ymmv. + if ((annotations == null) || (annotations.size() < 1)) return; + DateTime dt = null; + for (Annotation ann : annotations) { + MediaAsset ma = ann.getMediaAsset(); + if (ma == null) continue; + dt = ma.getDateTime(); + if (dt != null) break; // we just take the first one + } + if (dt != null) setDateInMilliseconds(dt.getMillis()); + } + + // this can(should?) fail in a lot of cases, since we may not know + public void setSpeciesFromAnnotations() { + if ((annotations == null) || (annotations.size() < 1)) return; + String[] sp = null; + for (Annotation ann : annotations) { + sp = IBEISIA.convertSpecies(annotations.get(0).getIAClass()); + if (sp != null) break; // use first one we get + } + // note: now we require (exactly) two parts ... please fix this, Taxonomy class! + if ((sp == null) || (sp.length != 2)) return; + this.setGenus(sp[0]); + this.setSpecificEpithet(sp[1]); + } + + // find the first one(s) we can + public void setLatLonFromAssets() { + if ((annotations == null) || (annotations.size() < 1)) return; + Double lat = null; + Double lon = null; + for (Annotation ann : annotations) { + MediaAsset ma = ann.getMediaAsset(); + if (ma == null) continue; + if (lat == null) lat = ma.getLatitude(); + if (lon == null) lon = ma.getLongitude(); + if ((lat != null) && (lon != null)) break; + } + if (lat != null) this.setDecimalLatitude(lat); + if (lon != null) this.setDecimalLongitude(lon); + } + + // sets date to the closes we have to "not set" :) + public void zeroOutDate() { + year = 0; + month = 0; + day = 0; + hour = -1; + minutes = "00"; + resetDateInMilliseconds(); // should set that to null as well + } + + public void resetDateInMilliseconds() { + dateInMilliseconds = computeDateInMilliseconds(); + } + + public Long computeDateInMilliseconds() { + if (year > 0) { + int localMonth = 0; + if (month > 0) { localMonth = month - 1; } + int localDay = 1; + if (day > 0) { localDay = day; } + int localHour = 0; + if (hour > -1) { localHour = hour; } + int myMinutes = 0; + try { myMinutes = Integer.parseInt(minutes); } catch (Exception e) {} + TimeZone tz = TimeZone.getTimeZone("UTC"); + Calendar calendar = Calendar.getInstance(tz); + calendar.set(year, localMonth, localDay, localHour, myMinutes); + return new Long(calendar.getTimeInMillis()); + } + return null; + } + + public java.lang.Long getDateInMilliseconds() { return dateInMilliseconds; } + + public Long getDateInMillisecondsFallback() { + if (dateInMilliseconds != null) return dateInMilliseconds; + return computeDateInMilliseconds(); + } + + // this will set all date stuff based on ms since epoch + public void setDateInMilliseconds(long ms) { + Calendar cal = Calendar.getInstance(TimeZone.getTimeZone("UTC")); + + cal.setTimeInMillis(ms); + this.year = cal.get(Calendar.YEAR); + this.month = cal.get(Calendar.MONTH) + 1; + this.day = cal.get(Calendar.DAY_OF_MONTH); + this.hour = cal.get(Calendar.HOUR); + this.minutes = Integer.toString(cal.get(Calendar.MINUTE)); + if (this.minutes.length() == 1) this.minutes = "0" + this.minutes; + this.dateInMilliseconds = ms; + } + + // also supports YYYY and YYYY-MM + // per issue 1489, cannot set a future date + public void setDateFromISO8601String(String iso8601) + throws ApiException { + if (!validISO8601String(iso8601)) return; + + // this is for potential ApiException + org.json.JSONObject error = new org.json.JSONObject(); + error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); + + if (iso8601.length() == 4) { // assume year + try { + this.year = Integer.parseInt(iso8601); + } catch (Exception ex) {} + + // got an int year, but lets see if it is valid + if (Util.dateIsInFuture(this.year, null, null)) { + error.put("fieldName", "year"); + error.put("value", this.year); + throw new ApiException("date is in the future", error); + } + resetDateInMilliseconds(); + return; + } + // this format should already be validated so we can trust it (flw) + if (iso8601.length() == 7) { + try { + this.year = Integer.parseInt(iso8601.substring(0, 4)); + this.month = Integer.parseInt(iso8601.substring(5, 7)); + } catch (Exception ex) {} + if (Util.dateIsInFuture(this.year, this.month, null)) { + // if we wanted to be super thorough we could do errors array of year & month + error.put("fieldName", "month"); + error.put("value", this.month); + throw new ApiException("date is in the future", error); + } + resetDateInMilliseconds(); + return; + } + try { + String adjusted = Util.getISO8601Date(iso8601); + DateTime dt = new DateTime(adjusted); + if (Util.dateIsInFuture(dt.getYear(), dt.getMonthOfYear(), dt.getDayOfMonth())) { + error.put("fieldName", "day"); + error.put("value", dt.getDayOfMonth()); + throw new ApiException("date is in the future", error); + } + this.setDateInMilliseconds(dt.getMillis()); + // pass this flavor out... + } catch (ApiException ex) { + throw ex; + // this catches failure of new DateTime() basically, so we make this an ApiException + } catch (Exception ex) { + System.out.println("setDateFromISO8601String(" + iso8601 + ") failed: " + ex); + throw new ApiException("date/time values are invalid"); + } + resetDateInMilliseconds(); + } + + // also supports YYYY and YYYY-MM + public static boolean validISO8601String(String iso8601) { + if (iso8601 == null) return false; + if (iso8601.length() == 4) { + Integer yr = null; + try { + yr = Integer.parseInt(iso8601); + } catch (Exception ex) {} + return (yr != null); + } + if (iso8601.length() == 7) { + Integer yr = null; + Integer mo = null; + try { + yr = Integer.parseInt(iso8601.substring(0, 4)); + mo = Integer.parseInt(iso8601.substring(5, 7)); + } catch (Exception ex) {} + if ((yr == null) || (mo == null)) return false; + if ((mo < 1) || (mo > 12)) return false; + return true; + } + long test = Util.getVersionFromModified(iso8601); + return (test > 0); + } + + public Long getEndDateInMilliseconds() { + return endDateInMilliseconds; + } + + public void setEndDateInMilliseconds(long ms) { + this.endDateInMilliseconds = ms; + } + + private String milliToMonthDayYear(Long millis) { + DateTime dt = new DateTime(millis); + DateTimeFormatter dtf = DateTimeFormat.forPattern("yyyy-MM-dd hh:mm a"); + + return dtf.print(dt); + } + + public String getStartDateTime() { + return milliToMonthDayYear(dateInMilliseconds); + } + + public String getEndDateTime() { + return milliToMonthDayYear(endDateInMilliseconds); + } + + public String getDecimalLatitude() { + if (decimalLatitude != null) { return Double.toString(decimalLatitude); } + return null; + } + + public String getDecimalLongitude() { + if (decimalLongitude != null) { return Double.toString(decimalLongitude); } + return null; + } + + public String getEndDecimalLongitude() { + if (endDecimalLongitude != null) { return Double.toString(endDecimalLongitude); } + return null; + } + + public String getEndDecimalLatitude() { + if (endDecimalLatitude != null) { return Double.toString(endDecimalLatitude); } + return null; + } + + public String getSubmitterProject() { + return submitterProject; + } + + public void setSubmitterProject(String newProject) { + if (newProject != null) { submitterProject = newProject; } else { submitterProject = null; } + } + + public String getSubmitterOrganization() { + return submitterOrganization; + } + + public void setSubmitterOrganization(String newOrg) { + if (newOrg != null) { submitterOrganization = newOrg; } else { + submitterOrganization = null; + } + } + + public List getSubmitterResearchers() { + return submitterResearchers; + } + + public void addSubmitterResearcher(String researcher) { + if (submitterResearchers == null) submitterResearchers = new ArrayList(); + submitterResearchers.add(researcher); + } + + public void setSubmitterResearchers(Collection researchers) { + if (researchers != null) this.submitterResearchers = new ArrayList(researchers); + } + + public List getProjects(Shepherd myShepherd) { + return myShepherd.getProjectsForEncounter(this); + } + + public void addTissueSample(TissueSample dce) { + if (tissueSamples == null) { tissueSamples = new ArrayList(); } + if (!tissueSamples.contains(dce)) { tissueSamples.add(dce); } + dce.setCorrespondingEncounterNumber(getCatalogNumber()); + } + + public void setTissueSamples(List samps) { + this.tissueSamples = samps; + } + + public void removeTissueSample(int num) { tissueSamples.remove(num); } + public List getTissueSamples() { return tissueSamples; } + public Set getTissueSampleIDs() { + Set ids = new HashSet(); + + if (tissueSamples != null) + for (TissueSample ts : tissueSamples) { + ids.add(ts.getSampleID()); + } + return ids; + } + + public void removeTissueSample(TissueSample num) { tissueSamples.remove(num); } + + public void addSinglePhotoVideo(SinglePhotoVideo dce) { + if (images == null) { images = new ArrayList(); } + if (!images.contains(dce)) { images.add(dce); } + } + + public void removeSinglePhotoVideo(int num) { images.remove(num); } + public List getSinglePhotoVideo() { return images; } + public void removeSinglePhotoVideo(SinglePhotoVideo num) { images.remove(num); } + + public void setMeasurements(List measurements) { + this.measurements = measurements; + } + + public void setMeasurement(Measurement measurement, Shepherd myShepherd) { + // if measurements are null, set the empty list + if (measurements == null) { measurements = new ArrayList(); } + // now start checking for existence of a previous measurement + // if we have it but the new value is null, remove the measurement + if ((this.hasMeasurement(measurement.getType())) && (measurement.getValue() == null)) { + Measurement m = this.getMeasurement(measurement.getType()); + measurements.remove(m); + myShepherd.getPM().deletePersistent(m); + myShepherd.commitDBTransaction(); + myShepherd.beginDBTransaction(); + } + // just add the measurement it if we did not have it before + else if (!this.hasMeasurement(measurement.getType())) { + measurements.add(measurement); + myShepherd.commitDBTransaction(); + myShepherd.beginDBTransaction(); + } + // if we had it before then just update the value + else if ((this.hasMeasurement(measurement.getType())) && (measurement != null)) { + Measurement m = this.getMeasurement(measurement.getType()); + m.setValue(measurement.getValue()); + m.setSamplingProtocol(measurement.getSamplingProtocol()); + myShepherd.commitDBTransaction(); + myShepherd.beginDBTransaction(); + } + } + + public Measurement removeMeasurementByType(String type) { + // findMeasurementOfType() seems to return even ones with value=null + // (versus getMeasurement())... so this seems the better choice? + Measurement m = findMeasurementOfType(type); + + if (m != null) measurements.remove(m); + return m; + } + + // will find the Measurement (by type) and modify it *or* make a new one + public Measurement getOrCreateMeasurement(org.json.JSONObject jdata) { + if (jdata == null) return null; + String type = jdata.optString("type", null); + if (type == null) return null; + Measurement m = findMeasurementOfType(type); + if (m == null) { + m = new Measurement(this.getId(), type, jdata.optDouble("value", 0.0D), + jdata.optString("units", null), jdata.optString("samplingProtocol", null)); + } else { + m.setValue(jdata.optDouble("value", 0.0D)); + m.setUnits(jdata.optString("units", null)); + m.setSamplingProtocol(jdata.optString("samplingProtocol", null)); + } + return m; + } + + // like above but way less persisty + public void setMeasurement(Measurement measurement) { + if (measurement == null) return; + if (measurements == null) measurements = new ArrayList(); + Measurement hasType = this.getMeasurement(measurement.getType()); + if (hasType == null) { + measurements.add(measurement); + } else if (measurement.getValue() == null) { + // i guess this means we remove it + measurements.remove(hasType); + } else { + // update existing + hasType.setValue(measurement.getValue()); + hasType.setSamplingProtocol(measurement.getSamplingProtocol()); + } + } + + // like above but less..... checky (trust the caller!) + public void addMeasurement(Measurement meas) { + if (meas == null) return; + if (measurements == null) measurements = new ArrayList(); + measurements.add(meas); + } + + public void removeMeasurement(int num) { measurements.remove(num); } + public List getMeasurements() { return measurements; } + public void removeMeasurement(Measurement num) { measurements.remove(num); } + // FIXME this seems suspiciously just like getMeasurement(type) + public Measurement findMeasurementOfType(String type) { + List measurements = getMeasurements(); + + if (measurements != null) { + for (Measurement measurement : measurements) { + if (type.equals(measurement.getType())) { + return measurement; + } + } + } + return null; + } + + public void addMetalTag(MetalTag metalTag) { + if (metalTags == null) { + metalTags = new ArrayList(); + } + metalTags.add(metalTag); + } + + // this does NOT validate values + public MetalTag addOrUpdateMetalTag(String location, String number) { + if ((location == null) || (number == null)) return null; + MetalTag tag = findMetalTagForLocation(location); + if (tag == null) { + tag = new MetalTag(number, location); + addMetalTag(tag); + } else { + tag.setTagNumber(number); + } + return tag; + } + + public void removeMetalTag(MetalTag metalTag) { + metalTags.remove(metalTag); + } + + // this will clear out ALL tags with this location, but i think we + // are supposed to only have [at most] one anyway! + public void removeMetalTag(String location) { + if ((location == null) || (metalTags == null)) return; + ListIterator it = metalTags.listIterator(); + while (it.hasNext()) { + MetalTag next = it.next(); + if (location.equals(next.getLocation())) it.remove(); + } + } + + public void setMetalTags(List metalTags) { + this.metalTags = metalTags; + } + + public List getMetalTags() { + return metalTags; + } + + public MetalTag findMetalTagForLocation(String location) { + List metalTags = getMetalTags(); + + if (metalTags != null) { + for (MetalTag metalTag : metalTags) { + if (location.equals(metalTag.getLocation())) { + return metalTag; + } + } + } + return null; + } + + public AcousticTag getAcousticTag() { + return acousticTag; + } + + public void setAcousticTag(AcousticTag acousticTag) { + this.acousticTag = acousticTag; + } + + public SatelliteTag getSatelliteTag() { + return satelliteTag; + } + + public void setSatelliteTag(SatelliteTag satelliteTag) { + this.satelliteTag = satelliteTag; + } + + public DigitalArchiveTag getDTag() { + return digitalArchiveTag; + } + + public void setDTag(DigitalArchiveTag dt) { + this.digitalArchiveTag = dt; + } + + public String getLifeStage() { return lifeStage; } + public void setLifeStage(String newStage) { + if (newStage != null) { lifeStage = newStage; } else { lifeStage = null; } + } + + // A convenience method that returns the first haplotype found in the TissueSamples for this Encounter. + public String getHaplotype() { + if (tissueSamples != null) { + int numTissueSamples = tissueSamples.size(); + if (numTissueSamples > 0) { + for (int j = 0; j < numTissueSamples; j++) { + TissueSample thisSample = tissueSamples.get(j); + int numAnalyses = thisSample.getNumAnalyses(); + if (numAnalyses > 0) { + List gAnalyses = thisSample.getGeneticAnalyses(); + for (int g = 0; g < numAnalyses; g++) { + GeneticAnalysis ga = gAnalyses.get(g); + if (ga.getAnalysisType().equals("MitochondrialDNA")) { + MitochondrialDNAAnalysis mito = (MitochondrialDNAAnalysis)ga; + if (mito.getHaplotype() != null) { return mito.getHaplotype(); } + } + } + } + } + } + } + return null; + } + + // A convenience method that returns the first genetic sex found in the TissueSamples for this Encounter. + public String getGeneticSex() { + if (tissueSamples != null) { + int numTissueSamples = tissueSamples.size(); + if (numTissueSamples > 0) { + for (int j = 0; j < numTissueSamples; j++) { + TissueSample thisSample = tissueSamples.get(j); + int numAnalyses = thisSample.getNumAnalyses(); + if (numAnalyses > 0) { + List gAnalyses = thisSample.getGeneticAnalyses(); + for (int g = 0; g < numAnalyses; g++) { + GeneticAnalysis ga = gAnalyses.get(g); + if (ga.getAnalysisType().equals("SexAnalysis")) { + SexAnalysis mito = (SexAnalysis)ga; + if (mito.getSex() != null) { return mito.getSex(); } + } + } + } + } + } + } + return null; + } + + public List getMicrosatelliteMarkers() { + List markers = + new ArrayList(); + + if (tissueSamples == null) return markers; + for (TissueSample tsamp : tissueSamples) { + for (GeneticAnalysis gan : tsamp.getGeneticAnalyses()) { + if (!"MicrosatelliteMarkers".equals(gan.getAnalysisType())) continue; + markers.add((MicrosatelliteMarkersAnalysis)gan); + } + } + return markers; + } + + public List getImages() { return images; } + + public boolean hasAnnotation(Annotation ann) { + return (annotations != null && annotations.contains(ann)); + } + + public boolean hasAnnotations() { + return (annotations != null && annotations.size() > 0); + } + + public int numAnnotations() { + if (annotations == null) return 0; + return annotations.size(); + } + + public int numNonTrivialAnnotations() { + if (annotations == null) return 0; + int ct = 0; + for (Annotation ann : annotations) { + if (!ann.isTrivial()) ct++; + } + return ct; + } + + public ArrayList getAnnotations() { + return annotations; + } + + public Annotation getAnnotation(String annId) { + if ((annId == null) || (annotations == null)) return null; + for (Annotation ann : annotations) { + if (annId.equals(ann.getId())) return ann; + } + return null; + } + + public Set getAnnotationViewpoints() { + Set vps = new HashSet(); + + if (!hasAnnotations()) return vps; + for (Annotation ann : annotations) { + if (ann.getViewpoint() != null) vps.add(ann.getViewpoint()); + } + return vps; + } + + public Set getAnnotationIAClasses() { + Set classes = new HashSet(); + + if (!hasAnnotations()) return classes; + for (Annotation ann : annotations) { + if (ann.getIAClass() != null) classes.add(ann.getIAClass()); + } + // TODO: we should find out how/where bunk iaClass values are getting set + // and stop the via isValidIAClass() or similar + // also should be considered for any data integrity/repair tools + classes.remove("____"); + return classes; + } + + // all an enc's annotations on a given asset (might be multiple if parts are involved) + public List getAnnotations(MediaAsset ma) { + List anns = new ArrayList(); + + for (Annotation ann : getAnnotations()) { + if (ann.getMediaAsset() == ma) anns.add(ann); + } + return anns; + } + + public void setAnnotations(ArrayList anns) { + annotations = anns; + } + + public void addAnnotations(List anns) { + if (annotations == null) annotations = new ArrayList(); + for (Annotation ann : anns) { + if (!annotations.contains(ann)) annotations.add(ann); + } + } + + public void addAnnotation(Annotation ann) { + if (annotations == null) annotations = new ArrayList(); + if (!annotations.contains(ann)) annotations.add(ann); + } + + public void useAnnotationsForMatching(boolean use) { + if (getAnnotations() != null && getAnnotations().size() >= 1) { + for (Annotation ann : getAnnotations()) { + ann.setMatchAgainst(use); + } + } + } + + public Annotation getAnnotationWithKeyword(String word) { + System.out.println("getAnnotationWithKeyword called for " + word); + System.out.println("getAnnotationWithKeyword called, annotations = " + annotations); + if (annotations == null) return null; + for (Annotation ann : annotations) { + if (ann == null) continue; + MediaAsset ma = ann.getMediaAsset(); + if (ma != null && ma.hasKeyword(word)) return ann; + } + return null; + } + + // pretty much only useful for frames pulled from video (after detection, to be made into encounters) + public static List collateFrameAnnotations(List anns, + Shepherd myShepherd) { + if ((anns == null) || (anns.size() < 1)) return null; + // Determine skipped frames before another encounter should be made. + int minGapSize = 4; + try { + String gapFromProperties = IA.getProperty(myShepherd.getContext(), + "newEncounterFrameGap"); + if (gapFromProperties != null) { + minGapSize = Integer.parseInt(gapFromProperties); + } + } catch (NumberFormatException nfe) {} + SortedMap > ordered = new TreeMap >(); + MediaAsset parentRoot = null; + for (Annotation ann : anns) { + System.out.println("========================== >>>>>> " + ann); + if (ann.getFeatures().get(0).isUnity()) continue; // makes big assumption there is one-and-only-one feature btw (detection should have + // bbox) + MediaAsset ma = ann.getMediaAsset(); + if (parentRoot == null) parentRoot = ma.getParentRoot(myShepherd); + System.out.println(" -->>> ma = " + ma); + if (!ma.hasLabel("_frame") || (ma.getParentId() == null)) continue; // nope thx + int offset = ma.getParameters().optInt("extractOffset", -1); + System.out.println(" -->>> offset = " + offset); + if (offset < 0) continue; + if (ordered.get(offset) == null) ordered.put(offset, new ArrayList()); + ordered.get(offset).add(ann); + } + if (ordered.size() < 1) return null; // none used! + + // now construct Encounters based upon spacing of frame-clusters + List newEncs = new ArrayList(); + int prevOffset = -1; + int groupsMade = 1; + ArrayList tmpAnns = new ArrayList(); + for (Integer i : ordered.keySet()) { + if ((prevOffset > -1) && ((i - prevOffset) >= minGapSize)) { + Encounter newEnc = __encForCollate(tmpAnns, parentRoot); + if (newEnc != null) { // null means none of the frames met minimum detection confidence + newEnc.setDynamicProperty("frameSplitNumber", Integer.toString(groupsMade + 1)); + newEncs.add(newEnc); + System.out.println(" cluster [" + (groupsMade) + "] -> " + newEnc); + groupsMade++; + tmpAnns = new ArrayList(); + } + } + prevOffset = i; + tmpAnns.addAll(ordered.get(i)); + } + // deal with dangling tmpAnns content + if (tmpAnns.size() > 0) { + Encounter newEnc = __encForCollate(tmpAnns, parentRoot); + if (newEnc != null) { + newEnc.setDynamicProperty("frameSplitNumber", Integer.toString(groupsMade + 1)); + newEncs.add(newEnc); + System.out.println(" (final)cluster [" + groupsMade + "] -> " + newEnc); + groupsMade++; + } + } + return newEncs; + } + + // this is really only for above method + private static Encounter __encForCollate(ArrayList tmpAnns, MediaAsset parentRoot) { + if ((tmpAnns == null) || (tmpAnns.size() < 1)) return null; + // make sure we even can use these annots first + double bestConfidence = 0.0; + for (Annotation ann : tmpAnns) { + if ((ann.getFeatures() == null) || (ann.getFeatures().size() < 1) || + (ann.getFeatures().get(0).getParameters() == null)) continue; + double conf = ann.getFeatures().get(0).getParameters().optDouble("detectionConfidence", + -1.0); + if (conf > bestConfidence) bestConfidence = conf; + } + if (bestConfidence < ENCOUNTER_AUTO_SOURCE_CONFIDENCE_CUTOFF) { + System.out.println("[INFO] bestConfidence=" + bestConfidence + + " below threshold; rejecting 1 enc from " + parentRoot); + return null; + } + Encounter newEnc = new Encounter(tmpAnns); + newEnc.setState(STATE_AUTO_SOURCED); + newEnc.zeroOutDate(); // do *not* want it using the video source date + newEnc.setDynamicProperty("bestDetectionConfidence", Double.toString(bestConfidence)); + if (parentRoot == null) { + newEnc.setSubmitterName("Unknown video source"); + newEnc.addComments("unable to determine video source - possibly YouTube error?"); + } else { + newEnc.addComments("

    YouTube ID: " + parentRoot.getParameters().optString("id") + + "

    "); + String consolidatedRemarks = + "

    Auto-sourced from YouTube Parent Video: " + + parentRoot.getParameters().optString("id") + "

    "; + // set the video ID as the EventID for distinct access later + newEnc.setEventID("youtube:" + parentRoot.getParameters().optString("id")); + if ((parentRoot.getMetadata() != null) && + (parentRoot.getMetadata().getData() != null)) { + if (parentRoot.getMetadata().getData().optJSONObject("basic") != null) { + newEnc.setSubmitterName(parentRoot.getMetadata().getData().getJSONObject( + "basic").optString("author_name", "[unknown]") + " (by way of YouTube)"); + consolidatedRemarks += "

    From YouTube video: " + + parentRoot.getMetadata().getData().getJSONObject("basic").optString("title", + "[unknown]") + "

    "; + newEnc.addComments(consolidatedRemarks); + + // add a dynamic property to make a quick link to the video + } + if (parentRoot.getMetadata().getData().optJSONObject("detailed") != null) { + String desc = "

    " + + parentRoot.getMetadata().getData().getJSONObject("detailed").optString( + "description", "[no description]") + "

    "; + if (parentRoot.getMetadata().getData().getJSONObject("detailed").optJSONArray( + "tags") != null) { + desc += "

    tags: " + + parentRoot.getMetadata().getData().getJSONObject( + "detailed").getJSONArray("tags").toString() + "

    "; + } + consolidatedRemarks += desc; + } + } + newEnc.setOccurrenceRemarks(consolidatedRemarks); + } + return newEnc; + } + + // convenience method + public ArrayList getMedia() { + ArrayList m = new ArrayList(); + + if ((annotations == null) || (annotations.size() < 1)) return m; + for (Annotation ann : annotations) { + if (ann == null) continue; // really weird that this happens sometimes + MediaAsset ma = ann.getMediaAsset(); + if (ma != null) m.add(ma); + } + return m; + } + + public MediaAsset getMediaAssetByFilename(String filename) { + if (!Util.stringExists(filename)) return null; + for (MediaAsset ma : getMedia()) { + if (Util.stringsEqualish(filename, ma.getFilename())) return ma; + } + return null; + } + + // only checks top-level MediaAssets, not children or resized images + public boolean hasTopLevelMediaAsset(int id) { + return (indexOfMediaAsset(id) >= 0); + } + + // finds the index of the MA we're looking for + public int indexOfMediaAsset(int id) { + if (annotations == null) return -1; + for (int i = 0; i < annotations.size(); i++) { + MediaAsset ma = annotations.get(i).getMediaAsset(); + if (ma == null) continue; + if (ma.getIdInt() == id) return i; + } + return -1; + } + + // creates a new annotation and attaches the asset + public void addMediaAsset(MediaAsset ma) { + Annotation ann = new Annotation(getTaxonomyString(), ma); + + if (annotations == null) annotations = new ArrayList(); + annotations.add(ann); + } + + public void removeAnnotation(Annotation ann) { + if (annotations == null) return; + annotations.remove(ann); + } + + public void removeAnnotation(int index) { + annotations.remove(index); + } + + // this removes an Annotation from Encounter (and from its MediaAsset!!) and replaces it with a new one + // please note: the oldAnn gets killed off (not orphaned) + public void replaceAnnotation(Annotation oldAnn, Annotation newAnn) { + oldAnn.detachFromMediaAsset(); + // note: newAnn should already attached to a MediaAsset + removeAnnotation(oldAnn); + addAnnotation(newAnn); + } + + public void removeMediaAsset(MediaAsset ma) { + removeAnnotation(indexOfMediaAsset(ma.getIdInt())); + } + + // this is a kinda hacky way to find media ... really used by encounter.jsp now but likely should go away? + public ArrayList findAllMediaByFeatureId(Shepherd myShepherd, String[] featureIds) { + ArrayList mas = new ArrayList(); + + for (MediaAsset ma : getMedia()) { + if (ma.hasFeatures(featureIds)) mas.add(ma); + ArrayList kids = ma.findChildren(myShepherd); // note: does not recurse, but... meh? + if ((kids == null) || (kids.size() < 1)) continue; + for (MediaAsset kma : kids) { + if (kma.hasFeatures(featureIds)) mas.add(kma); + } + } + return mas; + } + + // down-n-dirty with no myShepherd passed! :/ + public ArrayList findAllMediaByFeatureId(String[] featureIds) { + Shepherd myShepherd = new Shepherd("context0"); + + myShepherd.setAction("Encounter.class.findAllMediaByFeatureID"); + myShepherd.beginDBTransaction(); + ArrayList all = findAllMediaByFeatureId(myShepherd, featureIds); + myShepherd.rollbackDBTransaction(); + myShepherd.closeDBTransaction(); + return all; + } + + public ArrayList findAllMediaByLabel(Shepherd myShepherd, String label) { + return MediaAsset.findAllByLabel(getMedia(), myShepherd, label); + } + + public boolean hasKeyword(Keyword word) { + int imagesSize = images.size(); + + for (int i = 0; i < imagesSize; i++) { + SinglePhotoVideo image = images.get(i); + if (image.getKeywords().contains(word)) { return true; } + } + return false; + } + + public Set getMediaAssetKeywords() { + Set mak = new HashSet(); + + for (MediaAsset ma : this.getMedia()) { + ArrayList kws = ma.getKeywords(); + if (kws != null) mak.addAll(kws); + } + return mak; + } + + public String getState() { return state; } + + public void setState(String newState) { this.state = newState; } + + // DO NOT USE - LEGACY MIGRATION ONLY + /* + public boolean getApproved(){return approved;} + public boolean getUnidentifiable(){return unidentifiable;} + */ + public Vector getOldAdditionalImageNames() { return additionalImageNames; } + + public Double getLatitudeAsDouble() { return decimalLatitude; } + public Double getLongitudeAsDouble() { return decimalLongitude; } + + public boolean hasMeasurements() { + if ((measurements != null) && (measurements.size() > 0)) { + int numMeasurements = measurements.size(); + for (int i = 0; i < numMeasurements; i++) { + Measurement m = measurements.get(i); + if (m.getValue() != null) { return true; } + } + } + return false; + } + + public boolean hasMeasurement(String type) { + if ((measurements != null) && (measurements.size() > 0)) { + int numMeasurements = measurements.size(); + for (int i = 0; i < numMeasurements; i++) { + Measurement m = measurements.get(i); + if ((m.getValue() != null) && (m.getType().equals(type))) { return true; } + } + } + return false; + } + + public boolean hasBiologicalMeasurement(String type) { + if ((tissueSamples != null) && (tissueSamples.size() > 0)) { + int numTissueSamples = tissueSamples.size(); + for (int i = 0; i < numTissueSamples; i++) { + TissueSample ts = tissueSamples.get(i); + if (ts.getBiologicalMeasurement(type) != null) { + BiologicalMeasurement bm = ts.getBiologicalMeasurement(type); + if (bm.getValue() != null) { return true; } + } + } + } + return false; + } + + // Returns the first measurement of the specified type + public Measurement getMeasurement(String type) { + if ((measurements != null) && (measurements.size() > 0)) { + int numMeasurements = measurements.size(); + for (int i = 0; i < numMeasurements; i++) { + Measurement m = measurements.get(i); + if ((m.getValue() != null) && (m.getType().equals(type))) { return m; } + } + } + return null; + } + + public Map getBiologicalMeasurementsByType() { + Map meas = new HashMap(); + + for (MeasurementDesc mdesc : Util.findBiologicalMeasurementDescs("en", "context0")) { + BiologicalMeasurement bm = getBiologicalMeasurement(mdesc.getType()); + if (bm != null) meas.put(mdesc.getType(), bm); + } + return meas; + } + + public BiologicalMeasurement getBiologicalMeasurement(String type) { + if (tissueSamples != null) { + int numTissueSamples = tissueSamples.size(); + for (int y = 0; y < numTissueSamples; y++) { + TissueSample ts = tissueSamples.get(y); + if ((ts.getGeneticAnalyses() != null) && (ts.getGeneticAnalyses().size() > 0)) { + int numMeasurements = ts.getGeneticAnalyses().size(); + for (int i = 0; i < numMeasurements; i++) { + GeneticAnalysis m = ts.getGeneticAnalyses().get(i); + if (m.getAnalysisType().equals("BiologicalMeasurement")) { + BiologicalMeasurement f = (BiologicalMeasurement)m; + if ((f.getMeasurementType().equals(type)) && (f.getValue() != null)) { + return f; + } + } + } + } + } + } + return null; + } + + public String getCountry() { return country; } + + public void setCountry(String newCountry) { + if (newCountry != null) { country = newCountry; } else { country = null; } + } + + public void setOccurrenceID(String vet) { + if (vet != null) { this.occurrenceID = vet; } else { this.occurrenceID = null; } + } + + public String getOccurrenceID() { return occurrenceID; } + + public Occurrence getOccurrence(Shepherd myShepherd) { + return myShepherd.getOccurrence(this); + } + + public DateTime getOccurrenceDateTime(Shepherd myShepherd) { + Occurrence occ = this.getOccurrence(myShepherd); + + if (occ == null) return null; + return occ.getDateTime(); + } + + public boolean hasSinglePhotoVideoByFileName(String filename) { + int numImages = images.size(); + + for (int i = 0; i < numImages; i++) { + SinglePhotoVideo single = images.get(i); + if (single.getFilename().trim().toLowerCase().equals(filename.trim().toLowerCase())) { + return true; + } + } + return false; + } + + // convenience function to Collaboration permissions + public boolean canUserAccess(HttpServletRequest request) { + return Collaboration.canUserAccessEncounter(this, request); + } + + public boolean canUserAccess(User user, String context) { + if (user == null) return false; + // see comment below on canUserEdit(); substituting isUserOwner() now + // if (canUserEdit(user)) return true; + if (isUserOwner(user)) return true; + String username = user.getUsername(); + if (username == null) return false; + return Collaboration.canUserAccessEncounter(this, context, username); + } + + /* + this really is ugly cuz what is "view" vs "access", but i do NOT want to futz with canUserAccess() and + cause unintended consequences. so, for now, canUserView() is pretty much exclusively for search + */ + public boolean canUserView(User user, Shepherd myShepherd) { + return (user != null) && (user.isAdmin(myShepherd) || this.canUserAccess(user, + myShepherd.getContext())); + } + + // as part of 10.9, canUserEdit() was modified. it was not +/* + public boolean canUserEdit(User user) { + return isUserOwner(user); + } + */ + + // rewrite for 10.9 tries to actually do the right thing and (maybe) make sense + @Override public boolean canUserEdit(User user, Shepherd myShepherd) { + if (user == null) return false; + if (isUserOwner(user)) return true; + if (user.isAdmin(myShepherd)) return true; + if (Collaboration.canEditEncounter(this, user, myShepherd.getContext())) return true; + // TODO there seems to be some legacy stuff about roles based on location. is this real? + return false; + } + + public boolean isUserOwner(User user) { // the definition of this might change? + if (user == null) return false; + if ((submitters != null) && submitters.contains(user)) return true; + if ((submitterID != null) && submitterID.equals(user.getUsername())) return true; + return false; + } + + // new logic means we only need users who are in collab with submitting user + // and if public, we dont need to do this at all + public List userIdsWithViewAccess(Shepherd myShepherd) { + List ids = new ArrayList(); + + if (this.isPubliclyReadable()) return ids; + List collabs = Collaboration.collaborationsForUser(myShepherd, + this.getSubmitterID()); + for (Collaboration collab : collabs) { + User user = myShepherd.getUser(collab.getOtherUsername(this.getSubmitterID())); + if (user != null) ids.add(user.getId()); + } + return ids; + } + +/* + public List userIdsWithEditAccess(Shepherd myShepherd) { + List ids = new ArrayList(); + + for (User user : myShepherd.getUsersWithUsername()) { + if ((user.getId() != null) && this.canUserEdit(user)) ids.add(user.getId()); + } + return ids; + } + */ + public JSONObject sanitizeJson(HttpServletRequest request, JSONObject jobj) + throws JSONException { + boolean fullAccess = this.canUserAccess(request); + String useProjectContext = "false"; + + if (request.getParameter("useProjectContext") != null) { + useProjectContext = request.getParameter("useProjectContext"); + } + if (fullAccess) { + if (this.individual != null) { + jobj.put("individualID", this.individual.getIndividualID()); + if ("true".equals(useProjectContext)) { + jobj.put("displayName", this.individual.getDisplayName(request)); + } else { + jobj.put("displayName", this.individual.getDisplayName()); + } + } + return jobj; + } + jobj.remove("gpsLatitude"); + jobj.remove("location"); + jobj.remove("gpsLongitude"); + jobj.remove("verbatimLocality"); + jobj.remove("locationID"); + jobj.remove("gpsLongitude"); + jobj.remove("genus"); + jobj.remove("specificEpithet"); + jobj.put("_sanitized", true); + + return jobj; + } + + public JSONObject decorateJsonNoAnnots(HttpServletRequest request, JSONObject jobj) + throws JSONException { + jobj.put("location", this.getLocation()); + // these are for convenience, like .hasImages above (for use in table building e.g.) + if ((this.getTissueSamples() != null) && (this.getTissueSamples().size() > 0)) + jobj.put("hasTissueSamples", true); + if (this.hasMeasurements()) jobj.put("hasMeasurements", true); + return jobj; + } + + public JSONObject decorateJson(HttpServletRequest request, JSONObject jobj) + throws JSONException { + jobj = decorateJsonNoAnnots(request, jobj); + + jobj.put("_imagesNote", + ".images have been deprecated! long live MediaAssets! (see: .annotations)"); + + boolean fullAccess = this.canUserAccess(request); + if ((this.getAnnotations() != null) && (this.getAnnotations().size() > 0)) { + jobj.put("hasAnnotations", true); + JSONArray jarr = new JSONArray(); + for (Annotation ann : this.getAnnotations()) { + jarr.put(ann.sanitizeJson(request, fullAccess)); + } + jobj.put("annotations", jarr); + } + return jobj; + } + + public JSONObject uiJson(HttpServletRequest request) + throws JSONException { + JSONObject jobj = new JSONObject(); + + jobj.put("individualID", this.getIndividualID()); + jobj.put("url", this.getUrl(request)); + jobj.put("year", this.getYear()); + jobj.put("month", this.getMonth()); + jobj.put("day", this.getDay()); + jobj.put("gpsLatitude", this.getGPSLatitude()); + jobj.put("gpsLongitude", this.getGPSLongitude()); + jobj.put("location", this.getLocation()); + jobj.put("locationID", this.getLocationID()); + + jobj = sanitizeJson(request, jobj); + // we don't want annotations, which are added by sanitizeJson + jobj.remove("annotations"); + return jobj; + } + + public String getUrl(HttpServletRequest request) { + return request.getScheme() + "://" + CommonConfiguration.getURLLocation(request) + + "/encounters/encounter.jsp?number=" + this.getCatalogNumber(); + } + + /** + * returns an array of the MediaAsset sanitized JSON, because whenever UI queries our DB (regardless of class query), all they want in return are + * MediaAssets TODO: decorate with metadata + **/ + public org.datanucleus.api.rest.orgjson.JSONArray sanitizeMedia(HttpServletRequest request) + throws org.datanucleus.api.rest.orgjson.JSONException { + org.datanucleus.api.rest.orgjson.JSONArray jarr = + new org.datanucleus.api.rest.orgjson.JSONArray(); + boolean fullAccess = this.canUserAccess(request); + if ((this.getAnnotations() != null) && (this.getAnnotations().size() > 0)) { + for (Annotation ann : this.getAnnotations()) { + jarr.put(ann.sanitizeMedia(request, fullAccess)); + } + } + return jarr; + } + + // this simple version makes some assumptions: you already have list of collabs, and it is not visible + public String collaborationLockHtml(List collabs) { + Collaboration c = Collaboration.findCollaborationWithUser(this.getAssignedUsername(), + collabs); + String collabClass = "pending"; + + if ((c == null) || (c.getState() == null)) { + collabClass = "new"; + } else if (c.getState().equals(Collaboration.STATE_REJECTED)) { + collabClass = "blocked"; + } + return "
     
    "; + } + + // pass in a Vector of Encounters, get out a list that the user can NOT see + public static Vector blocked(Vector encs, HttpServletRequest request) { + Vector blk = new Vector(); + + for (int i = 0; i < encs.size(); i++) { + Encounter e = (Encounter)encs.get(i); + if (!e.canUserAccess(request)) blk.add(e); + } + return blk; + } + +/* + in short, this rebuilds (or builds for the first time) ALL *derived* images (etc?) for this encounter. + it is a baby step into the future of MediaAssets that hopefully will provide a smooth(er) transition to that. + right now its primary purpose is to create derived formats upon encounter creation; but that is obviously subject to change. + it should be considered an asyncronous action that happens in the background magickally + */ +/////other possiblity: only pass basedir??? do we need context if we do that? + + public boolean refreshAssetFormats(Shepherd myShepherd) { + ArrayList mas = this.getMedia(); + + if ((mas == null) || (mas.size() < 1)) return true; + for (MediaAsset ma : mas) { + ma.updateStandardChildren(myShepherd); + } + return true; + } + +/* + NOTE on "thumb.jpg" ... we only get one of these per encounter; and we do not have stored (i dont think?) which SPV it came from! + this is a problem, as we cant make a thumb in refreshAssetFormats(req, spv) since we dont know if that is the "right" spv. + thus, we have to treat it as a special case. + */ + // see also: future, MediaAssets + public String getThumbnailUrl(String context) { + MediaAsset ma = getPrimaryMediaAsset(); + + if (ma == null) return null; + String url = null; + Shepherd myShepherd = new Shepherd(context); + myShepherd.setAction("Encounter.class.getThumbnailUrl"); + myShepherd.beginDBTransaction(); + ArrayList kids = ma.findChildrenByLabel(myShepherd, "_thumb"); + if ((kids == null) || (kids.size() <= 0)) { + myShepherd.rollbackDBTransaction(); + myShepherd.closeDBTransaction(); + return null; + } + ma = kids.get(0); + if (ma.webURL() == null) { + myShepherd.rollbackDBTransaction(); + myShepherd.closeDBTransaction(); + return null; + } + url = ma.webURL().toString(); + myShepherd.rollbackDBTransaction(); + myShepherd.closeDBTransaction(); + return url; + } + + // this probably needs a better name and should allow for something more like an ordered list; that said, + // knowing we can always try to get THE ONE is probably useful too + public MediaAsset getPrimaryMediaAsset() { + ArrayList mas = getMedia(); + + if (mas.size() < 1) return null; + // here we could walk thru and find keywords, for example + return mas.get(0); + } + + public boolean restAccess(HttpServletRequest request, org.json.JSONObject jsonobj) + throws Exception { + ApiAccess access = new ApiAccess(); + + System.out.println("hello i am in restAccess() on Encounter"); + + String fail = access.checkRequest(this, request, jsonobj); + System.out.println("fail -----> " + fail); + if (fail != null) throw new Exception(fail); + return true; + } + +///////// this is bunk now: see fix for findAllByMediaAsset() if you need this + public static Encounter findByMediaAsset(MediaAsset ma, Shepherd myShepherd) { + String queryString = + "SELECT FROM org.ecocean.Encounter WHERE annotations.contains(ann) && ann.mediaAsset.id ==" + + ma.getId(); + Encounter returnEnc = null; + Query query = myShepherd.getPM().newQuery(queryString); + List results = (List)query.execute(); + + if ((results != null) && (results.size() >= 1)) { + returnEnc = (Encounter)results.get(0); + } + query.closeAll(); + return returnEnc; + } + + public static List findAllByMediaAsset(MediaAsset ma, Shepherd myShepherd) { + List returnEncs = new ArrayList(); + + try { + String queryString = + "SELECT FROM org.ecocean.Encounter WHERE annotations.contains(ann) && ann.features.contains(feat) && mediaAsset.features.contains(feat) && mediaAsset.id ==" + + ma.getId() + + " VARIABLES org.ecocean.media.MediaAsset mediaAsset; org.ecocean.Annotation ann; org.ecocean.media.Feature feat"; + Query query = myShepherd.getPM().newQuery(queryString); + Collection results = (Collection)query.execute(); + returnEncs = new ArrayList(results); + query.closeAll(); + } catch (Exception e) {} + return returnEncs; + } + + public String getPrefixForLocationID() { // convenience function + return LocationID.getPrefixForLocationID(this.getLocationID(), null); + } + + public int getPrefixDigitPaddingForLocationID() { // convenience function + return LocationID.getPrefixDigitPaddingForLocationID(this.getLocationID(), null); + } + + public static Encounter findByAnnotation(Annotation annot, Shepherd myShepherd) { + String queryString = + "SELECT FROM org.ecocean.Encounter WHERE annotations.contains(ann) && ann.id =='" + + annot.getId() + "'"; + Encounter returnEnc = null; + Query query = myShepherd.getPM().newQuery(queryString); + List results = (List)query.execute(); + + if ((results != null) && (results.size() >= 1)) { + if (results.size() > 1) + System.out.println("WARNING: Encounter.findByAnnotation() found " + results.size() + + " Encounters that contain Annotation " + annot.getId()); + returnEnc = (Encounter)results.get(0); + } + query.closeAll(); + return returnEnc; + } + + public static Encounter findByAnnotationId(String annid, Shepherd myShepherd) { + Annotation ann = ((Annotation)(myShepherd.getPM().getObjectById( + myShepherd.getPM().newObjectIdInstance(Annotation.class, annid), true))); + + if (ann == null) return null; + return findByAnnotation(ann, myShepherd); + } + + public static ArrayList getEncountersForMatching(String taxonomyString, + Shepherd myShepherd) { + if (_matchEncounterCache.get(taxonomyString) != null) + return _matchEncounterCache.get(taxonomyString); + ArrayList encs = new ArrayList(); + String queryString = "SELECT FROM org.ecocean.media.MediaAsset WHERE !features.isEmpty()"; + Query query = myShepherd.getPM().newQuery(queryString); + List results = (List)query.execute(); + for (int i = 0; i < results.size(); i++) { + MediaAsset ma = (MediaAsset)results.get(i); + MediaAsset top = ma.getParentRoot(myShepherd); + if (top == null) continue; + Encounter enc = Encounter.findByMediaAsset(top, myShepherd); + if (enc == null) System.out.println("could not find enc for ma " + ma); + if (enc == null) continue; + if (!enc.getTaxonomyString().equals(taxonomyString)) continue; + if (!encs.contains(enc)) encs.add(enc); + } + query.closeAll(); + _matchEncounterCache.put(taxonomyString, encs); + return encs; + } + +/* + this section are intentionally hacky backwards-compatible ways to get spots on an encounter in the new world of Features/Annotations/MediaAssets + ... do not use these, of course... and SOON we must weed out all the encounter-based-spot calls from everywhere and clean all this mess up! + */ + public ArrayList HACKgetSpots() { + return HACKgetAnySpots("spotsLeft"); + } + + public ArrayList HACKgetRightSpots() { + return HACKgetAnySpots("spotsRight"); + } + + public ArrayList HACKgetAnySpots(String which) { + ArrayList mas = findAllMediaByFeatureId( + new String[] { "org.ecocean.flukeEdge.edgeSpots", "org.ecocean.dorsalEdge.edgeSpots" }); + + if ((mas == null) || (mas.size() < 1)) return new ArrayList(); + for (Feature f : mas.get(0).getFeatures()) { + if (f.isType("org.ecocean.flukeEdge.edgeSpots") || + f.isType("org.ecocean.dorsalEdge.edgeSpots")) { + if (f.getParameters() != null) + return SuperSpot.listFromJSONArray(f.getParameters().optJSONArray(which)); + } + } + return new ArrayList(); + } + + // err, i think ref spots are the same right or left.... at least for flukes/dorsals. :/ good luck with mantas and whalesharks! + public ArrayList HACKgetAnyReferenceSpots() { + ArrayList mas = findAllMediaByFeatureId( + new String[] { "org.ecocean.flukeEdge.referenceSpots", + "org.ecocean.referenceEdge.edgeSpots" }); + + if ((mas == null) || (mas.size() < 1)) return new ArrayList(); + for (Feature f : mas.get(0).getFeatures()) { + if (f.isType("org.ecocean.flukeEdge.referenceSpots") || + f.isType("org.ecocean.dorsalEdge.referenceSpots")) { + if (f.getParameters() != null) + return SuperSpot.listFromJSONArray(f.getParameters().optJSONArray("spots")); + } + } + return new ArrayList(); + } + + // note this sets some things (e.g. species) which might (should!) need to be adjusted after, e.g. with setSpeciesFromAnnotations() + public Encounter cloneWithoutAnnotations(Shepherd myShepherd) { + Encounter enc = new Encounter(this.day, this.month, this.year, this.hour, this.minutes, + this.size_guess, this.verbatimLocality); + + enc.setCatalogNumber(Util.generateUUID()); + System.out.println("NOTE: cloneWithoutAnnotations(" + this.catalogNumber + ") -> " + + enc.getCatalogNumber()); + enc.setGenus(this.getGenus()); + enc.setSpecificEpithet(this.getSpecificEpithet()); + enc.setDecimalLatitude(this.getDecimalLatitudeAsDouble()); + enc.setDecimalLongitude(this.getDecimalLongitudeAsDouble()); + // just going to go ahead and go nuts here and copy most "logical"(?) things. reset on clone if needed + enc.setSubmitterID(this.getSubmitterID()); + enc.setSubmitters(this.submitters); + enc.setPhotographers(this.photographers); + enc.setSex(this.getSex()); + enc.setLocationID(this.getLocationID()); + enc.setVerbatimLocality(this.getVerbatimLocality()); + if (this.getCountry() != null && !"".equals(this.getCountry())) { + enc.setCountry(this.getCountry()); + } + Occurrence occ = myShepherd.getOccurrence(this); + if (occ != null) { + occ.addEncounter(enc); + enc.setOccurrenceID(occ.getOccurrenceID()); + } + // WB-1949: clone into same projects too + ArrayList projects = myShepherd.getAllProjectsForEncounter(this); + if (projects != null) { + for (Project proj : projects) { + proj.addEncounter(enc); + } + } + enc.setRecordedBy(this.getRecordedBy()); + enc.setState(this.getState()); // not too sure about this one? + + enc.setAlternateID(this.getAlternateID()); + enc.setOccurrenceRemarks(this.getOccurrenceRemarks()); + enc.addComments("NOTE: cloneWithoutAnnotations(" + this.catalogNumber + ") -> " + + enc.getCatalogNumber()); + + ImportTask itask = getImportTask(myShepherd); + if (itask != null) itask.addEncounter(enc); + return enc; + } + + // for convenience + public ImportTask getImportTask(Shepherd myShepherd) { + return myShepherd.getImportTaskForEncounter(this); + } + + // this is a special state only used now for match.jsp but basically means the data should be mostly hidden and soon deleted, roughly speaking??? + // TODO: figure out what this really means + public void setMatchingOnly() { + this.setState(STATE_MATCHING_ONLY); + } + + // ann is the Annotation that was created after IA detection. mostly this is just to notify... someone + // note: this is for singly-made encounters; see also Occurrence.fromDetection() + public void detectedAnnotation(Shepherd myShepherd, Annotation ann) { + System.out.println(">>>>> detectedAnnotation() on " + this); + } + + /* + note: these are baby steps into proper ownership of Encounters. a similar (but cleaner) attempt is done in MediaAssets... however, really this + probably should be upon some (mythical) BASE CLASS!!!! ... for now, this Encounter variation kinda fudges with existing "ownership" stuff, + namely, the submitterID - which maps (in theory!) to a User username. TODO: much much much ... incl call via constructor maybe ?? etc. + */ + // NOTE: not going to currently persist the AccessControl object yet, but create on the fly... clever? stupid? + public AccessControl getAccessControl() { + if ((submitterID == null) || submitterID.equals("")) return new AccessControl(); // not sure if we really have some "" but lets be safe + return new AccessControl(submitterID); + } + + public void setAccessControl(HttpServletRequest request) { // really just setting submitterID duh + this.submitterID = AccessControl.simpleUserString(request); // null if anon + } + + public String toString() { + return new ToStringBuilder(this) + .append("catalogNumber", catalogNumber) + .append("individualID", (hasMarkedIndividual() ? individual.getId() : null)) + .append("species", getTaxonomyString()) + .append("sex", getSex()) + .append("shortDate", getShortDate()) + .append("numAnnotations", ((annotations == null) ? 0 : annotations.size())) + .toString(); + } + + public boolean hasMediaFromAssetStoreType(AssetStoreType aType) { + System.out.println("Entering Encounter.hasMediaFromAssetStoreType"); + if (getMediaAssetsOfType(aType).size() > 0) { return true; } + return false; + } + + public ArrayList getMediaAssetsOfType(AssetStoreType aType) { + System.out.println("Entering Encounter.getMediaAssetsOfType"); + ArrayList results = new ArrayList(); + try { + ArrayList assets = getMedia(); + int numAssets = assets.size(); + for (int i = 0; i < numAssets; i++) { + MediaAsset ma = assets.get(i); + if (ma.getStore().getType() == aType) { results.add(ma); } + } + } catch (Exception e) { e.printStackTrace(); } + System.out.println("Exiting Encounter.getMediaAssetsOfType with this num results: " + + results.size()); + return results; + } + + public void setObservationArrayList(ArrayList obs) { + this.observations = obs; + } + + public ArrayList getObservationArrayList() { + return observations; + } + + public void addObservationArrayList(ArrayList arr) { + if (observations.isEmpty()) { + observations = arr; + } else { + observations.addAll(arr); + } + } + + public void addObservation(Observation obs) { + boolean found = false; + + // System.out.println("Adding Observation in Base Class... : "+obs.toString()); + if (observations != null && observations.size() > 0) { + for (Observation ob : observations) { + if (ob.getName() != null) { + if (ob.getName().toLowerCase().trim().equals( + obs.getName().toLowerCase().trim())) { + found = true; + break; + } + } + } + if (!found) { + observations.add(obs); + } + } else { + observations.add(obs); + } + } + + public Observation getObservationByName(String obName) { + if (observations != null && observations.size() > 0) { + for (Observation ob : observations) { + if (ob.getName() != null) { + if (ob.getName().toLowerCase().trim().equals(obName.toLowerCase().trim())) { + return ob; + } + } + } + } + return null; + } + + public Observation getObservationByID(String obId) { + if (observations != null && observations.size() > 0) { + for (Observation ob : observations) { + if (ob.getID() != null && ob.getID().equals(obId)) { + return ob; + } + } + } + return null; + } + + public void removeObservation(String name) { + int counter = 0; + + if (observations != null && observations.size() > 0) { + System.out.println("Looking for the Observation to delete..."); + for (Observation ob : observations) { + if (ob.getName() != null) { + if (ob.getName().toLowerCase().trim().equals(name.toLowerCase().trim())) { + System.out.println("Match! Trying to delete Observation " + name + + " at index " + counter); + observations.remove(counter); + break; + } + } + counter++; + } + } + } + + public List getSubmitters() { + return submitters; + } + + public List getInformOthers() { + return informOthers; + } + + public List getSubmitterEmails() { + ArrayList listy = new ArrayList(); + ArrayList subs = new ArrayList(); + + if (getSubmitters() != null) subs.addAll(getSubmitters()); + int numUsers = subs.size(); + for (int k = 0; k < numUsers; k++) { + User use = subs.get(k); + if ((use.getEmailAddress() != null) && (!use.getEmailAddress().trim().equals(""))) { + listy.add(use.getEmailAddress()); + } + } + return listy; + } + + public List getHashedSubmitterEmails() { + ArrayList listy = new ArrayList(); + ArrayList subs = new ArrayList(); + + if (getSubmitters() != null) subs.addAll(getSubmitters()); + int numUsers = subs.size(); + for (int k = 0; k < numUsers; k++) { + User use = subs.get(k); + if ((use.getHashedEmailAddress() != null) && + (!use.getHashedEmailAddress().trim().equals(""))) { + listy.add(use.getHashedEmailAddress()); + } + } + return listy; + } + + public List getPhotographers() { + return photographers; + } + + public List getPhotographerEmails() { + ArrayList listy = new ArrayList(); + ArrayList subs = new ArrayList(); + + if (getPhotographers() != null) subs.addAll(getPhotographers()); + int numUsers = subs.size(); + for (int k = 0; k < numUsers; k++) { + User use = subs.get(k); + if ((use.getEmailAddress() != null) && (!use.getEmailAddress().trim().equals(""))) { + listy.add(use.getEmailAddress()); + } + } + return listy; + } + + public List getInformOthersEmails() { + ArrayList listy = new ArrayList(); + ArrayList subs = new ArrayList(); + + if (getInformOthers() != null) subs.addAll(getInformOthers()); + int numUsers = subs.size(); + for (int k = 0; k < numUsers; k++) { + User use = subs.get(k); + if ((use.getEmailAddress() != null) && (!use.getEmailAddress().trim().equals(""))) { + listy.add(use.getEmailAddress()); + } + } + return listy; + } + + public List getHashedPhotographerEmails() { + ArrayList listy = new ArrayList(); + ArrayList subs = new ArrayList(); + + if (getPhotographers() != null) subs.addAll(getPhotographers()); + int numUsers = subs.size(); + for (int k = 0; k < numUsers; k++) { + User use = subs.get(k); + if ((use.getHashedEmailAddress() != null) && + (!use.getHashedEmailAddress().trim().equals(""))) { + listy.add(use.getHashedEmailAddress()); + } + } + return listy; + } + + public void addSubmitter(User user) { + if (user == null) return; + if (submitters == null) submitters = new ArrayList(); + if (!submitters.contains(user)) submitters.add(user); + } + + public void removeSubmitter(User user) { + if ((user == null) || (submitters == null)) return; + submitters.remove(user); + } + + public void addPhotographer(User user) { + if (user == null) return; + if (photographers == null) photographers = new ArrayList(); + if (!photographers.contains(user)) photographers.add(user); + } + + public void setSubmitters(List submitters) { + if (submitters == null) { this.submitters = null; } else { + this.submitters = submitters; + } + } + + public void setPhotographers(List photographers) { + if (photographers == null) { this.photographers = null; } else { + this.photographers = photographers; + } + } + + public void removePhotographer(User user) { + if ((user == null) || (photographers == null)) return; + photographers.remove(user); + } + + public void addInformOther(User user) { + if (user == null) return; + if (informOthers == null) informOthers = new ArrayList(); + if (!informOthers.contains(user)) informOthers.add(user); + } + + public void setInformOthers(List users) { + if (users == null) { this.informOthers = null; } else { + this.informOthers = users; + } + } + + public void removeInformOther(User user) { + if ((user == null) || (informOthers == null)) return; + informOthers.remove(user); + } + + public static List getIndividualIDs(Collection encs) { + Set idSet = new HashSet(); + + for (Encounter enc : encs) { + if (enc.hasMarkedIndividual()) idSet.add(enc.getIndividualID()); + } + return Util.asSortedList(idSet); + } + + public void refreshAnnotationLiteTaxonomy() { + if (!this.hasAnnotations()) return; + String tax = this.getTaxonomyString(); + for (Annotation ann : this.annotations) { + ann.refreshLiteTaxonomy(tax); + } + } + + public void refreshAnnotationLiteIndividual() { + if (!this.hasAnnotations()) return; + String indivId = "____"; + if (this.individual != null) indivId = this.individual.getIndividualID(); + for (Annotation ann : this.annotations) { + ann.refreshLiteIndividual(indivId); + } + } + + public int hashCode() { // we need this along with equals() for collections methods (contains etc) to work!! + if (this.getCatalogNumber() == null) return Util.generateUUID().hashCode(); // random(ish) so we dont get two identical for null values + return this.getCatalogNumber().hashCode(); + } + + // sadly, this mess needs to carry on the tradition set up in User.isUsernameAnonymous() + // thanks to the logic in Collaboration.canUserAccessOwnedObject() + public boolean isPubliclyReadable() { + if (!Collaboration.securityEnabled("context0")) return true; + return User.isUsernameAnonymous(this.submitterID); + } + + public boolean getOpensearchProcessPermissions() { + return opensearchProcessPermissions; + } + + public void setOpensearchProcessPermissions(boolean value) { + opensearchProcessPermissions = value; + } + + // wrapper for below, that checks if we really need to be run + public static void opensearchIndexPermissionsBackground(Shepherd myShepherd) { + boolean runIt = false; + Long lastRun = OpenSearch.getPermissionsTimestamp(myShepherd); + long now = System.currentTimeMillis(); + + if ((lastRun == null) || + ((now - lastRun) > OpenSearch.BACKGROUND_PERMISSIONS_MAX_FORCE_MINUTES * 60000)) { + System.out.println( + "opensearchIndexPermissionsBackground: forced run due to max time since previous"); + runIt = true; + } + boolean needed = OpenSearch.getPermissionsNeeded(myShepherd); + if (needed && !runIt) { + System.out.println("opensearchIndexPermissionsBackground: running due to needed=true"); + runIt = true; + } + if (!runIt) { + System.out.println("opensearchIndexPermissionsBackground: running not required; done"); + return; + } + // i think we should set these first... tho they may not get persisted til after? + OpenSearch.setPermissionsTimestamp(myShepherd); + OpenSearch.setPermissionsNeeded(myShepherd, false); + opensearchIndexPermissions(); + System.out.println("opensearchIndexPermissionsBackground: running completed"); + } + +/* note: there are a great deal of users with *no username* that seem to appear in enc.submitters array. + however, very few (2 out of 5600+) encounters with such .submitters have a blank submitterID value + therefore: submitterID will be assumed to be a required value on users which need to be + + this seems further validated by the facts that: + - canUserAccess(user) returns false if no username on user + - a user wihtout a username cant be logged in (and thus cant search) + + "admin" users are just ignored entirely, as they will be exempt from the viewUsers criteria during searching. + + other than "ownership" (via submitterID), a user can view if they have view or edit collab with + another user. so we frontload *approved* collabs for every user here too. + + in terms of "public" encounters, it seems that (based on Collaboration.canUserAccessEncounter()), + encounters with submitterID in (NULL, "public", "", "N/A" [ugh]) is readable by anyone; so we will + skip these from processing as they should be flagged with the boolean isPubliclyReadable in indexing + */ + public static void opensearchIndexPermissions() { + Util.mark("perm start"); + long startT = System.currentTimeMillis(); + System.out.println("opensearchIndexPermissions(): begin..."); + // no security => everything publiclyReadable - saves us work, no? + if (!Collaboration.securityEnabled("context0")) return; + OpenSearch os = new OpenSearch(); + Map > collab = new HashMap >(); + Map usernameToId = new HashMap(); + + // PHASE 1: load all DB data we need into in-memory structures, then close the Shepherd. + // The per-encounter OpenSearch HTTP calls in PHASE 2 below were previously made while + // this Shepherd's Postgres connection was still pinned, which on installs with hundreds + // of thousands of encounters could starve the JDO connection pool for tens of minutes + // and cause every concurrent request to queue at "begin" on dbconnections.jsp. + List encounterRows = new ArrayList(); + Shepherd myShepherd = new Shepherd("context0"); + myShepherd.setAction("Encounter.opensearchIndexPermissions"); + myShepherd.beginDBTransaction(); + try { + // it seems as though user.uuid is *required* so we can trust that + for (User user : myShepherd.getUsersWithUsername()) { + usernameToId.put(user.getUsername(), user.getId()); + List collabsFor = Collaboration.collaborationsForUser(myShepherd, + user.getUsername()); + if (Util.collectionIsEmptyOrNull(collabsFor)) continue; + for (Collaboration col : collabsFor) { + if (!col.isApproved() && !col.isEditApproved()) continue; + if (!collab.containsKey(user.getId())) + collab.put(user.getId(), new HashSet()); + collab.get(user.getId()).add(col.getOtherUsername(user.getUsername())); + } + } + Util.mark("perm: user build done", startT); + System.out.println("opensearchIndexPermissions(): " + usernameToId.size() + + " total users; " + collab.size() + " have active collab"); + + // we do not need full Encounter objects here to update index docs, so lets do this via sql/fields - much faster + String sql = + "SELECT \"CATALOGNUMBER\", \"SUBMITTERID\" FROM \"ENCOUNTER\" WHERE \"SUBMITTERID\" IS NOT NULL AND \"SUBMITTERID\" != '' AND \"SUBMITTERID\" != 'N/A' AND \"SUBMITTERID\" != 'public'"; + Query q = null; + try { + q = myShepherd.getPM().newQuery("javax.jdo.query.SQL", sql); + List results = (List)q.execute(); + Util.mark("perm: loading encs into memory, size=" + results.size(), startT); + Iterator it = results.iterator(); + while (it.hasNext()) { + Object[] row = (Object[])it.next(); + encounterRows.add(new String[] { (String)row[0], (String)row[1] }); + } + } finally { + if (q != null) q.closeAll(); + } + } catch (Exception ex) { + System.out.println( + "opensearchIndexPermissions(): failed during DB load phase: " + ex); + ex.printStackTrace(); + } finally { + myShepherd.rollbackAndClose(); + } + Util.mark("perm: DB load done; shepherd closed", startT); + + // PHASE 2: iterate the in-memory rows and update OpenSearch (no DB connection held). + int encCount = 0; + for (String[] row : encounterRows) { + String id = row[0]; + String submitterId = row[1]; + String uid = usernameToId.get(submitterId); + if (uid == null) { + // see issue 939 for example :( + System.out.println("opensearchIndexPermissions(): WARNING invalid username " + + submitterId + " on enc " + id); + continue; + } + encCount++; + if (encCount % 1000 == 0) Util.mark("enc[" + encCount + "]", startT); + + // ask the question, who else can see this encounter via collaboration? + org.json.JSONArray viewUsers = new org.json.JSONArray(); + for (Map.Entry > entry : collab.entrySet()) { + if (entry.getValue().contains(submitterId)) { + viewUsers.put(entry.getKey()); + } + } + if (viewUsers.length() > 0) { + org.json.JSONObject updateData = new org.json.JSONObject(); + updateData.put("viewUsers", viewUsers); + try { + os.indexUpdate("encounter", id, updateData); + } catch (Exception ex) { + // keeping this quiet cuz it can get noise while index builds + } + } + } + Util.mark("perm: done encs", startT); + System.out.println("opensearchIndexPermissions(): ...end [" + encCount + " encs; " + + Math.round((System.currentTimeMillis() - startT) / 1000) + "sec]"); + } + + public static org.json.JSONObject opensearchQuery(final org.json.JSONObject query, int numFrom, + int pageSize, String sort, String sortOrder) + throws IOException { + return Base.opensearchQuery("encounter", query, numFrom, pageSize, sort, sortOrder); + } + + public void opensearchDocumentSerializer(JsonGenerator jgen) + throws IOException, JsonProcessingException { + Shepherd myShepherd = new Shepherd("context0"); + + myShepherd.setAction("Encounter.opensearchDocumentSerializer"); + myShepherd.beginDBTransaction(); + try { + opensearchDocumentSerializer(jgen, myShepherd); + } catch (Exception ex) { + ex.printStackTrace(); + } finally { + myShepherd.rollbackAndClose(); + } + } + + public void opensearchDocumentSerializer(JsonGenerator jgen, Shepherd myShepherd) + throws IOException, JsonProcessingException { + super.opensearchDocumentSerializer(jgen, myShepherd); + + jgen.writeStringField("locationId", this.getLocationID()); + jgen.writeStringField("locationName", this.getLocationName()); + Long dim = this.getDateInMillisecondsFallback(); + if (dim != null) jgen.writeNumberField("dateMillis", dim); + String date = Util.getISO8601Date(this.getDate()); + if (date != null) jgen.writeStringField("date", date); + date = Util.getISO8601Date(this.getDWCDateAdded()); + if (date != null) jgen.writeStringField("dateSubmitted", date); + jgen.writeStringField("verbatimEventDate", this.getVerbatimEventDate()); + jgen.writeStringField("sex", this.getSex()); + jgen.writeStringField("taxonomy", this.getTaxonomyString()); + jgen.writeStringField("lifeStage", this.getLifeStage()); + jgen.writeStringField("livingStatus", this.getLivingStatus()); + jgen.writeStringField("verbatimLocality", this.getVerbatimLocality()); + jgen.writeStringField("country", this.getCountry()); + jgen.writeStringField("behavior", this.getBehavior()); + jgen.writeStringField("patterningCode", this.getPatterningCode()); + jgen.writeStringField("state", this.getState()); + jgen.writeStringField("occurrenceRemarks", this.getOccurrenceRemarks()); + jgen.writeStringField("otherCatalogNumbers", this.getOtherCatalogNumbers()); + jgen.writeBooleanField("publiclyReadable", this.isPubliclyReadable()); + jgen.writeStringField("distinguishingScar", this.getDistinguishingScar()); + String featuredAssetId = null; + List mas = this.getMedia(); + jgen.writeNumberField("numberAnnotations", this.numNonTrivialAnnotations()); + jgen.writeNumberField("numberMediaAssets", mas.size()); + jgen.writeArrayFieldStart("mediaAssets"); + for (MediaAsset ma : mas) { + jgen.writeStartObject(); + jgen.writeNumberField("id", ma.getIdInt()); + jgen.writeStringField("uuid", ma.getUUID()); + jgen.writeNumberField("width", ma.getWidth()); + jgen.writeNumberField("height", ma.getHeight()); + jgen.writeStringField("mimeTypeMajor", ma.getMimeTypeMajor()); + jgen.writeStringField("mimeTypeMinor", ma.getMimeTypeMinor()); + try { + // historic data might throw IllegalArgumentException: Path not under given root + URL url = ma.safeURL(myShepherd, null, "master"); + if (url != null) jgen.writeStringField("url", url.toString()); + } catch (Exception ex) {} + // we (likely) dont need annotations to search on, but they are needed for + // many of the usages (export, gallery, etc) of search *results* + jgen.writeArrayFieldStart("annotations"); + if (ma.hasAnnotations()) + for (Annotation ann : ma.getAnnotations()) { + jgen.writeStartObject(); + jgen.writeStringField("id", ann.getId()); + jgen.writeStringField("iaClass", ann.getIAClass()); + jgen.writeStringField("viewpoint", ann.getViewpoint()); + jgen.writeBooleanField("isTrivial", ann.isTrivial()); + jgen.writeNumberField("theta", ann.getTheta()); + jgen.writeArrayFieldStart("boundingBox"); + Feature ft = ann.getFeature(); // attempt force loading features for getBbox() + int[] bbox = ann.getBbox(); + if (bbox != null) + for (int i : bbox) { + jgen.writeNumber(i); + } + jgen.writeEndArray(); + Encounter annEnc = ann.findEncounter(myShepherd); + if (annEnc != null) jgen.writeStringField("encounterId", annEnc.getId()); + jgen.writeEndObject(); + } + jgen.writeEndArray(); + jgen.writeEndObject(); + if (featuredAssetId == null) featuredAssetId = ma.getUUID(); + } + jgen.writeEndArray(); + if (featuredAssetId != null) jgen.writeStringField("featuredAssetUuid", featuredAssetId); + if (this.submitterID == null) { + jgen.writeNullField("assignedUsername"); + } else { + jgen.writeStringField("assignedUsername", this.submitterID); + User submitter = this.getSubmitterUser(myShepherd); + if (submitter != null) jgen.writeStringField("submitterUserId", submitter.getId()); + } + jgen.writeArrayFieldStart("submitters"); + for (String id : this.getAllSubmitterIds(myShepherd)) { + jgen.writeString(id); + } + jgen.writeEndArray(); + jgen.writeArrayFieldStart("photographers"); + for (String id : this.getAllPhotographerIds()) { + jgen.writeString(id); + } + jgen.writeEndArray(); + jgen.writeArrayFieldStart("informOthers"); + for (String id : this.getAllInformOtherIds()) { + jgen.writeString(id); + } + jgen.writeEndArray(); + + List kws = new ArrayList(); + Map lkws = new HashMap(); + for (Keyword kw : this.getMediaAssetKeywords()) { + if (kw instanceof LabeledKeyword) { + LabeledKeyword lkw = (LabeledKeyword)kw; + lkws.put(lkw.getLabel(), lkw.getValue()); + } else { + String name = kw.getDisplayName(); + if (!kws.contains(name)) kws.add(name); + } + } + jgen.writeArrayFieldStart("mediaAssetKeywords"); + for (String kw : kws) { + jgen.writeString(kw); + } + jgen.writeEndArray(); + jgen.writeObjectFieldStart("mediaAssetLabeledKeywords"); + for (String kwLabel : lkws.keySet()) { + jgen.writeStringField(kwLabel, lkws.get(kwLabel)); + } + jgen.writeEndObject(); + + List projs = this.getProjects(myShepherd); + jgen.writeArrayFieldStart("projects"); + if (projs != null) + for (Project proj : projs) { + jgen.writeString(proj.getId()); + } + jgen.writeEndArray(); + + ImportTask itask = this.getImportTask(myShepherd); + if (itask != null) { + jgen.writeStringField("importTaskId", itask.getId()); + if (itask.getCreator() != null) + jgen.writeStringField("importTaskCreatorId", itask.getCreator().getId()); + String sourceName = itask.getSourceName(); + if (sourceName != null) + jgen.writeStringField("importTaskSourceName", sourceName); + } + jgen.writeArrayFieldStart("annotationViewpoints"); + for (String vp : this.getAnnotationViewpoints()) { + jgen.writeString(vp); + } + jgen.writeEndArray(); + + jgen.writeArrayFieldStart("annotationIAClasses"); + for (String cls : this.getAnnotationIAClasses()) { + jgen.writeString(cls); + } + jgen.writeEndArray(); + + jgen.writeArrayFieldStart("measurements"); + if (this.measurements != null) + for (Measurement meas : this.measurements) { + if (meas.getValue() == null) continue; // no value means we should skip + jgen.writeStartObject(); + jgen.writeNumberField("value", meas.getValue()); + if (meas.getType() != null) jgen.writeStringField("type", meas.getType()); + if (meas.getUnits() != null) jgen.writeStringField("units", meas.getUnits()); + if (meas.getSamplingProtocol() != null) + jgen.writeStringField("samplingProtocol", meas.getSamplingProtocol()); + jgen.writeEndObject(); + } + jgen.writeEndArray(); + + jgen.writeArrayFieldStart("metalTags"); + if (this.getMetalTags() != null) + for (MetalTag tag : this.getMetalTags()) { + jgen.writeStartObject(); + jgen.writeStringField("number", tag.getTagNumber()); + jgen.writeStringField("location", tag.getLocation()); + jgen.writeEndObject(); + } + jgen.writeEndArray(); + if (this.getAcousticTag() != null) { + jgen.writeObjectFieldStart("acousticTag"); + jgen.writeStringField("idNumber", this.getAcousticTag().getIdNumber()); + jgen.writeStringField("serialNumber", this.getAcousticTag().getSerialNumber()); + jgen.writeEndObject(); + } + if (this.getSatelliteTag() != null) { + jgen.writeObjectFieldStart("satelliteTag"); + jgen.writeStringField("name", this.getSatelliteTag().getName()); + jgen.writeStringField("serialNumber", this.getSatelliteTag().getSerialNumber()); + jgen.writeStringField("argosPttNumber", this.getSatelliteTag().getArgosPttNumber()); + jgen.writeEndObject(); + } + if (this.getDTag() != null) { + jgen.writeObjectFieldStart("digitalArchiveTag"); + jgen.writeStringField("dTagID", this.getDTag().getDTagID()); + jgen.writeStringField("serialNumber", this.getDTag().getSerialNumber()); + jgen.writeEndObject(); + } + org.json.JSONObject dpj = this.getDynamicPropertiesJSONObject(); + jgen.writeObjectFieldStart("dynamicProperties"); + for (String key : (Set)dpj.keySet()) { + jgen.writeStringField(key, dpj.optString(key, null)); + } + jgen.writeEndObject(); + + Double dlat = this.getDecimalLatitudeAsDouble(); + Double dlon = this.getDecimalLongitudeAsDouble(); + if ((dlat == null) || !Util.isValidDecimalLatitude(dlat) || (dlon == null) || + !Util.isValidDecimalLongitude(dlon)) { + jgen.writeNullField("locationGeoPoint"); + } else { + jgen.writeObjectFieldStart("locationGeoPoint"); + jgen.writeNumberField("lat", dlat); + jgen.writeNumberField("lon", dlon); + jgen.writeEndObject(); + } + MarkedIndividual indiv = this.getIndividual(); + if (indiv == null) { + jgen.writeNullField("individualId"); + } else { + jgen.writeStringField("individualId", indiv.getId()); + jgen.writeStringField("individualSex", indiv.getSex()); + jgen.writeStringField("individualTaxonomy", indiv.getTaxonomyString()); + jgen.writeNumberField("individualNumberEncounters", indiv.getNumEncounters()); + jgen.writeStringField("individualDisplayName", indiv.getDisplayName()); + jgen.writeArrayFieldStart("individualNames"); + Set names = indiv.getAllNamesList(); + if (names != null) + for (String name : names) { + jgen.writeString(name); + } + jgen.writeEndArray(); + jgen.writeStringField("individualNickName", indiv.getNickName()); + if (indiv.getTimeOfBirth() > 0) { + String birthTime = Util.getISO8601Date(new DateTime( + indiv.getTimeOfBirth()).toString()); + jgen.writeStringField("individualTimeOfBirth", birthTime); + } + if (indiv.getTimeOfDeath() > 0) { + String deathTime = Util.getISO8601Date(new DateTime( + indiv.getTimeOfDeath()).toString()); + jgen.writeStringField("individualTimeOfDeath", deathTime); + } + Encounter[] encs = indiv.getDateSortedEncounters(true); + if ((encs != null) && (encs.length > 0)) { + String encDate = Util.getISO8601Date(encs[0].getDate()); + if (encDate != null) jgen.writeStringField("individualFirstEncounterDate", encDate); + encDate = Util.getISO8601Date(encs[encs.length - 1].getDate()); + if (encDate != null) jgen.writeStringField("individualLastEncounterDate", encDate); + } + jgen.writeArrayFieldStart("individualSocialUnits"); + for (SocialUnit su : myShepherd.getAllSocialUnitsForMarkedIndividual(indiv)) { + Membership mem = su.getMembershipForMarkedIndividual(indiv); + if (mem != null) jgen.writeString(su.getSocialUnitName()); + } + jgen.writeEndArray(); + + jgen.writeArrayFieldStart("individualRelationshipRoles"); + for (String relRole : myShepherd.getAllRoleNamesForMarkedIndividual(indiv.getId())) { + jgen.writeString(relRole); + } + jgen.writeEndArray(); + } + DateTime occdt = getOccurrenceDateTime(myShepherd); + if (occdt != null) jgen.writeStringField("occurrenceDate", occdt.toString()); + jgen.writeStringField("geneticSex", this.getGeneticSex()); + jgen.writeStringField("haplotype", this.getHaplotype()); + + jgen.writeArrayFieldStart("microsatelliteMarkers"); + for (MicrosatelliteMarkersAnalysis msm : getMicrosatelliteMarkers()) { + jgen.writeStartObject(); + jgen.writeStringField("analysisId", msm.getAnalysisID()); + jgen.writeObjectFieldStart("loci"); + if (msm.getLoci() != null) + for (Locus locus : msm.getLoci()) { + if (locus.getName() == null) continue; // snh + jgen.writeObjectFieldStart(locus.getName()); + for (int i = 0; i < 4; i++) { + Integer allele = locus.getAllele(i); + if (allele != null) jgen.writeNumberField("allele" + i, allele); + } + jgen.writeEndObject(); + } + jgen.writeEndObject(); + jgen.writeEndObject(); + } + jgen.writeEndArray(); + + Occurrence occ = this.getOccurrence(myShepherd); + if (occ == null) { + jgen.writeNullField("occurrenceId"); + } else { + jgen.writeStringField("occurrenceId", occ.getId()); + jgen.writeStringField("occurrenceGroupBehavior", occ.getGroupBehavior()); + jgen.writeStringField("occurrenceGroupComposition", occ.getGroupComposition()); + jgen.writeStringField("occurrenceComments", occ.getComments()); + if (occ.getVisibilityIndex() != null) + jgen.writeNumberField("occurrenceVisibilityIndex", occ.getVisibilityIndex()); + if (occ.getIndividualCount() != null) + jgen.writeNumberField("occurrenceIndividualCount", occ.getIndividualCount()); + if (occ.getMinGroupSizeEstimate() != null) + jgen.writeNumberField("occurrenceMinGroupSizeEstimate", + occ.getMinGroupSizeEstimate()); + if (occ.getMaxGroupSizeEstimate() != null) + jgen.writeNumberField("occurrenceMaxGroupSizeEstimate", + occ.getMaxGroupSizeEstimate()); + if (occ.getBestGroupSizeEstimate() != null) + jgen.writeNumberField("occurrenceBestGroupSizeEstimate", + occ.getBestGroupSizeEstimate()); + if (occ.getBearing() != null) + jgen.writeNumberField("occurrenceBearing", occ.getBearing()); + if (occ.getDistance() != null) + jgen.writeNumberField("occurrenceDistance", occ.getDistance()); + Double odlat = occ.getDecimalLatitude(); + Double odlon = occ.getDecimalLongitude(); + if ((odlat == null) || !Util.isValidDecimalLatitude(odlat) || (odlon == null) || + !Util.isValidDecimalLongitude(odlon)) { + jgen.writeNullField("occurrenceLocationGeoPoint"); + } else { + jgen.writeObjectFieldStart("occurrenceLocationGeoPoint"); + jgen.writeNumberField("lat", odlat); + jgen.writeNumberField("lon", odlon); + jgen.writeEndObject(); + } + } + jgen.writeArrayFieldStart("organizations"); + User owner = this.getSubmitterUser(myShepherd); + if ((owner != null) && (owner.getOrganizations() != null)) + for (Organization org : owner.getOrganizations()) { + jgen.writeString(org.getId()); + } + jgen.writeEndArray(); + + jgen.writeArrayFieldStart("tissueSampleIds"); + for (String id : this.getTissueSampleIDs()) { + jgen.writeString(id); + } + jgen.writeEndArray(); + + Map bmeas = this.getBiologicalMeasurementsByType(); + jgen.writeObjectFieldStart("biologicalMeasurements"); + for (String type : (Set)bmeas.keySet()) { + jgen.writeNumberField(type, bmeas.get(type).getValue()); + } + jgen.writeEndObject(); + // this gets set on specific single-encounter-only actions, when extra expense is okay + // otherwise this will be computed by permissions backgrounding + if (this.getOpensearchProcessPermissions()) { + System.out.println("opensearchProcessPermissions=true for " + this.getId() + + "; indexing permissions"); + jgen.writeFieldName("viewUsers"); + jgen.writeStartArray(); + for (String id : this.userIdsWithViewAccess(myShepherd)) { + System.out.println("opensearch whhhh: " + id); + jgen.writeString(id); + } + jgen.writeEndArray(); + } + } + + public void opensearchIndexDeep() + throws IOException { + this.opensearchIndex(); + + final String encId = this.getId(); + ExecutorService executor = Executors.newFixedThreadPool(4); + Runnable rn = new Runnable() { + public void run() { + Shepherd bgShepherd = new Shepherd("context0"); + bgShepherd.setAction("Encounter.opensearchIndexDeep_" + encId); + bgShepherd.beginDBTransaction(); + try { + Encounter enc = bgShepherd.getEncounter(encId); + if ((enc == null) || (!enc.hasMarkedIndividual() && !enc.hasAnnotations())) { + // bgShepherd.rollbackAndClose(); + executor.shutdown(); + return; + } + MarkedIndividual indiv = enc.getIndividual(); + if (indiv != null) { + System.out.println("opensearchIndexDeep() background indexing indiv " + + indiv.getId() + " via enc " + encId); + try { + indiv.opensearchIndex(); + } catch (Exception ex) { + System.out.println("opensearchIndexDeep() background indexing " + + indiv.getId() + " FAILED: " + ex.toString()); + ex.printStackTrace(); + } + } + Occurrence occ = enc.getOccurrence(bgShepherd); + if (occ != null) { + System.out.println("opensearchIndexDeep() background indexing occ " + + occ.getId() + " via enc " + encId); + try { + occ.opensearchIndex(); + } catch (Exception ex) { + System.out.println("opensearchIndexDeep() background indexing " + + occ.getId() + " FAILED: " + ex.toString()); + ex.printStackTrace(); + } + } + if (enc.hasAnnotations()) { + for (Annotation ann : enc.getAnnotations()) { + System.out.println("opensearchIndexDeep() background indexing annot " + + ann.getId() + " via enc " + encId); + try { + ann.opensearchIndex(); + } catch (Exception ex) { + System.out.println("opensearchIndexDeep() background indexing " + + ann.getId() + " FAILED: " + ex.toString()); + ex.printStackTrace(); + } + } + } + } catch (Exception e) { + System.out.println("opensearchIndexDeep() backgrounding Encounter " + encId + + " hit an exception."); + e.printStackTrace(); + } finally { + bgShepherd.rollbackAndClose(); + } + System.out.println("opensearchIndexDeep() backgrounding Encounter " + encId + + " finished."); + executor.shutdown(); + } + }; + System.out.println("opensearchIndexDeep() begin backgrounding for " + this); + executor.execute(rn); + System.out.println("opensearchIndexDeep() [foreground] finished for Encounter " + encId); + } + + // given a doc from opensearch, can user access it? + public static boolean opensearchAccess(org.json.JSONObject doc, User user, + Shepherd myShepherd) { + if ((doc == null) || (user == null)) return false; + if (doc.optBoolean("publiclyReadable", false)) return true; + if (doc.optString("submitterUserId", "__FAIL__").equals(user.getId())) return true; + if (user.isAdmin(myShepherd)) return true; + org.json.JSONArray viewUsers = doc.optJSONArray("viewUsers"); + if (viewUsers == null) return false; + for (int i = 0; i < viewUsers.length(); i++) { + if (viewUsers.optString(i, "__FAIL__").equals(user.getId())) return true; + } + return false; + } + + @Override public Base getById(Shepherd myShepherd, String id) { + return myShepherd.getEncounter(id); + } + + @Override public String getAllVersionsSql() { + return + "SELECT \"CATALOGNUMBER\", CAST(COALESCE(EXTRACT(EPOCH FROM CAST(\"MODIFIED\" AS TIMESTAMP))*1000,-1) AS BIGINT) AS version FROM \"ENCOUNTER\" ORDER BY version"; + } + + @Override public long getVersion() { + return Util.getVersionFromModified(modified); + } + + public org.json.JSONObject opensearchMapping() { + org.json.JSONObject map = super.opensearchMapping(); + org.json.JSONObject keywordType = new org.json.JSONObject("{\"type\": \"keyword\"}"); + org.json.JSONObject keywordNormalType = new org.json.JSONObject( + "{\"type\": \"keyword\", \"normalizer\": \"wildbook_keyword_normalizer\"}"); + map.put("date", new org.json.JSONObject("{\"type\": \"date\"}")); + map.put("dateSubmitted", new org.json.JSONObject("{\"type\": \"date\"}")); + map.put("verbatimEventDate", new org.json.JSONObject("{\"type\": \"text\"}")); + map.put("individualTimeOfBirth", new org.json.JSONObject("{\"type\": \"date\"}")); + map.put("individualTimeOfDeath", new org.json.JSONObject("{\"type\": \"date\"}")); + map.put("locationGeoPoint", new org.json.JSONObject("{\"type\": \"geo_point\"}")); + map.put("occurrenceLocationGeoPoint", new org.json.JSONObject("{\"type\": \"geo_point\"}")); + + // if we want to sort on it (and it is texty), it needs to be keyword + // (ints, dates, etc are all sortable) + // note: "id" is done in Base.java + map.put("taxonomy", keywordType); + map.put("occurrenceId", keywordType); + map.put("state", keywordType); + map.put("submitterUserId", keywordType); + map.put("individualTaxonomy", keywordType); + map.put("individualId", keywordType); + map.put("importTaskId", keywordType); + map.put("importTaskCreatorId", keywordType); + map.put("importTaskSourceName", keywordType); + + // all case-insensitive keyword-ish types + map.put("locationId", keywordNormalType); + map.put("locationName", keywordNormalType); + map.put("country", keywordNormalType); + map.put("assignedUsername", keywordNormalType); + map.put("projects", keywordNormalType); + map.put("behavior", keywordNormalType); + map.put("patterningCode", keywordNormalType); + map.put("annotationViewpoints", keywordNormalType); + map.put("mediaAssetKeywords", keywordNormalType); + map.put("annotationIAClasses", keywordNormalType); + map.put("haplotype", keywordNormalType); + map.put("individualSocialUnits", keywordNormalType); + map.put("individualRelationshipRoles", keywordNormalType); + map.put("individualDisplayName", keywordNormalType); + map.put("organizations", keywordNormalType); + map.put("otherCatalogNumbers", keywordNormalType); + map.put("lifeStage", keywordNormalType); + map.put("submitters", keywordNormalType); + map.put("photographers", keywordNormalType); + map.put("informOthers", keywordNormalType); + + // https://stackoverflow.com/questions/68760699/matching-documents-where-multiple-fields-match-in-an-array-of-objects + map.put("measurements", new org.json.JSONObject("{\"type\": \"nested\"}")); + map.put("metalTags", new org.json.JSONObject("{\"type\": \"nested\"}")); + return map; + } + + // for encounters, we allow null user to see *some* things + public org.json.JSONObject jsonForApiGet(Shepherd myShepherd, User user) + throws IOException { + org.json.JSONObject rtn = new org.json.JSONObject(); + boolean isPublic = isPubliclyReadable(); + // anon-user can only see public, so we 401 here + if ((user == null) && !isPublic) { + rtn.put("statusCode", 401); + rtn.put("success", false); + return rtn; + } + rtn = opensearchDocumentAsJSONObject(myShepherd); + rtn.put("success", true); + rtn.put("statusCode", 200); + rtn.put("access", "read"); + rtn.put("isPublic", isPublic); + + boolean hideUserEmail = true; + User submitter = getSubmitterUser(myShepherd); + if (submitter != null) + rtn.put("submitterInfo", + submitter.infoJSONObject(myShepherd, user != null, hideUserEmail)); + // check to see if logged-in-user is outright blocked + if (user != null) { + boolean blocked = true; + if (canUserEdit(user, myShepherd)) { + rtn.put("access", "write"); + blocked = false; + // we can allow email being shown when access=write + hideUserEmail = false; + if (submitter != null) + rtn.put("submitterInfo", + submitter.infoJSONObject(myShepherd, true, hideUserEmail)); + } else if (canUserView(user, myShepherd)) { + blocked = false; + } + if (blocked) { + // we keep this very minimal + org.json.JSONObject blockedRtn = new org.json.JSONObject(); + blockedRtn.put("success", true); + blockedRtn.put("statusCode", 200); + blockedRtn.put("access", "none"); + blockedRtn.put("id", rtn.get("id")); + // need this to know who to collab with + Collaboration col = Collaboration.collaborationBetweenUsers(user, submitter, + myShepherd.getContext()); + if (col != null) { + blockedRtn.put("collaborationState", col.getState()); + blockedRtn.put("collaborationCreated", col.getDateStringCreated()); + } + blockedRtn.put("assignedUsername", rtn.optString("assignedUsername", null)); + blockedRtn.put("submitterUserId", rtn.optString("submitterUserId", null)); + blockedRtn.put("submitterInfo", rtn.optJSONObject("submitterInfo")); + return blockedRtn; + } + } + // additional fields we want + rtn.put("dateValues", getDateValuesJson()); + rtn.put("researcherComments", getRComments()); + rtn.put("groupRole", getGroupRole()); + rtn.put("identificationRemarks", getIdentificationRemarks()); + rtn.put("spotMapping", spotMappingJsonForApiGet()); + + // the user-listy things + rtn.put("submitters", + userListJSONArray(myShepherd, this.submitters, user != null, hideUserEmail)); + rtn.put("photographers", + userListJSONArray(myShepherd, this.photographers, user != null, hideUserEmail)); + rtn.put("informOthers", + userListJSONArray(myShepherd, this.informOthers, user != null, hideUserEmail)); + // sanitize for non-logged-in users (hence, on public data) + if (user == null) { + rtn.put("access", "read"); + String[] blocked = { + "importTaskSourceName", "locationId", "locationName", "country", "verbatimLocality", + "microsatelliteMarkers", "locationGeoPoint", "occurrenceLocationGeoPoint", + "mediaAssetKeywords", "mediaAssetLabeledKeywords", "biologicalMeasurements", + "importTaskCreatorId", "annotationIAClasses", "annotationViewpoints", + "researcherComments", "informOthers", "photographers", "submitters", + "assignedUsername" + }; + for (String field : blocked) { + rtn.remove(field); + } + // we redo mediaAssets, with no annots and mid size + org.json.JSONArray mas = new org.json.JSONArray(); + for (MediaAsset ma : getMedia()) { + org.json.JSONObject maj = new org.json.JSONObject(); + maj.put("uuid", ma.getUUID()); + maj.put("mimeTypeMajor", ma.getMimeTypeMajor()); + maj.put("mimeTypeMinor", ma.getMimeTypeMinor()); + maj.put("rotationInfo", ma.getRotationInfo()); + try { + // historic data might throw IllegalArgumentException: Path not under given root + java.net.URL url = ma.safeURL(myShepherd, null, "mid"); + if (url != null) maj.put("url", url.toString()); + } catch (Exception ex) {} + mas.put(maj); + } + rtn.put("mediaAssets", mas); + } else { + // for real users we add some extras to assets and annotations + if (rtn.optJSONArray("mediaAssets") != null) { + for (int i = 0; i < rtn.getJSONArray("mediaAssets").length(); i++) { + if (rtn.getJSONArray("mediaAssets").optJSONObject(i) != null) { + MediaAsset ma = MediaAssetFactory.loadByUuid(rtn.getJSONArray( + "mediaAssets").getJSONObject(i).optString("uuid"), myShepherd); + if (ma != null) { + rtn.getJSONArray("mediaAssets").getJSONObject(i).put("keywords", + ma.getKeywordsJSONArray()); + rtn.getJSONArray("mediaAssets").getJSONObject(i).put("detectionStatus", + ma.getDetectionStatus()); + rtn.getJSONArray("mediaAssets").getJSONObject(i).put("userFilename", + ma.getUserFilename()); + rtn.getJSONArray("mediaAssets").getJSONObject(i).put("rotationInfo", + ma.getRotationInfo()); + } + // now we cram some stuff into each annotation as well + if (rtn.getJSONArray("mediaAssets").getJSONObject(i).optJSONArray( + "annotations") != null) { + for (int j = 0; + j < + rtn.getJSONArray("mediaAssets").getJSONObject(i).getJSONArray( + "annotations").length(); + j++) { + if (rtn.getJSONArray("mediaAssets").getJSONObject(i).getJSONArray( + "annotations").optJSONObject(j) == null) continue; + // this parsing of nested json really makes me miss perl + Annotation ann = myShepherd.getAnnotation(rtn.getJSONArray( + "mediaAssets").getJSONObject(i).getJSONArray( + "annotations").getJSONObject(j).optString("id", null)); + if (ann == null) continue; + rtn.getJSONArray("mediaAssets").getJSONObject(i).getJSONArray( + "annotations").getJSONObject(j).put("identificationStatus", + ann.getIdentificationStatus()); + // annTasks are in chron order so most recent will be at end + List annTasks = ann.getRootIATasks(myShepherd); + int ntasks = Util.collectionSize(annTasks); + if (ntasks > 0) { + rtn.getJSONArray("mediaAssets").getJSONObject(i).getJSONArray( + "annotations").getJSONObject(j).put("iaTaskId", + annTasks.get(ntasks - 1).getId()); + rtn.getJSONArray("mediaAssets").getJSONObject(i).getJSONArray( + "annotations").getJSONObject(j).put("iaTaskParameters", + annTasks.get(ntasks - 1).getParameters()); + } + } + } + } + } + } + } + return rtn; + } + + // internal utility function + private org.json.JSONArray userListJSONArray(Shepherd myShepherd, List users, + boolean includeSensitive, boolean hideEmail) { + org.json.JSONArray arr = new org.json.JSONArray(); + if (Util.collectionIsEmptyOrNull(users)) return arr; + for (User user : users) { + arr.put(user.infoJSONObject(myShepherd, includeSensitive, hideEmail)); + } + return arr; + } + + public static Base createFromApi(org.json.JSONObject payload, List files, + Shepherd myShepherd) + throws ApiException { + if (payload == null) throw new ApiException("empty payload"); + User user = (User)payload.opt("_currentUser"); + + // these need validation (will throw ApiException if fail) + String locationID = (String)validateFieldValue("locationId", payload); + String dateTime = (String)validateFieldValue("dateTime", payload); + String txStr = (String)validateFieldValue("taxonomy", payload); + String submitterEmail = (String)validateFieldValue("submitterEmail", payload); + String photographerEmail = (String)validateFieldValue("photographerEmail", payload); + Double decimalLatitude = (Double)validateFieldValue("decimalLatitude", payload); + Double decimalLongitude = (Double)validateFieldValue("decimalLongitude", payload); + if (((decimalLatitude == null) && (decimalLongitude != null)) || + ((decimalLatitude != null) && (decimalLongitude == null))) { + org.json.JSONObject error = new org.json.JSONObject(); + error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); + // i guess we pick one, since both are wrong + error.put("fieldName", "decimalLatitude"); + error.put("value", decimalLatitude); + throw new ApiException("cannot send just one of decimalLatitude and decimalLongitude", + error); + } + String additionalEmailsValue = payload.optString("additionalEmails", null); + String[] additionalEmails = null; + if (!Util.stringIsEmptyOrNull(additionalEmailsValue)) + additionalEmails = additionalEmailsValue.split("[,\\s]+"); + if (additionalEmails != null) { + org.json.JSONObject error = new org.json.JSONObject(); + error.put("fieldName", "additionalEmails"); + for (String email : additionalEmails) { + if (!Util.isValidEmailAddress(email)) { + error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); + error.put("value", email); + throw new ApiException("invalid email address", error); + } + } + } + Encounter enc = new Encounter(false); + if (Util.isUUID(payload.optString("_id"))) enc.setId(payload.getString("_id")); + enc.setLocationID(locationID); + enc.setDecimalLatitude(decimalLatitude); + enc.setDecimalLongitude(decimalLongitude); + enc.setDateFromISO8601String(dateTime); + enc.setTaxonomyFromString(txStr); + if (CommonConfiguration.getProperty("encounterState0", myShepherd.getContext()) != null) { + enc.setState(CommonConfiguration.getProperty("encounterState0", + myShepherd.getContext())); + } + enc.setComments(payload.optString("comments", null)); + if (user == null) { + enc.setSubmitterID("public"); // this seems to be what EncounterForm servlet does so... + } else { + enc.setSubmitterID(user.getUsername()); + enc.addSubmitter(user); + } + if (!Util.stringIsEmptyOrNull(submitterEmail)) { + User submitterUser = myShepherd.getOrCreateUserByEmailAddress(submitterEmail, + payload.optString("submitterName", null)); + // set this after the owner-submitter being set + enc.addSubmitter(submitterUser); + } + if (!Util.stringIsEmptyOrNull(photographerEmail)) { + User photographerUser = myShepherd.getOrCreateUserByEmailAddress(photographerEmail, + payload.optString("photographerName", null)); + enc.addPhotographer(photographerUser); + } + if (additionalEmails != null) { + for (String email : additionalEmails) { + User addlUser = myShepherd.getOrCreateUserByEmailAddress(email, null); + enc.addInformOther(addlUser); + } + } + // this will get/make an Occurrence no matter what + Occurrence occ = myShepherd.getOrCreateOccurrence(payload.optString("occurrenceId", null)); + occ.addEncounterAndUpdateIt(enc); + myShepherd.getPM().makePersistent(occ); + return enc; + } + + // user should already have been validated -- via obj.canUserEdit() -- in api/BaseObject, so this + // does not need to be tested here. however, more detailed checks may require user (e.g. can user + // also alter another object, such as Occurrence) + public org.json.JSONObject processPatch(org.json.JSONArray patchArr, User user, + Shepherd myShepherd) + throws ApiException { + if (patchArr == null) + throw new ApiException("null patch array", ApiException.ERROR_RETURN_CODE_REQUIRED); + this.setSkipAutoIndexing(true); + org.json.JSONArray resArr = new org.json.JSONArray(); + Set occNeedPruning = new HashSet(); + Set indivNeedPruning = new HashSet(); + for (int i = 0; i < patchArr.length(); i++) { + System.out.println("applied patch at [i=" + i + "]: " + patchArr.optJSONObject(i)); + org.json.JSONObject patchRes = EncounterPatchValidator.applyPatch(this, + patchArr.optJSONObject(i), user, myShepherd); + for (int j = 0; j < patchRes.getJSONArray("_mayNeedPruning").length(); j++) { + Object p = patchRes.getJSONArray("_mayNeedPruning").get(j); + if (p instanceof Occurrence) { + occNeedPruning.add((Occurrence)p); + } else if (p instanceof MarkedIndividual) { + indivNeedPruning.add((MarkedIndividual)p); + } + } + patchRes.remove("_mayNeedPruning"); + System.out.println("patch returned at [i=" + i + "]: " + patchRes); + resArr.put(patchRes); + } + org.json.JSONObject rtn = new org.json.JSONObject(); + rtn.put("patchResults", resArr); + // after applying each patch, make sure nothing is wrong + EncounterPatchValidator.finalValidation(this, myShepherd); + // now we need to look at modified objects which may be empty (and thus need pruning) + for (Occurrence occ : occNeedPruning) { + if (!occ.pruneIfNeeded(myShepherd)) { + occ.setSkipAutoIndexing(false); + } + } + for (MarkedIndividual indiv : indivNeedPruning) { + if (!indiv.pruneIfNeeded(myShepherd)) { + indiv.setSkipAutoIndexing(false); + } + } + // no exceptions means success + rtn.put("success", true); + rtn.put("statusCode", 200); + this.setDWCDateLastModified(); + this._log(resArr); + this.setSkipAutoIndexing(false); + return rtn; + } + + // see note on painful redundancy with bulk import and createFromApi on + // Base.applyPatchOp() + public Object applyPatchOp(String fieldName, Object value, String op) + throws ApiException { + System.out.println("[DEBUG] applyPatchOp(): " + op + " " + fieldName + "=>" + value + + " on: " + this); + if (op == null) + throw new ApiException("op is required", ApiException.ERROR_RETURN_CODE_REQUIRED); + // TODO future enhancement: op=remove path=annotations/ANNOT_ID should perform + // functionality of servlet/EncounterRemoveAnnotation.java + User user = null; // needed for some options below + switch (fieldName) { + case "decimalLatitude": + setDecimalLatitude((Double)value); + break; + case "decimalLongitude": + setDecimalLongitude((Double)value); + break; + case "alternateId": + // note: is same as otherCatalogNumbers + setAlternateID((String)value); + break; + case "behavior": + setBehavior((String)value); + break; + case "country": + setCountry((String)value); + break; + case "dateInMilliseconds": + if (value != null) setDateInMilliseconds((Long)value); + break; + case "year": + if (value == null) { + setYear(0); + } else { + setYear((Integer)value); + } + break; + case "month": + if (value == null) { + setMonth(0); + } else { + setMonth((Integer)value); + } + break; + case "day": + if (value == null) { + setDay(0); + } else { + setDay((Integer)value); + } + break; + case "hour": + if (value == null) { + setHour(-1); // grr + } else { + setHour((Integer)value); + } + break; + case "minutes": + if (value == null) { + setMinutes(null); + } else { + setMinutes(value.toString()); + } + break; + case "depth": + setDepth((Double)value); + break; + case "elevation": + setMaximumElevationInMeters((Double)value); + break; + case "genus": + setGenus((String)value); + break; + case "specificEpithet": + setSpecificEpithet((String)value); + break; + case "lifeStage": + setLifeStage((String)value); + break; + case "livingStatus": + setLivingStatus((String)value); + break; + case "locationId": + setLocationID((String)value); + break; + case "sex": + setSex((String)value); + break; + case "state": + setState((String)value); + break; + case "submitterID": + setSubmitterID((String)value); + break; + case "submitterName": + setSubmitterName((String)value); + break; + case "submitterOrganization": + setSubmitterOrganization((String)value); + break; + case "distinguishingScar": + setDistinguishingScar((String)value); + break; + case "groupRole": + setGroupRole((String)value); + break; + case "identificationRemarks": + setIdentificationRemarks((String)value); + break; + case "occurrenceRemarks": + case "sightingRemarks": + setOccurrenceRemarks((String)value); + break; + case "otherCatalogNumbers": + setOtherCatalogNumbers((String)value); + break; + case "patterningCode": + setPatterningCode((String)value); + break; + case "satelliteTag": + setSatelliteTag((SatelliteTag)value); + break; + case "acousticTag": + setAcousticTag((AcousticTag)value); + break; + case "metalTags": + // we only need location to remove + if ("remove".equals(op) && (value != null)) { + removeMetalTag(value.toString()); + } else if (("add".equals(op) || "replace".equals(op)) && + (value instanceof org.json.JSONObject)) { + // add or replace will update based on location if exists + org.json.JSONObject jval = (org.json.JSONObject)value; + addOrUpdateMetalTag(jval.optString("location", null), + jval.optString("number", null)); + } + break; + case "measurements": + if ("remove".equals(op) && (value != null)) { + removeMeasurementByType(value.toString()); + } else if (value instanceof Measurement) { + // for op=add or op=replace, if it has the measurement (i.e. by type), it means + // it should be changed in place already so dont do anything + Measurement meas = (Measurement)value; + if (findMeasurementOfType(meas.getType()) == null) addMeasurement(meas); + } + break; + case "annotations": + // for now we can only patch op=remove on path=annotations + // adding annots is done through legacy servlet + if ("remove".equals(op) && (value instanceof Annotation)) { + // enc.removeAnnotation and deletePersistent (from db/shepherd) done in EncounterPatchValidator + // so we only need to clean up some loose ends here + Annotation goneAnnot = (Annotation)value; + goneAnnot.setSkipAutoIndexing(true); + goneAnnot.opensearchUnindexQuiet(); + } + break; + // these we really only want to append to (i think??) + // so this should only happen when op=add/replace and + // value is non-null + case "researcherComments": + if (value != null) addComments((String)value); + break; + case "verbatimLocality": + setVerbatimLocality((String)value); + break; + case "verbatimEventDate": + setVerbatimEventDate((String)value); + break; + // we should get value as a MarkedIndividual here (or null) + case "individualId": + if ("remove".equals(op) || (value == null)) { + MarkedIndividual current = removeIndividual(); + if (current != null) { + System.out.println("enc.applyPatchOp() removed " + this + " from " + current); + } + } else { + // value should be an individual (new or existing) + MarkedIndividual indiv = (MarkedIndividual)value; + MarkedIndividual current = getIndividual(); + if (indiv.equals(current)) { + System.out.println( + "enc.applyPatchOp() ignoring adding existing individual to " + this); + break; + } + current = removeIndividual(); + if (current != null) { + current.setSkipAutoIndexing(false); + setIndividual(null); + System.out.println("enc.applyPatchOp() removed (prior to re-setting) " + this + + " from " + current); + } + indiv.addEncounter(this); + setIndividual(indiv); + // this will only set indiv taxonomy if NOT set + // so for new indiv and existing with no taxonomy + if (indiv.getTaxonomyString() == null) + indiv.setTaxonomyString(this.getTaxonomyString()); + // indiv.version will be updated by above calls + System.out.println("enc.applyPatchOp() added " + this + " to " + indiv); + } + break; + // value should be an Occurrence here (already validated and permission-checked) + case "occurrenceId": + // if EncounterPatchValidator let thru null value, we do nothing + if (value == null) break; + Occurrence occ = (Occurrence)value; + if ("remove".equals(op)) { + // in remove case, we are given occ to remove from + occ.removeEncounter(this); + this.occurrenceID = null; + } else { + // otherwise it is occ we add to + occ.addEncounterAndUpdateIt(this); + } + break; + case "assets": + if ("add".equals(op) && (value != null)) { + MediaAsset ma = (MediaAsset)value; + ma.setDetectionStatus("_new"); + addMediaAsset(ma); + } + break; + // value should be a user here + case "informOthers": + user = (User)value; + if (op.equals("remove")) { + removeInformOther(user); + } else { + addInformOther(user); + } + break; + case "submitters": + user = (User)value; + if (op.equals("remove")) { + removeSubmitter(user); + } else { + addSubmitter(user); + } + break; + case "photographers": + user = (User)value; + if (op.equals("remove")) { + removePhotographer(user); + } else { + addPhotographer(user); + } + break; + default: + throw new ApiException("unknown fieldName: " + fieldName, + ApiException.ERROR_RETURN_CODE_INVALID); + } + return value; + } + + public org.json.JSONObject afterPatch(Shepherd myShepherd) { + org.json.JSONObject res = new org.json.JSONObject(); + List needsIndexing = new ArrayList(); + org.json.JSONArray newAssetsArr = new org.json.JSONArray(); + // we update children here (not backgrounded) since we need them available + // once the api returns the results + for (MediaAsset ma : this.getMedia()) { + if ("_new".equals(ma.getDetectionStatus())) { + // _post_new is meant to be temporary, as it + // will get overwritten once put into IA pipeline + ma.setDetectionStatus("_post_new"); + ma.updateStandardChildren(myShepherd); + needsIndexing.add(ma); + org.json.JSONObject maj = new org.json.JSONObject(); + maj.put("id", ma.getIdInt()); + try { + URL url = ma.safeURL(myShepherd, null, "master"); + if (url != null) maj.put("url", url.toString()); + } catch (Exception ex) {} + newAssetsArr.put(maj); + } + } + if (newAssetsArr.length() > 0) res.put("newMediaAssets", newAssetsArr); + BulkImportUtil.bulkOpensearchIndex(needsIndexing); + return res; + } + + // this is allowed to have its own new thread since encounter is persisted + public org.json.JSONObject afterPatchTransaction(String context) { + List ids = new ArrayList(); + + // we use _post_new state to determine what needs to go to IA + // see: afterPatch() above + for (MediaAsset ma : this.getMedia()) { + if ("_post_new".equals(ma.getDetectionStatus())) { + ids.add(ma.getIdInt()); + } + } + if (ids.size() < 1) return null; + Task task = this.sendToIA(ids, context); + if (task == null) return null; + org.json.JSONObject rtn = new org.json.JSONObject(); + rtn.put("taskId", task.getId()); + return rtn; + } + + public MarkedIndividual removeIndividual() { + MarkedIndividual current = getIndividual(); + + if (current == null) return null; + // skip auto indexing cuz race conditions; must manually index later + current.setSkipAutoIndexing(true); + current.removeEncounter(this); + setIndividual(null); + return current; + } + + public static Object validateFieldValue(String fieldName, org.json.JSONObject data) + throws ApiException { + if (data == null) throw new ApiException("empty payload"); + org.json.JSONObject error = new org.json.JSONObject(); + error.put("fieldName", fieldName); + String exMessage = "invalid value for " + fieldName; + Object returnValue = null; + double UNSET_LATLON = 9999.99; + switch (fieldName) { + case "locationId": + returnValue = data.optString(fieldName, null); + if (returnValue == null) { + error.put("code", ApiException.ERROR_RETURN_CODE_REQUIRED); + throw new ApiException(exMessage, error); + } + if (!LocationID.isValidLocationID((String)returnValue)) { + error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); + error.put("value", returnValue); + throw new ApiException(exMessage, error); + } + break; + + case "dateTime": + returnValue = data.optString(fieldName, null); + if (returnValue == null) { + error.put("code", ApiException.ERROR_RETURN_CODE_REQUIRED); + throw new ApiException(exMessage, error); + } + if (!validISO8601String((String)returnValue)) { + error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); + error.put("value", returnValue); + throw new ApiException(exMessage, error); + } + break; + + case "taxonomy": + returnValue = data.optString(fieldName, null); + if (returnValue != null) { // null is allowed, but will not pass validity + // this is throwaway read-only shepherd + Shepherd myShepherd = new Shepherd("context0"); + myShepherd.setAction("Encounter.validateFieldValue"); + boolean validTaxonomy = false; + myShepherd.beginDBTransaction(); + try { + validTaxonomy = myShepherd.isValidTaxonomyName((String)returnValue); + } catch (Exception e) { e.printStackTrace(); } finally { + myShepherd.rollbackAndClose(); + } + if (!validTaxonomy) { + error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); + error.put("value", returnValue); + throw new ApiException(exMessage, error); + } + } + break; + + case "photographerEmail": + case "submitterEmail": + returnValue = data.optString(fieldName, null); + if ((returnValue != null) && !Util.isValidEmailAddress((String)returnValue)) { + error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); + error.put("value", returnValue); + throw new ApiException(exMessage, error); + } + break; + + case "decimalLatitude": + returnValue = data.optDouble(fieldName, UNSET_LATLON); + if ((double)returnValue == UNSET_LATLON) { + returnValue = null; + } else if (!Util.isValidDecimalLatitude((double)returnValue)) { + error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); + error.put("value", returnValue); + throw new ApiException(exMessage, error); + } + break; + + case "decimalLongitude": + returnValue = data.optDouble(fieldName, UNSET_LATLON); + if ((double)returnValue == UNSET_LATLON) { + returnValue = null; + } else if (!Util.isValidDecimalLongitude((double)returnValue)) { + error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); + error.put("value", returnValue); + throw new ApiException(exMessage, error); + } + break; + + default: + System.out.println("Encounter.validateFieldValue(): WARNING unsupported fieldName=" + + fieldName); + } + // must be okay! + return returnValue; + } + + // basically ripped from servlet/EncounterForm + public Task sendToIA(Shepherd myShepherd) { + Task task = null; + + try { + IAJsonProperties iaConfig = IAJsonProperties.iaConfig(); + if (iaConfig.hasIA(this, myShepherd)) { + for (MediaAsset ma : this.getMedia()) { + ma.setDetectionStatus(IBEISIA.STATUS_INITIATED); + } + Task parentTask = null; // this is *not* persisted, but only used so intakeMediaAssets will inherit its params + if (this.getLocationID() != null) { + parentTask = new Task(); + org.json.JSONObject tp = new org.json.JSONObject(); + org.json.JSONObject mf = new org.json.JSONObject(); + mf.put("locationId", this.getLocationID()); + tp.put("matchingSetFilter", mf); + parentTask.setParameters(tp); + } + task = IA.intakeMediaAssets(myShepherd, this.getMedia(), parentTask); + myShepherd.storeNewTask(task); + System.out.println("sendToIA() success on " + this + " => " + task); + } else { + System.out.println("sendToIA() skipped; no config for " + this); + } + } catch (Exception ex) { + System.out.println("sendToIA() failed on " + this + ": " + ex); + ex.printStackTrace(); + } + return task; + } + + // this is based on servlet/MediaAssetCreate and differs only slightly from + // above - mainly in that it can handle multiple assets and creates own shepherd + // (note: all assets assumed to be using *this encounter* + public Task sendToIA(List ids, String context) { + Task task = null; + Shepherd myShepherd = new Shepherd(context); + + myShepherd.setAction("Encounter.sendToIA()"); + myShepherd.beginDBTransaction(); + try { + IAJsonProperties iaConfig = IAJsonProperties.iaConfig(); + boolean hasConfig = iaConfig.hasIA(this, myShepherd); + List allMAs = new ArrayList(); + for (Integer id : ids) { + if (id < 0) continue; + MediaAsset ma = MediaAssetFactory.load(id, myShepherd); + if (ma != null) { + ma.setDetectionStatus(hasConfig ? IBEISIA.STATUS_INITIATED : IBEISIA.STATUS_COMPLETE); + allMAs.add(ma); + } + } + if (!hasConfig) { + System.out.println("sendToIA() skipped; no config for " + this); + } else if (allMAs.size() > 0) { + Task parentTask = null; // not persisted + if (this.getLocationID() != null) { + parentTask = new Task(); + org.json.JSONObject tp = new org.json.JSONObject(); + org.json.JSONObject mf = new org.json.JSONObject(); + mf.put("locationId", this.getLocationID()); + tp.put("matchingSetFilter", mf); + parentTask.setParameters(tp); + } + Taxonomy taxy = this.getTaxonomy(myShepherd); + if (taxy != null) { + task = IA.intakeMediaAssetsOneSpecies(myShepherd, allMAs, taxy, parentTask); + } else { + task = IA.intakeMediaAssets(myShepherd, allMAs); + } + myShepherd.storeNewTask(task); + System.out.println("sendToIA() created " + task + " for " + this); + } + // persist will catch change on asset detectionStatus regardless + myShepherd.commitDBTransaction(); + } catch (Exception ex) { + ex.printStackTrace(); + myShepherd.rollbackDBTransaction(); + } finally { + myShepherd.closeDBTransaction(); + } + return task; + } + + public Set getNotificationEmailAddresses() { + Set addrs = new HashSet(); + + addrs.addAll(Util.getUserEmailAddresses(this.getSubmitters())); + addrs.addAll(Util.getUserEmailAddresses(this.getPhotographers())); + addrs.addAll(Util.getUserEmailAddresses(this.getInformOthers())); + return addrs; + } + + // FIXME passing the langCode is dumb imho, but this is "standard practice" + // better would be that each recipient user's language preference would be used for their email + public void sendCreationEmails(Shepherd myShepherd, String langCode) { + String context = myShepherd.getContext(); + + if (!CommonConfiguration.sendEmailNotifications(context)) return; + myShepherd.beginDBTransaction(); + try { + URI uri = CommonConfiguration.getServerURI(myShepherd); + if (uri == null) throw new IOException("could not find server uri"); + ThreadPoolExecutor es = MailThreadExecutorService.getExecutorService(); + Properties submitProps = ShepherdProperties.getProperties("submit.properties", langCode, + context); + Map tagMap = NotificationMailer.createBasicTagMap(this); + tagMap.put(NotificationMailer.WILDBOOK_COMMUNITY_URL, + CommonConfiguration.getWildbookCommunityURL(context)); + List mailTo = NotificationMailer.splitEmails( + CommonConfiguration.getNewSubmissionEmail(context)); + String mailSubj = submitProps.getProperty("newEncounter") + this.getCatalogNumber(); + for (String emailTo : mailTo) { + NotificationMailer mailer = new NotificationMailer(context, emailTo, langCode, + "newSubmission-summary", tagMap); + mailer.setUrlScheme(uri.getScheme()); + es.execute(mailer); + } + // this will be empty if no locationID + Set locEmails = myShepherd.getAllUserEmailAddressesForLocationIDAsSet( + this.getLocationID(), context); + for (String emailTo : locEmails) { + NotificationMailer mailer = new NotificationMailer(context, langCode, emailTo, + "newSubmission-summary", tagMap); + mailer.setUrlScheme(uri.getScheme()); + es.execute(mailer); + } + // Add encounter dont-track tag for remaining notifications (still needs email-hash assigned). + tagMap.put(NotificationMailer.EMAIL_NOTRACK, "number=" + this.getCatalogNumber()); + // this is a mashup of: submitters, photographers, informOthers.... + for (String emailTo : this.getNotificationEmailAddresses()) { + tagMap.put(NotificationMailer.EMAIL_HASH_TAG, getHashOfEmailString(emailTo)); + NotificationMailer mailer = new NotificationMailer(context, langCode, emailTo, + "newSubmission", tagMap); + mailer.setUrlScheme(uri.getScheme()); + es.execute(mailer); + } + es.shutdown(); + } catch (Exception ex) { + System.out.println("sendCreationEmails() on " + this + " failed: " + ex); + ex.printStackTrace(); + } finally { + myShepherd.rollbackDBTransaction(); + } + } + +/* + in anticipation of 10.10.0, this is a sketchy of what logging might look like + for a change in an Encounter via PATCH. + + FIXME this should be fully replaced (or wrapped around) the more basic log functionality + that is yet to be written. this can serve as an idea of some things which might be + desirable to support in general logging. take with a grain of salt. + */ + public void _log(org.json.JSONArray arr) { + if ((arr == null) || (arr.length() == 0)) return; + String actionId = Util.generateUUID(); + for (int i = 0; i < arr.length(); i++) { + if (arr.optJSONObject(i) == null) continue; + org.json.JSONObject p = arr.getJSONObject(i).optJSONObject("_patch"); + if (p == null) continue; + String op = p.optString("op", "UNKNOWN_OP"); + String path = p.optString("path", "UNKNOWN_PATH"); + Object value = null; + if (p.has("value") && !p.isNull("value")) value = p.get("value"); + String logMessage = "modified by PATCH op=" + op + ", path " + path + " with value: " + + ((value == null) ? "NULL" : value.toString()); + _log2(null, null, null, "Encounter", this.getId(), actionId, logMessage); + // legacy "audit log" (aka some random comment) + // TODO really need to add the user/who part here + this.addComments("

    " + Util.prettyTimeStamp() + + " modified " + path + " with operation " + op + "" + ((value == + null) ? "" : " and value " + value.toString() + "") + "

    "); + } + } + + // one of many dilemmas: we need a request object to get user + ip address, but dont have + // it at this point. so we likely need to pass it all around somehow. maybe on a shepherd or + // some other more common object? FIXME TODO + public void _log2( + // "standard" levels (null should be some reasonable default???) + String logLevel, + // reference to who did it, could be multiple users etc. probably should be id _and_ username? + String user, + // pretty obvious? + String ip, + // class of object acted upon + String objectClass, + // primary key + String objectId, + // for groupin multiple logs into one "action" (e.g. a PATCH on object) + String actionId, + // message + String message) { + System.out.println(String.join("\t", "[TMPLOG]", + new Long(System.currentTimeMillis()).toString(), user, ip, objectClass, objectId, + actionId, message)); + } +} diff --git a/src/main/resources/bundles/jdoconfig.properties b/src/main/resources/bundles/jdoconfig.properties index 8eb0b427d1..456db6d770 100755 --- a/src/main/resources/bundles/jdoconfig.properties +++ b/src/main/resources/bundles/jdoconfig.properties @@ -1,63 +1,66 @@ -#DataNucleus parameters for object persistence - -# The following two lines create a connection to an embedded Apache Derby database. -#datanucleus.ConnectionDriverName=org.apache.derby.jdbc.EmbeddedDriver -#datanucleus.ConnectionURL=jdbc:derby:shepherd_derby_database;create=true - -# The following two lines create a connection to a SQLite database. -# You will also need to add the JDBC JAR file for your SQLite version to /WEB-INF/lib. -#datanucleus.ConnectionDriverName=org.sqlite.JDBC -#datanucleus.ConnectionURL=jdbc:sqlite:shepherd_sqlite_database - -# The following two lines create a connection to a SQL Server or SQL Azure database. -#datanucleus.ConnectionDriverName=com.microsoft.sqlserver.jdbc.SQLServerDriver -#datanucleus.ConnectionURL=jdbc:sqlserver://.database.windows.net:1433;database=;user=@;password=;encrypt=true;hostNameInCertificate=*.database.windows.net;loginTimeout=30;create=true - - -# The following two lines create a connection to an H2 database. -# You will also need to add the JDBC JAR file for your H2 version to /WEB-INF/lib. -#datanucleus.ConnectionDriverName=org.h2.Driver -#datanucleus.ConnectionURL=jdbc:h2:shepherd_h2_database - -# The following three lines create a connection to a MySQL database. -# You will also need to add the JDBC JAR file for your MySQL version to /WEB-INF/lib. -#datanucleus.ConnectionDriverName=com.mysql.jdbc.Driver -#datanucleus.ConnectionURL=jdbc:mysql://localhost:3306/shepherd - -# The following lines can be used for PostgreSQL data storage. -# You will also need to add the JDBC JAR file for your PostgreSQL version to /WEB-INF/lib. -datanucleus.ConnectionDriverName=org.postgresql.Driver -datanucleus.ConnectionURL = jdbc:postgresql://localhost:5432/wildbook - - -javax.jdo.PersistenceManagerFactoryClass = org.datanucleus.api.jdo.JDOPersistenceManagerFactory -datanucleus.ConnectionUserName = wildbook -datanucleus.ConnectionPassword = wildbook -datanucleus.schema.autoCreateAll = true -#datanucleus.generateSchema.database.mode = create - -# deprecated: -#datanucleus.NontransactionalRead = true -#datanucleus.storeManagerType = rdbms - -datanucleus.Multithreaded = true -datanucleus.RestoreValues = true -datanucleus.maxFetchDepth = -1 -datanucleus.cache.collections.lazy = false - -# Connection pooling -datanucleus.connectionPoolingType = dbcp2 -datanucleus.connectionPool.maxIdle=10 -datanucleus.connectionPool.minIdle=5 -datanucleus.connectionPool.timeBetweenEvictionRunsMillis=240000 -# Standard DataNucleus keys (that map internally to DBCP2) -datanucleus.connectionPool.maxPoolSize = 300 -datanucleus.connectionPool.maxWait = -1 -datanucleus.connectionPool.testSQL = SELECT 1 - -# HikariCP Pooling of Connections -#datanucleus.connectionPool.maxPoolSize=30 -#datanucleus.connectionPool.maxIdle=10 -#datanucleus.connectionPool.leakThreshold=1 -#datanucleus.connectionPool.maxLifetime=1800000 - +#DataNucleus parameters for object persistence + +# The following two lines create a connection to an embedded Apache Derby database. +#datanucleus.ConnectionDriverName=org.apache.derby.jdbc.EmbeddedDriver +#datanucleus.ConnectionURL=jdbc:derby:shepherd_derby_database;create=true + +# The following two lines create a connection to a SQLite database. +# You will also need to add the JDBC JAR file for your SQLite version to /WEB-INF/lib. +#datanucleus.ConnectionDriverName=org.sqlite.JDBC +#datanucleus.ConnectionURL=jdbc:sqlite:shepherd_sqlite_database + +# The following two lines create a connection to a SQL Server or SQL Azure database. +#datanucleus.ConnectionDriverName=com.microsoft.sqlserver.jdbc.SQLServerDriver +#datanucleus.ConnectionURL=jdbc:sqlserver://.database.windows.net:1433;database=;user=@;password=;encrypt=true;hostNameInCertificate=*.database.windows.net;loginTimeout=30;create=true + + +# The following two lines create a connection to an H2 database. +# You will also need to add the JDBC JAR file for your H2 version to /WEB-INF/lib. +#datanucleus.ConnectionDriverName=org.h2.Driver +#datanucleus.ConnectionURL=jdbc:h2:shepherd_h2_database + +# The following three lines create a connection to a MySQL database. +# You will also need to add the JDBC JAR file for your MySQL version to /WEB-INF/lib. +#datanucleus.ConnectionDriverName=com.mysql.jdbc.Driver +#datanucleus.ConnectionURL=jdbc:mysql://localhost:3306/shepherd + +# The following lines can be used for PostgreSQL data storage. +# You will also need to add the JDBC JAR file for your PostgreSQL version to /WEB-INF/lib. +datanucleus.ConnectionDriverName=org.postgresql.Driver +datanucleus.ConnectionURL = jdbc:postgresql://localhost:5432/wildbook + + +javax.jdo.PersistenceManagerFactoryClass = org.datanucleus.api.jdo.JDOPersistenceManagerFactory +datanucleus.ConnectionUserName = wildbook +datanucleus.ConnectionPassword = wildbook +datanucleus.schema.autoCreateAll = true +#datanucleus.generateSchema.database.mode = create + +# deprecated: +#datanucleus.NontransactionalRead = true +#datanucleus.storeManagerType = rdbms + +datanucleus.Multithreaded = true +datanucleus.RestoreValues = true +datanucleus.maxFetchDepth = -1 +datanucleus.cache.collections.lazy = false + +# Connection pooling +datanucleus.connectionPoolingType = dbcp2 +datanucleus.connectionPool.maxIdle=10 +datanucleus.connectionPool.minIdle=5 +datanucleus.connectionPool.timeBetweenEvictionRunsMillis=240000 +# Standard DataNucleus keys (that map internally to DBCP2) +datanucleus.connectionPool.maxPoolSize = 300 +# maxWait in milliseconds. -1 means wait forever, which on contention causes threads to silently +# pile up at "begin" on dbconnections.jsp until Tomcat is restarted. 30s lets a request fail +# fast with a clear error instead, so operators see the problem and pool slots free up. +datanucleus.connectionPool.maxWait = 30000 +datanucleus.connectionPool.testSQL = SELECT 1 + +# HikariCP Pooling of Connections +#datanucleus.connectionPool.maxPoolSize=30 +#datanucleus.connectionPool.maxIdle=10 +#datanucleus.connectionPool.leakThreshold=1 +#datanucleus.connectionPool.maxLifetime=1800000 + From 6f089c2be3b5c45289f65428450d14b01ae083b8 Mon Sep 17 00:00:00 2001 From: JasonWildMe Date: Tue, 28 Apr 2026 16:48:00 -0700 Subject: [PATCH 4/7] =?UTF-8?q?Normalize=20line=20endings=20to=20LF=20(CRL?= =?UTF-8?q?F=E2=86=92LF)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Earlier commits on this branch saved Encounter.java, scanEndApplet.jsp and jdoconfig.properties with CRLF line endings, which made the GitHub PR diff display each file as entirely changed. main has these files as LF, so this commit normalizes back so reviewers see only the actual code changes from this branch. No functional change. Co-Authored-By: Claude Opus 4.7 (1M context) --- src/main/java/org/ecocean/Encounter.java | 11298 ++++++++-------- .../resources/bundles/jdoconfig.properties | 132 +- src/main/webapp/encounters/scanEndApplet.jsp | 1648 +-- 3 files changed, 6539 insertions(+), 6539 deletions(-) diff --git a/src/main/java/org/ecocean/Encounter.java b/src/main/java/org/ecocean/Encounter.java index c339e4d3b6..1696c3c793 100644 --- a/src/main/java/org/ecocean/Encounter.java +++ b/src/main/java/org/ecocean/Encounter.java @@ -1,5649 +1,5649 @@ -package org.ecocean; - -import org.apache.commons.codec.digest.DigestUtils; - -import java.io.*; -import java.lang.Math; -import java.net.URI; -import java.net.URL; -import java.text.SimpleDateFormat; -import java.util.*; -import java.util.concurrent.Executors; -import java.util.concurrent.ExecutorService; -import java.util.concurrent.ThreadPoolExecutor; - -import javax.jdo.Query; - -import org.apache.commons.lang3.builder.ToStringBuilder; - -import com.fasterxml.jackson.core.JsonGenerator; -import com.fasterxml.jackson.core.JsonProcessingException; -import javax.servlet.http.HttpServletRequest; - -import org.ecocean.api.ApiException; -import org.ecocean.api.bulk.BulkImportUtil; -import org.ecocean.api.bulk.BulkValidatorException; -import org.ecocean.api.patch.EncounterPatchValidator; -import org.ecocean.genetics.*; -import org.ecocean.ia.IA; -import org.ecocean.ia.Task; -import org.ecocean.identity.IBEISIA; -import org.ecocean.media.*; -import org.ecocean.security.Collaboration; -import org.ecocean.servlet.importer.ImportTask; -import org.ecocean.shepherd.core.Shepherd; -import org.ecocean.shepherd.core.ShepherdProperties; -import org.ecocean.social.Membership; -import org.ecocean.social.SocialUnit; -import org.ecocean.tag.AcousticTag; -import org.ecocean.tag.DigitalArchiveTag; -import org.ecocean.tag.MetalTag; -import org.ecocean.tag.SatelliteTag; -import org.ecocean.Util.MeasurementDesc; -import org.joda.time.DateTime; -import org.joda.time.format.DateTimeFormat; -import org.joda.time.format.DateTimeFormatter; -import org.joda.time.LocalDateTime; - -import org.datanucleus.api.rest.orgjson.JSONArray; -import org.datanucleus.api.rest.orgjson.JSONException; -import org.datanucleus.api.rest.orgjson.JSONObject; - -/** - * An encounter object stores the complete data for a single sighting/capture report. - * Encounters are added to MarkedIndividual objects as multiple encounters are associated with known individuals. - *

    - * - * @author Jason Holmberg - * @version 2.0 - */ -public class Encounter extends Base implements java.io.Serializable { - static final long serialVersionUID = -146404246317385604L; - - public static final String STATE_MATCHING_ONLY = "matching_only"; - - @Override public String opensearchIndexName() { return "encounter"; } - - public static final double ENCOUNTER_AUTO_SOURCE_CONFIDENCE_CUTOFF = 0.7; - public static final String STATE_AUTO_SOURCED = "auto_sourced"; - - private String sex = null; - private String locationID = null; - private Double maximumDepthInMeters; - private Double maximumElevationInMeters; - private String catalogNumber = ""; - private MarkedIndividual individual; - private int day = 0; - private int month = -1; - private int year = 0; - private Double decimalLatitude; - private Double decimalLongitude; - - private Double endDecimalLatitude; - private Double endDecimalLongitude; - - private String verbatimLocality; - private String occurrenceRemarks = ""; - private String modified; - private String occurrenceID; - private String recordedBy; - private String otherCatalogNumbers; - private String behavior; - private String eventID; - private String measurementUnit; - private String verbatimEventDate; - private String dynamicProperties; - public String identificationRemarks = ""; - public String genus = ""; - public String specificEpithet; - public String lifeStage; - public String country; - public String zebraClass = ""; // via lewa: lactating female, territorial male, etc etc - - private String imageSet; - private String soil; - - private String reproductiveStage; - private Double bodyCondition; - private Double parasiteLoad; - private Double immunoglobin; - private Boolean sampleTakenForDiet; - private Boolean injured; - private boolean opensearchProcessPermissions = false; - - private ArrayList observations = new ArrayList(); - - public String getSoil() { return soil; } - public void setSoil(String soil) { this.soil = soil; } - - public String getReproductiveStage() { return reproductiveStage; } - public void setReproductiveStage(String reproductiveStage) { - this.reproductiveStage = reproductiveStage; - } - - public Double getBodyCondition() { return bodyCondition; } - public void setBodyCondition(Double bodyCondition) { this.bodyCondition = bodyCondition; } - - public Double getParasiteLoad() { return parasiteLoad; } - public void setParasiteLoad(Double parasiteLoad) { this.parasiteLoad = parasiteLoad; } - - public Double getImmunoglobin() { return immunoglobin; } - public void setImmunoglobin(Double immunoglobin) { this.immunoglobin = immunoglobin; } - - public Boolean getSampleTakenForDiet() { return sampleTakenForDiet; } - public void setSampleTakenForDiet(Boolean sampleTakenForDiet) { - this.sampleTakenForDiet = sampleTakenForDiet; - } - - public Boolean getInjured() { return injured; } - public void setInjured(Boolean injured) { this.injured = injured; } - - // for searchability - private String imageNames; - - private List submitters; - private List photographers; - private List informOthers; - - private static HashMap > _matchEncounterCache = new HashMap >(); - - // An URL to a thumbnail image representing the encounter. - private String dwcImageURL; - - // Defines whether the sighting represents a living or deceased individual. - // Currently supported values are: "alive" and "dead". - private String livingStatus; - - // observed age (if any) via IBEIS zebra projects - private Double age; - - // Date the encounter was added to the library. - private String dwcDateAdded; - private Long dwcDateAddedLong; - - // If Encounter spanned more than one day, date of release - private Date releaseDate; - - private Long releaseDateLong; - - // Size of the individual in meters - private Double size; - - // Additional comments added by library users - private String researcherComments = "None"; - - // username of the logged in researcher assigned to the encounter - // this String is matched to an org.ecocean.User object to obtain more information - private String submitterID; - - // name, email, phone, address of the encounter reporter - private String submitterEmail, submitterPhone, submitterAddress; - private String hashedSubmitterEmail; - private String hashedPhotographerEmail; - private String hashedInformOthers; - private String informothers; - - // name, email, phone, address of the encounter photographer - private String photographerName, photographerEmail, photographerPhone, photographerAddress; - - // a Vector of Strings defining the relative path to each photo. The path is relative to the servlet base directory - public Vector additionalImageNames = new Vector(); - - // a Vector of Strings of email addresses to notify when this encounter is modified - private Vector interestedResearchers = new Vector(); - - // time metrics of the report - private int hour = 0; - private String minutes = "00"; - - private String state = ""; - - // the globally unique identifier (GUID) for this Encounter - private String guid; - - private Long endDateInMilliseconds; - private Long dateInMilliseconds; - - // describes how the shark was measured - private String size_guess = "none provided"; - - // String reported GPS values for lat and long of the encounter - private String gpsLongitude = "", gpsLatitude = ""; - private String gpsEndLongitude = "", gpsEndLatitude = ""; - - // Indicates whether this record can be exposed via TapirLink - private boolean okExposeViaTapirLink = false; - - public String spotImageFileName = ""; - - // name of the stored file from which the right-side spots were extracted - public String rightSpotImageFileName = ""; - - // string descriptor of the most obvious scar (if any) as reported by the original submitter - // we also use keywords to be more specific - public String distinguishingScar = "None"; - // describes how this encounter was matched to an existing shark - by eye, by pattern recognition algorithm etc. - - // SPOTS - // an array of the extracted left-side superSpots - // private superSpot[] spots; - private ArrayList spots; - - // an array of the extracted right-side superSpots - // private superSpot[] rightSpots; - private ArrayList rightSpots; - - // an array of the three extracted left-side superSpots used for the affine transform of the I3S algorithm - // private superSpot[] leftReferenceSpots; - private ArrayList leftReferenceSpots; - - // an array of the three extracted right-side superSpots used for the affine transform of the I3S algorithm - // private superSpot[] rightReferenceSpots; - private ArrayList rightReferenceSpots; - - // an open ended string that allows a type of patterning to be identified. - // as an example, see the use of color codes at splashcatalog.org, allowing pre-defined fluke patterning types - // to be used to help narrow the search for a marked individual - private String patterningCode; - - // submitting organization and project further detail the scope of who submitted this project - private String submitterOrganization; - private String submitterProject; - private List submitterResearchers; - - // hold submittedData - // private List collectedData; - private List tissueSamples; - private List images; - // private ArrayList media; - private ArrayList annotations; - private List measurements; - private List metalTags; - private AcousticTag acousticTag; - private SatelliteTag satelliteTag; - private DigitalArchiveTag digitalArchiveTag; - - private Boolean mmaCompatible = false; - - // Variables used in the Survey, SurveyTrack, Path, Location model - - private String correspondingSurveyTrackID = null; - private String correspondingSurveyID = null; - - // This is the eventual replacement for the old decimal lat lon and other location data. - private PointLocation pointLocation; - - // This is the number used to cross reference with dates to find occurances. (Read Lab) - private String sightNo = ""; - - // This is what researchers eyeball is the individual's ID in the field - // it could be a name that only has meaning in the context of that day's work - // (not necessarily an individual name from the WB database) - private String fieldID; - - // This is a standard 1-5 color scale used by cetacean researchers - private Integer flukeType; - - // added by request for ASWN, this is the role an individual served in its occurrence - // (from a standard list like Escort Male) - private String groupRole; - - // identifies the import/dataset this came from for data provenance - private String dataSource; - - // start constructors - - /** - * empty constructor required by the JDO Enhancer - */ - public Encounter() {} - - public Encounter(boolean skipSetup) { - if (skipSetup) return; - this.catalogNumber = Util.generateUUID(); - this.setDWCDateAdded(); - this.setDWCDateLastModified(); - this.resetDateInMilliseconds(); - this.annotations = new ArrayList(); - } - - /** - * Use this constructor to add the minimum level of information for a new encounter The Vector additionalImages must be a Vector of - * Blob objects - * - * TODO: evaluate and remove if this is DEPRECATED cuz, SinglePhotoVideos? really? - */ - public Encounter(int day, int month, int year, int hour, String minutes, String size_guess, - String location) { - if (images != null) - System.out.println( - "WARNING: danger! deprecated SinglePhotoVideo-based Encounter constructor used!"); - this.verbatimLocality = location; - - this.images = images; - this.day = day; - this.month = month; - this.year = year; - this.hour = hour; - this.minutes = minutes; - this.size_guess = size_guess; - - this.setDWCDateAdded(); - this.setDWCDateLastModified(); - this.resetDateInMilliseconds(); - } - - public Encounter(Annotation ann) { - this(new ArrayList(Arrays.asList(ann))); - } - - public Encounter(ArrayList anns) { - this.catalogNumber = Util.generateUUID(); - this.annotations = anns; - if (!this.annotationsAreEmpty()) { - this.setDateFromAssets(); - this.setSpeciesFromAnnotations(); - this.setLatLonFromAssets(); - } - this.setDWCDateAdded(); - this.setDWCDateLastModified(); - this.resetDateInMilliseconds(); - } - private boolean annotationsAreEmpty() { - return (this.annotations == null || this.annotations.size() == 0 || - (this.annotations.size() == 1 && (this.annotations.get(0) == null))); - } - - // space saver since we're about to use this hundreds of times - private boolean shouldReplace(String str1, String str2) { - return Util.shouldReplace(str1, str2); - } - - // also returns true when str1 is a superstring of str2. - private boolean shouldReplaceSuperStr(String str1, String str2) { - return (shouldReplace(str1, str2) || (Util.stringExists(str1) && str1.contains(str2))); - } - - public void mergeAndDelete(Encounter enc2, Shepherd myShepherd) { - mergeDataFrom(enc2); - MarkedIndividual ind = myShepherd.getMarkedIndividual(enc2); - if (ind != null) { - ind.removeEncounter(enc2); - ind.addEncounter(this); // duplicate-safe - } - Occurrence occ = myShepherd.getOccurrence(enc2); - if (occ != null) { - occ.removeEncounter(enc2); - occ.addEncounter(this); // duplicate-safe - } - // Remove it from an ImportTask if needed - ImportTask task = myShepherd.getImportTaskForEncounter(enc2.getCatalogNumber()); - if (task != null) { - task.removeEncounter(enc2); - myShepherd.updateDBTransaction(); - } - // Remove from Project if needed - List projects = myShepherd.getProjectsForEncounter(enc2); - if (projects != null && !projects.isEmpty()) { - for (Project project : projects) { - project.removeEncounter(enc2); - myShepherd.updateDBTransaction(); - } - } - // remove tissue samples because of bogus foreign key constraint that prevents deletion - int numTissueSamples = 0; - if (enc2.getTissueSamples() != null) numTissueSamples = enc2.getTissueSamples().size(); - for (int i = 0; i < numTissueSamples; i++) { - enc2.removeTissueSample(0); - } - this.addComments("

    Merged in encounter " + enc2.getCatalogNumber() + "."); - - myShepherd.throwAwayEncounter(enc2); - } - - // copies otherEnc's data into thisEnc, not overwriting anything - public void mergeDataFrom(Encounter enc2) { - if (enc2.getIndividual() != null) setIndividual(enc2.getIndividual()); - // simple string fields - if (shouldReplace(enc2.getSex(), getSex())) setSex(enc2.getSex()); - if (shouldReplace(enc2.getLocationID(), getLocationID())) - setLocationID(enc2.getLocationID()); - if (shouldReplace(enc2.getVerbatimLocality(), getVerbatimLocality())) - setVerbatimLocality(enc2.getVerbatimLocality()); - if (shouldReplace(enc2.getOccurrenceID(), getOccurrenceID())) - setOccurrenceID(enc2.getOccurrenceID()); - if (shouldReplace(enc2.getRecordedBy(), getRecordedBy())) - setRecordedBy(enc2.getRecordedBy()); - if (shouldReplace(enc2.getEventID(), getEventID())) setEventID(enc2.getEventID()); - if (shouldReplace(enc2.getGenus(), getGenus())) setGenus(enc2.getGenus()); - if (shouldReplace(enc2.getSpecificEpithet(), getSpecificEpithet())) - setSpecificEpithet(enc2.getSpecificEpithet()); - if (shouldReplace(enc2.getLifeStage(), getLifeStage())) setLifeStage(enc2.getLifeStage()); - if (shouldReplace(enc2.getCountry(), getCountry())) setCountry(enc2.getCountry()); - if (shouldReplace(enc2.getZebraClass(), getZebraClass())) - setZebraClass(enc2.getZebraClass()); - if (shouldReplace(enc2.getSoil(), getSoil())) setSoil(enc2.getSoil()); - if (shouldReplace(enc2.getReproductiveStage(), getReproductiveStage())) - setReproductiveStage(enc2.getReproductiveStage()); - if (shouldReplace(enc2.getLivingStatus(), getLivingStatus())) - setLivingStatus(enc2.getLivingStatus()); - if (shouldReplace(enc2.getSubmitterEmail(), getSubmitterEmail())) - setSubmitterEmail(enc2.getSubmitterEmail()); - if (shouldReplace(enc2.getSubmitterPhone(), getSubmitterPhone())) - setSubmitterPhone(enc2.getSubmitterPhone()); - if (shouldReplace(enc2.getSubmitterAddress(), getSubmitterAddress())) - setSubmitterAddress(enc2.getSubmitterAddress()); - if (shouldReplace(enc2.getState(), getState())) setState(enc2.getState()); - if (shouldReplace(enc2.getGPSLongitude(), getGPSLongitude())) - setGPSLongitude(enc2.getGPSLongitude()); - if (shouldReplace(enc2.getGPSLatitude(), getGPSLatitude())) - setGPSLatitude(enc2.getGPSLatitude()); - if (shouldReplace(enc2.getPatterningCode(), getPatterningCode())) - setPatterningCode(enc2.getPatterningCode()); - if (shouldReplace(enc2.getSubmitterOrganization(), getSubmitterOrganization())) - setSubmitterOrganization(enc2.getSubmitterOrganization()); - if (shouldReplace(enc2.getSubmitterProject(), getSubmitterProject())) - setSubmitterProject(enc2.getSubmitterProject()); - if (shouldReplace(enc2.getFieldID(), getFieldID())) setFieldID(enc2.getFieldID()); - if (shouldReplace(enc2.getGroupRole(), getGroupRole())) setGroupRole(enc2.getGroupRole()); - // now string fields that might need to be combined rather than replaced - if (shouldReplaceSuperStr(enc2.getDynamicProperties(), getDynamicProperties())) { - setDynamicProperties(enc2.getDynamicProperties()); - } else if (Util.stringExists(enc2.getDynamicProperties())) { // shouldn't replace, should combine - addDynamicProperties(enc2.getDynamicProperties()); - } - if (shouldReplaceSuperStr(enc2.getOccurrenceRemarks(), getOccurrenceRemarks())) { - setOccurrenceRemarks(enc2.getOccurrenceRemarks()); - } else if (Util.stringExists(enc2.getOccurrenceRemarks())) { // shouldn't replace, should combine - setOccurrenceRemarks(getOccurrenceRemarks() + " " + enc2.getOccurrenceRemarks()); - } - // now combine list fields making sure not to add duplicate entries - setAnnotations(Util.combineArrayListsInPlace(getAnnotations(), enc2.getAnnotations())); - setObservationArrayList(Util.combineArrayListsInPlace(getObservationArrayList(), - enc2.getObservationArrayList())); - setSubmitterResearchers(Util.combineListsInPlace(getSubmitterResearchers(), - enc2.getSubmitterResearchers())); - // custom no-duplicate logic bc the same sampleID may have been added on both encounters, but this would create unique tissuesample objects - Set sampleIDs = getTissueSampleIDs(); - for (TissueSample samp : enc2.getTissueSamples()) { - if (!sampleIDs.contains(samp.getSampleID())) addTissueSample(samp); - } - setMeasurements(Util.combineListsInPlace(getMeasurements(), enc2.getMeasurements())); - setMetalTags(Util.combineListsInPlace(getMetalTags(), enc2.getMetalTags())); - - // spot lists - setSpots(Util.combineArrayListsInPlace(getSpots(), enc2.getSpots())); - setRightSpots(Util.combineArrayListsInPlace(getRightSpots(), enc2.getRightSpots())); - setLeftReferenceSpots(Util.combineArrayListsInPlace(getLeftReferenceSpots(), - enc2.getLeftReferenceSpots())); - setRightReferenceSpots(Util.combineArrayListsInPlace(getRightReferenceSpots(), - enc2.getRightReferenceSpots())); - // tags - if (enc2.getAcousticTag() != null && getAcousticTag() == null) - setAcousticTag(enc2.getAcousticTag()); - if (enc2.getSatelliteTag() != null && getSatelliteTag() == null) - setSatelliteTag(enc2.getSatelliteTag()); - if (enc2.getDTag() != null && getDTag() == null) setDTag(enc2.getDTag()); - // skip time stuff bc if the time is different we probably don't want to combine the encounters anyway. - } - - public String getZebraClass() { - return zebraClass; - } - - public void setZebraClass(String c) { - zebraClass = c; - } - - public String getImageNames() { - return imageNames; - } - - public void addImageName(String name) { - if (imageNames == null) imageNames = name; - else if (name != null) imageNames += (", " + name); - } - - public String addAllImageNamesFromAnnots(boolean overwrite) { - if (overwrite) imageNames = null; - return addAllImageNamesFromAnnots(); - } - - public String addAllImageNamesFromAnnots() { - for (Annotation ann : getAnnotations()) { - for (Feature feat : ann.getFeatures()) { - try { - MediaAsset ma = feat.getMediaAsset(); - addImageName(ma.getFilename()); - } catch (Exception e) { - System.out.println("exception parsing image name from feature " + feat); - } - } - } - return imageNames; - } - - /** - * Returns an array of all of the superSpots for this encounter. - * - * @return the array of superSpots, taken from the croppedImage, that make up the digital fingerprint for this encounter - */ - public ArrayList getSpots() { - return spots; - } - - public ArrayList getRightSpots() { - return rightSpots; - } - - /** - * Returns an array of all of the superSpots for this encounter. - * - * @return the array of superSpots, taken from the croppedImage, that make up the digital fingerprint for this encounter - */ -/* TODO: evaluate if this is deprecate and can be removed - these have gone away! dont be setting spots on Encounter any more .... NOT SO FAST... we regress for whaleshark.org... */ - public void setSpots(ArrayList newSpots) { - spots = newSpots; - } - - public void setRightSpots(ArrayList newSpots) { - rightSpots = newSpots; - } - - /** - * Removes any spot data - */ - public void removeSpots() { - spots = null; - } - - public void removeRightSpots() { - rightSpots = null; - } - - public Integer getFlukeType() { return this.flukeType; } - public void setFlukeType(Integer flukeType) { this.flukeType = flukeType; } - // this averages all the fluketypes - public void setFlukeTypeFromKeywords() { - int totalFlukeType = 0; - int numFlukes = 0; - - for (Annotation ann : getAnnotations()) { - Integer thisFlukeType = getFlukeTypeFromAnnotation(ann); - if (thisFlukeType != null) { - totalFlukeType += thisFlukeType; - numFlukes++; - } - } - if (numFlukes == 0) return; - setFlukeType(totalFlukeType / numFlukes); - } - - // assuming the list is of erroneously-duplicated encounters, returns the one we want to keep - public static Encounter chooseFromDupes(List encs) { - int maxAnns = -1; - int encWithMax = 0; - - for (int i = 0; i < encs.size(); i++) { - Encounter enc = encs.get(i); - if (enc.numAnnotations() > maxAnns) { - maxAnns = enc.numAnnotations(); - encWithMax = i; - } - } - return encs.get(encWithMax); - } - - public static Integer getFlukeTypeFromAnnotation(Annotation ann) { - return getFlukeTypeFromAnnotation(ann, 5); - } - - // int maxScore is used because some people store flukeType on a 5 point (most standard), some on a 9 point scale - public static Integer getFlukeTypeFromAnnotation(Annotation ann, int maxScore) { - MediaAsset ma = ann.getMediaAsset(); - - if (ma == null || !ma.hasKeywords()) return null; - String flukeTypeKwPrefix = "fluke" + maxScore + ":"; - for (Keyword kw : ma.getKeywords()) { - String kwName = kw.getReadableName(); - if (kwName.contains(flukeTypeKwPrefix)) { - String justScore = kwName.split(flukeTypeKwPrefix)[1]; - try { - Integer score = Integer.parseInt(justScore); - if (score != null) return score; - } catch (NumberFormatException nfe) { - System.out.println("NFE on getFlukeTypeFromAnnotation! For ann " + ann + - " and kwPrefix " + flukeTypeKwPrefix); - } - } - } - return null; - } - - // yes, there "should" be only one of each of these, but we be thorough! - public void removeLeftSpotMediaAssets(Shepherd myShepherd) { - ArrayList spotMAs = this.findAllMediaByLabel(myShepherd, "_spot"); - - for (MediaAsset ma : spotMAs) { - System.out.println("INFO: removeLeftSpotMediaAsset() detaching " + ma + - " from parent id=" + ma.getParentId()); - ma.setParentId(null); - } - } - - public void removeRightSpotMediaAssets(Shepherd myShepherd) { - ArrayList spotMAs = this.findAllMediaByLabel(myShepherd, "_spotRight"); - - for (MediaAsset ma : spotMAs) { - System.out.println("INFO: removeRightSpotMediaAsset() detaching " + ma + - " from parent id=" + ma.getParentId()); - ma.setParentId(null); - } - } - - public void nukeAllSpots() { - leftReferenceSpots = null; - rightReferenceSpots = null; - spots = null; - rightSpots = null; - } - - /** - * Returns the number of spots in the cropped image stored for this encounter. - * - * @return the number of superSpots that make up the digital fingerprint for this encounter - */ - public int getNumSpots() { - return (spots == null) ? 0 : spots.size(); - } - - public int getNumRightSpots() { - return (rightSpots == null) ? 0 : rightSpots.size(); - } - - public boolean hasLeftSpotImage() { - return (this.getNumSpots() > 0); - } - - public boolean hasRightSpotImage() { - return (this.getNumRightSpots() > 0); - } - - // Sets the recorded length of the shark for this encounter. - public void setSize(Double mysize) { - if (mysize != null) { size = mysize; } else { size = null; } - } - - // @return the length of the shark - public double getSize() { - return size.doubleValue(); - } - - public Double getSizeAsDouble() { - return size; - } - - // Sets the units of the recorded size and depth of the shark for this encounter. Acceptable entries are either "Feet" or "Meters" - public void setMeasureUnits(String measure) { - measurementUnit = measure; - } - - // @return the units of measure used by the recorded of this encounter, either "feet" or "meters" - public String getMeasureUnits() { - return measurementUnit; - } - - public String getMeasurementUnit() { - return measurementUnit; - } - - // @return the location of this encounter - public String getLocation() { - return verbatimLocality; - } - - public void setLocation(String location) { - this.verbatimLocality = location; - } - - // Sets the recorded sex of the shark in this encounter. Acceptable values are "Male" or "Female" - public void setSex(String thesex) { - if (thesex != null) { sex = thesex; } else { sex = null; } - } - - // @return the sex of the shark, either "male" or "female" - public String getSex() { - return sex; - } - - // @return any comments regarding observed scarring on the shark's body - public boolean getMmaCompatible() { - if (mmaCompatible == null) return false; - return mmaCompatible; - } - - public void setMmaCompatible(boolean b) { - mmaCompatible = b; - } - - // @return Occurrence Remarks String - @Override public String getComments() { - return occurrenceRemarks; - } - - // FIXME why is setComments() affecting occurrenceRemarks, and yet - // addComments() affecting researchComments !!!!!???? - // @param newComments Occurrence remarks to set - @Override public void setComments(String newComments) { - occurrenceRemarks = newComments; - } - - // @return any comments added by authroized researchers - public String getRComments() { - return researcherComments; - } - - // @param newComments any additional comments to be added to the encounter - @Override public void addComments(String newComments) { - if ((researcherComments != null) && (!(researcherComments.equals("None")))) { - researcherComments += newComments; - } else { - researcherComments = newComments; - } - } - - // @return the name of the person who submitted this encounter to the database - public String getSubmitterName() { - return recordedBy; - } - - public void setSubmitterName(String newname) { - if (newname == null) { - recordedBy = null; - } else { - recordedBy = newname; - } - } - - // @return the e-mail address of the person who submitted this encounter data - public String getSubmitterEmail() { - return submitterEmail; - } - - public void setSubmitterEmail(String newemail) { - if (newemail == null) { - submitterEmail = null; - this.hashedSubmitterEmail = null; - } else { - submitterEmail = newemail; - this.hashedSubmitterEmail = Encounter.getHashOfEmailString(newemail); - } - } - - // @return the phone number of the person who submitted this encounter data - public String getSubmitterPhone() { - return submitterPhone; - } - - // Sets the phone number of the person who submitted this encounter data. - public void setSubmitterPhone(String newphone) { - if (newphone == null) { - submitterPhone = null; - } else { - submitterPhone = newphone; - } - } - - // @return the mailing address of the person who submitted this encounter data - public String getSubmitterAddress() { - return submitterAddress; - } - - // Sets the mailing address of the person who submitted this encounter data. - public void setSubmitterAddress(String address) { - if (address == null) { - submitterAddress = null; - } else { - submitterAddress = address; - } - } - - // @return the name of the photographer who took the primary image for this encounter - public String getPhotographerName() { - return photographerName; - } - - // @return the name of the photographer who took the primary image for this encounter - public void setPhotographerName(String name) { - if (name == null) { - photographerName = null; - } else { - photographerName = name; - } - } - - // @return the e-mail address of the photographer who took the primary image for this encounter - public String getPhotographerEmail() { - return photographerEmail; - } - - // Sets the e-mail address of the person who took the primaryImage this encounter. - public void setPhotographerEmail(String email) { - if (email == null) { - photographerEmail = null; - this.hashedPhotographerEmail = null; - } else { - photographerEmail = email; - this.hashedPhotographerEmail = Encounter.getHashOfEmailString(email); - } - } - - // @return the phone number of the photographer who took the primary image for this encounter - public String getPhotographerPhone() { - return photographerPhone; - } - - // this is a cruddy "solution" to .submitterName and .submitters existing simultaneously - public Set getAllSubmitterIds(Shepherd myShepherd) { - Set all = new HashSet(); - User owner = this.getSubmitterUser(myShepherd); - - if (owner == null) { - all.add(this.submitterID); - all.add(this.submitterEmail); - } else { - all.add(owner.getUsername()); - all.add(owner.getFullName()); - all.add(owner.getId()); - all.add(owner.getEmailAddress()); - } - if (this.submitters != null) - for (User user : this.submitters) { - all.add(user.getUsername()); - all.add(user.getFullName()); - all.add(user.getId()); - all.add(user.getEmailAddress()); - } - all.remove(null); - all.remove(""); - return all; - } - - // similar to above - public Set getAllPhotographerIds() { - Set all = new HashSet(); - - all.add(this.photographerName); - if (this.photographers != null) - for (User user : this.photographers) { - all.add(user.getUsername()); - all.add(user.getFullName()); - all.add(user.getId()); - all.add(user.getEmailAddress()); - } - all.remove(null); - all.remove(""); - return all; - } - - public Set getAllInformOtherIds() { - Set all = new HashSet(); - - if (this.informOthers != null) - for (User user : this.informOthers) { - all.add(user.getUsername()); - all.add(user.getFullName()); - all.add(user.getId()); - all.add(user.getEmailAddress()); - } - all.remove(null); - all.remove(""); - return all; - } - - public String getWebUrl(HttpServletRequest req) { - return getWebUrl(this.getCatalogNumber(), req); - } - - public static String getWebUrl(String encId, HttpServletRequest req) { - return getWebUrl(encId, CommonConfiguration.getServerURL(req)); - } - - public static String getWebUrl(String encId, String serverUrl) { - return (serverUrl + "/encounters/encounter.jsp?number=" + encId); - } - - // Sets the phone number of the person who took the primaryImage this encounter. - public void setPhotographerPhone(String phone) { - if (phone == null) { - photographerPhone = null; - } else { - photographerPhone = phone; - } - } - - // @return the mailing address of the photographer who took the primary image for this encounter - public String getPhotographerAddress() { - return photographerAddress; - } - - // Sets the mailing address of the person who took the primaryImage this encounter. - public void setPhotographerAddress(String address) { - if (address == null) { - photographerAddress = null; - } else { - photographerAddress = address; - } - } - - // Sets the recorded depth of this encounter. - public void setDepth(Double myDepth) { - if (myDepth != null) { maximumDepthInMeters = myDepth; } else { - maximumDepthInMeters = null; - } - } - - // @return the recorded depth for this encounter - public double getDepth() { - return maximumDepthInMeters.doubleValue(); - } - - public Double getDepthAsDouble() { - return maximumDepthInMeters; - } - - // @return a vector of image name Strings - public Vector getAdditionalImageNames() { - Vector imageNamesOnly = new Vector(); - - if ((images != null) && (images.size() > 0)) { - int imagesSize = images.size(); - for (int i = 0; i < imagesSize; i++) { - SinglePhotoVideo dce = (SinglePhotoVideo)images.get(i); - imageNamesOnly.add(dce.getFilename()); - } - } - return imageNamesOnly; - } - - public String getFieldID() { - return this.fieldID; - } - - public void setFieldID(String fieldID) { - this.fieldID = fieldID; - } - - public String getGroupRole() { - return this.groupRole; - } - - public void setGroupRole(String role) { - this.groupRole = role; - } - - public String getDataSource() { - return dataSource; - } - - public void setDataSource(String dataSource) { - this.dataSource = dataSource; - } - - public String getImageOriginalName() { - MediaAsset ma = getPrimaryMediaAsset(); - - if (ma == null) return null; - return ma.getFilename(); - } - - // @return a unique integer String used to identify this encounter in the database - public String getEncounterNumber() { - return catalogNumber; - } - - public String generateEncounterNumber() { - return Util.generateUUID(); - } - - public String dir(String baseDir) { - return baseDir + File.separator + "encounters" + File.separator + this.subdir(); - } - - // like above, but class method so you pass the encID - public static String dir(String baseDir, String id) { - return baseDir + File.separator + "encounters" + File.separator + subdir(id); - } - - // like above, but can pass a File in for base - public static String dir(File baseDir, String id) { - return baseDir.getAbsolutePath() + File.separator + "encounters" + File.separator + - subdir(id); - } - - // subdir() is kind of a utility function, which can be called as enc.subdir() or Encounter.subdir(IDSTRING) as needed - public String subdir() { - return subdir(this.getEncounterNumber()); - } - - public static String subdir(String id) { - String d = id; // old-world - - if (Util.isUUID(id)) { // new-world - d = id.charAt(0) + File.separator + id.charAt(1) + File.separator + id; - } - return d; - } - - // @return a Date object - public String getDate() { - String date = ""; - String time = ""; - - if (year <= 0) { - return "Unknown"; - } else if (month == -1) { - return Integer.toString(year); - } - if (hour != -1) { - String localMinutes = minutes; - if (!Util.stringExists(localMinutes)) { - localMinutes = "00"; - } else if (localMinutes.length() == 1) { - localMinutes = "0" + localMinutes; - } - time = String.format("%02d:%s", hour, localMinutes); - } - if (day > 0) { - date = String.format("%04d-%02d-%02d %s", year, month, day, time); - } else if (month > 0) { - date = String.format("%04d-%02d %s", year, month, time); - } else { - date = String.format("%04d %s", year, time); - } - return date.trim(); - } - - public String getShortDate() { - String date = ""; - - if (year <= 0) { - return "Unknown"; - } else if (month == -1) { - return Integer.toString(year); - } - if (day > 0) { - date = String.format("%02d/%02d/%04d", day, month, year); - } else { - date = String.format("%02d/%04d", month, year); - } - return date; - } - - public org.json.JSONObject getDateValuesJson() { - org.json.JSONObject dv = new org.json.JSONObject(); - // in theory we *always* should have at least a year, but our data probably says otherwise - // sadly we just bail empty if we dont have a year - if (getYear() < 1900) return dv; - dv.put("year", getYear()); - // from here on out we only add things if the previous one existed; hence the short-circuit return - // e.g. we do not add a day if there was no month - if ((getMonth() < 1) || (getMonth() > 12)) return dv; - dv.put("month", getMonth()); - // sorry not checking actual days-per-month here - if ((getDay() < 1) || (getDay() > 31)) return dv; - dv.put("day", getDay()); - if ((getHour() < 0) || (getHour() > 23)) return dv; - dv.put("hour", getHour()); - // sigh, deal with string-based minutes... - Integer min = getMinutesInteger(); - if ((min != null) && (min >= 0) && (min < 60)) { - dv.put("minutes", min); - } else { - // choosing to do this because we *must* have hour value here, so dumb to leave null? - dv.put("minutes", 0); - } - return dv; - } - - // @return a String with text about how the size of this animal was estimated/measured - public String getSizeGuess() { - return size_guess; - } - - public void setDay(int day) { - this.day = day; - resetDateInMilliseconds(); - } - - public void setHour(int hour) { - this.hour = hour; - resetDateInMilliseconds(); - } - - public void setMinutes(String minutes) { - this.minutes = minutes; - resetDateInMilliseconds(); - } - - public String getMinutes() { - return minutes; - } - - public Integer getMinutesInteger() { - Integer min = null; - - try { min = Integer.parseInt(minutes); } catch (Exception e) {} - return min; - } - - public int getHour() { - return hour; - } - - public void setMonth(int month) { - this.month = month; - resetDateInMilliseconds(); - } - - public void setYear(int year) { - this.year = year; - resetDateInMilliseconds(); - } - - // this does not reset year/month/etc - public void setDateInMillisOnly(long ms) { - this.dateInMilliseconds = ms; - } - - public int getDay() { - return day; - } - - public int getMonth() { - return month; - } - - public int getYear() { - return year; - } - - public boolean wasInPeriod(DateTime start, DateTime end) { - Long thisTime = getDateInMilliseconds(); - - if (thisTime == null) return false; - long endOfDay = end.withTime(23, 59, 59, 999).getMillis(); - return (start.getMillis() <= thisTime && endOfDay >= thisTime); - } - - // @return the String holding specific location data used for searching - public String getLocationCode() { - return locationID; - } - - // TODO: Verify and remove if this is deprecated: A legacy method replaced by setLocationID(...). - public void setLocationCode(String newLoc) { - setLocationID(newLoc); - } - - // @return the String holding specific location data used for searching - public String getDistinguishingScar() { - return distinguishingScar; - } - - // Sets the String holding scarring information for the encounter - public void setDistinguishingScar(String scar) { - distinguishingScar = scar; - } - - // Sets the String documenting how the size of this animal was approximated. - public void setSizeGuess(String newGuess) { - size_guess = newGuess; - } - - public String getMatchedBy() { - if ((identificationRemarks == null) || (identificationRemarks.equals(""))) { - return "Unknown"; - } - return identificationRemarks; - } - - public void setMatchedBy(String matchType) { - identificationRemarks = matchType; - } - - public void setIdentificationRemarks(String matchType) { - identificationRemarks = matchType; - } - - /** - * Sets the unique encounter identifier to be usd with this encounter. Once this is set, it cannot be changed without possible impact to the - * database structure. - * - * @param num the unique integer to be used to uniquely identify this encoun ter in the database - */ - public void setEncounterNumber(String num) { - catalogNumber = num; - } - - public boolean hasMarkedIndividual() { - return (individual != null); - } - - public boolean hasMarkedIndividual(MarkedIndividual match) { - if (match == null) return false; - if (individual == null) return false; - return (match.getId().equals(individual.getId())); - } - - public void assignToMarkedIndividual(MarkedIndividual indiv) { - setIndividual(indiv); - } - - public void setIndividual(MarkedIndividual indiv) { - if (indiv == null) { this.individual = null; } else { this.individual = indiv; } - this.refreshAnnotationLiteIndividual(); - } - - public MarkedIndividual getIndividual() { - return individual; - } - - public String getDisplayName() { - return (individual == null) ? null : individual.getDisplayName(); - } - - public String getIndividualID() { - if (individual == null) return null; - return individual.getId(); - } - - public String getGPSLongitude() { - if (gpsLongitude == null) { - return ""; - } else { - return gpsLongitude; - } - } - - public void setGPSLongitude(String newLong) { - gpsLongitude = newLong; - } - - public String getGPSLatitude() { - if (gpsLatitude == null) { - return ""; - } else { - return gpsLatitude; - } - } - - public void setGPSLatitude(String newLat) { - gpsLatitude = newLat; - } - - public Encounter getClone() { - Encounter tempEnc = new Encounter(); - - try { - tempEnc = (Encounter)this.clone(); - } catch (java.lang.CloneNotSupportedException e) { - e.printStackTrace(); - } - return tempEnc; - } - - public String getSpotImageFileName() { - return spotImageFileName; - } - - public void setSpotImageFileName(String name) { - spotImageFileName = name; - } - - // ------------- - // for the right side spot image - - public String getRightSpotImageFileName() { - return rightSpotImageFileName; - } - - public void setRightSpotImageFileName(String name) { - rightSpotImageFileName = name; - } - - // ---------------- - - // TODO: evaluate and remove if this has been deprecated: really only intended to convert legacy SinglePhotoVideo to MediaAsset/Annotation world - public ArrayList generateAnnotations(String baseDir, Shepherd myShepherd) { - if ((annotations != null) && (annotations.size() > 0)) return annotations; - if ((images == null) || (images.size() < 1)) return null; // probably pointless, so... - if (annotations == null) annotations = new ArrayList(); - boolean thumbDone = false; - ArrayList haveMedia = new ArrayList(); // so we dont add duplicates! - for (SinglePhotoVideo spv : images) { - MediaAsset ma = spv.toMediaAsset(myShepherd); - if (ma == null) { - System.out.println( - "WARNING: Encounter.generateAnnotations() could not create MediaAsset from SinglePhotoVideo " - + spv.getDataCollectionEventID() + "; skipping"); - continue; - } - if (haveMedia.contains(ma)) { - System.out.println( - "WARNING: Encounter.generateAnnotations() found a duplicate MediaAsset in the SinglePhotoVideo images; skipping -- " - + ma); - continue; - } - // note: we need at least minimal metadata (w,h) in order to make annotation, so if this fails, we are no-go - try { - ma.updateMetadata(); - } catch (IOException ioe) { - System.out.println( - "WARNING: Encounter.generateAnnotations() failed to updateMetadata() on original MediaAsset " - + ma + " (skipping): " + ioe.toString()); - continue; - } - ma.addLabel("_original"); - haveMedia.add(ma); - - annotations.add(new Annotation(getTaxonomyString(), ma)); - File idir = new File(spv.getFullFileSystemPath()).getParentFile(); - - addMediaIfNeeded(myShepherd, new File(idir, spv.getDataCollectionEventID() + ".jpg"), - "spv/" + spv.getDataCollectionEventID() + "/" + spv.getDataCollectionEventID() + - ".jpg", ma, "_watermark"); - addMediaIfNeeded(myShepherd, - new File(idir, spv.getDataCollectionEventID() + "-mid.jpg"), - "spv/" + spv.getDataCollectionEventID() + "/" + spv.getDataCollectionEventID() + - "-mid.jpg", ma, "_mid"); - // note: we "assume" thumb was created from 0th spv, cuz we simply dont know but want it living somewhere - if (!thumbDone) - addMediaIfNeeded(myShepherd, new File(idir, "/thumb.jpg"), - "spv/" + spv.getDataCollectionEventID() + "/thumb.jpg", ma, "_thumb"); - thumbDone = true; - } - // we need to have the spot image as a child under *some* MediaAsset from above, but unfortunately we do not know its lineage. so we just - // pick one. :/ - MediaAsset sma = spotImageAsMediaAsset(((annotations.size() < - 1) ? null : annotations.get(0).getMediaAsset()), baseDir, myShepherd); - return annotations; - } - - // utility method for created MediaAssets - // note: also will check for existence of mpath and fail silently if doesnt exist - private MediaAsset addMediaIfNeeded(Shepherd myShepherd, File mpath, String key, - MediaAsset parentMA, String label) { - if ((mpath == null) || !mpath.exists()) return null; - AssetStore astore = AssetStore.getDefault(myShepherd); - org.json.JSONObject sp = astore.createParameters(mpath); - if (key != null) sp.put("key", key); // will use default from createParameters() (if there was one even) - MediaAsset ma = astore.find(sp, myShepherd); - if (ma != null) { - ma.addLabel(label); - if (parentMA != null) ma.setParentId(parentMA.getIdInt()); - return ma; - } - System.out.println("creating new MediaAsset for key=" + key); - try { - ma = astore.copyIn(mpath, sp); - } catch (IOException ioe) { - System.out.println("Could not create MediaAsset for key=" + key + ": " + - ioe.toString()); - return null; - } - if (parentMA != null) { - ma.setParentId(parentMA.getIdInt()); - ma.updateMinimalMetadata(); // for children (ostensibly derived?) MediaAssets, really only need minimal metadata or so i claim - } else { - try { - ma.updateMetadata(); // root images get the whole deal (guess this sh/could key off label=_original ?) - } catch (IOException ioe) { - // we dont care (well sorta) ... since IOException usually means we couldnt open file or some nonsense that we cant recover from - } - } - ma.addLabel(label); - MediaAssetFactory.save(ma, myShepherd); - return ma; - } - - // this makes assumption (for flukes) that both right and left image files are identical - public MediaAsset spotImageAsMediaAsset(MediaAsset parent, String baseDir, - Shepherd myShepherd) { - if ((spotImageFileName == null) || spotImageFileName.equals("")) return null; - File fullPath = new File(this.dir(baseDir) + "/" + spotImageFileName); -// System.out.println("**** * ***** looking for spot file " + fullPath.toString()); - if (!fullPath.exists()) return null; // note: this only technically matters if we are *creating* the MediaAsset - if (parent == null) { - System.out.println("seems like we do not have a parent MediaAsset on enc " + - this.getCatalogNumber() + ", so cannot add spot MediaAsset for " + - fullPath.toString()); - return null; - } - AssetStore astore = AssetStore.getDefault(myShepherd); - if (astore == null) { - System.out.println("No AssetStore in Encounter.spotImageAsMediaAsset()"); - return null; - } - System.out.println("trying spotImageAsMediaAsset with file=" + fullPath.toString()); - org.json.JSONObject sp = astore.createParameters(fullPath); - sp.put("key", this.subdir() + "/spotImage-" + spotImageFileName); - // others? - MediaAsset ma = astore.find(sp, myShepherd); - if (ma == null) { - System.out.println("did not find MediaAsset for params=" + sp + "; creating one?"); - try { - ma = astore.copyIn(fullPath, sp); - ma.addDerivationMethod("historicSpotImageConversion", true); - ma.updateMinimalMetadata(); -// System.out.println("params? " + ma.getParameters()); - ma.addLabel("_spot"); - ma.addLabel("_annotation"); - MediaAssetFactory.save(ma, myShepherd); -// System.out.println("params? " + ma.getParameters()); - } catch (java.io.IOException ex) { - System.out.println("spotImageAsMediaAsset threw IOException " + ex.toString()); - } - } - ma.setParentId(parent.getIdInt()); - return ma; - } - - public void setSubmitterID(String username) { - if (username != null) { submitterID = username; } else { submitterID = null; } - } - - // old method. use getAssignedUser() instead - public String getSubmitterID() { - return getAssignedUsername(); - } - - public String getAssignedUsername() { - return submitterID; - } - - public User getSubmitterUser(Shepherd myShepherd) { - return myShepherd.getUser(submitterID); - } - - public Vector getInterestedResearchers() { - return interestedResearchers; - } - - public void addInterestedResearcher(String email) { - interestedResearchers.add(email); - } - - public double getRightmostSpot() { - double rightest = 0; - ArrayList spots = getSpots(); - - for (int iter = 0; iter < spots.size(); iter++) { - if (spots.get(iter).getTheSpot().getCentroidX() > rightest) { - rightest = spots.get(iter).getTheSpot().getCentroidX(); - } - } - return rightest; - } - - public double getLeftmostSpot() { - double leftest = getRightmostSpot(); - ArrayList spots = getSpots(); - - for (int iter = 0; iter < spots.size(); iter++) { - if (spots.get(iter).getTheSpot().getCentroidX() < leftest) { - leftest = spots.get(iter).getTheSpot().getCentroidX(); - } - } - return leftest; - } - - public double getHighestSpot() { - double highest = getLowestSpot(); - ArrayList spots = getSpots(); - - for (int iter = 0; iter < spots.size(); iter++) { - if (spots.get(iter).getTheSpot().getCentroidY() < highest) { - highest = spots.get(iter).getTheSpot().getCentroidY(); - } - } - return highest; - } - - public double getLowestSpot() { - double lowest = 0; - ArrayList spots = getSpots(); - - for (int iter = 0; iter < spots.size(); iter++) { - if (spots.get(iter).getTheSpot().getCentroidY() > lowest) { - lowest = spots.get(iter).getTheSpot().getCentroidY(); - } - } - return lowest; - } - - public com.reijns.I3S.Point2D[] getThreeLeftFiducialPoints() { - com.reijns.I3S.Point2D[] Rray = new com.reijns.I3S.Point2D[3]; - if (getLeftReferenceSpots() != null) { - ArrayList refsLeft = getLeftReferenceSpots(); - - Rray[0] = new com.reijns.I3S.Point2D(refsLeft.get(0).getTheSpot().getCentroidX(), - refsLeft.get(0).getTheSpot().getCentroidY()); - Rray[1] = new com.reijns.I3S.Point2D(refsLeft.get(1).getTheSpot().getCentroidX(), - refsLeft.get(1).getTheSpot().getCentroidY()); - Rray[2] = new com.reijns.I3S.Point2D(refsLeft.get(2).getTheSpot().getCentroidX(), - refsLeft.get(2).getTheSpot().getCentroidY()); - System.out.println("\tI found three left reference points!"); - } else { - com.reijns.I3S.Point2D topLeft = new com.reijns.I3S.Point2D(getLeftmostSpot(), - getHighestSpot()); - com.reijns.I3S.Point2D bottomLeft = new com.reijns.I3S.Point2D(getLeftmostSpot(), - getLowestSpot()); - com.reijns.I3S.Point2D bottomRight = new com.reijns.I3S.Point2D(getRightmostSpot(), - getLowestSpot()); - Rray[0] = topLeft; - Rray[1] = bottomLeft; - Rray[2] = bottomRight; - } - return Rray; - } - - public com.reijns.I3S.Point2D[] getThreeRightFiducialPoints() { - com.reijns.I3S.Point2D[] Rray = new com.reijns.I3S.Point2D[3]; - if (getRightReferenceSpots() != null) { - ArrayList refsRight = getRightReferenceSpots(); - Rray[0] = new com.reijns.I3S.Point2D(refsRight.get(0).getTheSpot().getCentroidX(), - refsRight.get(0).getTheSpot().getCentroidY()); - Rray[1] = new com.reijns.I3S.Point2D(refsRight.get(1).getTheSpot().getCentroidX(), - refsRight.get(1).getTheSpot().getCentroidY()); - Rray[2] = new com.reijns.I3S.Point2D(refsRight.get(2).getTheSpot().getCentroidX(), - refsRight.get(2).getTheSpot().getCentroidY()); - } else { - com.reijns.I3S.Point2D topRight = new com.reijns.I3S.Point2D(getRightmostRightSpot(), - getHighestRightSpot()); - com.reijns.I3S.Point2D bottomRight = new com.reijns.I3S.Point2D(getRightmostRightSpot(), - getLowestRightSpot()); - com.reijns.I3S.Point2D bottomLeft = new com.reijns.I3S.Point2D(getLeftmostRightSpot(), - getLowestRightSpot()); - - Rray[0] = topRight; - Rray[1] = bottomRight; - Rray[2] = bottomLeft; - } - return Rray; - } - - public double getRightmostRightSpot() { - double rightest = 0; - ArrayList rightSpots = getRightSpots(); - - for (int iter = 0; iter < rightSpots.size(); iter++) { - if (rightSpots.get(iter).getTheSpot().getCentroidX() > rightest) { - rightest = rightSpots.get(iter).getTheSpot().getCentroidX(); - } - } - return rightest; - } - - public double getLeftmostRightSpot() { - double leftest = getRightmostRightSpot(); - ArrayList rightSpots = getRightSpots(); - - for (int iter = 0; iter < rightSpots.size(); iter++) { - if (rightSpots.get(iter).getTheSpot().getCentroidX() < leftest) { - leftest = rightSpots.get(iter).getTheSpot().getCentroidX(); - } - } - return leftest; - } - - public double getHighestRightSpot() { - double highest = getLowestRightSpot(); - ArrayList rightSpots = getRightSpots(); - - for (int iter = 0; iter < rightSpots.size(); iter++) { - if (rightSpots.get(iter).getTheSpot().getCentroidY() < highest) { - highest = rightSpots.get(iter).getTheSpot().getCentroidY(); - } - } - return highest; - } - - public double getLowestRightSpot() { - double lowest = 0; - ArrayList rightSpots = getRightSpots(); - - for (int iter = 0; iter < rightSpots.size(); iter++) { - if (rightSpots.get(iter).getTheSpot().getCentroidY() > lowest) { - lowest = rightSpots.get(iter).getTheSpot().getCentroidY(); - } - } - return lowest; - } - - public ArrayList getLeftReferenceSpots() { - // return HACKgetAnyReferenceSpots(); - return leftReferenceSpots; - } - - public ArrayList getRightReferenceSpots() { - // return HACKgetAnyReferenceSpots(); - return rightReferenceSpots; - } - -/* gone! no more setting spots on encounters! ... whoa there, yes there is for whaleshark.org */ - public void setLeftReferenceSpots(ArrayList leftReferenceSpots) { - this.leftReferenceSpots = leftReferenceSpots; - } - - public void setRightReferenceSpots(ArrayList rightReferenceSpots) { - this.rightReferenceSpots = rightReferenceSpots; - } - - // this is for jsonForApiGet() - public org.json.JSONObject spotMappingJsonForApiGet() { - org.json.JSONObject rtn = new org.json.JSONObject(); - boolean enabled = CommonConfiguration.useSpotPatternRecognition("context0"); - rtn.put("enabled", enabled); - if (!enabled) return rtn; - rtn.put("numberLeftSpots", getNumSpots()); - rtn.put("numberRightSpots", getNumRightSpots()); - rtn.put("hasLeftSpots", getNumSpots() > 0); - rtn.put("hasRightSpots", getNumRightSpots() > 0); - rtn.put("hasSpots", (getNumSpots() + getNumRightSpots()) > 0); - - // check where results xml is stored (per spotMappingAlgorith.jsp) - File ddir = Util.getDataDir(); - String encDir = dir(ddir.toString()); - rtn.put("resultsGrothLeft", new File(encDir, "lastFullScan.xml").exists()); - rtn.put("resultsGrothRight", new File(encDir, "lastFullRightScan.xml").exists()); - rtn.put("resultsI3SLeft", new File(encDir, "lastFullI3SScan.xml").exists()); - rtn.put("resultsI3SRight", new File(encDir, "lastFullRightI3SScan.xml").exists()); - return rtn; - } - - // @return the variance for population - public double variance(double[] population) { - long n = 0; - double mean = 0; - double s = 0.0; - - for (double x : population) { - n++; - double delta = x - mean; - mean += delta / n; - s += delta * (x - mean); - } - // if you want to calculate std deviation - // of a sample change this to (s/(n-1)) - // return (s / n); - return (s / (n - 1)); - } - - // @return the standard deviation for population - public double standard_deviation(double[] population) { - return Math.sqrt(variance(population)); - } - - public void setDWCGlobalUniqueIdentifier(String guid) { - this.guid = guid; - } - - public String getDWCGlobalUniqueIdentifier() { - return guid; - } - - public void setDWCImageURL(String link) { - dwcImageURL = link; - } - - // lmao, we have this capitalization of the getter for reflexivity purposes - public String getModified() { - return modified; - } - - public String getDWCDateLastModified() { - return modified; - } - - public void setDWCDateLastModified(String lastModified) { - modified = lastModified; - } - - public void setDWCDateLastModified() { - modified = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(new Date()); - } - - public String getDWCDateAdded() { - return dwcDateAdded; - } - - // lmao, we have this capitalization of the getter for reflexivity purposes - public String getDwcDateAdded() { - return dwcDateAdded; - } - - public Long getDWCDateAddedLong() { - return dwcDateAddedLong; - } - - public Long getDwcDateAddedLong() { - return dwcDateAddedLong; - } - - public void setDWCDateAdded(String m_dateAdded) { - dwcDateAdded = m_dateAdded; - } - - public void setDWCDateAdded() { - Date myDate = new Date(); - - dwcDateAddedLong = new Long(myDate.getTime()); - dwcDateAdded = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(myDate); - } - - public void setDWCDateAdded(Long m_dateAdded) { - dwcDateAddedLong = m_dateAdded; - } - - // TODO: evaluate and remove if deprecated - public Date getReleaseDateDONOTUSE() { - return releaseDate; - } - - public Date getReleaseDate() { - if ((releaseDateLong != null) && (releaseDateLong > 0)) { - Date mDate = new Date(releaseDateLong); - return mDate; - } - return null; - } - - public Long getReleaseDateLong() { return releaseDateLong; } - - public void setReleaseDate(Long releaseDate) { - this.releaseDateLong = releaseDate; - } - - // Survey ect associations... - - public void setSurveyTrackID(String id) { - if (id != null && !id.equals("")) { - this.correspondingSurveyTrackID = id; - } - } - - public String getSurveyTrackID() { - if (correspondingSurveyTrackID != null) { - return correspondingSurveyTrackID; - } - return null; - } - - public void setPointLocation(PointLocation loc) { - if (loc.getID() != null) { - this.pointLocation = loc; - } - } - - public PointLocation getPointLocation() { - if (pointLocation != null) { - return pointLocation; - } - return null; - } - - public String getSurveyID() { - if (correspondingSurveyID != null && !correspondingSurveyID.equals("")) { - return correspondingSurveyID; - } - return null; - } - - public void setSurveyID(String id) { - if (id != null && !id.equals("")) { - this.correspondingSurveyID = id; - } - } - - public void setSurvey() { - } - - // TODO: Get all this lat lon over to Locations - - public void setDWCDecimalLatitude(double lat) { - if (lat == -9999.0) { - decimalLatitude = null; - } else { - decimalLatitude = (new Double(lat)); - } - } - - public void setDWCDecimalLatitude(Double lat) { - if ((lat != null) && (lat <= 90) && (lat >= -90)) { - this.decimalLatitude = lat; - } else { this.decimalLatitude = null; } - } - - public String getDWCDecimalLatitude() { - if (decimalLatitude != null) { return Double.toString(decimalLatitude); } - return null; - } - - public void setDWCDecimalLongitude(double longit) { - if ((longit >= -180) && (longit <= 180)) { - this.decimalLongitude = longit; - } - } - - public String getDWCDecimalLongitude() { - if (decimalLongitude != null) { - return Double.toString(decimalLongitude); - } - return null; - } - - public boolean getOKExposeViaTapirLink() { - return okExposeViaTapirLink; - } - - public void setOKExposeViaTapirLink(boolean ok) { - okExposeViaTapirLink = ok; - } - - public void setAlternateID(String newID) { - this.otherCatalogNumbers = newID; - } - - public String getAlternateID() { - if (otherCatalogNumbers == null) { - return null; - } - return otherCatalogNumbers; - } - - public String getOLDInformOthersFORLEGACYCONVERSION() { - if (informothers == null) { - return ""; - } - return informothers; - } - - public String getLocationID() { - return locationID; - } - - public String getLocationName() { - if (locationID == null) return null; - return LocationID.getNameForLocationID(locationID, null); - } - - public void setLocationID(String newLocationID) { - if (newLocationID != null) { - this.locationID = newLocationID.trim(); - } else { - this.locationID = null; - } - } - - public Double getMaximumDepthInMeters() { - return maximumDepthInMeters; - } - - public void setMaximumDepthInMeters(Double newDepth) { - this.maximumDepthInMeters = newDepth; - } - - public Double getMaximumElevationInMeters() { - return maximumElevationInMeters; - } - - public void setMaximumElevationInMeters(Double newElev) { - this.maximumElevationInMeters = newElev; - } - - // @return Catalog Number String - @Override public String getId() { - return catalogNumber; - } - - // @param newNumber The Catalog Number to set. - @Override public void setId(String newNumber) { - this.catalogNumber = newNumber; - } - - // TODO: remove if actually deprecated and unused - // ##DEPRECATED #509 - Base class getId() method - public String getCatalogNumber() { - return catalogNumber; - } - - // TODO: remove if actually deprecated and unused - // ##DEPRECATED #509 - Base class setId() method - public void setCatalogNumber(String newNumber) { - this.catalogNumber = newNumber; - } - - // TODO: remove if actually deprecated and unused - // ##DEPRECATED #509 - Base class getId() method - public String getID() { - return catalogNumber; - } - - // TODO: remove if actually deprecated and unused - // ##DEPRECATED #509 - Base class setId() method - public void setID(String newNumber) { - this.catalogNumber = newNumber; - } - - public String getVerbatimLocality() { - return verbatimLocality; - } - - public void setVerbatimLocality(String vlcl) { - this.verbatimLocality = vlcl; - } - - public Double getDecimalLatitudeAsDouble() { - return (decimalLatitude == null) ? null : decimalLatitude.doubleValue(); - } - - public void setDecimalLatitude(Double lat) { - this.decimalLatitude = lat; - gpsLatitude = Util.decimalLatLonToString(lat); - } - - public Double getDecimalLongitudeAsDouble() { - return (decimalLongitude == null) ? null : decimalLongitude.doubleValue(); - } - - public void setDecimalLongitude(Double lon) { - this.decimalLongitude = lon; - gpsLongitude = Util.decimalLatLonToString(lon); - } - - public Double getEndDecimalLatitudeAsDouble() { - return (endDecimalLatitude == null) ? null : endDecimalLatitude.doubleValue(); - } - - public void setEndDecimalLatitude(Double lat) { - this.endDecimalLatitude = lat; - gpsEndLatitude = Util.decimalLatLonToString(lat); - } - - public Double getEndDecimalLongitudeAsDouble() { - return (endDecimalLongitude == null) ? null : endDecimalLongitude.doubleValue(); - } - - public void setEndDecimalLongitude(Double lon) { - this.endDecimalLongitude = lon; - gpsEndLongitude = Util.decimalLatLonToString(lon); - } - - public String getOccurrenceRemarks() { - return occurrenceRemarks; - } - - public void setOccurrenceRemarks(String remarks) { - this.occurrenceRemarks = remarks; - } - - public String getRecordedBy() { - return recordedBy; - } - - public void setRecordedBy(String submitterName) { - this.recordedBy = submitterName; - } - - public String getOtherCatalogNumbers() { - return otherCatalogNumbers; - } - - public void setOtherCatalogNumbers(String otherNums) { - this.otherCatalogNumbers = otherNums; - } - - public String getLivingStatus() { - return livingStatus; - } - - public void setLivingStatus(String status) { - this.livingStatus = status; - } - - public void setAge(Double a) { - age = a; - } - - public Double getAge() { - return age; - } - - public String getBehavior() { - return behavior; - } - - public void setBehavior(String beh) { - this.behavior = beh; - } - - public String getEventID() { - return eventID; - } - - public void setEventID(String id) { - this.eventID = id; - } - - public String getVerbatimEventDate() { - return verbatimEventDate; - } - - public void setVerbatimEventDate(String vet) { - if (vet != null) { this.verbatimEventDate = vet; } else { this.verbatimEventDate = null; } - } - - public String getDynamicProperties() { - return dynamicProperties; - } - - public org.json.JSONObject getDynamicPropertiesJSONObject() { - org.json.JSONObject dp = new org.json.JSONObject(); - if (dynamicProperties == null) return dp; - StringTokenizer st = new StringTokenizer(dynamicProperties, ";"); - while (st.hasMoreTokens()) { - String token = st.nextToken(); - int equalPlace = token.indexOf("="); - if (equalPlace > 0) - dp.put(token.substring(0, equalPlace), token.substring(equalPlace + 1)); - } - return dp; - } - - public void setDynamicProperties(String allDynamicProperties) { - this.dynamicProperties = allDynamicProperties; - } - - public void addDynamicProperties(String allDynamicProperties) { - this.dynamicProperties += allDynamicProperties; - } - - public void setDynamicProperty(String name, String value) { - name = name.replaceAll(";", "_").trim().replaceAll("%20", " "); - value = value.replaceAll(";", "_").trim(); - if (dynamicProperties == null) { dynamicProperties = name + "=" + value + ";"; } else { - // let's create a TreeMap of the properties - TreeMap tm = new TreeMap(); - StringTokenizer st = new StringTokenizer(dynamicProperties, ";"); - while (st.hasMoreTokens()) { - String token = st.nextToken(); - int equalPlace = token.indexOf("="); - try { - tm.put(token.substring(0, equalPlace), token.substring(equalPlace + 1)); - } catch (java.lang.StringIndexOutOfBoundsException soe) { - // this is a badly formatted pair that should be ignored - } - } - if (tm.containsKey(name)) { - tm.remove(name); - tm.put(name, value); - - // now let's recreate the dynamicProperties String - String newProps = tm.toString(); - int stringSize = newProps.length(); - dynamicProperties = newProps.substring(1, (stringSize - 1)).replaceAll(", ", - ";") + ";"; - } else { - dynamicProperties = dynamicProperties + name + "=" + value + ";"; - } - } - } - - public String getDynamicPropertyValue(String name) { - if (dynamicProperties != null) { - name = name.replaceAll("%20", " "); - // let's create a TreeMap of the properties - TreeMap tm = new TreeMap(); - StringTokenizer st = new StringTokenizer(dynamicProperties, ";"); - while (st.hasMoreTokens()) { - String token = st.nextToken(); - int equalPlace = token.indexOf("="); - tm.put(token.substring(0, equalPlace), token.substring(equalPlace + 1)); - } - if (tm.containsKey(name)) { - return tm.get(name); - } - } - return null; - } - - public boolean hasDynamicProperty(String name) { - return (this.getDynamicPropertyValue(name) != null); - } - - public void removeDynamicProperty(String name) { - name = name.replaceAll(";", "_").trim().replaceAll("%20", " "); - if (dynamicProperties != null) { - // let's create a TreeMap of the properties - TreeMap tm = new TreeMap(); - StringTokenizer st = new StringTokenizer(dynamicProperties, ";"); - while (st.hasMoreTokens()) { - String token = st.nextToken(); - int equalPlace = token.indexOf("="); - tm.put(token.substring(0, (equalPlace)), token.substring(equalPlace + 1)); - } - if (tm.containsKey(name)) { - tm.remove(name); - - // now let's recreate the dynamicProperties String - String newProps = tm.toString(); - int stringSize = newProps.length(); - dynamicProperties = newProps.substring(1, (stringSize - 1)).replaceAll(", ", - ";") + ";"; - } - } - } - - public String getIdentificationRemarks() { - return identificationRemarks; - } - - public String getHashedSubmitterEmail() { - return hashedSubmitterEmail; - } - - public String getHashedPhotographerEmail() { - return hashedPhotographerEmail; - } - - public String getHashedInformOthers() { - return hashedInformOthers; - } - - public static String getHashOfEmailString(String hashMe) { - if (hashMe == null) return null; - String returnString = ""; - StringTokenizer tokenizer = new StringTokenizer(hashMe, ","); - while (tokenizer.hasMoreTokens()) { - String emailAddress = tokenizer.nextToken().trim().toLowerCase(); - if (!emailAddress.equals("")) { - String md5 = DigestUtils.md5Hex(emailAddress); - if (returnString.equals("")) { - returnString += md5; - } else { - returnString += "," + md5; - } - } - } - return returnString; - } - - public String getGenus() { - return genus; - } - - public void setGenus(String newGenus) { - if (newGenus != null) { genus = newGenus; } else { genus = null; } - this.refreshAnnotationLiteTaxonomy(); - } - - // we need these methods because our side-effected setGenus will silently break an import (!!!!!) in an edge case I cannot identify - public void setGenusOnly(String genus) { - this.genus = genus; - this.refreshAnnotationLiteTaxonomy(); - } - - public void setSpeciesOnly(String species) { - setSpecificEpithet(species); - this.refreshAnnotationLiteTaxonomy(); - } - - public String getSpecificEpithet() { - return specificEpithet; - } - - public void setSpecificEpithet(String newEpithet) { - if (newEpithet != null) { specificEpithet = newEpithet.replaceAll("_", " "); } else { - specificEpithet = null; - } - this.refreshAnnotationLiteTaxonomy(); - } - - public String getTaxonomyString() { - return Util.taxonomyString(getGenus(), getSpecificEpithet()); - } - - // hacky (as generates new Taxonomy -- with random uuid) but still should work for tax1.equals(tax2); - // TODO: FIXME this should be superceded by the getter for Taxonomy property in the future.... - public Taxonomy getTaxonomy(Shepherd myShepherd) { - String sciname = this.getTaxonomyString(); - - if (sciname == null) return null; - return myShepherd.getOrCreateTaxonomy(sciname, false); // false means don't commit the taxonomy - } - - // right now this updates .genus and .specificEpithet ... but in some glorious future we will just store Taxonomy! - // note that "null" cases will leave *current values untouched* (does not reset them) - public void setTaxonomy(Taxonomy tax) { - if (tax == null) return; - String[] gs = tax.getGenusSpecificEpithet(); - if ((gs == null) || (gs.length < 1)) return; - if (gs.length == 1) { - this.genus = gs[0]; - this.specificEpithet = null; - } else { - this.genus = gs[0]; - this.specificEpithet = gs[1].replaceAll("_", " "); - } - this.refreshAnnotationLiteTaxonomy(); - } - - public void setTaxonomyFromString(String s) { // basically scientific name (will get split on space) - String[] gs = Util.stringToGenusSpecificEpithet(s); - - if ((gs == null) || (gs.length < 1)) return; - if (gs.length == 1) { - this.genus = gs[0]; - this.specificEpithet = null; - } else { - this.genus = gs[0]; - this.specificEpithet = gs[1].replaceAll("_", " "); - } - this.refreshAnnotationLiteTaxonomy(); - } - - public void setTaxonomyFromIAClass(String iaClass, Shepherd myShepherd) { - setTaxonomy(IBEISIA.iaClassToTaxonomy(iaClass, myShepherd)); - } - - public String getPatterningCode() { return patterningCode; } - public void setPatterningCode(String newCode) { this.patterningCode = newCode; } - - // crawls thru assets and sets date - public void setDateFromAssets() { - // FIXME if you dare. i can *promise you* there are some timezone problems here. ymmv. - if ((annotations == null) || (annotations.size() < 1)) return; - DateTime dt = null; - for (Annotation ann : annotations) { - MediaAsset ma = ann.getMediaAsset(); - if (ma == null) continue; - dt = ma.getDateTime(); - if (dt != null) break; // we just take the first one - } - if (dt != null) setDateInMilliseconds(dt.getMillis()); - } - - // this can(should?) fail in a lot of cases, since we may not know - public void setSpeciesFromAnnotations() { - if ((annotations == null) || (annotations.size() < 1)) return; - String[] sp = null; - for (Annotation ann : annotations) { - sp = IBEISIA.convertSpecies(annotations.get(0).getIAClass()); - if (sp != null) break; // use first one we get - } - // note: now we require (exactly) two parts ... please fix this, Taxonomy class! - if ((sp == null) || (sp.length != 2)) return; - this.setGenus(sp[0]); - this.setSpecificEpithet(sp[1]); - } - - // find the first one(s) we can - public void setLatLonFromAssets() { - if ((annotations == null) || (annotations.size() < 1)) return; - Double lat = null; - Double lon = null; - for (Annotation ann : annotations) { - MediaAsset ma = ann.getMediaAsset(); - if (ma == null) continue; - if (lat == null) lat = ma.getLatitude(); - if (lon == null) lon = ma.getLongitude(); - if ((lat != null) && (lon != null)) break; - } - if (lat != null) this.setDecimalLatitude(lat); - if (lon != null) this.setDecimalLongitude(lon); - } - - // sets date to the closes we have to "not set" :) - public void zeroOutDate() { - year = 0; - month = 0; - day = 0; - hour = -1; - minutes = "00"; - resetDateInMilliseconds(); // should set that to null as well - } - - public void resetDateInMilliseconds() { - dateInMilliseconds = computeDateInMilliseconds(); - } - - public Long computeDateInMilliseconds() { - if (year > 0) { - int localMonth = 0; - if (month > 0) { localMonth = month - 1; } - int localDay = 1; - if (day > 0) { localDay = day; } - int localHour = 0; - if (hour > -1) { localHour = hour; } - int myMinutes = 0; - try { myMinutes = Integer.parseInt(minutes); } catch (Exception e) {} - TimeZone tz = TimeZone.getTimeZone("UTC"); - Calendar calendar = Calendar.getInstance(tz); - calendar.set(year, localMonth, localDay, localHour, myMinutes); - return new Long(calendar.getTimeInMillis()); - } - return null; - } - - public java.lang.Long getDateInMilliseconds() { return dateInMilliseconds; } - - public Long getDateInMillisecondsFallback() { - if (dateInMilliseconds != null) return dateInMilliseconds; - return computeDateInMilliseconds(); - } - - // this will set all date stuff based on ms since epoch - public void setDateInMilliseconds(long ms) { - Calendar cal = Calendar.getInstance(TimeZone.getTimeZone("UTC")); - - cal.setTimeInMillis(ms); - this.year = cal.get(Calendar.YEAR); - this.month = cal.get(Calendar.MONTH) + 1; - this.day = cal.get(Calendar.DAY_OF_MONTH); - this.hour = cal.get(Calendar.HOUR); - this.minutes = Integer.toString(cal.get(Calendar.MINUTE)); - if (this.minutes.length() == 1) this.minutes = "0" + this.minutes; - this.dateInMilliseconds = ms; - } - - // also supports YYYY and YYYY-MM - // per issue 1489, cannot set a future date - public void setDateFromISO8601String(String iso8601) - throws ApiException { - if (!validISO8601String(iso8601)) return; - - // this is for potential ApiException - org.json.JSONObject error = new org.json.JSONObject(); - error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); - - if (iso8601.length() == 4) { // assume year - try { - this.year = Integer.parseInt(iso8601); - } catch (Exception ex) {} - - // got an int year, but lets see if it is valid - if (Util.dateIsInFuture(this.year, null, null)) { - error.put("fieldName", "year"); - error.put("value", this.year); - throw new ApiException("date is in the future", error); - } - resetDateInMilliseconds(); - return; - } - // this format should already be validated so we can trust it (flw) - if (iso8601.length() == 7) { - try { - this.year = Integer.parseInt(iso8601.substring(0, 4)); - this.month = Integer.parseInt(iso8601.substring(5, 7)); - } catch (Exception ex) {} - if (Util.dateIsInFuture(this.year, this.month, null)) { - // if we wanted to be super thorough we could do errors array of year & month - error.put("fieldName", "month"); - error.put("value", this.month); - throw new ApiException("date is in the future", error); - } - resetDateInMilliseconds(); - return; - } - try { - String adjusted = Util.getISO8601Date(iso8601); - DateTime dt = new DateTime(adjusted); - if (Util.dateIsInFuture(dt.getYear(), dt.getMonthOfYear(), dt.getDayOfMonth())) { - error.put("fieldName", "day"); - error.put("value", dt.getDayOfMonth()); - throw new ApiException("date is in the future", error); - } - this.setDateInMilliseconds(dt.getMillis()); - // pass this flavor out... - } catch (ApiException ex) { - throw ex; - // this catches failure of new DateTime() basically, so we make this an ApiException - } catch (Exception ex) { - System.out.println("setDateFromISO8601String(" + iso8601 + ") failed: " + ex); - throw new ApiException("date/time values are invalid"); - } - resetDateInMilliseconds(); - } - - // also supports YYYY and YYYY-MM - public static boolean validISO8601String(String iso8601) { - if (iso8601 == null) return false; - if (iso8601.length() == 4) { - Integer yr = null; - try { - yr = Integer.parseInt(iso8601); - } catch (Exception ex) {} - return (yr != null); - } - if (iso8601.length() == 7) { - Integer yr = null; - Integer mo = null; - try { - yr = Integer.parseInt(iso8601.substring(0, 4)); - mo = Integer.parseInt(iso8601.substring(5, 7)); - } catch (Exception ex) {} - if ((yr == null) || (mo == null)) return false; - if ((mo < 1) || (mo > 12)) return false; - return true; - } - long test = Util.getVersionFromModified(iso8601); - return (test > 0); - } - - public Long getEndDateInMilliseconds() { - return endDateInMilliseconds; - } - - public void setEndDateInMilliseconds(long ms) { - this.endDateInMilliseconds = ms; - } - - private String milliToMonthDayYear(Long millis) { - DateTime dt = new DateTime(millis); - DateTimeFormatter dtf = DateTimeFormat.forPattern("yyyy-MM-dd hh:mm a"); - - return dtf.print(dt); - } - - public String getStartDateTime() { - return milliToMonthDayYear(dateInMilliseconds); - } - - public String getEndDateTime() { - return milliToMonthDayYear(endDateInMilliseconds); - } - - public String getDecimalLatitude() { - if (decimalLatitude != null) { return Double.toString(decimalLatitude); } - return null; - } - - public String getDecimalLongitude() { - if (decimalLongitude != null) { return Double.toString(decimalLongitude); } - return null; - } - - public String getEndDecimalLongitude() { - if (endDecimalLongitude != null) { return Double.toString(endDecimalLongitude); } - return null; - } - - public String getEndDecimalLatitude() { - if (endDecimalLatitude != null) { return Double.toString(endDecimalLatitude); } - return null; - } - - public String getSubmitterProject() { - return submitterProject; - } - - public void setSubmitterProject(String newProject) { - if (newProject != null) { submitterProject = newProject; } else { submitterProject = null; } - } - - public String getSubmitterOrganization() { - return submitterOrganization; - } - - public void setSubmitterOrganization(String newOrg) { - if (newOrg != null) { submitterOrganization = newOrg; } else { - submitterOrganization = null; - } - } - - public List getSubmitterResearchers() { - return submitterResearchers; - } - - public void addSubmitterResearcher(String researcher) { - if (submitterResearchers == null) submitterResearchers = new ArrayList(); - submitterResearchers.add(researcher); - } - - public void setSubmitterResearchers(Collection researchers) { - if (researchers != null) this.submitterResearchers = new ArrayList(researchers); - } - - public List getProjects(Shepherd myShepherd) { - return myShepherd.getProjectsForEncounter(this); - } - - public void addTissueSample(TissueSample dce) { - if (tissueSamples == null) { tissueSamples = new ArrayList(); } - if (!tissueSamples.contains(dce)) { tissueSamples.add(dce); } - dce.setCorrespondingEncounterNumber(getCatalogNumber()); - } - - public void setTissueSamples(List samps) { - this.tissueSamples = samps; - } - - public void removeTissueSample(int num) { tissueSamples.remove(num); } - public List getTissueSamples() { return tissueSamples; } - public Set getTissueSampleIDs() { - Set ids = new HashSet(); - - if (tissueSamples != null) - for (TissueSample ts : tissueSamples) { - ids.add(ts.getSampleID()); - } - return ids; - } - - public void removeTissueSample(TissueSample num) { tissueSamples.remove(num); } - - public void addSinglePhotoVideo(SinglePhotoVideo dce) { - if (images == null) { images = new ArrayList(); } - if (!images.contains(dce)) { images.add(dce); } - } - - public void removeSinglePhotoVideo(int num) { images.remove(num); } - public List getSinglePhotoVideo() { return images; } - public void removeSinglePhotoVideo(SinglePhotoVideo num) { images.remove(num); } - - public void setMeasurements(List measurements) { - this.measurements = measurements; - } - - public void setMeasurement(Measurement measurement, Shepherd myShepherd) { - // if measurements are null, set the empty list - if (measurements == null) { measurements = new ArrayList(); } - // now start checking for existence of a previous measurement - // if we have it but the new value is null, remove the measurement - if ((this.hasMeasurement(measurement.getType())) && (measurement.getValue() == null)) { - Measurement m = this.getMeasurement(measurement.getType()); - measurements.remove(m); - myShepherd.getPM().deletePersistent(m); - myShepherd.commitDBTransaction(); - myShepherd.beginDBTransaction(); - } - // just add the measurement it if we did not have it before - else if (!this.hasMeasurement(measurement.getType())) { - measurements.add(measurement); - myShepherd.commitDBTransaction(); - myShepherd.beginDBTransaction(); - } - // if we had it before then just update the value - else if ((this.hasMeasurement(measurement.getType())) && (measurement != null)) { - Measurement m = this.getMeasurement(measurement.getType()); - m.setValue(measurement.getValue()); - m.setSamplingProtocol(measurement.getSamplingProtocol()); - myShepherd.commitDBTransaction(); - myShepherd.beginDBTransaction(); - } - } - - public Measurement removeMeasurementByType(String type) { - // findMeasurementOfType() seems to return even ones with value=null - // (versus getMeasurement())... so this seems the better choice? - Measurement m = findMeasurementOfType(type); - - if (m != null) measurements.remove(m); - return m; - } - - // will find the Measurement (by type) and modify it *or* make a new one - public Measurement getOrCreateMeasurement(org.json.JSONObject jdata) { - if (jdata == null) return null; - String type = jdata.optString("type", null); - if (type == null) return null; - Measurement m = findMeasurementOfType(type); - if (m == null) { - m = new Measurement(this.getId(), type, jdata.optDouble("value", 0.0D), - jdata.optString("units", null), jdata.optString("samplingProtocol", null)); - } else { - m.setValue(jdata.optDouble("value", 0.0D)); - m.setUnits(jdata.optString("units", null)); - m.setSamplingProtocol(jdata.optString("samplingProtocol", null)); - } - return m; - } - - // like above but way less persisty - public void setMeasurement(Measurement measurement) { - if (measurement == null) return; - if (measurements == null) measurements = new ArrayList(); - Measurement hasType = this.getMeasurement(measurement.getType()); - if (hasType == null) { - measurements.add(measurement); - } else if (measurement.getValue() == null) { - // i guess this means we remove it - measurements.remove(hasType); - } else { - // update existing - hasType.setValue(measurement.getValue()); - hasType.setSamplingProtocol(measurement.getSamplingProtocol()); - } - } - - // like above but less..... checky (trust the caller!) - public void addMeasurement(Measurement meas) { - if (meas == null) return; - if (measurements == null) measurements = new ArrayList(); - measurements.add(meas); - } - - public void removeMeasurement(int num) { measurements.remove(num); } - public List getMeasurements() { return measurements; } - public void removeMeasurement(Measurement num) { measurements.remove(num); } - // FIXME this seems suspiciously just like getMeasurement(type) - public Measurement findMeasurementOfType(String type) { - List measurements = getMeasurements(); - - if (measurements != null) { - for (Measurement measurement : measurements) { - if (type.equals(measurement.getType())) { - return measurement; - } - } - } - return null; - } - - public void addMetalTag(MetalTag metalTag) { - if (metalTags == null) { - metalTags = new ArrayList(); - } - metalTags.add(metalTag); - } - - // this does NOT validate values - public MetalTag addOrUpdateMetalTag(String location, String number) { - if ((location == null) || (number == null)) return null; - MetalTag tag = findMetalTagForLocation(location); - if (tag == null) { - tag = new MetalTag(number, location); - addMetalTag(tag); - } else { - tag.setTagNumber(number); - } - return tag; - } - - public void removeMetalTag(MetalTag metalTag) { - metalTags.remove(metalTag); - } - - // this will clear out ALL tags with this location, but i think we - // are supposed to only have [at most] one anyway! - public void removeMetalTag(String location) { - if ((location == null) || (metalTags == null)) return; - ListIterator it = metalTags.listIterator(); - while (it.hasNext()) { - MetalTag next = it.next(); - if (location.equals(next.getLocation())) it.remove(); - } - } - - public void setMetalTags(List metalTags) { - this.metalTags = metalTags; - } - - public List getMetalTags() { - return metalTags; - } - - public MetalTag findMetalTagForLocation(String location) { - List metalTags = getMetalTags(); - - if (metalTags != null) { - for (MetalTag metalTag : metalTags) { - if (location.equals(metalTag.getLocation())) { - return metalTag; - } - } - } - return null; - } - - public AcousticTag getAcousticTag() { - return acousticTag; - } - - public void setAcousticTag(AcousticTag acousticTag) { - this.acousticTag = acousticTag; - } - - public SatelliteTag getSatelliteTag() { - return satelliteTag; - } - - public void setSatelliteTag(SatelliteTag satelliteTag) { - this.satelliteTag = satelliteTag; - } - - public DigitalArchiveTag getDTag() { - return digitalArchiveTag; - } - - public void setDTag(DigitalArchiveTag dt) { - this.digitalArchiveTag = dt; - } - - public String getLifeStage() { return lifeStage; } - public void setLifeStage(String newStage) { - if (newStage != null) { lifeStage = newStage; } else { lifeStage = null; } - } - - // A convenience method that returns the first haplotype found in the TissueSamples for this Encounter. - public String getHaplotype() { - if (tissueSamples != null) { - int numTissueSamples = tissueSamples.size(); - if (numTissueSamples > 0) { - for (int j = 0; j < numTissueSamples; j++) { - TissueSample thisSample = tissueSamples.get(j); - int numAnalyses = thisSample.getNumAnalyses(); - if (numAnalyses > 0) { - List gAnalyses = thisSample.getGeneticAnalyses(); - for (int g = 0; g < numAnalyses; g++) { - GeneticAnalysis ga = gAnalyses.get(g); - if (ga.getAnalysisType().equals("MitochondrialDNA")) { - MitochondrialDNAAnalysis mito = (MitochondrialDNAAnalysis)ga; - if (mito.getHaplotype() != null) { return mito.getHaplotype(); } - } - } - } - } - } - } - return null; - } - - // A convenience method that returns the first genetic sex found in the TissueSamples for this Encounter. - public String getGeneticSex() { - if (tissueSamples != null) { - int numTissueSamples = tissueSamples.size(); - if (numTissueSamples > 0) { - for (int j = 0; j < numTissueSamples; j++) { - TissueSample thisSample = tissueSamples.get(j); - int numAnalyses = thisSample.getNumAnalyses(); - if (numAnalyses > 0) { - List gAnalyses = thisSample.getGeneticAnalyses(); - for (int g = 0; g < numAnalyses; g++) { - GeneticAnalysis ga = gAnalyses.get(g); - if (ga.getAnalysisType().equals("SexAnalysis")) { - SexAnalysis mito = (SexAnalysis)ga; - if (mito.getSex() != null) { return mito.getSex(); } - } - } - } - } - } - } - return null; - } - - public List getMicrosatelliteMarkers() { - List markers = - new ArrayList(); - - if (tissueSamples == null) return markers; - for (TissueSample tsamp : tissueSamples) { - for (GeneticAnalysis gan : tsamp.getGeneticAnalyses()) { - if (!"MicrosatelliteMarkers".equals(gan.getAnalysisType())) continue; - markers.add((MicrosatelliteMarkersAnalysis)gan); - } - } - return markers; - } - - public List getImages() { return images; } - - public boolean hasAnnotation(Annotation ann) { - return (annotations != null && annotations.contains(ann)); - } - - public boolean hasAnnotations() { - return (annotations != null && annotations.size() > 0); - } - - public int numAnnotations() { - if (annotations == null) return 0; - return annotations.size(); - } - - public int numNonTrivialAnnotations() { - if (annotations == null) return 0; - int ct = 0; - for (Annotation ann : annotations) { - if (!ann.isTrivial()) ct++; - } - return ct; - } - - public ArrayList getAnnotations() { - return annotations; - } - - public Annotation getAnnotation(String annId) { - if ((annId == null) || (annotations == null)) return null; - for (Annotation ann : annotations) { - if (annId.equals(ann.getId())) return ann; - } - return null; - } - - public Set getAnnotationViewpoints() { - Set vps = new HashSet(); - - if (!hasAnnotations()) return vps; - for (Annotation ann : annotations) { - if (ann.getViewpoint() != null) vps.add(ann.getViewpoint()); - } - return vps; - } - - public Set getAnnotationIAClasses() { - Set classes = new HashSet(); - - if (!hasAnnotations()) return classes; - for (Annotation ann : annotations) { - if (ann.getIAClass() != null) classes.add(ann.getIAClass()); - } - // TODO: we should find out how/where bunk iaClass values are getting set - // and stop the via isValidIAClass() or similar - // also should be considered for any data integrity/repair tools - classes.remove("____"); - return classes; - } - - // all an enc's annotations on a given asset (might be multiple if parts are involved) - public List getAnnotations(MediaAsset ma) { - List anns = new ArrayList(); - - for (Annotation ann : getAnnotations()) { - if (ann.getMediaAsset() == ma) anns.add(ann); - } - return anns; - } - - public void setAnnotations(ArrayList anns) { - annotations = anns; - } - - public void addAnnotations(List anns) { - if (annotations == null) annotations = new ArrayList(); - for (Annotation ann : anns) { - if (!annotations.contains(ann)) annotations.add(ann); - } - } - - public void addAnnotation(Annotation ann) { - if (annotations == null) annotations = new ArrayList(); - if (!annotations.contains(ann)) annotations.add(ann); - } - - public void useAnnotationsForMatching(boolean use) { - if (getAnnotations() != null && getAnnotations().size() >= 1) { - for (Annotation ann : getAnnotations()) { - ann.setMatchAgainst(use); - } - } - } - - public Annotation getAnnotationWithKeyword(String word) { - System.out.println("getAnnotationWithKeyword called for " + word); - System.out.println("getAnnotationWithKeyword called, annotations = " + annotations); - if (annotations == null) return null; - for (Annotation ann : annotations) { - if (ann == null) continue; - MediaAsset ma = ann.getMediaAsset(); - if (ma != null && ma.hasKeyword(word)) return ann; - } - return null; - } - - // pretty much only useful for frames pulled from video (after detection, to be made into encounters) - public static List collateFrameAnnotations(List anns, - Shepherd myShepherd) { - if ((anns == null) || (anns.size() < 1)) return null; - // Determine skipped frames before another encounter should be made. - int minGapSize = 4; - try { - String gapFromProperties = IA.getProperty(myShepherd.getContext(), - "newEncounterFrameGap"); - if (gapFromProperties != null) { - minGapSize = Integer.parseInt(gapFromProperties); - } - } catch (NumberFormatException nfe) {} - SortedMap > ordered = new TreeMap >(); - MediaAsset parentRoot = null; - for (Annotation ann : anns) { - System.out.println("========================== >>>>>> " + ann); - if (ann.getFeatures().get(0).isUnity()) continue; // makes big assumption there is one-and-only-one feature btw (detection should have - // bbox) - MediaAsset ma = ann.getMediaAsset(); - if (parentRoot == null) parentRoot = ma.getParentRoot(myShepherd); - System.out.println(" -->>> ma = " + ma); - if (!ma.hasLabel("_frame") || (ma.getParentId() == null)) continue; // nope thx - int offset = ma.getParameters().optInt("extractOffset", -1); - System.out.println(" -->>> offset = " + offset); - if (offset < 0) continue; - if (ordered.get(offset) == null) ordered.put(offset, new ArrayList()); - ordered.get(offset).add(ann); - } - if (ordered.size() < 1) return null; // none used! - - // now construct Encounters based upon spacing of frame-clusters - List newEncs = new ArrayList(); - int prevOffset = -1; - int groupsMade = 1; - ArrayList tmpAnns = new ArrayList(); - for (Integer i : ordered.keySet()) { - if ((prevOffset > -1) && ((i - prevOffset) >= minGapSize)) { - Encounter newEnc = __encForCollate(tmpAnns, parentRoot); - if (newEnc != null) { // null means none of the frames met minimum detection confidence - newEnc.setDynamicProperty("frameSplitNumber", Integer.toString(groupsMade + 1)); - newEncs.add(newEnc); - System.out.println(" cluster [" + (groupsMade) + "] -> " + newEnc); - groupsMade++; - tmpAnns = new ArrayList(); - } - } - prevOffset = i; - tmpAnns.addAll(ordered.get(i)); - } - // deal with dangling tmpAnns content - if (tmpAnns.size() > 0) { - Encounter newEnc = __encForCollate(tmpAnns, parentRoot); - if (newEnc != null) { - newEnc.setDynamicProperty("frameSplitNumber", Integer.toString(groupsMade + 1)); - newEncs.add(newEnc); - System.out.println(" (final)cluster [" + groupsMade + "] -> " + newEnc); - groupsMade++; - } - } - return newEncs; - } - - // this is really only for above method - private static Encounter __encForCollate(ArrayList tmpAnns, MediaAsset parentRoot) { - if ((tmpAnns == null) || (tmpAnns.size() < 1)) return null; - // make sure we even can use these annots first - double bestConfidence = 0.0; - for (Annotation ann : tmpAnns) { - if ((ann.getFeatures() == null) || (ann.getFeatures().size() < 1) || - (ann.getFeatures().get(0).getParameters() == null)) continue; - double conf = ann.getFeatures().get(0).getParameters().optDouble("detectionConfidence", - -1.0); - if (conf > bestConfidence) bestConfidence = conf; - } - if (bestConfidence < ENCOUNTER_AUTO_SOURCE_CONFIDENCE_CUTOFF) { - System.out.println("[INFO] bestConfidence=" + bestConfidence + - " below threshold; rejecting 1 enc from " + parentRoot); - return null; - } - Encounter newEnc = new Encounter(tmpAnns); - newEnc.setState(STATE_AUTO_SOURCED); - newEnc.zeroOutDate(); // do *not* want it using the video source date - newEnc.setDynamicProperty("bestDetectionConfidence", Double.toString(bestConfidence)); - if (parentRoot == null) { - newEnc.setSubmitterName("Unknown video source"); - newEnc.addComments("unable to determine video source - possibly YouTube error?"); - } else { - newEnc.addComments("

    YouTube ID: " + parentRoot.getParameters().optString("id") + - "

    "); - String consolidatedRemarks = - "

    Auto-sourced from YouTube Parent Video: " + - parentRoot.getParameters().optString("id") + "

    "; - // set the video ID as the EventID for distinct access later - newEnc.setEventID("youtube:" + parentRoot.getParameters().optString("id")); - if ((parentRoot.getMetadata() != null) && - (parentRoot.getMetadata().getData() != null)) { - if (parentRoot.getMetadata().getData().optJSONObject("basic") != null) { - newEnc.setSubmitterName(parentRoot.getMetadata().getData().getJSONObject( - "basic").optString("author_name", "[unknown]") + " (by way of YouTube)"); - consolidatedRemarks += "

    From YouTube video: " + - parentRoot.getMetadata().getData().getJSONObject("basic").optString("title", - "[unknown]") + "

    "; - newEnc.addComments(consolidatedRemarks); - - // add a dynamic property to make a quick link to the video - } - if (parentRoot.getMetadata().getData().optJSONObject("detailed") != null) { - String desc = "

    " + - parentRoot.getMetadata().getData().getJSONObject("detailed").optString( - "description", "[no description]") + "

    "; - if (parentRoot.getMetadata().getData().getJSONObject("detailed").optJSONArray( - "tags") != null) { - desc += "

    tags: " + - parentRoot.getMetadata().getData().getJSONObject( - "detailed").getJSONArray("tags").toString() + "

    "; - } - consolidatedRemarks += desc; - } - } - newEnc.setOccurrenceRemarks(consolidatedRemarks); - } - return newEnc; - } - - // convenience method - public ArrayList getMedia() { - ArrayList m = new ArrayList(); - - if ((annotations == null) || (annotations.size() < 1)) return m; - for (Annotation ann : annotations) { - if (ann == null) continue; // really weird that this happens sometimes - MediaAsset ma = ann.getMediaAsset(); - if (ma != null) m.add(ma); - } - return m; - } - - public MediaAsset getMediaAssetByFilename(String filename) { - if (!Util.stringExists(filename)) return null; - for (MediaAsset ma : getMedia()) { - if (Util.stringsEqualish(filename, ma.getFilename())) return ma; - } - return null; - } - - // only checks top-level MediaAssets, not children or resized images - public boolean hasTopLevelMediaAsset(int id) { - return (indexOfMediaAsset(id) >= 0); - } - - // finds the index of the MA we're looking for - public int indexOfMediaAsset(int id) { - if (annotations == null) return -1; - for (int i = 0; i < annotations.size(); i++) { - MediaAsset ma = annotations.get(i).getMediaAsset(); - if (ma == null) continue; - if (ma.getIdInt() == id) return i; - } - return -1; - } - - // creates a new annotation and attaches the asset - public void addMediaAsset(MediaAsset ma) { - Annotation ann = new Annotation(getTaxonomyString(), ma); - - if (annotations == null) annotations = new ArrayList(); - annotations.add(ann); - } - - public void removeAnnotation(Annotation ann) { - if (annotations == null) return; - annotations.remove(ann); - } - - public void removeAnnotation(int index) { - annotations.remove(index); - } - - // this removes an Annotation from Encounter (and from its MediaAsset!!) and replaces it with a new one - // please note: the oldAnn gets killed off (not orphaned) - public void replaceAnnotation(Annotation oldAnn, Annotation newAnn) { - oldAnn.detachFromMediaAsset(); - // note: newAnn should already attached to a MediaAsset - removeAnnotation(oldAnn); - addAnnotation(newAnn); - } - - public void removeMediaAsset(MediaAsset ma) { - removeAnnotation(indexOfMediaAsset(ma.getIdInt())); - } - - // this is a kinda hacky way to find media ... really used by encounter.jsp now but likely should go away? - public ArrayList findAllMediaByFeatureId(Shepherd myShepherd, String[] featureIds) { - ArrayList mas = new ArrayList(); - - for (MediaAsset ma : getMedia()) { - if (ma.hasFeatures(featureIds)) mas.add(ma); - ArrayList kids = ma.findChildren(myShepherd); // note: does not recurse, but... meh? - if ((kids == null) || (kids.size() < 1)) continue; - for (MediaAsset kma : kids) { - if (kma.hasFeatures(featureIds)) mas.add(kma); - } - } - return mas; - } - - // down-n-dirty with no myShepherd passed! :/ - public ArrayList findAllMediaByFeatureId(String[] featureIds) { - Shepherd myShepherd = new Shepherd("context0"); - - myShepherd.setAction("Encounter.class.findAllMediaByFeatureID"); - myShepherd.beginDBTransaction(); - ArrayList all = findAllMediaByFeatureId(myShepherd, featureIds); - myShepherd.rollbackDBTransaction(); - myShepherd.closeDBTransaction(); - return all; - } - - public ArrayList findAllMediaByLabel(Shepherd myShepherd, String label) { - return MediaAsset.findAllByLabel(getMedia(), myShepherd, label); - } - - public boolean hasKeyword(Keyword word) { - int imagesSize = images.size(); - - for (int i = 0; i < imagesSize; i++) { - SinglePhotoVideo image = images.get(i); - if (image.getKeywords().contains(word)) { return true; } - } - return false; - } - - public Set getMediaAssetKeywords() { - Set mak = new HashSet(); - - for (MediaAsset ma : this.getMedia()) { - ArrayList kws = ma.getKeywords(); - if (kws != null) mak.addAll(kws); - } - return mak; - } - - public String getState() { return state; } - - public void setState(String newState) { this.state = newState; } - - // DO NOT USE - LEGACY MIGRATION ONLY - /* - public boolean getApproved(){return approved;} - public boolean getUnidentifiable(){return unidentifiable;} - */ - public Vector getOldAdditionalImageNames() { return additionalImageNames; } - - public Double getLatitudeAsDouble() { return decimalLatitude; } - public Double getLongitudeAsDouble() { return decimalLongitude; } - - public boolean hasMeasurements() { - if ((measurements != null) && (measurements.size() > 0)) { - int numMeasurements = measurements.size(); - for (int i = 0; i < numMeasurements; i++) { - Measurement m = measurements.get(i); - if (m.getValue() != null) { return true; } - } - } - return false; - } - - public boolean hasMeasurement(String type) { - if ((measurements != null) && (measurements.size() > 0)) { - int numMeasurements = measurements.size(); - for (int i = 0; i < numMeasurements; i++) { - Measurement m = measurements.get(i); - if ((m.getValue() != null) && (m.getType().equals(type))) { return true; } - } - } - return false; - } - - public boolean hasBiologicalMeasurement(String type) { - if ((tissueSamples != null) && (tissueSamples.size() > 0)) { - int numTissueSamples = tissueSamples.size(); - for (int i = 0; i < numTissueSamples; i++) { - TissueSample ts = tissueSamples.get(i); - if (ts.getBiologicalMeasurement(type) != null) { - BiologicalMeasurement bm = ts.getBiologicalMeasurement(type); - if (bm.getValue() != null) { return true; } - } - } - } - return false; - } - - // Returns the first measurement of the specified type - public Measurement getMeasurement(String type) { - if ((measurements != null) && (measurements.size() > 0)) { - int numMeasurements = measurements.size(); - for (int i = 0; i < numMeasurements; i++) { - Measurement m = measurements.get(i); - if ((m.getValue() != null) && (m.getType().equals(type))) { return m; } - } - } - return null; - } - - public Map getBiologicalMeasurementsByType() { - Map meas = new HashMap(); - - for (MeasurementDesc mdesc : Util.findBiologicalMeasurementDescs("en", "context0")) { - BiologicalMeasurement bm = getBiologicalMeasurement(mdesc.getType()); - if (bm != null) meas.put(mdesc.getType(), bm); - } - return meas; - } - - public BiologicalMeasurement getBiologicalMeasurement(String type) { - if (tissueSamples != null) { - int numTissueSamples = tissueSamples.size(); - for (int y = 0; y < numTissueSamples; y++) { - TissueSample ts = tissueSamples.get(y); - if ((ts.getGeneticAnalyses() != null) && (ts.getGeneticAnalyses().size() > 0)) { - int numMeasurements = ts.getGeneticAnalyses().size(); - for (int i = 0; i < numMeasurements; i++) { - GeneticAnalysis m = ts.getGeneticAnalyses().get(i); - if (m.getAnalysisType().equals("BiologicalMeasurement")) { - BiologicalMeasurement f = (BiologicalMeasurement)m; - if ((f.getMeasurementType().equals(type)) && (f.getValue() != null)) { - return f; - } - } - } - } - } - } - return null; - } - - public String getCountry() { return country; } - - public void setCountry(String newCountry) { - if (newCountry != null) { country = newCountry; } else { country = null; } - } - - public void setOccurrenceID(String vet) { - if (vet != null) { this.occurrenceID = vet; } else { this.occurrenceID = null; } - } - - public String getOccurrenceID() { return occurrenceID; } - - public Occurrence getOccurrence(Shepherd myShepherd) { - return myShepherd.getOccurrence(this); - } - - public DateTime getOccurrenceDateTime(Shepherd myShepherd) { - Occurrence occ = this.getOccurrence(myShepherd); - - if (occ == null) return null; - return occ.getDateTime(); - } - - public boolean hasSinglePhotoVideoByFileName(String filename) { - int numImages = images.size(); - - for (int i = 0; i < numImages; i++) { - SinglePhotoVideo single = images.get(i); - if (single.getFilename().trim().toLowerCase().equals(filename.trim().toLowerCase())) { - return true; - } - } - return false; - } - - // convenience function to Collaboration permissions - public boolean canUserAccess(HttpServletRequest request) { - return Collaboration.canUserAccessEncounter(this, request); - } - - public boolean canUserAccess(User user, String context) { - if (user == null) return false; - // see comment below on canUserEdit(); substituting isUserOwner() now - // if (canUserEdit(user)) return true; - if (isUserOwner(user)) return true; - String username = user.getUsername(); - if (username == null) return false; - return Collaboration.canUserAccessEncounter(this, context, username); - } - - /* - this really is ugly cuz what is "view" vs "access", but i do NOT want to futz with canUserAccess() and - cause unintended consequences. so, for now, canUserView() is pretty much exclusively for search - */ - public boolean canUserView(User user, Shepherd myShepherd) { - return (user != null) && (user.isAdmin(myShepherd) || this.canUserAccess(user, - myShepherd.getContext())); - } - - // as part of 10.9, canUserEdit() was modified. it was not -/* - public boolean canUserEdit(User user) { - return isUserOwner(user); - } - */ - - // rewrite for 10.9 tries to actually do the right thing and (maybe) make sense - @Override public boolean canUserEdit(User user, Shepherd myShepherd) { - if (user == null) return false; - if (isUserOwner(user)) return true; - if (user.isAdmin(myShepherd)) return true; - if (Collaboration.canEditEncounter(this, user, myShepherd.getContext())) return true; - // TODO there seems to be some legacy stuff about roles based on location. is this real? - return false; - } - - public boolean isUserOwner(User user) { // the definition of this might change? - if (user == null) return false; - if ((submitters != null) && submitters.contains(user)) return true; - if ((submitterID != null) && submitterID.equals(user.getUsername())) return true; - return false; - } - - // new logic means we only need users who are in collab with submitting user - // and if public, we dont need to do this at all - public List userIdsWithViewAccess(Shepherd myShepherd) { - List ids = new ArrayList(); - - if (this.isPubliclyReadable()) return ids; - List collabs = Collaboration.collaborationsForUser(myShepherd, - this.getSubmitterID()); - for (Collaboration collab : collabs) { - User user = myShepherd.getUser(collab.getOtherUsername(this.getSubmitterID())); - if (user != null) ids.add(user.getId()); - } - return ids; - } - -/* - public List userIdsWithEditAccess(Shepherd myShepherd) { - List ids = new ArrayList(); - - for (User user : myShepherd.getUsersWithUsername()) { - if ((user.getId() != null) && this.canUserEdit(user)) ids.add(user.getId()); - } - return ids; - } - */ - public JSONObject sanitizeJson(HttpServletRequest request, JSONObject jobj) - throws JSONException { - boolean fullAccess = this.canUserAccess(request); - String useProjectContext = "false"; - - if (request.getParameter("useProjectContext") != null) { - useProjectContext = request.getParameter("useProjectContext"); - } - if (fullAccess) { - if (this.individual != null) { - jobj.put("individualID", this.individual.getIndividualID()); - if ("true".equals(useProjectContext)) { - jobj.put("displayName", this.individual.getDisplayName(request)); - } else { - jobj.put("displayName", this.individual.getDisplayName()); - } - } - return jobj; - } - jobj.remove("gpsLatitude"); - jobj.remove("location"); - jobj.remove("gpsLongitude"); - jobj.remove("verbatimLocality"); - jobj.remove("locationID"); - jobj.remove("gpsLongitude"); - jobj.remove("genus"); - jobj.remove("specificEpithet"); - jobj.put("_sanitized", true); - - return jobj; - } - - public JSONObject decorateJsonNoAnnots(HttpServletRequest request, JSONObject jobj) - throws JSONException { - jobj.put("location", this.getLocation()); - // these are for convenience, like .hasImages above (for use in table building e.g.) - if ((this.getTissueSamples() != null) && (this.getTissueSamples().size() > 0)) - jobj.put("hasTissueSamples", true); - if (this.hasMeasurements()) jobj.put("hasMeasurements", true); - return jobj; - } - - public JSONObject decorateJson(HttpServletRequest request, JSONObject jobj) - throws JSONException { - jobj = decorateJsonNoAnnots(request, jobj); - - jobj.put("_imagesNote", - ".images have been deprecated! long live MediaAssets! (see: .annotations)"); - - boolean fullAccess = this.canUserAccess(request); - if ((this.getAnnotations() != null) && (this.getAnnotations().size() > 0)) { - jobj.put("hasAnnotations", true); - JSONArray jarr = new JSONArray(); - for (Annotation ann : this.getAnnotations()) { - jarr.put(ann.sanitizeJson(request, fullAccess)); - } - jobj.put("annotations", jarr); - } - return jobj; - } - - public JSONObject uiJson(HttpServletRequest request) - throws JSONException { - JSONObject jobj = new JSONObject(); - - jobj.put("individualID", this.getIndividualID()); - jobj.put("url", this.getUrl(request)); - jobj.put("year", this.getYear()); - jobj.put("month", this.getMonth()); - jobj.put("day", this.getDay()); - jobj.put("gpsLatitude", this.getGPSLatitude()); - jobj.put("gpsLongitude", this.getGPSLongitude()); - jobj.put("location", this.getLocation()); - jobj.put("locationID", this.getLocationID()); - - jobj = sanitizeJson(request, jobj); - // we don't want annotations, which are added by sanitizeJson - jobj.remove("annotations"); - return jobj; - } - - public String getUrl(HttpServletRequest request) { - return request.getScheme() + "://" + CommonConfiguration.getURLLocation(request) + - "/encounters/encounter.jsp?number=" + this.getCatalogNumber(); - } - - /** - * returns an array of the MediaAsset sanitized JSON, because whenever UI queries our DB (regardless of class query), all they want in return are - * MediaAssets TODO: decorate with metadata - **/ - public org.datanucleus.api.rest.orgjson.JSONArray sanitizeMedia(HttpServletRequest request) - throws org.datanucleus.api.rest.orgjson.JSONException { - org.datanucleus.api.rest.orgjson.JSONArray jarr = - new org.datanucleus.api.rest.orgjson.JSONArray(); - boolean fullAccess = this.canUserAccess(request); - if ((this.getAnnotations() != null) && (this.getAnnotations().size() > 0)) { - for (Annotation ann : this.getAnnotations()) { - jarr.put(ann.sanitizeMedia(request, fullAccess)); - } - } - return jarr; - } - - // this simple version makes some assumptions: you already have list of collabs, and it is not visible - public String collaborationLockHtml(List collabs) { - Collaboration c = Collaboration.findCollaborationWithUser(this.getAssignedUsername(), - collabs); - String collabClass = "pending"; - - if ((c == null) || (c.getState() == null)) { - collabClass = "new"; - } else if (c.getState().equals(Collaboration.STATE_REJECTED)) { - collabClass = "blocked"; - } - return "
     
    "; - } - - // pass in a Vector of Encounters, get out a list that the user can NOT see - public static Vector blocked(Vector encs, HttpServletRequest request) { - Vector blk = new Vector(); - - for (int i = 0; i < encs.size(); i++) { - Encounter e = (Encounter)encs.get(i); - if (!e.canUserAccess(request)) blk.add(e); - } - return blk; - } - -/* - in short, this rebuilds (or builds for the first time) ALL *derived* images (etc?) for this encounter. - it is a baby step into the future of MediaAssets that hopefully will provide a smooth(er) transition to that. - right now its primary purpose is to create derived formats upon encounter creation; but that is obviously subject to change. - it should be considered an asyncronous action that happens in the background magickally - */ -/////other possiblity: only pass basedir??? do we need context if we do that? - - public boolean refreshAssetFormats(Shepherd myShepherd) { - ArrayList mas = this.getMedia(); - - if ((mas == null) || (mas.size() < 1)) return true; - for (MediaAsset ma : mas) { - ma.updateStandardChildren(myShepherd); - } - return true; - } - -/* - NOTE on "thumb.jpg" ... we only get one of these per encounter; and we do not have stored (i dont think?) which SPV it came from! - this is a problem, as we cant make a thumb in refreshAssetFormats(req, spv) since we dont know if that is the "right" spv. - thus, we have to treat it as a special case. - */ - // see also: future, MediaAssets - public String getThumbnailUrl(String context) { - MediaAsset ma = getPrimaryMediaAsset(); - - if (ma == null) return null; - String url = null; - Shepherd myShepherd = new Shepherd(context); - myShepherd.setAction("Encounter.class.getThumbnailUrl"); - myShepherd.beginDBTransaction(); - ArrayList kids = ma.findChildrenByLabel(myShepherd, "_thumb"); - if ((kids == null) || (kids.size() <= 0)) { - myShepherd.rollbackDBTransaction(); - myShepherd.closeDBTransaction(); - return null; - } - ma = kids.get(0); - if (ma.webURL() == null) { - myShepherd.rollbackDBTransaction(); - myShepherd.closeDBTransaction(); - return null; - } - url = ma.webURL().toString(); - myShepherd.rollbackDBTransaction(); - myShepherd.closeDBTransaction(); - return url; - } - - // this probably needs a better name and should allow for something more like an ordered list; that said, - // knowing we can always try to get THE ONE is probably useful too - public MediaAsset getPrimaryMediaAsset() { - ArrayList mas = getMedia(); - - if (mas.size() < 1) return null; - // here we could walk thru and find keywords, for example - return mas.get(0); - } - - public boolean restAccess(HttpServletRequest request, org.json.JSONObject jsonobj) - throws Exception { - ApiAccess access = new ApiAccess(); - - System.out.println("hello i am in restAccess() on Encounter"); - - String fail = access.checkRequest(this, request, jsonobj); - System.out.println("fail -----> " + fail); - if (fail != null) throw new Exception(fail); - return true; - } - -///////// this is bunk now: see fix for findAllByMediaAsset() if you need this - public static Encounter findByMediaAsset(MediaAsset ma, Shepherd myShepherd) { - String queryString = - "SELECT FROM org.ecocean.Encounter WHERE annotations.contains(ann) && ann.mediaAsset.id ==" - + ma.getId(); - Encounter returnEnc = null; - Query query = myShepherd.getPM().newQuery(queryString); - List results = (List)query.execute(); - - if ((results != null) && (results.size() >= 1)) { - returnEnc = (Encounter)results.get(0); - } - query.closeAll(); - return returnEnc; - } - - public static List findAllByMediaAsset(MediaAsset ma, Shepherd myShepherd) { - List returnEncs = new ArrayList(); - - try { - String queryString = - "SELECT FROM org.ecocean.Encounter WHERE annotations.contains(ann) && ann.features.contains(feat) && mediaAsset.features.contains(feat) && mediaAsset.id ==" - + ma.getId() + - " VARIABLES org.ecocean.media.MediaAsset mediaAsset; org.ecocean.Annotation ann; org.ecocean.media.Feature feat"; - Query query = myShepherd.getPM().newQuery(queryString); - Collection results = (Collection)query.execute(); - returnEncs = new ArrayList(results); - query.closeAll(); - } catch (Exception e) {} - return returnEncs; - } - - public String getPrefixForLocationID() { // convenience function - return LocationID.getPrefixForLocationID(this.getLocationID(), null); - } - - public int getPrefixDigitPaddingForLocationID() { // convenience function - return LocationID.getPrefixDigitPaddingForLocationID(this.getLocationID(), null); - } - - public static Encounter findByAnnotation(Annotation annot, Shepherd myShepherd) { - String queryString = - "SELECT FROM org.ecocean.Encounter WHERE annotations.contains(ann) && ann.id =='" + - annot.getId() + "'"; - Encounter returnEnc = null; - Query query = myShepherd.getPM().newQuery(queryString); - List results = (List)query.execute(); - - if ((results != null) && (results.size() >= 1)) { - if (results.size() > 1) - System.out.println("WARNING: Encounter.findByAnnotation() found " + results.size() + - " Encounters that contain Annotation " + annot.getId()); - returnEnc = (Encounter)results.get(0); - } - query.closeAll(); - return returnEnc; - } - - public static Encounter findByAnnotationId(String annid, Shepherd myShepherd) { - Annotation ann = ((Annotation)(myShepherd.getPM().getObjectById( - myShepherd.getPM().newObjectIdInstance(Annotation.class, annid), true))); - - if (ann == null) return null; - return findByAnnotation(ann, myShepherd); - } - - public static ArrayList getEncountersForMatching(String taxonomyString, - Shepherd myShepherd) { - if (_matchEncounterCache.get(taxonomyString) != null) - return _matchEncounterCache.get(taxonomyString); - ArrayList encs = new ArrayList(); - String queryString = "SELECT FROM org.ecocean.media.MediaAsset WHERE !features.isEmpty()"; - Query query = myShepherd.getPM().newQuery(queryString); - List results = (List)query.execute(); - for (int i = 0; i < results.size(); i++) { - MediaAsset ma = (MediaAsset)results.get(i); - MediaAsset top = ma.getParentRoot(myShepherd); - if (top == null) continue; - Encounter enc = Encounter.findByMediaAsset(top, myShepherd); - if (enc == null) System.out.println("could not find enc for ma " + ma); - if (enc == null) continue; - if (!enc.getTaxonomyString().equals(taxonomyString)) continue; - if (!encs.contains(enc)) encs.add(enc); - } - query.closeAll(); - _matchEncounterCache.put(taxonomyString, encs); - return encs; - } - -/* - this section are intentionally hacky backwards-compatible ways to get spots on an encounter in the new world of Features/Annotations/MediaAssets - ... do not use these, of course... and SOON we must weed out all the encounter-based-spot calls from everywhere and clean all this mess up! - */ - public ArrayList HACKgetSpots() { - return HACKgetAnySpots("spotsLeft"); - } - - public ArrayList HACKgetRightSpots() { - return HACKgetAnySpots("spotsRight"); - } - - public ArrayList HACKgetAnySpots(String which) { - ArrayList mas = findAllMediaByFeatureId( - new String[] { "org.ecocean.flukeEdge.edgeSpots", "org.ecocean.dorsalEdge.edgeSpots" }); - - if ((mas == null) || (mas.size() < 1)) return new ArrayList(); - for (Feature f : mas.get(0).getFeatures()) { - if (f.isType("org.ecocean.flukeEdge.edgeSpots") || - f.isType("org.ecocean.dorsalEdge.edgeSpots")) { - if (f.getParameters() != null) - return SuperSpot.listFromJSONArray(f.getParameters().optJSONArray(which)); - } - } - return new ArrayList(); - } - - // err, i think ref spots are the same right or left.... at least for flukes/dorsals. :/ good luck with mantas and whalesharks! - public ArrayList HACKgetAnyReferenceSpots() { - ArrayList mas = findAllMediaByFeatureId( - new String[] { "org.ecocean.flukeEdge.referenceSpots", - "org.ecocean.referenceEdge.edgeSpots" }); - - if ((mas == null) || (mas.size() < 1)) return new ArrayList(); - for (Feature f : mas.get(0).getFeatures()) { - if (f.isType("org.ecocean.flukeEdge.referenceSpots") || - f.isType("org.ecocean.dorsalEdge.referenceSpots")) { - if (f.getParameters() != null) - return SuperSpot.listFromJSONArray(f.getParameters().optJSONArray("spots")); - } - } - return new ArrayList(); - } - - // note this sets some things (e.g. species) which might (should!) need to be adjusted after, e.g. with setSpeciesFromAnnotations() - public Encounter cloneWithoutAnnotations(Shepherd myShepherd) { - Encounter enc = new Encounter(this.day, this.month, this.year, this.hour, this.minutes, - this.size_guess, this.verbatimLocality); - - enc.setCatalogNumber(Util.generateUUID()); - System.out.println("NOTE: cloneWithoutAnnotations(" + this.catalogNumber + ") -> " + - enc.getCatalogNumber()); - enc.setGenus(this.getGenus()); - enc.setSpecificEpithet(this.getSpecificEpithet()); - enc.setDecimalLatitude(this.getDecimalLatitudeAsDouble()); - enc.setDecimalLongitude(this.getDecimalLongitudeAsDouble()); - // just going to go ahead and go nuts here and copy most "logical"(?) things. reset on clone if needed - enc.setSubmitterID(this.getSubmitterID()); - enc.setSubmitters(this.submitters); - enc.setPhotographers(this.photographers); - enc.setSex(this.getSex()); - enc.setLocationID(this.getLocationID()); - enc.setVerbatimLocality(this.getVerbatimLocality()); - if (this.getCountry() != null && !"".equals(this.getCountry())) { - enc.setCountry(this.getCountry()); - } - Occurrence occ = myShepherd.getOccurrence(this); - if (occ != null) { - occ.addEncounter(enc); - enc.setOccurrenceID(occ.getOccurrenceID()); - } - // WB-1949: clone into same projects too - ArrayList projects = myShepherd.getAllProjectsForEncounter(this); - if (projects != null) { - for (Project proj : projects) { - proj.addEncounter(enc); - } - } - enc.setRecordedBy(this.getRecordedBy()); - enc.setState(this.getState()); // not too sure about this one? - - enc.setAlternateID(this.getAlternateID()); - enc.setOccurrenceRemarks(this.getOccurrenceRemarks()); - enc.addComments("NOTE: cloneWithoutAnnotations(" + this.catalogNumber + ") -> " + - enc.getCatalogNumber()); - - ImportTask itask = getImportTask(myShepherd); - if (itask != null) itask.addEncounter(enc); - return enc; - } - - // for convenience - public ImportTask getImportTask(Shepherd myShepherd) { - return myShepherd.getImportTaskForEncounter(this); - } - - // this is a special state only used now for match.jsp but basically means the data should be mostly hidden and soon deleted, roughly speaking??? - // TODO: figure out what this really means - public void setMatchingOnly() { - this.setState(STATE_MATCHING_ONLY); - } - - // ann is the Annotation that was created after IA detection. mostly this is just to notify... someone - // note: this is for singly-made encounters; see also Occurrence.fromDetection() - public void detectedAnnotation(Shepherd myShepherd, Annotation ann) { - System.out.println(">>>>> detectedAnnotation() on " + this); - } - - /* - note: these are baby steps into proper ownership of Encounters. a similar (but cleaner) attempt is done in MediaAssets... however, really this - probably should be upon some (mythical) BASE CLASS!!!! ... for now, this Encounter variation kinda fudges with existing "ownership" stuff, - namely, the submitterID - which maps (in theory!) to a User username. TODO: much much much ... incl call via constructor maybe ?? etc. - */ - // NOTE: not going to currently persist the AccessControl object yet, but create on the fly... clever? stupid? - public AccessControl getAccessControl() { - if ((submitterID == null) || submitterID.equals("")) return new AccessControl(); // not sure if we really have some "" but lets be safe - return new AccessControl(submitterID); - } - - public void setAccessControl(HttpServletRequest request) { // really just setting submitterID duh - this.submitterID = AccessControl.simpleUserString(request); // null if anon - } - - public String toString() { - return new ToStringBuilder(this) - .append("catalogNumber", catalogNumber) - .append("individualID", (hasMarkedIndividual() ? individual.getId() : null)) - .append("species", getTaxonomyString()) - .append("sex", getSex()) - .append("shortDate", getShortDate()) - .append("numAnnotations", ((annotations == null) ? 0 : annotations.size())) - .toString(); - } - - public boolean hasMediaFromAssetStoreType(AssetStoreType aType) { - System.out.println("Entering Encounter.hasMediaFromAssetStoreType"); - if (getMediaAssetsOfType(aType).size() > 0) { return true; } - return false; - } - - public ArrayList getMediaAssetsOfType(AssetStoreType aType) { - System.out.println("Entering Encounter.getMediaAssetsOfType"); - ArrayList results = new ArrayList(); - try { - ArrayList assets = getMedia(); - int numAssets = assets.size(); - for (int i = 0; i < numAssets; i++) { - MediaAsset ma = assets.get(i); - if (ma.getStore().getType() == aType) { results.add(ma); } - } - } catch (Exception e) { e.printStackTrace(); } - System.out.println("Exiting Encounter.getMediaAssetsOfType with this num results: " + - results.size()); - return results; - } - - public void setObservationArrayList(ArrayList obs) { - this.observations = obs; - } - - public ArrayList getObservationArrayList() { - return observations; - } - - public void addObservationArrayList(ArrayList arr) { - if (observations.isEmpty()) { - observations = arr; - } else { - observations.addAll(arr); - } - } - - public void addObservation(Observation obs) { - boolean found = false; - - // System.out.println("Adding Observation in Base Class... : "+obs.toString()); - if (observations != null && observations.size() > 0) { - for (Observation ob : observations) { - if (ob.getName() != null) { - if (ob.getName().toLowerCase().trim().equals( - obs.getName().toLowerCase().trim())) { - found = true; - break; - } - } - } - if (!found) { - observations.add(obs); - } - } else { - observations.add(obs); - } - } - - public Observation getObservationByName(String obName) { - if (observations != null && observations.size() > 0) { - for (Observation ob : observations) { - if (ob.getName() != null) { - if (ob.getName().toLowerCase().trim().equals(obName.toLowerCase().trim())) { - return ob; - } - } - } - } - return null; - } - - public Observation getObservationByID(String obId) { - if (observations != null && observations.size() > 0) { - for (Observation ob : observations) { - if (ob.getID() != null && ob.getID().equals(obId)) { - return ob; - } - } - } - return null; - } - - public void removeObservation(String name) { - int counter = 0; - - if (observations != null && observations.size() > 0) { - System.out.println("Looking for the Observation to delete..."); - for (Observation ob : observations) { - if (ob.getName() != null) { - if (ob.getName().toLowerCase().trim().equals(name.toLowerCase().trim())) { - System.out.println("Match! Trying to delete Observation " + name + - " at index " + counter); - observations.remove(counter); - break; - } - } - counter++; - } - } - } - - public List getSubmitters() { - return submitters; - } - - public List getInformOthers() { - return informOthers; - } - - public List getSubmitterEmails() { - ArrayList listy = new ArrayList(); - ArrayList subs = new ArrayList(); - - if (getSubmitters() != null) subs.addAll(getSubmitters()); - int numUsers = subs.size(); - for (int k = 0; k < numUsers; k++) { - User use = subs.get(k); - if ((use.getEmailAddress() != null) && (!use.getEmailAddress().trim().equals(""))) { - listy.add(use.getEmailAddress()); - } - } - return listy; - } - - public List getHashedSubmitterEmails() { - ArrayList listy = new ArrayList(); - ArrayList subs = new ArrayList(); - - if (getSubmitters() != null) subs.addAll(getSubmitters()); - int numUsers = subs.size(); - for (int k = 0; k < numUsers; k++) { - User use = subs.get(k); - if ((use.getHashedEmailAddress() != null) && - (!use.getHashedEmailAddress().trim().equals(""))) { - listy.add(use.getHashedEmailAddress()); - } - } - return listy; - } - - public List getPhotographers() { - return photographers; - } - - public List getPhotographerEmails() { - ArrayList listy = new ArrayList(); - ArrayList subs = new ArrayList(); - - if (getPhotographers() != null) subs.addAll(getPhotographers()); - int numUsers = subs.size(); - for (int k = 0; k < numUsers; k++) { - User use = subs.get(k); - if ((use.getEmailAddress() != null) && (!use.getEmailAddress().trim().equals(""))) { - listy.add(use.getEmailAddress()); - } - } - return listy; - } - - public List getInformOthersEmails() { - ArrayList listy = new ArrayList(); - ArrayList subs = new ArrayList(); - - if (getInformOthers() != null) subs.addAll(getInformOthers()); - int numUsers = subs.size(); - for (int k = 0; k < numUsers; k++) { - User use = subs.get(k); - if ((use.getEmailAddress() != null) && (!use.getEmailAddress().trim().equals(""))) { - listy.add(use.getEmailAddress()); - } - } - return listy; - } - - public List getHashedPhotographerEmails() { - ArrayList listy = new ArrayList(); - ArrayList subs = new ArrayList(); - - if (getPhotographers() != null) subs.addAll(getPhotographers()); - int numUsers = subs.size(); - for (int k = 0; k < numUsers; k++) { - User use = subs.get(k); - if ((use.getHashedEmailAddress() != null) && - (!use.getHashedEmailAddress().trim().equals(""))) { - listy.add(use.getHashedEmailAddress()); - } - } - return listy; - } - - public void addSubmitter(User user) { - if (user == null) return; - if (submitters == null) submitters = new ArrayList(); - if (!submitters.contains(user)) submitters.add(user); - } - - public void removeSubmitter(User user) { - if ((user == null) || (submitters == null)) return; - submitters.remove(user); - } - - public void addPhotographer(User user) { - if (user == null) return; - if (photographers == null) photographers = new ArrayList(); - if (!photographers.contains(user)) photographers.add(user); - } - - public void setSubmitters(List submitters) { - if (submitters == null) { this.submitters = null; } else { - this.submitters = submitters; - } - } - - public void setPhotographers(List photographers) { - if (photographers == null) { this.photographers = null; } else { - this.photographers = photographers; - } - } - - public void removePhotographer(User user) { - if ((user == null) || (photographers == null)) return; - photographers.remove(user); - } - - public void addInformOther(User user) { - if (user == null) return; - if (informOthers == null) informOthers = new ArrayList(); - if (!informOthers.contains(user)) informOthers.add(user); - } - - public void setInformOthers(List users) { - if (users == null) { this.informOthers = null; } else { - this.informOthers = users; - } - } - - public void removeInformOther(User user) { - if ((user == null) || (informOthers == null)) return; - informOthers.remove(user); - } - - public static List getIndividualIDs(Collection encs) { - Set idSet = new HashSet(); - - for (Encounter enc : encs) { - if (enc.hasMarkedIndividual()) idSet.add(enc.getIndividualID()); - } - return Util.asSortedList(idSet); - } - - public void refreshAnnotationLiteTaxonomy() { - if (!this.hasAnnotations()) return; - String tax = this.getTaxonomyString(); - for (Annotation ann : this.annotations) { - ann.refreshLiteTaxonomy(tax); - } - } - - public void refreshAnnotationLiteIndividual() { - if (!this.hasAnnotations()) return; - String indivId = "____"; - if (this.individual != null) indivId = this.individual.getIndividualID(); - for (Annotation ann : this.annotations) { - ann.refreshLiteIndividual(indivId); - } - } - - public int hashCode() { // we need this along with equals() for collections methods (contains etc) to work!! - if (this.getCatalogNumber() == null) return Util.generateUUID().hashCode(); // random(ish) so we dont get two identical for null values - return this.getCatalogNumber().hashCode(); - } - - // sadly, this mess needs to carry on the tradition set up in User.isUsernameAnonymous() - // thanks to the logic in Collaboration.canUserAccessOwnedObject() - public boolean isPubliclyReadable() { - if (!Collaboration.securityEnabled("context0")) return true; - return User.isUsernameAnonymous(this.submitterID); - } - - public boolean getOpensearchProcessPermissions() { - return opensearchProcessPermissions; - } - - public void setOpensearchProcessPermissions(boolean value) { - opensearchProcessPermissions = value; - } - - // wrapper for below, that checks if we really need to be run - public static void opensearchIndexPermissionsBackground(Shepherd myShepherd) { - boolean runIt = false; - Long lastRun = OpenSearch.getPermissionsTimestamp(myShepherd); - long now = System.currentTimeMillis(); - - if ((lastRun == null) || - ((now - lastRun) > OpenSearch.BACKGROUND_PERMISSIONS_MAX_FORCE_MINUTES * 60000)) { - System.out.println( - "opensearchIndexPermissionsBackground: forced run due to max time since previous"); - runIt = true; - } - boolean needed = OpenSearch.getPermissionsNeeded(myShepherd); - if (needed && !runIt) { - System.out.println("opensearchIndexPermissionsBackground: running due to needed=true"); - runIt = true; - } - if (!runIt) { - System.out.println("opensearchIndexPermissionsBackground: running not required; done"); - return; - } - // i think we should set these first... tho they may not get persisted til after? - OpenSearch.setPermissionsTimestamp(myShepherd); - OpenSearch.setPermissionsNeeded(myShepherd, false); - opensearchIndexPermissions(); - System.out.println("opensearchIndexPermissionsBackground: running completed"); - } - -/* note: there are a great deal of users with *no username* that seem to appear in enc.submitters array. - however, very few (2 out of 5600+) encounters with such .submitters have a blank submitterID value - therefore: submitterID will be assumed to be a required value on users which need to be - - this seems further validated by the facts that: - - canUserAccess(user) returns false if no username on user - - a user wihtout a username cant be logged in (and thus cant search) - - "admin" users are just ignored entirely, as they will be exempt from the viewUsers criteria during searching. - - other than "ownership" (via submitterID), a user can view if they have view or edit collab with - another user. so we frontload *approved* collabs for every user here too. - - in terms of "public" encounters, it seems that (based on Collaboration.canUserAccessEncounter()), - encounters with submitterID in (NULL, "public", "", "N/A" [ugh]) is readable by anyone; so we will - skip these from processing as they should be flagged with the boolean isPubliclyReadable in indexing - */ - public static void opensearchIndexPermissions() { - Util.mark("perm start"); - long startT = System.currentTimeMillis(); - System.out.println("opensearchIndexPermissions(): begin..."); - // no security => everything publiclyReadable - saves us work, no? - if (!Collaboration.securityEnabled("context0")) return; - OpenSearch os = new OpenSearch(); - Map > collab = new HashMap >(); - Map usernameToId = new HashMap(); - - // PHASE 1: load all DB data we need into in-memory structures, then close the Shepherd. - // The per-encounter OpenSearch HTTP calls in PHASE 2 below were previously made while - // this Shepherd's Postgres connection was still pinned, which on installs with hundreds - // of thousands of encounters could starve the JDO connection pool for tens of minutes - // and cause every concurrent request to queue at "begin" on dbconnections.jsp. - List encounterRows = new ArrayList(); - Shepherd myShepherd = new Shepherd("context0"); - myShepherd.setAction("Encounter.opensearchIndexPermissions"); - myShepherd.beginDBTransaction(); - try { - // it seems as though user.uuid is *required* so we can trust that - for (User user : myShepherd.getUsersWithUsername()) { - usernameToId.put(user.getUsername(), user.getId()); - List collabsFor = Collaboration.collaborationsForUser(myShepherd, - user.getUsername()); - if (Util.collectionIsEmptyOrNull(collabsFor)) continue; - for (Collaboration col : collabsFor) { - if (!col.isApproved() && !col.isEditApproved()) continue; - if (!collab.containsKey(user.getId())) - collab.put(user.getId(), new HashSet()); - collab.get(user.getId()).add(col.getOtherUsername(user.getUsername())); - } - } - Util.mark("perm: user build done", startT); - System.out.println("opensearchIndexPermissions(): " + usernameToId.size() + - " total users; " + collab.size() + " have active collab"); - - // we do not need full Encounter objects here to update index docs, so lets do this via sql/fields - much faster - String sql = - "SELECT \"CATALOGNUMBER\", \"SUBMITTERID\" FROM \"ENCOUNTER\" WHERE \"SUBMITTERID\" IS NOT NULL AND \"SUBMITTERID\" != '' AND \"SUBMITTERID\" != 'N/A' AND \"SUBMITTERID\" != 'public'"; - Query q = null; - try { - q = myShepherd.getPM().newQuery("javax.jdo.query.SQL", sql); - List results = (List)q.execute(); - Util.mark("perm: loading encs into memory, size=" + results.size(), startT); - Iterator it = results.iterator(); - while (it.hasNext()) { - Object[] row = (Object[])it.next(); - encounterRows.add(new String[] { (String)row[0], (String)row[1] }); - } - } finally { - if (q != null) q.closeAll(); - } - } catch (Exception ex) { - System.out.println( - "opensearchIndexPermissions(): failed during DB load phase: " + ex); - ex.printStackTrace(); - } finally { - myShepherd.rollbackAndClose(); - } - Util.mark("perm: DB load done; shepherd closed", startT); - - // PHASE 2: iterate the in-memory rows and update OpenSearch (no DB connection held). - int encCount = 0; - for (String[] row : encounterRows) { - String id = row[0]; - String submitterId = row[1]; - String uid = usernameToId.get(submitterId); - if (uid == null) { - // see issue 939 for example :( - System.out.println("opensearchIndexPermissions(): WARNING invalid username " + - submitterId + " on enc " + id); - continue; - } - encCount++; - if (encCount % 1000 == 0) Util.mark("enc[" + encCount + "]", startT); - - // ask the question, who else can see this encounter via collaboration? - org.json.JSONArray viewUsers = new org.json.JSONArray(); - for (Map.Entry > entry : collab.entrySet()) { - if (entry.getValue().contains(submitterId)) { - viewUsers.put(entry.getKey()); - } - } - if (viewUsers.length() > 0) { - org.json.JSONObject updateData = new org.json.JSONObject(); - updateData.put("viewUsers", viewUsers); - try { - os.indexUpdate("encounter", id, updateData); - } catch (Exception ex) { - // keeping this quiet cuz it can get noise while index builds - } - } - } - Util.mark("perm: done encs", startT); - System.out.println("opensearchIndexPermissions(): ...end [" + encCount + " encs; " + - Math.round((System.currentTimeMillis() - startT) / 1000) + "sec]"); - } - - public static org.json.JSONObject opensearchQuery(final org.json.JSONObject query, int numFrom, - int pageSize, String sort, String sortOrder) - throws IOException { - return Base.opensearchQuery("encounter", query, numFrom, pageSize, sort, sortOrder); - } - - public void opensearchDocumentSerializer(JsonGenerator jgen) - throws IOException, JsonProcessingException { - Shepherd myShepherd = new Shepherd("context0"); - - myShepherd.setAction("Encounter.opensearchDocumentSerializer"); - myShepherd.beginDBTransaction(); - try { - opensearchDocumentSerializer(jgen, myShepherd); - } catch (Exception ex) { - ex.printStackTrace(); - } finally { - myShepherd.rollbackAndClose(); - } - } - - public void opensearchDocumentSerializer(JsonGenerator jgen, Shepherd myShepherd) - throws IOException, JsonProcessingException { - super.opensearchDocumentSerializer(jgen, myShepherd); - - jgen.writeStringField("locationId", this.getLocationID()); - jgen.writeStringField("locationName", this.getLocationName()); - Long dim = this.getDateInMillisecondsFallback(); - if (dim != null) jgen.writeNumberField("dateMillis", dim); - String date = Util.getISO8601Date(this.getDate()); - if (date != null) jgen.writeStringField("date", date); - date = Util.getISO8601Date(this.getDWCDateAdded()); - if (date != null) jgen.writeStringField("dateSubmitted", date); - jgen.writeStringField("verbatimEventDate", this.getVerbatimEventDate()); - jgen.writeStringField("sex", this.getSex()); - jgen.writeStringField("taxonomy", this.getTaxonomyString()); - jgen.writeStringField("lifeStage", this.getLifeStage()); - jgen.writeStringField("livingStatus", this.getLivingStatus()); - jgen.writeStringField("verbatimLocality", this.getVerbatimLocality()); - jgen.writeStringField("country", this.getCountry()); - jgen.writeStringField("behavior", this.getBehavior()); - jgen.writeStringField("patterningCode", this.getPatterningCode()); - jgen.writeStringField("state", this.getState()); - jgen.writeStringField("occurrenceRemarks", this.getOccurrenceRemarks()); - jgen.writeStringField("otherCatalogNumbers", this.getOtherCatalogNumbers()); - jgen.writeBooleanField("publiclyReadable", this.isPubliclyReadable()); - jgen.writeStringField("distinguishingScar", this.getDistinguishingScar()); - String featuredAssetId = null; - List mas = this.getMedia(); - jgen.writeNumberField("numberAnnotations", this.numNonTrivialAnnotations()); - jgen.writeNumberField("numberMediaAssets", mas.size()); - jgen.writeArrayFieldStart("mediaAssets"); - for (MediaAsset ma : mas) { - jgen.writeStartObject(); - jgen.writeNumberField("id", ma.getIdInt()); - jgen.writeStringField("uuid", ma.getUUID()); - jgen.writeNumberField("width", ma.getWidth()); - jgen.writeNumberField("height", ma.getHeight()); - jgen.writeStringField("mimeTypeMajor", ma.getMimeTypeMajor()); - jgen.writeStringField("mimeTypeMinor", ma.getMimeTypeMinor()); - try { - // historic data might throw IllegalArgumentException: Path not under given root - URL url = ma.safeURL(myShepherd, null, "master"); - if (url != null) jgen.writeStringField("url", url.toString()); - } catch (Exception ex) {} - // we (likely) dont need annotations to search on, but they are needed for - // many of the usages (export, gallery, etc) of search *results* - jgen.writeArrayFieldStart("annotations"); - if (ma.hasAnnotations()) - for (Annotation ann : ma.getAnnotations()) { - jgen.writeStartObject(); - jgen.writeStringField("id", ann.getId()); - jgen.writeStringField("iaClass", ann.getIAClass()); - jgen.writeStringField("viewpoint", ann.getViewpoint()); - jgen.writeBooleanField("isTrivial", ann.isTrivial()); - jgen.writeNumberField("theta", ann.getTheta()); - jgen.writeArrayFieldStart("boundingBox"); - Feature ft = ann.getFeature(); // attempt force loading features for getBbox() - int[] bbox = ann.getBbox(); - if (bbox != null) - for (int i : bbox) { - jgen.writeNumber(i); - } - jgen.writeEndArray(); - Encounter annEnc = ann.findEncounter(myShepherd); - if (annEnc != null) jgen.writeStringField("encounterId", annEnc.getId()); - jgen.writeEndObject(); - } - jgen.writeEndArray(); - jgen.writeEndObject(); - if (featuredAssetId == null) featuredAssetId = ma.getUUID(); - } - jgen.writeEndArray(); - if (featuredAssetId != null) jgen.writeStringField("featuredAssetUuid", featuredAssetId); - if (this.submitterID == null) { - jgen.writeNullField("assignedUsername"); - } else { - jgen.writeStringField("assignedUsername", this.submitterID); - User submitter = this.getSubmitterUser(myShepherd); - if (submitter != null) jgen.writeStringField("submitterUserId", submitter.getId()); - } - jgen.writeArrayFieldStart("submitters"); - for (String id : this.getAllSubmitterIds(myShepherd)) { - jgen.writeString(id); - } - jgen.writeEndArray(); - jgen.writeArrayFieldStart("photographers"); - for (String id : this.getAllPhotographerIds()) { - jgen.writeString(id); - } - jgen.writeEndArray(); - jgen.writeArrayFieldStart("informOthers"); - for (String id : this.getAllInformOtherIds()) { - jgen.writeString(id); - } - jgen.writeEndArray(); - - List kws = new ArrayList(); - Map lkws = new HashMap(); - for (Keyword kw : this.getMediaAssetKeywords()) { - if (kw instanceof LabeledKeyword) { - LabeledKeyword lkw = (LabeledKeyword)kw; - lkws.put(lkw.getLabel(), lkw.getValue()); - } else { - String name = kw.getDisplayName(); - if (!kws.contains(name)) kws.add(name); - } - } - jgen.writeArrayFieldStart("mediaAssetKeywords"); - for (String kw : kws) { - jgen.writeString(kw); - } - jgen.writeEndArray(); - jgen.writeObjectFieldStart("mediaAssetLabeledKeywords"); - for (String kwLabel : lkws.keySet()) { - jgen.writeStringField(kwLabel, lkws.get(kwLabel)); - } - jgen.writeEndObject(); - - List projs = this.getProjects(myShepherd); - jgen.writeArrayFieldStart("projects"); - if (projs != null) - for (Project proj : projs) { - jgen.writeString(proj.getId()); - } - jgen.writeEndArray(); - - ImportTask itask = this.getImportTask(myShepherd); - if (itask != null) { - jgen.writeStringField("importTaskId", itask.getId()); - if (itask.getCreator() != null) - jgen.writeStringField("importTaskCreatorId", itask.getCreator().getId()); - String sourceName = itask.getSourceName(); - if (sourceName != null) - jgen.writeStringField("importTaskSourceName", sourceName); - } - jgen.writeArrayFieldStart("annotationViewpoints"); - for (String vp : this.getAnnotationViewpoints()) { - jgen.writeString(vp); - } - jgen.writeEndArray(); - - jgen.writeArrayFieldStart("annotationIAClasses"); - for (String cls : this.getAnnotationIAClasses()) { - jgen.writeString(cls); - } - jgen.writeEndArray(); - - jgen.writeArrayFieldStart("measurements"); - if (this.measurements != null) - for (Measurement meas : this.measurements) { - if (meas.getValue() == null) continue; // no value means we should skip - jgen.writeStartObject(); - jgen.writeNumberField("value", meas.getValue()); - if (meas.getType() != null) jgen.writeStringField("type", meas.getType()); - if (meas.getUnits() != null) jgen.writeStringField("units", meas.getUnits()); - if (meas.getSamplingProtocol() != null) - jgen.writeStringField("samplingProtocol", meas.getSamplingProtocol()); - jgen.writeEndObject(); - } - jgen.writeEndArray(); - - jgen.writeArrayFieldStart("metalTags"); - if (this.getMetalTags() != null) - for (MetalTag tag : this.getMetalTags()) { - jgen.writeStartObject(); - jgen.writeStringField("number", tag.getTagNumber()); - jgen.writeStringField("location", tag.getLocation()); - jgen.writeEndObject(); - } - jgen.writeEndArray(); - if (this.getAcousticTag() != null) { - jgen.writeObjectFieldStart("acousticTag"); - jgen.writeStringField("idNumber", this.getAcousticTag().getIdNumber()); - jgen.writeStringField("serialNumber", this.getAcousticTag().getSerialNumber()); - jgen.writeEndObject(); - } - if (this.getSatelliteTag() != null) { - jgen.writeObjectFieldStart("satelliteTag"); - jgen.writeStringField("name", this.getSatelliteTag().getName()); - jgen.writeStringField("serialNumber", this.getSatelliteTag().getSerialNumber()); - jgen.writeStringField("argosPttNumber", this.getSatelliteTag().getArgosPttNumber()); - jgen.writeEndObject(); - } - if (this.getDTag() != null) { - jgen.writeObjectFieldStart("digitalArchiveTag"); - jgen.writeStringField("dTagID", this.getDTag().getDTagID()); - jgen.writeStringField("serialNumber", this.getDTag().getSerialNumber()); - jgen.writeEndObject(); - } - org.json.JSONObject dpj = this.getDynamicPropertiesJSONObject(); - jgen.writeObjectFieldStart("dynamicProperties"); - for (String key : (Set)dpj.keySet()) { - jgen.writeStringField(key, dpj.optString(key, null)); - } - jgen.writeEndObject(); - - Double dlat = this.getDecimalLatitudeAsDouble(); - Double dlon = this.getDecimalLongitudeAsDouble(); - if ((dlat == null) || !Util.isValidDecimalLatitude(dlat) || (dlon == null) || - !Util.isValidDecimalLongitude(dlon)) { - jgen.writeNullField("locationGeoPoint"); - } else { - jgen.writeObjectFieldStart("locationGeoPoint"); - jgen.writeNumberField("lat", dlat); - jgen.writeNumberField("lon", dlon); - jgen.writeEndObject(); - } - MarkedIndividual indiv = this.getIndividual(); - if (indiv == null) { - jgen.writeNullField("individualId"); - } else { - jgen.writeStringField("individualId", indiv.getId()); - jgen.writeStringField("individualSex", indiv.getSex()); - jgen.writeStringField("individualTaxonomy", indiv.getTaxonomyString()); - jgen.writeNumberField("individualNumberEncounters", indiv.getNumEncounters()); - jgen.writeStringField("individualDisplayName", indiv.getDisplayName()); - jgen.writeArrayFieldStart("individualNames"); - Set names = indiv.getAllNamesList(); - if (names != null) - for (String name : names) { - jgen.writeString(name); - } - jgen.writeEndArray(); - jgen.writeStringField("individualNickName", indiv.getNickName()); - if (indiv.getTimeOfBirth() > 0) { - String birthTime = Util.getISO8601Date(new DateTime( - indiv.getTimeOfBirth()).toString()); - jgen.writeStringField("individualTimeOfBirth", birthTime); - } - if (indiv.getTimeOfDeath() > 0) { - String deathTime = Util.getISO8601Date(new DateTime( - indiv.getTimeOfDeath()).toString()); - jgen.writeStringField("individualTimeOfDeath", deathTime); - } - Encounter[] encs = indiv.getDateSortedEncounters(true); - if ((encs != null) && (encs.length > 0)) { - String encDate = Util.getISO8601Date(encs[0].getDate()); - if (encDate != null) jgen.writeStringField("individualFirstEncounterDate", encDate); - encDate = Util.getISO8601Date(encs[encs.length - 1].getDate()); - if (encDate != null) jgen.writeStringField("individualLastEncounterDate", encDate); - } - jgen.writeArrayFieldStart("individualSocialUnits"); - for (SocialUnit su : myShepherd.getAllSocialUnitsForMarkedIndividual(indiv)) { - Membership mem = su.getMembershipForMarkedIndividual(indiv); - if (mem != null) jgen.writeString(su.getSocialUnitName()); - } - jgen.writeEndArray(); - - jgen.writeArrayFieldStart("individualRelationshipRoles"); - for (String relRole : myShepherd.getAllRoleNamesForMarkedIndividual(indiv.getId())) { - jgen.writeString(relRole); - } - jgen.writeEndArray(); - } - DateTime occdt = getOccurrenceDateTime(myShepherd); - if (occdt != null) jgen.writeStringField("occurrenceDate", occdt.toString()); - jgen.writeStringField("geneticSex", this.getGeneticSex()); - jgen.writeStringField("haplotype", this.getHaplotype()); - - jgen.writeArrayFieldStart("microsatelliteMarkers"); - for (MicrosatelliteMarkersAnalysis msm : getMicrosatelliteMarkers()) { - jgen.writeStartObject(); - jgen.writeStringField("analysisId", msm.getAnalysisID()); - jgen.writeObjectFieldStart("loci"); - if (msm.getLoci() != null) - for (Locus locus : msm.getLoci()) { - if (locus.getName() == null) continue; // snh - jgen.writeObjectFieldStart(locus.getName()); - for (int i = 0; i < 4; i++) { - Integer allele = locus.getAllele(i); - if (allele != null) jgen.writeNumberField("allele" + i, allele); - } - jgen.writeEndObject(); - } - jgen.writeEndObject(); - jgen.writeEndObject(); - } - jgen.writeEndArray(); - - Occurrence occ = this.getOccurrence(myShepherd); - if (occ == null) { - jgen.writeNullField("occurrenceId"); - } else { - jgen.writeStringField("occurrenceId", occ.getId()); - jgen.writeStringField("occurrenceGroupBehavior", occ.getGroupBehavior()); - jgen.writeStringField("occurrenceGroupComposition", occ.getGroupComposition()); - jgen.writeStringField("occurrenceComments", occ.getComments()); - if (occ.getVisibilityIndex() != null) - jgen.writeNumberField("occurrenceVisibilityIndex", occ.getVisibilityIndex()); - if (occ.getIndividualCount() != null) - jgen.writeNumberField("occurrenceIndividualCount", occ.getIndividualCount()); - if (occ.getMinGroupSizeEstimate() != null) - jgen.writeNumberField("occurrenceMinGroupSizeEstimate", - occ.getMinGroupSizeEstimate()); - if (occ.getMaxGroupSizeEstimate() != null) - jgen.writeNumberField("occurrenceMaxGroupSizeEstimate", - occ.getMaxGroupSizeEstimate()); - if (occ.getBestGroupSizeEstimate() != null) - jgen.writeNumberField("occurrenceBestGroupSizeEstimate", - occ.getBestGroupSizeEstimate()); - if (occ.getBearing() != null) - jgen.writeNumberField("occurrenceBearing", occ.getBearing()); - if (occ.getDistance() != null) - jgen.writeNumberField("occurrenceDistance", occ.getDistance()); - Double odlat = occ.getDecimalLatitude(); - Double odlon = occ.getDecimalLongitude(); - if ((odlat == null) || !Util.isValidDecimalLatitude(odlat) || (odlon == null) || - !Util.isValidDecimalLongitude(odlon)) { - jgen.writeNullField("occurrenceLocationGeoPoint"); - } else { - jgen.writeObjectFieldStart("occurrenceLocationGeoPoint"); - jgen.writeNumberField("lat", odlat); - jgen.writeNumberField("lon", odlon); - jgen.writeEndObject(); - } - } - jgen.writeArrayFieldStart("organizations"); - User owner = this.getSubmitterUser(myShepherd); - if ((owner != null) && (owner.getOrganizations() != null)) - for (Organization org : owner.getOrganizations()) { - jgen.writeString(org.getId()); - } - jgen.writeEndArray(); - - jgen.writeArrayFieldStart("tissueSampleIds"); - for (String id : this.getTissueSampleIDs()) { - jgen.writeString(id); - } - jgen.writeEndArray(); - - Map bmeas = this.getBiologicalMeasurementsByType(); - jgen.writeObjectFieldStart("biologicalMeasurements"); - for (String type : (Set)bmeas.keySet()) { - jgen.writeNumberField(type, bmeas.get(type).getValue()); - } - jgen.writeEndObject(); - // this gets set on specific single-encounter-only actions, when extra expense is okay - // otherwise this will be computed by permissions backgrounding - if (this.getOpensearchProcessPermissions()) { - System.out.println("opensearchProcessPermissions=true for " + this.getId() + - "; indexing permissions"); - jgen.writeFieldName("viewUsers"); - jgen.writeStartArray(); - for (String id : this.userIdsWithViewAccess(myShepherd)) { - System.out.println("opensearch whhhh: " + id); - jgen.writeString(id); - } - jgen.writeEndArray(); - } - } - - public void opensearchIndexDeep() - throws IOException { - this.opensearchIndex(); - - final String encId = this.getId(); - ExecutorService executor = Executors.newFixedThreadPool(4); - Runnable rn = new Runnable() { - public void run() { - Shepherd bgShepherd = new Shepherd("context0"); - bgShepherd.setAction("Encounter.opensearchIndexDeep_" + encId); - bgShepherd.beginDBTransaction(); - try { - Encounter enc = bgShepherd.getEncounter(encId); - if ((enc == null) || (!enc.hasMarkedIndividual() && !enc.hasAnnotations())) { - // bgShepherd.rollbackAndClose(); - executor.shutdown(); - return; - } - MarkedIndividual indiv = enc.getIndividual(); - if (indiv != null) { - System.out.println("opensearchIndexDeep() background indexing indiv " + - indiv.getId() + " via enc " + encId); - try { - indiv.opensearchIndex(); - } catch (Exception ex) { - System.out.println("opensearchIndexDeep() background indexing " + - indiv.getId() + " FAILED: " + ex.toString()); - ex.printStackTrace(); - } - } - Occurrence occ = enc.getOccurrence(bgShepherd); - if (occ != null) { - System.out.println("opensearchIndexDeep() background indexing occ " + - occ.getId() + " via enc " + encId); - try { - occ.opensearchIndex(); - } catch (Exception ex) { - System.out.println("opensearchIndexDeep() background indexing " + - occ.getId() + " FAILED: " + ex.toString()); - ex.printStackTrace(); - } - } - if (enc.hasAnnotations()) { - for (Annotation ann : enc.getAnnotations()) { - System.out.println("opensearchIndexDeep() background indexing annot " + - ann.getId() + " via enc " + encId); - try { - ann.opensearchIndex(); - } catch (Exception ex) { - System.out.println("opensearchIndexDeep() background indexing " + - ann.getId() + " FAILED: " + ex.toString()); - ex.printStackTrace(); - } - } - } - } catch (Exception e) { - System.out.println("opensearchIndexDeep() backgrounding Encounter " + encId + - " hit an exception."); - e.printStackTrace(); - } finally { - bgShepherd.rollbackAndClose(); - } - System.out.println("opensearchIndexDeep() backgrounding Encounter " + encId + - " finished."); - executor.shutdown(); - } - }; - System.out.println("opensearchIndexDeep() begin backgrounding for " + this); - executor.execute(rn); - System.out.println("opensearchIndexDeep() [foreground] finished for Encounter " + encId); - } - - // given a doc from opensearch, can user access it? - public static boolean opensearchAccess(org.json.JSONObject doc, User user, - Shepherd myShepherd) { - if ((doc == null) || (user == null)) return false; - if (doc.optBoolean("publiclyReadable", false)) return true; - if (doc.optString("submitterUserId", "__FAIL__").equals(user.getId())) return true; - if (user.isAdmin(myShepherd)) return true; - org.json.JSONArray viewUsers = doc.optJSONArray("viewUsers"); - if (viewUsers == null) return false; - for (int i = 0; i < viewUsers.length(); i++) { - if (viewUsers.optString(i, "__FAIL__").equals(user.getId())) return true; - } - return false; - } - - @Override public Base getById(Shepherd myShepherd, String id) { - return myShepherd.getEncounter(id); - } - - @Override public String getAllVersionsSql() { - return - "SELECT \"CATALOGNUMBER\", CAST(COALESCE(EXTRACT(EPOCH FROM CAST(\"MODIFIED\" AS TIMESTAMP))*1000,-1) AS BIGINT) AS version FROM \"ENCOUNTER\" ORDER BY version"; - } - - @Override public long getVersion() { - return Util.getVersionFromModified(modified); - } - - public org.json.JSONObject opensearchMapping() { - org.json.JSONObject map = super.opensearchMapping(); - org.json.JSONObject keywordType = new org.json.JSONObject("{\"type\": \"keyword\"}"); - org.json.JSONObject keywordNormalType = new org.json.JSONObject( - "{\"type\": \"keyword\", \"normalizer\": \"wildbook_keyword_normalizer\"}"); - map.put("date", new org.json.JSONObject("{\"type\": \"date\"}")); - map.put("dateSubmitted", new org.json.JSONObject("{\"type\": \"date\"}")); - map.put("verbatimEventDate", new org.json.JSONObject("{\"type\": \"text\"}")); - map.put("individualTimeOfBirth", new org.json.JSONObject("{\"type\": \"date\"}")); - map.put("individualTimeOfDeath", new org.json.JSONObject("{\"type\": \"date\"}")); - map.put("locationGeoPoint", new org.json.JSONObject("{\"type\": \"geo_point\"}")); - map.put("occurrenceLocationGeoPoint", new org.json.JSONObject("{\"type\": \"geo_point\"}")); - - // if we want to sort on it (and it is texty), it needs to be keyword - // (ints, dates, etc are all sortable) - // note: "id" is done in Base.java - map.put("taxonomy", keywordType); - map.put("occurrenceId", keywordType); - map.put("state", keywordType); - map.put("submitterUserId", keywordType); - map.put("individualTaxonomy", keywordType); - map.put("individualId", keywordType); - map.put("importTaskId", keywordType); - map.put("importTaskCreatorId", keywordType); - map.put("importTaskSourceName", keywordType); - - // all case-insensitive keyword-ish types - map.put("locationId", keywordNormalType); - map.put("locationName", keywordNormalType); - map.put("country", keywordNormalType); - map.put("assignedUsername", keywordNormalType); - map.put("projects", keywordNormalType); - map.put("behavior", keywordNormalType); - map.put("patterningCode", keywordNormalType); - map.put("annotationViewpoints", keywordNormalType); - map.put("mediaAssetKeywords", keywordNormalType); - map.put("annotationIAClasses", keywordNormalType); - map.put("haplotype", keywordNormalType); - map.put("individualSocialUnits", keywordNormalType); - map.put("individualRelationshipRoles", keywordNormalType); - map.put("individualDisplayName", keywordNormalType); - map.put("organizations", keywordNormalType); - map.put("otherCatalogNumbers", keywordNormalType); - map.put("lifeStage", keywordNormalType); - map.put("submitters", keywordNormalType); - map.put("photographers", keywordNormalType); - map.put("informOthers", keywordNormalType); - - // https://stackoverflow.com/questions/68760699/matching-documents-where-multiple-fields-match-in-an-array-of-objects - map.put("measurements", new org.json.JSONObject("{\"type\": \"nested\"}")); - map.put("metalTags", new org.json.JSONObject("{\"type\": \"nested\"}")); - return map; - } - - // for encounters, we allow null user to see *some* things - public org.json.JSONObject jsonForApiGet(Shepherd myShepherd, User user) - throws IOException { - org.json.JSONObject rtn = new org.json.JSONObject(); - boolean isPublic = isPubliclyReadable(); - // anon-user can only see public, so we 401 here - if ((user == null) && !isPublic) { - rtn.put("statusCode", 401); - rtn.put("success", false); - return rtn; - } - rtn = opensearchDocumentAsJSONObject(myShepherd); - rtn.put("success", true); - rtn.put("statusCode", 200); - rtn.put("access", "read"); - rtn.put("isPublic", isPublic); - - boolean hideUserEmail = true; - User submitter = getSubmitterUser(myShepherd); - if (submitter != null) - rtn.put("submitterInfo", - submitter.infoJSONObject(myShepherd, user != null, hideUserEmail)); - // check to see if logged-in-user is outright blocked - if (user != null) { - boolean blocked = true; - if (canUserEdit(user, myShepherd)) { - rtn.put("access", "write"); - blocked = false; - // we can allow email being shown when access=write - hideUserEmail = false; - if (submitter != null) - rtn.put("submitterInfo", - submitter.infoJSONObject(myShepherd, true, hideUserEmail)); - } else if (canUserView(user, myShepherd)) { - blocked = false; - } - if (blocked) { - // we keep this very minimal - org.json.JSONObject blockedRtn = new org.json.JSONObject(); - blockedRtn.put("success", true); - blockedRtn.put("statusCode", 200); - blockedRtn.put("access", "none"); - blockedRtn.put("id", rtn.get("id")); - // need this to know who to collab with - Collaboration col = Collaboration.collaborationBetweenUsers(user, submitter, - myShepherd.getContext()); - if (col != null) { - blockedRtn.put("collaborationState", col.getState()); - blockedRtn.put("collaborationCreated", col.getDateStringCreated()); - } - blockedRtn.put("assignedUsername", rtn.optString("assignedUsername", null)); - blockedRtn.put("submitterUserId", rtn.optString("submitterUserId", null)); - blockedRtn.put("submitterInfo", rtn.optJSONObject("submitterInfo")); - return blockedRtn; - } - } - // additional fields we want - rtn.put("dateValues", getDateValuesJson()); - rtn.put("researcherComments", getRComments()); - rtn.put("groupRole", getGroupRole()); - rtn.put("identificationRemarks", getIdentificationRemarks()); - rtn.put("spotMapping", spotMappingJsonForApiGet()); - - // the user-listy things - rtn.put("submitters", - userListJSONArray(myShepherd, this.submitters, user != null, hideUserEmail)); - rtn.put("photographers", - userListJSONArray(myShepherd, this.photographers, user != null, hideUserEmail)); - rtn.put("informOthers", - userListJSONArray(myShepherd, this.informOthers, user != null, hideUserEmail)); - // sanitize for non-logged-in users (hence, on public data) - if (user == null) { - rtn.put("access", "read"); - String[] blocked = { - "importTaskSourceName", "locationId", "locationName", "country", "verbatimLocality", - "microsatelliteMarkers", "locationGeoPoint", "occurrenceLocationGeoPoint", - "mediaAssetKeywords", "mediaAssetLabeledKeywords", "biologicalMeasurements", - "importTaskCreatorId", "annotationIAClasses", "annotationViewpoints", - "researcherComments", "informOthers", "photographers", "submitters", - "assignedUsername" - }; - for (String field : blocked) { - rtn.remove(field); - } - // we redo mediaAssets, with no annots and mid size - org.json.JSONArray mas = new org.json.JSONArray(); - for (MediaAsset ma : getMedia()) { - org.json.JSONObject maj = new org.json.JSONObject(); - maj.put("uuid", ma.getUUID()); - maj.put("mimeTypeMajor", ma.getMimeTypeMajor()); - maj.put("mimeTypeMinor", ma.getMimeTypeMinor()); - maj.put("rotationInfo", ma.getRotationInfo()); - try { - // historic data might throw IllegalArgumentException: Path not under given root - java.net.URL url = ma.safeURL(myShepherd, null, "mid"); - if (url != null) maj.put("url", url.toString()); - } catch (Exception ex) {} - mas.put(maj); - } - rtn.put("mediaAssets", mas); - } else { - // for real users we add some extras to assets and annotations - if (rtn.optJSONArray("mediaAssets") != null) { - for (int i = 0; i < rtn.getJSONArray("mediaAssets").length(); i++) { - if (rtn.getJSONArray("mediaAssets").optJSONObject(i) != null) { - MediaAsset ma = MediaAssetFactory.loadByUuid(rtn.getJSONArray( - "mediaAssets").getJSONObject(i).optString("uuid"), myShepherd); - if (ma != null) { - rtn.getJSONArray("mediaAssets").getJSONObject(i).put("keywords", - ma.getKeywordsJSONArray()); - rtn.getJSONArray("mediaAssets").getJSONObject(i).put("detectionStatus", - ma.getDetectionStatus()); - rtn.getJSONArray("mediaAssets").getJSONObject(i).put("userFilename", - ma.getUserFilename()); - rtn.getJSONArray("mediaAssets").getJSONObject(i).put("rotationInfo", - ma.getRotationInfo()); - } - // now we cram some stuff into each annotation as well - if (rtn.getJSONArray("mediaAssets").getJSONObject(i).optJSONArray( - "annotations") != null) { - for (int j = 0; - j < - rtn.getJSONArray("mediaAssets").getJSONObject(i).getJSONArray( - "annotations").length(); - j++) { - if (rtn.getJSONArray("mediaAssets").getJSONObject(i).getJSONArray( - "annotations").optJSONObject(j) == null) continue; - // this parsing of nested json really makes me miss perl - Annotation ann = myShepherd.getAnnotation(rtn.getJSONArray( - "mediaAssets").getJSONObject(i).getJSONArray( - "annotations").getJSONObject(j).optString("id", null)); - if (ann == null) continue; - rtn.getJSONArray("mediaAssets").getJSONObject(i).getJSONArray( - "annotations").getJSONObject(j).put("identificationStatus", - ann.getIdentificationStatus()); - // annTasks are in chron order so most recent will be at end - List annTasks = ann.getRootIATasks(myShepherd); - int ntasks = Util.collectionSize(annTasks); - if (ntasks > 0) { - rtn.getJSONArray("mediaAssets").getJSONObject(i).getJSONArray( - "annotations").getJSONObject(j).put("iaTaskId", - annTasks.get(ntasks - 1).getId()); - rtn.getJSONArray("mediaAssets").getJSONObject(i).getJSONArray( - "annotations").getJSONObject(j).put("iaTaskParameters", - annTasks.get(ntasks - 1).getParameters()); - } - } - } - } - } - } - } - return rtn; - } - - // internal utility function - private org.json.JSONArray userListJSONArray(Shepherd myShepherd, List users, - boolean includeSensitive, boolean hideEmail) { - org.json.JSONArray arr = new org.json.JSONArray(); - if (Util.collectionIsEmptyOrNull(users)) return arr; - for (User user : users) { - arr.put(user.infoJSONObject(myShepherd, includeSensitive, hideEmail)); - } - return arr; - } - - public static Base createFromApi(org.json.JSONObject payload, List files, - Shepherd myShepherd) - throws ApiException { - if (payload == null) throw new ApiException("empty payload"); - User user = (User)payload.opt("_currentUser"); - - // these need validation (will throw ApiException if fail) - String locationID = (String)validateFieldValue("locationId", payload); - String dateTime = (String)validateFieldValue("dateTime", payload); - String txStr = (String)validateFieldValue("taxonomy", payload); - String submitterEmail = (String)validateFieldValue("submitterEmail", payload); - String photographerEmail = (String)validateFieldValue("photographerEmail", payload); - Double decimalLatitude = (Double)validateFieldValue("decimalLatitude", payload); - Double decimalLongitude = (Double)validateFieldValue("decimalLongitude", payload); - if (((decimalLatitude == null) && (decimalLongitude != null)) || - ((decimalLatitude != null) && (decimalLongitude == null))) { - org.json.JSONObject error = new org.json.JSONObject(); - error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); - // i guess we pick one, since both are wrong - error.put("fieldName", "decimalLatitude"); - error.put("value", decimalLatitude); - throw new ApiException("cannot send just one of decimalLatitude and decimalLongitude", - error); - } - String additionalEmailsValue = payload.optString("additionalEmails", null); - String[] additionalEmails = null; - if (!Util.stringIsEmptyOrNull(additionalEmailsValue)) - additionalEmails = additionalEmailsValue.split("[,\\s]+"); - if (additionalEmails != null) { - org.json.JSONObject error = new org.json.JSONObject(); - error.put("fieldName", "additionalEmails"); - for (String email : additionalEmails) { - if (!Util.isValidEmailAddress(email)) { - error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); - error.put("value", email); - throw new ApiException("invalid email address", error); - } - } - } - Encounter enc = new Encounter(false); - if (Util.isUUID(payload.optString("_id"))) enc.setId(payload.getString("_id")); - enc.setLocationID(locationID); - enc.setDecimalLatitude(decimalLatitude); - enc.setDecimalLongitude(decimalLongitude); - enc.setDateFromISO8601String(dateTime); - enc.setTaxonomyFromString(txStr); - if (CommonConfiguration.getProperty("encounterState0", myShepherd.getContext()) != null) { - enc.setState(CommonConfiguration.getProperty("encounterState0", - myShepherd.getContext())); - } - enc.setComments(payload.optString("comments", null)); - if (user == null) { - enc.setSubmitterID("public"); // this seems to be what EncounterForm servlet does so... - } else { - enc.setSubmitterID(user.getUsername()); - enc.addSubmitter(user); - } - if (!Util.stringIsEmptyOrNull(submitterEmail)) { - User submitterUser = myShepherd.getOrCreateUserByEmailAddress(submitterEmail, - payload.optString("submitterName", null)); - // set this after the owner-submitter being set - enc.addSubmitter(submitterUser); - } - if (!Util.stringIsEmptyOrNull(photographerEmail)) { - User photographerUser = myShepherd.getOrCreateUserByEmailAddress(photographerEmail, - payload.optString("photographerName", null)); - enc.addPhotographer(photographerUser); - } - if (additionalEmails != null) { - for (String email : additionalEmails) { - User addlUser = myShepherd.getOrCreateUserByEmailAddress(email, null); - enc.addInformOther(addlUser); - } - } - // this will get/make an Occurrence no matter what - Occurrence occ = myShepherd.getOrCreateOccurrence(payload.optString("occurrenceId", null)); - occ.addEncounterAndUpdateIt(enc); - myShepherd.getPM().makePersistent(occ); - return enc; - } - - // user should already have been validated -- via obj.canUserEdit() -- in api/BaseObject, so this - // does not need to be tested here. however, more detailed checks may require user (e.g. can user - // also alter another object, such as Occurrence) - public org.json.JSONObject processPatch(org.json.JSONArray patchArr, User user, - Shepherd myShepherd) - throws ApiException { - if (patchArr == null) - throw new ApiException("null patch array", ApiException.ERROR_RETURN_CODE_REQUIRED); - this.setSkipAutoIndexing(true); - org.json.JSONArray resArr = new org.json.JSONArray(); - Set occNeedPruning = new HashSet(); - Set indivNeedPruning = new HashSet(); - for (int i = 0; i < patchArr.length(); i++) { - System.out.println("applied patch at [i=" + i + "]: " + patchArr.optJSONObject(i)); - org.json.JSONObject patchRes = EncounterPatchValidator.applyPatch(this, - patchArr.optJSONObject(i), user, myShepherd); - for (int j = 0; j < patchRes.getJSONArray("_mayNeedPruning").length(); j++) { - Object p = patchRes.getJSONArray("_mayNeedPruning").get(j); - if (p instanceof Occurrence) { - occNeedPruning.add((Occurrence)p); - } else if (p instanceof MarkedIndividual) { - indivNeedPruning.add((MarkedIndividual)p); - } - } - patchRes.remove("_mayNeedPruning"); - System.out.println("patch returned at [i=" + i + "]: " + patchRes); - resArr.put(patchRes); - } - org.json.JSONObject rtn = new org.json.JSONObject(); - rtn.put("patchResults", resArr); - // after applying each patch, make sure nothing is wrong - EncounterPatchValidator.finalValidation(this, myShepherd); - // now we need to look at modified objects which may be empty (and thus need pruning) - for (Occurrence occ : occNeedPruning) { - if (!occ.pruneIfNeeded(myShepherd)) { - occ.setSkipAutoIndexing(false); - } - } - for (MarkedIndividual indiv : indivNeedPruning) { - if (!indiv.pruneIfNeeded(myShepherd)) { - indiv.setSkipAutoIndexing(false); - } - } - // no exceptions means success - rtn.put("success", true); - rtn.put("statusCode", 200); - this.setDWCDateLastModified(); - this._log(resArr); - this.setSkipAutoIndexing(false); - return rtn; - } - - // see note on painful redundancy with bulk import and createFromApi on - // Base.applyPatchOp() - public Object applyPatchOp(String fieldName, Object value, String op) - throws ApiException { - System.out.println("[DEBUG] applyPatchOp(): " + op + " " + fieldName + "=>" + value + - " on: " + this); - if (op == null) - throw new ApiException("op is required", ApiException.ERROR_RETURN_CODE_REQUIRED); - // TODO future enhancement: op=remove path=annotations/ANNOT_ID should perform - // functionality of servlet/EncounterRemoveAnnotation.java - User user = null; // needed for some options below - switch (fieldName) { - case "decimalLatitude": - setDecimalLatitude((Double)value); - break; - case "decimalLongitude": - setDecimalLongitude((Double)value); - break; - case "alternateId": - // note: is same as otherCatalogNumbers - setAlternateID((String)value); - break; - case "behavior": - setBehavior((String)value); - break; - case "country": - setCountry((String)value); - break; - case "dateInMilliseconds": - if (value != null) setDateInMilliseconds((Long)value); - break; - case "year": - if (value == null) { - setYear(0); - } else { - setYear((Integer)value); - } - break; - case "month": - if (value == null) { - setMonth(0); - } else { - setMonth((Integer)value); - } - break; - case "day": - if (value == null) { - setDay(0); - } else { - setDay((Integer)value); - } - break; - case "hour": - if (value == null) { - setHour(-1); // grr - } else { - setHour((Integer)value); - } - break; - case "minutes": - if (value == null) { - setMinutes(null); - } else { - setMinutes(value.toString()); - } - break; - case "depth": - setDepth((Double)value); - break; - case "elevation": - setMaximumElevationInMeters((Double)value); - break; - case "genus": - setGenus((String)value); - break; - case "specificEpithet": - setSpecificEpithet((String)value); - break; - case "lifeStage": - setLifeStage((String)value); - break; - case "livingStatus": - setLivingStatus((String)value); - break; - case "locationId": - setLocationID((String)value); - break; - case "sex": - setSex((String)value); - break; - case "state": - setState((String)value); - break; - case "submitterID": - setSubmitterID((String)value); - break; - case "submitterName": - setSubmitterName((String)value); - break; - case "submitterOrganization": - setSubmitterOrganization((String)value); - break; - case "distinguishingScar": - setDistinguishingScar((String)value); - break; - case "groupRole": - setGroupRole((String)value); - break; - case "identificationRemarks": - setIdentificationRemarks((String)value); - break; - case "occurrenceRemarks": - case "sightingRemarks": - setOccurrenceRemarks((String)value); - break; - case "otherCatalogNumbers": - setOtherCatalogNumbers((String)value); - break; - case "patterningCode": - setPatterningCode((String)value); - break; - case "satelliteTag": - setSatelliteTag((SatelliteTag)value); - break; - case "acousticTag": - setAcousticTag((AcousticTag)value); - break; - case "metalTags": - // we only need location to remove - if ("remove".equals(op) && (value != null)) { - removeMetalTag(value.toString()); - } else if (("add".equals(op) || "replace".equals(op)) && - (value instanceof org.json.JSONObject)) { - // add or replace will update based on location if exists - org.json.JSONObject jval = (org.json.JSONObject)value; - addOrUpdateMetalTag(jval.optString("location", null), - jval.optString("number", null)); - } - break; - case "measurements": - if ("remove".equals(op) && (value != null)) { - removeMeasurementByType(value.toString()); - } else if (value instanceof Measurement) { - // for op=add or op=replace, if it has the measurement (i.e. by type), it means - // it should be changed in place already so dont do anything - Measurement meas = (Measurement)value; - if (findMeasurementOfType(meas.getType()) == null) addMeasurement(meas); - } - break; - case "annotations": - // for now we can only patch op=remove on path=annotations - // adding annots is done through legacy servlet - if ("remove".equals(op) && (value instanceof Annotation)) { - // enc.removeAnnotation and deletePersistent (from db/shepherd) done in EncounterPatchValidator - // so we only need to clean up some loose ends here - Annotation goneAnnot = (Annotation)value; - goneAnnot.setSkipAutoIndexing(true); - goneAnnot.opensearchUnindexQuiet(); - } - break; - // these we really only want to append to (i think??) - // so this should only happen when op=add/replace and - // value is non-null - case "researcherComments": - if (value != null) addComments((String)value); - break; - case "verbatimLocality": - setVerbatimLocality((String)value); - break; - case "verbatimEventDate": - setVerbatimEventDate((String)value); - break; - // we should get value as a MarkedIndividual here (or null) - case "individualId": - if ("remove".equals(op) || (value == null)) { - MarkedIndividual current = removeIndividual(); - if (current != null) { - System.out.println("enc.applyPatchOp() removed " + this + " from " + current); - } - } else { - // value should be an individual (new or existing) - MarkedIndividual indiv = (MarkedIndividual)value; - MarkedIndividual current = getIndividual(); - if (indiv.equals(current)) { - System.out.println( - "enc.applyPatchOp() ignoring adding existing individual to " + this); - break; - } - current = removeIndividual(); - if (current != null) { - current.setSkipAutoIndexing(false); - setIndividual(null); - System.out.println("enc.applyPatchOp() removed (prior to re-setting) " + this + - " from " + current); - } - indiv.addEncounter(this); - setIndividual(indiv); - // this will only set indiv taxonomy if NOT set - // so for new indiv and existing with no taxonomy - if (indiv.getTaxonomyString() == null) - indiv.setTaxonomyString(this.getTaxonomyString()); - // indiv.version will be updated by above calls - System.out.println("enc.applyPatchOp() added " + this + " to " + indiv); - } - break; - // value should be an Occurrence here (already validated and permission-checked) - case "occurrenceId": - // if EncounterPatchValidator let thru null value, we do nothing - if (value == null) break; - Occurrence occ = (Occurrence)value; - if ("remove".equals(op)) { - // in remove case, we are given occ to remove from - occ.removeEncounter(this); - this.occurrenceID = null; - } else { - // otherwise it is occ we add to - occ.addEncounterAndUpdateIt(this); - } - break; - case "assets": - if ("add".equals(op) && (value != null)) { - MediaAsset ma = (MediaAsset)value; - ma.setDetectionStatus("_new"); - addMediaAsset(ma); - } - break; - // value should be a user here - case "informOthers": - user = (User)value; - if (op.equals("remove")) { - removeInformOther(user); - } else { - addInformOther(user); - } - break; - case "submitters": - user = (User)value; - if (op.equals("remove")) { - removeSubmitter(user); - } else { - addSubmitter(user); - } - break; - case "photographers": - user = (User)value; - if (op.equals("remove")) { - removePhotographer(user); - } else { - addPhotographer(user); - } - break; - default: - throw new ApiException("unknown fieldName: " + fieldName, - ApiException.ERROR_RETURN_CODE_INVALID); - } - return value; - } - - public org.json.JSONObject afterPatch(Shepherd myShepherd) { - org.json.JSONObject res = new org.json.JSONObject(); - List needsIndexing = new ArrayList(); - org.json.JSONArray newAssetsArr = new org.json.JSONArray(); - // we update children here (not backgrounded) since we need them available - // once the api returns the results - for (MediaAsset ma : this.getMedia()) { - if ("_new".equals(ma.getDetectionStatus())) { - // _post_new is meant to be temporary, as it - // will get overwritten once put into IA pipeline - ma.setDetectionStatus("_post_new"); - ma.updateStandardChildren(myShepherd); - needsIndexing.add(ma); - org.json.JSONObject maj = new org.json.JSONObject(); - maj.put("id", ma.getIdInt()); - try { - URL url = ma.safeURL(myShepherd, null, "master"); - if (url != null) maj.put("url", url.toString()); - } catch (Exception ex) {} - newAssetsArr.put(maj); - } - } - if (newAssetsArr.length() > 0) res.put("newMediaAssets", newAssetsArr); - BulkImportUtil.bulkOpensearchIndex(needsIndexing); - return res; - } - - // this is allowed to have its own new thread since encounter is persisted - public org.json.JSONObject afterPatchTransaction(String context) { - List ids = new ArrayList(); - - // we use _post_new state to determine what needs to go to IA - // see: afterPatch() above - for (MediaAsset ma : this.getMedia()) { - if ("_post_new".equals(ma.getDetectionStatus())) { - ids.add(ma.getIdInt()); - } - } - if (ids.size() < 1) return null; - Task task = this.sendToIA(ids, context); - if (task == null) return null; - org.json.JSONObject rtn = new org.json.JSONObject(); - rtn.put("taskId", task.getId()); - return rtn; - } - - public MarkedIndividual removeIndividual() { - MarkedIndividual current = getIndividual(); - - if (current == null) return null; - // skip auto indexing cuz race conditions; must manually index later - current.setSkipAutoIndexing(true); - current.removeEncounter(this); - setIndividual(null); - return current; - } - - public static Object validateFieldValue(String fieldName, org.json.JSONObject data) - throws ApiException { - if (data == null) throw new ApiException("empty payload"); - org.json.JSONObject error = new org.json.JSONObject(); - error.put("fieldName", fieldName); - String exMessage = "invalid value for " + fieldName; - Object returnValue = null; - double UNSET_LATLON = 9999.99; - switch (fieldName) { - case "locationId": - returnValue = data.optString(fieldName, null); - if (returnValue == null) { - error.put("code", ApiException.ERROR_RETURN_CODE_REQUIRED); - throw new ApiException(exMessage, error); - } - if (!LocationID.isValidLocationID((String)returnValue)) { - error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); - error.put("value", returnValue); - throw new ApiException(exMessage, error); - } - break; - - case "dateTime": - returnValue = data.optString(fieldName, null); - if (returnValue == null) { - error.put("code", ApiException.ERROR_RETURN_CODE_REQUIRED); - throw new ApiException(exMessage, error); - } - if (!validISO8601String((String)returnValue)) { - error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); - error.put("value", returnValue); - throw new ApiException(exMessage, error); - } - break; - - case "taxonomy": - returnValue = data.optString(fieldName, null); - if (returnValue != null) { // null is allowed, but will not pass validity - // this is throwaway read-only shepherd - Shepherd myShepherd = new Shepherd("context0"); - myShepherd.setAction("Encounter.validateFieldValue"); - boolean validTaxonomy = false; - myShepherd.beginDBTransaction(); - try { - validTaxonomy = myShepherd.isValidTaxonomyName((String)returnValue); - } catch (Exception e) { e.printStackTrace(); } finally { - myShepherd.rollbackAndClose(); - } - if (!validTaxonomy) { - error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); - error.put("value", returnValue); - throw new ApiException(exMessage, error); - } - } - break; - - case "photographerEmail": - case "submitterEmail": - returnValue = data.optString(fieldName, null); - if ((returnValue != null) && !Util.isValidEmailAddress((String)returnValue)) { - error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); - error.put("value", returnValue); - throw new ApiException(exMessage, error); - } - break; - - case "decimalLatitude": - returnValue = data.optDouble(fieldName, UNSET_LATLON); - if ((double)returnValue == UNSET_LATLON) { - returnValue = null; - } else if (!Util.isValidDecimalLatitude((double)returnValue)) { - error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); - error.put("value", returnValue); - throw new ApiException(exMessage, error); - } - break; - - case "decimalLongitude": - returnValue = data.optDouble(fieldName, UNSET_LATLON); - if ((double)returnValue == UNSET_LATLON) { - returnValue = null; - } else if (!Util.isValidDecimalLongitude((double)returnValue)) { - error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); - error.put("value", returnValue); - throw new ApiException(exMessage, error); - } - break; - - default: - System.out.println("Encounter.validateFieldValue(): WARNING unsupported fieldName=" + - fieldName); - } - // must be okay! - return returnValue; - } - - // basically ripped from servlet/EncounterForm - public Task sendToIA(Shepherd myShepherd) { - Task task = null; - - try { - IAJsonProperties iaConfig = IAJsonProperties.iaConfig(); - if (iaConfig.hasIA(this, myShepherd)) { - for (MediaAsset ma : this.getMedia()) { - ma.setDetectionStatus(IBEISIA.STATUS_INITIATED); - } - Task parentTask = null; // this is *not* persisted, but only used so intakeMediaAssets will inherit its params - if (this.getLocationID() != null) { - parentTask = new Task(); - org.json.JSONObject tp = new org.json.JSONObject(); - org.json.JSONObject mf = new org.json.JSONObject(); - mf.put("locationId", this.getLocationID()); - tp.put("matchingSetFilter", mf); - parentTask.setParameters(tp); - } - task = IA.intakeMediaAssets(myShepherd, this.getMedia(), parentTask); - myShepherd.storeNewTask(task); - System.out.println("sendToIA() success on " + this + " => " + task); - } else { - System.out.println("sendToIA() skipped; no config for " + this); - } - } catch (Exception ex) { - System.out.println("sendToIA() failed on " + this + ": " + ex); - ex.printStackTrace(); - } - return task; - } - - // this is based on servlet/MediaAssetCreate and differs only slightly from - // above - mainly in that it can handle multiple assets and creates own shepherd - // (note: all assets assumed to be using *this encounter* - public Task sendToIA(List ids, String context) { - Task task = null; - Shepherd myShepherd = new Shepherd(context); - - myShepherd.setAction("Encounter.sendToIA()"); - myShepherd.beginDBTransaction(); - try { - IAJsonProperties iaConfig = IAJsonProperties.iaConfig(); - boolean hasConfig = iaConfig.hasIA(this, myShepherd); - List allMAs = new ArrayList(); - for (Integer id : ids) { - if (id < 0) continue; - MediaAsset ma = MediaAssetFactory.load(id, myShepherd); - if (ma != null) { - ma.setDetectionStatus(hasConfig ? IBEISIA.STATUS_INITIATED : IBEISIA.STATUS_COMPLETE); - allMAs.add(ma); - } - } - if (!hasConfig) { - System.out.println("sendToIA() skipped; no config for " + this); - } else if (allMAs.size() > 0) { - Task parentTask = null; // not persisted - if (this.getLocationID() != null) { - parentTask = new Task(); - org.json.JSONObject tp = new org.json.JSONObject(); - org.json.JSONObject mf = new org.json.JSONObject(); - mf.put("locationId", this.getLocationID()); - tp.put("matchingSetFilter", mf); - parentTask.setParameters(tp); - } - Taxonomy taxy = this.getTaxonomy(myShepherd); - if (taxy != null) { - task = IA.intakeMediaAssetsOneSpecies(myShepherd, allMAs, taxy, parentTask); - } else { - task = IA.intakeMediaAssets(myShepherd, allMAs); - } - myShepherd.storeNewTask(task); - System.out.println("sendToIA() created " + task + " for " + this); - } - // persist will catch change on asset detectionStatus regardless - myShepherd.commitDBTransaction(); - } catch (Exception ex) { - ex.printStackTrace(); - myShepherd.rollbackDBTransaction(); - } finally { - myShepherd.closeDBTransaction(); - } - return task; - } - - public Set getNotificationEmailAddresses() { - Set addrs = new HashSet(); - - addrs.addAll(Util.getUserEmailAddresses(this.getSubmitters())); - addrs.addAll(Util.getUserEmailAddresses(this.getPhotographers())); - addrs.addAll(Util.getUserEmailAddresses(this.getInformOthers())); - return addrs; - } - - // FIXME passing the langCode is dumb imho, but this is "standard practice" - // better would be that each recipient user's language preference would be used for their email - public void sendCreationEmails(Shepherd myShepherd, String langCode) { - String context = myShepherd.getContext(); - - if (!CommonConfiguration.sendEmailNotifications(context)) return; - myShepherd.beginDBTransaction(); - try { - URI uri = CommonConfiguration.getServerURI(myShepherd); - if (uri == null) throw new IOException("could not find server uri"); - ThreadPoolExecutor es = MailThreadExecutorService.getExecutorService(); - Properties submitProps = ShepherdProperties.getProperties("submit.properties", langCode, - context); - Map tagMap = NotificationMailer.createBasicTagMap(this); - tagMap.put(NotificationMailer.WILDBOOK_COMMUNITY_URL, - CommonConfiguration.getWildbookCommunityURL(context)); - List mailTo = NotificationMailer.splitEmails( - CommonConfiguration.getNewSubmissionEmail(context)); - String mailSubj = submitProps.getProperty("newEncounter") + this.getCatalogNumber(); - for (String emailTo : mailTo) { - NotificationMailer mailer = new NotificationMailer(context, emailTo, langCode, - "newSubmission-summary", tagMap); - mailer.setUrlScheme(uri.getScheme()); - es.execute(mailer); - } - // this will be empty if no locationID - Set locEmails = myShepherd.getAllUserEmailAddressesForLocationIDAsSet( - this.getLocationID(), context); - for (String emailTo : locEmails) { - NotificationMailer mailer = new NotificationMailer(context, langCode, emailTo, - "newSubmission-summary", tagMap); - mailer.setUrlScheme(uri.getScheme()); - es.execute(mailer); - } - // Add encounter dont-track tag for remaining notifications (still needs email-hash assigned). - tagMap.put(NotificationMailer.EMAIL_NOTRACK, "number=" + this.getCatalogNumber()); - // this is a mashup of: submitters, photographers, informOthers.... - for (String emailTo : this.getNotificationEmailAddresses()) { - tagMap.put(NotificationMailer.EMAIL_HASH_TAG, getHashOfEmailString(emailTo)); - NotificationMailer mailer = new NotificationMailer(context, langCode, emailTo, - "newSubmission", tagMap); - mailer.setUrlScheme(uri.getScheme()); - es.execute(mailer); - } - es.shutdown(); - } catch (Exception ex) { - System.out.println("sendCreationEmails() on " + this + " failed: " + ex); - ex.printStackTrace(); - } finally { - myShepherd.rollbackDBTransaction(); - } - } - -/* - in anticipation of 10.10.0, this is a sketchy of what logging might look like - for a change in an Encounter via PATCH. - - FIXME this should be fully replaced (or wrapped around) the more basic log functionality - that is yet to be written. this can serve as an idea of some things which might be - desirable to support in general logging. take with a grain of salt. - */ - public void _log(org.json.JSONArray arr) { - if ((arr == null) || (arr.length() == 0)) return; - String actionId = Util.generateUUID(); - for (int i = 0; i < arr.length(); i++) { - if (arr.optJSONObject(i) == null) continue; - org.json.JSONObject p = arr.getJSONObject(i).optJSONObject("_patch"); - if (p == null) continue; - String op = p.optString("op", "UNKNOWN_OP"); - String path = p.optString("path", "UNKNOWN_PATH"); - Object value = null; - if (p.has("value") && !p.isNull("value")) value = p.get("value"); - String logMessage = "modified by PATCH op=" + op + ", path " + path + " with value: " + - ((value == null) ? "NULL" : value.toString()); - _log2(null, null, null, "Encounter", this.getId(), actionId, logMessage); - // legacy "audit log" (aka some random comment) - // TODO really need to add the user/who part here - this.addComments("

    " + Util.prettyTimeStamp() + - " modified " + path + " with operation " + op + "" + ((value == - null) ? "" : " and value " + value.toString() + "") + "

    "); - } - } - - // one of many dilemmas: we need a request object to get user + ip address, but dont have - // it at this point. so we likely need to pass it all around somehow. maybe on a shepherd or - // some other more common object? FIXME TODO - public void _log2( - // "standard" levels (null should be some reasonable default???) - String logLevel, - // reference to who did it, could be multiple users etc. probably should be id _and_ username? - String user, - // pretty obvious? - String ip, - // class of object acted upon - String objectClass, - // primary key - String objectId, - // for groupin multiple logs into one "action" (e.g. a PATCH on object) - String actionId, - // message - String message) { - System.out.println(String.join("\t", "[TMPLOG]", - new Long(System.currentTimeMillis()).toString(), user, ip, objectClass, objectId, - actionId, message)); - } -} +package org.ecocean; + +import org.apache.commons.codec.digest.DigestUtils; + +import java.io.*; +import java.lang.Math; +import java.net.URI; +import java.net.URL; +import java.text.SimpleDateFormat; +import java.util.*; +import java.util.concurrent.Executors; +import java.util.concurrent.ExecutorService; +import java.util.concurrent.ThreadPoolExecutor; + +import javax.jdo.Query; + +import org.apache.commons.lang3.builder.ToStringBuilder; + +import com.fasterxml.jackson.core.JsonGenerator; +import com.fasterxml.jackson.core.JsonProcessingException; +import javax.servlet.http.HttpServletRequest; + +import org.ecocean.api.ApiException; +import org.ecocean.api.bulk.BulkImportUtil; +import org.ecocean.api.bulk.BulkValidatorException; +import org.ecocean.api.patch.EncounterPatchValidator; +import org.ecocean.genetics.*; +import org.ecocean.ia.IA; +import org.ecocean.ia.Task; +import org.ecocean.identity.IBEISIA; +import org.ecocean.media.*; +import org.ecocean.security.Collaboration; +import org.ecocean.servlet.importer.ImportTask; +import org.ecocean.shepherd.core.Shepherd; +import org.ecocean.shepherd.core.ShepherdProperties; +import org.ecocean.social.Membership; +import org.ecocean.social.SocialUnit; +import org.ecocean.tag.AcousticTag; +import org.ecocean.tag.DigitalArchiveTag; +import org.ecocean.tag.MetalTag; +import org.ecocean.tag.SatelliteTag; +import org.ecocean.Util.MeasurementDesc; +import org.joda.time.DateTime; +import org.joda.time.format.DateTimeFormat; +import org.joda.time.format.DateTimeFormatter; +import org.joda.time.LocalDateTime; + +import org.datanucleus.api.rest.orgjson.JSONArray; +import org.datanucleus.api.rest.orgjson.JSONException; +import org.datanucleus.api.rest.orgjson.JSONObject; + +/** + * An encounter object stores the complete data for a single sighting/capture report. + * Encounters are added to MarkedIndividual objects as multiple encounters are associated with known individuals. + *

    + * + * @author Jason Holmberg + * @version 2.0 + */ +public class Encounter extends Base implements java.io.Serializable { + static final long serialVersionUID = -146404246317385604L; + + public static final String STATE_MATCHING_ONLY = "matching_only"; + + @Override public String opensearchIndexName() { return "encounter"; } + + public static final double ENCOUNTER_AUTO_SOURCE_CONFIDENCE_CUTOFF = 0.7; + public static final String STATE_AUTO_SOURCED = "auto_sourced"; + + private String sex = null; + private String locationID = null; + private Double maximumDepthInMeters; + private Double maximumElevationInMeters; + private String catalogNumber = ""; + private MarkedIndividual individual; + private int day = 0; + private int month = -1; + private int year = 0; + private Double decimalLatitude; + private Double decimalLongitude; + + private Double endDecimalLatitude; + private Double endDecimalLongitude; + + private String verbatimLocality; + private String occurrenceRemarks = ""; + private String modified; + private String occurrenceID; + private String recordedBy; + private String otherCatalogNumbers; + private String behavior; + private String eventID; + private String measurementUnit; + private String verbatimEventDate; + private String dynamicProperties; + public String identificationRemarks = ""; + public String genus = ""; + public String specificEpithet; + public String lifeStage; + public String country; + public String zebraClass = ""; // via lewa: lactating female, territorial male, etc etc + + private String imageSet; + private String soil; + + private String reproductiveStage; + private Double bodyCondition; + private Double parasiteLoad; + private Double immunoglobin; + private Boolean sampleTakenForDiet; + private Boolean injured; + private boolean opensearchProcessPermissions = false; + + private ArrayList observations = new ArrayList(); + + public String getSoil() { return soil; } + public void setSoil(String soil) { this.soil = soil; } + + public String getReproductiveStage() { return reproductiveStage; } + public void setReproductiveStage(String reproductiveStage) { + this.reproductiveStage = reproductiveStage; + } + + public Double getBodyCondition() { return bodyCondition; } + public void setBodyCondition(Double bodyCondition) { this.bodyCondition = bodyCondition; } + + public Double getParasiteLoad() { return parasiteLoad; } + public void setParasiteLoad(Double parasiteLoad) { this.parasiteLoad = parasiteLoad; } + + public Double getImmunoglobin() { return immunoglobin; } + public void setImmunoglobin(Double immunoglobin) { this.immunoglobin = immunoglobin; } + + public Boolean getSampleTakenForDiet() { return sampleTakenForDiet; } + public void setSampleTakenForDiet(Boolean sampleTakenForDiet) { + this.sampleTakenForDiet = sampleTakenForDiet; + } + + public Boolean getInjured() { return injured; } + public void setInjured(Boolean injured) { this.injured = injured; } + + // for searchability + private String imageNames; + + private List submitters; + private List photographers; + private List informOthers; + + private static HashMap > _matchEncounterCache = new HashMap >(); + + // An URL to a thumbnail image representing the encounter. + private String dwcImageURL; + + // Defines whether the sighting represents a living or deceased individual. + // Currently supported values are: "alive" and "dead". + private String livingStatus; + + // observed age (if any) via IBEIS zebra projects + private Double age; + + // Date the encounter was added to the library. + private String dwcDateAdded; + private Long dwcDateAddedLong; + + // If Encounter spanned more than one day, date of release + private Date releaseDate; + + private Long releaseDateLong; + + // Size of the individual in meters + private Double size; + + // Additional comments added by library users + private String researcherComments = "None"; + + // username of the logged in researcher assigned to the encounter + // this String is matched to an org.ecocean.User object to obtain more information + private String submitterID; + + // name, email, phone, address of the encounter reporter + private String submitterEmail, submitterPhone, submitterAddress; + private String hashedSubmitterEmail; + private String hashedPhotographerEmail; + private String hashedInformOthers; + private String informothers; + + // name, email, phone, address of the encounter photographer + private String photographerName, photographerEmail, photographerPhone, photographerAddress; + + // a Vector of Strings defining the relative path to each photo. The path is relative to the servlet base directory + public Vector additionalImageNames = new Vector(); + + // a Vector of Strings of email addresses to notify when this encounter is modified + private Vector interestedResearchers = new Vector(); + + // time metrics of the report + private int hour = 0; + private String minutes = "00"; + + private String state = ""; + + // the globally unique identifier (GUID) for this Encounter + private String guid; + + private Long endDateInMilliseconds; + private Long dateInMilliseconds; + + // describes how the shark was measured + private String size_guess = "none provided"; + + // String reported GPS values for lat and long of the encounter + private String gpsLongitude = "", gpsLatitude = ""; + private String gpsEndLongitude = "", gpsEndLatitude = ""; + + // Indicates whether this record can be exposed via TapirLink + private boolean okExposeViaTapirLink = false; + + public String spotImageFileName = ""; + + // name of the stored file from which the right-side spots were extracted + public String rightSpotImageFileName = ""; + + // string descriptor of the most obvious scar (if any) as reported by the original submitter + // we also use keywords to be more specific + public String distinguishingScar = "None"; + // describes how this encounter was matched to an existing shark - by eye, by pattern recognition algorithm etc. + + // SPOTS + // an array of the extracted left-side superSpots + // private superSpot[] spots; + private ArrayList spots; + + // an array of the extracted right-side superSpots + // private superSpot[] rightSpots; + private ArrayList rightSpots; + + // an array of the three extracted left-side superSpots used for the affine transform of the I3S algorithm + // private superSpot[] leftReferenceSpots; + private ArrayList leftReferenceSpots; + + // an array of the three extracted right-side superSpots used for the affine transform of the I3S algorithm + // private superSpot[] rightReferenceSpots; + private ArrayList rightReferenceSpots; + + // an open ended string that allows a type of patterning to be identified. + // as an example, see the use of color codes at splashcatalog.org, allowing pre-defined fluke patterning types + // to be used to help narrow the search for a marked individual + private String patterningCode; + + // submitting organization and project further detail the scope of who submitted this project + private String submitterOrganization; + private String submitterProject; + private List submitterResearchers; + + // hold submittedData + // private List collectedData; + private List tissueSamples; + private List images; + // private ArrayList media; + private ArrayList annotations; + private List measurements; + private List metalTags; + private AcousticTag acousticTag; + private SatelliteTag satelliteTag; + private DigitalArchiveTag digitalArchiveTag; + + private Boolean mmaCompatible = false; + + // Variables used in the Survey, SurveyTrack, Path, Location model + + private String correspondingSurveyTrackID = null; + private String correspondingSurveyID = null; + + // This is the eventual replacement for the old decimal lat lon and other location data. + private PointLocation pointLocation; + + // This is the number used to cross reference with dates to find occurances. (Read Lab) + private String sightNo = ""; + + // This is what researchers eyeball is the individual's ID in the field + // it could be a name that only has meaning in the context of that day's work + // (not necessarily an individual name from the WB database) + private String fieldID; + + // This is a standard 1-5 color scale used by cetacean researchers + private Integer flukeType; + + // added by request for ASWN, this is the role an individual served in its occurrence + // (from a standard list like Escort Male) + private String groupRole; + + // identifies the import/dataset this came from for data provenance + private String dataSource; + + // start constructors + + /** + * empty constructor required by the JDO Enhancer + */ + public Encounter() {} + + public Encounter(boolean skipSetup) { + if (skipSetup) return; + this.catalogNumber = Util.generateUUID(); + this.setDWCDateAdded(); + this.setDWCDateLastModified(); + this.resetDateInMilliseconds(); + this.annotations = new ArrayList(); + } + + /** + * Use this constructor to add the minimum level of information for a new encounter The Vector additionalImages must be a Vector of + * Blob objects + * + * TODO: evaluate and remove if this is DEPRECATED cuz, SinglePhotoVideos? really? + */ + public Encounter(int day, int month, int year, int hour, String minutes, String size_guess, + String location) { + if (images != null) + System.out.println( + "WARNING: danger! deprecated SinglePhotoVideo-based Encounter constructor used!"); + this.verbatimLocality = location; + + this.images = images; + this.day = day; + this.month = month; + this.year = year; + this.hour = hour; + this.minutes = minutes; + this.size_guess = size_guess; + + this.setDWCDateAdded(); + this.setDWCDateLastModified(); + this.resetDateInMilliseconds(); + } + + public Encounter(Annotation ann) { + this(new ArrayList(Arrays.asList(ann))); + } + + public Encounter(ArrayList anns) { + this.catalogNumber = Util.generateUUID(); + this.annotations = anns; + if (!this.annotationsAreEmpty()) { + this.setDateFromAssets(); + this.setSpeciesFromAnnotations(); + this.setLatLonFromAssets(); + } + this.setDWCDateAdded(); + this.setDWCDateLastModified(); + this.resetDateInMilliseconds(); + } + private boolean annotationsAreEmpty() { + return (this.annotations == null || this.annotations.size() == 0 || + (this.annotations.size() == 1 && (this.annotations.get(0) == null))); + } + + // space saver since we're about to use this hundreds of times + private boolean shouldReplace(String str1, String str2) { + return Util.shouldReplace(str1, str2); + } + + // also returns true when str1 is a superstring of str2. + private boolean shouldReplaceSuperStr(String str1, String str2) { + return (shouldReplace(str1, str2) || (Util.stringExists(str1) && str1.contains(str2))); + } + + public void mergeAndDelete(Encounter enc2, Shepherd myShepherd) { + mergeDataFrom(enc2); + MarkedIndividual ind = myShepherd.getMarkedIndividual(enc2); + if (ind != null) { + ind.removeEncounter(enc2); + ind.addEncounter(this); // duplicate-safe + } + Occurrence occ = myShepherd.getOccurrence(enc2); + if (occ != null) { + occ.removeEncounter(enc2); + occ.addEncounter(this); // duplicate-safe + } + // Remove it from an ImportTask if needed + ImportTask task = myShepherd.getImportTaskForEncounter(enc2.getCatalogNumber()); + if (task != null) { + task.removeEncounter(enc2); + myShepherd.updateDBTransaction(); + } + // Remove from Project if needed + List projects = myShepherd.getProjectsForEncounter(enc2); + if (projects != null && !projects.isEmpty()) { + for (Project project : projects) { + project.removeEncounter(enc2); + myShepherd.updateDBTransaction(); + } + } + // remove tissue samples because of bogus foreign key constraint that prevents deletion + int numTissueSamples = 0; + if (enc2.getTissueSamples() != null) numTissueSamples = enc2.getTissueSamples().size(); + for (int i = 0; i < numTissueSamples; i++) { + enc2.removeTissueSample(0); + } + this.addComments("

    Merged in encounter " + enc2.getCatalogNumber() + "."); + + myShepherd.throwAwayEncounter(enc2); + } + + // copies otherEnc's data into thisEnc, not overwriting anything + public void mergeDataFrom(Encounter enc2) { + if (enc2.getIndividual() != null) setIndividual(enc2.getIndividual()); + // simple string fields + if (shouldReplace(enc2.getSex(), getSex())) setSex(enc2.getSex()); + if (shouldReplace(enc2.getLocationID(), getLocationID())) + setLocationID(enc2.getLocationID()); + if (shouldReplace(enc2.getVerbatimLocality(), getVerbatimLocality())) + setVerbatimLocality(enc2.getVerbatimLocality()); + if (shouldReplace(enc2.getOccurrenceID(), getOccurrenceID())) + setOccurrenceID(enc2.getOccurrenceID()); + if (shouldReplace(enc2.getRecordedBy(), getRecordedBy())) + setRecordedBy(enc2.getRecordedBy()); + if (shouldReplace(enc2.getEventID(), getEventID())) setEventID(enc2.getEventID()); + if (shouldReplace(enc2.getGenus(), getGenus())) setGenus(enc2.getGenus()); + if (shouldReplace(enc2.getSpecificEpithet(), getSpecificEpithet())) + setSpecificEpithet(enc2.getSpecificEpithet()); + if (shouldReplace(enc2.getLifeStage(), getLifeStage())) setLifeStage(enc2.getLifeStage()); + if (shouldReplace(enc2.getCountry(), getCountry())) setCountry(enc2.getCountry()); + if (shouldReplace(enc2.getZebraClass(), getZebraClass())) + setZebraClass(enc2.getZebraClass()); + if (shouldReplace(enc2.getSoil(), getSoil())) setSoil(enc2.getSoil()); + if (shouldReplace(enc2.getReproductiveStage(), getReproductiveStage())) + setReproductiveStage(enc2.getReproductiveStage()); + if (shouldReplace(enc2.getLivingStatus(), getLivingStatus())) + setLivingStatus(enc2.getLivingStatus()); + if (shouldReplace(enc2.getSubmitterEmail(), getSubmitterEmail())) + setSubmitterEmail(enc2.getSubmitterEmail()); + if (shouldReplace(enc2.getSubmitterPhone(), getSubmitterPhone())) + setSubmitterPhone(enc2.getSubmitterPhone()); + if (shouldReplace(enc2.getSubmitterAddress(), getSubmitterAddress())) + setSubmitterAddress(enc2.getSubmitterAddress()); + if (shouldReplace(enc2.getState(), getState())) setState(enc2.getState()); + if (shouldReplace(enc2.getGPSLongitude(), getGPSLongitude())) + setGPSLongitude(enc2.getGPSLongitude()); + if (shouldReplace(enc2.getGPSLatitude(), getGPSLatitude())) + setGPSLatitude(enc2.getGPSLatitude()); + if (shouldReplace(enc2.getPatterningCode(), getPatterningCode())) + setPatterningCode(enc2.getPatterningCode()); + if (shouldReplace(enc2.getSubmitterOrganization(), getSubmitterOrganization())) + setSubmitterOrganization(enc2.getSubmitterOrganization()); + if (shouldReplace(enc2.getSubmitterProject(), getSubmitterProject())) + setSubmitterProject(enc2.getSubmitterProject()); + if (shouldReplace(enc2.getFieldID(), getFieldID())) setFieldID(enc2.getFieldID()); + if (shouldReplace(enc2.getGroupRole(), getGroupRole())) setGroupRole(enc2.getGroupRole()); + // now string fields that might need to be combined rather than replaced + if (shouldReplaceSuperStr(enc2.getDynamicProperties(), getDynamicProperties())) { + setDynamicProperties(enc2.getDynamicProperties()); + } else if (Util.stringExists(enc2.getDynamicProperties())) { // shouldn't replace, should combine + addDynamicProperties(enc2.getDynamicProperties()); + } + if (shouldReplaceSuperStr(enc2.getOccurrenceRemarks(), getOccurrenceRemarks())) { + setOccurrenceRemarks(enc2.getOccurrenceRemarks()); + } else if (Util.stringExists(enc2.getOccurrenceRemarks())) { // shouldn't replace, should combine + setOccurrenceRemarks(getOccurrenceRemarks() + " " + enc2.getOccurrenceRemarks()); + } + // now combine list fields making sure not to add duplicate entries + setAnnotations(Util.combineArrayListsInPlace(getAnnotations(), enc2.getAnnotations())); + setObservationArrayList(Util.combineArrayListsInPlace(getObservationArrayList(), + enc2.getObservationArrayList())); + setSubmitterResearchers(Util.combineListsInPlace(getSubmitterResearchers(), + enc2.getSubmitterResearchers())); + // custom no-duplicate logic bc the same sampleID may have been added on both encounters, but this would create unique tissuesample objects + Set sampleIDs = getTissueSampleIDs(); + for (TissueSample samp : enc2.getTissueSamples()) { + if (!sampleIDs.contains(samp.getSampleID())) addTissueSample(samp); + } + setMeasurements(Util.combineListsInPlace(getMeasurements(), enc2.getMeasurements())); + setMetalTags(Util.combineListsInPlace(getMetalTags(), enc2.getMetalTags())); + + // spot lists + setSpots(Util.combineArrayListsInPlace(getSpots(), enc2.getSpots())); + setRightSpots(Util.combineArrayListsInPlace(getRightSpots(), enc2.getRightSpots())); + setLeftReferenceSpots(Util.combineArrayListsInPlace(getLeftReferenceSpots(), + enc2.getLeftReferenceSpots())); + setRightReferenceSpots(Util.combineArrayListsInPlace(getRightReferenceSpots(), + enc2.getRightReferenceSpots())); + // tags + if (enc2.getAcousticTag() != null && getAcousticTag() == null) + setAcousticTag(enc2.getAcousticTag()); + if (enc2.getSatelliteTag() != null && getSatelliteTag() == null) + setSatelliteTag(enc2.getSatelliteTag()); + if (enc2.getDTag() != null && getDTag() == null) setDTag(enc2.getDTag()); + // skip time stuff bc if the time is different we probably don't want to combine the encounters anyway. + } + + public String getZebraClass() { + return zebraClass; + } + + public void setZebraClass(String c) { + zebraClass = c; + } + + public String getImageNames() { + return imageNames; + } + + public void addImageName(String name) { + if (imageNames == null) imageNames = name; + else if (name != null) imageNames += (", " + name); + } + + public String addAllImageNamesFromAnnots(boolean overwrite) { + if (overwrite) imageNames = null; + return addAllImageNamesFromAnnots(); + } + + public String addAllImageNamesFromAnnots() { + for (Annotation ann : getAnnotations()) { + for (Feature feat : ann.getFeatures()) { + try { + MediaAsset ma = feat.getMediaAsset(); + addImageName(ma.getFilename()); + } catch (Exception e) { + System.out.println("exception parsing image name from feature " + feat); + } + } + } + return imageNames; + } + + /** + * Returns an array of all of the superSpots for this encounter. + * + * @return the array of superSpots, taken from the croppedImage, that make up the digital fingerprint for this encounter + */ + public ArrayList getSpots() { + return spots; + } + + public ArrayList getRightSpots() { + return rightSpots; + } + + /** + * Returns an array of all of the superSpots for this encounter. + * + * @return the array of superSpots, taken from the croppedImage, that make up the digital fingerprint for this encounter + */ +/* TODO: evaluate if this is deprecate and can be removed + these have gone away! dont be setting spots on Encounter any more .... NOT SO FAST... we regress for whaleshark.org... */ + public void setSpots(ArrayList newSpots) { + spots = newSpots; + } + + public void setRightSpots(ArrayList newSpots) { + rightSpots = newSpots; + } + + /** + * Removes any spot data + */ + public void removeSpots() { + spots = null; + } + + public void removeRightSpots() { + rightSpots = null; + } + + public Integer getFlukeType() { return this.flukeType; } + public void setFlukeType(Integer flukeType) { this.flukeType = flukeType; } + // this averages all the fluketypes + public void setFlukeTypeFromKeywords() { + int totalFlukeType = 0; + int numFlukes = 0; + + for (Annotation ann : getAnnotations()) { + Integer thisFlukeType = getFlukeTypeFromAnnotation(ann); + if (thisFlukeType != null) { + totalFlukeType += thisFlukeType; + numFlukes++; + } + } + if (numFlukes == 0) return; + setFlukeType(totalFlukeType / numFlukes); + } + + // assuming the list is of erroneously-duplicated encounters, returns the one we want to keep + public static Encounter chooseFromDupes(List encs) { + int maxAnns = -1; + int encWithMax = 0; + + for (int i = 0; i < encs.size(); i++) { + Encounter enc = encs.get(i); + if (enc.numAnnotations() > maxAnns) { + maxAnns = enc.numAnnotations(); + encWithMax = i; + } + } + return encs.get(encWithMax); + } + + public static Integer getFlukeTypeFromAnnotation(Annotation ann) { + return getFlukeTypeFromAnnotation(ann, 5); + } + + // int maxScore is used because some people store flukeType on a 5 point (most standard), some on a 9 point scale + public static Integer getFlukeTypeFromAnnotation(Annotation ann, int maxScore) { + MediaAsset ma = ann.getMediaAsset(); + + if (ma == null || !ma.hasKeywords()) return null; + String flukeTypeKwPrefix = "fluke" + maxScore + ":"; + for (Keyword kw : ma.getKeywords()) { + String kwName = kw.getReadableName(); + if (kwName.contains(flukeTypeKwPrefix)) { + String justScore = kwName.split(flukeTypeKwPrefix)[1]; + try { + Integer score = Integer.parseInt(justScore); + if (score != null) return score; + } catch (NumberFormatException nfe) { + System.out.println("NFE on getFlukeTypeFromAnnotation! For ann " + ann + + " and kwPrefix " + flukeTypeKwPrefix); + } + } + } + return null; + } + + // yes, there "should" be only one of each of these, but we be thorough! + public void removeLeftSpotMediaAssets(Shepherd myShepherd) { + ArrayList spotMAs = this.findAllMediaByLabel(myShepherd, "_spot"); + + for (MediaAsset ma : spotMAs) { + System.out.println("INFO: removeLeftSpotMediaAsset() detaching " + ma + + " from parent id=" + ma.getParentId()); + ma.setParentId(null); + } + } + + public void removeRightSpotMediaAssets(Shepherd myShepherd) { + ArrayList spotMAs = this.findAllMediaByLabel(myShepherd, "_spotRight"); + + for (MediaAsset ma : spotMAs) { + System.out.println("INFO: removeRightSpotMediaAsset() detaching " + ma + + " from parent id=" + ma.getParentId()); + ma.setParentId(null); + } + } + + public void nukeAllSpots() { + leftReferenceSpots = null; + rightReferenceSpots = null; + spots = null; + rightSpots = null; + } + + /** + * Returns the number of spots in the cropped image stored for this encounter. + * + * @return the number of superSpots that make up the digital fingerprint for this encounter + */ + public int getNumSpots() { + return (spots == null) ? 0 : spots.size(); + } + + public int getNumRightSpots() { + return (rightSpots == null) ? 0 : rightSpots.size(); + } + + public boolean hasLeftSpotImage() { + return (this.getNumSpots() > 0); + } + + public boolean hasRightSpotImage() { + return (this.getNumRightSpots() > 0); + } + + // Sets the recorded length of the shark for this encounter. + public void setSize(Double mysize) { + if (mysize != null) { size = mysize; } else { size = null; } + } + + // @return the length of the shark + public double getSize() { + return size.doubleValue(); + } + + public Double getSizeAsDouble() { + return size; + } + + // Sets the units of the recorded size and depth of the shark for this encounter. Acceptable entries are either "Feet" or "Meters" + public void setMeasureUnits(String measure) { + measurementUnit = measure; + } + + // @return the units of measure used by the recorded of this encounter, either "feet" or "meters" + public String getMeasureUnits() { + return measurementUnit; + } + + public String getMeasurementUnit() { + return measurementUnit; + } + + // @return the location of this encounter + public String getLocation() { + return verbatimLocality; + } + + public void setLocation(String location) { + this.verbatimLocality = location; + } + + // Sets the recorded sex of the shark in this encounter. Acceptable values are "Male" or "Female" + public void setSex(String thesex) { + if (thesex != null) { sex = thesex; } else { sex = null; } + } + + // @return the sex of the shark, either "male" or "female" + public String getSex() { + return sex; + } + + // @return any comments regarding observed scarring on the shark's body + public boolean getMmaCompatible() { + if (mmaCompatible == null) return false; + return mmaCompatible; + } + + public void setMmaCompatible(boolean b) { + mmaCompatible = b; + } + + // @return Occurrence Remarks String + @Override public String getComments() { + return occurrenceRemarks; + } + + // FIXME why is setComments() affecting occurrenceRemarks, and yet + // addComments() affecting researchComments !!!!!???? + // @param newComments Occurrence remarks to set + @Override public void setComments(String newComments) { + occurrenceRemarks = newComments; + } + + // @return any comments added by authroized researchers + public String getRComments() { + return researcherComments; + } + + // @param newComments any additional comments to be added to the encounter + @Override public void addComments(String newComments) { + if ((researcherComments != null) && (!(researcherComments.equals("None")))) { + researcherComments += newComments; + } else { + researcherComments = newComments; + } + } + + // @return the name of the person who submitted this encounter to the database + public String getSubmitterName() { + return recordedBy; + } + + public void setSubmitterName(String newname) { + if (newname == null) { + recordedBy = null; + } else { + recordedBy = newname; + } + } + + // @return the e-mail address of the person who submitted this encounter data + public String getSubmitterEmail() { + return submitterEmail; + } + + public void setSubmitterEmail(String newemail) { + if (newemail == null) { + submitterEmail = null; + this.hashedSubmitterEmail = null; + } else { + submitterEmail = newemail; + this.hashedSubmitterEmail = Encounter.getHashOfEmailString(newemail); + } + } + + // @return the phone number of the person who submitted this encounter data + public String getSubmitterPhone() { + return submitterPhone; + } + + // Sets the phone number of the person who submitted this encounter data. + public void setSubmitterPhone(String newphone) { + if (newphone == null) { + submitterPhone = null; + } else { + submitterPhone = newphone; + } + } + + // @return the mailing address of the person who submitted this encounter data + public String getSubmitterAddress() { + return submitterAddress; + } + + // Sets the mailing address of the person who submitted this encounter data. + public void setSubmitterAddress(String address) { + if (address == null) { + submitterAddress = null; + } else { + submitterAddress = address; + } + } + + // @return the name of the photographer who took the primary image for this encounter + public String getPhotographerName() { + return photographerName; + } + + // @return the name of the photographer who took the primary image for this encounter + public void setPhotographerName(String name) { + if (name == null) { + photographerName = null; + } else { + photographerName = name; + } + } + + // @return the e-mail address of the photographer who took the primary image for this encounter + public String getPhotographerEmail() { + return photographerEmail; + } + + // Sets the e-mail address of the person who took the primaryImage this encounter. + public void setPhotographerEmail(String email) { + if (email == null) { + photographerEmail = null; + this.hashedPhotographerEmail = null; + } else { + photographerEmail = email; + this.hashedPhotographerEmail = Encounter.getHashOfEmailString(email); + } + } + + // @return the phone number of the photographer who took the primary image for this encounter + public String getPhotographerPhone() { + return photographerPhone; + } + + // this is a cruddy "solution" to .submitterName and .submitters existing simultaneously + public Set getAllSubmitterIds(Shepherd myShepherd) { + Set all = new HashSet(); + User owner = this.getSubmitterUser(myShepherd); + + if (owner == null) { + all.add(this.submitterID); + all.add(this.submitterEmail); + } else { + all.add(owner.getUsername()); + all.add(owner.getFullName()); + all.add(owner.getId()); + all.add(owner.getEmailAddress()); + } + if (this.submitters != null) + for (User user : this.submitters) { + all.add(user.getUsername()); + all.add(user.getFullName()); + all.add(user.getId()); + all.add(user.getEmailAddress()); + } + all.remove(null); + all.remove(""); + return all; + } + + // similar to above + public Set getAllPhotographerIds() { + Set all = new HashSet(); + + all.add(this.photographerName); + if (this.photographers != null) + for (User user : this.photographers) { + all.add(user.getUsername()); + all.add(user.getFullName()); + all.add(user.getId()); + all.add(user.getEmailAddress()); + } + all.remove(null); + all.remove(""); + return all; + } + + public Set getAllInformOtherIds() { + Set all = new HashSet(); + + if (this.informOthers != null) + for (User user : this.informOthers) { + all.add(user.getUsername()); + all.add(user.getFullName()); + all.add(user.getId()); + all.add(user.getEmailAddress()); + } + all.remove(null); + all.remove(""); + return all; + } + + public String getWebUrl(HttpServletRequest req) { + return getWebUrl(this.getCatalogNumber(), req); + } + + public static String getWebUrl(String encId, HttpServletRequest req) { + return getWebUrl(encId, CommonConfiguration.getServerURL(req)); + } + + public static String getWebUrl(String encId, String serverUrl) { + return (serverUrl + "/encounters/encounter.jsp?number=" + encId); + } + + // Sets the phone number of the person who took the primaryImage this encounter. + public void setPhotographerPhone(String phone) { + if (phone == null) { + photographerPhone = null; + } else { + photographerPhone = phone; + } + } + + // @return the mailing address of the photographer who took the primary image for this encounter + public String getPhotographerAddress() { + return photographerAddress; + } + + // Sets the mailing address of the person who took the primaryImage this encounter. + public void setPhotographerAddress(String address) { + if (address == null) { + photographerAddress = null; + } else { + photographerAddress = address; + } + } + + // Sets the recorded depth of this encounter. + public void setDepth(Double myDepth) { + if (myDepth != null) { maximumDepthInMeters = myDepth; } else { + maximumDepthInMeters = null; + } + } + + // @return the recorded depth for this encounter + public double getDepth() { + return maximumDepthInMeters.doubleValue(); + } + + public Double getDepthAsDouble() { + return maximumDepthInMeters; + } + + // @return a vector of image name Strings + public Vector getAdditionalImageNames() { + Vector imageNamesOnly = new Vector(); + + if ((images != null) && (images.size() > 0)) { + int imagesSize = images.size(); + for (int i = 0; i < imagesSize; i++) { + SinglePhotoVideo dce = (SinglePhotoVideo)images.get(i); + imageNamesOnly.add(dce.getFilename()); + } + } + return imageNamesOnly; + } + + public String getFieldID() { + return this.fieldID; + } + + public void setFieldID(String fieldID) { + this.fieldID = fieldID; + } + + public String getGroupRole() { + return this.groupRole; + } + + public void setGroupRole(String role) { + this.groupRole = role; + } + + public String getDataSource() { + return dataSource; + } + + public void setDataSource(String dataSource) { + this.dataSource = dataSource; + } + + public String getImageOriginalName() { + MediaAsset ma = getPrimaryMediaAsset(); + + if (ma == null) return null; + return ma.getFilename(); + } + + // @return a unique integer String used to identify this encounter in the database + public String getEncounterNumber() { + return catalogNumber; + } + + public String generateEncounterNumber() { + return Util.generateUUID(); + } + + public String dir(String baseDir) { + return baseDir + File.separator + "encounters" + File.separator + this.subdir(); + } + + // like above, but class method so you pass the encID + public static String dir(String baseDir, String id) { + return baseDir + File.separator + "encounters" + File.separator + subdir(id); + } + + // like above, but can pass a File in for base + public static String dir(File baseDir, String id) { + return baseDir.getAbsolutePath() + File.separator + "encounters" + File.separator + + subdir(id); + } + + // subdir() is kind of a utility function, which can be called as enc.subdir() or Encounter.subdir(IDSTRING) as needed + public String subdir() { + return subdir(this.getEncounterNumber()); + } + + public static String subdir(String id) { + String d = id; // old-world + + if (Util.isUUID(id)) { // new-world + d = id.charAt(0) + File.separator + id.charAt(1) + File.separator + id; + } + return d; + } + + // @return a Date object + public String getDate() { + String date = ""; + String time = ""; + + if (year <= 0) { + return "Unknown"; + } else if (month == -1) { + return Integer.toString(year); + } + if (hour != -1) { + String localMinutes = minutes; + if (!Util.stringExists(localMinutes)) { + localMinutes = "00"; + } else if (localMinutes.length() == 1) { + localMinutes = "0" + localMinutes; + } + time = String.format("%02d:%s", hour, localMinutes); + } + if (day > 0) { + date = String.format("%04d-%02d-%02d %s", year, month, day, time); + } else if (month > 0) { + date = String.format("%04d-%02d %s", year, month, time); + } else { + date = String.format("%04d %s", year, time); + } + return date.trim(); + } + + public String getShortDate() { + String date = ""; + + if (year <= 0) { + return "Unknown"; + } else if (month == -1) { + return Integer.toString(year); + } + if (day > 0) { + date = String.format("%02d/%02d/%04d", day, month, year); + } else { + date = String.format("%02d/%04d", month, year); + } + return date; + } + + public org.json.JSONObject getDateValuesJson() { + org.json.JSONObject dv = new org.json.JSONObject(); + // in theory we *always* should have at least a year, but our data probably says otherwise + // sadly we just bail empty if we dont have a year + if (getYear() < 1900) return dv; + dv.put("year", getYear()); + // from here on out we only add things if the previous one existed; hence the short-circuit return + // e.g. we do not add a day if there was no month + if ((getMonth() < 1) || (getMonth() > 12)) return dv; + dv.put("month", getMonth()); + // sorry not checking actual days-per-month here + if ((getDay() < 1) || (getDay() > 31)) return dv; + dv.put("day", getDay()); + if ((getHour() < 0) || (getHour() > 23)) return dv; + dv.put("hour", getHour()); + // sigh, deal with string-based minutes... + Integer min = getMinutesInteger(); + if ((min != null) && (min >= 0) && (min < 60)) { + dv.put("minutes", min); + } else { + // choosing to do this because we *must* have hour value here, so dumb to leave null? + dv.put("minutes", 0); + } + return dv; + } + + // @return a String with text about how the size of this animal was estimated/measured + public String getSizeGuess() { + return size_guess; + } + + public void setDay(int day) { + this.day = day; + resetDateInMilliseconds(); + } + + public void setHour(int hour) { + this.hour = hour; + resetDateInMilliseconds(); + } + + public void setMinutes(String minutes) { + this.minutes = minutes; + resetDateInMilliseconds(); + } + + public String getMinutes() { + return minutes; + } + + public Integer getMinutesInteger() { + Integer min = null; + + try { min = Integer.parseInt(minutes); } catch (Exception e) {} + return min; + } + + public int getHour() { + return hour; + } + + public void setMonth(int month) { + this.month = month; + resetDateInMilliseconds(); + } + + public void setYear(int year) { + this.year = year; + resetDateInMilliseconds(); + } + + // this does not reset year/month/etc + public void setDateInMillisOnly(long ms) { + this.dateInMilliseconds = ms; + } + + public int getDay() { + return day; + } + + public int getMonth() { + return month; + } + + public int getYear() { + return year; + } + + public boolean wasInPeriod(DateTime start, DateTime end) { + Long thisTime = getDateInMilliseconds(); + + if (thisTime == null) return false; + long endOfDay = end.withTime(23, 59, 59, 999).getMillis(); + return (start.getMillis() <= thisTime && endOfDay >= thisTime); + } + + // @return the String holding specific location data used for searching + public String getLocationCode() { + return locationID; + } + + // TODO: Verify and remove if this is deprecated: A legacy method replaced by setLocationID(...). + public void setLocationCode(String newLoc) { + setLocationID(newLoc); + } + + // @return the String holding specific location data used for searching + public String getDistinguishingScar() { + return distinguishingScar; + } + + // Sets the String holding scarring information for the encounter + public void setDistinguishingScar(String scar) { + distinguishingScar = scar; + } + + // Sets the String documenting how the size of this animal was approximated. + public void setSizeGuess(String newGuess) { + size_guess = newGuess; + } + + public String getMatchedBy() { + if ((identificationRemarks == null) || (identificationRemarks.equals(""))) { + return "Unknown"; + } + return identificationRemarks; + } + + public void setMatchedBy(String matchType) { + identificationRemarks = matchType; + } + + public void setIdentificationRemarks(String matchType) { + identificationRemarks = matchType; + } + + /** + * Sets the unique encounter identifier to be usd with this encounter. Once this is set, it cannot be changed without possible impact to the + * database structure. + * + * @param num the unique integer to be used to uniquely identify this encoun ter in the database + */ + public void setEncounterNumber(String num) { + catalogNumber = num; + } + + public boolean hasMarkedIndividual() { + return (individual != null); + } + + public boolean hasMarkedIndividual(MarkedIndividual match) { + if (match == null) return false; + if (individual == null) return false; + return (match.getId().equals(individual.getId())); + } + + public void assignToMarkedIndividual(MarkedIndividual indiv) { + setIndividual(indiv); + } + + public void setIndividual(MarkedIndividual indiv) { + if (indiv == null) { this.individual = null; } else { this.individual = indiv; } + this.refreshAnnotationLiteIndividual(); + } + + public MarkedIndividual getIndividual() { + return individual; + } + + public String getDisplayName() { + return (individual == null) ? null : individual.getDisplayName(); + } + + public String getIndividualID() { + if (individual == null) return null; + return individual.getId(); + } + + public String getGPSLongitude() { + if (gpsLongitude == null) { + return ""; + } else { + return gpsLongitude; + } + } + + public void setGPSLongitude(String newLong) { + gpsLongitude = newLong; + } + + public String getGPSLatitude() { + if (gpsLatitude == null) { + return ""; + } else { + return gpsLatitude; + } + } + + public void setGPSLatitude(String newLat) { + gpsLatitude = newLat; + } + + public Encounter getClone() { + Encounter tempEnc = new Encounter(); + + try { + tempEnc = (Encounter)this.clone(); + } catch (java.lang.CloneNotSupportedException e) { + e.printStackTrace(); + } + return tempEnc; + } + + public String getSpotImageFileName() { + return spotImageFileName; + } + + public void setSpotImageFileName(String name) { + spotImageFileName = name; + } + + // ------------- + // for the right side spot image + + public String getRightSpotImageFileName() { + return rightSpotImageFileName; + } + + public void setRightSpotImageFileName(String name) { + rightSpotImageFileName = name; + } + + // ---------------- + + // TODO: evaluate and remove if this has been deprecated: really only intended to convert legacy SinglePhotoVideo to MediaAsset/Annotation world + public ArrayList generateAnnotations(String baseDir, Shepherd myShepherd) { + if ((annotations != null) && (annotations.size() > 0)) return annotations; + if ((images == null) || (images.size() < 1)) return null; // probably pointless, so... + if (annotations == null) annotations = new ArrayList(); + boolean thumbDone = false; + ArrayList haveMedia = new ArrayList(); // so we dont add duplicates! + for (SinglePhotoVideo spv : images) { + MediaAsset ma = spv.toMediaAsset(myShepherd); + if (ma == null) { + System.out.println( + "WARNING: Encounter.generateAnnotations() could not create MediaAsset from SinglePhotoVideo " + + spv.getDataCollectionEventID() + "; skipping"); + continue; + } + if (haveMedia.contains(ma)) { + System.out.println( + "WARNING: Encounter.generateAnnotations() found a duplicate MediaAsset in the SinglePhotoVideo images; skipping -- " + + ma); + continue; + } + // note: we need at least minimal metadata (w,h) in order to make annotation, so if this fails, we are no-go + try { + ma.updateMetadata(); + } catch (IOException ioe) { + System.out.println( + "WARNING: Encounter.generateAnnotations() failed to updateMetadata() on original MediaAsset " + + ma + " (skipping): " + ioe.toString()); + continue; + } + ma.addLabel("_original"); + haveMedia.add(ma); + + annotations.add(new Annotation(getTaxonomyString(), ma)); + File idir = new File(spv.getFullFileSystemPath()).getParentFile(); + + addMediaIfNeeded(myShepherd, new File(idir, spv.getDataCollectionEventID() + ".jpg"), + "spv/" + spv.getDataCollectionEventID() + "/" + spv.getDataCollectionEventID() + + ".jpg", ma, "_watermark"); + addMediaIfNeeded(myShepherd, + new File(idir, spv.getDataCollectionEventID() + "-mid.jpg"), + "spv/" + spv.getDataCollectionEventID() + "/" + spv.getDataCollectionEventID() + + "-mid.jpg", ma, "_mid"); + // note: we "assume" thumb was created from 0th spv, cuz we simply dont know but want it living somewhere + if (!thumbDone) + addMediaIfNeeded(myShepherd, new File(idir, "/thumb.jpg"), + "spv/" + spv.getDataCollectionEventID() + "/thumb.jpg", ma, "_thumb"); + thumbDone = true; + } + // we need to have the spot image as a child under *some* MediaAsset from above, but unfortunately we do not know its lineage. so we just + // pick one. :/ + MediaAsset sma = spotImageAsMediaAsset(((annotations.size() < + 1) ? null : annotations.get(0).getMediaAsset()), baseDir, myShepherd); + return annotations; + } + + // utility method for created MediaAssets + // note: also will check for existence of mpath and fail silently if doesnt exist + private MediaAsset addMediaIfNeeded(Shepherd myShepherd, File mpath, String key, + MediaAsset parentMA, String label) { + if ((mpath == null) || !mpath.exists()) return null; + AssetStore astore = AssetStore.getDefault(myShepherd); + org.json.JSONObject sp = astore.createParameters(mpath); + if (key != null) sp.put("key", key); // will use default from createParameters() (if there was one even) + MediaAsset ma = astore.find(sp, myShepherd); + if (ma != null) { + ma.addLabel(label); + if (parentMA != null) ma.setParentId(parentMA.getIdInt()); + return ma; + } + System.out.println("creating new MediaAsset for key=" + key); + try { + ma = astore.copyIn(mpath, sp); + } catch (IOException ioe) { + System.out.println("Could not create MediaAsset for key=" + key + ": " + + ioe.toString()); + return null; + } + if (parentMA != null) { + ma.setParentId(parentMA.getIdInt()); + ma.updateMinimalMetadata(); // for children (ostensibly derived?) MediaAssets, really only need minimal metadata or so i claim + } else { + try { + ma.updateMetadata(); // root images get the whole deal (guess this sh/could key off label=_original ?) + } catch (IOException ioe) { + // we dont care (well sorta) ... since IOException usually means we couldnt open file or some nonsense that we cant recover from + } + } + ma.addLabel(label); + MediaAssetFactory.save(ma, myShepherd); + return ma; + } + + // this makes assumption (for flukes) that both right and left image files are identical + public MediaAsset spotImageAsMediaAsset(MediaAsset parent, String baseDir, + Shepherd myShepherd) { + if ((spotImageFileName == null) || spotImageFileName.equals("")) return null; + File fullPath = new File(this.dir(baseDir) + "/" + spotImageFileName); +// System.out.println("**** * ***** looking for spot file " + fullPath.toString()); + if (!fullPath.exists()) return null; // note: this only technically matters if we are *creating* the MediaAsset + if (parent == null) { + System.out.println("seems like we do not have a parent MediaAsset on enc " + + this.getCatalogNumber() + ", so cannot add spot MediaAsset for " + + fullPath.toString()); + return null; + } + AssetStore astore = AssetStore.getDefault(myShepherd); + if (astore == null) { + System.out.println("No AssetStore in Encounter.spotImageAsMediaAsset()"); + return null; + } + System.out.println("trying spotImageAsMediaAsset with file=" + fullPath.toString()); + org.json.JSONObject sp = astore.createParameters(fullPath); + sp.put("key", this.subdir() + "/spotImage-" + spotImageFileName); + // others? + MediaAsset ma = astore.find(sp, myShepherd); + if (ma == null) { + System.out.println("did not find MediaAsset for params=" + sp + "; creating one?"); + try { + ma = astore.copyIn(fullPath, sp); + ma.addDerivationMethod("historicSpotImageConversion", true); + ma.updateMinimalMetadata(); +// System.out.println("params? " + ma.getParameters()); + ma.addLabel("_spot"); + ma.addLabel("_annotation"); + MediaAssetFactory.save(ma, myShepherd); +// System.out.println("params? " + ma.getParameters()); + } catch (java.io.IOException ex) { + System.out.println("spotImageAsMediaAsset threw IOException " + ex.toString()); + } + } + ma.setParentId(parent.getIdInt()); + return ma; + } + + public void setSubmitterID(String username) { + if (username != null) { submitterID = username; } else { submitterID = null; } + } + + // old method. use getAssignedUser() instead + public String getSubmitterID() { + return getAssignedUsername(); + } + + public String getAssignedUsername() { + return submitterID; + } + + public User getSubmitterUser(Shepherd myShepherd) { + return myShepherd.getUser(submitterID); + } + + public Vector getInterestedResearchers() { + return interestedResearchers; + } + + public void addInterestedResearcher(String email) { + interestedResearchers.add(email); + } + + public double getRightmostSpot() { + double rightest = 0; + ArrayList spots = getSpots(); + + for (int iter = 0; iter < spots.size(); iter++) { + if (spots.get(iter).getTheSpot().getCentroidX() > rightest) { + rightest = spots.get(iter).getTheSpot().getCentroidX(); + } + } + return rightest; + } + + public double getLeftmostSpot() { + double leftest = getRightmostSpot(); + ArrayList spots = getSpots(); + + for (int iter = 0; iter < spots.size(); iter++) { + if (spots.get(iter).getTheSpot().getCentroidX() < leftest) { + leftest = spots.get(iter).getTheSpot().getCentroidX(); + } + } + return leftest; + } + + public double getHighestSpot() { + double highest = getLowestSpot(); + ArrayList spots = getSpots(); + + for (int iter = 0; iter < spots.size(); iter++) { + if (spots.get(iter).getTheSpot().getCentroidY() < highest) { + highest = spots.get(iter).getTheSpot().getCentroidY(); + } + } + return highest; + } + + public double getLowestSpot() { + double lowest = 0; + ArrayList spots = getSpots(); + + for (int iter = 0; iter < spots.size(); iter++) { + if (spots.get(iter).getTheSpot().getCentroidY() > lowest) { + lowest = spots.get(iter).getTheSpot().getCentroidY(); + } + } + return lowest; + } + + public com.reijns.I3S.Point2D[] getThreeLeftFiducialPoints() { + com.reijns.I3S.Point2D[] Rray = new com.reijns.I3S.Point2D[3]; + if (getLeftReferenceSpots() != null) { + ArrayList refsLeft = getLeftReferenceSpots(); + + Rray[0] = new com.reijns.I3S.Point2D(refsLeft.get(0).getTheSpot().getCentroidX(), + refsLeft.get(0).getTheSpot().getCentroidY()); + Rray[1] = new com.reijns.I3S.Point2D(refsLeft.get(1).getTheSpot().getCentroidX(), + refsLeft.get(1).getTheSpot().getCentroidY()); + Rray[2] = new com.reijns.I3S.Point2D(refsLeft.get(2).getTheSpot().getCentroidX(), + refsLeft.get(2).getTheSpot().getCentroidY()); + System.out.println("\tI found three left reference points!"); + } else { + com.reijns.I3S.Point2D topLeft = new com.reijns.I3S.Point2D(getLeftmostSpot(), + getHighestSpot()); + com.reijns.I3S.Point2D bottomLeft = new com.reijns.I3S.Point2D(getLeftmostSpot(), + getLowestSpot()); + com.reijns.I3S.Point2D bottomRight = new com.reijns.I3S.Point2D(getRightmostSpot(), + getLowestSpot()); + Rray[0] = topLeft; + Rray[1] = bottomLeft; + Rray[2] = bottomRight; + } + return Rray; + } + + public com.reijns.I3S.Point2D[] getThreeRightFiducialPoints() { + com.reijns.I3S.Point2D[] Rray = new com.reijns.I3S.Point2D[3]; + if (getRightReferenceSpots() != null) { + ArrayList refsRight = getRightReferenceSpots(); + Rray[0] = new com.reijns.I3S.Point2D(refsRight.get(0).getTheSpot().getCentroidX(), + refsRight.get(0).getTheSpot().getCentroidY()); + Rray[1] = new com.reijns.I3S.Point2D(refsRight.get(1).getTheSpot().getCentroidX(), + refsRight.get(1).getTheSpot().getCentroidY()); + Rray[2] = new com.reijns.I3S.Point2D(refsRight.get(2).getTheSpot().getCentroidX(), + refsRight.get(2).getTheSpot().getCentroidY()); + } else { + com.reijns.I3S.Point2D topRight = new com.reijns.I3S.Point2D(getRightmostRightSpot(), + getHighestRightSpot()); + com.reijns.I3S.Point2D bottomRight = new com.reijns.I3S.Point2D(getRightmostRightSpot(), + getLowestRightSpot()); + com.reijns.I3S.Point2D bottomLeft = new com.reijns.I3S.Point2D(getLeftmostRightSpot(), + getLowestRightSpot()); + + Rray[0] = topRight; + Rray[1] = bottomRight; + Rray[2] = bottomLeft; + } + return Rray; + } + + public double getRightmostRightSpot() { + double rightest = 0; + ArrayList rightSpots = getRightSpots(); + + for (int iter = 0; iter < rightSpots.size(); iter++) { + if (rightSpots.get(iter).getTheSpot().getCentroidX() > rightest) { + rightest = rightSpots.get(iter).getTheSpot().getCentroidX(); + } + } + return rightest; + } + + public double getLeftmostRightSpot() { + double leftest = getRightmostRightSpot(); + ArrayList rightSpots = getRightSpots(); + + for (int iter = 0; iter < rightSpots.size(); iter++) { + if (rightSpots.get(iter).getTheSpot().getCentroidX() < leftest) { + leftest = rightSpots.get(iter).getTheSpot().getCentroidX(); + } + } + return leftest; + } + + public double getHighestRightSpot() { + double highest = getLowestRightSpot(); + ArrayList rightSpots = getRightSpots(); + + for (int iter = 0; iter < rightSpots.size(); iter++) { + if (rightSpots.get(iter).getTheSpot().getCentroidY() < highest) { + highest = rightSpots.get(iter).getTheSpot().getCentroidY(); + } + } + return highest; + } + + public double getLowestRightSpot() { + double lowest = 0; + ArrayList rightSpots = getRightSpots(); + + for (int iter = 0; iter < rightSpots.size(); iter++) { + if (rightSpots.get(iter).getTheSpot().getCentroidY() > lowest) { + lowest = rightSpots.get(iter).getTheSpot().getCentroidY(); + } + } + return lowest; + } + + public ArrayList getLeftReferenceSpots() { + // return HACKgetAnyReferenceSpots(); + return leftReferenceSpots; + } + + public ArrayList getRightReferenceSpots() { + // return HACKgetAnyReferenceSpots(); + return rightReferenceSpots; + } + +/* gone! no more setting spots on encounters! ... whoa there, yes there is for whaleshark.org */ + public void setLeftReferenceSpots(ArrayList leftReferenceSpots) { + this.leftReferenceSpots = leftReferenceSpots; + } + + public void setRightReferenceSpots(ArrayList rightReferenceSpots) { + this.rightReferenceSpots = rightReferenceSpots; + } + + // this is for jsonForApiGet() + public org.json.JSONObject spotMappingJsonForApiGet() { + org.json.JSONObject rtn = new org.json.JSONObject(); + boolean enabled = CommonConfiguration.useSpotPatternRecognition("context0"); + rtn.put("enabled", enabled); + if (!enabled) return rtn; + rtn.put("numberLeftSpots", getNumSpots()); + rtn.put("numberRightSpots", getNumRightSpots()); + rtn.put("hasLeftSpots", getNumSpots() > 0); + rtn.put("hasRightSpots", getNumRightSpots() > 0); + rtn.put("hasSpots", (getNumSpots() + getNumRightSpots()) > 0); + + // check where results xml is stored (per spotMappingAlgorith.jsp) + File ddir = Util.getDataDir(); + String encDir = dir(ddir.toString()); + rtn.put("resultsGrothLeft", new File(encDir, "lastFullScan.xml").exists()); + rtn.put("resultsGrothRight", new File(encDir, "lastFullRightScan.xml").exists()); + rtn.put("resultsI3SLeft", new File(encDir, "lastFullI3SScan.xml").exists()); + rtn.put("resultsI3SRight", new File(encDir, "lastFullRightI3SScan.xml").exists()); + return rtn; + } + + // @return the variance for population + public double variance(double[] population) { + long n = 0; + double mean = 0; + double s = 0.0; + + for (double x : population) { + n++; + double delta = x - mean; + mean += delta / n; + s += delta * (x - mean); + } + // if you want to calculate std deviation + // of a sample change this to (s/(n-1)) + // return (s / n); + return (s / (n - 1)); + } + + // @return the standard deviation for population + public double standard_deviation(double[] population) { + return Math.sqrt(variance(population)); + } + + public void setDWCGlobalUniqueIdentifier(String guid) { + this.guid = guid; + } + + public String getDWCGlobalUniqueIdentifier() { + return guid; + } + + public void setDWCImageURL(String link) { + dwcImageURL = link; + } + + // lmao, we have this capitalization of the getter for reflexivity purposes + public String getModified() { + return modified; + } + + public String getDWCDateLastModified() { + return modified; + } + + public void setDWCDateLastModified(String lastModified) { + modified = lastModified; + } + + public void setDWCDateLastModified() { + modified = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(new Date()); + } + + public String getDWCDateAdded() { + return dwcDateAdded; + } + + // lmao, we have this capitalization of the getter for reflexivity purposes + public String getDwcDateAdded() { + return dwcDateAdded; + } + + public Long getDWCDateAddedLong() { + return dwcDateAddedLong; + } + + public Long getDwcDateAddedLong() { + return dwcDateAddedLong; + } + + public void setDWCDateAdded(String m_dateAdded) { + dwcDateAdded = m_dateAdded; + } + + public void setDWCDateAdded() { + Date myDate = new Date(); + + dwcDateAddedLong = new Long(myDate.getTime()); + dwcDateAdded = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(myDate); + } + + public void setDWCDateAdded(Long m_dateAdded) { + dwcDateAddedLong = m_dateAdded; + } + + // TODO: evaluate and remove if deprecated + public Date getReleaseDateDONOTUSE() { + return releaseDate; + } + + public Date getReleaseDate() { + if ((releaseDateLong != null) && (releaseDateLong > 0)) { + Date mDate = new Date(releaseDateLong); + return mDate; + } + return null; + } + + public Long getReleaseDateLong() { return releaseDateLong; } + + public void setReleaseDate(Long releaseDate) { + this.releaseDateLong = releaseDate; + } + + // Survey ect associations... + + public void setSurveyTrackID(String id) { + if (id != null && !id.equals("")) { + this.correspondingSurveyTrackID = id; + } + } + + public String getSurveyTrackID() { + if (correspondingSurveyTrackID != null) { + return correspondingSurveyTrackID; + } + return null; + } + + public void setPointLocation(PointLocation loc) { + if (loc.getID() != null) { + this.pointLocation = loc; + } + } + + public PointLocation getPointLocation() { + if (pointLocation != null) { + return pointLocation; + } + return null; + } + + public String getSurveyID() { + if (correspondingSurveyID != null && !correspondingSurveyID.equals("")) { + return correspondingSurveyID; + } + return null; + } + + public void setSurveyID(String id) { + if (id != null && !id.equals("")) { + this.correspondingSurveyID = id; + } + } + + public void setSurvey() { + } + + // TODO: Get all this lat lon over to Locations + + public void setDWCDecimalLatitude(double lat) { + if (lat == -9999.0) { + decimalLatitude = null; + } else { + decimalLatitude = (new Double(lat)); + } + } + + public void setDWCDecimalLatitude(Double lat) { + if ((lat != null) && (lat <= 90) && (lat >= -90)) { + this.decimalLatitude = lat; + } else { this.decimalLatitude = null; } + } + + public String getDWCDecimalLatitude() { + if (decimalLatitude != null) { return Double.toString(decimalLatitude); } + return null; + } + + public void setDWCDecimalLongitude(double longit) { + if ((longit >= -180) && (longit <= 180)) { + this.decimalLongitude = longit; + } + } + + public String getDWCDecimalLongitude() { + if (decimalLongitude != null) { + return Double.toString(decimalLongitude); + } + return null; + } + + public boolean getOKExposeViaTapirLink() { + return okExposeViaTapirLink; + } + + public void setOKExposeViaTapirLink(boolean ok) { + okExposeViaTapirLink = ok; + } + + public void setAlternateID(String newID) { + this.otherCatalogNumbers = newID; + } + + public String getAlternateID() { + if (otherCatalogNumbers == null) { + return null; + } + return otherCatalogNumbers; + } + + public String getOLDInformOthersFORLEGACYCONVERSION() { + if (informothers == null) { + return ""; + } + return informothers; + } + + public String getLocationID() { + return locationID; + } + + public String getLocationName() { + if (locationID == null) return null; + return LocationID.getNameForLocationID(locationID, null); + } + + public void setLocationID(String newLocationID) { + if (newLocationID != null) { + this.locationID = newLocationID.trim(); + } else { + this.locationID = null; + } + } + + public Double getMaximumDepthInMeters() { + return maximumDepthInMeters; + } + + public void setMaximumDepthInMeters(Double newDepth) { + this.maximumDepthInMeters = newDepth; + } + + public Double getMaximumElevationInMeters() { + return maximumElevationInMeters; + } + + public void setMaximumElevationInMeters(Double newElev) { + this.maximumElevationInMeters = newElev; + } + + // @return Catalog Number String + @Override public String getId() { + return catalogNumber; + } + + // @param newNumber The Catalog Number to set. + @Override public void setId(String newNumber) { + this.catalogNumber = newNumber; + } + + // TODO: remove if actually deprecated and unused + // ##DEPRECATED #509 - Base class getId() method + public String getCatalogNumber() { + return catalogNumber; + } + + // TODO: remove if actually deprecated and unused + // ##DEPRECATED #509 - Base class setId() method + public void setCatalogNumber(String newNumber) { + this.catalogNumber = newNumber; + } + + // TODO: remove if actually deprecated and unused + // ##DEPRECATED #509 - Base class getId() method + public String getID() { + return catalogNumber; + } + + // TODO: remove if actually deprecated and unused + // ##DEPRECATED #509 - Base class setId() method + public void setID(String newNumber) { + this.catalogNumber = newNumber; + } + + public String getVerbatimLocality() { + return verbatimLocality; + } + + public void setVerbatimLocality(String vlcl) { + this.verbatimLocality = vlcl; + } + + public Double getDecimalLatitudeAsDouble() { + return (decimalLatitude == null) ? null : decimalLatitude.doubleValue(); + } + + public void setDecimalLatitude(Double lat) { + this.decimalLatitude = lat; + gpsLatitude = Util.decimalLatLonToString(lat); + } + + public Double getDecimalLongitudeAsDouble() { + return (decimalLongitude == null) ? null : decimalLongitude.doubleValue(); + } + + public void setDecimalLongitude(Double lon) { + this.decimalLongitude = lon; + gpsLongitude = Util.decimalLatLonToString(lon); + } + + public Double getEndDecimalLatitudeAsDouble() { + return (endDecimalLatitude == null) ? null : endDecimalLatitude.doubleValue(); + } + + public void setEndDecimalLatitude(Double lat) { + this.endDecimalLatitude = lat; + gpsEndLatitude = Util.decimalLatLonToString(lat); + } + + public Double getEndDecimalLongitudeAsDouble() { + return (endDecimalLongitude == null) ? null : endDecimalLongitude.doubleValue(); + } + + public void setEndDecimalLongitude(Double lon) { + this.endDecimalLongitude = lon; + gpsEndLongitude = Util.decimalLatLonToString(lon); + } + + public String getOccurrenceRemarks() { + return occurrenceRemarks; + } + + public void setOccurrenceRemarks(String remarks) { + this.occurrenceRemarks = remarks; + } + + public String getRecordedBy() { + return recordedBy; + } + + public void setRecordedBy(String submitterName) { + this.recordedBy = submitterName; + } + + public String getOtherCatalogNumbers() { + return otherCatalogNumbers; + } + + public void setOtherCatalogNumbers(String otherNums) { + this.otherCatalogNumbers = otherNums; + } + + public String getLivingStatus() { + return livingStatus; + } + + public void setLivingStatus(String status) { + this.livingStatus = status; + } + + public void setAge(Double a) { + age = a; + } + + public Double getAge() { + return age; + } + + public String getBehavior() { + return behavior; + } + + public void setBehavior(String beh) { + this.behavior = beh; + } + + public String getEventID() { + return eventID; + } + + public void setEventID(String id) { + this.eventID = id; + } + + public String getVerbatimEventDate() { + return verbatimEventDate; + } + + public void setVerbatimEventDate(String vet) { + if (vet != null) { this.verbatimEventDate = vet; } else { this.verbatimEventDate = null; } + } + + public String getDynamicProperties() { + return dynamicProperties; + } + + public org.json.JSONObject getDynamicPropertiesJSONObject() { + org.json.JSONObject dp = new org.json.JSONObject(); + if (dynamicProperties == null) return dp; + StringTokenizer st = new StringTokenizer(dynamicProperties, ";"); + while (st.hasMoreTokens()) { + String token = st.nextToken(); + int equalPlace = token.indexOf("="); + if (equalPlace > 0) + dp.put(token.substring(0, equalPlace), token.substring(equalPlace + 1)); + } + return dp; + } + + public void setDynamicProperties(String allDynamicProperties) { + this.dynamicProperties = allDynamicProperties; + } + + public void addDynamicProperties(String allDynamicProperties) { + this.dynamicProperties += allDynamicProperties; + } + + public void setDynamicProperty(String name, String value) { + name = name.replaceAll(";", "_").trim().replaceAll("%20", " "); + value = value.replaceAll(";", "_").trim(); + if (dynamicProperties == null) { dynamicProperties = name + "=" + value + ";"; } else { + // let's create a TreeMap of the properties + TreeMap tm = new TreeMap(); + StringTokenizer st = new StringTokenizer(dynamicProperties, ";"); + while (st.hasMoreTokens()) { + String token = st.nextToken(); + int equalPlace = token.indexOf("="); + try { + tm.put(token.substring(0, equalPlace), token.substring(equalPlace + 1)); + } catch (java.lang.StringIndexOutOfBoundsException soe) { + // this is a badly formatted pair that should be ignored + } + } + if (tm.containsKey(name)) { + tm.remove(name); + tm.put(name, value); + + // now let's recreate the dynamicProperties String + String newProps = tm.toString(); + int stringSize = newProps.length(); + dynamicProperties = newProps.substring(1, (stringSize - 1)).replaceAll(", ", + ";") + ";"; + } else { + dynamicProperties = dynamicProperties + name + "=" + value + ";"; + } + } + } + + public String getDynamicPropertyValue(String name) { + if (dynamicProperties != null) { + name = name.replaceAll("%20", " "); + // let's create a TreeMap of the properties + TreeMap tm = new TreeMap(); + StringTokenizer st = new StringTokenizer(dynamicProperties, ";"); + while (st.hasMoreTokens()) { + String token = st.nextToken(); + int equalPlace = token.indexOf("="); + tm.put(token.substring(0, equalPlace), token.substring(equalPlace + 1)); + } + if (tm.containsKey(name)) { + return tm.get(name); + } + } + return null; + } + + public boolean hasDynamicProperty(String name) { + return (this.getDynamicPropertyValue(name) != null); + } + + public void removeDynamicProperty(String name) { + name = name.replaceAll(";", "_").trim().replaceAll("%20", " "); + if (dynamicProperties != null) { + // let's create a TreeMap of the properties + TreeMap tm = new TreeMap(); + StringTokenizer st = new StringTokenizer(dynamicProperties, ";"); + while (st.hasMoreTokens()) { + String token = st.nextToken(); + int equalPlace = token.indexOf("="); + tm.put(token.substring(0, (equalPlace)), token.substring(equalPlace + 1)); + } + if (tm.containsKey(name)) { + tm.remove(name); + + // now let's recreate the dynamicProperties String + String newProps = tm.toString(); + int stringSize = newProps.length(); + dynamicProperties = newProps.substring(1, (stringSize - 1)).replaceAll(", ", + ";") + ";"; + } + } + } + + public String getIdentificationRemarks() { + return identificationRemarks; + } + + public String getHashedSubmitterEmail() { + return hashedSubmitterEmail; + } + + public String getHashedPhotographerEmail() { + return hashedPhotographerEmail; + } + + public String getHashedInformOthers() { + return hashedInformOthers; + } + + public static String getHashOfEmailString(String hashMe) { + if (hashMe == null) return null; + String returnString = ""; + StringTokenizer tokenizer = new StringTokenizer(hashMe, ","); + while (tokenizer.hasMoreTokens()) { + String emailAddress = tokenizer.nextToken().trim().toLowerCase(); + if (!emailAddress.equals("")) { + String md5 = DigestUtils.md5Hex(emailAddress); + if (returnString.equals("")) { + returnString += md5; + } else { + returnString += "," + md5; + } + } + } + return returnString; + } + + public String getGenus() { + return genus; + } + + public void setGenus(String newGenus) { + if (newGenus != null) { genus = newGenus; } else { genus = null; } + this.refreshAnnotationLiteTaxonomy(); + } + + // we need these methods because our side-effected setGenus will silently break an import (!!!!!) in an edge case I cannot identify + public void setGenusOnly(String genus) { + this.genus = genus; + this.refreshAnnotationLiteTaxonomy(); + } + + public void setSpeciesOnly(String species) { + setSpecificEpithet(species); + this.refreshAnnotationLiteTaxonomy(); + } + + public String getSpecificEpithet() { + return specificEpithet; + } + + public void setSpecificEpithet(String newEpithet) { + if (newEpithet != null) { specificEpithet = newEpithet.replaceAll("_", " "); } else { + specificEpithet = null; + } + this.refreshAnnotationLiteTaxonomy(); + } + + public String getTaxonomyString() { + return Util.taxonomyString(getGenus(), getSpecificEpithet()); + } + + // hacky (as generates new Taxonomy -- with random uuid) but still should work for tax1.equals(tax2); + // TODO: FIXME this should be superceded by the getter for Taxonomy property in the future.... + public Taxonomy getTaxonomy(Shepherd myShepherd) { + String sciname = this.getTaxonomyString(); + + if (sciname == null) return null; + return myShepherd.getOrCreateTaxonomy(sciname, false); // false means don't commit the taxonomy + } + + // right now this updates .genus and .specificEpithet ... but in some glorious future we will just store Taxonomy! + // note that "null" cases will leave *current values untouched* (does not reset them) + public void setTaxonomy(Taxonomy tax) { + if (tax == null) return; + String[] gs = tax.getGenusSpecificEpithet(); + if ((gs == null) || (gs.length < 1)) return; + if (gs.length == 1) { + this.genus = gs[0]; + this.specificEpithet = null; + } else { + this.genus = gs[0]; + this.specificEpithet = gs[1].replaceAll("_", " "); + } + this.refreshAnnotationLiteTaxonomy(); + } + + public void setTaxonomyFromString(String s) { // basically scientific name (will get split on space) + String[] gs = Util.stringToGenusSpecificEpithet(s); + + if ((gs == null) || (gs.length < 1)) return; + if (gs.length == 1) { + this.genus = gs[0]; + this.specificEpithet = null; + } else { + this.genus = gs[0]; + this.specificEpithet = gs[1].replaceAll("_", " "); + } + this.refreshAnnotationLiteTaxonomy(); + } + + public void setTaxonomyFromIAClass(String iaClass, Shepherd myShepherd) { + setTaxonomy(IBEISIA.iaClassToTaxonomy(iaClass, myShepherd)); + } + + public String getPatterningCode() { return patterningCode; } + public void setPatterningCode(String newCode) { this.patterningCode = newCode; } + + // crawls thru assets and sets date + public void setDateFromAssets() { + // FIXME if you dare. i can *promise you* there are some timezone problems here. ymmv. + if ((annotations == null) || (annotations.size() < 1)) return; + DateTime dt = null; + for (Annotation ann : annotations) { + MediaAsset ma = ann.getMediaAsset(); + if (ma == null) continue; + dt = ma.getDateTime(); + if (dt != null) break; // we just take the first one + } + if (dt != null) setDateInMilliseconds(dt.getMillis()); + } + + // this can(should?) fail in a lot of cases, since we may not know + public void setSpeciesFromAnnotations() { + if ((annotations == null) || (annotations.size() < 1)) return; + String[] sp = null; + for (Annotation ann : annotations) { + sp = IBEISIA.convertSpecies(annotations.get(0).getIAClass()); + if (sp != null) break; // use first one we get + } + // note: now we require (exactly) two parts ... please fix this, Taxonomy class! + if ((sp == null) || (sp.length != 2)) return; + this.setGenus(sp[0]); + this.setSpecificEpithet(sp[1]); + } + + // find the first one(s) we can + public void setLatLonFromAssets() { + if ((annotations == null) || (annotations.size() < 1)) return; + Double lat = null; + Double lon = null; + for (Annotation ann : annotations) { + MediaAsset ma = ann.getMediaAsset(); + if (ma == null) continue; + if (lat == null) lat = ma.getLatitude(); + if (lon == null) lon = ma.getLongitude(); + if ((lat != null) && (lon != null)) break; + } + if (lat != null) this.setDecimalLatitude(lat); + if (lon != null) this.setDecimalLongitude(lon); + } + + // sets date to the closes we have to "not set" :) + public void zeroOutDate() { + year = 0; + month = 0; + day = 0; + hour = -1; + minutes = "00"; + resetDateInMilliseconds(); // should set that to null as well + } + + public void resetDateInMilliseconds() { + dateInMilliseconds = computeDateInMilliseconds(); + } + + public Long computeDateInMilliseconds() { + if (year > 0) { + int localMonth = 0; + if (month > 0) { localMonth = month - 1; } + int localDay = 1; + if (day > 0) { localDay = day; } + int localHour = 0; + if (hour > -1) { localHour = hour; } + int myMinutes = 0; + try { myMinutes = Integer.parseInt(minutes); } catch (Exception e) {} + TimeZone tz = TimeZone.getTimeZone("UTC"); + Calendar calendar = Calendar.getInstance(tz); + calendar.set(year, localMonth, localDay, localHour, myMinutes); + return new Long(calendar.getTimeInMillis()); + } + return null; + } + + public java.lang.Long getDateInMilliseconds() { return dateInMilliseconds; } + + public Long getDateInMillisecondsFallback() { + if (dateInMilliseconds != null) return dateInMilliseconds; + return computeDateInMilliseconds(); + } + + // this will set all date stuff based on ms since epoch + public void setDateInMilliseconds(long ms) { + Calendar cal = Calendar.getInstance(TimeZone.getTimeZone("UTC")); + + cal.setTimeInMillis(ms); + this.year = cal.get(Calendar.YEAR); + this.month = cal.get(Calendar.MONTH) + 1; + this.day = cal.get(Calendar.DAY_OF_MONTH); + this.hour = cal.get(Calendar.HOUR); + this.minutes = Integer.toString(cal.get(Calendar.MINUTE)); + if (this.minutes.length() == 1) this.minutes = "0" + this.minutes; + this.dateInMilliseconds = ms; + } + + // also supports YYYY and YYYY-MM + // per issue 1489, cannot set a future date + public void setDateFromISO8601String(String iso8601) + throws ApiException { + if (!validISO8601String(iso8601)) return; + + // this is for potential ApiException + org.json.JSONObject error = new org.json.JSONObject(); + error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); + + if (iso8601.length() == 4) { // assume year + try { + this.year = Integer.parseInt(iso8601); + } catch (Exception ex) {} + + // got an int year, but lets see if it is valid + if (Util.dateIsInFuture(this.year, null, null)) { + error.put("fieldName", "year"); + error.put("value", this.year); + throw new ApiException("date is in the future", error); + } + resetDateInMilliseconds(); + return; + } + // this format should already be validated so we can trust it (flw) + if (iso8601.length() == 7) { + try { + this.year = Integer.parseInt(iso8601.substring(0, 4)); + this.month = Integer.parseInt(iso8601.substring(5, 7)); + } catch (Exception ex) {} + if (Util.dateIsInFuture(this.year, this.month, null)) { + // if we wanted to be super thorough we could do errors array of year & month + error.put("fieldName", "month"); + error.put("value", this.month); + throw new ApiException("date is in the future", error); + } + resetDateInMilliseconds(); + return; + } + try { + String adjusted = Util.getISO8601Date(iso8601); + DateTime dt = new DateTime(adjusted); + if (Util.dateIsInFuture(dt.getYear(), dt.getMonthOfYear(), dt.getDayOfMonth())) { + error.put("fieldName", "day"); + error.put("value", dt.getDayOfMonth()); + throw new ApiException("date is in the future", error); + } + this.setDateInMilliseconds(dt.getMillis()); + // pass this flavor out... + } catch (ApiException ex) { + throw ex; + // this catches failure of new DateTime() basically, so we make this an ApiException + } catch (Exception ex) { + System.out.println("setDateFromISO8601String(" + iso8601 + ") failed: " + ex); + throw new ApiException("date/time values are invalid"); + } + resetDateInMilliseconds(); + } + + // also supports YYYY and YYYY-MM + public static boolean validISO8601String(String iso8601) { + if (iso8601 == null) return false; + if (iso8601.length() == 4) { + Integer yr = null; + try { + yr = Integer.parseInt(iso8601); + } catch (Exception ex) {} + return (yr != null); + } + if (iso8601.length() == 7) { + Integer yr = null; + Integer mo = null; + try { + yr = Integer.parseInt(iso8601.substring(0, 4)); + mo = Integer.parseInt(iso8601.substring(5, 7)); + } catch (Exception ex) {} + if ((yr == null) || (mo == null)) return false; + if ((mo < 1) || (mo > 12)) return false; + return true; + } + long test = Util.getVersionFromModified(iso8601); + return (test > 0); + } + + public Long getEndDateInMilliseconds() { + return endDateInMilliseconds; + } + + public void setEndDateInMilliseconds(long ms) { + this.endDateInMilliseconds = ms; + } + + private String milliToMonthDayYear(Long millis) { + DateTime dt = new DateTime(millis); + DateTimeFormatter dtf = DateTimeFormat.forPattern("yyyy-MM-dd hh:mm a"); + + return dtf.print(dt); + } + + public String getStartDateTime() { + return milliToMonthDayYear(dateInMilliseconds); + } + + public String getEndDateTime() { + return milliToMonthDayYear(endDateInMilliseconds); + } + + public String getDecimalLatitude() { + if (decimalLatitude != null) { return Double.toString(decimalLatitude); } + return null; + } + + public String getDecimalLongitude() { + if (decimalLongitude != null) { return Double.toString(decimalLongitude); } + return null; + } + + public String getEndDecimalLongitude() { + if (endDecimalLongitude != null) { return Double.toString(endDecimalLongitude); } + return null; + } + + public String getEndDecimalLatitude() { + if (endDecimalLatitude != null) { return Double.toString(endDecimalLatitude); } + return null; + } + + public String getSubmitterProject() { + return submitterProject; + } + + public void setSubmitterProject(String newProject) { + if (newProject != null) { submitterProject = newProject; } else { submitterProject = null; } + } + + public String getSubmitterOrganization() { + return submitterOrganization; + } + + public void setSubmitterOrganization(String newOrg) { + if (newOrg != null) { submitterOrganization = newOrg; } else { + submitterOrganization = null; + } + } + + public List getSubmitterResearchers() { + return submitterResearchers; + } + + public void addSubmitterResearcher(String researcher) { + if (submitterResearchers == null) submitterResearchers = new ArrayList(); + submitterResearchers.add(researcher); + } + + public void setSubmitterResearchers(Collection researchers) { + if (researchers != null) this.submitterResearchers = new ArrayList(researchers); + } + + public List getProjects(Shepherd myShepherd) { + return myShepherd.getProjectsForEncounter(this); + } + + public void addTissueSample(TissueSample dce) { + if (tissueSamples == null) { tissueSamples = new ArrayList(); } + if (!tissueSamples.contains(dce)) { tissueSamples.add(dce); } + dce.setCorrespondingEncounterNumber(getCatalogNumber()); + } + + public void setTissueSamples(List samps) { + this.tissueSamples = samps; + } + + public void removeTissueSample(int num) { tissueSamples.remove(num); } + public List getTissueSamples() { return tissueSamples; } + public Set getTissueSampleIDs() { + Set ids = new HashSet(); + + if (tissueSamples != null) + for (TissueSample ts : tissueSamples) { + ids.add(ts.getSampleID()); + } + return ids; + } + + public void removeTissueSample(TissueSample num) { tissueSamples.remove(num); } + + public void addSinglePhotoVideo(SinglePhotoVideo dce) { + if (images == null) { images = new ArrayList(); } + if (!images.contains(dce)) { images.add(dce); } + } + + public void removeSinglePhotoVideo(int num) { images.remove(num); } + public List getSinglePhotoVideo() { return images; } + public void removeSinglePhotoVideo(SinglePhotoVideo num) { images.remove(num); } + + public void setMeasurements(List measurements) { + this.measurements = measurements; + } + + public void setMeasurement(Measurement measurement, Shepherd myShepherd) { + // if measurements are null, set the empty list + if (measurements == null) { measurements = new ArrayList(); } + // now start checking for existence of a previous measurement + // if we have it but the new value is null, remove the measurement + if ((this.hasMeasurement(measurement.getType())) && (measurement.getValue() == null)) { + Measurement m = this.getMeasurement(measurement.getType()); + measurements.remove(m); + myShepherd.getPM().deletePersistent(m); + myShepherd.commitDBTransaction(); + myShepherd.beginDBTransaction(); + } + // just add the measurement it if we did not have it before + else if (!this.hasMeasurement(measurement.getType())) { + measurements.add(measurement); + myShepherd.commitDBTransaction(); + myShepherd.beginDBTransaction(); + } + // if we had it before then just update the value + else if ((this.hasMeasurement(measurement.getType())) && (measurement != null)) { + Measurement m = this.getMeasurement(measurement.getType()); + m.setValue(measurement.getValue()); + m.setSamplingProtocol(measurement.getSamplingProtocol()); + myShepherd.commitDBTransaction(); + myShepherd.beginDBTransaction(); + } + } + + public Measurement removeMeasurementByType(String type) { + // findMeasurementOfType() seems to return even ones with value=null + // (versus getMeasurement())... so this seems the better choice? + Measurement m = findMeasurementOfType(type); + + if (m != null) measurements.remove(m); + return m; + } + + // will find the Measurement (by type) and modify it *or* make a new one + public Measurement getOrCreateMeasurement(org.json.JSONObject jdata) { + if (jdata == null) return null; + String type = jdata.optString("type", null); + if (type == null) return null; + Measurement m = findMeasurementOfType(type); + if (m == null) { + m = new Measurement(this.getId(), type, jdata.optDouble("value", 0.0D), + jdata.optString("units", null), jdata.optString("samplingProtocol", null)); + } else { + m.setValue(jdata.optDouble("value", 0.0D)); + m.setUnits(jdata.optString("units", null)); + m.setSamplingProtocol(jdata.optString("samplingProtocol", null)); + } + return m; + } + + // like above but way less persisty + public void setMeasurement(Measurement measurement) { + if (measurement == null) return; + if (measurements == null) measurements = new ArrayList(); + Measurement hasType = this.getMeasurement(measurement.getType()); + if (hasType == null) { + measurements.add(measurement); + } else if (measurement.getValue() == null) { + // i guess this means we remove it + measurements.remove(hasType); + } else { + // update existing + hasType.setValue(measurement.getValue()); + hasType.setSamplingProtocol(measurement.getSamplingProtocol()); + } + } + + // like above but less..... checky (trust the caller!) + public void addMeasurement(Measurement meas) { + if (meas == null) return; + if (measurements == null) measurements = new ArrayList(); + measurements.add(meas); + } + + public void removeMeasurement(int num) { measurements.remove(num); } + public List getMeasurements() { return measurements; } + public void removeMeasurement(Measurement num) { measurements.remove(num); } + // FIXME this seems suspiciously just like getMeasurement(type) + public Measurement findMeasurementOfType(String type) { + List measurements = getMeasurements(); + + if (measurements != null) { + for (Measurement measurement : measurements) { + if (type.equals(measurement.getType())) { + return measurement; + } + } + } + return null; + } + + public void addMetalTag(MetalTag metalTag) { + if (metalTags == null) { + metalTags = new ArrayList(); + } + metalTags.add(metalTag); + } + + // this does NOT validate values + public MetalTag addOrUpdateMetalTag(String location, String number) { + if ((location == null) || (number == null)) return null; + MetalTag tag = findMetalTagForLocation(location); + if (tag == null) { + tag = new MetalTag(number, location); + addMetalTag(tag); + } else { + tag.setTagNumber(number); + } + return tag; + } + + public void removeMetalTag(MetalTag metalTag) { + metalTags.remove(metalTag); + } + + // this will clear out ALL tags with this location, but i think we + // are supposed to only have [at most] one anyway! + public void removeMetalTag(String location) { + if ((location == null) || (metalTags == null)) return; + ListIterator it = metalTags.listIterator(); + while (it.hasNext()) { + MetalTag next = it.next(); + if (location.equals(next.getLocation())) it.remove(); + } + } + + public void setMetalTags(List metalTags) { + this.metalTags = metalTags; + } + + public List getMetalTags() { + return metalTags; + } + + public MetalTag findMetalTagForLocation(String location) { + List metalTags = getMetalTags(); + + if (metalTags != null) { + for (MetalTag metalTag : metalTags) { + if (location.equals(metalTag.getLocation())) { + return metalTag; + } + } + } + return null; + } + + public AcousticTag getAcousticTag() { + return acousticTag; + } + + public void setAcousticTag(AcousticTag acousticTag) { + this.acousticTag = acousticTag; + } + + public SatelliteTag getSatelliteTag() { + return satelliteTag; + } + + public void setSatelliteTag(SatelliteTag satelliteTag) { + this.satelliteTag = satelliteTag; + } + + public DigitalArchiveTag getDTag() { + return digitalArchiveTag; + } + + public void setDTag(DigitalArchiveTag dt) { + this.digitalArchiveTag = dt; + } + + public String getLifeStage() { return lifeStage; } + public void setLifeStage(String newStage) { + if (newStage != null) { lifeStage = newStage; } else { lifeStage = null; } + } + + // A convenience method that returns the first haplotype found in the TissueSamples for this Encounter. + public String getHaplotype() { + if (tissueSamples != null) { + int numTissueSamples = tissueSamples.size(); + if (numTissueSamples > 0) { + for (int j = 0; j < numTissueSamples; j++) { + TissueSample thisSample = tissueSamples.get(j); + int numAnalyses = thisSample.getNumAnalyses(); + if (numAnalyses > 0) { + List gAnalyses = thisSample.getGeneticAnalyses(); + for (int g = 0; g < numAnalyses; g++) { + GeneticAnalysis ga = gAnalyses.get(g); + if (ga.getAnalysisType().equals("MitochondrialDNA")) { + MitochondrialDNAAnalysis mito = (MitochondrialDNAAnalysis)ga; + if (mito.getHaplotype() != null) { return mito.getHaplotype(); } + } + } + } + } + } + } + return null; + } + + // A convenience method that returns the first genetic sex found in the TissueSamples for this Encounter. + public String getGeneticSex() { + if (tissueSamples != null) { + int numTissueSamples = tissueSamples.size(); + if (numTissueSamples > 0) { + for (int j = 0; j < numTissueSamples; j++) { + TissueSample thisSample = tissueSamples.get(j); + int numAnalyses = thisSample.getNumAnalyses(); + if (numAnalyses > 0) { + List gAnalyses = thisSample.getGeneticAnalyses(); + for (int g = 0; g < numAnalyses; g++) { + GeneticAnalysis ga = gAnalyses.get(g); + if (ga.getAnalysisType().equals("SexAnalysis")) { + SexAnalysis mito = (SexAnalysis)ga; + if (mito.getSex() != null) { return mito.getSex(); } + } + } + } + } + } + } + return null; + } + + public List getMicrosatelliteMarkers() { + List markers = + new ArrayList(); + + if (tissueSamples == null) return markers; + for (TissueSample tsamp : tissueSamples) { + for (GeneticAnalysis gan : tsamp.getGeneticAnalyses()) { + if (!"MicrosatelliteMarkers".equals(gan.getAnalysisType())) continue; + markers.add((MicrosatelliteMarkersAnalysis)gan); + } + } + return markers; + } + + public List getImages() { return images; } + + public boolean hasAnnotation(Annotation ann) { + return (annotations != null && annotations.contains(ann)); + } + + public boolean hasAnnotations() { + return (annotations != null && annotations.size() > 0); + } + + public int numAnnotations() { + if (annotations == null) return 0; + return annotations.size(); + } + + public int numNonTrivialAnnotations() { + if (annotations == null) return 0; + int ct = 0; + for (Annotation ann : annotations) { + if (!ann.isTrivial()) ct++; + } + return ct; + } + + public ArrayList getAnnotations() { + return annotations; + } + + public Annotation getAnnotation(String annId) { + if ((annId == null) || (annotations == null)) return null; + for (Annotation ann : annotations) { + if (annId.equals(ann.getId())) return ann; + } + return null; + } + + public Set getAnnotationViewpoints() { + Set vps = new HashSet(); + + if (!hasAnnotations()) return vps; + for (Annotation ann : annotations) { + if (ann.getViewpoint() != null) vps.add(ann.getViewpoint()); + } + return vps; + } + + public Set getAnnotationIAClasses() { + Set classes = new HashSet(); + + if (!hasAnnotations()) return classes; + for (Annotation ann : annotations) { + if (ann.getIAClass() != null) classes.add(ann.getIAClass()); + } + // TODO: we should find out how/where bunk iaClass values are getting set + // and stop the via isValidIAClass() or similar + // also should be considered for any data integrity/repair tools + classes.remove("____"); + return classes; + } + + // all an enc's annotations on a given asset (might be multiple if parts are involved) + public List getAnnotations(MediaAsset ma) { + List anns = new ArrayList(); + + for (Annotation ann : getAnnotations()) { + if (ann.getMediaAsset() == ma) anns.add(ann); + } + return anns; + } + + public void setAnnotations(ArrayList anns) { + annotations = anns; + } + + public void addAnnotations(List anns) { + if (annotations == null) annotations = new ArrayList(); + for (Annotation ann : anns) { + if (!annotations.contains(ann)) annotations.add(ann); + } + } + + public void addAnnotation(Annotation ann) { + if (annotations == null) annotations = new ArrayList(); + if (!annotations.contains(ann)) annotations.add(ann); + } + + public void useAnnotationsForMatching(boolean use) { + if (getAnnotations() != null && getAnnotations().size() >= 1) { + for (Annotation ann : getAnnotations()) { + ann.setMatchAgainst(use); + } + } + } + + public Annotation getAnnotationWithKeyword(String word) { + System.out.println("getAnnotationWithKeyword called for " + word); + System.out.println("getAnnotationWithKeyword called, annotations = " + annotations); + if (annotations == null) return null; + for (Annotation ann : annotations) { + if (ann == null) continue; + MediaAsset ma = ann.getMediaAsset(); + if (ma != null && ma.hasKeyword(word)) return ann; + } + return null; + } + + // pretty much only useful for frames pulled from video (after detection, to be made into encounters) + public static List collateFrameAnnotations(List anns, + Shepherd myShepherd) { + if ((anns == null) || (anns.size() < 1)) return null; + // Determine skipped frames before another encounter should be made. + int minGapSize = 4; + try { + String gapFromProperties = IA.getProperty(myShepherd.getContext(), + "newEncounterFrameGap"); + if (gapFromProperties != null) { + minGapSize = Integer.parseInt(gapFromProperties); + } + } catch (NumberFormatException nfe) {} + SortedMap > ordered = new TreeMap >(); + MediaAsset parentRoot = null; + for (Annotation ann : anns) { + System.out.println("========================== >>>>>> " + ann); + if (ann.getFeatures().get(0).isUnity()) continue; // makes big assumption there is one-and-only-one feature btw (detection should have + // bbox) + MediaAsset ma = ann.getMediaAsset(); + if (parentRoot == null) parentRoot = ma.getParentRoot(myShepherd); + System.out.println(" -->>> ma = " + ma); + if (!ma.hasLabel("_frame") || (ma.getParentId() == null)) continue; // nope thx + int offset = ma.getParameters().optInt("extractOffset", -1); + System.out.println(" -->>> offset = " + offset); + if (offset < 0) continue; + if (ordered.get(offset) == null) ordered.put(offset, new ArrayList()); + ordered.get(offset).add(ann); + } + if (ordered.size() < 1) return null; // none used! + + // now construct Encounters based upon spacing of frame-clusters + List newEncs = new ArrayList(); + int prevOffset = -1; + int groupsMade = 1; + ArrayList tmpAnns = new ArrayList(); + for (Integer i : ordered.keySet()) { + if ((prevOffset > -1) && ((i - prevOffset) >= minGapSize)) { + Encounter newEnc = __encForCollate(tmpAnns, parentRoot); + if (newEnc != null) { // null means none of the frames met minimum detection confidence + newEnc.setDynamicProperty("frameSplitNumber", Integer.toString(groupsMade + 1)); + newEncs.add(newEnc); + System.out.println(" cluster [" + (groupsMade) + "] -> " + newEnc); + groupsMade++; + tmpAnns = new ArrayList(); + } + } + prevOffset = i; + tmpAnns.addAll(ordered.get(i)); + } + // deal with dangling tmpAnns content + if (tmpAnns.size() > 0) { + Encounter newEnc = __encForCollate(tmpAnns, parentRoot); + if (newEnc != null) { + newEnc.setDynamicProperty("frameSplitNumber", Integer.toString(groupsMade + 1)); + newEncs.add(newEnc); + System.out.println(" (final)cluster [" + groupsMade + "] -> " + newEnc); + groupsMade++; + } + } + return newEncs; + } + + // this is really only for above method + private static Encounter __encForCollate(ArrayList tmpAnns, MediaAsset parentRoot) { + if ((tmpAnns == null) || (tmpAnns.size() < 1)) return null; + // make sure we even can use these annots first + double bestConfidence = 0.0; + for (Annotation ann : tmpAnns) { + if ((ann.getFeatures() == null) || (ann.getFeatures().size() < 1) || + (ann.getFeatures().get(0).getParameters() == null)) continue; + double conf = ann.getFeatures().get(0).getParameters().optDouble("detectionConfidence", + -1.0); + if (conf > bestConfidence) bestConfidence = conf; + } + if (bestConfidence < ENCOUNTER_AUTO_SOURCE_CONFIDENCE_CUTOFF) { + System.out.println("[INFO] bestConfidence=" + bestConfidence + + " below threshold; rejecting 1 enc from " + parentRoot); + return null; + } + Encounter newEnc = new Encounter(tmpAnns); + newEnc.setState(STATE_AUTO_SOURCED); + newEnc.zeroOutDate(); // do *not* want it using the video source date + newEnc.setDynamicProperty("bestDetectionConfidence", Double.toString(bestConfidence)); + if (parentRoot == null) { + newEnc.setSubmitterName("Unknown video source"); + newEnc.addComments("unable to determine video source - possibly YouTube error?"); + } else { + newEnc.addComments("

    YouTube ID: " + parentRoot.getParameters().optString("id") + + "

    "); + String consolidatedRemarks = + "

    Auto-sourced from YouTube Parent Video: " + + parentRoot.getParameters().optString("id") + "

    "; + // set the video ID as the EventID for distinct access later + newEnc.setEventID("youtube:" + parentRoot.getParameters().optString("id")); + if ((parentRoot.getMetadata() != null) && + (parentRoot.getMetadata().getData() != null)) { + if (parentRoot.getMetadata().getData().optJSONObject("basic") != null) { + newEnc.setSubmitterName(parentRoot.getMetadata().getData().getJSONObject( + "basic").optString("author_name", "[unknown]") + " (by way of YouTube)"); + consolidatedRemarks += "

    From YouTube video: " + + parentRoot.getMetadata().getData().getJSONObject("basic").optString("title", + "[unknown]") + "

    "; + newEnc.addComments(consolidatedRemarks); + + // add a dynamic property to make a quick link to the video + } + if (parentRoot.getMetadata().getData().optJSONObject("detailed") != null) { + String desc = "

    " + + parentRoot.getMetadata().getData().getJSONObject("detailed").optString( + "description", "[no description]") + "

    "; + if (parentRoot.getMetadata().getData().getJSONObject("detailed").optJSONArray( + "tags") != null) { + desc += "

    tags: " + + parentRoot.getMetadata().getData().getJSONObject( + "detailed").getJSONArray("tags").toString() + "

    "; + } + consolidatedRemarks += desc; + } + } + newEnc.setOccurrenceRemarks(consolidatedRemarks); + } + return newEnc; + } + + // convenience method + public ArrayList getMedia() { + ArrayList m = new ArrayList(); + + if ((annotations == null) || (annotations.size() < 1)) return m; + for (Annotation ann : annotations) { + if (ann == null) continue; // really weird that this happens sometimes + MediaAsset ma = ann.getMediaAsset(); + if (ma != null) m.add(ma); + } + return m; + } + + public MediaAsset getMediaAssetByFilename(String filename) { + if (!Util.stringExists(filename)) return null; + for (MediaAsset ma : getMedia()) { + if (Util.stringsEqualish(filename, ma.getFilename())) return ma; + } + return null; + } + + // only checks top-level MediaAssets, not children or resized images + public boolean hasTopLevelMediaAsset(int id) { + return (indexOfMediaAsset(id) >= 0); + } + + // finds the index of the MA we're looking for + public int indexOfMediaAsset(int id) { + if (annotations == null) return -1; + for (int i = 0; i < annotations.size(); i++) { + MediaAsset ma = annotations.get(i).getMediaAsset(); + if (ma == null) continue; + if (ma.getIdInt() == id) return i; + } + return -1; + } + + // creates a new annotation and attaches the asset + public void addMediaAsset(MediaAsset ma) { + Annotation ann = new Annotation(getTaxonomyString(), ma); + + if (annotations == null) annotations = new ArrayList(); + annotations.add(ann); + } + + public void removeAnnotation(Annotation ann) { + if (annotations == null) return; + annotations.remove(ann); + } + + public void removeAnnotation(int index) { + annotations.remove(index); + } + + // this removes an Annotation from Encounter (and from its MediaAsset!!) and replaces it with a new one + // please note: the oldAnn gets killed off (not orphaned) + public void replaceAnnotation(Annotation oldAnn, Annotation newAnn) { + oldAnn.detachFromMediaAsset(); + // note: newAnn should already attached to a MediaAsset + removeAnnotation(oldAnn); + addAnnotation(newAnn); + } + + public void removeMediaAsset(MediaAsset ma) { + removeAnnotation(indexOfMediaAsset(ma.getIdInt())); + } + + // this is a kinda hacky way to find media ... really used by encounter.jsp now but likely should go away? + public ArrayList findAllMediaByFeatureId(Shepherd myShepherd, String[] featureIds) { + ArrayList mas = new ArrayList(); + + for (MediaAsset ma : getMedia()) { + if (ma.hasFeatures(featureIds)) mas.add(ma); + ArrayList kids = ma.findChildren(myShepherd); // note: does not recurse, but... meh? + if ((kids == null) || (kids.size() < 1)) continue; + for (MediaAsset kma : kids) { + if (kma.hasFeatures(featureIds)) mas.add(kma); + } + } + return mas; + } + + // down-n-dirty with no myShepherd passed! :/ + public ArrayList findAllMediaByFeatureId(String[] featureIds) { + Shepherd myShepherd = new Shepherd("context0"); + + myShepherd.setAction("Encounter.class.findAllMediaByFeatureID"); + myShepherd.beginDBTransaction(); + ArrayList all = findAllMediaByFeatureId(myShepherd, featureIds); + myShepherd.rollbackDBTransaction(); + myShepherd.closeDBTransaction(); + return all; + } + + public ArrayList findAllMediaByLabel(Shepherd myShepherd, String label) { + return MediaAsset.findAllByLabel(getMedia(), myShepherd, label); + } + + public boolean hasKeyword(Keyword word) { + int imagesSize = images.size(); + + for (int i = 0; i < imagesSize; i++) { + SinglePhotoVideo image = images.get(i); + if (image.getKeywords().contains(word)) { return true; } + } + return false; + } + + public Set getMediaAssetKeywords() { + Set mak = new HashSet(); + + for (MediaAsset ma : this.getMedia()) { + ArrayList kws = ma.getKeywords(); + if (kws != null) mak.addAll(kws); + } + return mak; + } + + public String getState() { return state; } + + public void setState(String newState) { this.state = newState; } + + // DO NOT USE - LEGACY MIGRATION ONLY + /* + public boolean getApproved(){return approved;} + public boolean getUnidentifiable(){return unidentifiable;} + */ + public Vector getOldAdditionalImageNames() { return additionalImageNames; } + + public Double getLatitudeAsDouble() { return decimalLatitude; } + public Double getLongitudeAsDouble() { return decimalLongitude; } + + public boolean hasMeasurements() { + if ((measurements != null) && (measurements.size() > 0)) { + int numMeasurements = measurements.size(); + for (int i = 0; i < numMeasurements; i++) { + Measurement m = measurements.get(i); + if (m.getValue() != null) { return true; } + } + } + return false; + } + + public boolean hasMeasurement(String type) { + if ((measurements != null) && (measurements.size() > 0)) { + int numMeasurements = measurements.size(); + for (int i = 0; i < numMeasurements; i++) { + Measurement m = measurements.get(i); + if ((m.getValue() != null) && (m.getType().equals(type))) { return true; } + } + } + return false; + } + + public boolean hasBiologicalMeasurement(String type) { + if ((tissueSamples != null) && (tissueSamples.size() > 0)) { + int numTissueSamples = tissueSamples.size(); + for (int i = 0; i < numTissueSamples; i++) { + TissueSample ts = tissueSamples.get(i); + if (ts.getBiologicalMeasurement(type) != null) { + BiologicalMeasurement bm = ts.getBiologicalMeasurement(type); + if (bm.getValue() != null) { return true; } + } + } + } + return false; + } + + // Returns the first measurement of the specified type + public Measurement getMeasurement(String type) { + if ((measurements != null) && (measurements.size() > 0)) { + int numMeasurements = measurements.size(); + for (int i = 0; i < numMeasurements; i++) { + Measurement m = measurements.get(i); + if ((m.getValue() != null) && (m.getType().equals(type))) { return m; } + } + } + return null; + } + + public Map getBiologicalMeasurementsByType() { + Map meas = new HashMap(); + + for (MeasurementDesc mdesc : Util.findBiologicalMeasurementDescs("en", "context0")) { + BiologicalMeasurement bm = getBiologicalMeasurement(mdesc.getType()); + if (bm != null) meas.put(mdesc.getType(), bm); + } + return meas; + } + + public BiologicalMeasurement getBiologicalMeasurement(String type) { + if (tissueSamples != null) { + int numTissueSamples = tissueSamples.size(); + for (int y = 0; y < numTissueSamples; y++) { + TissueSample ts = tissueSamples.get(y); + if ((ts.getGeneticAnalyses() != null) && (ts.getGeneticAnalyses().size() > 0)) { + int numMeasurements = ts.getGeneticAnalyses().size(); + for (int i = 0; i < numMeasurements; i++) { + GeneticAnalysis m = ts.getGeneticAnalyses().get(i); + if (m.getAnalysisType().equals("BiologicalMeasurement")) { + BiologicalMeasurement f = (BiologicalMeasurement)m; + if ((f.getMeasurementType().equals(type)) && (f.getValue() != null)) { + return f; + } + } + } + } + } + } + return null; + } + + public String getCountry() { return country; } + + public void setCountry(String newCountry) { + if (newCountry != null) { country = newCountry; } else { country = null; } + } + + public void setOccurrenceID(String vet) { + if (vet != null) { this.occurrenceID = vet; } else { this.occurrenceID = null; } + } + + public String getOccurrenceID() { return occurrenceID; } + + public Occurrence getOccurrence(Shepherd myShepherd) { + return myShepherd.getOccurrence(this); + } + + public DateTime getOccurrenceDateTime(Shepherd myShepherd) { + Occurrence occ = this.getOccurrence(myShepherd); + + if (occ == null) return null; + return occ.getDateTime(); + } + + public boolean hasSinglePhotoVideoByFileName(String filename) { + int numImages = images.size(); + + for (int i = 0; i < numImages; i++) { + SinglePhotoVideo single = images.get(i); + if (single.getFilename().trim().toLowerCase().equals(filename.trim().toLowerCase())) { + return true; + } + } + return false; + } + + // convenience function to Collaboration permissions + public boolean canUserAccess(HttpServletRequest request) { + return Collaboration.canUserAccessEncounter(this, request); + } + + public boolean canUserAccess(User user, String context) { + if (user == null) return false; + // see comment below on canUserEdit(); substituting isUserOwner() now + // if (canUserEdit(user)) return true; + if (isUserOwner(user)) return true; + String username = user.getUsername(); + if (username == null) return false; + return Collaboration.canUserAccessEncounter(this, context, username); + } + + /* + this really is ugly cuz what is "view" vs "access", but i do NOT want to futz with canUserAccess() and + cause unintended consequences. so, for now, canUserView() is pretty much exclusively for search + */ + public boolean canUserView(User user, Shepherd myShepherd) { + return (user != null) && (user.isAdmin(myShepherd) || this.canUserAccess(user, + myShepherd.getContext())); + } + + // as part of 10.9, canUserEdit() was modified. it was not +/* + public boolean canUserEdit(User user) { + return isUserOwner(user); + } + */ + + // rewrite for 10.9 tries to actually do the right thing and (maybe) make sense + @Override public boolean canUserEdit(User user, Shepherd myShepherd) { + if (user == null) return false; + if (isUserOwner(user)) return true; + if (user.isAdmin(myShepherd)) return true; + if (Collaboration.canEditEncounter(this, user, myShepherd.getContext())) return true; + // TODO there seems to be some legacy stuff about roles based on location. is this real? + return false; + } + + public boolean isUserOwner(User user) { // the definition of this might change? + if (user == null) return false; + if ((submitters != null) && submitters.contains(user)) return true; + if ((submitterID != null) && submitterID.equals(user.getUsername())) return true; + return false; + } + + // new logic means we only need users who are in collab with submitting user + // and if public, we dont need to do this at all + public List userIdsWithViewAccess(Shepherd myShepherd) { + List ids = new ArrayList(); + + if (this.isPubliclyReadable()) return ids; + List collabs = Collaboration.collaborationsForUser(myShepherd, + this.getSubmitterID()); + for (Collaboration collab : collabs) { + User user = myShepherd.getUser(collab.getOtherUsername(this.getSubmitterID())); + if (user != null) ids.add(user.getId()); + } + return ids; + } + +/* + public List userIdsWithEditAccess(Shepherd myShepherd) { + List ids = new ArrayList(); + + for (User user : myShepherd.getUsersWithUsername()) { + if ((user.getId() != null) && this.canUserEdit(user)) ids.add(user.getId()); + } + return ids; + } + */ + public JSONObject sanitizeJson(HttpServletRequest request, JSONObject jobj) + throws JSONException { + boolean fullAccess = this.canUserAccess(request); + String useProjectContext = "false"; + + if (request.getParameter("useProjectContext") != null) { + useProjectContext = request.getParameter("useProjectContext"); + } + if (fullAccess) { + if (this.individual != null) { + jobj.put("individualID", this.individual.getIndividualID()); + if ("true".equals(useProjectContext)) { + jobj.put("displayName", this.individual.getDisplayName(request)); + } else { + jobj.put("displayName", this.individual.getDisplayName()); + } + } + return jobj; + } + jobj.remove("gpsLatitude"); + jobj.remove("location"); + jobj.remove("gpsLongitude"); + jobj.remove("verbatimLocality"); + jobj.remove("locationID"); + jobj.remove("gpsLongitude"); + jobj.remove("genus"); + jobj.remove("specificEpithet"); + jobj.put("_sanitized", true); + + return jobj; + } + + public JSONObject decorateJsonNoAnnots(HttpServletRequest request, JSONObject jobj) + throws JSONException { + jobj.put("location", this.getLocation()); + // these are for convenience, like .hasImages above (for use in table building e.g.) + if ((this.getTissueSamples() != null) && (this.getTissueSamples().size() > 0)) + jobj.put("hasTissueSamples", true); + if (this.hasMeasurements()) jobj.put("hasMeasurements", true); + return jobj; + } + + public JSONObject decorateJson(HttpServletRequest request, JSONObject jobj) + throws JSONException { + jobj = decorateJsonNoAnnots(request, jobj); + + jobj.put("_imagesNote", + ".images have been deprecated! long live MediaAssets! (see: .annotations)"); + + boolean fullAccess = this.canUserAccess(request); + if ((this.getAnnotations() != null) && (this.getAnnotations().size() > 0)) { + jobj.put("hasAnnotations", true); + JSONArray jarr = new JSONArray(); + for (Annotation ann : this.getAnnotations()) { + jarr.put(ann.sanitizeJson(request, fullAccess)); + } + jobj.put("annotations", jarr); + } + return jobj; + } + + public JSONObject uiJson(HttpServletRequest request) + throws JSONException { + JSONObject jobj = new JSONObject(); + + jobj.put("individualID", this.getIndividualID()); + jobj.put("url", this.getUrl(request)); + jobj.put("year", this.getYear()); + jobj.put("month", this.getMonth()); + jobj.put("day", this.getDay()); + jobj.put("gpsLatitude", this.getGPSLatitude()); + jobj.put("gpsLongitude", this.getGPSLongitude()); + jobj.put("location", this.getLocation()); + jobj.put("locationID", this.getLocationID()); + + jobj = sanitizeJson(request, jobj); + // we don't want annotations, which are added by sanitizeJson + jobj.remove("annotations"); + return jobj; + } + + public String getUrl(HttpServletRequest request) { + return request.getScheme() + "://" + CommonConfiguration.getURLLocation(request) + + "/encounters/encounter.jsp?number=" + this.getCatalogNumber(); + } + + /** + * returns an array of the MediaAsset sanitized JSON, because whenever UI queries our DB (regardless of class query), all they want in return are + * MediaAssets TODO: decorate with metadata + **/ + public org.datanucleus.api.rest.orgjson.JSONArray sanitizeMedia(HttpServletRequest request) + throws org.datanucleus.api.rest.orgjson.JSONException { + org.datanucleus.api.rest.orgjson.JSONArray jarr = + new org.datanucleus.api.rest.orgjson.JSONArray(); + boolean fullAccess = this.canUserAccess(request); + if ((this.getAnnotations() != null) && (this.getAnnotations().size() > 0)) { + for (Annotation ann : this.getAnnotations()) { + jarr.put(ann.sanitizeMedia(request, fullAccess)); + } + } + return jarr; + } + + // this simple version makes some assumptions: you already have list of collabs, and it is not visible + public String collaborationLockHtml(List collabs) { + Collaboration c = Collaboration.findCollaborationWithUser(this.getAssignedUsername(), + collabs); + String collabClass = "pending"; + + if ((c == null) || (c.getState() == null)) { + collabClass = "new"; + } else if (c.getState().equals(Collaboration.STATE_REJECTED)) { + collabClass = "blocked"; + } + return "
     
    "; + } + + // pass in a Vector of Encounters, get out a list that the user can NOT see + public static Vector blocked(Vector encs, HttpServletRequest request) { + Vector blk = new Vector(); + + for (int i = 0; i < encs.size(); i++) { + Encounter e = (Encounter)encs.get(i); + if (!e.canUserAccess(request)) blk.add(e); + } + return blk; + } + +/* + in short, this rebuilds (or builds for the first time) ALL *derived* images (etc?) for this encounter. + it is a baby step into the future of MediaAssets that hopefully will provide a smooth(er) transition to that. + right now its primary purpose is to create derived formats upon encounter creation; but that is obviously subject to change. + it should be considered an asyncronous action that happens in the background magickally + */ +/////other possiblity: only pass basedir??? do we need context if we do that? + + public boolean refreshAssetFormats(Shepherd myShepherd) { + ArrayList mas = this.getMedia(); + + if ((mas == null) || (mas.size() < 1)) return true; + for (MediaAsset ma : mas) { + ma.updateStandardChildren(myShepherd); + } + return true; + } + +/* + NOTE on "thumb.jpg" ... we only get one of these per encounter; and we do not have stored (i dont think?) which SPV it came from! + this is a problem, as we cant make a thumb in refreshAssetFormats(req, spv) since we dont know if that is the "right" spv. + thus, we have to treat it as a special case. + */ + // see also: future, MediaAssets + public String getThumbnailUrl(String context) { + MediaAsset ma = getPrimaryMediaAsset(); + + if (ma == null) return null; + String url = null; + Shepherd myShepherd = new Shepherd(context); + myShepherd.setAction("Encounter.class.getThumbnailUrl"); + myShepherd.beginDBTransaction(); + ArrayList kids = ma.findChildrenByLabel(myShepherd, "_thumb"); + if ((kids == null) || (kids.size() <= 0)) { + myShepherd.rollbackDBTransaction(); + myShepherd.closeDBTransaction(); + return null; + } + ma = kids.get(0); + if (ma.webURL() == null) { + myShepherd.rollbackDBTransaction(); + myShepherd.closeDBTransaction(); + return null; + } + url = ma.webURL().toString(); + myShepherd.rollbackDBTransaction(); + myShepherd.closeDBTransaction(); + return url; + } + + // this probably needs a better name and should allow for something more like an ordered list; that said, + // knowing we can always try to get THE ONE is probably useful too + public MediaAsset getPrimaryMediaAsset() { + ArrayList mas = getMedia(); + + if (mas.size() < 1) return null; + // here we could walk thru and find keywords, for example + return mas.get(0); + } + + public boolean restAccess(HttpServletRequest request, org.json.JSONObject jsonobj) + throws Exception { + ApiAccess access = new ApiAccess(); + + System.out.println("hello i am in restAccess() on Encounter"); + + String fail = access.checkRequest(this, request, jsonobj); + System.out.println("fail -----> " + fail); + if (fail != null) throw new Exception(fail); + return true; + } + +///////// this is bunk now: see fix for findAllByMediaAsset() if you need this + public static Encounter findByMediaAsset(MediaAsset ma, Shepherd myShepherd) { + String queryString = + "SELECT FROM org.ecocean.Encounter WHERE annotations.contains(ann) && ann.mediaAsset.id ==" + + ma.getId(); + Encounter returnEnc = null; + Query query = myShepherd.getPM().newQuery(queryString); + List results = (List)query.execute(); + + if ((results != null) && (results.size() >= 1)) { + returnEnc = (Encounter)results.get(0); + } + query.closeAll(); + return returnEnc; + } + + public static List findAllByMediaAsset(MediaAsset ma, Shepherd myShepherd) { + List returnEncs = new ArrayList(); + + try { + String queryString = + "SELECT FROM org.ecocean.Encounter WHERE annotations.contains(ann) && ann.features.contains(feat) && mediaAsset.features.contains(feat) && mediaAsset.id ==" + + ma.getId() + + " VARIABLES org.ecocean.media.MediaAsset mediaAsset; org.ecocean.Annotation ann; org.ecocean.media.Feature feat"; + Query query = myShepherd.getPM().newQuery(queryString); + Collection results = (Collection)query.execute(); + returnEncs = new ArrayList(results); + query.closeAll(); + } catch (Exception e) {} + return returnEncs; + } + + public String getPrefixForLocationID() { // convenience function + return LocationID.getPrefixForLocationID(this.getLocationID(), null); + } + + public int getPrefixDigitPaddingForLocationID() { // convenience function + return LocationID.getPrefixDigitPaddingForLocationID(this.getLocationID(), null); + } + + public static Encounter findByAnnotation(Annotation annot, Shepherd myShepherd) { + String queryString = + "SELECT FROM org.ecocean.Encounter WHERE annotations.contains(ann) && ann.id =='" + + annot.getId() + "'"; + Encounter returnEnc = null; + Query query = myShepherd.getPM().newQuery(queryString); + List results = (List)query.execute(); + + if ((results != null) && (results.size() >= 1)) { + if (results.size() > 1) + System.out.println("WARNING: Encounter.findByAnnotation() found " + results.size() + + " Encounters that contain Annotation " + annot.getId()); + returnEnc = (Encounter)results.get(0); + } + query.closeAll(); + return returnEnc; + } + + public static Encounter findByAnnotationId(String annid, Shepherd myShepherd) { + Annotation ann = ((Annotation)(myShepherd.getPM().getObjectById( + myShepherd.getPM().newObjectIdInstance(Annotation.class, annid), true))); + + if (ann == null) return null; + return findByAnnotation(ann, myShepherd); + } + + public static ArrayList getEncountersForMatching(String taxonomyString, + Shepherd myShepherd) { + if (_matchEncounterCache.get(taxonomyString) != null) + return _matchEncounterCache.get(taxonomyString); + ArrayList encs = new ArrayList(); + String queryString = "SELECT FROM org.ecocean.media.MediaAsset WHERE !features.isEmpty()"; + Query query = myShepherd.getPM().newQuery(queryString); + List results = (List)query.execute(); + for (int i = 0; i < results.size(); i++) { + MediaAsset ma = (MediaAsset)results.get(i); + MediaAsset top = ma.getParentRoot(myShepherd); + if (top == null) continue; + Encounter enc = Encounter.findByMediaAsset(top, myShepherd); + if (enc == null) System.out.println("could not find enc for ma " + ma); + if (enc == null) continue; + if (!enc.getTaxonomyString().equals(taxonomyString)) continue; + if (!encs.contains(enc)) encs.add(enc); + } + query.closeAll(); + _matchEncounterCache.put(taxonomyString, encs); + return encs; + } + +/* + this section are intentionally hacky backwards-compatible ways to get spots on an encounter in the new world of Features/Annotations/MediaAssets + ... do not use these, of course... and SOON we must weed out all the encounter-based-spot calls from everywhere and clean all this mess up! + */ + public ArrayList HACKgetSpots() { + return HACKgetAnySpots("spotsLeft"); + } + + public ArrayList HACKgetRightSpots() { + return HACKgetAnySpots("spotsRight"); + } + + public ArrayList HACKgetAnySpots(String which) { + ArrayList mas = findAllMediaByFeatureId( + new String[] { "org.ecocean.flukeEdge.edgeSpots", "org.ecocean.dorsalEdge.edgeSpots" }); + + if ((mas == null) || (mas.size() < 1)) return new ArrayList(); + for (Feature f : mas.get(0).getFeatures()) { + if (f.isType("org.ecocean.flukeEdge.edgeSpots") || + f.isType("org.ecocean.dorsalEdge.edgeSpots")) { + if (f.getParameters() != null) + return SuperSpot.listFromJSONArray(f.getParameters().optJSONArray(which)); + } + } + return new ArrayList(); + } + + // err, i think ref spots are the same right or left.... at least for flukes/dorsals. :/ good luck with mantas and whalesharks! + public ArrayList HACKgetAnyReferenceSpots() { + ArrayList mas = findAllMediaByFeatureId( + new String[] { "org.ecocean.flukeEdge.referenceSpots", + "org.ecocean.referenceEdge.edgeSpots" }); + + if ((mas == null) || (mas.size() < 1)) return new ArrayList(); + for (Feature f : mas.get(0).getFeatures()) { + if (f.isType("org.ecocean.flukeEdge.referenceSpots") || + f.isType("org.ecocean.dorsalEdge.referenceSpots")) { + if (f.getParameters() != null) + return SuperSpot.listFromJSONArray(f.getParameters().optJSONArray("spots")); + } + } + return new ArrayList(); + } + + // note this sets some things (e.g. species) which might (should!) need to be adjusted after, e.g. with setSpeciesFromAnnotations() + public Encounter cloneWithoutAnnotations(Shepherd myShepherd) { + Encounter enc = new Encounter(this.day, this.month, this.year, this.hour, this.minutes, + this.size_guess, this.verbatimLocality); + + enc.setCatalogNumber(Util.generateUUID()); + System.out.println("NOTE: cloneWithoutAnnotations(" + this.catalogNumber + ") -> " + + enc.getCatalogNumber()); + enc.setGenus(this.getGenus()); + enc.setSpecificEpithet(this.getSpecificEpithet()); + enc.setDecimalLatitude(this.getDecimalLatitudeAsDouble()); + enc.setDecimalLongitude(this.getDecimalLongitudeAsDouble()); + // just going to go ahead and go nuts here and copy most "logical"(?) things. reset on clone if needed + enc.setSubmitterID(this.getSubmitterID()); + enc.setSubmitters(this.submitters); + enc.setPhotographers(this.photographers); + enc.setSex(this.getSex()); + enc.setLocationID(this.getLocationID()); + enc.setVerbatimLocality(this.getVerbatimLocality()); + if (this.getCountry() != null && !"".equals(this.getCountry())) { + enc.setCountry(this.getCountry()); + } + Occurrence occ = myShepherd.getOccurrence(this); + if (occ != null) { + occ.addEncounter(enc); + enc.setOccurrenceID(occ.getOccurrenceID()); + } + // WB-1949: clone into same projects too + ArrayList projects = myShepherd.getAllProjectsForEncounter(this); + if (projects != null) { + for (Project proj : projects) { + proj.addEncounter(enc); + } + } + enc.setRecordedBy(this.getRecordedBy()); + enc.setState(this.getState()); // not too sure about this one? + + enc.setAlternateID(this.getAlternateID()); + enc.setOccurrenceRemarks(this.getOccurrenceRemarks()); + enc.addComments("NOTE: cloneWithoutAnnotations(" + this.catalogNumber + ") -> " + + enc.getCatalogNumber()); + + ImportTask itask = getImportTask(myShepherd); + if (itask != null) itask.addEncounter(enc); + return enc; + } + + // for convenience + public ImportTask getImportTask(Shepherd myShepherd) { + return myShepherd.getImportTaskForEncounter(this); + } + + // this is a special state only used now for match.jsp but basically means the data should be mostly hidden and soon deleted, roughly speaking??? + // TODO: figure out what this really means + public void setMatchingOnly() { + this.setState(STATE_MATCHING_ONLY); + } + + // ann is the Annotation that was created after IA detection. mostly this is just to notify... someone + // note: this is for singly-made encounters; see also Occurrence.fromDetection() + public void detectedAnnotation(Shepherd myShepherd, Annotation ann) { + System.out.println(">>>>> detectedAnnotation() on " + this); + } + + /* + note: these are baby steps into proper ownership of Encounters. a similar (but cleaner) attempt is done in MediaAssets... however, really this + probably should be upon some (mythical) BASE CLASS!!!! ... for now, this Encounter variation kinda fudges with existing "ownership" stuff, + namely, the submitterID - which maps (in theory!) to a User username. TODO: much much much ... incl call via constructor maybe ?? etc. + */ + // NOTE: not going to currently persist the AccessControl object yet, but create on the fly... clever? stupid? + public AccessControl getAccessControl() { + if ((submitterID == null) || submitterID.equals("")) return new AccessControl(); // not sure if we really have some "" but lets be safe + return new AccessControl(submitterID); + } + + public void setAccessControl(HttpServletRequest request) { // really just setting submitterID duh + this.submitterID = AccessControl.simpleUserString(request); // null if anon + } + + public String toString() { + return new ToStringBuilder(this) + .append("catalogNumber", catalogNumber) + .append("individualID", (hasMarkedIndividual() ? individual.getId() : null)) + .append("species", getTaxonomyString()) + .append("sex", getSex()) + .append("shortDate", getShortDate()) + .append("numAnnotations", ((annotations == null) ? 0 : annotations.size())) + .toString(); + } + + public boolean hasMediaFromAssetStoreType(AssetStoreType aType) { + System.out.println("Entering Encounter.hasMediaFromAssetStoreType"); + if (getMediaAssetsOfType(aType).size() > 0) { return true; } + return false; + } + + public ArrayList getMediaAssetsOfType(AssetStoreType aType) { + System.out.println("Entering Encounter.getMediaAssetsOfType"); + ArrayList results = new ArrayList(); + try { + ArrayList assets = getMedia(); + int numAssets = assets.size(); + for (int i = 0; i < numAssets; i++) { + MediaAsset ma = assets.get(i); + if (ma.getStore().getType() == aType) { results.add(ma); } + } + } catch (Exception e) { e.printStackTrace(); } + System.out.println("Exiting Encounter.getMediaAssetsOfType with this num results: " + + results.size()); + return results; + } + + public void setObservationArrayList(ArrayList obs) { + this.observations = obs; + } + + public ArrayList getObservationArrayList() { + return observations; + } + + public void addObservationArrayList(ArrayList arr) { + if (observations.isEmpty()) { + observations = arr; + } else { + observations.addAll(arr); + } + } + + public void addObservation(Observation obs) { + boolean found = false; + + // System.out.println("Adding Observation in Base Class... : "+obs.toString()); + if (observations != null && observations.size() > 0) { + for (Observation ob : observations) { + if (ob.getName() != null) { + if (ob.getName().toLowerCase().trim().equals( + obs.getName().toLowerCase().trim())) { + found = true; + break; + } + } + } + if (!found) { + observations.add(obs); + } + } else { + observations.add(obs); + } + } + + public Observation getObservationByName(String obName) { + if (observations != null && observations.size() > 0) { + for (Observation ob : observations) { + if (ob.getName() != null) { + if (ob.getName().toLowerCase().trim().equals(obName.toLowerCase().trim())) { + return ob; + } + } + } + } + return null; + } + + public Observation getObservationByID(String obId) { + if (observations != null && observations.size() > 0) { + for (Observation ob : observations) { + if (ob.getID() != null && ob.getID().equals(obId)) { + return ob; + } + } + } + return null; + } + + public void removeObservation(String name) { + int counter = 0; + + if (observations != null && observations.size() > 0) { + System.out.println("Looking for the Observation to delete..."); + for (Observation ob : observations) { + if (ob.getName() != null) { + if (ob.getName().toLowerCase().trim().equals(name.toLowerCase().trim())) { + System.out.println("Match! Trying to delete Observation " + name + + " at index " + counter); + observations.remove(counter); + break; + } + } + counter++; + } + } + } + + public List getSubmitters() { + return submitters; + } + + public List getInformOthers() { + return informOthers; + } + + public List getSubmitterEmails() { + ArrayList listy = new ArrayList(); + ArrayList subs = new ArrayList(); + + if (getSubmitters() != null) subs.addAll(getSubmitters()); + int numUsers = subs.size(); + for (int k = 0; k < numUsers; k++) { + User use = subs.get(k); + if ((use.getEmailAddress() != null) && (!use.getEmailAddress().trim().equals(""))) { + listy.add(use.getEmailAddress()); + } + } + return listy; + } + + public List getHashedSubmitterEmails() { + ArrayList listy = new ArrayList(); + ArrayList subs = new ArrayList(); + + if (getSubmitters() != null) subs.addAll(getSubmitters()); + int numUsers = subs.size(); + for (int k = 0; k < numUsers; k++) { + User use = subs.get(k); + if ((use.getHashedEmailAddress() != null) && + (!use.getHashedEmailAddress().trim().equals(""))) { + listy.add(use.getHashedEmailAddress()); + } + } + return listy; + } + + public List getPhotographers() { + return photographers; + } + + public List getPhotographerEmails() { + ArrayList listy = new ArrayList(); + ArrayList subs = new ArrayList(); + + if (getPhotographers() != null) subs.addAll(getPhotographers()); + int numUsers = subs.size(); + for (int k = 0; k < numUsers; k++) { + User use = subs.get(k); + if ((use.getEmailAddress() != null) && (!use.getEmailAddress().trim().equals(""))) { + listy.add(use.getEmailAddress()); + } + } + return listy; + } + + public List getInformOthersEmails() { + ArrayList listy = new ArrayList(); + ArrayList subs = new ArrayList(); + + if (getInformOthers() != null) subs.addAll(getInformOthers()); + int numUsers = subs.size(); + for (int k = 0; k < numUsers; k++) { + User use = subs.get(k); + if ((use.getEmailAddress() != null) && (!use.getEmailAddress().trim().equals(""))) { + listy.add(use.getEmailAddress()); + } + } + return listy; + } + + public List getHashedPhotographerEmails() { + ArrayList listy = new ArrayList(); + ArrayList subs = new ArrayList(); + + if (getPhotographers() != null) subs.addAll(getPhotographers()); + int numUsers = subs.size(); + for (int k = 0; k < numUsers; k++) { + User use = subs.get(k); + if ((use.getHashedEmailAddress() != null) && + (!use.getHashedEmailAddress().trim().equals(""))) { + listy.add(use.getHashedEmailAddress()); + } + } + return listy; + } + + public void addSubmitter(User user) { + if (user == null) return; + if (submitters == null) submitters = new ArrayList(); + if (!submitters.contains(user)) submitters.add(user); + } + + public void removeSubmitter(User user) { + if ((user == null) || (submitters == null)) return; + submitters.remove(user); + } + + public void addPhotographer(User user) { + if (user == null) return; + if (photographers == null) photographers = new ArrayList(); + if (!photographers.contains(user)) photographers.add(user); + } + + public void setSubmitters(List submitters) { + if (submitters == null) { this.submitters = null; } else { + this.submitters = submitters; + } + } + + public void setPhotographers(List photographers) { + if (photographers == null) { this.photographers = null; } else { + this.photographers = photographers; + } + } + + public void removePhotographer(User user) { + if ((user == null) || (photographers == null)) return; + photographers.remove(user); + } + + public void addInformOther(User user) { + if (user == null) return; + if (informOthers == null) informOthers = new ArrayList(); + if (!informOthers.contains(user)) informOthers.add(user); + } + + public void setInformOthers(List users) { + if (users == null) { this.informOthers = null; } else { + this.informOthers = users; + } + } + + public void removeInformOther(User user) { + if ((user == null) || (informOthers == null)) return; + informOthers.remove(user); + } + + public static List getIndividualIDs(Collection encs) { + Set idSet = new HashSet(); + + for (Encounter enc : encs) { + if (enc.hasMarkedIndividual()) idSet.add(enc.getIndividualID()); + } + return Util.asSortedList(idSet); + } + + public void refreshAnnotationLiteTaxonomy() { + if (!this.hasAnnotations()) return; + String tax = this.getTaxonomyString(); + for (Annotation ann : this.annotations) { + ann.refreshLiteTaxonomy(tax); + } + } + + public void refreshAnnotationLiteIndividual() { + if (!this.hasAnnotations()) return; + String indivId = "____"; + if (this.individual != null) indivId = this.individual.getIndividualID(); + for (Annotation ann : this.annotations) { + ann.refreshLiteIndividual(indivId); + } + } + + public int hashCode() { // we need this along with equals() for collections methods (contains etc) to work!! + if (this.getCatalogNumber() == null) return Util.generateUUID().hashCode(); // random(ish) so we dont get two identical for null values + return this.getCatalogNumber().hashCode(); + } + + // sadly, this mess needs to carry on the tradition set up in User.isUsernameAnonymous() + // thanks to the logic in Collaboration.canUserAccessOwnedObject() + public boolean isPubliclyReadable() { + if (!Collaboration.securityEnabled("context0")) return true; + return User.isUsernameAnonymous(this.submitterID); + } + + public boolean getOpensearchProcessPermissions() { + return opensearchProcessPermissions; + } + + public void setOpensearchProcessPermissions(boolean value) { + opensearchProcessPermissions = value; + } + + // wrapper for below, that checks if we really need to be run + public static void opensearchIndexPermissionsBackground(Shepherd myShepherd) { + boolean runIt = false; + Long lastRun = OpenSearch.getPermissionsTimestamp(myShepherd); + long now = System.currentTimeMillis(); + + if ((lastRun == null) || + ((now - lastRun) > OpenSearch.BACKGROUND_PERMISSIONS_MAX_FORCE_MINUTES * 60000)) { + System.out.println( + "opensearchIndexPermissionsBackground: forced run due to max time since previous"); + runIt = true; + } + boolean needed = OpenSearch.getPermissionsNeeded(myShepherd); + if (needed && !runIt) { + System.out.println("opensearchIndexPermissionsBackground: running due to needed=true"); + runIt = true; + } + if (!runIt) { + System.out.println("opensearchIndexPermissionsBackground: running not required; done"); + return; + } + // i think we should set these first... tho they may not get persisted til after? + OpenSearch.setPermissionsTimestamp(myShepherd); + OpenSearch.setPermissionsNeeded(myShepherd, false); + opensearchIndexPermissions(); + System.out.println("opensearchIndexPermissionsBackground: running completed"); + } + +/* note: there are a great deal of users with *no username* that seem to appear in enc.submitters array. + however, very few (2 out of 5600+) encounters with such .submitters have a blank submitterID value + therefore: submitterID will be assumed to be a required value on users which need to be + + this seems further validated by the facts that: + - canUserAccess(user) returns false if no username on user + - a user wihtout a username cant be logged in (and thus cant search) + + "admin" users are just ignored entirely, as they will be exempt from the viewUsers criteria during searching. + + other than "ownership" (via submitterID), a user can view if they have view or edit collab with + another user. so we frontload *approved* collabs for every user here too. + + in terms of "public" encounters, it seems that (based on Collaboration.canUserAccessEncounter()), + encounters with submitterID in (NULL, "public", "", "N/A" [ugh]) is readable by anyone; so we will + skip these from processing as they should be flagged with the boolean isPubliclyReadable in indexing + */ + public static void opensearchIndexPermissions() { + Util.mark("perm start"); + long startT = System.currentTimeMillis(); + System.out.println("opensearchIndexPermissions(): begin..."); + // no security => everything publiclyReadable - saves us work, no? + if (!Collaboration.securityEnabled("context0")) return; + OpenSearch os = new OpenSearch(); + Map > collab = new HashMap >(); + Map usernameToId = new HashMap(); + + // PHASE 1: load all DB data we need into in-memory structures, then close the Shepherd. + // The per-encounter OpenSearch HTTP calls in PHASE 2 below were previously made while + // this Shepherd's Postgres connection was still pinned, which on installs with hundreds + // of thousands of encounters could starve the JDO connection pool for tens of minutes + // and cause every concurrent request to queue at "begin" on dbconnections.jsp. + List encounterRows = new ArrayList(); + Shepherd myShepherd = new Shepherd("context0"); + myShepherd.setAction("Encounter.opensearchIndexPermissions"); + myShepherd.beginDBTransaction(); + try { + // it seems as though user.uuid is *required* so we can trust that + for (User user : myShepherd.getUsersWithUsername()) { + usernameToId.put(user.getUsername(), user.getId()); + List collabsFor = Collaboration.collaborationsForUser(myShepherd, + user.getUsername()); + if (Util.collectionIsEmptyOrNull(collabsFor)) continue; + for (Collaboration col : collabsFor) { + if (!col.isApproved() && !col.isEditApproved()) continue; + if (!collab.containsKey(user.getId())) + collab.put(user.getId(), new HashSet()); + collab.get(user.getId()).add(col.getOtherUsername(user.getUsername())); + } + } + Util.mark("perm: user build done", startT); + System.out.println("opensearchIndexPermissions(): " + usernameToId.size() + + " total users; " + collab.size() + " have active collab"); + + // we do not need full Encounter objects here to update index docs, so lets do this via sql/fields - much faster + String sql = + "SELECT \"CATALOGNUMBER\", \"SUBMITTERID\" FROM \"ENCOUNTER\" WHERE \"SUBMITTERID\" IS NOT NULL AND \"SUBMITTERID\" != '' AND \"SUBMITTERID\" != 'N/A' AND \"SUBMITTERID\" != 'public'"; + Query q = null; + try { + q = myShepherd.getPM().newQuery("javax.jdo.query.SQL", sql); + List results = (List)q.execute(); + Util.mark("perm: loading encs into memory, size=" + results.size(), startT); + Iterator it = results.iterator(); + while (it.hasNext()) { + Object[] row = (Object[])it.next(); + encounterRows.add(new String[] { (String)row[0], (String)row[1] }); + } + } finally { + if (q != null) q.closeAll(); + } + } catch (Exception ex) { + System.out.println( + "opensearchIndexPermissions(): failed during DB load phase: " + ex); + ex.printStackTrace(); + } finally { + myShepherd.rollbackAndClose(); + } + Util.mark("perm: DB load done; shepherd closed", startT); + + // PHASE 2: iterate the in-memory rows and update OpenSearch (no DB connection held). + int encCount = 0; + for (String[] row : encounterRows) { + String id = row[0]; + String submitterId = row[1]; + String uid = usernameToId.get(submitterId); + if (uid == null) { + // see issue 939 for example :( + System.out.println("opensearchIndexPermissions(): WARNING invalid username " + + submitterId + " on enc " + id); + continue; + } + encCount++; + if (encCount % 1000 == 0) Util.mark("enc[" + encCount + "]", startT); + + // ask the question, who else can see this encounter via collaboration? + org.json.JSONArray viewUsers = new org.json.JSONArray(); + for (Map.Entry > entry : collab.entrySet()) { + if (entry.getValue().contains(submitterId)) { + viewUsers.put(entry.getKey()); + } + } + if (viewUsers.length() > 0) { + org.json.JSONObject updateData = new org.json.JSONObject(); + updateData.put("viewUsers", viewUsers); + try { + os.indexUpdate("encounter", id, updateData); + } catch (Exception ex) { + // keeping this quiet cuz it can get noise while index builds + } + } + } + Util.mark("perm: done encs", startT); + System.out.println("opensearchIndexPermissions(): ...end [" + encCount + " encs; " + + Math.round((System.currentTimeMillis() - startT) / 1000) + "sec]"); + } + + public static org.json.JSONObject opensearchQuery(final org.json.JSONObject query, int numFrom, + int pageSize, String sort, String sortOrder) + throws IOException { + return Base.opensearchQuery("encounter", query, numFrom, pageSize, sort, sortOrder); + } + + public void opensearchDocumentSerializer(JsonGenerator jgen) + throws IOException, JsonProcessingException { + Shepherd myShepherd = new Shepherd("context0"); + + myShepherd.setAction("Encounter.opensearchDocumentSerializer"); + myShepherd.beginDBTransaction(); + try { + opensearchDocumentSerializer(jgen, myShepherd); + } catch (Exception ex) { + ex.printStackTrace(); + } finally { + myShepherd.rollbackAndClose(); + } + } + + public void opensearchDocumentSerializer(JsonGenerator jgen, Shepherd myShepherd) + throws IOException, JsonProcessingException { + super.opensearchDocumentSerializer(jgen, myShepherd); + + jgen.writeStringField("locationId", this.getLocationID()); + jgen.writeStringField("locationName", this.getLocationName()); + Long dim = this.getDateInMillisecondsFallback(); + if (dim != null) jgen.writeNumberField("dateMillis", dim); + String date = Util.getISO8601Date(this.getDate()); + if (date != null) jgen.writeStringField("date", date); + date = Util.getISO8601Date(this.getDWCDateAdded()); + if (date != null) jgen.writeStringField("dateSubmitted", date); + jgen.writeStringField("verbatimEventDate", this.getVerbatimEventDate()); + jgen.writeStringField("sex", this.getSex()); + jgen.writeStringField("taxonomy", this.getTaxonomyString()); + jgen.writeStringField("lifeStage", this.getLifeStage()); + jgen.writeStringField("livingStatus", this.getLivingStatus()); + jgen.writeStringField("verbatimLocality", this.getVerbatimLocality()); + jgen.writeStringField("country", this.getCountry()); + jgen.writeStringField("behavior", this.getBehavior()); + jgen.writeStringField("patterningCode", this.getPatterningCode()); + jgen.writeStringField("state", this.getState()); + jgen.writeStringField("occurrenceRemarks", this.getOccurrenceRemarks()); + jgen.writeStringField("otherCatalogNumbers", this.getOtherCatalogNumbers()); + jgen.writeBooleanField("publiclyReadable", this.isPubliclyReadable()); + jgen.writeStringField("distinguishingScar", this.getDistinguishingScar()); + String featuredAssetId = null; + List mas = this.getMedia(); + jgen.writeNumberField("numberAnnotations", this.numNonTrivialAnnotations()); + jgen.writeNumberField("numberMediaAssets", mas.size()); + jgen.writeArrayFieldStart("mediaAssets"); + for (MediaAsset ma : mas) { + jgen.writeStartObject(); + jgen.writeNumberField("id", ma.getIdInt()); + jgen.writeStringField("uuid", ma.getUUID()); + jgen.writeNumberField("width", ma.getWidth()); + jgen.writeNumberField("height", ma.getHeight()); + jgen.writeStringField("mimeTypeMajor", ma.getMimeTypeMajor()); + jgen.writeStringField("mimeTypeMinor", ma.getMimeTypeMinor()); + try { + // historic data might throw IllegalArgumentException: Path not under given root + URL url = ma.safeURL(myShepherd, null, "master"); + if (url != null) jgen.writeStringField("url", url.toString()); + } catch (Exception ex) {} + // we (likely) dont need annotations to search on, but they are needed for + // many of the usages (export, gallery, etc) of search *results* + jgen.writeArrayFieldStart("annotations"); + if (ma.hasAnnotations()) + for (Annotation ann : ma.getAnnotations()) { + jgen.writeStartObject(); + jgen.writeStringField("id", ann.getId()); + jgen.writeStringField("iaClass", ann.getIAClass()); + jgen.writeStringField("viewpoint", ann.getViewpoint()); + jgen.writeBooleanField("isTrivial", ann.isTrivial()); + jgen.writeNumberField("theta", ann.getTheta()); + jgen.writeArrayFieldStart("boundingBox"); + Feature ft = ann.getFeature(); // attempt force loading features for getBbox() + int[] bbox = ann.getBbox(); + if (bbox != null) + for (int i : bbox) { + jgen.writeNumber(i); + } + jgen.writeEndArray(); + Encounter annEnc = ann.findEncounter(myShepherd); + if (annEnc != null) jgen.writeStringField("encounterId", annEnc.getId()); + jgen.writeEndObject(); + } + jgen.writeEndArray(); + jgen.writeEndObject(); + if (featuredAssetId == null) featuredAssetId = ma.getUUID(); + } + jgen.writeEndArray(); + if (featuredAssetId != null) jgen.writeStringField("featuredAssetUuid", featuredAssetId); + if (this.submitterID == null) { + jgen.writeNullField("assignedUsername"); + } else { + jgen.writeStringField("assignedUsername", this.submitterID); + User submitter = this.getSubmitterUser(myShepherd); + if (submitter != null) jgen.writeStringField("submitterUserId", submitter.getId()); + } + jgen.writeArrayFieldStart("submitters"); + for (String id : this.getAllSubmitterIds(myShepherd)) { + jgen.writeString(id); + } + jgen.writeEndArray(); + jgen.writeArrayFieldStart("photographers"); + for (String id : this.getAllPhotographerIds()) { + jgen.writeString(id); + } + jgen.writeEndArray(); + jgen.writeArrayFieldStart("informOthers"); + for (String id : this.getAllInformOtherIds()) { + jgen.writeString(id); + } + jgen.writeEndArray(); + + List kws = new ArrayList(); + Map lkws = new HashMap(); + for (Keyword kw : this.getMediaAssetKeywords()) { + if (kw instanceof LabeledKeyword) { + LabeledKeyword lkw = (LabeledKeyword)kw; + lkws.put(lkw.getLabel(), lkw.getValue()); + } else { + String name = kw.getDisplayName(); + if (!kws.contains(name)) kws.add(name); + } + } + jgen.writeArrayFieldStart("mediaAssetKeywords"); + for (String kw : kws) { + jgen.writeString(kw); + } + jgen.writeEndArray(); + jgen.writeObjectFieldStart("mediaAssetLabeledKeywords"); + for (String kwLabel : lkws.keySet()) { + jgen.writeStringField(kwLabel, lkws.get(kwLabel)); + } + jgen.writeEndObject(); + + List projs = this.getProjects(myShepherd); + jgen.writeArrayFieldStart("projects"); + if (projs != null) + for (Project proj : projs) { + jgen.writeString(proj.getId()); + } + jgen.writeEndArray(); + + ImportTask itask = this.getImportTask(myShepherd); + if (itask != null) { + jgen.writeStringField("importTaskId", itask.getId()); + if (itask.getCreator() != null) + jgen.writeStringField("importTaskCreatorId", itask.getCreator().getId()); + String sourceName = itask.getSourceName(); + if (sourceName != null) + jgen.writeStringField("importTaskSourceName", sourceName); + } + jgen.writeArrayFieldStart("annotationViewpoints"); + for (String vp : this.getAnnotationViewpoints()) { + jgen.writeString(vp); + } + jgen.writeEndArray(); + + jgen.writeArrayFieldStart("annotationIAClasses"); + for (String cls : this.getAnnotationIAClasses()) { + jgen.writeString(cls); + } + jgen.writeEndArray(); + + jgen.writeArrayFieldStart("measurements"); + if (this.measurements != null) + for (Measurement meas : this.measurements) { + if (meas.getValue() == null) continue; // no value means we should skip + jgen.writeStartObject(); + jgen.writeNumberField("value", meas.getValue()); + if (meas.getType() != null) jgen.writeStringField("type", meas.getType()); + if (meas.getUnits() != null) jgen.writeStringField("units", meas.getUnits()); + if (meas.getSamplingProtocol() != null) + jgen.writeStringField("samplingProtocol", meas.getSamplingProtocol()); + jgen.writeEndObject(); + } + jgen.writeEndArray(); + + jgen.writeArrayFieldStart("metalTags"); + if (this.getMetalTags() != null) + for (MetalTag tag : this.getMetalTags()) { + jgen.writeStartObject(); + jgen.writeStringField("number", tag.getTagNumber()); + jgen.writeStringField("location", tag.getLocation()); + jgen.writeEndObject(); + } + jgen.writeEndArray(); + if (this.getAcousticTag() != null) { + jgen.writeObjectFieldStart("acousticTag"); + jgen.writeStringField("idNumber", this.getAcousticTag().getIdNumber()); + jgen.writeStringField("serialNumber", this.getAcousticTag().getSerialNumber()); + jgen.writeEndObject(); + } + if (this.getSatelliteTag() != null) { + jgen.writeObjectFieldStart("satelliteTag"); + jgen.writeStringField("name", this.getSatelliteTag().getName()); + jgen.writeStringField("serialNumber", this.getSatelliteTag().getSerialNumber()); + jgen.writeStringField("argosPttNumber", this.getSatelliteTag().getArgosPttNumber()); + jgen.writeEndObject(); + } + if (this.getDTag() != null) { + jgen.writeObjectFieldStart("digitalArchiveTag"); + jgen.writeStringField("dTagID", this.getDTag().getDTagID()); + jgen.writeStringField("serialNumber", this.getDTag().getSerialNumber()); + jgen.writeEndObject(); + } + org.json.JSONObject dpj = this.getDynamicPropertiesJSONObject(); + jgen.writeObjectFieldStart("dynamicProperties"); + for (String key : (Set)dpj.keySet()) { + jgen.writeStringField(key, dpj.optString(key, null)); + } + jgen.writeEndObject(); + + Double dlat = this.getDecimalLatitudeAsDouble(); + Double dlon = this.getDecimalLongitudeAsDouble(); + if ((dlat == null) || !Util.isValidDecimalLatitude(dlat) || (dlon == null) || + !Util.isValidDecimalLongitude(dlon)) { + jgen.writeNullField("locationGeoPoint"); + } else { + jgen.writeObjectFieldStart("locationGeoPoint"); + jgen.writeNumberField("lat", dlat); + jgen.writeNumberField("lon", dlon); + jgen.writeEndObject(); + } + MarkedIndividual indiv = this.getIndividual(); + if (indiv == null) { + jgen.writeNullField("individualId"); + } else { + jgen.writeStringField("individualId", indiv.getId()); + jgen.writeStringField("individualSex", indiv.getSex()); + jgen.writeStringField("individualTaxonomy", indiv.getTaxonomyString()); + jgen.writeNumberField("individualNumberEncounters", indiv.getNumEncounters()); + jgen.writeStringField("individualDisplayName", indiv.getDisplayName()); + jgen.writeArrayFieldStart("individualNames"); + Set names = indiv.getAllNamesList(); + if (names != null) + for (String name : names) { + jgen.writeString(name); + } + jgen.writeEndArray(); + jgen.writeStringField("individualNickName", indiv.getNickName()); + if (indiv.getTimeOfBirth() > 0) { + String birthTime = Util.getISO8601Date(new DateTime( + indiv.getTimeOfBirth()).toString()); + jgen.writeStringField("individualTimeOfBirth", birthTime); + } + if (indiv.getTimeOfDeath() > 0) { + String deathTime = Util.getISO8601Date(new DateTime( + indiv.getTimeOfDeath()).toString()); + jgen.writeStringField("individualTimeOfDeath", deathTime); + } + Encounter[] encs = indiv.getDateSortedEncounters(true); + if ((encs != null) && (encs.length > 0)) { + String encDate = Util.getISO8601Date(encs[0].getDate()); + if (encDate != null) jgen.writeStringField("individualFirstEncounterDate", encDate); + encDate = Util.getISO8601Date(encs[encs.length - 1].getDate()); + if (encDate != null) jgen.writeStringField("individualLastEncounterDate", encDate); + } + jgen.writeArrayFieldStart("individualSocialUnits"); + for (SocialUnit su : myShepherd.getAllSocialUnitsForMarkedIndividual(indiv)) { + Membership mem = su.getMembershipForMarkedIndividual(indiv); + if (mem != null) jgen.writeString(su.getSocialUnitName()); + } + jgen.writeEndArray(); + + jgen.writeArrayFieldStart("individualRelationshipRoles"); + for (String relRole : myShepherd.getAllRoleNamesForMarkedIndividual(indiv.getId())) { + jgen.writeString(relRole); + } + jgen.writeEndArray(); + } + DateTime occdt = getOccurrenceDateTime(myShepherd); + if (occdt != null) jgen.writeStringField("occurrenceDate", occdt.toString()); + jgen.writeStringField("geneticSex", this.getGeneticSex()); + jgen.writeStringField("haplotype", this.getHaplotype()); + + jgen.writeArrayFieldStart("microsatelliteMarkers"); + for (MicrosatelliteMarkersAnalysis msm : getMicrosatelliteMarkers()) { + jgen.writeStartObject(); + jgen.writeStringField("analysisId", msm.getAnalysisID()); + jgen.writeObjectFieldStart("loci"); + if (msm.getLoci() != null) + for (Locus locus : msm.getLoci()) { + if (locus.getName() == null) continue; // snh + jgen.writeObjectFieldStart(locus.getName()); + for (int i = 0; i < 4; i++) { + Integer allele = locus.getAllele(i); + if (allele != null) jgen.writeNumberField("allele" + i, allele); + } + jgen.writeEndObject(); + } + jgen.writeEndObject(); + jgen.writeEndObject(); + } + jgen.writeEndArray(); + + Occurrence occ = this.getOccurrence(myShepherd); + if (occ == null) { + jgen.writeNullField("occurrenceId"); + } else { + jgen.writeStringField("occurrenceId", occ.getId()); + jgen.writeStringField("occurrenceGroupBehavior", occ.getGroupBehavior()); + jgen.writeStringField("occurrenceGroupComposition", occ.getGroupComposition()); + jgen.writeStringField("occurrenceComments", occ.getComments()); + if (occ.getVisibilityIndex() != null) + jgen.writeNumberField("occurrenceVisibilityIndex", occ.getVisibilityIndex()); + if (occ.getIndividualCount() != null) + jgen.writeNumberField("occurrenceIndividualCount", occ.getIndividualCount()); + if (occ.getMinGroupSizeEstimate() != null) + jgen.writeNumberField("occurrenceMinGroupSizeEstimate", + occ.getMinGroupSizeEstimate()); + if (occ.getMaxGroupSizeEstimate() != null) + jgen.writeNumberField("occurrenceMaxGroupSizeEstimate", + occ.getMaxGroupSizeEstimate()); + if (occ.getBestGroupSizeEstimate() != null) + jgen.writeNumberField("occurrenceBestGroupSizeEstimate", + occ.getBestGroupSizeEstimate()); + if (occ.getBearing() != null) + jgen.writeNumberField("occurrenceBearing", occ.getBearing()); + if (occ.getDistance() != null) + jgen.writeNumberField("occurrenceDistance", occ.getDistance()); + Double odlat = occ.getDecimalLatitude(); + Double odlon = occ.getDecimalLongitude(); + if ((odlat == null) || !Util.isValidDecimalLatitude(odlat) || (odlon == null) || + !Util.isValidDecimalLongitude(odlon)) { + jgen.writeNullField("occurrenceLocationGeoPoint"); + } else { + jgen.writeObjectFieldStart("occurrenceLocationGeoPoint"); + jgen.writeNumberField("lat", odlat); + jgen.writeNumberField("lon", odlon); + jgen.writeEndObject(); + } + } + jgen.writeArrayFieldStart("organizations"); + User owner = this.getSubmitterUser(myShepherd); + if ((owner != null) && (owner.getOrganizations() != null)) + for (Organization org : owner.getOrganizations()) { + jgen.writeString(org.getId()); + } + jgen.writeEndArray(); + + jgen.writeArrayFieldStart("tissueSampleIds"); + for (String id : this.getTissueSampleIDs()) { + jgen.writeString(id); + } + jgen.writeEndArray(); + + Map bmeas = this.getBiologicalMeasurementsByType(); + jgen.writeObjectFieldStart("biologicalMeasurements"); + for (String type : (Set)bmeas.keySet()) { + jgen.writeNumberField(type, bmeas.get(type).getValue()); + } + jgen.writeEndObject(); + // this gets set on specific single-encounter-only actions, when extra expense is okay + // otherwise this will be computed by permissions backgrounding + if (this.getOpensearchProcessPermissions()) { + System.out.println("opensearchProcessPermissions=true for " + this.getId() + + "; indexing permissions"); + jgen.writeFieldName("viewUsers"); + jgen.writeStartArray(); + for (String id : this.userIdsWithViewAccess(myShepherd)) { + System.out.println("opensearch whhhh: " + id); + jgen.writeString(id); + } + jgen.writeEndArray(); + } + } + + public void opensearchIndexDeep() + throws IOException { + this.opensearchIndex(); + + final String encId = this.getId(); + ExecutorService executor = Executors.newFixedThreadPool(4); + Runnable rn = new Runnable() { + public void run() { + Shepherd bgShepherd = new Shepherd("context0"); + bgShepherd.setAction("Encounter.opensearchIndexDeep_" + encId); + bgShepherd.beginDBTransaction(); + try { + Encounter enc = bgShepherd.getEncounter(encId); + if ((enc == null) || (!enc.hasMarkedIndividual() && !enc.hasAnnotations())) { + // bgShepherd.rollbackAndClose(); + executor.shutdown(); + return; + } + MarkedIndividual indiv = enc.getIndividual(); + if (indiv != null) { + System.out.println("opensearchIndexDeep() background indexing indiv " + + indiv.getId() + " via enc " + encId); + try { + indiv.opensearchIndex(); + } catch (Exception ex) { + System.out.println("opensearchIndexDeep() background indexing " + + indiv.getId() + " FAILED: " + ex.toString()); + ex.printStackTrace(); + } + } + Occurrence occ = enc.getOccurrence(bgShepherd); + if (occ != null) { + System.out.println("opensearchIndexDeep() background indexing occ " + + occ.getId() + " via enc " + encId); + try { + occ.opensearchIndex(); + } catch (Exception ex) { + System.out.println("opensearchIndexDeep() background indexing " + + occ.getId() + " FAILED: " + ex.toString()); + ex.printStackTrace(); + } + } + if (enc.hasAnnotations()) { + for (Annotation ann : enc.getAnnotations()) { + System.out.println("opensearchIndexDeep() background indexing annot " + + ann.getId() + " via enc " + encId); + try { + ann.opensearchIndex(); + } catch (Exception ex) { + System.out.println("opensearchIndexDeep() background indexing " + + ann.getId() + " FAILED: " + ex.toString()); + ex.printStackTrace(); + } + } + } + } catch (Exception e) { + System.out.println("opensearchIndexDeep() backgrounding Encounter " + encId + + " hit an exception."); + e.printStackTrace(); + } finally { + bgShepherd.rollbackAndClose(); + } + System.out.println("opensearchIndexDeep() backgrounding Encounter " + encId + + " finished."); + executor.shutdown(); + } + }; + System.out.println("opensearchIndexDeep() begin backgrounding for " + this); + executor.execute(rn); + System.out.println("opensearchIndexDeep() [foreground] finished for Encounter " + encId); + } + + // given a doc from opensearch, can user access it? + public static boolean opensearchAccess(org.json.JSONObject doc, User user, + Shepherd myShepherd) { + if ((doc == null) || (user == null)) return false; + if (doc.optBoolean("publiclyReadable", false)) return true; + if (doc.optString("submitterUserId", "__FAIL__").equals(user.getId())) return true; + if (user.isAdmin(myShepherd)) return true; + org.json.JSONArray viewUsers = doc.optJSONArray("viewUsers"); + if (viewUsers == null) return false; + for (int i = 0; i < viewUsers.length(); i++) { + if (viewUsers.optString(i, "__FAIL__").equals(user.getId())) return true; + } + return false; + } + + @Override public Base getById(Shepherd myShepherd, String id) { + return myShepherd.getEncounter(id); + } + + @Override public String getAllVersionsSql() { + return + "SELECT \"CATALOGNUMBER\", CAST(COALESCE(EXTRACT(EPOCH FROM CAST(\"MODIFIED\" AS TIMESTAMP))*1000,-1) AS BIGINT) AS version FROM \"ENCOUNTER\" ORDER BY version"; + } + + @Override public long getVersion() { + return Util.getVersionFromModified(modified); + } + + public org.json.JSONObject opensearchMapping() { + org.json.JSONObject map = super.opensearchMapping(); + org.json.JSONObject keywordType = new org.json.JSONObject("{\"type\": \"keyword\"}"); + org.json.JSONObject keywordNormalType = new org.json.JSONObject( + "{\"type\": \"keyword\", \"normalizer\": \"wildbook_keyword_normalizer\"}"); + map.put("date", new org.json.JSONObject("{\"type\": \"date\"}")); + map.put("dateSubmitted", new org.json.JSONObject("{\"type\": \"date\"}")); + map.put("verbatimEventDate", new org.json.JSONObject("{\"type\": \"text\"}")); + map.put("individualTimeOfBirth", new org.json.JSONObject("{\"type\": \"date\"}")); + map.put("individualTimeOfDeath", new org.json.JSONObject("{\"type\": \"date\"}")); + map.put("locationGeoPoint", new org.json.JSONObject("{\"type\": \"geo_point\"}")); + map.put("occurrenceLocationGeoPoint", new org.json.JSONObject("{\"type\": \"geo_point\"}")); + + // if we want to sort on it (and it is texty), it needs to be keyword + // (ints, dates, etc are all sortable) + // note: "id" is done in Base.java + map.put("taxonomy", keywordType); + map.put("occurrenceId", keywordType); + map.put("state", keywordType); + map.put("submitterUserId", keywordType); + map.put("individualTaxonomy", keywordType); + map.put("individualId", keywordType); + map.put("importTaskId", keywordType); + map.put("importTaskCreatorId", keywordType); + map.put("importTaskSourceName", keywordType); + + // all case-insensitive keyword-ish types + map.put("locationId", keywordNormalType); + map.put("locationName", keywordNormalType); + map.put("country", keywordNormalType); + map.put("assignedUsername", keywordNormalType); + map.put("projects", keywordNormalType); + map.put("behavior", keywordNormalType); + map.put("patterningCode", keywordNormalType); + map.put("annotationViewpoints", keywordNormalType); + map.put("mediaAssetKeywords", keywordNormalType); + map.put("annotationIAClasses", keywordNormalType); + map.put("haplotype", keywordNormalType); + map.put("individualSocialUnits", keywordNormalType); + map.put("individualRelationshipRoles", keywordNormalType); + map.put("individualDisplayName", keywordNormalType); + map.put("organizations", keywordNormalType); + map.put("otherCatalogNumbers", keywordNormalType); + map.put("lifeStage", keywordNormalType); + map.put("submitters", keywordNormalType); + map.put("photographers", keywordNormalType); + map.put("informOthers", keywordNormalType); + + // https://stackoverflow.com/questions/68760699/matching-documents-where-multiple-fields-match-in-an-array-of-objects + map.put("measurements", new org.json.JSONObject("{\"type\": \"nested\"}")); + map.put("metalTags", new org.json.JSONObject("{\"type\": \"nested\"}")); + return map; + } + + // for encounters, we allow null user to see *some* things + public org.json.JSONObject jsonForApiGet(Shepherd myShepherd, User user) + throws IOException { + org.json.JSONObject rtn = new org.json.JSONObject(); + boolean isPublic = isPubliclyReadable(); + // anon-user can only see public, so we 401 here + if ((user == null) && !isPublic) { + rtn.put("statusCode", 401); + rtn.put("success", false); + return rtn; + } + rtn = opensearchDocumentAsJSONObject(myShepherd); + rtn.put("success", true); + rtn.put("statusCode", 200); + rtn.put("access", "read"); + rtn.put("isPublic", isPublic); + + boolean hideUserEmail = true; + User submitter = getSubmitterUser(myShepherd); + if (submitter != null) + rtn.put("submitterInfo", + submitter.infoJSONObject(myShepherd, user != null, hideUserEmail)); + // check to see if logged-in-user is outright blocked + if (user != null) { + boolean blocked = true; + if (canUserEdit(user, myShepherd)) { + rtn.put("access", "write"); + blocked = false; + // we can allow email being shown when access=write + hideUserEmail = false; + if (submitter != null) + rtn.put("submitterInfo", + submitter.infoJSONObject(myShepherd, true, hideUserEmail)); + } else if (canUserView(user, myShepherd)) { + blocked = false; + } + if (blocked) { + // we keep this very minimal + org.json.JSONObject blockedRtn = new org.json.JSONObject(); + blockedRtn.put("success", true); + blockedRtn.put("statusCode", 200); + blockedRtn.put("access", "none"); + blockedRtn.put("id", rtn.get("id")); + // need this to know who to collab with + Collaboration col = Collaboration.collaborationBetweenUsers(user, submitter, + myShepherd.getContext()); + if (col != null) { + blockedRtn.put("collaborationState", col.getState()); + blockedRtn.put("collaborationCreated", col.getDateStringCreated()); + } + blockedRtn.put("assignedUsername", rtn.optString("assignedUsername", null)); + blockedRtn.put("submitterUserId", rtn.optString("submitterUserId", null)); + blockedRtn.put("submitterInfo", rtn.optJSONObject("submitterInfo")); + return blockedRtn; + } + } + // additional fields we want + rtn.put("dateValues", getDateValuesJson()); + rtn.put("researcherComments", getRComments()); + rtn.put("groupRole", getGroupRole()); + rtn.put("identificationRemarks", getIdentificationRemarks()); + rtn.put("spotMapping", spotMappingJsonForApiGet()); + + // the user-listy things + rtn.put("submitters", + userListJSONArray(myShepherd, this.submitters, user != null, hideUserEmail)); + rtn.put("photographers", + userListJSONArray(myShepherd, this.photographers, user != null, hideUserEmail)); + rtn.put("informOthers", + userListJSONArray(myShepherd, this.informOthers, user != null, hideUserEmail)); + // sanitize for non-logged-in users (hence, on public data) + if (user == null) { + rtn.put("access", "read"); + String[] blocked = { + "importTaskSourceName", "locationId", "locationName", "country", "verbatimLocality", + "microsatelliteMarkers", "locationGeoPoint", "occurrenceLocationGeoPoint", + "mediaAssetKeywords", "mediaAssetLabeledKeywords", "biologicalMeasurements", + "importTaskCreatorId", "annotationIAClasses", "annotationViewpoints", + "researcherComments", "informOthers", "photographers", "submitters", + "assignedUsername" + }; + for (String field : blocked) { + rtn.remove(field); + } + // we redo mediaAssets, with no annots and mid size + org.json.JSONArray mas = new org.json.JSONArray(); + for (MediaAsset ma : getMedia()) { + org.json.JSONObject maj = new org.json.JSONObject(); + maj.put("uuid", ma.getUUID()); + maj.put("mimeTypeMajor", ma.getMimeTypeMajor()); + maj.put("mimeTypeMinor", ma.getMimeTypeMinor()); + maj.put("rotationInfo", ma.getRotationInfo()); + try { + // historic data might throw IllegalArgumentException: Path not under given root + java.net.URL url = ma.safeURL(myShepherd, null, "mid"); + if (url != null) maj.put("url", url.toString()); + } catch (Exception ex) {} + mas.put(maj); + } + rtn.put("mediaAssets", mas); + } else { + // for real users we add some extras to assets and annotations + if (rtn.optJSONArray("mediaAssets") != null) { + for (int i = 0; i < rtn.getJSONArray("mediaAssets").length(); i++) { + if (rtn.getJSONArray("mediaAssets").optJSONObject(i) != null) { + MediaAsset ma = MediaAssetFactory.loadByUuid(rtn.getJSONArray( + "mediaAssets").getJSONObject(i).optString("uuid"), myShepherd); + if (ma != null) { + rtn.getJSONArray("mediaAssets").getJSONObject(i).put("keywords", + ma.getKeywordsJSONArray()); + rtn.getJSONArray("mediaAssets").getJSONObject(i).put("detectionStatus", + ma.getDetectionStatus()); + rtn.getJSONArray("mediaAssets").getJSONObject(i).put("userFilename", + ma.getUserFilename()); + rtn.getJSONArray("mediaAssets").getJSONObject(i).put("rotationInfo", + ma.getRotationInfo()); + } + // now we cram some stuff into each annotation as well + if (rtn.getJSONArray("mediaAssets").getJSONObject(i).optJSONArray( + "annotations") != null) { + for (int j = 0; + j < + rtn.getJSONArray("mediaAssets").getJSONObject(i).getJSONArray( + "annotations").length(); + j++) { + if (rtn.getJSONArray("mediaAssets").getJSONObject(i).getJSONArray( + "annotations").optJSONObject(j) == null) continue; + // this parsing of nested json really makes me miss perl + Annotation ann = myShepherd.getAnnotation(rtn.getJSONArray( + "mediaAssets").getJSONObject(i).getJSONArray( + "annotations").getJSONObject(j).optString("id", null)); + if (ann == null) continue; + rtn.getJSONArray("mediaAssets").getJSONObject(i).getJSONArray( + "annotations").getJSONObject(j).put("identificationStatus", + ann.getIdentificationStatus()); + // annTasks are in chron order so most recent will be at end + List annTasks = ann.getRootIATasks(myShepherd); + int ntasks = Util.collectionSize(annTasks); + if (ntasks > 0) { + rtn.getJSONArray("mediaAssets").getJSONObject(i).getJSONArray( + "annotations").getJSONObject(j).put("iaTaskId", + annTasks.get(ntasks - 1).getId()); + rtn.getJSONArray("mediaAssets").getJSONObject(i).getJSONArray( + "annotations").getJSONObject(j).put("iaTaskParameters", + annTasks.get(ntasks - 1).getParameters()); + } + } + } + } + } + } + } + return rtn; + } + + // internal utility function + private org.json.JSONArray userListJSONArray(Shepherd myShepherd, List users, + boolean includeSensitive, boolean hideEmail) { + org.json.JSONArray arr = new org.json.JSONArray(); + if (Util.collectionIsEmptyOrNull(users)) return arr; + for (User user : users) { + arr.put(user.infoJSONObject(myShepherd, includeSensitive, hideEmail)); + } + return arr; + } + + public static Base createFromApi(org.json.JSONObject payload, List files, + Shepherd myShepherd) + throws ApiException { + if (payload == null) throw new ApiException("empty payload"); + User user = (User)payload.opt("_currentUser"); + + // these need validation (will throw ApiException if fail) + String locationID = (String)validateFieldValue("locationId", payload); + String dateTime = (String)validateFieldValue("dateTime", payload); + String txStr = (String)validateFieldValue("taxonomy", payload); + String submitterEmail = (String)validateFieldValue("submitterEmail", payload); + String photographerEmail = (String)validateFieldValue("photographerEmail", payload); + Double decimalLatitude = (Double)validateFieldValue("decimalLatitude", payload); + Double decimalLongitude = (Double)validateFieldValue("decimalLongitude", payload); + if (((decimalLatitude == null) && (decimalLongitude != null)) || + ((decimalLatitude != null) && (decimalLongitude == null))) { + org.json.JSONObject error = new org.json.JSONObject(); + error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); + // i guess we pick one, since both are wrong + error.put("fieldName", "decimalLatitude"); + error.put("value", decimalLatitude); + throw new ApiException("cannot send just one of decimalLatitude and decimalLongitude", + error); + } + String additionalEmailsValue = payload.optString("additionalEmails", null); + String[] additionalEmails = null; + if (!Util.stringIsEmptyOrNull(additionalEmailsValue)) + additionalEmails = additionalEmailsValue.split("[,\\s]+"); + if (additionalEmails != null) { + org.json.JSONObject error = new org.json.JSONObject(); + error.put("fieldName", "additionalEmails"); + for (String email : additionalEmails) { + if (!Util.isValidEmailAddress(email)) { + error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); + error.put("value", email); + throw new ApiException("invalid email address", error); + } + } + } + Encounter enc = new Encounter(false); + if (Util.isUUID(payload.optString("_id"))) enc.setId(payload.getString("_id")); + enc.setLocationID(locationID); + enc.setDecimalLatitude(decimalLatitude); + enc.setDecimalLongitude(decimalLongitude); + enc.setDateFromISO8601String(dateTime); + enc.setTaxonomyFromString(txStr); + if (CommonConfiguration.getProperty("encounterState0", myShepherd.getContext()) != null) { + enc.setState(CommonConfiguration.getProperty("encounterState0", + myShepherd.getContext())); + } + enc.setComments(payload.optString("comments", null)); + if (user == null) { + enc.setSubmitterID("public"); // this seems to be what EncounterForm servlet does so... + } else { + enc.setSubmitterID(user.getUsername()); + enc.addSubmitter(user); + } + if (!Util.stringIsEmptyOrNull(submitterEmail)) { + User submitterUser = myShepherd.getOrCreateUserByEmailAddress(submitterEmail, + payload.optString("submitterName", null)); + // set this after the owner-submitter being set + enc.addSubmitter(submitterUser); + } + if (!Util.stringIsEmptyOrNull(photographerEmail)) { + User photographerUser = myShepherd.getOrCreateUserByEmailAddress(photographerEmail, + payload.optString("photographerName", null)); + enc.addPhotographer(photographerUser); + } + if (additionalEmails != null) { + for (String email : additionalEmails) { + User addlUser = myShepherd.getOrCreateUserByEmailAddress(email, null); + enc.addInformOther(addlUser); + } + } + // this will get/make an Occurrence no matter what + Occurrence occ = myShepherd.getOrCreateOccurrence(payload.optString("occurrenceId", null)); + occ.addEncounterAndUpdateIt(enc); + myShepherd.getPM().makePersistent(occ); + return enc; + } + + // user should already have been validated -- via obj.canUserEdit() -- in api/BaseObject, so this + // does not need to be tested here. however, more detailed checks may require user (e.g. can user + // also alter another object, such as Occurrence) + public org.json.JSONObject processPatch(org.json.JSONArray patchArr, User user, + Shepherd myShepherd) + throws ApiException { + if (patchArr == null) + throw new ApiException("null patch array", ApiException.ERROR_RETURN_CODE_REQUIRED); + this.setSkipAutoIndexing(true); + org.json.JSONArray resArr = new org.json.JSONArray(); + Set occNeedPruning = new HashSet(); + Set indivNeedPruning = new HashSet(); + for (int i = 0; i < patchArr.length(); i++) { + System.out.println("applied patch at [i=" + i + "]: " + patchArr.optJSONObject(i)); + org.json.JSONObject patchRes = EncounterPatchValidator.applyPatch(this, + patchArr.optJSONObject(i), user, myShepherd); + for (int j = 0; j < patchRes.getJSONArray("_mayNeedPruning").length(); j++) { + Object p = patchRes.getJSONArray("_mayNeedPruning").get(j); + if (p instanceof Occurrence) { + occNeedPruning.add((Occurrence)p); + } else if (p instanceof MarkedIndividual) { + indivNeedPruning.add((MarkedIndividual)p); + } + } + patchRes.remove("_mayNeedPruning"); + System.out.println("patch returned at [i=" + i + "]: " + patchRes); + resArr.put(patchRes); + } + org.json.JSONObject rtn = new org.json.JSONObject(); + rtn.put("patchResults", resArr); + // after applying each patch, make sure nothing is wrong + EncounterPatchValidator.finalValidation(this, myShepherd); + // now we need to look at modified objects which may be empty (and thus need pruning) + for (Occurrence occ : occNeedPruning) { + if (!occ.pruneIfNeeded(myShepherd)) { + occ.setSkipAutoIndexing(false); + } + } + for (MarkedIndividual indiv : indivNeedPruning) { + if (!indiv.pruneIfNeeded(myShepherd)) { + indiv.setSkipAutoIndexing(false); + } + } + // no exceptions means success + rtn.put("success", true); + rtn.put("statusCode", 200); + this.setDWCDateLastModified(); + this._log(resArr); + this.setSkipAutoIndexing(false); + return rtn; + } + + // see note on painful redundancy with bulk import and createFromApi on + // Base.applyPatchOp() + public Object applyPatchOp(String fieldName, Object value, String op) + throws ApiException { + System.out.println("[DEBUG] applyPatchOp(): " + op + " " + fieldName + "=>" + value + + " on: " + this); + if (op == null) + throw new ApiException("op is required", ApiException.ERROR_RETURN_CODE_REQUIRED); + // TODO future enhancement: op=remove path=annotations/ANNOT_ID should perform + // functionality of servlet/EncounterRemoveAnnotation.java + User user = null; // needed for some options below + switch (fieldName) { + case "decimalLatitude": + setDecimalLatitude((Double)value); + break; + case "decimalLongitude": + setDecimalLongitude((Double)value); + break; + case "alternateId": + // note: is same as otherCatalogNumbers + setAlternateID((String)value); + break; + case "behavior": + setBehavior((String)value); + break; + case "country": + setCountry((String)value); + break; + case "dateInMilliseconds": + if (value != null) setDateInMilliseconds((Long)value); + break; + case "year": + if (value == null) { + setYear(0); + } else { + setYear((Integer)value); + } + break; + case "month": + if (value == null) { + setMonth(0); + } else { + setMonth((Integer)value); + } + break; + case "day": + if (value == null) { + setDay(0); + } else { + setDay((Integer)value); + } + break; + case "hour": + if (value == null) { + setHour(-1); // grr + } else { + setHour((Integer)value); + } + break; + case "minutes": + if (value == null) { + setMinutes(null); + } else { + setMinutes(value.toString()); + } + break; + case "depth": + setDepth((Double)value); + break; + case "elevation": + setMaximumElevationInMeters((Double)value); + break; + case "genus": + setGenus((String)value); + break; + case "specificEpithet": + setSpecificEpithet((String)value); + break; + case "lifeStage": + setLifeStage((String)value); + break; + case "livingStatus": + setLivingStatus((String)value); + break; + case "locationId": + setLocationID((String)value); + break; + case "sex": + setSex((String)value); + break; + case "state": + setState((String)value); + break; + case "submitterID": + setSubmitterID((String)value); + break; + case "submitterName": + setSubmitterName((String)value); + break; + case "submitterOrganization": + setSubmitterOrganization((String)value); + break; + case "distinguishingScar": + setDistinguishingScar((String)value); + break; + case "groupRole": + setGroupRole((String)value); + break; + case "identificationRemarks": + setIdentificationRemarks((String)value); + break; + case "occurrenceRemarks": + case "sightingRemarks": + setOccurrenceRemarks((String)value); + break; + case "otherCatalogNumbers": + setOtherCatalogNumbers((String)value); + break; + case "patterningCode": + setPatterningCode((String)value); + break; + case "satelliteTag": + setSatelliteTag((SatelliteTag)value); + break; + case "acousticTag": + setAcousticTag((AcousticTag)value); + break; + case "metalTags": + // we only need location to remove + if ("remove".equals(op) && (value != null)) { + removeMetalTag(value.toString()); + } else if (("add".equals(op) || "replace".equals(op)) && + (value instanceof org.json.JSONObject)) { + // add or replace will update based on location if exists + org.json.JSONObject jval = (org.json.JSONObject)value; + addOrUpdateMetalTag(jval.optString("location", null), + jval.optString("number", null)); + } + break; + case "measurements": + if ("remove".equals(op) && (value != null)) { + removeMeasurementByType(value.toString()); + } else if (value instanceof Measurement) { + // for op=add or op=replace, if it has the measurement (i.e. by type), it means + // it should be changed in place already so dont do anything + Measurement meas = (Measurement)value; + if (findMeasurementOfType(meas.getType()) == null) addMeasurement(meas); + } + break; + case "annotations": + // for now we can only patch op=remove on path=annotations + // adding annots is done through legacy servlet + if ("remove".equals(op) && (value instanceof Annotation)) { + // enc.removeAnnotation and deletePersistent (from db/shepherd) done in EncounterPatchValidator + // so we only need to clean up some loose ends here + Annotation goneAnnot = (Annotation)value; + goneAnnot.setSkipAutoIndexing(true); + goneAnnot.opensearchUnindexQuiet(); + } + break; + // these we really only want to append to (i think??) + // so this should only happen when op=add/replace and + // value is non-null + case "researcherComments": + if (value != null) addComments((String)value); + break; + case "verbatimLocality": + setVerbatimLocality((String)value); + break; + case "verbatimEventDate": + setVerbatimEventDate((String)value); + break; + // we should get value as a MarkedIndividual here (or null) + case "individualId": + if ("remove".equals(op) || (value == null)) { + MarkedIndividual current = removeIndividual(); + if (current != null) { + System.out.println("enc.applyPatchOp() removed " + this + " from " + current); + } + } else { + // value should be an individual (new or existing) + MarkedIndividual indiv = (MarkedIndividual)value; + MarkedIndividual current = getIndividual(); + if (indiv.equals(current)) { + System.out.println( + "enc.applyPatchOp() ignoring adding existing individual to " + this); + break; + } + current = removeIndividual(); + if (current != null) { + current.setSkipAutoIndexing(false); + setIndividual(null); + System.out.println("enc.applyPatchOp() removed (prior to re-setting) " + this + + " from " + current); + } + indiv.addEncounter(this); + setIndividual(indiv); + // this will only set indiv taxonomy if NOT set + // so for new indiv and existing with no taxonomy + if (indiv.getTaxonomyString() == null) + indiv.setTaxonomyString(this.getTaxonomyString()); + // indiv.version will be updated by above calls + System.out.println("enc.applyPatchOp() added " + this + " to " + indiv); + } + break; + // value should be an Occurrence here (already validated and permission-checked) + case "occurrenceId": + // if EncounterPatchValidator let thru null value, we do nothing + if (value == null) break; + Occurrence occ = (Occurrence)value; + if ("remove".equals(op)) { + // in remove case, we are given occ to remove from + occ.removeEncounter(this); + this.occurrenceID = null; + } else { + // otherwise it is occ we add to + occ.addEncounterAndUpdateIt(this); + } + break; + case "assets": + if ("add".equals(op) && (value != null)) { + MediaAsset ma = (MediaAsset)value; + ma.setDetectionStatus("_new"); + addMediaAsset(ma); + } + break; + // value should be a user here + case "informOthers": + user = (User)value; + if (op.equals("remove")) { + removeInformOther(user); + } else { + addInformOther(user); + } + break; + case "submitters": + user = (User)value; + if (op.equals("remove")) { + removeSubmitter(user); + } else { + addSubmitter(user); + } + break; + case "photographers": + user = (User)value; + if (op.equals("remove")) { + removePhotographer(user); + } else { + addPhotographer(user); + } + break; + default: + throw new ApiException("unknown fieldName: " + fieldName, + ApiException.ERROR_RETURN_CODE_INVALID); + } + return value; + } + + public org.json.JSONObject afterPatch(Shepherd myShepherd) { + org.json.JSONObject res = new org.json.JSONObject(); + List needsIndexing = new ArrayList(); + org.json.JSONArray newAssetsArr = new org.json.JSONArray(); + // we update children here (not backgrounded) since we need them available + // once the api returns the results + for (MediaAsset ma : this.getMedia()) { + if ("_new".equals(ma.getDetectionStatus())) { + // _post_new is meant to be temporary, as it + // will get overwritten once put into IA pipeline + ma.setDetectionStatus("_post_new"); + ma.updateStandardChildren(myShepherd); + needsIndexing.add(ma); + org.json.JSONObject maj = new org.json.JSONObject(); + maj.put("id", ma.getIdInt()); + try { + URL url = ma.safeURL(myShepherd, null, "master"); + if (url != null) maj.put("url", url.toString()); + } catch (Exception ex) {} + newAssetsArr.put(maj); + } + } + if (newAssetsArr.length() > 0) res.put("newMediaAssets", newAssetsArr); + BulkImportUtil.bulkOpensearchIndex(needsIndexing); + return res; + } + + // this is allowed to have its own new thread since encounter is persisted + public org.json.JSONObject afterPatchTransaction(String context) { + List ids = new ArrayList(); + + // we use _post_new state to determine what needs to go to IA + // see: afterPatch() above + for (MediaAsset ma : this.getMedia()) { + if ("_post_new".equals(ma.getDetectionStatus())) { + ids.add(ma.getIdInt()); + } + } + if (ids.size() < 1) return null; + Task task = this.sendToIA(ids, context); + if (task == null) return null; + org.json.JSONObject rtn = new org.json.JSONObject(); + rtn.put("taskId", task.getId()); + return rtn; + } + + public MarkedIndividual removeIndividual() { + MarkedIndividual current = getIndividual(); + + if (current == null) return null; + // skip auto indexing cuz race conditions; must manually index later + current.setSkipAutoIndexing(true); + current.removeEncounter(this); + setIndividual(null); + return current; + } + + public static Object validateFieldValue(String fieldName, org.json.JSONObject data) + throws ApiException { + if (data == null) throw new ApiException("empty payload"); + org.json.JSONObject error = new org.json.JSONObject(); + error.put("fieldName", fieldName); + String exMessage = "invalid value for " + fieldName; + Object returnValue = null; + double UNSET_LATLON = 9999.99; + switch (fieldName) { + case "locationId": + returnValue = data.optString(fieldName, null); + if (returnValue == null) { + error.put("code", ApiException.ERROR_RETURN_CODE_REQUIRED); + throw new ApiException(exMessage, error); + } + if (!LocationID.isValidLocationID((String)returnValue)) { + error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); + error.put("value", returnValue); + throw new ApiException(exMessage, error); + } + break; + + case "dateTime": + returnValue = data.optString(fieldName, null); + if (returnValue == null) { + error.put("code", ApiException.ERROR_RETURN_CODE_REQUIRED); + throw new ApiException(exMessage, error); + } + if (!validISO8601String((String)returnValue)) { + error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); + error.put("value", returnValue); + throw new ApiException(exMessage, error); + } + break; + + case "taxonomy": + returnValue = data.optString(fieldName, null); + if (returnValue != null) { // null is allowed, but will not pass validity + // this is throwaway read-only shepherd + Shepherd myShepherd = new Shepherd("context0"); + myShepherd.setAction("Encounter.validateFieldValue"); + boolean validTaxonomy = false; + myShepherd.beginDBTransaction(); + try { + validTaxonomy = myShepherd.isValidTaxonomyName((String)returnValue); + } catch (Exception e) { e.printStackTrace(); } finally { + myShepherd.rollbackAndClose(); + } + if (!validTaxonomy) { + error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); + error.put("value", returnValue); + throw new ApiException(exMessage, error); + } + } + break; + + case "photographerEmail": + case "submitterEmail": + returnValue = data.optString(fieldName, null); + if ((returnValue != null) && !Util.isValidEmailAddress((String)returnValue)) { + error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); + error.put("value", returnValue); + throw new ApiException(exMessage, error); + } + break; + + case "decimalLatitude": + returnValue = data.optDouble(fieldName, UNSET_LATLON); + if ((double)returnValue == UNSET_LATLON) { + returnValue = null; + } else if (!Util.isValidDecimalLatitude((double)returnValue)) { + error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); + error.put("value", returnValue); + throw new ApiException(exMessage, error); + } + break; + + case "decimalLongitude": + returnValue = data.optDouble(fieldName, UNSET_LATLON); + if ((double)returnValue == UNSET_LATLON) { + returnValue = null; + } else if (!Util.isValidDecimalLongitude((double)returnValue)) { + error.put("code", ApiException.ERROR_RETURN_CODE_INVALID); + error.put("value", returnValue); + throw new ApiException(exMessage, error); + } + break; + + default: + System.out.println("Encounter.validateFieldValue(): WARNING unsupported fieldName=" + + fieldName); + } + // must be okay! + return returnValue; + } + + // basically ripped from servlet/EncounterForm + public Task sendToIA(Shepherd myShepherd) { + Task task = null; + + try { + IAJsonProperties iaConfig = IAJsonProperties.iaConfig(); + if (iaConfig.hasIA(this, myShepherd)) { + for (MediaAsset ma : this.getMedia()) { + ma.setDetectionStatus(IBEISIA.STATUS_INITIATED); + } + Task parentTask = null; // this is *not* persisted, but only used so intakeMediaAssets will inherit its params + if (this.getLocationID() != null) { + parentTask = new Task(); + org.json.JSONObject tp = new org.json.JSONObject(); + org.json.JSONObject mf = new org.json.JSONObject(); + mf.put("locationId", this.getLocationID()); + tp.put("matchingSetFilter", mf); + parentTask.setParameters(tp); + } + task = IA.intakeMediaAssets(myShepherd, this.getMedia(), parentTask); + myShepherd.storeNewTask(task); + System.out.println("sendToIA() success on " + this + " => " + task); + } else { + System.out.println("sendToIA() skipped; no config for " + this); + } + } catch (Exception ex) { + System.out.println("sendToIA() failed on " + this + ": " + ex); + ex.printStackTrace(); + } + return task; + } + + // this is based on servlet/MediaAssetCreate and differs only slightly from + // above - mainly in that it can handle multiple assets and creates own shepherd + // (note: all assets assumed to be using *this encounter* + public Task sendToIA(List ids, String context) { + Task task = null; + Shepherd myShepherd = new Shepherd(context); + + myShepherd.setAction("Encounter.sendToIA()"); + myShepherd.beginDBTransaction(); + try { + IAJsonProperties iaConfig = IAJsonProperties.iaConfig(); + boolean hasConfig = iaConfig.hasIA(this, myShepherd); + List allMAs = new ArrayList(); + for (Integer id : ids) { + if (id < 0) continue; + MediaAsset ma = MediaAssetFactory.load(id, myShepherd); + if (ma != null) { + ma.setDetectionStatus(hasConfig ? IBEISIA.STATUS_INITIATED : IBEISIA.STATUS_COMPLETE); + allMAs.add(ma); + } + } + if (!hasConfig) { + System.out.println("sendToIA() skipped; no config for " + this); + } else if (allMAs.size() > 0) { + Task parentTask = null; // not persisted + if (this.getLocationID() != null) { + parentTask = new Task(); + org.json.JSONObject tp = new org.json.JSONObject(); + org.json.JSONObject mf = new org.json.JSONObject(); + mf.put("locationId", this.getLocationID()); + tp.put("matchingSetFilter", mf); + parentTask.setParameters(tp); + } + Taxonomy taxy = this.getTaxonomy(myShepherd); + if (taxy != null) { + task = IA.intakeMediaAssetsOneSpecies(myShepherd, allMAs, taxy, parentTask); + } else { + task = IA.intakeMediaAssets(myShepherd, allMAs); + } + myShepherd.storeNewTask(task); + System.out.println("sendToIA() created " + task + " for " + this); + } + // persist will catch change on asset detectionStatus regardless + myShepherd.commitDBTransaction(); + } catch (Exception ex) { + ex.printStackTrace(); + myShepherd.rollbackDBTransaction(); + } finally { + myShepherd.closeDBTransaction(); + } + return task; + } + + public Set getNotificationEmailAddresses() { + Set addrs = new HashSet(); + + addrs.addAll(Util.getUserEmailAddresses(this.getSubmitters())); + addrs.addAll(Util.getUserEmailAddresses(this.getPhotographers())); + addrs.addAll(Util.getUserEmailAddresses(this.getInformOthers())); + return addrs; + } + + // FIXME passing the langCode is dumb imho, but this is "standard practice" + // better would be that each recipient user's language preference would be used for their email + public void sendCreationEmails(Shepherd myShepherd, String langCode) { + String context = myShepherd.getContext(); + + if (!CommonConfiguration.sendEmailNotifications(context)) return; + myShepherd.beginDBTransaction(); + try { + URI uri = CommonConfiguration.getServerURI(myShepherd); + if (uri == null) throw new IOException("could not find server uri"); + ThreadPoolExecutor es = MailThreadExecutorService.getExecutorService(); + Properties submitProps = ShepherdProperties.getProperties("submit.properties", langCode, + context); + Map tagMap = NotificationMailer.createBasicTagMap(this); + tagMap.put(NotificationMailer.WILDBOOK_COMMUNITY_URL, + CommonConfiguration.getWildbookCommunityURL(context)); + List mailTo = NotificationMailer.splitEmails( + CommonConfiguration.getNewSubmissionEmail(context)); + String mailSubj = submitProps.getProperty("newEncounter") + this.getCatalogNumber(); + for (String emailTo : mailTo) { + NotificationMailer mailer = new NotificationMailer(context, emailTo, langCode, + "newSubmission-summary", tagMap); + mailer.setUrlScheme(uri.getScheme()); + es.execute(mailer); + } + // this will be empty if no locationID + Set locEmails = myShepherd.getAllUserEmailAddressesForLocationIDAsSet( + this.getLocationID(), context); + for (String emailTo : locEmails) { + NotificationMailer mailer = new NotificationMailer(context, langCode, emailTo, + "newSubmission-summary", tagMap); + mailer.setUrlScheme(uri.getScheme()); + es.execute(mailer); + } + // Add encounter dont-track tag for remaining notifications (still needs email-hash assigned). + tagMap.put(NotificationMailer.EMAIL_NOTRACK, "number=" + this.getCatalogNumber()); + // this is a mashup of: submitters, photographers, informOthers.... + for (String emailTo : this.getNotificationEmailAddresses()) { + tagMap.put(NotificationMailer.EMAIL_HASH_TAG, getHashOfEmailString(emailTo)); + NotificationMailer mailer = new NotificationMailer(context, langCode, emailTo, + "newSubmission", tagMap); + mailer.setUrlScheme(uri.getScheme()); + es.execute(mailer); + } + es.shutdown(); + } catch (Exception ex) { + System.out.println("sendCreationEmails() on " + this + " failed: " + ex); + ex.printStackTrace(); + } finally { + myShepherd.rollbackDBTransaction(); + } + } + +/* + in anticipation of 10.10.0, this is a sketchy of what logging might look like + for a change in an Encounter via PATCH. + + FIXME this should be fully replaced (or wrapped around) the more basic log functionality + that is yet to be written. this can serve as an idea of some things which might be + desirable to support in general logging. take with a grain of salt. + */ + public void _log(org.json.JSONArray arr) { + if ((arr == null) || (arr.length() == 0)) return; + String actionId = Util.generateUUID(); + for (int i = 0; i < arr.length(); i++) { + if (arr.optJSONObject(i) == null) continue; + org.json.JSONObject p = arr.getJSONObject(i).optJSONObject("_patch"); + if (p == null) continue; + String op = p.optString("op", "UNKNOWN_OP"); + String path = p.optString("path", "UNKNOWN_PATH"); + Object value = null; + if (p.has("value") && !p.isNull("value")) value = p.get("value"); + String logMessage = "modified by PATCH op=" + op + ", path " + path + " with value: " + + ((value == null) ? "NULL" : value.toString()); + _log2(null, null, null, "Encounter", this.getId(), actionId, logMessage); + // legacy "audit log" (aka some random comment) + // TODO really need to add the user/who part here + this.addComments("

    " + Util.prettyTimeStamp() + + " modified " + path + " with operation " + op + "" + ((value == + null) ? "" : " and value " + value.toString() + "") + "

    "); + } + } + + // one of many dilemmas: we need a request object to get user + ip address, but dont have + // it at this point. so we likely need to pass it all around somehow. maybe on a shepherd or + // some other more common object? FIXME TODO + public void _log2( + // "standard" levels (null should be some reasonable default???) + String logLevel, + // reference to who did it, could be multiple users etc. probably should be id _and_ username? + String user, + // pretty obvious? + String ip, + // class of object acted upon + String objectClass, + // primary key + String objectId, + // for groupin multiple logs into one "action" (e.g. a PATCH on object) + String actionId, + // message + String message) { + System.out.println(String.join("\t", "[TMPLOG]", + new Long(System.currentTimeMillis()).toString(), user, ip, objectClass, objectId, + actionId, message)); + } +} diff --git a/src/main/resources/bundles/jdoconfig.properties b/src/main/resources/bundles/jdoconfig.properties index 456db6d770..50e31a5ebc 100755 --- a/src/main/resources/bundles/jdoconfig.properties +++ b/src/main/resources/bundles/jdoconfig.properties @@ -1,66 +1,66 @@ -#DataNucleus parameters for object persistence - -# The following two lines create a connection to an embedded Apache Derby database. -#datanucleus.ConnectionDriverName=org.apache.derby.jdbc.EmbeddedDriver -#datanucleus.ConnectionURL=jdbc:derby:shepherd_derby_database;create=true - -# The following two lines create a connection to a SQLite database. -# You will also need to add the JDBC JAR file for your SQLite version to /WEB-INF/lib. -#datanucleus.ConnectionDriverName=org.sqlite.JDBC -#datanucleus.ConnectionURL=jdbc:sqlite:shepherd_sqlite_database - -# The following two lines create a connection to a SQL Server or SQL Azure database. -#datanucleus.ConnectionDriverName=com.microsoft.sqlserver.jdbc.SQLServerDriver -#datanucleus.ConnectionURL=jdbc:sqlserver://.database.windows.net:1433;database=;user=@;password=;encrypt=true;hostNameInCertificate=*.database.windows.net;loginTimeout=30;create=true - - -# The following two lines create a connection to an H2 database. -# You will also need to add the JDBC JAR file for your H2 version to /WEB-INF/lib. -#datanucleus.ConnectionDriverName=org.h2.Driver -#datanucleus.ConnectionURL=jdbc:h2:shepherd_h2_database - -# The following three lines create a connection to a MySQL database. -# You will also need to add the JDBC JAR file for your MySQL version to /WEB-INF/lib. -#datanucleus.ConnectionDriverName=com.mysql.jdbc.Driver -#datanucleus.ConnectionURL=jdbc:mysql://localhost:3306/shepherd - -# The following lines can be used for PostgreSQL data storage. -# You will also need to add the JDBC JAR file for your PostgreSQL version to /WEB-INF/lib. -datanucleus.ConnectionDriverName=org.postgresql.Driver -datanucleus.ConnectionURL = jdbc:postgresql://localhost:5432/wildbook - - -javax.jdo.PersistenceManagerFactoryClass = org.datanucleus.api.jdo.JDOPersistenceManagerFactory -datanucleus.ConnectionUserName = wildbook -datanucleus.ConnectionPassword = wildbook -datanucleus.schema.autoCreateAll = true -#datanucleus.generateSchema.database.mode = create - -# deprecated: -#datanucleus.NontransactionalRead = true -#datanucleus.storeManagerType = rdbms - -datanucleus.Multithreaded = true -datanucleus.RestoreValues = true -datanucleus.maxFetchDepth = -1 -datanucleus.cache.collections.lazy = false - -# Connection pooling -datanucleus.connectionPoolingType = dbcp2 -datanucleus.connectionPool.maxIdle=10 -datanucleus.connectionPool.minIdle=5 -datanucleus.connectionPool.timeBetweenEvictionRunsMillis=240000 -# Standard DataNucleus keys (that map internally to DBCP2) -datanucleus.connectionPool.maxPoolSize = 300 -# maxWait in milliseconds. -1 means wait forever, which on contention causes threads to silently -# pile up at "begin" on dbconnections.jsp until Tomcat is restarted. 30s lets a request fail -# fast with a clear error instead, so operators see the problem and pool slots free up. -datanucleus.connectionPool.maxWait = 30000 -datanucleus.connectionPool.testSQL = SELECT 1 - -# HikariCP Pooling of Connections -#datanucleus.connectionPool.maxPoolSize=30 -#datanucleus.connectionPool.maxIdle=10 -#datanucleus.connectionPool.leakThreshold=1 -#datanucleus.connectionPool.maxLifetime=1800000 - +#DataNucleus parameters for object persistence + +# The following two lines create a connection to an embedded Apache Derby database. +#datanucleus.ConnectionDriverName=org.apache.derby.jdbc.EmbeddedDriver +#datanucleus.ConnectionURL=jdbc:derby:shepherd_derby_database;create=true + +# The following two lines create a connection to a SQLite database. +# You will also need to add the JDBC JAR file for your SQLite version to /WEB-INF/lib. +#datanucleus.ConnectionDriverName=org.sqlite.JDBC +#datanucleus.ConnectionURL=jdbc:sqlite:shepherd_sqlite_database + +# The following two lines create a connection to a SQL Server or SQL Azure database. +#datanucleus.ConnectionDriverName=com.microsoft.sqlserver.jdbc.SQLServerDriver +#datanucleus.ConnectionURL=jdbc:sqlserver://.database.windows.net:1433;database=;user=@;password=;encrypt=true;hostNameInCertificate=*.database.windows.net;loginTimeout=30;create=true + + +# The following two lines create a connection to an H2 database. +# You will also need to add the JDBC JAR file for your H2 version to /WEB-INF/lib. +#datanucleus.ConnectionDriverName=org.h2.Driver +#datanucleus.ConnectionURL=jdbc:h2:shepherd_h2_database + +# The following three lines create a connection to a MySQL database. +# You will also need to add the JDBC JAR file for your MySQL version to /WEB-INF/lib. +#datanucleus.ConnectionDriverName=com.mysql.jdbc.Driver +#datanucleus.ConnectionURL=jdbc:mysql://localhost:3306/shepherd + +# The following lines can be used for PostgreSQL data storage. +# You will also need to add the JDBC JAR file for your PostgreSQL version to /WEB-INF/lib. +datanucleus.ConnectionDriverName=org.postgresql.Driver +datanucleus.ConnectionURL = jdbc:postgresql://localhost:5432/wildbook + + +javax.jdo.PersistenceManagerFactoryClass = org.datanucleus.api.jdo.JDOPersistenceManagerFactory +datanucleus.ConnectionUserName = wildbook +datanucleus.ConnectionPassword = wildbook +datanucleus.schema.autoCreateAll = true +#datanucleus.generateSchema.database.mode = create + +# deprecated: +#datanucleus.NontransactionalRead = true +#datanucleus.storeManagerType = rdbms + +datanucleus.Multithreaded = true +datanucleus.RestoreValues = true +datanucleus.maxFetchDepth = -1 +datanucleus.cache.collections.lazy = false + +# Connection pooling +datanucleus.connectionPoolingType = dbcp2 +datanucleus.connectionPool.maxIdle=10 +datanucleus.connectionPool.minIdle=5 +datanucleus.connectionPool.timeBetweenEvictionRunsMillis=240000 +# Standard DataNucleus keys (that map internally to DBCP2) +datanucleus.connectionPool.maxPoolSize = 300 +# maxWait in milliseconds. -1 means wait forever, which on contention causes threads to silently +# pile up at "begin" on dbconnections.jsp until Tomcat is restarted. 30s lets a request fail +# fast with a clear error instead, so operators see the problem and pool slots free up. +datanucleus.connectionPool.maxWait = 30000 +datanucleus.connectionPool.testSQL = SELECT 1 + +# HikariCP Pooling of Connections +#datanucleus.connectionPool.maxPoolSize=30 +#datanucleus.connectionPool.maxIdle=10 +#datanucleus.connectionPool.leakThreshold=1 +#datanucleus.connectionPool.maxLifetime=1800000 + diff --git a/src/main/webapp/encounters/scanEndApplet.jsp b/src/main/webapp/encounters/scanEndApplet.jsp index 46eac65762..0accbd5225 100755 --- a/src/main/webapp/encounters/scanEndApplet.jsp +++ b/src/main/webapp/encounters/scanEndApplet.jsp @@ -1,824 +1,824 @@ - - - -<%@ page contentType="text/html; charset=iso-8859-1" language="java" - import="org.ecocean.servlet.ServletUtilities,org.dom4j.Document, org.dom4j.Element,org.dom4j.io.SAXReader, org.ecocean.*, org.ecocean.grid.MatchComparator, org.ecocean.grid.MatchObject, org.ecocean.grid.GridManager, org.ecocean.grid.GridManagerFactory, java.io.File, java.util.Arrays, java.util.Iterator, java.util.List, -org.ecocean.grid.ScanTask, -java.util.ArrayList, -org.json.JSONArray, -java.text.MessageFormat, -java.util.Properties, -java.util.Vector" %> -<%@ page import="org.ecocean.shepherd.core.Shepherd" %> -<%@ page import="org.ecocean.shepherd.core.ShepherdProperties" %> - -<% - -String context="context0"; -context=ServletUtilities.getContext(request); - -//let's set up references to our file system components -String rootWebappPath = getServletContext().getRealPath("/"); -File webappsDir = new File(rootWebappPath).getParentFile(); -File shepherdDataDir = new File(webappsDir, CommonConfiguration.getDataDirectoryName(context)); -File encountersDir=new File(shepherdDataDir.getAbsolutePath()+"/encounters"); - - String num=""; - ArrayList locationIDs = new ArrayList(); - boolean scanInProgress = false; - boolean scanTaskExists = false; - int numComplete = 0; - int numTotal = 0; - long scanTaskStartTime = -1; - - if(request.getParameter("number")!=null){ - Shepherd myShepherd=new Shepherd(context); - myShepherd.setAction("scanEndApplet.jsp"); - myShepherd.beginDBTransaction(); - try { - if(myShepherd.isEncounter(ServletUtilities.preventCrossSiteScriptingAttacks(request.getParameter("number")))){ - num = ServletUtilities.preventCrossSiteScriptingAttacks(request.getParameter("number")); - } - - //get any scantask locationID lists and check scan status - String taskID = request.getParameter("taskID"); - boolean isRightSide = (request.getParameter("rightSide") != null) && request.getParameter("rightSide").equals("true"); - if (taskID == null) taskID = "scan" + (isRightSide ? "R" : "L") + num; - if(taskID != null) { - ScanTask st=myShepherd.getScanTask(taskID); - if(st!=null){ - scanTaskExists = true; - if(st.getLocationIDFilters()!=null){ - locationIDs=st.getLocationIDFilters(); - } - if(!st.hasFinished()){ - scanInProgress = true; - scanTaskStartTime = st.getStartTime(); - // Check how much work is done via GridManager - GridManager gm = GridManagerFactory.getGridManager(); - numComplete = gm.getNumWorkItemsCompleteForTask(taskID); - numTotal = numComplete + gm.getNumWorkItemsIncompleteForTask(taskID); - } - } - } - } finally { - myShepherd.rollbackAndClose(); - } - } - String encSubdir = Encounter.subdir(num); - - String sessionId = session.getId(); - boolean xmlOK = false; - SAXReader xmlReader = new SAXReader(); - File file = new File("foo"); - String scanDate = ""; - String C = ""; - String R = ""; - String epsilon = ""; - String Sizelim = ""; - String maxTriangleRotation = ""; - String side2 = ""; - - // Determine the language for i18n - String langCode = "en"; - if (session.getAttribute("langCode") != null) langCode = (String) session.getAttribute("langCode"); - Properties i18n = ShepherdProperties.getProperties("commonConfigurationLabels.properties", langCode, context); -%> - - - - -<% -// If scan is in progress, add auto-refresh -if (scanInProgress) { -%> - -<% -} -%> - -
    - -
      -
    • Encounter - <%=num%> -
      • - - - <% - String fileSider = ""; - File finalXMLFile; - File locationIDXMLFile; - if ((request.getParameter("rightSide") != null) && (request.getParameter("rightSide").equals("true"))) { - finalXMLFile = new File(encountersDir.getAbsolutePath()+"/"+ encSubdir + "/lastFullRightI3SScan.xml"); - locationIDXMLFile = new File(encountersDir.getAbsolutePath()+"/"+ encSubdir + "/lastFullRightLocationIDScan.xml"); - - - side2 = "right"; - fileSider = "&rightSide=true"; - } else { - finalXMLFile = new File(encountersDir.getAbsolutePath()+"/" + encSubdir + "/lastFullI3SScan.xml"); - locationIDXMLFile = new File(encountersDir.getAbsolutePath()+"/" + encSubdir + "/lastFullLocationIDScan.xml"); - } - - - if (locationIDXMLFile.exists()) { - %> - - <% - } - %> - -
    • Modified Groth (Full)
      • - <% - - if (finalXMLFile.exists()) { - %> - -
    • I3S -
      • - <% - } - - - %> - - -
    - -<% - // ============================================================ - // SCAN IN PROGRESS: Show waiting message with progress - // ============================================================ - if (scanInProgress) { -%> - -
    - -

    <%=MessageFormat.format(i18n.getProperty("scanInProgress.title", "Scan in progress for encounter {0}"), num)%>

    -

    <%=i18n.getProperty("scanInProgress.message", "The pattern matching scan is running. Results will appear here when complete.")%>

    - - <% - if (numTotal > 0) { - int pct = (int) ((numComplete * 100.0) / numTotal); - %> -
    - <%=MessageFormat.format(i18n.getProperty("scanInProgress.progress", "{0} of {1} comparisons complete"), String.valueOf(numComplete), String.valueOf(numTotal))%> -
    -
    -
    -
    - <% - } else { - %> -

    <%=i18n.getProperty("scanInProgress.queuing", "Preparing comparisons...")%>

    - <% - } - %> -

    <%=i18n.getProperty("scanInProgress.autoRefresh", "This page will automatically refresh every 15 seconds.")%>

    -
    - -<% - } else { - // ============================================================ - // SCAN COMPLETE or NO SCAN: Show results - // ============================================================ -%> - -<% - Vector initresults = new Vector(); - Document doc; - Element root; - String side = "left"; - - try { - if ((request.getParameter("rightSide") != null) && (request.getParameter("rightSide").equals("true"))) { - file = new File(encountersDir.getAbsolutePath()+"/" + encSubdir + "/lastFullRightScan.xml"); - side = "right"; - } else { - file = new File(encountersDir.getAbsolutePath()+"/" + encSubdir + "/lastFullScan.xml"); - } - doc = xmlReader.read(file); - root = doc.getRootElement(); - scanDate = root.attributeValue("scanDate"); - xmlOK = true; - R = root.attributeValue("R"); - C = root.attributeValue("C"); - maxTriangleRotation = root.attributeValue("maxTriangleRotation"); - Sizelim = root.attributeValue("Sizelim"); - epsilon = root.attributeValue("epsilon"); - } catch (Exception ioe) { - System.out.println("Error accessing the stored scan XML data for encounter: " + num); - ioe.printStackTrace(); - xmlOK = false; - } - - MatchObject[] matches = new MatchObject[0]; - if (!xmlOK) { - int resultsSize = initresults.size(); - System.out.println(resultsSize); - matches = new MatchObject[resultsSize]; - for (int a = 0; a < resultsSize; a++) { - matches[a] = (MatchObject) initresults.get(a); - } - R = request.getParameter("R"); - C = request.getParameter("C"); - maxTriangleRotation = request.getParameter("maxTriangleRotation"); - Sizelim = request.getParameter("Sizelim"); - epsilon = request.getParameter("epsilon"); - } -%> - -

    - -<% - if (!xmlOK && !scanTaskExists) { - // No scan has ever been run and no XML exists -%> -

    <%=i18n.getProperty("scanResults.noResults.title", "No Scan Results")%>

    -

    <%=i18n.getProperty("scanResults.noResults.message", "No pattern matching scan has been run for this encounter yet.")%>

    -<% - } else if (!xmlOK && scanTaskExists) { - // Scan task finished but XML was not written (failed or partial write) -%> -

    <%=i18n.getProperty("scanResults.failed.title", "Scan Failed")%>

    -

    <%=i18n.getProperty("scanResults.failed.message", "The scan task completed but results could not be written. Please try running the scan again.")%>

    -<% - } else if (xmlOK) { - // We have results to display -%> -

    Modified Groth Scan Results

    -

    -

    The following encounter(s) received the highest - match values against a <%=side%>-side scan of encounter <%=num%>.

    - - -<% - if (xmlOK) {%> -

     Saved - scan data may be old and invalid. Check the date below and run a fresh - scan for the latest results.

    - -

    Date of scan: <%=scanDate%> -

    -<%}%> - -

    See the table below for score breakdowns.

    - - - - -<% - String feedURL = "//" + CommonConfiguration.getURLLocation(request) + "/TrackerFeed?number=" + num; - String baseURL = "/"+CommonConfiguration.getDataDirectoryName(context)+"/encounters/"; - - if (xmlOK) { - if ((request.getParameter("rightSide") != null) && (request.getParameter("rightSide").equals("true"))) { - feedURL = baseURL + encSubdir + "/lastFullRightScan.xml?"; - } else { - feedURL = baseURL + encSubdir + "/lastFullScan.xml?"; - } - } - String rightSA = ""; - if ((request.getParameter("rightSide") != null) && (request.getParameter("rightSide").equals("true"))) { - rightSA = "&filePrefix=extractRight"; - } - -java.util.Random rnd = new java.util.Random(); -%> -"); - %> - - - - - -
    -
    -
    - -
    -
    -
    -
    -
    - -
    -
    -
    -
    -
    -
    - - -
    -
    -
    - - - -
    -
    - - -
    -

    - - - - - - - - - - - - - - - - - - - <% - Shepherd indShepherd = new Shepherd(context); - indShepherd.setAction("scanEndApplet.jsp_displayNames"); - indShepherd.beginDBTransaction(); - try { - java.util.HashMap displayNameCache = new java.util.HashMap<>(); - - if (!xmlOK) { - - MatchObject[] results = new MatchObject[1]; - results = matches; - Arrays.sort(results, new MatchComparator()); - for (int p = 0; p < results.length; p++) { - if ((results[p].matchValue != 0) || (request.getAttribute("singleComparison") != null)) { - String indId_mo = results[p].getIndividualName(); - String displayName_mo = displayNameCache.get(indId_mo); - if (displayName_mo == null && indId_mo != null) { - MarkedIndividual ind_mo = indShepherd.getMarkedIndividual(indId_mo); - displayName_mo = (ind_mo != null) ? ind_mo.getDisplayName() : indId_mo; - displayNameCache.put(indId_mo, displayName_mo); - } - if (displayName_mo == null) displayName_mo = "Unknown"; - %> - - - <%if (results[p].encounterNumber.equals("N/A")) {%> - - <%} else {%> - - <% - } - String adjustedMatchValueString = (new Double(results[p].adjustedMatchValue)).toString(); - if (adjustedMatchValueString.length() > 5) { - adjustedMatchValueString = adjustedMatchValueString.substring(0, 5); - } - %> - - <% - String finalscore2 = (new Double(results[p].matchValue * results[p].adjustedMatchValue)).toString(); - - //trim the length of finalscore - if (finalscore2.length() > 7) { - finalscore2 = finalscore2.substring(0, 6); - } - %> - - - - - - - - <% - //end if matchValue!=0 loop - } - //end for loop - } - -//or use XML output here - } else { - doc = xmlReader.read(file); - root = doc.getRootElement(); - - Iterator matchsets = root.elementIterator("match"); - int ct = 0; - while (matchsets.hasNext()) { - Element match = (Element) matchsets.next(); - List encounters = match.elements("encounter"); - Element enc1 = (Element) encounters.get(0); - Element enc2 = (Element) encounters.get(1); - String indId_xml = enc1.attributeValue("assignedToShark"); - String displayName_xml = displayNameCache.get(indId_xml); - if (displayName_xml == null && indId_xml != null) { - MarkedIndividual ind_xml = indShepherd.getMarkedIndividual(indId_xml); - displayName_xml = (ind_xml != null) ? ind_xml.getDisplayName() : indId_xml; - displayNameCache.put(indId_xml, displayName_xml); - } - if (displayName_xml == null) displayName_xml = "Unknown"; - %> - - " - style="cursor: pointer;" onClick="spotDisplayPair(<%=ct%>);" title="jump to this match pair"> - - <%if (enc1.attributeValue("number").equals("N/A")) {%> - - <%} else {%> - - <% - } - String adjustedpoints = "No Adj."; - adjustedpoints = match.attributeValue("adjustedpoints"); - if (adjustedpoints == null) { - adjustedpoints = " "; - } - if (adjustedpoints.length() > 5) { - adjustedpoints = adjustedpoints.substring(0, 5); - } else { - adjustedpoints = adjustedpoints + "
    "; - } - %> - - <% - String finalscore = " "; - try { - if (match.attributeValue("finalscore") != null) { - finalscore = match.attributeValue("finalscore"); - } - } catch (NullPointerException npe) { - } - - //trim the length of finalscore - if (finalscore.length() > 7) { - finalscore = finalscore.substring(0, 6); - } - - %> - - - - - <% - String evaluation = "No Adj."; - evaluation = match.attributeValue("evaluation"); - if (evaluation == null) { - evaluation = " "; - } - - %> - - - - - <% - - - ct++; - } - } - - %> - -
    Individual ID EncounterFraction Matched Triangles Match Score logM std. dev.ConfidenceMatched Keywords
    - <%=displayName_mo%> - - N/A<%=results[p].encounterNumber%> - <%=(adjustedMatchValueString)%>
    -     		<%=finalscore2%> - <%=results[p].getLogMStdDev()%> - <%=results[p].getEvaluation()%> -
    - - <%=displayName_xml%> - - N/A">Link - <%=adjustedpoints%> - <%=finalscore%> - <%=match.attributeValue("logMStdDev")%> - <%=evaluation%> - - <% - String keywords = ""; - for (Iterator i = match.elementIterator("keywords"); i.hasNext();) { - Element kws = (Element) i.next(); - // iterate the keywords themselves - for (Iterator j = kws.elementIterator("keyword"); j.hasNext();) { - Element kws2 = (Element) j.next(); - keywords = keywords + "
  • " + kws2.attributeValue("name") + "
    • "; - } - } - if (keywords.length() <= 1) { - keywords = " "; - } - %> -
      <%=keywords%> -
    -
    - - - - <% - } finally { - indShepherd.rollbackAndClose(); - } - - //myShepherd.closeDBTransaction(); - //myShepherd = null; - doc = null; - root = null; - initresults = null; - file = null; - xmlReader = null; - -if ((request.getParameter("epsilon") != null) && (request.getParameter("R") != null)) {%> -

    Custom Scan

    - <%} else {%> -

    Standard Scan

    - <%}%> -

    For this scan, the following variables were used:

    -
      - - -
    • epsilon (<%=epsilon%>)
      • -
    • R (<%=R%>)
      • -
    • Sizelim (<%=Sizelim%>)
      • -
    • C (<%=C%>)
      • -
    • Max. Triangle Rotation (<%=maxTriangleRotation%>)
      • - -
    -<% - } // end if xmlOK -%> -
    -<% - } // end else (not scanInProgress) -%> -
    - + + + +<%@ page contentType="text/html; charset=iso-8859-1" language="java" + import="org.ecocean.servlet.ServletUtilities,org.dom4j.Document, org.dom4j.Element,org.dom4j.io.SAXReader, org.ecocean.*, org.ecocean.grid.MatchComparator, org.ecocean.grid.MatchObject, org.ecocean.grid.GridManager, org.ecocean.grid.GridManagerFactory, java.io.File, java.util.Arrays, java.util.Iterator, java.util.List, +org.ecocean.grid.ScanTask, +java.util.ArrayList, +org.json.JSONArray, +java.text.MessageFormat, +java.util.Properties, +java.util.Vector" %> +<%@ page import="org.ecocean.shepherd.core.Shepherd" %> +<%@ page import="org.ecocean.shepherd.core.ShepherdProperties" %> + +<% + +String context="context0"; +context=ServletUtilities.getContext(request); + +//let's set up references to our file system components +String rootWebappPath = getServletContext().getRealPath("/"); +File webappsDir = new File(rootWebappPath).getParentFile(); +File shepherdDataDir = new File(webappsDir, CommonConfiguration.getDataDirectoryName(context)); +File encountersDir=new File(shepherdDataDir.getAbsolutePath()+"/encounters"); + + String num=""; + ArrayList locationIDs = new ArrayList(); + boolean scanInProgress = false; + boolean scanTaskExists = false; + int numComplete = 0; + int numTotal = 0; + long scanTaskStartTime = -1; + + if(request.getParameter("number")!=null){ + Shepherd myShepherd=new Shepherd(context); + myShepherd.setAction("scanEndApplet.jsp"); + myShepherd.beginDBTransaction(); + try { + if(myShepherd.isEncounter(ServletUtilities.preventCrossSiteScriptingAttacks(request.getParameter("number")))){ + num = ServletUtilities.preventCrossSiteScriptingAttacks(request.getParameter("number")); + } + + //get any scantask locationID lists and check scan status + String taskID = request.getParameter("taskID"); + boolean isRightSide = (request.getParameter("rightSide") != null) && request.getParameter("rightSide").equals("true"); + if (taskID == null) taskID = "scan" + (isRightSide ? "R" : "L") + num; + if(taskID != null) { + ScanTask st=myShepherd.getScanTask(taskID); + if(st!=null){ + scanTaskExists = true; + if(st.getLocationIDFilters()!=null){ + locationIDs=st.getLocationIDFilters(); + } + if(!st.hasFinished()){ + scanInProgress = true; + scanTaskStartTime = st.getStartTime(); + // Check how much work is done via GridManager + GridManager gm = GridManagerFactory.getGridManager(); + numComplete = gm.getNumWorkItemsCompleteForTask(taskID); + numTotal = numComplete + gm.getNumWorkItemsIncompleteForTask(taskID); + } + } + } + } finally { + myShepherd.rollbackAndClose(); + } + } + String encSubdir = Encounter.subdir(num); + + String sessionId = session.getId(); + boolean xmlOK = false; + SAXReader xmlReader = new SAXReader(); + File file = new File("foo"); + String scanDate = ""; + String C = ""; + String R = ""; + String epsilon = ""; + String Sizelim = ""; + String maxTriangleRotation = ""; + String side2 = ""; + + // Determine the language for i18n + String langCode = "en"; + if (session.getAttribute("langCode") != null) langCode = (String) session.getAttribute("langCode"); + Properties i18n = ShepherdProperties.getProperties("commonConfigurationLabels.properties", langCode, context); +%> + + + + +<% +// If scan is in progress, add auto-refresh +if (scanInProgress) { +%> + +<% +} +%> + +
    + +
      +
    • Encounter + <%=num%> +
      • + + + <% + String fileSider = ""; + File finalXMLFile; + File locationIDXMLFile; + if ((request.getParameter("rightSide") != null) && (request.getParameter("rightSide").equals("true"))) { + finalXMLFile = new File(encountersDir.getAbsolutePath()+"/"+ encSubdir + "/lastFullRightI3SScan.xml"); + locationIDXMLFile = new File(encountersDir.getAbsolutePath()+"/"+ encSubdir + "/lastFullRightLocationIDScan.xml"); + + + side2 = "right"; + fileSider = "&rightSide=true"; + } else { + finalXMLFile = new File(encountersDir.getAbsolutePath()+"/" + encSubdir + "/lastFullI3SScan.xml"); + locationIDXMLFile = new File(encountersDir.getAbsolutePath()+"/" + encSubdir + "/lastFullLocationIDScan.xml"); + } + + + if (locationIDXMLFile.exists()) { + %> + + <% + } + %> + +
    • Modified Groth (Full)
      • + <% + + if (finalXMLFile.exists()) { + %> + +
    • I3S +
      • + <% + } + + + %> + + +
    + +<% + // ============================================================ + // SCAN IN PROGRESS: Show waiting message with progress + // ============================================================ + if (scanInProgress) { +%> + +
    + +

    <%=MessageFormat.format(i18n.getProperty("scanInProgress.title", "Scan in progress for encounter {0}"), num)%>

    +

    <%=i18n.getProperty("scanInProgress.message", "The pattern matching scan is running. Results will appear here when complete.")%>

    + + <% + if (numTotal > 0) { + int pct = (int) ((numComplete * 100.0) / numTotal); + %> +
    + <%=MessageFormat.format(i18n.getProperty("scanInProgress.progress", "{0} of {1} comparisons complete"), String.valueOf(numComplete), String.valueOf(numTotal))%> +
    +
    +
    +
    + <% + } else { + %> +

    <%=i18n.getProperty("scanInProgress.queuing", "Preparing comparisons...")%>

    + <% + } + %> +

    <%=i18n.getProperty("scanInProgress.autoRefresh", "This page will automatically refresh every 15 seconds.")%>

    +
    + +<% + } else { + // ============================================================ + // SCAN COMPLETE or NO SCAN: Show results + // ============================================================ +%> + +<% + Vector initresults = new Vector(); + Document doc; + Element root; + String side = "left"; + + try { + if ((request.getParameter("rightSide") != null) && (request.getParameter("rightSide").equals("true"))) { + file = new File(encountersDir.getAbsolutePath()+"/" + encSubdir + "/lastFullRightScan.xml"); + side = "right"; + } else { + file = new File(encountersDir.getAbsolutePath()+"/" + encSubdir + "/lastFullScan.xml"); + } + doc = xmlReader.read(file); + root = doc.getRootElement(); + scanDate = root.attributeValue("scanDate"); + xmlOK = true; + R = root.attributeValue("R"); + C = root.attributeValue("C"); + maxTriangleRotation = root.attributeValue("maxTriangleRotation"); + Sizelim = root.attributeValue("Sizelim"); + epsilon = root.attributeValue("epsilon"); + } catch (Exception ioe) { + System.out.println("Error accessing the stored scan XML data for encounter: " + num); + ioe.printStackTrace(); + xmlOK = false; + } + + MatchObject[] matches = new MatchObject[0]; + if (!xmlOK) { + int resultsSize = initresults.size(); + System.out.println(resultsSize); + matches = new MatchObject[resultsSize]; + for (int a = 0; a < resultsSize; a++) { + matches[a] = (MatchObject) initresults.get(a); + } + R = request.getParameter("R"); + C = request.getParameter("C"); + maxTriangleRotation = request.getParameter("maxTriangleRotation"); + Sizelim = request.getParameter("Sizelim"); + epsilon = request.getParameter("epsilon"); + } +%> + +

    + +<% + if (!xmlOK && !scanTaskExists) { + // No scan has ever been run and no XML exists +%> +

    <%=i18n.getProperty("scanResults.noResults.title", "No Scan Results")%>

    +

    <%=i18n.getProperty("scanResults.noResults.message", "No pattern matching scan has been run for this encounter yet.")%>

    +<% + } else if (!xmlOK && scanTaskExists) { + // Scan task finished but XML was not written (failed or partial write) +%> +

    <%=i18n.getProperty("scanResults.failed.title", "Scan Failed")%>

    +

    <%=i18n.getProperty("scanResults.failed.message", "The scan task completed but results could not be written. Please try running the scan again.")%>

    +<% + } else if (xmlOK) { + // We have results to display +%> +

    Modified Groth Scan Results

    +

    +

    The following encounter(s) received the highest + match values against a <%=side%>-side scan of encounter <%=num%>.

    + + +<% + if (xmlOK) {%> +

     Saved + scan data may be old and invalid. Check the date below and run a fresh + scan for the latest results.

    + +

    Date of scan: <%=scanDate%> +

    +<%}%> + +

    See the table below for score breakdowns.

    + + + + +<% + String feedURL = "//" + CommonConfiguration.getURLLocation(request) + "/TrackerFeed?number=" + num; + String baseURL = "/"+CommonConfiguration.getDataDirectoryName(context)+"/encounters/"; + + if (xmlOK) { + if ((request.getParameter("rightSide") != null) && (request.getParameter("rightSide").equals("true"))) { + feedURL = baseURL + encSubdir + "/lastFullRightScan.xml?"; + } else { + feedURL = baseURL + encSubdir + "/lastFullScan.xml?"; + } + } + String rightSA = ""; + if ((request.getParameter("rightSide") != null) && (request.getParameter("rightSide").equals("true"))) { + rightSA = "&filePrefix=extractRight"; + } + +java.util.Random rnd = new java.util.Random(); +%> +"); + %> + + + + + +
    +
    +
    + +
    +
    +
    +
    +
    + +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + + + +
    +
    + + +
    +

    + + + + + + + + + + + + + + + + + + + <% + Shepherd indShepherd = new Shepherd(context); + indShepherd.setAction("scanEndApplet.jsp_displayNames"); + indShepherd.beginDBTransaction(); + try { + java.util.HashMap displayNameCache = new java.util.HashMap<>(); + + if (!xmlOK) { + + MatchObject[] results = new MatchObject[1]; + results = matches; + Arrays.sort(results, new MatchComparator()); + for (int p = 0; p < results.length; p++) { + if ((results[p].matchValue != 0) || (request.getAttribute("singleComparison") != null)) { + String indId_mo = results[p].getIndividualName(); + String displayName_mo = displayNameCache.get(indId_mo); + if (displayName_mo == null && indId_mo != null) { + MarkedIndividual ind_mo = indShepherd.getMarkedIndividual(indId_mo); + displayName_mo = (ind_mo != null) ? ind_mo.getDisplayName() : indId_mo; + displayNameCache.put(indId_mo, displayName_mo); + } + if (displayName_mo == null) displayName_mo = "Unknown"; + %> + + + <%if (results[p].encounterNumber.equals("N/A")) {%> + + <%} else {%> + + <% + } + String adjustedMatchValueString = (new Double(results[p].adjustedMatchValue)).toString(); + if (adjustedMatchValueString.length() > 5) { + adjustedMatchValueString = adjustedMatchValueString.substring(0, 5); + } + %> + + <% + String finalscore2 = (new Double(results[p].matchValue * results[p].adjustedMatchValue)).toString(); + + //trim the length of finalscore + if (finalscore2.length() > 7) { + finalscore2 = finalscore2.substring(0, 6); + } + %> + + + + + + + + <% + //end if matchValue!=0 loop + } + //end for loop + } + +//or use XML output here + } else { + doc = xmlReader.read(file); + root = doc.getRootElement(); + + Iterator matchsets = root.elementIterator("match"); + int ct = 0; + while (matchsets.hasNext()) { + Element match = (Element) matchsets.next(); + List encounters = match.elements("encounter"); + Element enc1 = (Element) encounters.get(0); + Element enc2 = (Element) encounters.get(1); + String indId_xml = enc1.attributeValue("assignedToShark"); + String displayName_xml = displayNameCache.get(indId_xml); + if (displayName_xml == null && indId_xml != null) { + MarkedIndividual ind_xml = indShepherd.getMarkedIndividual(indId_xml); + displayName_xml = (ind_xml != null) ? ind_xml.getDisplayName() : indId_xml; + displayNameCache.put(indId_xml, displayName_xml); + } + if (displayName_xml == null) displayName_xml = "Unknown"; + %> + + " + style="cursor: pointer;" onClick="spotDisplayPair(<%=ct%>);" title="jump to this match pair"> + + <%if (enc1.attributeValue("number").equals("N/A")) {%> + + <%} else {%> + + <% + } + String adjustedpoints = "No Adj."; + adjustedpoints = match.attributeValue("adjustedpoints"); + if (adjustedpoints == null) { + adjustedpoints = " "; + } + if (adjustedpoints.length() > 5) { + adjustedpoints = adjustedpoints.substring(0, 5); + } else { + adjustedpoints = adjustedpoints + "
    "; + } + %> + + <% + String finalscore = " "; + try { + if (match.attributeValue("finalscore") != null) { + finalscore = match.attributeValue("finalscore"); + } + } catch (NullPointerException npe) { + } + + //trim the length of finalscore + if (finalscore.length() > 7) { + finalscore = finalscore.substring(0, 6); + } + + %> + + + + + <% + String evaluation = "No Adj."; + evaluation = match.attributeValue("evaluation"); + if (evaluation == null) { + evaluation = " "; + } + + %> + + + + + <% + + + ct++; + } + } + + %> + +
    Individual ID EncounterFraction Matched Triangles Match Score logM std. dev.ConfidenceMatched Keywords
    + <%=displayName_mo%> + + N/A<%=results[p].encounterNumber%> + <%=(adjustedMatchValueString)%>
    +     		<%=finalscore2%> + <%=results[p].getLogMStdDev()%> + <%=results[p].getEvaluation()%> +
    + + <%=displayName_xml%> + + N/A">Link + <%=adjustedpoints%> + <%=finalscore%> + <%=match.attributeValue("logMStdDev")%> + <%=evaluation%> + + <% + String keywords = ""; + for (Iterator i = match.elementIterator("keywords"); i.hasNext();) { + Element kws = (Element) i.next(); + // iterate the keywords themselves + for (Iterator j = kws.elementIterator("keyword"); j.hasNext();) { + Element kws2 = (Element) j.next(); + keywords = keywords + "
  • " + kws2.attributeValue("name") + "
    • "; + } + } + if (keywords.length() <= 1) { + keywords = " "; + } + %> +
      <%=keywords%> +
    +
    + + + + <% + } finally { + indShepherd.rollbackAndClose(); + } + + //myShepherd.closeDBTransaction(); + //myShepherd = null; + doc = null; + root = null; + initresults = null; + file = null; + xmlReader = null; + +if ((request.getParameter("epsilon") != null) && (request.getParameter("R") != null)) {%> +

    Custom Scan

    + <%} else {%> +

    Standard Scan

    + <%}%> +

    For this scan, the following variables were used:

    +
      + + +
    • epsilon (<%=epsilon%>)
      • +
    • R (<%=R%>)
      • +
    • Sizelim (<%=Sizelim%>)
      • +
    • C (<%=C%>)
      • +
    • Max. Triangle Rotation (<%=maxTriangleRotation%>)
      • + +
    +<% + } // end if xmlOK +%> +
    +<% + } // end else (not scanInProgress) +%> +
    + From a6d9942d7bee1cb10bef6282bac86f25a5380d3d Mon Sep 17 00:00:00 2001 From: JasonWildMe Date: Wed, 29 Apr 2026 09:25:12 -0700 Subject: [PATCH 5/7] Wrap IBEISIA.sendIdentify in try/finally MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The method opened a Shepherd at line 241 and only closed it on three specific success/early-return paths (lines 290, 339, 375). Anything that threw between begin and one of those closes leaked the PM: - IBEISIAIdentificationMatchingState.allAsJSONArray() — a JDO query - WildbookIAM.getIASpecies() and other lazy-loading getters in the qanns/tanns iteration loops - qanns.get(0).getMatchingSet() — runs an OpenSearch HTTP call while the Postgres tx is still open; fails on slow/hung OpenSearch - annotGetIndiv() — a JDO query - Any unchecked Throwable Wraps the body in try { ... } finally { rollbackAndClose() }, removes the three explicit close pairs, and hoists the HashMap declaration out of the try so the post-try RestClient.post() (which intentionally runs after the DB connection is released) can still see it. Same JSONObject results on every path; same "close DB before HTTP" ordering preserved. Co-Authored-By: Claude Opus 4.7 (1M context) --- src/main/java/org/ecocean/identity/IBEISIA.java | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/main/java/org/ecocean/identity/IBEISIA.java b/src/main/java/org/ecocean/identity/IBEISIA.java index 6cd456c41c..96077cc4ea 100644 --- a/src/main/java/org/ecocean/identity/IBEISIA.java +++ b/src/main/java/org/ecocean/identity/IBEISIA.java @@ -240,7 +240,10 @@ public static JSONObject sendIdentify(ArrayList qanns, ArrayList map = new HashMap(); + try { map.put("callback_url", callbackUrl(baseUrl)); map.put("jobid", taskId); if (queryConfigDict != null) map.put("query_config_dict", queryConfigDict); @@ -286,8 +289,6 @@ public static JSONObject sendIdentify(ArrayList qanns, ArrayList qanns, ArrayList qanns, ArrayList Date: Thu, 7 May 2026 09:05:07 -0700 Subject: [PATCH 6/7] Clean try-catch-finally block --- src/main/java/org/ecocean/identity/IBEISIA.java | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/src/main/java/org/ecocean/identity/IBEISIA.java b/src/main/java/org/ecocean/identity/IBEISIA.java index 31751641ef..0f6e03f517 100644 --- a/src/main/java/org/ecocean/identity/IBEISIA.java +++ b/src/main/java/org/ecocean/identity/IBEISIA.java @@ -240,6 +240,7 @@ public static JSONObject sendIdentify(ArrayList qanns, ArrayList map = new HashMap(); map.put("callback_url", callbackUrl(baseUrl)); @@ -287,8 +288,6 @@ public static JSONObject sendIdentify(ArrayList qanns, ArrayList qanns, ArrayList qanns, ArrayList Date: Thu, 28 May 2026 19:31:58 -0700 Subject: [PATCH 7/7] fix(ia): close Shepherds in processCallback; release before POST in sendIdentify Addresses code-review findings on PR #1553. processCallback (the stated headline fix, previously missing): wrap both Shepherds in try/finally so the no-log early `return rtn` (after beginDBTransaction) and any throw from the detect/identify or IA.intake branches release the connection. These were the source of the IBEISIA.processCallback:* stuck entries on dbconnections.jsp. `newAnns` is hoisted above the try so the post-commit identification block still reads it. sendIdentify: the earlier try/finally wrap held the DB connection across the RestClient.post(...) call to IA. Move the POST to after the finally so the pooled connection is released before the network round-trip (matching the pre-PR behavior, which closed before posting). `map` is hoisted above the try. Early-return paths stay inside the try, so they still close on the way out. Compiles clean; reviewed by Codex. Co-Authored-By: Claude Opus 4.8 (1M context) --- .../java/org/ecocean/identity/IBEISIA.java | 30 +++++++++++++++---- 1 file changed, 25 insertions(+), 5 deletions(-) diff --git a/src/main/java/org/ecocean/identity/IBEISIA.java b/src/main/java/org/ecocean/identity/IBEISIA.java index 2890549d07..75059dd6ef 100644 --- a/src/main/java/org/ecocean/identity/IBEISIA.java +++ b/src/main/java/org/ecocean/identity/IBEISIA.java @@ -242,9 +242,11 @@ public static JSONObject sendIdentify(ArrayList qanns, ArrayList map = new HashMap(); try { - HashMap map = new HashMap(); map.put("callback_url", callbackUrl(baseUrl)); map.put("jobid", taskId); if (queryConfigDict != null) map.put("query_config_dict", queryConfigDict); @@ -371,10 +373,14 @@ public static JSONObject sendIdentify(ArrayList qanns, ArrayList logs = IdentityServiceLog.loadByTaskID(taskID, "IBEISIA", myShepherd); rtn.put("_logs", logs); if (((logs == null) || (logs.size() < 1)) && !fromEmbeddingExtraction) return rtn; - JSONObject newAnns = null; String type = getTaskType(logs); System.out.println("**** type ---------------> [" + type + "]"); if ("detect".equals(type)) { @@ -1438,7 +1447,13 @@ a few lines below here still has output (in mlservice-free IA.json) such as: rtn.put("error", "unknown task action type " + type); } myShepherd.commitDBTransaction(); - myShepherd.closeDBTransaction(); + } finally { + // Always release the connection: the no-log early return above and + // any throw from the detect/identify branches previously leaked this + // Shepherd (the IBEISIA.processCallback:* stuck dbconnections entries). + // rollbackAndClose after a successful commit is a no-op rollback + close. + myShepherd.rollbackAndClose(); + } boolean skipIdent = Util.booleanNotFalse(IA.getProperty(context, "IBEISIADisableIdentification")); @@ -1449,6 +1464,7 @@ a few lines below here still has output (in mlservice-free IA.json) such as: Shepherd myShepherd2 = new Shepherd(context); myShepherd2.setAction("IBEISIA.processCallback-IA.intake"); myShepherd2.beginDBTransaction(); + try { Task parentTask = Task.load(taskID, myShepherd2); // Task parametersSkipIdent looks at the parent task.. It works for non-ID Wildbooks. If you are sending multiple annotations from a // single image, and some need @@ -1525,7 +1541,11 @@ a few lines below here still has output (in mlservice-free IA.json) such as: "[INFO]: No annotations were suitable for identification. Check resulting identification class(es)."); myShepherd2.rollbackDBTransaction(); } - myShepherd2.rollbackAndClose(); + } finally { + // Guarantee release if Task.load / getObjectById / intakeAnnotations + // throws; previously a throw here skipped rollbackAndClose entirely. + myShepherd2.rollbackAndClose(); + } } return rtn; }