Extensions to the SOP classes and Transfer Syntaxes hardcoded lists. (#…

…516) * New datastructs to support schema upcoming change * New attributes and functions to support confs/server.xml schema upcoming change * Planned #498 course of action (TODOs) * Implemented support for extended SOP classes and Transfer Syntaxes * Tweaks in comments * Tweaks in comments * Added licence to new files * Fixed licence header on new datastructures * Fixed* uninitialized server settings problems. *shadowed TransfersStorage's changes in this branch temporarily Signed-off-by: Almeida-a <[email protected]> * Implemented the recently added signatures in LegacyServerSettings's interfaces Signed-off-by: Almeida-a <[email protected]> * Parser from AdditionalTransferSyntax to TransferSyntax from dcm4che; Code rearrangement for readability Signed-off-by: Almeida-a <[email protected]> * TransfersStorage refactor, tweaks and tests * Everything working, with the only task missing being the new configs appearing in the dicoogle's GUI Signed-off-by: Almeida-a <[email protected]> * New SOP classes now appear on transfer options; New transfer syntaxes appear now only on new SOP Classes; * Problem on new SOP classes not showing on the list was because I forgot to add them to SOP array (SOPList.updateList) * The new transfer syntaxes don't appear on the hardcoded SOP list because it is static. To be solved asap Signed-off-by: Almeida-a <[email protected]> * Fixed problem of hardcoded SOP list not containing added transfer syntaxes Signed-off-by: Almeida-a <[email protected]> * Set default TSs for new SOP classes Signed-off-by: Almeida-a <[email protected]> * Minor tweaks/cleanup and optimization. * Optimized the use of TransfersStorage.namesUidMapping (updated to static variable) * TODO#498 in ServerSettingsManager was marked with feedback keyword, as the issue is a mere conceptual one, and doesn't affect any functional operations in dicoogle. Signed-off-by: Almeida-a <[email protected]> * "Additionals" related functions are now a no-op Signed-off-by: Almeida-a <[email protected]> * Refactored additional datastructs following the first feedback from #516 pull request. * Format was switched to more verbose parameters, like explicitVR, encapsulated, etc.; * Invalid, and therefore, suppressed additionals leave a logger warning indicating the problem in concrete; * ServerSettingsTest.testAdditionals cover the referenced additions. Signed-off-by: Almeida-a <[email protected]> * #516 pull request's 2nd review changes. * Changed defaults * Removed Additional datastructs' id and thus refactored isValid logs * Changed JacksonXmlProperty notations to JsonProperty (and fixed typo on attribute' name reference) * Other suggested minor changes Signed-off-by: Almeida-a <[email protected]> * Minor changes in code for readability Signed-off-by: Almeida-a <[email protected]> * #498 #516 Reference fix Signed-off-by: Almeida-a <[email protected]> * #516 Moved from JsonProperty to JacksonXmlProperty Also, removed unused imports * #516 Suppressed logs in ServerSettingsTest$testAdditionals --------- Signed-off-by: Almeida-a <[email protected]>
bioinformatics-ua · Jun 7, 2023 · 3a84aba · 3a84aba
1 parent ecafbad
commit 3a84aba
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Showing 13 changed files with 666 additions and 81 deletions.
diff --git a/dicoogle/src/main/java/pt/ua/dicoogle/core/settings/LegacyServerSettings.java b/dicoogle/src/main/java/pt/ua/dicoogle/core/settings/LegacyServerSettings.java
@@ -23,6 +23,8 @@
 import org.dcm4che2.data.UID;
 import org.slf4j.LoggerFactory;
 import pt.ua.dicoogle.core.XMLSupport;
+import pt.ua.dicoogle.sdk.datastructs.AdditionalSOPClass;
+import pt.ua.dicoogle.sdk.datastructs.AdditionalTransferSyntax;
 import pt.ua.dicoogle.sdk.datastructs.MoveDestination;
 import pt.ua.dicoogle.sdk.datastructs.SOPClass;
 import pt.ua.dicoogle.sdk.settings.server.ServerSettings;
@@ -664,10 +666,28 @@ public void setSOPClasses(Collection<SOPClass> classes) {
                 + " in legacy configuration file \"config.xml\". Please upgrade your server to use the latest format.");
     }
 
+    public void setAdditionalSOPClasses(Collection<AdditionalSOPClass> classes) {
+        // No-op
+    }
+
+    public void setAdditionalTransferSyntaxes(Collection<AdditionalTransferSyntax> syntaxes) {
+        // No-op
+    }
+
     public List<SOPClass> getSOPClasses() {
         return SOPList.getInstance().asSOPClassList();
     }
 
+    public List<AdditionalSOPClass> getAdditionalSOPClass() {
+        // No-op
+        return Collections.emptyList();
+    }
+
+    public List<AdditionalTransferSyntax> getAdditionalTransferSyntax() {
+        // No-op
+        return Collections.emptyList();
+    }
+
     public void setDIMSERspTimeout(int timeout) {
         this.DIMSERspTimeout = timeout;
     }
@@ -1264,7 +1284,7 @@ public List<String> getDefaultStorage() {
         public String getNodeName() {
             return LegacyServerSettings.this.getNodeName();
         }
-
+        
         @JsonGetter("encrypt-users-file")
         @Override
         public boolean isEncryptUsersFile() {
@@ -1292,6 +1312,7 @@ public Archive getArchiveSettings() {
     @JsonAutoDetect(isGetterVisibility = JsonAutoDetect.Visibility.NONE,
             getterVisibility = JsonAutoDetect.Visibility.NONE, setterVisibility = JsonAutoDetect.Visibility.NONE)
     protected class StubDicomServices implements DicomServices {
+
         @Override
         public void setAETitle(String aetitle) {
             LegacyServerSettings.this.setAETitle(aetitle);
@@ -1342,6 +1363,16 @@ public void setSOPClasses(Collection<SOPClass> sopClasses) {
             LegacyServerSettings.this.setSOPClasses(sopClasses);
         }
 
+        @Override
+        public void setAdditionalSOPClasses(Collection<AdditionalSOPClass> additionalSOPClasses) {
+            LegacyServerSettings.this.setAdditionalSOPClasses(additionalSOPClasses);
+        }
+
+        @Override
+        public void setAdditionalTransferSyntaxes(Collection<AdditionalTransferSyntax> additionalTransferSyntaxes) {
+            LegacyServerSettings.this.setAdditionalTransferSyntaxes(additionalTransferSyntaxes);
+        }
+
         @Override
         public ServiceBase getStorageSettings() {
             return LegacyServerSettings.this.getStorageSettings();
@@ -1387,6 +1418,16 @@ public Collection<SOPClass> getSOPClasses() {
             return LegacyServerSettings.this.getSOPClasses();
         }
 
+        @Override
+        public Collection<AdditionalSOPClass> getAdditionalSOPClasses() {
+            return LegacyServerSettings.this.getAdditionalSOPClass();
+        }
+
+        @Override
+        public Collection<AdditionalTransferSyntax> getAdditionalTransferSyntaxes() {
+            return LegacyServerSettings.this.getAdditionalTransferSyntax();
+        }
+
         @Override
         public List<MoveDestination> getMoveDestinations() {
             return LegacyServerSettings.this.getMoveDestinations();

diff --git a/dicoogle/src/main/java/pt/ua/dicoogle/core/settings/ServerSettingsManager.java b/dicoogle/src/main/java/pt/ua/dicoogle/core/settings/ServerSettingsManager.java
@@ -25,15 +25,20 @@
 import org.slf4j.LoggerFactory;
 import org.xml.sax.SAXException;
 import pt.ua.dicoogle.core.XMLSupport;
-import pt.ua.dicoogle.utils.Platform;
+import pt.ua.dicoogle.sdk.datastructs.AdditionalSOPClass;
+import pt.ua.dicoogle.sdk.datastructs.AdditionalTransferSyntax;
 import pt.ua.dicoogle.sdk.settings.server.ServerSettings;
+import pt.ua.dicoogle.server.SOPList;
+import pt.ua.dicoogle.server.TransfersStorage;
+import pt.ua.dicoogle.utils.Platform;
 
 import java.io.*;
 import java.net.URL;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.Objects;
+import java.util.stream.Collectors;
 
 /**
  * @author Eduardo Pinho <[email protected]>
@@ -98,6 +103,21 @@ public static void init() throws IOException {
         } else {
             // use main configuration file
             inner = loadSettingsAt(MAIN_CONFIG_PATH);
+            /*
+             TODO#498 (feedback needed) export this following block of code to somewhere more fitting
+             Check which new UIDs from "additional*" tags are valid (SOP Class UIDs can skip this if
+             they are already present in the transfer options: e.g. in SOPList) and filter them
+             Validate and filter Transfer Syntaxes;
+            */
+            inner.getDicomServicesSettings()
+                    .setAdditionalTransferSyntaxes(inner.getDicomServicesSettings().getAdditionalTransferSyntaxes()
+                            .stream().filter(AdditionalTransferSyntax::isValid).collect(Collectors.toList()));
+            TransfersStorage.completeList();
+            // Validate and filter SOP Classes; add them to SOPList
+            inner.getDicomServicesSettings()
+                    .setAdditionalSOPClasses(inner.getDicomServicesSettings().getAdditionalSOPClasses().stream()
+                            .filter(AdditionalSOPClass::isValid).collect(Collectors.toList()));
+            SOPList.getInstance().updateList();
         }
     }
 

diff --git a/dicoogle/src/main/java/pt/ua/dicoogle/core/settings/part/DicomServicesImpl.java b/dicoogle/src/main/java/pt/ua/dicoogle/core/settings/part/DicomServicesImpl.java
@@ -21,6 +21,8 @@
 import com.fasterxml.jackson.annotation.*;
 import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlElementWrapper;
 import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlProperty;
+import pt.ua.dicoogle.sdk.datastructs.AdditionalSOPClass;
+import pt.ua.dicoogle.sdk.datastructs.AdditionalTransferSyntax;
 import pt.ua.dicoogle.sdk.datastructs.MoveDestination;
 import pt.ua.dicoogle.sdk.datastructs.SOPClass;
 import pt.ua.dicoogle.sdk.settings.server.ServerSettings;
@@ -118,6 +120,12 @@ private void setAllowedHostnames_(Object o) {
     @JsonProperty("sop-classes")
     private Collection<SOPClass> sopClasses = Collections.emptyList();
 
+    @JsonProperty("additional-sop-classes")
+    private Collection<AdditionalSOPClass> additionalSOPClasses = Collections.emptyList();
+
+    @JsonProperty("additional-transfer-syntaxes")
+    private Collection<AdditionalTransferSyntax> additionalTransferSyntaxes = Collections.emptyList();
+
     @JacksonXmlElementWrapper(localName = "move-destinations")
     private List<MoveDestination> moveDestinations;
 
@@ -212,6 +220,35 @@ public void setSOPClasses(Collection<SOPClass> sopClasses) {
         this.sopClasses = sopClasses;
     }
 
+    @Override
+    @JsonGetter("additional-sop-classes")
+    public Collection<AdditionalSOPClass> getAdditionalSOPClasses() {
+        return this.additionalSOPClasses;
+    }
+
+    @Override
+    @JsonSetter("additional-sop-classes")
+    public void setAdditionalSOPClasses(Collection<AdditionalSOPClass> additionalSOPClasses) {
+        if (additionalSOPClasses == null)
+            return; // Keep default emptyList value
+
+        this.additionalSOPClasses = additionalSOPClasses;
+    }
+
+    @Override
+    @JsonGetter("additional-transfer-syntaxes")
+    public Collection<AdditionalTransferSyntax> getAdditionalTransferSyntaxes() {
+        return this.additionalTransferSyntaxes;
+    }
+
+    @Override
+    @JsonSetter("additional-transfer-syntaxes")
+    public void setAdditionalTransferSyntaxes(Collection<AdditionalTransferSyntax> additionalTransferSyntaxes) {
+        if (additionalTransferSyntaxes == null)
+            return; // Keep default emptyList value
+        this.additionalTransferSyntaxes = additionalTransferSyntaxes;
+    }
+
     @Override
     @JsonGetter("move-destinations")
     public List<MoveDestination> getMoveDestinations() {
@@ -258,10 +295,14 @@ public boolean removeMoveDestination(String aetitle) {
 
     @Override
     public String toString() {
-        return "DicomServicesImpl{" + "aetitle='" + aetitle + '\'' + ", deviceDescription='" + deviceDescription + '\''
-                + ", allowedAETitles=" + allowedAETitles + ", priorityAETitles=" + priorityAETitles
-                + ", allowedLocalInterfaces=" + allowedLocalInterfaces + ", allowedHosts=" + allowedHosts
-                + ", defaultTS=" + defaultTS + ", sopClasses=" + sopClasses + ", moveDestinations=" + moveDestinations
-                + ", storage=" + storage + ", queryRetrieve=" + queryRetrieve + '}';
+        return new StringJoiner(", ", DicomServicesImpl.class.getSimpleName() + "[", "]")
+                .add("aetitle='" + aetitle + "'").add("deviceDescription='" + deviceDescription + "'")
+                .add("allowedAETitles=" + allowedAETitles).add("priorityAETitles=" + priorityAETitles)
+                .add("allowedLocalInterfaces=" + allowedLocalInterfaces).add("allowedHosts=" + allowedHosts)
+                .add("defaultTS=" + defaultTS).add("sopClasses=" + sopClasses)
+                .add("additionalSOPClasses=" + additionalSOPClasses)
+                .add("additionalTransferSyntaxes=" + additionalTransferSyntaxes)
+                .add("moveDestinations=" + moveDestinations).add("storage=" + storage)
+                .add("queryRetrieve=" + queryRetrieve).toString();
     }
 }
diff --git a/dicoogle/src/main/java/pt/ua/dicoogle/server/SOPList.java b/dicoogle/src/main/java/pt/ua/dicoogle/server/SOPList.java
@@ -23,10 +23,14 @@
 import org.dcm4che2.data.UID;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import pt.ua.dicoogle.core.settings.ServerSettingsManager;
+import pt.ua.dicoogle.sdk.datastructs.AdditionalSOPClass;
 import pt.ua.dicoogle.sdk.datastructs.SOPClass;
+import pt.ua.dicoogle.sdk.settings.server.ServerSettings;
 import pt.ua.dicoogle.server.web.management.SOPClassSettings;
 
 import java.util.*;
+import java.util.stream.Collectors;
 
 /**
  * Support class for keeping SOPClass/TransferSyntax association
@@ -142,6 +146,7 @@ public static synchronized SOPList getInstance() {
     private SOPList() {
         table = new Hashtable<>();
 
+        // Hardcoded (pre-#498) SOPs
         for (String sop : SOP) {
             table.put(sop, new TransfersStorage());
         }
@@ -206,7 +211,7 @@ public synchronized int updateTS(String UID, boolean[] p, boolean a) {
 
 
     public int updateTSFieldByTsUID(String sopUID, String tsUID, boolean value) {
-        return updateTSField(sopUID, TransfersStorage.globalTransferUIDsMap.get(tsUID), value);
+        return updateTSField(sopUID, TransfersStorage.getGlobalTransferUIDsMap().get(tsUID), value);
     }
 
 
@@ -224,8 +229,8 @@ public synchronized int updateTSField(String UID, String name, boolean value) {
         TS = table.get(UID);
 
         int index = -1;
-        for (int i = 0; i < TransfersStorage.globalTransferMap.size(); i++) {
-            if (TransfersStorage.globalTransferMap.get(i).equals(name)) {
+        for (int i = 0; i < TransfersStorage.getGlobalTransferMap().size(); i++) {
+            if (TransfersStorage.getGlobalTransferMap().get(i).equals(name)) {
                 index = i;
                 break;
             }
@@ -332,7 +337,7 @@ public String getSOPList() {
             TransfersStorage ts = getTS(uid);
             for (int i = 0; i < ts.getTS().length; i++) {
                 JSONObject tsobj = new JSONObject();
-                String name = ts.globalTransferMap.get(i);
+                String name = TransfersStorage.getGlobalTransferMap().get(i);
                 boolean value = ts.getTS()[i];
                 tsobj.put("name", name);
                 tsobj.put("value", value);
@@ -354,4 +359,31 @@ public List<SOPClass> asSOPClassList() {
         }
         return l;
     }
+
+    public void updateList() {
+
+        // Add the extras on SOP from getSettings()
+        ServerSettings settings = ServerSettingsManager.getSettings();
+        // Get all new SOP classes' UID (not existing in String[] SOP)
+        Collection<String> newSOPs = settings.getDicomServicesSettings().getAdditionalSOPClasses().stream()
+                .map(AdditionalSOPClass::getUid)
+                .filter(newSOPUID -> !Arrays.asList(SOP).contains(newSOPUID))
+                .collect(Collectors.toList());
+        // Refresh hardcoded SOPs (outdated TransfersStorage)
+        Arrays.asList(SOP).forEach(sop -> table.put(sop, new TransfersStorage()));
+        // Add "Additional" SOPs to table w/ default transfer syntaxes
+        newSOPs.forEach(sop -> {
+            TransfersStorage ts = new TransfersStorage();
+            ts.setDefaultSettings();
+            table.put(sop, ts);
+        });
+        // Add them to SOP
+        newSOPs.addAll(Arrays.asList(SOP));
+        SOP = newSOPs.toArray(new String[0]);
+    }
+
+    public void updateList(Collection<AdditionalSOPClass> additionalSOPClasses) {
+        additionalSOPClasses.forEach(elem -> table.put(elem.getUid(), new TransfersStorage()));
+    }
+
 }