Merge pull request #609 from robinschmid/tomasmaster_library_submit_tag

Small fix of parameter check of deselected/invalid library entries
mzmine · Jun 2, 2019 · 5acbc6e · 5acbc6e
2 parents 30505d6 + 0721b2d
commit 5acbc6e
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/...ain/java/net/sf/mzmine/modules/peaklistmethods/io/spectraldbsubmit/LibrarySubmitTask.java b/...ain/java/net/sf/mzmine/modules/peaklistmethods/io/spectraldbsubmit/LibrarySubmitTask.java
@@ -78,6 +78,8 @@ private enum Result {
   public static final String GNPS_LIBRARY_SUBMIT_URL =
       "http://dorresteinappshub.ucsd.edu:5050/depostsinglespectrum";
 
+  public static final String SOURCE_DESCRIPTION = "mzmine2 library entry submission";
+
   private Logger log = Logger.getLogger(this.getClass().getName());
   private Map<LibrarySubmitIonParameters, DataPoint[]> map;
   private int done = 0;
@@ -261,9 +263,12 @@ private void submitGNPS(String json) {
         // ######################################################
         // NEEDED
         // user pass and json entry
+        //
         entity.addPart("username", new StringBody(USER));
         entity.addPart("password", new StringBody(PASS));
         entity.addPart("spectrum", new StringBody(json));
+        // job description is not entry description
+        entity.addPart("description", new StringBody(SOURCE_DESCRIPTION));
 
         HttpPost httppost = new HttpPost(GNPS_LIBRARY_SUBMIT_URL);
         httppost.setEntity(entity);

diff --git a/.../mzmine/modules/peaklistmethods/io/spectraldbsubmit/view/MSMSLibrarySubmissionWindow.java b/.../mzmine/modules/peaklistmethods/io/spectraldbsubmit/view/MSMSLibrarySubmissionWindow.java
@@ -466,8 +466,8 @@ protected boolean checkParameters() {
     // check
     ArrayList<String> messages = new ArrayList<>();
 
-    boolean checkIon =
-        streamSelection().filter(pn -> !pn.checkParameterValues(messages)).count() == 0;
+    boolean checkIon = streamSelection().filter(ScanSelectPanel::isValidAndSelected)
+        .filter(pn -> !pn.checkParameterValues(messages)).count() == 0;
     boolean checkSubmit = paramSubmit.checkParameterValues(messages);
     boolean checkMeta = paramMeta.checkParameterValues(messages);
     if (checkMeta && checkSubmit && checkIon) {