update dev

.github/workflows/build_package.yml

@@ -14,9 +14,9 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up JDK 8
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           distribution: 'zulu'
           java-version: '8'

.github/workflows/codeql-analysis.yml

@@ -37,9 +37,9 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up JDK 8
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           distribution: 'zulu'
           java-version: '8'

.github/workflows/create-release.yml

@@ -12,9 +12,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up JDK 8
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           distribution: 'zulu'
           java-version: '8'
@@ -44,7 +44,7 @@ jobs:
           && !( contains(github.event.inputs.versionTag, 'alpha')
           || contains(github.event.inputs.versionTag, 'beta')
           || contains(github.event.inputs.versionTag, 'rc')) }}
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         with:
           github-token: ${{secrets.JOHNNY_Q5_REPORTS_TOKEN}}
           script: |
@@ -58,7 +58,7 @@ jobs:
           && ( contains(github.event.inputs.versionTag, 'alpha')
           || contains(github.event.inputs.versionTag, 'beta')
           || contains(github.event.inputs.versionTag, 'rc')) }}
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         with:
           github-token: ${{secrets.JOHNNY_Q5_REPORTS_TOKEN}}
           script: |
@@ -87,7 +87,7 @@ jobs:
         run: git push
 
       - name: Open PR with version bump
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         with:
           github-token: ${{secrets.JOHNNY_Q5_REPORTS_TOKEN}}
           script: |

.github/workflows/nexus-publish-snapshots.yml

@@ -16,9 +16,9 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up JDK 8
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           distribution: 'zulu'
           java-version: '8'

.github/workflows/run_tests.yml

@@ -14,9 +14,9 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up JDK 8
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           distribution: 'zulu'
           java-version: '8'

pom.xml

@@ -5,7 +5,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>projectwizard-portlet</artifactId>
 	<groupId>life.qbic</groupId>
-	<version>1.14.0</version>
+	<version>1.15.1</version>
 	<name>ProjectWizard Portlet</name>
 	<url>https://github.com/qbicsoftware/projectwizard-portlet</url>
 	<description>Creates hierarchical experiments using factorial design.</description>

src/main/java/life/qbic/projectwizard/control/ExperimentImportController.java

@@ -475,6 +475,9 @@ public void buttonClick(ClickEvent event) {
             }
             omero.registerSamples(project, description, imagableSamples);
           }
+          if(getImportType().equals(ExperimentalDesignType.Proteomics_MassSpectrometry)) {
+            correctFreeTextLCMSMethods(complexExperiments, new HashSet<>(vocabs.getLcmsMethods()));
+          }
           openbisCreator.registerProjectWithExperimentsAndSamplesBatchWise(samples, description,
               complexExperiments, view.getProgressBar(), view.getProgressLabel(),
               new RegisteredSamplesReadyRunnable(view, control), entitiesToUpdate,
@@ -535,7 +538,7 @@ private Map<String, Map<String, Object>> fixSamplePrepProperties(
 
       private Collection<? extends OpenbisExperiment> collectComplexExperiments(
           Map<String, Map<String, Object>> propsMap, ExperimentType type) {
-        List<OpenbisExperiment> res = new ArrayList<OpenbisExperiment>();
+        List<OpenbisExperiment> res = new ArrayList<>();
         if (propsMap != null) {
           for (String code : propsMap.keySet()) {
             res.add(new OpenbisExperiment(code, type, propsMap.get(code)));
@@ -547,6 +550,20 @@ private Collection<? extends OpenbisExperiment> collectComplexExperiments(
     view.getRegisterButton().addClickListener(cl);
   }
 
+  private void correctFreeTextLCMSMethods(List<OpenbisExperiment> complexExperiments, Set<String> lcmsMethods) {
+    String LCMS_KEY = "Q_MS_LCMS_METHOD";
+    for(OpenbisExperiment experiment : complexExperiments) {
+      if(experiment.getType().equals(ExperimentType.Q_MS_MEASUREMENT)) {
+        Map<String, Object> metadata = experiment.getMetadata();
+        String lcmsInput = (String) metadata.get(LCMS_KEY);
+        if(!lcmsMethods.contains(lcmsInput)) {
+          metadata.put(LCMS_KEY, "SPECIAL_METHOD");
+          metadata.put("Q_MS_LCMS_METHOD_INFO", lcmsInput);
+        }
+      }
+    }
+  }
+
   private String replaceChangedMetadata(String tsvContent,
       Map<String, String> metadataReplacements) {
     logger.warn("Debug: String replacement");
@@ -767,7 +784,7 @@ private void prepareCompletionDialog() {
       for (String method : vocabs.getLcmsMethods()) {
         lcmsMap.put(method, method);
       }
-      catToVocabulary.put("LCMS Method", lcmsMap);
+      //catToVocabulary.put("LCMS Method", lcmsMap); <- freetext now for Proteomics import
       //// MC Device : Q_MS_DEVICE : Q_MS_DEVICES
       catToVocabulary.put("MS Device", vocabs.getMSDeviceMap());
       //// Sample Cleanup (peptide) : Q_PROTEIN_PURIFICATION_METHODS
@@ -799,6 +816,7 @@ private void prepareCompletionDialog() {
               "MS Device", "Fractionation Type", "Enrichment Method", "Labeling Type",
               "LCMS Method", "Digestion Method", "Digestion Enzyme", "Sample Preparation",
               "Species", "Tissue", "Sample Cleanup (Protein)", "Sample Cleanup (Peptide)")));
+      parsedCategoryToValues.remove("LCMS Method");
       // logger.warn(parsedCategoryToValues);
     }
     if (!getImportType().equals(ExperimentalDesignType.Metabolomics_LCMS)) {
@@ -974,7 +992,7 @@ else if (b.getSampleType().contains("Sample Extract")) {
             // ms experiments
             keyToFields.put("Q_MS_DEVICE", new HashSet<>(Arrays.asList("MS Device")));
             keyToFields.put("Q_CHROMATOGRAPHY_TYPE", new HashSet<>(Arrays.asList("LC Column")));
-            keyToFields.put("Q_MS_LCMS_METHOD", new HashSet<>(Arrays.asList("LCMS Method")));
+            //keyToFields.put("Q_MS_LCMS_METHOD", new HashSet<>(Arrays.asList("LCMS Method")));
             keyToFields.put("Q_MS_PURIFICATION_METHOD", new HashSet<>(
                 Arrays.asList("Sample Cleanup (Protein)", "Sample Cleanup (Peptide)")));
             // TODO collisions between cleanup
@@ -1252,8 +1270,8 @@ else if (b.getSampleType().contains("Sample Extract")) {
                 uniqueCodeToBarcode.put(uniqueID, code);
                 uniqueNumericIDToBarcode.put(numericID, code);
                 List<String> parents = t.getParentIDs();
-                t.setParents(new ArrayList<ISampleBean>());
-                List<String> newParents = new ArrayList<String>();
+                t.setParents(new ArrayList<>());
+                List<String> newParents = new ArrayList<>();
                 for (String parentID : parents) {
                   if (getImportType().equals(ExperimentalDesignType.Proteomics_MassSpectrometry)
                       || getImportType().equals(ExperimentalDesignType.Metabolomics_LCMS)) {

src/main/java/life/qbic/projectwizard/control/WizardDataAggregator.java

@@ -742,7 +742,7 @@ public List<AOpenbisSample> createPoolingSamples(Map<String, List<AOpenbisSample
       else
         testPools = new ArrayList<AOpenbisSample>();
       String exp = dummy.getValueMap().get("EXPERIMENT");
-      List<Property> factors = new ArrayList<Property>();
+      List<Property> factors = new ArrayList<>();
       for (String secName : pools.keySet()) {
         incrementOrCreateBarcode();
         String parents = "";
@@ -778,9 +778,9 @@ public List<AOpenbisSample> createPoolingSamples(Map<String, List<AOpenbisSample
    */
   private List<List<AOpenbisSample>> buildTestSamples(List<AOpenbisSample> extracts,
       Map<String, Character> classChars) {
-    List<List<AOpenbisSample>> tests = new ArrayList<List<AOpenbisSample>>();
+    List<List<AOpenbisSample>> tests = new ArrayList<>();
     for (int j = 0; j < techTypeInfo.size(); j++) {// different technologies
-      List<AOpenbisSample> techTests = new ArrayList<AOpenbisSample>();
+      List<AOpenbisSample> techTests = new ArrayList<>();
       int techReps = techTypeInfo.get(j).getReplicates();
       String sampleType = techTypeInfo.get(j).getTechnology();
       int expNum = experiments.size() - techTypeInfo.size() + j;
@@ -847,7 +847,7 @@ public void setInheritExtracts(boolean inherit) {
   private List<AOpenbisSample> parseEntities(List<Sample> entities, boolean copy)
       throws JAXBException {
     oldCodesToNewCodes = new HashMap<String, String>();
-    List<AOpenbisSample> res = new ArrayList<AOpenbisSample>();
+    List<AOpenbisSample> res = new ArrayList<>();
     String expCode = "";
     if (entities.get(0).getExperiment() != null) {
       expCode = entities.get(0).getExperiment().getCode();
@@ -899,7 +899,7 @@ private List<AOpenbisSample> parseEntities(List<Sample> entities, boolean copy)
    */
   private List<AOpenbisSample> parseExtracts(List<Sample> extracts,
       Map<Sample, List<String>> childParentsMap) throws JAXBException {
-    List<AOpenbisSample> res = new ArrayList<AOpenbisSample>();
+    List<AOpenbisSample> res = new ArrayList<>();
     String exp = "";
     if (extracts.get(0).getExperiment() != null) {
       exp = extracts.get(0).getExperiment().getCode();