multiple features fix

MICommunity · Feb 19, 2025 · 149a9cb · 149a9cb
1 parent 8a7fc3e
commit 149a9cb
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Showing 5 changed files with 28 additions and 11 deletions.
diff --git a/src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/file/processing/FileFormater.java b/src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/file/processing/FileFormater.java
@@ -352,6 +352,8 @@ public void addInteractionType() {
      * This method includes adding feature columns for each participant (bait or prey) based on available features.
      */
     private void addAllFeatures() {
+        System.out.println("prey features: " + preyFeatures.size());
+        System.out.println("bait features: " + baitFeatures.size());
         int numberOfColumnsToAdd = getNumberOfFeaturesColumns() * 6;
         ArrayList<String> featuresHeader = getFeaturesHeader();
         String[] extendedHeader = Arrays.copyOf(header, header.length + numberOfColumnsToAdd);

diff --git a/...uk/ac/ebi/intact/psi/mi/xmlmaker/file/processing/ParticipantAndInteractionCreatorGui.java b/...uk/ac/ebi/intact/psi/mi/xmlmaker/file/processing/ParticipantAndInteractionCreatorGui.java
@@ -41,7 +41,6 @@ public class ParticipantAndInteractionCreatorGui {
     private final JComboBox<String> baitOrganism = new JComboBox<>();
     private final JComboBox<String> baitIdDatabase = new JComboBox<>();
 
-//    private final JComboBox<String> preyExperimentalPreparation = new JComboBox<>();
     private final List<JComboBox<String>> preyExperimentalPreparationList = new ArrayList<>();
     private final List<String> preyExperimentalPreparationNames = new ArrayList<>();
 
@@ -299,8 +298,6 @@ private void updateExperimentalPreparations(int count, JPanel experimentalPrepar
         experimentalPreparationsPanel.repaint();
     }
 
-
-
     /**
      * Retrieves the selected bait experimental preparations as a semicolon-separated string.
      *
@@ -480,11 +477,11 @@ private JPanel createFeatureOptionPanel(boolean bait) {
         numberOfFeature.addChangeListener(e -> {
             int value = (int) numberOfFeature.getValue();
             SwingUtilities.invokeLater(() -> {
-                if (bait){
-                    baitFeaturesComboBoxes.clear();
-                } else {
-                    preyFeaturesComboBoxes.clear();
-                }
+//                if (bait){
+//                    baitFeaturesComboBoxes.clear();
+//                } else {
+//                    preyFeaturesComboBoxes.clear();
+//                }
                 updateFeaturePanel(featureContainerPanel, value, bait);
             });
         });
@@ -512,6 +509,11 @@ private void updateFeaturePanel(JPanel featureContainerPanel, int count, boolean
         }
         for (int i = currentCount - 1; i >= count; i--) {
             featureContainerPanel.remove(i);
+            if (bait){
+                baitFeaturesComboBoxes.remove(i);
+            } else {
+                preyFeaturesComboBoxes.remove(i);
+            }
         }
 
         featureContainerPanel.revalidate();
@@ -572,8 +574,12 @@ public List<Map<String, String>> getFeaturesData(boolean bait){
         List<Map<String, String>> featuresData;
         if (bait) {
             featuresData = getFeaturesDataFromCombobox(baitFeaturesComboBoxes, true);
+            System.out.println("comboboxes: " + baitFeaturesComboBoxes.size());
+            System.out.println("features data:" + featuresData.size());
         } else {
             featuresData = getFeaturesDataFromCombobox(preyFeaturesComboBoxes, false);
+            System.out.println("comboboxes: " + preyFeaturesComboBoxes.size());
+            System.out.println("features data:" + featuresData.size());
         }
 
         return featuresData;

diff --git a/src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/jami/xml/InteractionWriter.java b/src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/jami/xml/InteractionWriter.java
@@ -53,6 +53,8 @@ public class InteractionWriter {
     @Getter @Setter
     private String name;
 
+    public final List<String> skippedParticipants = new ArrayList<>();
+
     /**
      * Constructs a InteractionWriter instance with the given dependencies.
      *
@@ -226,6 +228,7 @@ private void writeInteractionsToFile(List<XmlInteractionEvidence> interactions,
             LOGGER.error("Error during PSI-XML writing", e);
         } finally {
             closeWriter(xmlInteractionWriter);
+            XmlMakerUtils.showInfoDialog("Participant skipped because of missing data: " + skippedParticipants);
             XmlMakerUtils.showInfoDialog("PSI-XML writing completed successfully. File saved at: " + saveLocation);
         }
     }

diff --git a/src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/jami/xml/InteractionsCreator.java b/src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/jami/xml/InteractionsCreator.java
@@ -32,6 +32,7 @@ public class InteractionsCreator {
     public final List<XmlInteractionEvidence> xmlModelledInteractions = new ArrayList<>();
     public final List<Map<String, String>> dataList = new ArrayList<>();
 
+
     @Setter
     Map<String, Integer> columnAndIndex;
     public String sheetSelected;
@@ -105,6 +106,14 @@ public XmlParticipantEvidence createParticipant(Map<String, String> data) {
         for (DataTypeAndColumn requiredColumn : required) {
             if (data.get(requiredColumn.name) == null || data.get(requiredColumn.name).trim().isBlank()) {
                 LOGGER.warning(requiredColumn.name + " is required but missing or empty.");
+
+                if (!(data.get(PARTICIPANT_NAME.name) == null) || !data.get(PARTICIPANT_NAME.name).trim().isBlank()) {
+                    interactionWriter.skippedParticipants.add(data.get(PARTICIPANT_NAME.name));
+                }
+                else if (!(data.get(PARTICIPANT_ID.name) == null) || !data.get(PARTICIPANT_ID.name).trim().isBlank()) {
+                    interactionWriter.skippedParticipants.add(data.get(PARTICIPANT_ID.name));
+                }
+
                 return null;
             }
         }
@@ -210,8 +219,6 @@ private Interactor createParticipantByType(String participantType, String name,
                 break;
             case "gene":
                 participant = new XmlGene(name, organism, uniqueId);
-                CvTerm geneType = utils.fetchTerm("gene");
-                participant.setInteractorType(geneType); // needed as the type is not set automatically by jami here
                 break;
             default:
                 break;

diff --git a/src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/utils/XmlMakerUtils.java b/src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/utils/XmlMakerUtils.java
@@ -30,7 +30,6 @@ public class XmlMakerUtils {
     private static final Map<String, CvTerm> nameToCvTerm = new ConcurrentHashMap<>();
     private static final Map<String, String> nameToTaxIdCache = new ConcurrentHashMap<>();
     static final OLSClient olsClient = new OLSClient(new OLSWsConfig());
-
     static {
         try {
             FileHandler fileHandler = new FileHandler("xmlmakerutils.log", true);