code refactoring for readability

MICommunity · Feb 14, 2025 · ba04427 · ba04427
1 parent 2a3efd3
commit ba04427
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Showing 7 changed files with 150 additions and 104 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
@@ -50,7 +50,7 @@ public class FileFormater {
     private String[] header = {"Interaction Number", "Input Participant ID", "Input Participant Name",
             "Experimental role", "Input Participant ID database", "Interaction detection method",
             "Participant identification method", "Host organism", "Experimental preparation",
-            "Biological role", "Participant organism"};
+            "Biological role", "Participant organism", "Participant Expressed in organism",};
 
     private final Map<String, Integer> participantCountMap = new HashMap<>();
 
@@ -342,7 +342,7 @@ public void addInteractionType() {
             if (count > 2) {
                 row.add("association");
             } else {
-                row.add("physical interaction");
+                row.add("physical association"); //todo: check with kalpana
             }
         }
     }

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
@@ -43,6 +43,8 @@ public class ParticipantAndInteractionCreatorGui {
     private final JComboBox<String> preyOrganism = new JComboBox<>();
     private final JComboBox<String> preyIdDatabase = new JComboBox<>();
 
+    private final JComboBox<String> preyExpressedInOrganism = new JComboBox<>();
+
     @Getter
     private final JSpinner numberOfExperimentalPrep = new JSpinner(new SpinnerNumberModel(1, 1, 10, 1));
 
@@ -143,10 +145,12 @@ public void setOrganisms() {
         baitOrganism.setEditable(true);
         preyOrganism.setEditable(true);
         hostOrganism.setEditable(true);
+        preyExpressedInOrganism.setEditable(true);
         for (ParticipantOrganism participantOrganism : ParticipantOrganism.values()) {
             preyOrganism.addItem(participantOrganism.name + " (" + participantOrganism.taxId + ")");
             baitOrganism.addItem(participantOrganism.name + " (" + participantOrganism.taxId + ")");
             hostOrganism.addItem(participantOrganism.name + " (" + participantOrganism.taxId + ")");
+            preyExpressedInOrganism.addItem(participantOrganism.name + " (" + participantOrganism.taxId + ")");
         }
     }
 
@@ -180,6 +184,7 @@ public Map<String, String> getParticipantDetails() {
         participantDetails.put(DataForRawFile.PREY_ORGANISM.name,
                 isValueNull(XmlMakerUtils.fetchTaxIdForOrganism(Objects.requireNonNull(preyOrganism.getSelectedItem()).toString()), DataForRawFile.PREY_ORGANISM.name));
         participantDetails.put(DataForRawFile.HOST_ORGANSIM.name, isValueNull(XmlMakerUtils.fetchTaxIdForOrganism(Objects.requireNonNull(hostOrganism.getSelectedItem()).toString()), DataForRawFile.HOST_ORGANSIM.name));
+        participantDetails.put(DataForRawFile.PREY_EXPRESSED_IN_ORGANISM.name, isValueNull(XmlMakerUtils.fetchTaxIdForOrganism(Objects.requireNonNull(preyExpressedInOrganism.getSelectedItem()).toString()), DataForRawFile.PREY_EXPRESSED_IN_ORGANISM.name));
 
         return participantDetails;
     }
@@ -388,6 +393,7 @@ public JPanel createPreyPanel() {
         preyPanel.add(XmlMakerUtils.setComboBoxDimension(preyExperimentalPreparation, DataForRawFile.PREY_EXPERIMENTAL_PREPARATION.name));
         preyPanel.add(XmlMakerUtils.setComboBoxDimension(preyBiologicalRole, DataForRawFile.PREY_BIOLOGICAL_ROLE.name));
         preyPanel.add(XmlMakerUtils.setComboBoxDimension(preyOrganism, DataForRawFile.PREY_ORGANISM.name));
+        preyPanel.add(XmlMakerUtils.setComboBoxDimension(preyExpressedInOrganism, DataForRawFile.PREY_EXPRESSED_IN_ORGANISM.name));
         preyPanel.add(XmlMakerUtils.setComboBoxDimension(preyExperimentalPreparation, DataForRawFile.PREY_EXPERIMENTAL_PREPARATION.name));
 
         JButton createFeatureButton = new JButton("Create feature(s)");

diff --git a/src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/file/processing/content/DataForRawFile.java b/src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/file/processing/content/DataForRawFile.java
@@ -16,6 +16,7 @@ public enum DataForRawFile {
 
     BAIT_ORGANISM("Bait Organism", true, false, false),
     PREY_ORGANISM("Prey Organism", false, false, false),
+    PREY_EXPRESSED_IN_ORGANISM("Prey Expressed In Organism", false, false, false),
 
     FEATURE_TYPE("Feature type", false, false, true),
     FEATURE_START_LOCATION("Feature Start Location", false, false, true),

diff --git a/src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/jami/xml/DataTypeAndColumn.java b/src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/jami/xml/DataTypeAndColumn.java
@@ -18,6 +18,7 @@ public enum DataTypeAndColumn {
     PARTICIPANT_ID_DB("Participant ID database"),
     PARTICIPANT_TYPE("Participant type"),
     PARTICIPANT_ORGANISM("Participant organism"),
+    PARTICIPANT_EXPRESSED_IN_ORGANISM("Participant expressed in organism"),
     EXPERIMENTAL_ROLE("Experimental role"),
     PARTICIPANT_IDENTIFICATION_METHOD("Participant identification method"),
 

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
@@ -16,6 +16,7 @@
 import uk.ac.ebi.intact.psi.mi.xmlmaker.utils.FileUtils;
 
 import javax.xml.datatype.DatatypeConfigurationException;
+import javax.xml.datatype.DatatypeConstants;
 import javax.xml.datatype.DatatypeFactory;
 import javax.xml.datatype.XMLGregorianCalendar;
 import java.io.File;
@@ -143,10 +144,15 @@ private XmlSource initializeSource() {
      * @return the default release date as an {@link XMLGregorianCalendar}.
      * @throws RuntimeException if an error occurs while creating the release date.
      */
+
     private XMLGregorianCalendar createDefaultReleaseDate() {
         try {
             GregorianCalendar calendar = new GregorianCalendar();
-            return DatatypeFactory.newInstance().newXMLGregorianCalendar(calendar);
+            XMLGregorianCalendar xmlGregorianCalendar = DatatypeFactory.newInstance().newXMLGregorianCalendar(calendar);
+            xmlGregorianCalendar.setTimezone(DatatypeConstants.FIELD_UNDEFINED);
+            xmlGregorianCalendar.setTime(DatatypeConstants.FIELD_UNDEFINED, DatatypeConstants.FIELD_UNDEFINED, DatatypeConstants.FIELD_UNDEFINED);
+
+            return xmlGregorianCalendar;
         } catch (DatatypeConfigurationException e) {
             LOGGER.error("Error while creating default release date", e);
             throw new RuntimeException(e);