Code cleaning

README.md

@@ -7,7 +7,7 @@ The PSI-MI XML Maker is a tool designed to create XML files based on the [PSI-MI
 These XML files can later be used in the editor for further processing.
 
 ### How to download?
-- **MacOs** : download the .dmg file
+- **MacOS** : download the .dmg file
 - **Windows** : download the .zip file
 - **Linux** : download the .tar file
 

src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/XmlMakerGui.java

@@ -50,7 +50,7 @@ public XmlMakerGui() {
         this.fileFormaterGui = new FileFormaterGui(excelFileReader);
         this.interactionWriterGui = new InteractionWriterGui(excelFileReader);
         this.interactionsCreatorGui = new InteractionsCreatorGui(excelFileReader,
-                interactionWriterGui.getInteractionWriter(), uniprotMapperGui);
+                interactionWriterGui.getInteractionWriter());
         excelFileReader.registerInputSelectedEventHandler(event -> setUpSheets());
     }
 
@@ -284,11 +284,7 @@ public JPanel createFileFetcher() {
 
         JTextField publicationDatabase = new JTextField("Publication database");
         publicationDatabase.setEditable(true);
-//        JButton textValidationButton = new JButton("Submit");
-//        textValidationButton.addActionListener(e -> excelFileReader.setPublicationId(publicationDatabase.getText()));
         pubmedInputPanel.add(publicationDatabase);
-//        pubmedInputPanel.add(textValidationButton);
-
 
         JTextField publicationTitleField = new JTextField("Publication ID");
         publicationTitleField.setEditable(true);

src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/file/processing/ExcelFileReader.java

@@ -336,8 +336,8 @@ public void checkAndInsertUniprotResultsSeparatedFormat(String idColumnName, int
 
                 String updatedOrganism = null;
                 String participantName = null;
-                String uniprotResult = null;
-                String uniprotResultDb = null;
+                String uniprotResult;
+                String uniprotResultDb;
 
                 if (previousId == null || previousId.isEmpty()) {
                     LOGGER.warning("Skipping row with null or empty ID: " + row);
@@ -528,7 +528,7 @@ public void checkAndInsertUniprotResultsWorkbook(String sheetSelected, String id
      * @return A {@link UniprotResult} object representing the selected UniProt ID, or {@code null} if no entries exist.
      */
     private UniprotResult getOneUniprotId(String previousId, String previousIdDb, String organism) {
-        UniprotGeneralMapperGui mapperGui = new UniprotGeneralMapperGui(uniprotGeneralMapper);
+        UniprotGeneralMapperGui mapperGui = new UniprotGeneralMapperGui();
         ArrayList<UniprotResult> uniprotResults = uniprotGeneralMapper.fetchUniprotResult(previousId, previousIdDb, organism);
         UniprotResult oneUniprotId = null;
 

src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/file/processing/FileFormater.java

@@ -48,8 +48,8 @@ public class FileFormater {
     private List<Map<String, String>> preyFeatures = new ArrayList<>();
 
     private String[] header = {"Interaction Number", "Input Participant ID", "Input Participant Name",
-            "Experimental role", "Input Participant ID database",
-            "Interaction detection method", "Participant identification method", "Experimental preparation",
+            "Experimental role", "Input Participant ID database", "Interaction detection method",
+            "Participant identification method", "Experimental preparation",
             "Biological role", "Participant organism"};
 
     private final Map<String, Integer> participantCountMap = new HashMap<>();

src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/file/processing/FileFormaterGui.java

@@ -3,7 +3,6 @@
 import uk.ac.ebi.intact.psi.mi.xmlmaker.utils.XmlMakerUtils;
 import javax.swing.*;
 import java.awt.*;
-import java.util.List;
 import java.util.Map;
 import java.util.Objects;
 import java.util.logging.Logger;

src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/file/processing/ParticipantAndInteractionCreatorGui.java

@@ -7,10 +7,7 @@
 import javax.swing.*;
 import java.awt.*;
 import java.util.*;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
-import java.util.Objects;
 
 /**
  * The {@code ParticipantAndInteractionCreatorGui} class provides a graphical user interface
@@ -235,11 +232,6 @@ private void updateBaitExperimentalPreparations(int count) {
         int numberExperiments = baitExperimentalPanel.getComponents().length;
 //        baitExperimentalPreparationList.clear();
 
-//        if (numberExperiments > count) {
-//            baitExperimentalPanel.removeAll();
-//            baitExperimentalPreparationList.clear();
-//        }
-
         for (int i = numberExperiments; i < count; i++) {
             JComboBox<String> comboBox = new JComboBox<>();
             comboBox.addItem("Experimental Preparation");
@@ -405,7 +397,6 @@ private void updateFeaturePanels(JPanel featureContainerPanel, int count, boolea
 
     private JPanel createFeaturePanel(int featureNumber, boolean bait) {
         Map<String, JComboBox<String>> comboBoxMap = new HashMap<>();
-        Map<String, Map<String, String>> featureXrefs = new HashMap<>();
 
         JPanel featurePanel = new JPanel(new GridLayout(2, 1));
         featurePanel.setBorder(BorderFactory.createTitledBorder("Create feature " + (featureNumber + 1)));
@@ -423,8 +414,7 @@ private JPanel createFeaturePanel(int featureNumber, boolean bait) {
             featurePanel.add(XmlMakerUtils.setComboBoxDimension(comboBox, attribute.name));
         }
 
-        featurePanel.add(featureXrefPanel(featureNumber, bait));
-//        featureXrefs.put(featureNumber + )
+        featurePanel.add(featureXrefPanel(bait));
 
         setFeatureType(comboBoxMap.get(DataForRawFile.FEATURE_TYPE.name));
         setFeatureRangeType(comboBoxMap.get(DataForRawFile.FEATURE_RANGE_TYPE.name));
@@ -481,7 +471,7 @@ private List<Map<String, String>> getFeaturesDataFromCombobox(List<Map<String, J
         return featuresData;
     }
 
-    private JPanel featureXrefPanel(int featureNumber, boolean bait) {
+    private JPanel featureXrefPanel(boolean bait) {
         JPanel featureXrefPanel = new JPanel();
         featureXrefPanel.setBorder(BorderFactory.createTitledBorder("Feature Xref"));
         JSpinner numberOfXref = new JSpinner(new SpinnerNumberModel(1, 1, 10, 1));
@@ -490,17 +480,17 @@ private JPanel featureXrefPanel(int featureNumber, boolean bait) {
 
         JPanel xrefContainerPanel = new JPanel();
         xrefContainerPanel.setLayout(new BoxLayout(xrefContainerPanel, BoxLayout.Y_AXIS));
-        xrefContainerPanel.add(oneFeatureXrefPanel(featureNumber, bait));
+        xrefContainerPanel.add(oneFeatureXrefPanel(bait));
 
         featureXrefPanel.add(xrefContainerPanel);
 
         numberOfXref.addChangeListener(e -> updateXrefPanel(xrefContainerPanel,
-                (int) numberOfXref.getValue(), featureNumber, bait));
+                (int) numberOfXref.getValue(), bait));
 
         return featureXrefPanel;
     }
 
-    private JPanel oneFeatureXrefPanel(int featureNumber, boolean bait) {
+    private JPanel oneFeatureXrefPanel(boolean bait) {
         JPanel xrefPanel = new JPanel();
 
         JComboBox<String> xrefComboBox = new JComboBox<>();
@@ -524,12 +514,12 @@ private JPanel oneFeatureXrefPanel(int featureNumber, boolean bait) {
         return xrefPanel;
     }
 
-    private void updateXrefPanel(JPanel xrefPanel, int numberOfXref, int featureNumber, boolean bait) {
+    private void updateXrefPanel(JPanel xrefPanel, int numberOfXref, boolean bait) {
 //        xrefPanel.removeAll(); //TODO: CHECK HOW TO NOT REMOVE EVERYTHING
         //todo: check for decreasing number
         int length = xrefPanel.getComponents().length;
         for (int i = length; i < numberOfXref; i++) {
-            xrefPanel.add(oneFeatureXrefPanel(featureNumber, bait));
+            xrefPanel.add(oneFeatureXrefPanel(bait));
         }
         xrefPanel.revalidate();
         xrefPanel.repaint();

src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/jami/xml/InteractionsCreator.java

@@ -10,9 +10,8 @@
 import uk.ac.ebi.intact.psi.mi.xmlmaker.utils.FileUtils;
 import uk.ac.ebi.intact.psi.mi.xmlmaker.utils.XmlMakerUtils;
 import uk.ac.ebi.intact.psi.mi.xmlmaker.file.processing.ExcelFileReader;
-import uk.ac.ebi.intact.psi.mi.xmlmaker.uniprot.mapping.UniprotMapperGui;
+
 import java.util.*;
-import java.util.List;
 import java.util.concurrent.CompletableFuture;
 import java.util.logging.Logger;
 import java.util.stream.Collectors;
@@ -30,7 +29,7 @@ public class InteractionsCreator {
     private static int MAX_INTERACTIONS_PER_FILE = 1_000;
     final ExcelFileReader excelFileReader;
     final InteractionWriter interactionWriter;
-    final UniprotMapperGui uniprotMapperGui;
+//    final UniprotMapperGui uniprotMapperGui;
     final XmlMakerUtils utils = new XmlMakerUtils();
     public final List<XmlInteractionEvidence> xmlModelledInteractions = new ArrayList<>();
     public final List<Map<String, String>> dataList = new ArrayList<>();
@@ -55,13 +54,12 @@ public class InteractionsCreator {
      *
      * @param reader           the Excel file reader for fetching data from Excel files.
      * @param writer           the InteractionWriter
-     * @param uniprotMapperGui the Uniprot mapper GUI for mapping protein data.
      * @param columnAndIndex   the mapping of column names to their corresponding indices in the dataset.
      */
-    public InteractionsCreator(ExcelFileReader reader, InteractionWriter writer, UniprotMapperGui uniprotMapperGui, Map<String, Integer> columnAndIndex) {
+    public InteractionsCreator(ExcelFileReader reader, InteractionWriter writer, Map<String, Integer> columnAndIndex) {
         this.excelFileReader = reader;
         this.interactionWriter = writer;
-        this.uniprotMapperGui = uniprotMapperGui;
+//        this.uniprotMapperGui = uniprotMapperGui;
         this.columnAndIndex = columnAndIndex;
         this.publicationId = excelFileReader.publicationId;
     }
@@ -197,8 +195,7 @@ public XmlParticipantEvidence createParticipant(Map<String, String> data) {
         if (numberOfFeature > 0) {
             for (int i = 0; i < numberOfFeature; i++) {
                 XmlFeatureEvidence feature = createFeature(i, data);
-
-                participantEvidence.addFeature(feature); //todo: add feature xref here
+                participantEvidence.addFeature(feature);
             }
         }
 

src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/jami/xml/InteractionsCreatorGui.java

@@ -54,12 +54,11 @@ public class InteractionsCreatorGui extends JPanel {
      *
      * @param excelFileReader  The Excel file reader used to read data.
      * @param writer Interaction writer
-     * @param uniprotMapperGui The Uniprot mapper GUI for integrating with Uniprot.
      */
-    public InteractionsCreatorGui(ExcelFileReader excelFileReader, InteractionWriter writer, UniprotMapperGui uniprotMapperGui) {
+    public InteractionsCreatorGui(ExcelFileReader excelFileReader, InteractionWriter writer) {
         this.excelFileReader = excelFileReader;
         this.participantCreatorPanel = new JPanel(new BorderLayout());
-        this.interactionsCreator = new InteractionsCreator(excelFileReader, writer, uniprotMapperGui, getDataAndIndexes());
+        this.interactionsCreator = new InteractionsCreator(excelFileReader, writer, getDataAndIndexes());
     }
 
     /**

src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/uniprot/mapping/UniprotGeneralMapper.java

@@ -48,7 +48,7 @@ public class UniprotGeneralMapper {
      */
     public ArrayList<UniprotResult> fetchUniprotResult(String protein, String previousDb, String organism){
         try {
-            return getUniprotIds(getUniprotResponse(protein, previousDb, organism), protein, previousDb, organism);
+            return getUniprotIds(getUniprotResponse(protein, previousDb, organism));
         } catch (Exception e) {
             XmlMakerUtils.showErrorDialog("Error fetching UniProt results, please check your internet connection");
             LOGGER.error("Error fetching UniProt results for protein '{}': {}", protein, e.getMessage(), e);
@@ -109,7 +109,7 @@ public JsonObject getUniprotResponse(String protein, String previousDb, String o
      * @param results The JSON response from the UniProt API.
      * @return A list of {@link UniprotResult} objects representing the UniProt entries.
      */
-    public ArrayList<UniprotResult> getUniprotIds(JsonObject results, String protein, String previousDb, String inputOrganism) {
+    public ArrayList<UniprotResult> getUniprotIds(JsonObject results) {
         ArrayList<UniprotResult> uniprotResults = new ArrayList<>();
 
         if (results.isJsonNull()) {

src/main/java/uk/ac/ebi/intact/psi/mi/xmlmaker/uniprot/mapping/UniprotGeneralMapperGui.java

@@ -6,7 +6,6 @@
 import java.util.Enumeration;
 
 public class UniprotGeneralMapperGui {
-    final UniprotGeneralMapper generalMapper;
     @Getter
     String selectedId;
     @Getter
@@ -15,8 +14,7 @@ public class UniprotGeneralMapperGui {
     @Getter
     private String selectedParticipantType;
 
-    public UniprotGeneralMapperGui(UniprotGeneralMapper generalMapper) {
-        this.generalMapper = generalMapper;
+    public UniprotGeneralMapperGui() {
     }
 
     public void getUniprotIdChoicePanel(ButtonGroup uniprotIdsGroup, String previousId) {

src/test/java/uk/ac/ebi/intact/psi/mi/xmlmaker/XmlMakerGuiTest.java

@@ -38,7 +38,7 @@ public void setUp() {
         reader = new ExcelFileReader();
         UniprotMapperGui uniprotMapperGui = new UniprotMapperGui(reader, new LoadingSpinner());
         interactionWriter = new InteractionWriter(reader);
-        interactionsCreator = new InteractionsCreator(reader, interactionWriter, uniprotMapperGui, mockColumnAndIndex());
+        interactionsCreator = new InteractionsCreator(reader, interactionWriter, mockColumnAndIndex());
     }
 
     @Test