Add "Export candidates" button in the File menu

src/org/ohdsi/usagi/ui/Global.java

@@ -46,6 +46,7 @@ public class Global {
 	public static ReviewerAssignmentAction 			reviewerAssignmentAction;
 	public static ClearSelectedAction 				clearSelectedAction;
 	public static ConceptInformationAction			conceptInfoAction;
+	public static ExportCandidatesAction				    exportCandidatesAction;
 	public static AthenaAction						athenaAction;
 	public static GoogleSearchAction				googleSearchAction;
 	public static AboutAction						aboutAction;

src/org/ohdsi/usagi/ui/ImportDialog.java

@@ -455,6 +455,7 @@ public void run() {
 				Global.saveAsAction.setEnabled(true);
 				Global.exportAction.setEnabled(true);
 				Global.exportForReviewAction.setEnabled(true);
+				Global.exportCandidatesAction.setEnabled(true);
 			} catch (Exception e) {
 				JOptionPane.showMessageDialog(Global.frame, StringUtilities.wordWrap(e.getMessage(), 80), "Error", JOptionPane.ERROR_MESSAGE);
 			}

src/org/ohdsi/usagi/ui/UsagiMain.java

@@ -77,6 +77,7 @@ public UsagiMain(String[] args) {
 		Global.importAction = new ImportAction();
 		Global.exportAction = new ExportSourceToConceptMapAction();
 		Global.exportForReviewAction = new ExportForReviewAction();
+		Global.exportCandidatesAction = new ExportCandidatesAction();
 		Global.saveAction = new SaveAction();
 		Global.saveAsAction = new SaveAsAction();
 		Global.approveAction = new ApproveAction();
@@ -96,6 +97,7 @@ public UsagiMain(String[] args) {
 		Global.saveAsAction.setEnabled(false);
 		Global.exportAction.setEnabled(false);
 		Global.exportForReviewAction.setEnabled(false);
+		Global.exportCandidatesAction.setEnabled(false);
 		Global.approveAction.setEnabled(false);
 		Global.flagAction.setEnabled(false);
 		Global.clearSelectedAction = new ClearSelectedAction();

src/org/ohdsi/usagi/ui/UsagiMenubar.java

@@ -33,6 +33,7 @@ public UsagiMenubar() {
 		fileMenu.add(Global.applyPreviousMappingAction);
 		fileMenu.add(Global.exportAction);
 		fileMenu.add(Global.exportForReviewAction);
+		fileMenu.add(Global.exportCandidatesAction);
 		fileMenu.add(Global.saveAction);
 		fileMenu.add(Global.saveAsAction);
 		fileMenu.add(Global.exitAction);

src/org/ohdsi/usagi/ui/actions/ExportCandidatesAction.java

@@ -0,0 +1,148 @@
+package org.ohdsi.usagi.ui.actions;
+
+import java.awt.event.ActionEvent;
+import java.io.File;
+import java.util.List;
+import java.util.Set; // Added for Set<Integer>
+import java.util.Vector; // Added for Vector<String>
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.JFileChooser;
+import javax.swing.JOptionPane;
+import javax.swing.filechooser.FileNameExtensionFilter;
+
+import org.ohdsi.usagi.CodeMapping;
+import org.ohdsi.usagi.SourceCode;
+import org.ohdsi.usagi.UsagiSearchEngine.ScoredConcept;
+import org.ohdsi.usagi.ui.FilterPanel; // Added import for FilterPanel
+import org.ohdsi.usagi.ui.Global;
+import org.ohdsi.utilities.files.Row;
+import org.ohdsi.utilities.files.WriteCSVFileWithHeader;
+
+public class ExportCandidatesAction extends AbstractAction {
+    private static final long serialVersionUID = 1L;
+
+    public ExportCandidatesAction() {
+        putValue(Action.NAME, "Export candidates");
+        putValue(Action.SHORT_DESCRIPTION, "Export all source codes with their candidates and scores using specified filters");
+    }
+
+    @Override
+    public void actionPerformed(ActionEvent e) {
+        /* This function configure filters for exporting candidates and writes the
+         * exported data to a CSV file.
+         */
+        if (Global.mapping == null || Global.mapping.isEmpty()) {
+            JOptionPane.showMessageDialog(Global.frame, "No mappings to export.", "Export Candidates", JOptionPane.INFORMATION_MESSAGE);
+            return;
+        }
+
+        // 1. Create and show FilterPanel for user to specify filters
+        FilterPanel exportFilterPanel = new FilterPanel();
+
+        int filterConfigResult = JOptionPane.showConfirmDialog(Global.frame, exportFilterPanel,
+                "Configure Export Filters", JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE);
+
+        if (filterConfigResult != JOptionPane.OK_OPTION) {
+            return; // User cancelled filter configuration
+        }
+
+        // 2. Get File Path using JFileChooser
+        JFileChooser fileChooser = new JFileChooser();
+        fileChooser.setDialogTitle("Export Candidates to CSV");
+        fileChooser.setFileFilter(new FileNameExtensionFilter("CSV files", "csv"));
+        String suggestedFileName = "usagi_candidates_export.csv";
+        fileChooser.setSelectedFile(new File(suggestedFileName));
+
+        if (fileChooser.showSaveDialog(Global.frame) == JFileChooser.APPROVE_OPTION) {
+            File file = fileChooser.getSelectedFile();
+            if (!file.getName().toLowerCase().endsWith(".csv")) {
+                file = new File(file.getParentFile(), file.getName() + ".csv");
+            }
+
+            if (file.exists()) {
+                int response = JOptionPane.showConfirmDialog(Global.frame,
+                        "The file " + file.getName() + " already exists. Do you want to overwrite it?",
+                        "Confirm Overwrite", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE);
+                if (response == JOptionPane.NO_OPTION) {
+                    return;
+                }
+            }
+
+            WriteCSVFileWithHeader writer = null;
+            try {
+                writer = new WriteCSVFileWithHeader(file.getAbsolutePath());
+
+                // 3. Write data using filters from exportFilterPanel
+                for (CodeMapping codeMappingEntry : Global.mapping) {
+                    SourceCode sourceCode = codeMappingEntry.getSourceCode();
+
+                    // Get filter settings from the configured exportFilterPanel
+                    Set<Integer> conceptIdsForFilter = null;
+                    if (exportFilterPanel.getFilterByAuto()) {
+                        conceptIdsForFilter = sourceCode.sourceAutoAssignedConceptIds;
+                    }
+                    boolean standardFilter = exportFilterPanel.getFilterStandard();
+                    Vector<String> conceptClassesFilter = null;
+                    if (exportFilterPanel.getFilterByConceptClasses()) {
+                        conceptClassesFilter = exportFilterPanel.getConceptClass();
+                    }
+                    Vector<String> vocabulariesFilter = null;
+                    if (exportFilterPanel.getFilterByVocabularies()) {
+                        vocabulariesFilter = exportFilterPanel.getVocabulary();
+                    }
+                    Vector<String> domainsFilter = null;
+                    if (exportFilterPanel.getFilterByDomains()) {
+                        domainsFilter = exportFilterPanel.getDomain();
+                    }
+                    boolean includeSourceFilter = exportFilterPanel.getIncludeSourceTerms();
+                    boolean useMlt = true; // Default for search, can also be made a filter option if needed
+
+                    List<ScoredConcept> candidates = Global.usagiSearchEngine.search(
+                            sourceCode.sourceName,
+                            useMlt,
+                            conceptIdsForFilter,
+                            domainsFilter,
+                            conceptClassesFilter,
+                            vocabulariesFilter,
+                            standardFilter,
+                            includeSourceFilter
+                    ); 
+                    if (candidates == null || candidates.isEmpty()) {
+                        Row row = new Row();
+                        row.add("source_code", sourceCode.sourceCode);
+                        row.add("source_name", sourceCode.sourceName);
+                        // Add other source code fields as needed
+                        row.add("target_concept_id", "");
+                        row.add("target_domain_id", "");
+                        row.add("match_score", "");
+                        writer.write(row);
+                    } else {
+                        for (ScoredConcept candidate : candidates) {
+                            Row row = new Row();
+                            row.add("source_code", sourceCode.sourceCode);
+                            row.add("source_name", sourceCode.sourceName);
+                            // Add other source code fields
+                            row.add("target_concept_id", String.valueOf(candidate.concept.conceptId));
+                            row.add("target_domain_id", candidate.concept.domainId);
+                            row.add("match_score", String.valueOf(candidate.matchScore));
+                            writer.write(row);
+                        }
+                    }
+                }
+                JOptionPane.showMessageDialog(Global.frame, "Export completed successfully to " + file.getAbsolutePath(), "Export Candidates", JOptionPane.INFORMATION_MESSAGE);
+            } catch (Exception ex) {
+                JOptionPane.showMessageDialog(Global.frame, "Error during export: " + ex.getMessage(), "Export Error", JOptionPane.ERROR_MESSAGE);
+                ex.printStackTrace();
+            } finally {
+                if (writer != null) {
+                    try {
+                        writer.close();
+                    } catch (Exception ex) {
+                        ex.printStackTrace();
+                    }
+                }
+            }
+        }
+    }
+}

src/org/ohdsi/usagi/ui/actions/OpenAction.java

@@ -69,6 +69,7 @@ public static void open(File file) {
 		Global.saveAsAction.setEnabled(true);
 		Global.exportAction.setEnabled(true);
 		Global.exportForReviewAction.setEnabled(true);
+		Global.exportCandidatesAction.setEnabled(true);
 	}
 
 }