Export unapproved mappings

.gitignore

@@ -1,3 +1,104 @@
 /bin
 build/
 dist/
+
+### Usagi index files ###
+derivedIndex/
+mainIndex/
+sleepyCat/
+ConceptClassIds.txt
+DomainIds.txt
+VocabularyIds.txt
+vocabularyVersion.txt
+
+### Intellij ###
+# Created by https://www.gitignore.io/api/intellij
+# Edit at https://www.gitignore.io/?templates=intellij
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and WebStorm
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+.idea/
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn.  Uncomment if using
+# auto-import.
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based Rest Client
+.idea/httpRequests
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+
+### Intellij Patch ###
+# Comment Reason: https://github.com/joeblau/gitignore.io/issues/186#issuecomment-215987721
+
+# *.iml
+# modules.xml
+# .idea/misc.xml
+# *.ipr
+
+# Sonarlint plugin
+.idea/**/sonarlint/
+
+# SonarQube Plugin
+.idea/**/sonarIssues.xml
+
+# Markdown Navigator plugin
+.idea/**/markdown-navigator.xml
+.idea/**/markdown-navigator/
+
+# End of https://www.gitignore.io/api/intellij

Usagi.iml

@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="JAVA_MODULE" version="4">
+  <component name="NewModuleRootManager" inherit-compiler-output="true">
+    <exclude-output />
+    <content url="file://$MODULE_DIR$">
+      <sourceFolder url="file://$MODULE_DIR$/src" isTestSource="false" />
+    </content>
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="library" name="lib" level="project" />
+    <orderEntry type="library" name="R User Library" level="project" />
+    <orderEntry type="library" name="R Skeletons" level="application" />
+  </component>
+</module>

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

@@ -45,6 +45,7 @@ public class ExportSourceToConceptMapDialog extends JDialog {
 
 	private JTextField			sourceVocabularyIdField;
 	private static final long	serialVersionUID	= -6846083121849826818L;
+	private boolean exportUnapproved = false;
 
 	public ExportSourceToConceptMapDialog() {
 		setTitle("Export to source_to_concept_map");
@@ -73,23 +74,11 @@ public ExportSourceToConceptMapDialog() {
 		buttonPanel.add(Box.createHorizontalGlue());
 		JButton cancelButton = new JButton("Cancel");
 		cancelButton.setToolTipText("Cancel the export");
-		cancelButton.addActionListener(new ActionListener() {
-
-			@Override
-			public void actionPerformed(ActionEvent arg0) {
-				setVisible(false);
-			}
-		});
+		cancelButton.addActionListener(arg0 -> setVisible(false));
 		buttonPanel.add(cancelButton);
 		JButton exportButton = new JButton("Export");
 		exportButton.setToolTipText("Select the filename and export using these settings");
-		exportButton.addActionListener(new ActionListener() {
-
-			@Override
-			public void actionPerformed(ActionEvent arg0) {
-				export();
-			}
-		});
+		exportButton.addActionListener(arg0 -> export());
 		buttonPanel.add(exportButton);
 		add(buttonPanel, g);
 
@@ -98,13 +87,18 @@ public void actionPerformed(ActionEvent arg0) {
 		setLocationRelativeTo(Global.frame);
 	}
 
+	public void setExportUnapproved(boolean exportUnapproved) {
+		this.exportUnapproved = exportUnapproved;
+	}
+
 	private void export() {
 		JFileChooser fileChooser = new JFileChooser(Global.folder);
 		FileFilter csvFilter = new FileNameExtensionFilter("CSV files", "csv");
 		fileChooser.setFileFilter(csvFilter);
 		fileChooser.setDialogTitle("Export");
 		if (fileChooser.showSaveDialog(Global.frame) == JFileChooser.APPROVE_OPTION) {
 			File file = fileChooser.getSelectedFile();
+			Global.folder = file.getParentFile().getAbsolutePath();
 			if (!file.getName().toLowerCase().endsWith(".csv"))
 				file = new File(file.getAbsolutePath() + ".csv");
 
@@ -116,7 +110,7 @@ private void export() {
 	private void writeToCsvFile(String filename) {
 		WriteCSVFileWithHeader out = new WriteCSVFileWithHeader(filename);
 		for (CodeMapping mapping : Global.mapping)
-			if (mapping.mappingStatus == MappingStatus.APPROVED) {
+			if (exportUnapproved || mapping.mappingStatus == MappingStatus.APPROVED) {
 				List<Concept> targetConcepts;
 				if (mapping.targetConcepts.size() == 0) {
 					targetConcepts = new ArrayList<Concept>(1);
@@ -131,7 +125,7 @@ private void writeToCsvFile(String filename) {
 					row.add("source_vocabulary_id", sourceVocabularyIdField.getText());
 					row.add("source_code_description", mapping.sourceCode.sourceName);
 					row.add("target_concept_id", targetConcept.conceptId);
-					row.add("target_vocabulary_id", targetConcept.vocabularyId);
+					row.add("target_vocabulary_id", targetConcept.conceptId == 0 ? "None" : targetConcept.vocabularyId );
 					row.add("valid_start_date", "1970-01-01");
 					row.add("valid_end_date", "2099-12-31");
 					row.add("invalid_reason", "");

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

@@ -1,12 +1,12 @@
 /*******************************************************************************
  * Copyright 2019 Observational Health Data Sciences and Informatics
- * 
+ *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- * 
+ *
  *   http://www.apache.org/licenses/LICENSE-2.0
- * 
+ *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -28,50 +28,28 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.swing.JFrame;
-import javax.swing.JPanel;
-import javax.swing.JSplitPane;
+import javax.swing.*;
 
 import org.ohdsi.usagi.BerkeleyDbEngine;
 import org.ohdsi.usagi.UsagiSearchEngine;
-import org.ohdsi.usagi.ui.actions.AboutAction;
-import org.ohdsi.usagi.ui.actions.ApplyPreviousMappingAction;
-import org.ohdsi.usagi.ui.actions.ApproveAction;
-import org.ohdsi.usagi.ui.actions.ApproveAllAction;
-import org.ohdsi.usagi.ui.actions.ClearAllAction;
-import org.ohdsi.usagi.ui.actions.ConceptInformationAction;
-import org.ohdsi.usagi.ui.actions.ExitAction;
-import org.ohdsi.usagi.ui.actions.ExportForReviewAction;
-import org.ohdsi.usagi.ui.actions.ExportSourceToConceptMapAction;
-import org.ohdsi.usagi.ui.actions.ImportAction;
-import org.ohdsi.usagi.ui.actions.OpenAction;
-import org.ohdsi.usagi.ui.actions.RebuildIndexAction;
-import org.ohdsi.usagi.ui.actions.SaveAction;
-import org.ohdsi.usagi.ui.actions.SaveAsAction;
-import org.ohdsi.usagi.ui.actions.ShowStatsAction;
+import org.ohdsi.usagi.ui.actions.*;
 import org.ohdsi.utilities.files.ReadTextFile;
 
 /**
  * The main application class
  */
 public class UsagiMain implements ActionListener {
 
-	private JFrame	frame;
-
 	public static void main(String[] args) {
 		new UsagiMain(args);
 	}
 
 	public UsagiMain(String[] args) {
-		frame = new JFrame("Usagi");
+		JFrame frame = new JFrame("Usagi");
 
 		// Initialize global variables:
 		Global.mapping = new Mapping();
-		if (args.length != 0)
-			Global.folder = args[0];
-		else
-			Global.folder = new File("").getAbsolutePath();
-
+		Global.folder = new File("").getAbsolutePath();
 		Global.usagiSearchEngine = new UsagiSearchEngine(Global.folder);
 		Global.dbEngine = new BerkeleyDbEngine(Global.folder);
 		if (Global.usagiSearchEngine.mainIndexExists()) {
@@ -107,10 +85,13 @@ public UsagiMain(String[] args) {
 		Global.clearAllAction.setEnabled(false);
 		Global.conceptInfoAction.setEnabled(false);
 
+		frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);
 		frame.addWindowListener(new WindowAdapter() {
 			public void windowClosing(WindowEvent e) {
-				Global.dbEngine.shutdown();
-				System.exit(0);
+				if (UsagiDialogs.askBeforeExit()) {
+					Global.dbEngine.shutdown();
+					System.exit(0);
+				}
 			}
 		});
 		frame.setLayout(new BorderLayout());
@@ -139,6 +120,12 @@ public void windowClosing(WindowEvent e) {
 
 		if (!Global.usagiSearchEngine.mainIndexExists())
 			Global.rebuildIndexAction.actionPerformed(null);
+
+		if (args.length == 1) {
+			Global.folder = args[0];
+		} else if (args.length > 1 && args[0].equals("--file")) {
+			OpenAction.open(new File(args[1]));
+		}
 	}
 
 	private String loadVocabularyVersion(String folder) {
@@ -147,7 +134,7 @@ private String loadVocabularyVersion(String folder) {
 		if (new File(versionFileName).exists()) {
 			for (String line : new ReadTextFile(versionFileName))
 				version = line;
-		} 
+		}
 		return version;
 	}
 

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

@@ -15,10 +15,11 @@
  ******************************************************************************/
 package org.ohdsi.usagi.ui.actions;
 
+import org.ohdsi.usagi.ui.Global;
+
 import java.awt.event.ActionEvent;
 
-import javax.swing.AbstractAction;
-import javax.swing.Action;
+import javax.swing.*;
 
 public class ExitAction extends AbstractAction {
 
@@ -31,7 +32,10 @@ public ExitAction() {
 
 	@Override
 	public void actionPerformed(ActionEvent arg0) {
-		System.exit(0);
+		if (UsagiDialogs.askBeforeExit()) {
+			Global.dbEngine.shutdown();
+			System.exit(0);
+		}
 	}
 
 }