Release 1.2.9

.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/ReadCodeMappingsFromFile.java

@@ -22,6 +22,8 @@
 import org.ohdsi.utilities.files.ReadCSVFileWithHeader;
 import org.ohdsi.utilities.files.Row;
 
+import javax.swing.*;
+
 public class ReadCodeMappingsFromFile implements Iterable<CodeMapping> {
 	private String filename;
 
@@ -42,17 +44,29 @@ public class RowIterator implements Iterator<CodeMapping> {
 
 		public RowIterator() {
 			iterator = new ReadCSVFileWithHeader(filename).iterator();
+
 			if (iterator.hasNext()) {
 				row = iterator.next();
-				readNext();
-			} else
+				try {
+					readNext();
+				} catch (Exception e) {
+					JOptionPane.showMessageDialog(
+							Global.frame,
+							"Invalid File Format",
+							"Error",
+							JOptionPane.ERROR_MESSAGE
+					);
+					return;
+				}
+			} else {
 				buffer = null;
+			}
 		}
 
 		private void readNext() {
-			if (row == null)
+			if (row == null) {
 				buffer = null;
-			else {
+			} else {
 				buffer = new CodeMapping(new SourceCode(row));
 				buffer.matchScore = row.getDouble("matchScore");
 				buffer.mappingStatus = MappingStatus.valueOf(row.get("mappingStatus"));
@@ -66,7 +80,8 @@ && new SourceCode(row).sourceName.equals(buffer.sourceCode.sourceName)) {
 					if (row.getInt("conceptId") != 0) {
 						Concept concept = Global.dbEngine.getConcept(row.getInt("conceptId"));
 						if (concept == null) {
-							buffer.mappingStatus = CodeMapping.MappingStatus.INVALID_TARGET;
+							buffer.mappingStatus = MappingStatus.INVALID_TARGET;
+							buffer.comment = "Invalid existing target: " + row.get("conceptId");
 						} else {
 							buffer.targetConcepts.add(concept);
 						}

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

@@ -40,10 +40,9 @@
 public class AboutDialog extends JDialog {
 
 	private static final long	serialVersionUID	= 2028328868610404663L;
-	private JEditorPane			text;
 
 	public AboutDialog() {
-		setTitle("About Usagi");
+		setTitle("About Usagi v" + UsagiMain.version);
 		setLayout(new GridBagLayout());
 
 		GridBagConstraints g = new GridBagConstraints();
@@ -60,9 +59,11 @@ public AboutDialog() {
 		g.gridx = 1;
 		g.gridy = 0;
 
-		text = new JEditorPane(
+		JEditorPane text = new JEditorPane(
 				"text/html",
-				"Usagi was developed by Martijn Schuemie in <a href=\"http://ohdsi.org\">Observational Health Data Sciences and Informatics</a> (OHDSI).<br/><br/>For help, please review the <a href =\"http://www.ohdsi.org/web/wiki/doku.php?id=documentation:software:usagi\">Usagi Wiki</a>.");
+				"Usagi was developed by Martijn Schuemie" +
+						"<br/>in <a href=\"http://ohdsi.org\">Observational Health Data Sciences and Informatics</a> (OHDSI)." +
+						"<br/><br/>For help, please review the <a href =\"http://www.ohdsi.org/web/wiki/doku.php?id=documentation:software:usagi\">Usagi Wiki</a>.");
 
 		text.setEditable(false);
 		text.setOpaque(false);

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

@@ -18,5 +18,7 @@
 import org.ohdsi.usagi.CodeMapping;
 
 public interface CodeSelectedListener {
-	public void codeSelected(CodeMapping codeMapping);
+	void codeSelected(CodeMapping codeMapping);
+	void addCodeMultiSelected(CodeMapping codeMapping);
+	void clearCodeMultiSelected();
 }

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

@@ -130,7 +130,7 @@ public Class<?> getColumnClass(int col) {
 	}
 
 	public boolean isCellEditable(int row, int col) {
-		return true;
+		return false;
 	}
 
 	public void setValueAt(Object value, int row, int col) {

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

@@ -17,19 +17,22 @@
 
 public interface DataChangeListener {
 
-	public static DataChangeEvent	APPROVE_EVENT		= new DataChangeEvent(true, false);
-	public static DataChangeEvent	SIMPLE_UPDATE_EVENT	= new DataChangeEvent(false, false);
-	public static DataChangeEvent	RESTRUCTURE_EVENT	= new DataChangeEvent(false, true);
+	DataChangeEvent	APPROVE_EVENT		= new DataChangeEvent(true, false, false);
+	DataChangeEvent	SIMPLE_UPDATE_EVENT	= new DataChangeEvent(false, false, false);
+	DataChangeEvent	MULTI_UPDATE_EVENT	= new DataChangeEvent(false, false, true);
+	DataChangeEvent	RESTRUCTURE_EVENT	= new DataChangeEvent(false, true, false);
 
-	public void dataChanged(DataChangeEvent event);
+	void dataChanged(DataChangeEvent event);
 
-	public static class DataChangeEvent {
-		public DataChangeEvent(boolean approved, boolean structureChange) {
+	class DataChangeEvent {
+		public DataChangeEvent(boolean approved, boolean structureChange, boolean multiUpdate) {
 			this.approved = approved;
 			this.structureChange = structureChange;
+			this.multiUpdate = multiUpdate;
 		}
 
-		public boolean	approved		= false;
-		public boolean	structureChange	= false;
+		public boolean	approved;
+		public boolean	structureChange;
+		public boolean	multiUpdate	= false;
 	}
 }

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/Global.java

@@ -19,21 +19,7 @@
 
 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.*;
 
 public class Global {
 	public static JFrame							frame;
@@ -57,6 +43,8 @@ public class Global {
 	public static ApproveAllAction					approveAllAction;
 	public static ClearAllAction					clearAllAction;
 	public static ConceptInformationAction			conceptInfoAction;
+	public static AthenaAction						athenaAction;
+	public static GoogleSearchAction				googleSearchAction;
 	public static AboutAction						aboutAction;
 	public static ExportSourceToConceptMapAction	exportAction;
 	public static ExportForReviewAction				exportForReviewAction;

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

@@ -32,14 +32,21 @@ public class Mapping extends ArrayList<CodeMapping> {
 
 	public void loadFromFile(String filename) {
 		clear();
-		boolean invalidTargets = false;
+		int nInvalidTargets = 0;
 		for (CodeMapping codeMapping : new ReadCodeMappingsFromFile(filename)) {
 			add(codeMapping);
-			if (codeMapping.mappingStatus == CodeMapping.MappingStatus.INVALID_TARGET)
-				invalidTargets = true;
+			if (codeMapping.mappingStatus == CodeMapping.MappingStatus.INVALID_TARGET) {
+				nInvalidTargets += 1;
+			}
+		}
+		if (nInvalidTargets > 0) {
+			JOptionPane.showMessageDialog(
+					null,
+					nInvalidTargets + " illegal target concepts found. The corresponding source codes are marked in red.",
+					"Illegal target concepts",
+					JOptionPane.WARNING_MESSAGE
+			);
 		}
-		if (invalidTargets)
-			JOptionPane.showMessageDialog(null, "Illegal target concepts found. The corresponding source codes are marked in red.", "Illegal target concepts", JOptionPane.WARNING_MESSAGE);
 		fireDataChanged(DataChangeListener.RESTRUCTURE_EVENT);
 	}