Merge pull request #125 from OHDSI/release-1.4.3

Release 1.4.3

.gitignore

@@ -10,6 +10,7 @@ ConceptClassIds.txt
 DomainIds.txt
 VocabularyIds.txt
 vocabularyVersion.txt
+authorName.txt
 
 local_files/
 

src/org/ohdsi/usagi/Concept.java

@@ -20,6 +20,8 @@
 import com.sleepycat.persist.model.Entity;
 import com.sleepycat.persist.model.PrimaryKey;
 
+import java.util.Objects;
+
 /**
  * Class for holding information about a single (target) concept in the Vocabulary
  */
@@ -77,4 +79,18 @@ public static Concept createEmptyConcept() {
 
 	public Concept() {
 	}
+
+	@Override
+	public boolean equals(Object o) {
+		// Only compare conceptId
+		if (this == o) return true;
+		if (o == null || getClass() != o.getClass()) return false;
+		Concept concept = (Concept) o;
+		return conceptId == concept.conceptId;
+	}
+
+	@Override
+	public int hashCode() {
+		return Objects.hash(conceptId);
+	}
 }

src/org/ohdsi/usagi/MappingTarget.java

@@ -15,12 +15,24 @@
  ******************************************************************************/
 package org.ohdsi.usagi;
 
+import java.util.Objects;
+
 /**
  * Class for holding information about a single (target) concept in the Vocabulary
  */
 public class MappingTarget{
 	public enum Type {
-		MAPS_TO, MAPS_TO_VALUE, MAPS_TO_UNIT
+		MAPS_TO, MAPS_TO_VALUE, MAPS_TO_UNIT, MAPS_TO_OPERATOR, MAPS_TO_TYPE, MAPS_TO_NUMBER;
+
+		public static Type valueOfCompat(String value) {
+			// For backwards compatibility with old types
+			switch (value) {
+				case "EVENT": return MAPS_TO;
+				case "VALUE": return MAPS_TO_VALUE;
+				case "UNIT": return MAPS_TO_UNIT;
+				default: return valueOf(value);
+			}
+		}
 	}
 
 	private final Concept concept;
@@ -72,4 +84,18 @@ public Type getMappingType() {
 	public void setMappingType(Type mappingType) {
 		this.mappingType = mappingType;
 	}
+
+	@Override
+	public boolean equals(Object o) {
+		// Only compares target concept and mappingType.
+		if (this == o) return true;
+		if (o == null || getClass() != o.getClass()) return false;
+		MappingTarget that = (MappingTarget) o;
+		return Objects.equals(concept, that.concept) && mappingType == that.mappingType;
+	}
+
+	@Override
+	public int hashCode() {
+		return Objects.hash(concept, mappingType);
+	}
 }

src/org/ohdsi/usagi/ReadCodeMappingsFromFile.java

@@ -57,7 +57,7 @@ private void readNext() {
 				buffer = null;
 			} else {
 				buffer = new CodeMapping(new SourceCode(row));
-				buffer.setMatchScore(row.getDouble("matchScore"));
+				buffer.setMatchScore(row.getDouble("matchScore", "0"));
 				buffer.setMappingStatus(MappingStatus.valueOf(row.get("mappingStatus")));
 
 				// Status provenance and review need a default as these fields might not be available in older Usagi files
@@ -77,14 +77,9 @@ && new SourceCode(row).sourceName.equals(buffer.getSourceCode().sourceName)) {
 							buffer.setMappingStatus(MappingStatus.INVALID_TARGET);
 							buffer.setComment("Invalid existing target: " + row.get("conceptId"));
 						} else {
-							// Type and provenance might not be available in older Usagi files
 							MappingTarget mappingTarget = new MappingTarget(
 									concept,
-									MappingTarget.Type.valueOf(row.get("mappingType", "MAPS_TO")
-											.replace("EVENT", "MAPS_TO")
-											.replace("VALUE", "MAPS_TO_VALUE")
-											.replace("UNIT", "MAPS_TO_UNIT")
-									),
+									MappingTarget.Type.valueOfCompat(row.get("mappingType", "MAPS_TO")),
 									row.get("createdBy", ""),
 									row.getLong("createdOn", "0")
 							);

src/org/ohdsi/usagi/WriteCodeMappingsToFile.java

@@ -51,7 +51,8 @@ public void write(CodeMapping codeMapping) {
 			row.add("statusSetBy", codeMapping.getStatusSetBy());
 			row.add("statusSetOn", codeMapping.getStatusSetOn());
 			row.add("conceptId", targetConcept.getConcept().conceptId);
-			row.add("conceptName", targetConcept.getConcept().conceptName); // Never read in.
+			row.add("conceptName", targetConcept.getConcept().conceptName); // Redundant, not read in
+			row.add("domainId", targetConcept.getConcept().domainId); // Redundant, not read in
 			row.add("mappingType", targetConcept.getMappingType().toString());
 			row.add("comment", codeMapping.getComment());
 			row.add("createdBy", targetConcept.getCreatedBy());

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

@@ -15,15 +15,18 @@
  ******************************************************************************/
 package org.ohdsi.usagi.ui;
 
+import org.ohdsi.utilities.files.WriteTextFile;
+
 import javax.swing.*;
 import java.awt.*;
 
 public class AuthorDialog extends JDialog {
 
-	private static final long	serialVersionUID	= 8239922540117895957L;
+	private static final long serialVersionUID = 8239922540117895957L;
+	private String authorFileName;
 
 	public AuthorDialog() {
-		setTitle("Author");
+		setTitle("Usagi v" + UsagiMain.version);
 		setLayout(new GridBagLayout());
 		GridBagConstraints g = new GridBagConstraints();
 		g.fill = GridBagConstraints.BOTH;
@@ -32,7 +35,7 @@ public AuthorDialog() {
 
 		g.gridx = 0;
 		g.gridy = 0;
-		add(new JLabel("Author:"), g);
+		add(new JLabel(" Author:"), g);
 
 		g.gridx = 1;
 		g.gridy = 0;
@@ -41,6 +44,12 @@ public AuthorDialog() {
 		authorField.setPreferredSize(new Dimension(100, 10));
 		add(authorField, g);
 
+		g.gridx = 0;
+		g.gridy = 1;
+		g.gridwidth = 2;
+		JCheckBox saveBox = new JCheckBox("Remember me?");
+		add(saveBox, g);
+
 		g.gridx = 0;
 		g.gridy = 2;
 		g.gridwidth = 2;
@@ -52,6 +61,11 @@ public AuthorDialog() {
 		saveButton.addActionListener(event -> {
 			Global.author = authorField.getText();
 			setVisible(false);
+			if (saveBox.isSelected() && authorFileName != null) {
+				WriteTextFile out = new WriteTextFile(authorFileName);
+				out.writeln(authorField.getText());
+				out.close();
+			}
 		});
 		buttonPanel.add(saveButton);
 		add(buttonPanel, g);
@@ -60,4 +74,9 @@ public AuthorDialog() {
 		setModal(true);
 		setLocationRelativeTo(Global.frame);
 	}
+
+	public void setAuthorFileName(String authorFileName) {
+		this.authorFileName = authorFileName;
+	}
+
 }

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

@@ -101,10 +101,15 @@ private void loadData(String filename) {
 		if (!iterator.hasNext())
 			throw new RuntimeException("File contains no data");
 		columnNames = iterator.next();
-		Set<String> uniqueNames = new HashSet<String>();
-		for (String columnName : columnNames)
-			if (!uniqueNames.add(columnName))
+		Set<String> uniqueNames = new HashSet<>();
+		for (String columnName : columnNames) {
+			if (columnName.isEmpty()) {
+				continue;
+			}
+			if (!uniqueNames.add(columnName)) {
 				throw new RuntimeException("Found duplicate column name '" + columnName + "', duplicates are not allowed.");
+			}
+		}
 		comboBoxOptions = new String[columnNames.size() + 1];
 		comboBoxOptions[0] = "";
 		for (int i = 0; i < columnNames.size(); i++)

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

@@ -17,13 +17,15 @@
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.stream.Collectors;
 
 import javax.swing.JOptionPane;
 
 import org.ohdsi.usagi.CodeMapping;
 import org.ohdsi.usagi.ReadCodeMappingsFromFile;
 import org.ohdsi.usagi.SourceCode;
 import org.ohdsi.usagi.WriteCodeMappingsToFile;
+import org.ohdsi.utilities.collections.Pair;
 
 import static org.ohdsi.usagi.ui.DataChangeEvent.*;
 
@@ -83,9 +85,15 @@ public void saveToFile(String filename) {
 	}
 
 	public List<SourceCode> getSourceCodes() {
-		List<SourceCode> sourceCodes = new ArrayList<SourceCode>(size());
-		for (CodeMapping codeMapping : this)
-			sourceCodes.add(codeMapping.getSourceCode());
-		return sourceCodes;
+		return this.stream()
+				.map(CodeMapping::getSourceCode)
+				.collect(Collectors.toList());
+	}
+
+	public List<String> getAdditionalColumnNames() {
+		CodeMapping codeMapping = Global.mapping.get(0);
+		return codeMapping.getSourceCode().sourceAdditionalInfo.stream()
+				.map(Pair::getItem1)
+				.collect(Collectors.toList());
 	}
 }

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

@@ -53,7 +53,8 @@ public class MappingDetailPanel extends JPanel implements CodeSelectedListener,
 	private JComboBox 							equivalenceOptionChooser;
 	private JTextField							commentField;
 	private JButton								removeButton;
-	private JComboBox 							typesChooser;
+	private JComboBox 							targetMappingTypesChooser;
+	private JComboBox 							addMappingsTypesChooser;
 	private JButton								replaceButton;
 	private List<JButton> 						addButtons;
 	private JRadioButton 						autoQueryCodeButton;
@@ -179,9 +180,11 @@ private Component createSearchResultsPanel() {
 			if (viewRow == -1 || codeMapping.getMappingStatus() == MappingStatus.APPROVED) {
 				addButtons.forEach(x -> x.setEnabled(false));
 				replaceButton.setEnabled(false);
+				addMappingsTypesChooser.setEnabled(false);
 			} else {
 				addButtons.forEach(x -> x.setEnabled(true));
 				replaceButton.setEnabled(true);
+				addMappingsTypesChooser.setEnabled(true);
 				int modelRow = searchTable.convertRowIndexToModel(viewRow);
 				Global.conceptInfoAction.setEnabled(true);
 				Global.conceptInformationDialog.setActiveConcept(searchTableModel.getConcept(modelRow));
@@ -211,28 +214,23 @@ private Component createSearchResultsPanel() {
 		buttonPanel.add(replaceButton);
 
 		JButton button;
-		addButtons = new ArrayList<>();
-		for (MappingTarget.Type mappingType : MappingTarget.Type.values()) {
-			if (mappingType.equals(MappingTarget.Type.MAPS_TO)) {
-				button = new JButton("Add concept");
-			} else {
-				button = new JButton(String.format("Add %s", mappingType));
-			}
-			button.setToolTipText(String.format("Add selected concept as %s", mappingType));
-			button.addActionListener(e -> {
-				int viewRow = searchTable.getSelectedRow();
-				int modelRow = searchTable.convertRowIndexToModel(viewRow);
-				addConcept(searchTableModel.getConcept(modelRow), mappingType);
-			});
-			button.setEnabled(false);
-			addButtons.add(button);
-			// Add Maps_to button on the right, the other on the left.
-			if (mappingType.equals(MappingTarget.Type.MAPS_TO)) {
-				buttonPanel.add(button);
-			} else {
-				buttonPanel.add(button, 0);
-			}
-		}
+		button = new JButton("Add concept");
+		button.setToolTipText(String.format("Add selected concept"));
+		button.addActionListener(e -> {
+			int viewRow = searchTable.getSelectedRow();
+			int modelRow = searchTable.convertRowIndexToModel(viewRow);
+			addConcept(searchTableModel.getConcept(modelRow), (MappingTarget.Type) addMappingsTypesChooser.getSelectedItem());
+		});
+		button.setEnabled(false);
+		buttonPanel.add(button);
+		addButtons = new ArrayList<>(); // There used to be an add button for each mapping type
+		addButtons.add(button);
+
+		addMappingsTypesChooser = new JComboBox<>(MappingTarget.Type.values());
+		addMappingsTypesChooser.setToolTipText("Set type of the mapping to be added");
+		addMappingsTypesChooser.setMaximumSize(addMappingsTypesChooser.getPreferredSize());
+		addMappingsTypesChooser.setEnabled(false);
+		buttonPanel.add(addMappingsTypesChooser, 0);
 
 		panel.add(buttonPanel);
 
@@ -322,13 +320,13 @@ private JPanel createTargetConceptsPanel() {
 			int viewRow = targetConceptTable.getSelectedRow();
 			if (viewRow == -1 || codeMapping.getMappingStatus() == MappingStatus.APPROVED) {
 				removeButton.setEnabled(false);
-				typesChooser.setEnabled(false);
+				targetMappingTypesChooser.setEnabled(false);
 			} else {
 				removeButton.setEnabled(true);
-				typesChooser.setEnabled(true);
+				targetMappingTypesChooser.setEnabled(true);
 				int modelRow = targetConceptTable.convertRowIndexToModel(viewRow);
 				MappingTarget mappingTarget = targetConceptTableModel.getMappingTarget(modelRow);
-				typesChooser.setSelectedItem(mappingTarget.getMappingType());
+				targetMappingTypesChooser.setSelectedItem(mappingTarget.getMappingType());
 				Global.conceptInfoAction.setEnabled(true);
 				Global.conceptInformationDialog.setActiveConcept(mappingTarget.getConcept());
 				Global.athenaAction.setEnabled(true);
@@ -342,22 +340,22 @@ private JPanel createTargetConceptsPanel() {
 
 		JScrollPane pane = new JScrollPane(targetConceptTable);
 		pane.setBorder(BorderFactory.createEmptyBorder());
-		pane.setMinimumSize(new Dimension(500, 50));
-		pane.setPreferredSize(new Dimension(500, 50));
+		pane.setMinimumSize(new Dimension(500, 75));
+		pane.setPreferredSize(new Dimension(500, 75));
 		panel.add(pane);
 
 		JPanel buttonPanel = new JPanel();
 		buttonPanel.setLayout(new BoxLayout(buttonPanel, BoxLayout.X_AXIS));
 
-		typesChooser = new JComboBox<>(MappingTarget.Type.values());
-		typesChooser.setToolTipText("Set type of the mapping");
-		typesChooser.addActionListener(e -> {
+		targetMappingTypesChooser = new JComboBox<>(MappingTarget.Type.values());
+		targetMappingTypesChooser.setToolTipText("Set type of the mapping");
+		targetMappingTypesChooser.addActionListener(e -> {
 			if (((JComboBox)e.getSource()).hasFocus())
 				changeTargetType();
 		});
-		typesChooser.setMaximumSize(typesChooser.getPreferredSize());
-		typesChooser.setEnabled(false);
-		buttonPanel.add(typesChooser);
+		targetMappingTypesChooser.setMaximumSize(targetMappingTypesChooser.getPreferredSize());
+		targetMappingTypesChooser.setEnabled(false);
+		buttonPanel.add(targetMappingTypesChooser);
 
 		buttonPanel.add(Box.createHorizontalGlue());
 
@@ -448,6 +446,7 @@ public void uncheckSelected() {
 		if (searchTable.getSelectedRow() != -1) {
 			replaceButton.setEnabled(true);
 			addButtons.forEach(x -> x.setEnabled(true));
+			addMappingsTypesChooser.setEnabled(true);
 		}
 	}
 
@@ -523,7 +522,7 @@ private void remove() {
 	private void changeTargetType() {
 		for (int row : targetConceptTable.getSelectedRows()) {
 			MappingTarget mappingTarget = codeMapping.getTargetConcepts().get(row);
-			mappingTarget.setMappingType((MappingTarget.Type) typesChooser.getSelectedItem());
+			mappingTarget.setMappingType((MappingTarget.Type) targetMappingTypesChooser.getSelectedItem());
 		}
 
 		targetConceptTableModel.fireTableDataChanged();