Map variables

.gitignore

@@ -11,6 +11,8 @@ DomainIds.txt
 VocabularyIds.txt
 vocabularyVersion.txt
 
+local_files/
+
 ### Intellij ###
 # Created by https://www.gitignore.io/api/intellij
 # Edit at https://www.gitignore.io/?templates=intellij

src/org/ohdsi/usagi/CodeMapping.java

@@ -1,12 +1,12 @@
 /*******************************************************************************
- * Copyright 2019 Observational Health Data Sciences and Informatics
- * 
+ * Copyright 2020 Observational Health Data Sciences and Informatics & The Hyve
+ *
  * 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.
@@ -20,23 +20,43 @@
 
 /**
  * Data class for holding information on a single source code and its mapping
- * 
+ *
  * @author MSCHUEMI
- * 
  */
 public class CodeMapping {
-	public static enum MappingStatus {
-		APPROVED, UNCHECKED, AUTO_MAPPED, AUTO_MAPPED_TO_1, INVALID_TARGET
-	};
+    public enum MappingStatus {
+        APPROVED, UNCHECKED, AUTO_MAPPED, AUTO_MAPPED_TO_1, INVALID_TARGET, IGNORED, FLAGGED
+    };
 
-	public SourceCode		sourceCode;
-	public double			matchScore;
-	public MappingStatus	mappingStatus;
-	public List<Concept>	targetConcepts	= new ArrayList<Concept>(1);
-	public String			comment;
+    public SourceCode sourceCode;
+    public double matchScore;
+    public MappingStatus mappingStatus;
+    public List<MappingTarget> targetConcepts = new ArrayList<>(1);
+    public String comment;
+    public String statusSetBy;
+    public long statusSetOn;
 
-	public CodeMapping(SourceCode sourceCode) {
-		this.sourceCode = sourceCode;
-	}
+    public CodeMapping(SourceCode sourceCode) {
+        this.sourceCode = sourceCode;
+    }
 
+    public void setStatus(MappingStatus mappingStatus, String author) {
+        this.mappingStatus = mappingStatus;
+        this.statusSetOn = System.currentTimeMillis();
+        this.statusSetBy = author;
+    }
+
+    public void setUnchecked() {
+        this.mappingStatus = MappingStatus.UNCHECKED;
+        this.statusSetOn = 0;
+        this.statusSetBy = "";
+    }
+
+    public void approve(String approvedBy) {
+        setStatus(MappingStatus.APPROVED, approvedBy);
+    }
+
+    public void ignore(String ignoredBy) {
+        setStatus(MappingStatus.IGNORED, ignoredBy);
+    }
 }

src/org/ohdsi/usagi/MappingTarget.java

@@ -0,0 +1,71 @@
+/*******************************************************************************
+ * Copyright 2020 Observational Health Data Sciences and Informatics & The Hyve
+ * 
+ * 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.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ ******************************************************************************/
+package org.ohdsi.usagi;
+
+/**
+ * Class for holding information about a single (target) concept in the Vocabulary
+ */
+public class MappingTarget{
+	public enum Type {
+		EVENT, VALUE, UNIT // Maybe also OPERATOR, TYPE, etc.
+	};
+
+	public Concept concept;
+	public Type mappingType;
+	public String createdBy;
+	public long createdOn;
+
+	public MappingTarget() {
+		this.concept = Concept.createEmptyConcept();
+		this.mappingType = Type.EVENT;
+		this.createdBy = "";
+		this.createdOn = 0;
+	}
+
+	public MappingTarget(Concept concept, String createdBy) {
+		this(concept, Type.EVENT, createdBy);
+	}
+
+	public MappingTarget(Concept concept, Type mappingType, String createdBy) {
+		this.concept = concept;
+		this.mappingType = mappingType;
+		this.createdBy = createdBy;
+		this.createdOn = System.currentTimeMillis();
+	}
+
+	public MappingTarget(Concept concept, Type mappingType, String createdBy, long createdOn) {
+		this.concept = concept;
+		this.mappingType = mappingType;
+		this.createdBy = createdBy;
+		this.createdOn = createdOn;
+	}
+
+	public Concept getConcept() {
+		return concept;
+	}
+
+	public void setConcept(Concept concept) {
+		this.concept = concept;
+	}
+
+	public Type getMappingType() {
+		return mappingType;
+	}
+
+	public void setMappingType(Type mappingType) {
+		this.mappingType = mappingType;
+	}
+}

src/org/ohdsi/usagi/ReadCodeMappingsFromFile.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.
@@ -23,7 +23,7 @@
 import org.ohdsi.utilities.files.Row;
 
 public class ReadCodeMappingsFromFile implements Iterable<CodeMapping> {
-	private String filename;
+	private final String filename;
 
 	public ReadCodeMappingsFromFile(String filename) {
 		this.filename = filename;
@@ -36,9 +36,9 @@ public Iterator<CodeMapping> iterator() {
 
 	public class RowIterator implements Iterator<CodeMapping> {
 
-		private Iterator<Row>	iterator;
-		private CodeMapping		buffer;
-		private Row				row;
+		private Iterator<Row> iterator;
+		private CodeMapping buffer;
+		private Row row;
 
 		public RowIterator() {
 			iterator = new ReadCSVFileWithHeader(filename).iterator();
@@ -58,20 +58,35 @@ private void readNext() {
 				buffer = new CodeMapping(new SourceCode(row));
 				buffer.matchScore = row.getDouble("matchScore");
 				buffer.mappingStatus = MappingStatus.valueOf(row.get("mappingStatus"));
+
+				// Status provenance fields might not be available in older Usagi files
+				buffer.statusSetBy = row.get("statusSetBy", "");
+				buffer.statusSetOn = row.getLong("statusSetOn", "0");
+
 				try {
 					buffer.comment = row.get("comment");
 				} catch (Exception e) {
 					buffer.comment = "";
 				}
-				while (row != null && new SourceCode(row).sourceCode.equals(buffer.sourceCode.sourceCode)
-						&& new SourceCode(row).sourceName.equals(buffer.sourceCode.sourceName)) {
+				while (row != null
+						&& new SourceCode(row).sourceCode.equals(buffer.sourceCode.sourceCode)
+						&& new SourceCode(row).sourceName.equals(buffer.sourceCode.sourceName) // MM: is this needed?
+						&& new SourceCode(row).sourceValueCode.equals(buffer.sourceCode.sourceValueCode)) {
 					if (row.getInt("conceptId") != 0) {
 						Concept concept = Global.dbEngine.getConcept(row.getInt("conceptId"));
+
 						if (concept == null) {
 							buffer.mappingStatus = MappingStatus.INVALID_TARGET;
 							buffer.comment = "Invalid existing target: " + row.get("conceptId");
 						} else {
-							buffer.targetConcepts.add(concept);
+							// Type and provenance might not be available in older Usagi files
+							MappingTarget mappingTarget = new MappingTarget(
+									concept,
+									MappingTarget.Type.valueOf(row.get("mappingType", "EVENT")),
+									row.get("createdBy", ""),
+									row.getLong("createdOn", "0")
+							);
+							buffer.targetConcepts.add(mappingTarget);
 						}
 					}
 					if (iterator.hasNext())
@@ -98,7 +113,5 @@ public CodeMapping next() {
 		public void remove() {
 			throw new RuntimeException("Remove not supported");
 		}
-
 	}
-
 }

src/org/ohdsi/usagi/SourceCode.java

@@ -32,16 +32,22 @@ public class SourceCode {
 
 	public String						sourceCode;
 	public String						sourceName;
+	public String						sourceValueCode;
+	public String						sourceValueName;
+	public String						sourceUnitName;
 	public int							sourceFrequency;
 	public Set<Integer>					sourceAutoAssignedConceptIds	= new HashSet<Integer>();
 	public List<Pair<String, String>>	sourceAdditionalInfo			= new ArrayList<Pair<String, String>>();
 
-	private static String				ADDITIONAL_INFO_PREFIX			= "ADD_INFO:";
+	private final static String			ADDITIONAL_INFO_PREFIX			= "ADD_INFO:";
 
 	public Row toRow() {
 		Row row = new Row();
 		row.add("sourceCode", sourceCode);
 		row.add("sourceName", sourceName);
+		row.add("sourceValueCode", sourceValueCode);
+		row.add("sourceValueName", sourceValueName);
+		row.add("sourceUnitName", sourceUnitName);
 		row.add("sourceFrequency", sourceFrequency);
 		row.add("sourceAutoAssignedConceptIds", StringUtilities.join(sourceAutoAssignedConceptIds, ";"));
 		for (Pair<String, String> pair : sourceAdditionalInfo) {
@@ -56,6 +62,12 @@ public SourceCode() {
 	public SourceCode(Row row) {
 		sourceCode = row.get("sourceCode");
 		sourceName = row.get("sourceName");
+		if (row.getFieldNames().contains("sourceValueCode")) {
+			// Assume that if source value code exists, then other new fields as well
+			sourceValueCode = row.get("sourceValueCode");
+			sourceValueName = row.get("sourceValueName");
+			sourceUnitName = row.get("sourceUnitName");
+		}
 		sourceFrequency = row.getInt("sourceFrequency");
 		sourceAutoAssignedConceptIds = parse(row.get("sourceAutoAssignedConceptIds"));
 		for (String field : row.getFieldNames())

src/org/ohdsi/usagi/WriteCodeMappingsToFile.java

@@ -32,18 +32,23 @@ public WriteCodeMappingsToFile(String filename) {
 	}
 
 	public void write(CodeMapping codeMapping) {
-		List<Concept> targetConcepts;
+		List<MappingTarget> mappingTargets;
 		if (codeMapping.targetConcepts.size() == 0) {
-			targetConcepts = new ArrayList<Concept>(1);
-			targetConcepts.add(Concept.EMPTY_CONCEPT);
+			mappingTargets = new ArrayList<>(1);
+			mappingTargets.add(new MappingTarget());
 		} else
-			targetConcepts = codeMapping.targetConcepts;
-		for (Concept targetConcept : targetConcepts) {
+			mappingTargets = codeMapping.targetConcepts;
+		for (MappingTarget targetConcept : mappingTargets) {
 			Row row = codeMapping.sourceCode.toRow();
 			row.add("matchScore", codeMapping.matchScore);
 			row.add("mappingStatus", codeMapping.mappingStatus.toString());
-			row.add("conceptId", targetConcept.conceptId);
+			row.add("statusSetBy", codeMapping.statusSetBy);
+			row.add("statusSetOn", codeMapping.statusSetOn);
+			row.add("conceptId", targetConcept.concept.conceptId);
+			row.add("mappingType", targetConcept.mappingType.toString());
 			row.add("comment", codeMapping.comment);
+			row.add("createdBy", targetConcept.createdBy);
+			row.add("createdOn", targetConcept.createdOn);
 			out.write(row);
 		}
 	}

src/org/ohdsi/usagi/dataImport/ImportData.java

@@ -19,13 +19,9 @@
 import java.util.List;
 import java.util.Vector;
 
-import org.ohdsi.usagi.CodeMapping;
+import org.ohdsi.usagi.*;
 import org.ohdsi.usagi.CodeMapping.MappingStatus;
-import org.ohdsi.usagi.SourceCode;
-import org.ohdsi.usagi.Concept;
-import org.ohdsi.usagi.UsagiSearchEngine;
 import org.ohdsi.usagi.UsagiSearchEngine.ScoredConcept;
-import org.ohdsi.usagi.WriteCodeMappingsToFile;
 import org.ohdsi.utilities.collections.Pair;
 import org.ohdsi.utilities.files.ReadCSVFileWithHeader;
 import org.ohdsi.utilities.files.Row;
@@ -78,10 +74,10 @@ private void createInitialMapping(List<SourceCode> sourceCodes, ImportSettings s
 			List<ScoredConcept> concepts = usagiSearchEngine.search(sourceCode.sourceName, true, sourceCode.sourceAutoAssignedConceptIds,
 					settings.filterDomains, settings.filterConceptClasses, settings.filterVocabularies, settings.filterStandard, settings.includeSourceTerms);
 			if (concepts.size() > 0) {
-				codeMapping.targetConcepts.add(concepts.get(0).concept);
+				codeMapping.targetConcepts.add(new MappingTarget(concepts.get(0).concept, "<auto>"));
 				codeMapping.matchScore = concepts.get(0).matchScore;
 			} else {
-				codeMapping.targetConcepts.add(Concept.EMPTY_CONCEPT);
+				codeMapping.targetConcepts.add(new MappingTarget(Concept.EMPTY_CONCEPT, "<auto>"));
 				codeMapping.matchScore = 0;
 			}
 			codeMapping.mappingStatus = MappingStatus.UNCHECKED;

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

@@ -0,0 +1,63 @@
+/*******************************************************************************
+ * Copyright 2020 Observational Health Data Sciences and Informatics & The Hyve
+ * 
+ * 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.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ ******************************************************************************/
+package org.ohdsi.usagi.ui;
+
+import javax.swing.*;
+import java.awt.*;
+
+public class AuthorDialog extends JDialog {
+
+	private static final long	serialVersionUID	= 8239922540117895957L;
+
+	public AuthorDialog() {
+		setTitle("Author");
+		setLayout(new GridBagLayout());
+		GridBagConstraints g = new GridBagConstraints();
+		g.fill = GridBagConstraints.BOTH;
+		g.ipadx = 5;
+		g.ipady = 5;
+
+		g.gridx = 0;
+		g.gridy = 0;
+		add(new JLabel("Author:"), g);
+
+		g.gridx = 1;
+		g.gridy = 0;
+		JTextFieldLimit authorField = new JTextFieldLimit(20);
+		authorField.setToolTipText("Please enter your name");
+		authorField.setPreferredSize(new Dimension(100, 10));
+		add(authorField, g);
+
+		g.gridx = 0;
+		g.gridy = 2;
+		g.gridwidth = 2;
+		JPanel buttonPanel = new JPanel();
+		buttonPanel.setLayout(new BoxLayout(buttonPanel, BoxLayout.X_AXIS));
+		buttonPanel.add(Box.createHorizontalGlue());
+		JButton saveButton = new JButton("Save");
+		saveButton.setToolTipText("Save your name");
+		saveButton.addActionListener(event -> {
+			Global.author = authorField.getText();
+			setVisible(false);
+		});
+		buttonPanel.add(saveButton);
+		add(buttonPanel, g);
+
+		pack();
+		setModal(true);
+		setLocationRelativeTo(Global.frame);
+	}
+}