Merge pull request #108 from OHDSI/release-1.4.1

Release 1.4.1

.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.
@@ -15,28 +15,132 @@
  ******************************************************************************/
 package org.ohdsi.usagi;
 
+import org.ohdsi.usagi.ui.Global;
+
 import java.util.ArrayList;
 import java.util.List;
 
 /**
  * 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 {
+        // Includes IGNORED for backwards compatibility
+        APPROVED, UNCHECKED, AUTO_MAPPED, AUTO_MAPPED_TO_1, INVALID_TARGET, FLAGGED, IGNORED
+    }
+
+    public enum Equivalence {
+        EQUAL, EQUIVALENT, WIDER, NARROWER, INEXACT, UNMATCHED, UNREVIEWED
+    }
+
+    private SourceCode sourceCode;
+    private double matchScore;
+    private MappingStatus mappingStatus;
+    private Equivalence equivalence;
+    private List<MappingTarget> targetConcepts = new ArrayList<>(1);
+    private String comment;
+    private String statusSetBy;
+    private long statusSetOn;
+    private String assignedReviewer;
+
+    public CodeMapping(SourceCode sourceCode) {
+        this.setSourceCode(sourceCode);
+    }
+
+    public void approve(Equivalence equivalence) {
+        setStatus(MappingStatus.APPROVED);
+        this.setEquivalence(equivalence);
+    }
+
+    public void flag(Equivalence equivalence) {
+        setStatus(MappingStatus.FLAGGED);
+        this.setEquivalence(equivalence);
+    }
+
+    public void setStatus(MappingStatus mappingStatus) {
+        this.setMappingStatus(mappingStatus);
+        this.setStatusSetOn(System.currentTimeMillis());
+        this.setStatusSetBy(Global.author);
+    }
+
+    public void setUnchecked() {
+        this.setMappingStatus(MappingStatus.UNCHECKED);
+        this.setEquivalence(Equivalence.UNREVIEWED);
+        this.setStatusSetOn(0);
+        this.setStatusSetBy("");
+    }
+
+    public SourceCode getSourceCode() {
+        return sourceCode;
+    }
+
+    public void setSourceCode(SourceCode sourceCode) {
+        this.sourceCode = sourceCode;
+    }
+
+    public double getMatchScore() {
+        return matchScore;
+    }
+
+    public void setMatchScore(double matchScore) {
+        this.matchScore = matchScore;
+    }
+
+    public MappingStatus getMappingStatus() {
+        return mappingStatus;
+    }
+
+    public void setMappingStatus(MappingStatus mappingStatus) {
+        this.mappingStatus = mappingStatus;
+    }
+
+    public Equivalence getEquivalence() {
+        return equivalence;
+    }
+
+    public void setEquivalence(Equivalence equivalence) {
+        this.equivalence = equivalence;
+    }
+
+    public List<MappingTarget> getTargetConcepts() {
+        return targetConcepts;
+    }
+
+    public void setTargetConcepts(List<MappingTarget> targetConcepts) {
+        this.targetConcepts = targetConcepts;
+    }
+
+    public String getComment() {
+        return comment;
+    }
+
+    public void setComment(String comment) {
+        this.comment = comment;
+    }
+
+    public String getStatusSetBy() {
+        return statusSetBy;
+    }
+
+    public void setStatusSetBy(String statusSetBy) {
+        this.statusSetBy = statusSetBy;
+    }
+
+    public long getStatusSetOn() {
+        return statusSetOn;
+    }
 
-	public SourceCode		sourceCode;
-	public double			matchScore;
-	public MappingStatus	mappingStatus;
-	public List<Concept>	targetConcepts	= new ArrayList<Concept>(1);
-	public String			comment;
+    public void setStatusSetOn(long statusSetOn) {
+        this.statusSetOn = statusSetOn;
+    }
 
-	public CodeMapping(SourceCode sourceCode) {
-		this.sourceCode = sourceCode;
-	}
+    public String getAssignedReviewer() {
+        return assignedReviewer;
+    }
 
+    public void setAssignedReviewer(String assignedReviewer) {
+        this.assignedReviewer = assignedReviewer;
+    }
 }

src/org/ohdsi/usagi/MappingTarget.java

@@ -0,0 +1,75 @@
+/*******************************************************************************
+ * 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 {
+		MAPS_TO, MAPS_TO_VALUE, MAPS_TO_UNIT
+	}
+
+	private final Concept concept;
+	private final String createdBy;
+	private final long createdTime;
+	private Type mappingType;
+
+	public MappingTarget() {
+		this.concept = Concept.createEmptyConcept();
+		this.mappingType = Type.MAPS_TO;
+		this.createdBy = "";
+		this.createdTime = 0;
+	}
+
+	public MappingTarget(Concept concept, String createdBy) {
+		this(concept, Type.MAPS_TO, createdBy);
+	}
+
+	public MappingTarget(Concept concept, Type mappingType, String createdBy) {
+		this.concept = concept;
+		this.mappingType = mappingType;
+		this.createdBy = createdBy;
+		this.createdTime = System.currentTimeMillis();
+	}
+
+	public MappingTarget(Concept concept, Type mappingType, String createdBy, long createdTime) {
+		this.concept = concept;
+		this.mappingType = mappingType;
+		this.createdBy = createdBy;
+		this.createdTime = createdTime;
+	}
+
+	public Concept getConcept() {
+		return concept;
+	}
+
+	public String getCreatedBy() {
+		return createdBy;
+	}
+
+	public long getCreatedTime() {
+		return createdTime;
+	}
+
+	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.
@@ -18,12 +18,13 @@
 import java.util.Iterator;
 
 import org.ohdsi.usagi.CodeMapping.MappingStatus;
+import org.ohdsi.usagi.CodeMapping.Equivalence;
 import org.ohdsi.usagi.ui.Global;
 import org.ohdsi.utilities.files.ReadCSVFileWithHeader;
 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 +37,9 @@ 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();
@@ -56,22 +57,38 @@ private void readNext() {
 				buffer = null;
 			} else {
 				buffer = new CodeMapping(new SourceCode(row));
-				buffer.matchScore = row.getDouble("matchScore");
-				buffer.mappingStatus = MappingStatus.valueOf(row.get("mappingStatus"));
-				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)) {
+				buffer.setMatchScore(row.getDouble("matchScore"));
+				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
+				buffer.setStatusSetBy(row.get("statusSetBy", ""));
+				buffer.setStatusSetOn(row.getLong("statusSetOn", "0"));
+				buffer.setEquivalence(Equivalence.valueOf(row.get("equivalence", "UNREVIEWED")));
+				buffer.setAssignedReviewer(row.get("assignedReviewer", ""));
+				buffer.setComment(row.get("comment", ""));
+
+				while (row != null
+						&& new SourceCode(row).sourceCode.equals(buffer.getSourceCode().sourceCode)
+						&& new SourceCode(row).sourceName.equals(buffer.getSourceCode().sourceName)) {
 					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");
+							buffer.setMappingStatus(MappingStatus.INVALID_TARGET);
+							buffer.setComment("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", "MAPS_TO")
+											.replace("EVENT", "MAPS_TO")
+											.replace("VALUE", "MAPS_TO_VALUE")
+											.replace("UNIT", "MAPS_TO_UNIT")
+									),
+									row.get("createdBy", ""),
+									row.getLong("createdOn", "0")
+							);
+							buffer.getTargetConcepts().add(mappingTarget);
 						}
 					}
 					if (iterator.hasNext())
@@ -98,7 +115,5 @@ public CodeMapping next() {
 		public void remove() {
 			throw new RuntimeException("Remove not supported");
 		}
-
 	}
-
 }

src/org/ohdsi/usagi/SourceCode.java

@@ -36,7 +36,7 @@ public class SourceCode {
 	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();