Merge pull request #123 from EHDEN/fix-read-maptype

Fix compatibility and apply previous issues

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_OPERATOR, MAPS_TO_TYPE, MAPS_TO_NUMBER
+		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

@@ -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/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/MappingTablePanel.java

@@ -128,14 +128,14 @@ public void restructure() {
 			columnNames = defaultColumnNames;
 			addInfoColCount = 0;
 			if (Global.mapping.size() != 0) {
-				CodeMapping codeMapping = Global.mapping.get(0);
-				addInfoColCount = codeMapping.getSourceCode().sourceAdditionalInfo.size();
+				List<String> additionalColumns = Global.mapping.getAdditionalColumnNames();
+				addInfoColCount = additionalColumns.size();
 				columnNames = new String[defaultColumnNames.length + addInfoColCount];
 				for (int i = 0; i < ADD_INFO_START_COL; i++)
 					columnNames[i] = defaultColumnNames[i];
 
 				for (int i = 0; i < addInfoColCount; i++)
-					columnNames[i + ADD_INFO_START_COL] = codeMapping.getSourceCode().sourceAdditionalInfo.get(i).getItem1();
+					columnNames[i + ADD_INFO_START_COL] = additionalColumns.get(i);
 
 				for (int i = ADD_INFO_START_COL; i < defaultColumnNames.length; i++)
 					columnNames[i + addInfoColCount] = defaultColumnNames[i];

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

@@ -17,8 +17,11 @@
 
 import java.awt.event.ActionEvent;
 import java.io.File;
+import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.Map;
+import java.util.List;
+import java.util.stream.Collectors;
 
 import javax.swing.AbstractAction;
 import javax.swing.Action;
@@ -30,6 +33,7 @@
 import org.ohdsi.usagi.CodeMapping;
 import org.ohdsi.usagi.ui.Global;
 import org.ohdsi.usagi.ui.Mapping;
+import org.ohdsi.utilities.collections.Pair;
 
 import static org.ohdsi.usagi.ui.DataChangeEvent.*;
 
@@ -62,10 +66,15 @@ public void actionPerformed(ActionEvent arg0) {
 			Mapping mappingToBeApplied = new Mapping();
 			mappingToBeApplied.loadFromFile(file.getAbsolutePath());
 
+			// Additional columns
+			List<String> existingAdditionalColumnNames = Global.mapping.getAdditionalColumnNames();
+
 			// Apply mapping. Add mappings not currently present
+			ApplyPreviousChangeSummary summary = new ApplyPreviousChangeSummary();
 			for (CodeMapping codeMappingToBeApplied : mappingToBeApplied) {
 				CodeMapping existingMapping = codeToMapping.get(codeMappingToBeApplied.getSourceCode().sourceCode);
 				if (existingMapping != null) {
+					summary.compare(existingMapping, codeMappingToBeApplied);
 					existingMapping.getSourceCode().sourceName = codeMappingToBeApplied.getSourceCode().sourceName;
 					existingMapping.setTargetConcepts(codeMappingToBeApplied.getTargetConcepts());
 					existingMapping.setMappingStatus(codeMappingToBeApplied.getMappingStatus());
@@ -76,13 +85,17 @@ public void actionPerformed(ActionEvent arg0) {
 					existingMapping.setStatusSetOn(codeMappingToBeApplied.getStatusSetOn());
 					mappingsApplied++;
 				} else {
+					// Add empty additional columns if these existed in existing mapping
+					codeMappingToBeApplied.getSourceCode().sourceAdditionalInfo = existingAdditionalColumnNames.stream()
+							.map(x -> new Pair<>(x, ""))
+							.collect(Collectors.toList());
 					Global.mapping.add(codeMappingToBeApplied);
 					mappingsAdded++;
 				}
 			}
 
 			String message = "The applied mapping contained " + mappingToBeApplied.size() + " mappings of which " + mappingsApplied
-					+ " were applied to the current mapping and " + mappingsAdded + " were newly added.";
+					+ " were applied to the current mapping and " + mappingsAdded + " were newly added.\n\n" + summary.createReport();
 			Global.mappingTablePanel.updateUI();
 			Global.mappingDetailPanel.updateUI();
 			Global.mapping.fireDataChanged(APPROVE_EVENT); // To update the footer
@@ -91,7 +104,48 @@ public void actionPerformed(ActionEvent arg0) {
 				Global.usagiSearchEngine.createDerivedIndex(Global.mapping.getSourceCodes(), Global.frame);
 				Global.mappingDetailPanel.doSearch();
 			}
-			JOptionPane.showMessageDialog(Global.frame, message);
+			JOptionPane.showMessageDialog(Global.frame, message, "Summary", JOptionPane.INFORMATION_MESSAGE);
+		}
+	}
+
+	private static class ApplyPreviousChangeSummary {
+		private int nChanged = 0;
+		private int nSourceNameChanged = 0;
+		private int nTargetConceptsChanged = 0;
+		private int nMappingStatusChanged = 0;
+		private int nEquivalenceChanged = 0;
+
+		private void compare(CodeMapping A, CodeMapping B) {
+			boolean hasChanged = false;
+			if (!A.getSourceCode().sourceName.equals(B.getSourceCode().sourceName)) {
+				nSourceNameChanged++;
+				hasChanged = true;
+			}
+			if (!A.getTargetConcepts().equals(B.getTargetConcepts())) {
+				nTargetConceptsChanged++; // This could be target concept, size OR type
+				hasChanged = true;
+			}
+			if (!A.getMappingStatus().equals(B.getMappingStatus())) {
+				nMappingStatusChanged++;
+				hasChanged = true;
+			}
+			if (!A.getEquivalence().equals(B.getEquivalence())) {
+				nEquivalenceChanged++;
+				hasChanged = true;
+			}
+			if (hasChanged) {
+				nChanged++;
+			}
+		}
+
+		private String createReport() {
+			StringBuilder report = new StringBuilder();
+			report.append("Of the applied mappings, " + nChanged + " mappings changed.");
+			report.append("\n\tSource name: " + nSourceNameChanged);
+			report.append("\n\tTarget concept: " + nTargetConceptsChanged + "\t(changed target concept, target type AND/OR number of targets)");
+			report.append("\n\tMapping status: " + nMappingStatusChanged);
+			report.append("\n\tMapping equivalence: " + nEquivalenceChanged);
+			return report.toString();
 		}
 	}
 }