If last column of Athena file is empty, it is now represented as an e…

…mpty string instead of a null value. Fixes #52
OHDSI · Nov 21, 2018 · 284a2da · 284a2da
1 parent 4d2d203
commit 284a2da
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Showing 7 changed files with 8 additions and 8 deletions.
diff --git a/src/org/ohdsi/usagi/indexBuilding/BerkeleyDbBuilder.java b/src/org/ohdsi/usagi/indexBuilding/BerkeleyDbBuilder.java
@@ -51,7 +51,7 @@ private IntHashSet loadValidConceptIdsAndAtcCodes(String conceptFileName) {
 		conceptIdToAtcCode = new HashMap<Integer, String>();
 
 		for (Row row : new ReadAthenaFile(conceptFileName))
-			if (row.get("invalid_reason") == null) {
+			if (row.get("invalid_reason").length() == 0) {
 				validConceptIds.add(row.getInt("concept_id"));
 				if (row.get("vocabulary_id").equals("ATC"))
 					conceptIdToAtcCode.put(row.getInt("concept_id"), row.get("concept_code"));
@@ -109,7 +109,7 @@ private void loadConcepts(String conceptFileName, String loincFileName) {
 		int count = 0;
 		for (Row row : new ReadAthenaFile(conceptFileName)) {
 			Concept concept = new Concept(row);
-			if (concept.invalidReason == null) {
+			if (concept.invalidReason.length() == 0) {
 				if (loincToInfo != null) {
 					String info = loincToInfo.get(concept.conceptCode);
 					if (info != null)

diff --git a/src/org/ohdsi/usagi/indexBuilding/IndexBuildCoordinator.java b/src/org/ohdsi/usagi/indexBuilding/IndexBuildCoordinator.java
@@ -18,7 +18,7 @@ public class IndexBuildCoordinator {
 
 	public static void main(String[] args) {
 		Global.folder = "c:/data/usagi/";
-		String vocabFolder = "C:\\Data\\OMOP Standard Vocabulary V5\\Vocabulary-20180823";
+		String vocabFolder = "C:\\Data\\OMOP Standard Vocabulary V5\\Vocabulary-20181119";
 //		String loincFolder = "c:/Data/LOINC/loinc.csv";
 		String loincFolder = null;
 		IndexBuildCoordinator buildIndex = new IndexBuildCoordinator();

diff --git a/src/org/ohdsi/usagi/ui/ConceptInformationDialog.java b/src/org/ohdsi/usagi/ui/ConceptInformationDialog.java
@@ -304,7 +304,7 @@ private void showConcept(Concept concept) {
 		conceptInfo.append("Vocabulary ID: " + concept.vocabularyId + "\n");
 		conceptInfo.append("Concept ID: " + concept.conceptId + "\n");
 		conceptInfo.append("Concept code: " + concept.conceptCode + "\n");
-		conceptInfo.append("Invalid reason: " + (concept.invalidReason == null ? "" : concept.invalidReason) + "\n");
+		conceptInfo.append("Invalid reason: " + concept.invalidReason + "\n");
 		conceptInfo.append("Standard concept: " + concept.standardConcept + "\n");
 		if (concept.additionalInformation != null)
 			conceptInfo.append("\n" + concept.additionalInformation.replaceAll("\\\\n", "\n"));

diff --git a/src/org/ohdsi/usagi/ui/ConceptTableModel.java b/src/org/ohdsi/usagi/ui/ConceptTableModel.java
@@ -97,7 +97,7 @@ public Object getValueAt(int row, int col) {
 			case 7:
 				return targetConcept.validEndDate;
 			case 8:
-				return targetConcept.invalidReason == null ? "" : targetConcept.invalidReason;
+				return targetConcept.invalidReason;
 			case 9:
 				return targetConcept.standardConcept;
 			case 10:

diff --git a/src/org/ohdsi/usagi/ui/MappingTablePanel.java b/src/org/ohdsi/usagi/ui/MappingTablePanel.java
@@ -177,7 +177,7 @@ public Object getValueAt(int row, int col) {
 					case 12:
 						return targetConcept.validEndDate;
 					case 13:
-						return targetConcept.invalidReason == null ? "" : targetConcept.invalidReason;
+						return targetConcept.invalidReason;
 					case 14:
 						return targetConcept.standardConcept;
 					case 15:

diff --git a/src/org/ohdsi/usagi/ui/actions/ExportForReviewAction.java b/src/org/ohdsi/usagi/ui/actions/ExportForReviewAction.java
@@ -85,7 +85,7 @@ public void actionPerformed(ActionEvent arg0) {
 							row.add("targetConceptCode", targetConcept.conceptCode);
 							row.add("targetValidStartDate", targetConcept.validStartDate);
 							row.add("targetValidEndDate", targetConcept.validEndDate);
-							row.add("targetInvalidReason", targetConcept.invalidReason == null?"":targetConcept.invalidReason);
+							row.add("targetInvalidReason", targetConcept.invalidReason);
 							out.write(row);
 						}
 					}

diff --git a/src/org/ohdsi/utilities/files/Row.java b/src/org/ohdsi/utilities/files/Row.java
@@ -49,7 +49,7 @@ public String get(String fieldName) {
 			throw new RuntimeException("Field \"" + fieldName + "\" not found");
 		}
 		if (cells.size() <= index)
-			return null;
+			return "";
 		else
 			return cells.get(index);
 	}