From 284a2da1f1f87abd3119964e6d558208a4a36a20 Mon Sep 17 00:00:00 2001 From: schuemie Date: Wed, 21 Nov 2018 08:57:38 +0100 Subject: [PATCH] If last column of Athena file is empty, it is now represented as an empty string instead of a null value. Fixes #52 --- src/org/ohdsi/usagi/indexBuilding/BerkeleyDbBuilder.java | 4 ++-- src/org/ohdsi/usagi/indexBuilding/IndexBuildCoordinator.java | 2 +- src/org/ohdsi/usagi/ui/ConceptInformationDialog.java | 2 +- src/org/ohdsi/usagi/ui/ConceptTableModel.java | 2 +- src/org/ohdsi/usagi/ui/MappingTablePanel.java | 2 +- src/org/ohdsi/usagi/ui/actions/ExportForReviewAction.java | 2 +- src/org/ohdsi/utilities/files/Row.java | 2 +- 7 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/org/ohdsi/usagi/indexBuilding/BerkeleyDbBuilder.java b/src/org/ohdsi/usagi/indexBuilding/BerkeleyDbBuilder.java index eb4e17a..2eec03b 100644 --- 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(); 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 index 1e3d4f7..7ceda95 100644 --- 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 index a3b202a..b64f411 100644 --- 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 index 19be40a..637cddd 100644 --- 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 index a0e629a..42791f6 100644 --- 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 index 86111b1..83de995 100644 --- 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 index 693ba3c..23ccac6 100644 --- 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); }