ALS-4751: Clean up excepetion handling, per checkmarx

hms-dbmi · Jul 12, 2023 · befa929 · befa929
1 parent 7b7165f
commit befa929
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Showing 3 changed files with 2 additions and 3 deletions.
diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RemapIds.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RemapIds.java
@@ -124,7 +124,7 @@ private static void processRecord(final PhenoCube[] currentConcept, List<String>
 				store.allIds.add(patientId);
 			}
 		} catch (ExecutionException e) {
-			e.printStackTrace();
+			log.error("Error processing record", e);
 		}
 	}
 

diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/LoadingStore.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/LoadingStore.java
@@ -145,7 +145,6 @@ public void dumpStats() {
 			System.out.println("Total Number of Observations : " + totalNumberOfObservations);
 
 		} catch (IOException | ClassNotFoundException e) {
-			e.printStackTrace();
 			throw new RuntimeException("Could not load metastore");
 		}
 	}

diff --git a/...rc/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/SequentialLoadingStore.java b/...rc/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/SequentialLoadingStore.java
@@ -66,7 +66,7 @@ public void onRemoval(RemovalNotification<String, PhenoCube> cubeRemoval) {
 							columnMeta.setAllObservationsLength(allObservationsTemp.getFilePointer());
 							metadataMap.put(columnMeta.getName(), columnMeta);
 						} catch (IOException e1) {
-							e1.printStackTrace();
+							throw new UncheckedIOException(e1);
 						}
 					}
 				}