diff --git a/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationIncrementalImporter.java b/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationIncrementalImporter.java index 0b9b2515..e8e70149 100644 --- a/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationIncrementalImporter.java +++ b/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationIncrementalImporter.java @@ -24,7 +24,7 @@ public GeneticAlterationIncrementalImporter( List fileOrderedSampleList ) throws DaoException { - super.geneticProfileId = geneticProfileId; + this.geneticProfileId = geneticProfileId; this.geneticAlterationMap = daoGeneticAlteration.getGeneticAlterationMapForEntityIds(geneticProfileId, null); this.fileOrderedSampleList = fileOrderedSampleList; @@ -39,11 +39,11 @@ public GeneticAlterationIncrementalImporter( } }); // add all new sample ids at the end - super.orderedSampleList = new ArrayList<>(savedOrderedSampleList); + this.orderedSampleList = new ArrayList<>(savedOrderedSampleList); List newSampleIds = this.fileOrderedSampleList.stream().filter(sampleId -> !savedOrderedSampleList.contains(sampleId)).toList(); - super.orderedSampleList.addAll(newSampleIds); + this.orderedSampleList.addAll(newSampleIds); DaoGeneticProfileSamples.deleteAllSamplesInGeneticProfile(this.geneticProfileId); - super.storeOrderedSampleList(); + this.storeOrderedSampleList(); daoGeneticAlteration.deleteAllRecordsInGeneticProfile(this.geneticProfileId); }