@Override public URI preLoad(URI input, URI output) throws StorageEngineException { getOrCreateStudyConfiguration(false); int studyId = getStudyId(); VariantFileMetadata fileMetadata = readVariantFileMetadata(input); //Get the studyConfiguration. If there is no StudyConfiguration, create a empty one. dbAdaptor.getStudyConfigurationManager().lockAndUpdate(studyId, studyConfiguration -> { securePreLoad(studyConfiguration, fileMetadata); privateStudyConfiguration = studyConfiguration; return studyConfiguration; }); return input; }
@Override protected void securePreLoad(StudyConfiguration studyConfiguration, VariantFileMetadata source) throws StorageEngineException { super.securePreLoad(studyConfiguration, source); List<Integer> fileIds = Collections.singletonList(getFileId()); BatchFileOperation op = new BatchFileOperation("load", fileIds, 1, BatchFileOperation.Type.LOAD); op.addStatus(BatchFileOperation.Status.RUNNING); studyConfiguration.getBatches().add(op); }
@Override protected void securePreLoad(StudyConfiguration studyConfiguration, VariantFileMetadata fileMetadata) throws StorageEngineException { super.securePreLoad(studyConfiguration, fileMetadata); MergeMode mergeMode; if (!studyConfiguration.getAttributes().containsKey(Options.MERGE_MODE.key())) { mergeMode = MergeMode.from(options); studyConfiguration.getAttributes().put(Options.MERGE_MODE.key(), mergeMode); } else { options.put(MERGE_MODE.key(), MergeMode.from(studyConfiguration.getAttributes())); } }
@Override protected void securePreLoad(StudyConfiguration studyConfiguration, VariantFileMetadata source) throws StorageEngineException { super.securePreLoad(studyConfiguration, source); int fileId = getFileId();