if (File.RelatedFile.Relation.PRODUCED_FROM.equals(relatedFile.getRelation())) { Query query = new Query(FileDBAdaptor.QueryParams.UID.key(), relatedFile.getFileId()); file = get(studyStr, query, null, sessionId).first(); break;
transformedFromFileIds.addAll( fileAux.getRelatedFiles().stream() .filter(myFile -> myFile.getRelation() == File.RelatedFile.Relation.PRODUCED_FROM) .map(File.RelatedFile::getFileId) .collect(Collectors.toSet())
File.RelatedFile producedFromRelation = new File.RelatedFile(vcf.getUid(), File.RelatedFile.Relation.PRODUCED_FROM);
fileIds.addAll( transformedFile.getRelatedFiles().stream() .filter(myFile -> myFile.getRelation() == File.RelatedFile.Relation.PRODUCED_FROM) .map(File.RelatedFile::getFileId) .collect(Collectors.toSet())
.filter(relatedFile -> relatedFile.getRelation().equals(File.RelatedFile.Relation.PRODUCED_FROM)) .collect(Collectors.toList()); assertEquals(1, relatedFiles.size()); assertEquals(inputFile.getUid(), relatedFiles.get(0).getFileId());
.filter(relatedFile -> relatedFile.getRelation().equals(File.RelatedFile.Relation.PRODUCED_FROM)) .collect(Collectors.toList()); assertEquals(1, relatedFiles.size()); assertEquals(inputFile.getUid(), relatedFiles.get(0).getFileId());
private File getOriginalFromTransformed(String study, File file, String sessionId) throws URISyntaxException, CatalogException { // Look for the vcf file String vcfId = null; // Matchup variant files, if missing if (file.getRelatedFiles() == null || file.getRelatedFiles().isEmpty()) { catalogManager.getFileManager().matchUpVariantFiles(null, Collections.singletonList(file), sessionId); } for (File.RelatedFile relatedFile : file.getRelatedFiles()) { if (File.RelatedFile.Relation.PRODUCED_FROM.equals(relatedFile.getRelation())) { long fileUid = relatedFile.getFileId(); // FIXME!!! vcfId = catalogManager.getFileManager().get(study, new Query(UID.key(), fileUid), new QueryOptions(QueryOptions.INCLUDE, ID.key()), sessionId).first().getId(); break; } } if (vcfId == null) { logger.error("This code should never be executed. Every transformed avro file should come from a registered vcf file"); throw new CatalogException("Internal error. No vcf file could be found for file " + file.getPath()); } QueryResult<File> vcfQueryResult = fileManager.get(study, vcfId, FILE_GET_QUERY_OPTIONS, sessionId); if (vcfQueryResult.getNumResults() != 1) { logger.error("This code should never be executed. No vcf file could be found for vcf id " + vcfId); throw new CatalogException("Internal error. No vcf file could be found under id " + vcfId); } file = vcfQueryResult.first(); return file; }
protected void checkEtlResults(String studyId, List<StoragePipelineResult> etlResults, String expectedStatus) throws CatalogException { for (StoragePipelineResult etlResult : etlResults) { File input = catalogManager.getFileManager().get(studyId, new Query(FileDBAdaptor.QueryParams.URI.key(), etlResult.getInput()), null, sessionId).first(); String indexedFileId; if (input.getRelatedFiles().isEmpty()) { indexedFileId = input.getId(); } else { long indexedFileUid = input.getRelatedFiles().get(0).getFileId(); indexedFileId = catalogManager.getFileManager().get(studyId, new Query(FileDBAdaptor.QueryParams.UID.key(), indexedFileUid), new QueryOptions(), sessionId).first().getId(); } assertEquals(expectedStatus, catalogManager.getFileManager().get(studyId, indexedFileId, null, sessionId).first().getIndex().getStatus().getName()); System.out.println("etlResult = " + etlResult); } }