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; }
private void updateIndexStatusAfterDeletionOfTransformedFile(long studyId, File file) throws CatalogDBException { if (file.getType() == File.Type.FILE && (file.getRelatedFiles() == null || file.getRelatedFiles().isEmpty())) { return; for (File transformedFile : fileQR.getResult()) { fileIds.addAll( transformedFile.getRelatedFiles().stream() .filter(myFile -> myFile.getRelation() == File.RelatedFile.Relation.PRODUCED_FROM) .map(File.RelatedFile::getFileId)
if (fileAux.getRelatedFiles() != null && !fileAux.getRelatedFiles().isEmpty()) { transformedFromFileIds.addAll( fileAux.getRelatedFiles().stream() .filter(myFile -> myFile.getRelation() == File.RelatedFile.Relation.PRODUCED_FROM) .map(File.RelatedFile::getFileId)
if (file.getRelatedFiles() == null || file.getRelatedFiles().isEmpty()) { catalogManager.getFileManager().matchUpVariantFiles(studyStr, Collections.singletonList(file), sessionId); if (file.getRelatedFiles() != null) { for (File.RelatedFile relatedFile : file.getRelatedFiles()) { if (File.RelatedFile.Relation.PRODUCED_FROM.equals(relatedFile.getRelation())) { Query query = new Query(FileDBAdaptor.QueryParams.UID.key(), relatedFile.getFileId());
fileSolrModel.setNumRelatedFiles(file.getRelatedFiles() != null ? file.getRelatedFiles().size() : 0);
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); } }
List<File.RelatedFile> relatedFiles = ParamUtils.defaultObject(json.getRelatedFiles(), ArrayList::new); relatedFiles = ParamUtils.defaultObject(transformedFile.getRelatedFiles(), ArrayList::new);
List<File.RelatedFile> relatedFiles = transformedFile.getRelatedFiles().stream() .filter(relatedFile -> relatedFile.getRelation().equals(File.RelatedFile.Relation.PRODUCED_FROM)) .collect(Collectors.toList());
List<File.RelatedFile> relatedFiles = transformedFile.getRelatedFiles().stream() .filter(relatedFile -> relatedFile.getRelation().equals(File.RelatedFile.Relation.PRODUCED_FROM)) .collect(Collectors.toList());
file.setBioformat(ParamUtils.defaultObject(file.getBioformat(), File.Bioformat.NONE)); file.setDescription(ParamUtils.defaultString(file.getDescription(), "")); file.setRelatedFiles(ParamUtils.defaultObject(file.getRelatedFiles(), ArrayList::new)); file.setCreationDate(TimeUtils.getTime()); file.setModificationDate(file.getCreationDate());