public VariantFileMetadata readVariantFileMetadata(URI input) throws StorageEngineException { VariantFileMetadata variantFileMetadata = variantReaderUtils.readVariantFileMetadata(input); // Ensure correct fileId // FIXME // variantFileMetadata.setId(String.valueOf(getFileId())); variantFileMetadata.setId(null); return variantFileMetadata; }
public void stageSuccess(VariantFileMetadata metadata) throws StorageEngineException { // Stage loading finished. Save VariantSource and update BatchOperation int fileId = getFileId(); metadata.setId(String.valueOf(fileId)); getStudyConfigurationManager() .atomicSetStatus(getStudyId(), BatchFileOperation.Status.READY, STAGE.key(), Collections.singletonList(fileId)); metadata.setId(String.valueOf(fileId)); dbAdaptor.getStudyConfigurationManager().updateVariantFileMetadata(String.valueOf(getStudyId()), metadata); }
public static VariantFileMetadata readVariantFileMetadata(File file, URI fileUri) throws IOException { File.Format format = file.getFormat(); File.Format detectFormat = FileUtils.detectFormat(fileUri); if (format == File.Format.VCF || format == File.Format.GVCF || format == File.Format.BCF || detectFormat == File.Format.VCF || detectFormat == File.Format.GVCF || detectFormat == File.Format.BCF) { VariantFileMetadata metadata = new VariantFileMetadata(String.valueOf(file.getUid()), file.getName()); metadata.setId(String.valueOf(file.getUid())); return VariantMetadataUtils.readVariantFileMetadata(Paths.get(fileUri.getPath()), metadata); } else { return null; } }
protected VariantFileMetadata createEmptyVariantFileMetadata(Path input) { VariantFileMetadata fileMetadata = VariantReaderUtils.createEmptyVariantFileMetadata(input); int fileId; if (options.getBoolean(Options.ISOLATE_FILE_FROM_STUDY_CONFIGURATION.key(), Options.ISOLATE_FILE_FROM_STUDY_CONFIGURATION .defaultValue())) { fileId = -1; } else { fileId = getFileId(); } return fileMetadata.setId(Integer.toString(fileId)); }
meta.setId(String.valueOf(fileId)); storeMetaData(String.valueOf(studyId), meta, conf);
@Override public boolean pre() { if (metadataPath != null) { Files.exists(metadataPath); try (InputStream inputStream = FileUtils.newInputStream(metadataPath)) { // Read global JSON file and copy its info into the already available VariantSource object VariantFileMetadata readMetadata = VariantReaderUtils.readVariantFileMetadataFromJson(inputStream); fileMetadata.setId(readMetadata.getId()); fileMetadata.setPath(readMetadata.getPath()); fileMetadata.setHeader(readMetadata.getHeader()); fileMetadata.setSamplesPosition(readMetadata.getSamplesPosition()); fileMetadata.setStats(readMetadata.getStats()); } catch (IOException ex) { throw new UncheckedIOException(ex); } } if (fileMetadata != null) { Map<String, Integer> samplesPosition = fileMetadata.getSamplesPosition(); this.samplesPosition = new LinkedHashMap<>(samplesPosition.size()); String[] samples = new String[samplesPosition.size()]; for (Map.Entry<String, Integer> entry : samplesPosition.entrySet()) { samples[entry.getValue()] = entry.getKey(); } for (int i = 0; i < samples.length; i++) { this.samplesPosition.put(samples[i], i); } } return true; }
fileMetadata.setId(String.valueOf(fileId));
@Override public URI postLoad(URI input, URI output) throws StorageEngineException { StudyConfigurationManager scm = getStudyConfigurationManager(); try { int studyId = getStudyId(); VariantFileMetadata fileMetadata = readVariantFileMetadata(input); fileMetadata.setId(String.valueOf(getFileId())); scm.updateVariantFileMetadata(studyId, fileMetadata); dbAdaptor.getVariantFileMetadataDBAdaptor().updateLoadedFilesSummary(studyId, Collections.singletonList(getFileId())); } catch (IOException e) { throw new StorageEngineException("Error storing VariantFileMetadata for file " + getFileId(), e); } registerLoadedFiles(Collections.singletonList(getFileId())); // This method checks the loaded variants (if possible) and adds the loaded files to the studyConfiguration super.postLoad(input, output); return input; }
@Override public URI postLoad(URI input, URI output) throws StorageEngineException { logger.info("Post load file " + input); VariantFileMetadata fileMetadata = readVariantFileMetadata(input); fileMetadata.setId(String.valueOf(getFileId())); dbAdaptor.getStudyConfigurationManager().updateVariantFileMetadata(getStudyId(), fileMetadata); return super.postLoad(input, output); }
loadStats.append("writeResult", writeResult); fileMetadata.setId(String.valueOf(fileId)); dbAdaptor.getStudyConfigurationManager().updateVariantFileMetadata(String.valueOf(studyId), fileMetadata); } catch (ExecutionException e) {