public TieringAnalysis(String opencgaHome, String studyStr, String token, String clinicalAnalysisId, List<String> diseasePanelIds, ObjectMap config) { super(opencgaHome, studyStr, token); this.clinicalAnalysisId = clinicalAnalysisId; this.diseasePanelIds = diseasePanelIds; this.maxCoverage = 20; this.cellBaseClient = new CellBaseClient(storageConfiguration.getCellbase().toClientConfiguration()); this.alignmentStorageManager = new AlignmentStorageManager(catalogManager, StorageEngineFactory.get(storageConfiguration)); }
public CustomAnalysis(Query query, String opencgaHome, String studyStr, String token) { super(opencgaHome, studyStr, token); this.query = query; // this.clinicalAnalysisId = clinicalAnalysisId; // this.probandSampleId = probandSampleId; // this.diseaseName = diseaseName; // this.diseasePanelIds = diseasePanelIds; this.maxCoverage = 20; this.cellBaseClient = new CellBaseClient(storageConfiguration.getCellbase().toClientConfiguration()); this.alignmentStorageManager = new AlignmentStorageManager(catalogManager, StorageEngineFactory.get(storageConfiguration)); }
public CellBaseRestVariantAnnotator(StorageConfiguration storageConfiguration, ProjectMetadata projectMetadata, ObjectMap options) throws VariantAnnotatorException { super(storageConfiguration, projectMetadata, options); List<String> hosts = storageConfiguration.getCellbase().getHosts(); if (hosts.isEmpty()) { throw new VariantAnnotatorException("Missing defaultValue \"CellBase Hosts\""); } String cellbaseRest = hosts.get(0); checkNotNull(cellbaseRest, "cellbase hosts"); ClientConfiguration clientConfiguration = storageConfiguration.getCellbase().toClientConfiguration(); clientConfiguration.getRest().setTimeout(TIMEOUT); cellBaseClient = new CellBaseClient(species, assembly, clientConfiguration); logger.info("Annotating with Cellbase REST. host '{}', version '{}', species '{}', assembly '{}'", cellbaseRest, cellbaseVersion, species, assembly); if (impreciseVariants) { // If the cellbase sever supports imprecise variants, use the original toString, which adds the CIPOS and CIEND variantSerializer = Variant::toString; } else { variantSerializer = variant -> variant.getChromosome() + ':' + variant.getStart() + ':' + (variant.getReference().isEmpty() ? "-" : variant.getReference()) + ':' + (variant.getAlternate().isEmpty() ? "-" : variant.getAlternate()); } }
public CellBaseUtils getCellBaseUtils() throws StorageEngineException { if (cellBaseUtils == null) { final ProjectMetadata metadata = getStudyConfigurationManager().getProjectMetadata(getOptions()).first(); String species = metadata.getSpecies(); String assembly = metadata.getAssembly(); ClientConfiguration clientConfiguration = configuration.getCellbase().toClientConfiguration(); if (StringUtils.isEmpty(species)) { species = clientConfiguration.getDefaultSpecies(); } species = toCellBaseSpeciesName(species); cellBaseUtils = new CellBaseUtils(new CellBaseClient(species, assembly, clientConfiguration)); } return cellBaseUtils; }
public VariantSearchManager(StudyConfigurationManager studyConfigurationManager, StorageConfiguration storageConfiguration) { this.storageConfiguration = storageConfiguration; this.solrQueryParser = new SolrQueryParser(studyConfigurationManager); this.cellBaseClient = new CellBaseClient(storageConfiguration.getCellbase().toClientConfiguration()); this.variantSearchToVariantConverter = new VariantSearchToVariantConverter(); this.solrManager = new SolrManager(storageConfiguration.getSearch().getHosts(), storageConfiguration.getSearch().getMode(), storageConfiguration.getSearch().getTimeout()); // Set internal insert batch size from configuration and default value insertBatchSize = storageConfiguration.getSearch().getInsertBatchSize() > 0 ? storageConfiguration.getSearch().getInsertBatchSize() : DEFAULT_INSERT_BATCH_SIZE; logger = LoggerFactory.getLogger(VariantSearchManager.class); }
List<Variant> variants = reader.read(limit); CellBaseClient cellBaseClient = new CellBaseClient(variantStorageEngine.getConfiguration().getCellbase().toClientConfiguration()); QueryResponse<VariantAnnotation> queryResponse = cellBaseClient.getVariantClient().getAnnotationByVariantIds(variants.stream().map(Variant::toString).collect(Collectors.toList()), QueryOptions.empty());