@Override public void forEach(Query query, Consumer<? super Object> action, QueryOptions options) throws CatalogDBException { Objects.requireNonNull(action); try (DBIterator<Individual> catalogDBIterator = iterator(query, options)) { while (catalogDBIterator.hasNext()) { action.accept(catalogDBIterator.next()); } } }
@Override public void forEach(Query query, Consumer<? super Object> action, QueryOptions options) throws CatalogDBException { Objects.requireNonNull(action); try (DBIterator<Study> catalogDBIterator = iterator(query, options)) { while (catalogDBIterator.hasNext()) { action.accept(catalogDBIterator.next()); } } }
@Override public void forEach(Query query, Consumer<? super Object> action, QueryOptions options) throws CatalogDBException { Objects.requireNonNull(action); try (DBIterator<ClinicalAnalysis> catalogDBIterator = iterator(query, options)) { while (catalogDBIterator.hasNext()) { action.accept(catalogDBIterator.next()); } } }
@Override public void forEach(Query query, Consumer<? super Object> action, QueryOptions options) throws CatalogDBException { Objects.requireNonNull(action); try (DBIterator<File> catalogDBIterator = iterator(query, options)) { while (catalogDBIterator.hasNext()) { action.accept(catalogDBIterator.next()); } } }
@Override public void forEach(Query query, Consumer<? super Object> action, QueryOptions options) throws CatalogDBException { Objects.requireNonNull(action); try (DBIterator<Family> catalogDBIterator = iterator(query, options)) { while (catalogDBIterator.hasNext()) { action.accept(catalogDBIterator.next()); } } }
@Override public void forEach(Query query, Consumer<? super Object> action, QueryOptions options) throws CatalogDBException { Objects.requireNonNull(action); try (DBIterator<Interpretation> catalogDBIterator = iterator(query, options)) { while (catalogDBIterator.hasNext()) { action.accept(catalogDBIterator.next()); } } }
@Override public void forEach(Query query, Consumer<? super Object> action, QueryOptions options) throws CatalogDBException { Objects.requireNonNull(action); try (DBIterator<Cohort> catalogDBIterator = iterator(query, options)) { while (catalogDBIterator.hasNext()) { action.accept(catalogDBIterator.next()); } } }
@Override public void forEach(Query query, Consumer<? super Object> action, QueryOptions options) throws CatalogDBException { Objects.requireNonNull(action); try (DBIterator<Dataset> catalogDBIterator = iterator(query, options)) { while (catalogDBIterator.hasNext()) { action.accept(catalogDBIterator.next()); } } }
@Override public void forEach(Query query, Consumer<? super Object> action, QueryOptions options) throws CatalogDBException { Objects.requireNonNull(action); try (DBIterator<Job> catalogDBIterator = iterator(query, options)) { while (catalogDBIterator.hasNext()) { action.accept(catalogDBIterator.next()); } } }
@Override public void forEach(Query query, Consumer<? super Object> action, QueryOptions options) throws CatalogDBException { Objects.requireNonNull(action); try (DBIterator<Sample> catalogDBIterator = iterator(query, options)) { while (catalogDBIterator.hasNext()) { action.accept(catalogDBIterator.next()); } } }
@Override public void forEach(Query query, Consumer<? super Object> action, QueryOptions options) throws CatalogDBException { Objects.requireNonNull(action); try (DBIterator<Project> catalogDBIterator = iterator(query, options)) { while (catalogDBIterator.hasNext()) { action.accept(catalogDBIterator.next()); } } }
@Override public void forEach(Query query, Consumer<? super Object> action, QueryOptions options) throws CatalogDBException { Objects.requireNonNull(action); try (DBIterator<User> catalogDBIterator = iterator(query, options)) { while (catalogDBIterator.hasNext()) { action.accept(catalogDBIterator.next()); } } }
@Override public void forEach(Query query, Consumer<? super Object> action, QueryOptions options) throws CatalogDBException { Objects.requireNonNull(action); try (DBIterator<Panel> catalogDBIterator = iterator(query, options)) { while (catalogDBIterator.hasNext()) { action.accept(catalogDBIterator.next()); } } }
@Override public QueryResult nativeGet(Query query, QueryOptions options, String user) throws CatalogDBException, CatalogAuthorizationException { long startTime = startQuery(); List<Document> documentList = new ArrayList<>(); try (DBIterator<Document> dbIterator = nativeIterator(query, options, user)) { while (dbIterator.hasNext()) { documentList.add(dbIterator.next()); } } return endQuery("Native get", startTime, documentList); }
@Override public QueryResult<Document> nativeGet(Query query, QueryOptions options) throws CatalogDBException { long startTime = startQuery(); List<Document> documentList = new ArrayList<>(); try (DBIterator<Document> dbIterator = nativeIterator(query, options)) { while (dbIterator.hasNext()) { documentList.add(dbIterator.next()); } } return endQuery("Native get", startTime, documentList); }
@Override public QueryResult nativeGet(Query query, QueryOptions options) throws CatalogDBException { long startTime = startQuery(); List<Document> documentList = new ArrayList<>(); try (DBIterator<Document> dbIterator = nativeIterator(query, options)) { while (dbIterator.hasNext()) { documentList.add(dbIterator.next()); } } return endQuery("Native get", startTime, documentList); }
@Override public QueryResult nativeGet(Query query, QueryOptions options, String user) throws CatalogDBException, CatalogAuthorizationException { long startTime = startQuery(); List<Document> documentList = new ArrayList<>(); try (DBIterator<Document> dbIterator = nativeIterator(query, options, user)) { while (dbIterator.hasNext()) { documentList.add(dbIterator.next()); } } return endQuery("Native get", startTime, documentList); }
@Override public QueryResult<Study> get(Query query, QueryOptions options) throws CatalogDBException { long startTime = startQuery(); List<Study> documentList = new ArrayList<>(); QueryResult<Study> studyQueryResult; try (DBIterator<Study> dbIterator = iterator(query, options)) { while (dbIterator.hasNext()) { documentList.add(dbIterator.next()); } } studyQueryResult = endQuery("Get", startTime, documentList); for (Study study : studyQueryResult.getResult()) { joinFields(study, options); } return studyQueryResult; }
public QueryResult<ReportedVariant> index(String study, String token) throws IOException, ClinicalVariantException, CatalogException { DBIterator<ClinicalAnalysis> clinicalAnalysisDBIterator = clinicalAnalysisManager.iterator(study, new Query(), QueryOptions.empty(), token); while (clinicalAnalysisDBIterator.hasNext()) { ClinicalAnalysis clinicalAnalysis = clinicalAnalysisDBIterator.next(); for (Interpretation interpretation : clinicalAnalysis.getInterpretations()) { interpretation.getInterpretation().getAttributes().put("OPENCGA_CLINICAL_ANALYSIS", clinicalAnalysis); this.clinicalVariantEngine.insert(interpretation.getInterpretation(), database); } } return null; }
@Test public void testIteratorSamples() throws CatalogException { Query query = new Query(); DBIterator<Sample> iterator = catalogManager.getSampleManager().iterator(studyFqn, query, null, sessionIdUser); int count = 0; while (iterator.hasNext()) { iterator.next(); count++; } assertEquals(9, count); }