@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()); } } }
fileManager.iterator(studyFQN, query, new QueryOptions(QueryOptions.INCLUDE, Arrays.asList(UID.key(), FileDBAdaptor.QueryParams.URI.key())), sessionId) .forEachRemaining(transformed -> { foundTransformedFiles.add(transformed.getUid()); fileUris.add(transformed.getUri());
@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); }
public <T> void insertCatalogCollection(DBIterator<T> iterator, ComplexTypeConverter converter, String collectionName) throws IOException, CatalogException { int count = 0; List<T> records = new ArrayList<>(insertBatchSize); while (iterator.hasNext()) { T record = iterator.next(); records.add(record); count++; if (count % insertBatchSize == 0) { insertCatalogCollection(records, converter, collectionName); records.clear(); } } if (CollectionUtils.isNotEmpty(records)) { insertCatalogCollection(records, converter, collectionName); } }