private URI getStudyUri(long studyId) throws CatalogException { return studyDBAdaptor.get(studyId, INCLUDE_STUDY_URI).first().getUri(); }
variableSetId = Long.parseLong(variableStr); Query query = new Query(StudyDBAdaptor.QueryParams.VARIABLE_SET_UID.key(), variableSetId); QueryResult<Study> studyQueryResult = studyDBAdaptor.get(query, new QueryOptions(QueryOptions.INCLUDE, StudyDBAdaptor.QueryParams.UID.key())); if (studyQueryResult.getNumResults() == 0) {
QueryResult<Study> studyQueryResult = studyDBAdaptor.get(studyId, new QueryOptions(QueryOptions.INCLUDE, StudyDBAdaptor.QueryParams.VARIABLE_SET.key())); if (studyQueryResult.getNumResults() == 0) {
StudyDBAdaptor.QueryParams.FQN.key(), StudyDBAdaptor.QueryParams.VARIABLE_SET.key())) .append(DBAdaptor.INCLUDE_ACLS, true); QueryResult<Study> studyQueryResult = studyDBAdaptor.get(query, options); if (studyQueryResult.getNumResults() == 0) { throw new CatalogException("Could not index catalog into solr. No studies found");
/** * Fetch all the study objects matching the query. * * @param query Query to catalog. * @param options Query options, like "include", "exclude", "limit" and "skip" * @param sessionId sessionId * @return All matching elements. * @throws CatalogException CatalogException */ public QueryResult<Study> get(Query query, QueryOptions options, String sessionId) throws CatalogException { query = ParamUtils.defaultObject(query, Query::new); QueryOptions qOptions = options != null ? new QueryOptions(options) : new QueryOptions(); String userId = catalogManager.getUserManager().getUserId(sessionId); if (!qOptions.containsKey("include") || qOptions.get("include") == null || qOptions.getAsStringList("include").isEmpty()) { qOptions.addToListOption("exclude", "projects.studies.attributes.studyConfiguration"); } return studyDBAdaptor.get(query, qOptions, userId); }
@Test public void updateDiskUsage() throws Exception { catalogDBAdaptor.getCatalogStudyDBAdaptor().updateDiskUsage(5, 100); assertEquals(2100, catalogStudyDBAdaptor.get(5, null).getResult().get(0).getSize()); catalogDBAdaptor.getCatalogStudyDBAdaptor().updateDiskUsage(5, -200); assertEquals(1900, catalogStudyDBAdaptor.get(5, null).getResult().get(0).getSize()); }
.append(StudyDBAdaptor.QueryParams.PROJECT_ID.key(), projectId) .append(StudyDBAdaptor.QueryParams.RELEASE.key(), "<=" + release); QueryResult<Study> studyQueryResult = studyDBAdaptor.get(query, new QueryOptions(QueryOptions.INCLUDE, StudyDBAdaptor.QueryParams.UID.key())); if (studyQueryResult.getNumResults() == 0) {
/** * Fetch a study from Catalog given a study id or alias. * * @param studyStr Study id or alias. * @param options Read options * @param sessionId sessionId * @return The specified object * @throws CatalogException CatalogException */ public QueryResult<Study> get(String studyStr, QueryOptions options, String sessionId) throws CatalogException { options = ParamUtils.defaultObject(options, QueryOptions::new); String userId = catalogManager.getUserManager().getUserId(sessionId); Study study = catalogManager.getStudyManager().resolveId(studyStr, userId); Query query = new Query(StudyDBAdaptor.QueryParams.UID.key(), study.getUid()); QueryResult<Study> studyQueryResult = studyDBAdaptor.get(query, options, userId); if (studyQueryResult.getNumResults() <= 0) { throw CatalogAuthorizationException.deny(userId, "view", "study", study.getFqn(), ""); } return studyQueryResult; }
QueryResult<Study> studyQueryResult = studyDBAdaptor.get(resource.getStudy().getUid(), new QueryOptions(QueryOptions.INCLUDE, StudyDBAdaptor.QueryParams.VARIABLE_SET.key())); if (studyQueryResult.getNumResults() == 0) { QueryResult<Study> studyQueryResult = studyDBAdaptor.get(resource.getStudy().getUid(), new QueryOptions(QueryOptions.INCLUDE, StudyDBAdaptor.QueryParams.VARIABLE_SET.key()));
QueryResult<Study> studyQueryResult = studyDBAdaptor.get(query, queryOptions, userId);
public Study getStudy(File file, String sessionId) throws CatalogException { ParamUtils.checkObj(file, "file"); ParamUtils.checkObj(sessionId, "session id"); if (file.getStudyUid() <= 0) { throw new CatalogException("Missing study uid field in file"); } String user = catalogManager.getUserManager().getUserId(sessionId); Query query = new Query(StudyDBAdaptor.QueryParams.UID.key(), file.getStudyUid()); QueryResult<Study> studyQueryResult = studyDBAdaptor.get(query, QueryOptions.empty(), user); if (studyQueryResult.getNumResults() == 1) { return studyQueryResult.first(); } else { authorizationManager.checkCanViewStudy(file.getStudyUid(), user); throw new CatalogException("Incorrect study uid"); } }
public Study getStudy(Job job, String sessionId) throws CatalogException { ParamUtils.checkObj(job, "job"); ParamUtils.checkObj(sessionId, "session id"); if (job.getStudyUid() <= 0) { throw new CatalogException("Missing study uid field in file"); } String user = catalogManager.getUserManager().getUserId(sessionId); Query query = new Query(StudyDBAdaptor.QueryParams.UID.key(), job.getStudyUid()); QueryResult<Study> studyQueryResult = studyDBAdaptor.get(query, QueryOptions.empty(), user); if (studyQueryResult.getNumResults() == 1) { return studyQueryResult.first(); } else { authorizationManager.checkCanViewStudy(job.getStudyUid(), user); throw new CatalogException("Incorrect study uid"); } }