public QueryResult<File> link(String studyStr, URI uriOrigin, String pathDestiny, ObjectMap params, String sessionId) throws CatalogException, IOException { // We make two attempts to link to ensure the behaviour remains even if it is being called at the same time link from different // threads String userId = userManager.getUserId(sessionId); Study study = catalogManager.getStudyManager().resolveId(studyStr, userId); try { return privateLink(study, uriOrigin, pathDestiny, params, sessionId); } catch (CatalogException | IOException e) { return privateLink(study, uriOrigin, pathDestiny, params, sessionId); } }
public QueryResult<File> create(String studyStr, File file, boolean parents, String content, QueryOptions options, String sessionId) throws CatalogException { String userId = userManager.getUserId(sessionId); Study study = catalogManager.getStudyManager().resolveId(studyStr, userId); return create(study, file, parents, content, options, sessionId); }
public QueryResult<VariableSet> createVariableSet(String studyId, String id, String name, Boolean unique, Boolean confidential, String description, Map<String, Object> attributes, List<Variable> variables, String sessionId) throws CatalogException { String userId = catalogManager.getUserManager().getUserId(sessionId); Study study = resolveId(studyId, userId); return createVariableSet(study, id, name, unique, confidential, description, attributes, variables, sessionId); }
SampleManager(AuthorizationManager authorizationManager, AuditManager auditManager, CatalogManager catalogManager, DBAdaptorFactory catalogDBAdaptorFactory, CatalogIOManagerFactory ioManagerFactory, Configuration configuration) { super(authorizationManager, auditManager, catalogManager, catalogDBAdaptorFactory, ioManagerFactory, configuration); this.userManager = catalogManager.getUserManager(); this.studyManager = catalogManager.getStudyManager(); }
@Before public void setUp() throws IOException, CatalogException { catalogManager = catalogManagerResource.getCatalogManager(); panelManager = catalogManager.getPanelManager(); setUpCatalogManager(catalogManager); adminToken = catalogManager.getUserManager().login("admin", "admin"); }
public void clearCache(String studyId, String type, String sessionId) throws CatalogException { String userId = catalogManager.getUserManager().getUserId(sessionId); }
private String getAdminToken() throws CatalogException, IOException { return catalogManager.getUserManager().login("admin", "admin"); }
protected void updateCohorts(String studyId, List<String> cohortIds, String sessionId, String status, String message) throws CatalogException { for (String cohortId : cohortIds) { catalogManager.getCohortManager().setStatus(studyId, cohortId, status, message, sessionId); } }
@Before public void setUp() throws IOException, CatalogException { catalogManager = catalogManagerResource.getCatalogManager(); familyManager = catalogManager.getFamilyManager(); setUpCatalogManager(catalogManager); }
@Before public void setUp() throws IOException, CatalogException { catalogManager = catalogManagerResource.getCatalogManager(); familyManager = catalogManager.getFamilyManager(); setUpCatalogManager(catalogManager); }
@Before public void setUp() throws IOException, CatalogException { super.setUp(); fileManager = catalogManager.getFileManager(); }
@Before public void setUp() throws IOException, CatalogException { catalogManager = catalogManagerResource.getCatalogManager(); setUpCatalogManager(catalogManager); }
@Override public QueryResult<Interpretation> search(String studyStr, Query query, QueryOptions options, String sessionId) throws CatalogException { return get(studyStr, query, options, sessionId); }
private String getMetaFile(String path) { String file = getOriginalFile(path); if (file != null) { return file + ".file.json.gz"; } else { return null; } }
IndividualManager(AuthorizationManager authorizationManager, AuditManager auditManager, CatalogManager catalogManager, DBAdaptorFactory catalogDBAdaptorFactory, CatalogIOManagerFactory ioManagerFactory, Configuration configuration) { super(authorizationManager, auditManager, catalogManager, catalogDBAdaptorFactory, ioManagerFactory, configuration); this.userManager = catalogManager.getUserManager(); this.studyManager = catalogManager.getStudyManager(); }
public void clearCache(String studyId, String sessionId) throws CatalogException { String userId = catalogManager.getUserManager().getUserId(sessionId); }
PanelManager(AuthorizationManager authorizationManager, AuditManager auditManager, CatalogManager catalogManager, DBAdaptorFactory catalogDBAdaptorFactory, CatalogIOManagerFactory ioManagerFactory, Configuration configuration) { super(authorizationManager, auditManager, catalogManager, catalogDBAdaptorFactory, ioManagerFactory, configuration); this.userManager = catalogManager.getUserManager(); this.studyManager = catalogManager.getStudyManager(); }
public void clearCache(String sessionId) throws CatalogException { String userId = catalogManager.getUserManager().getUserId(sessionId); }
FamilyManager(AuthorizationManager authorizationManager, AuditManager auditManager, CatalogManager catalogManager, DBAdaptorFactory catalogDBAdaptorFactory, CatalogIOManagerFactory ioManagerFactory, Configuration configuration) { super(authorizationManager, auditManager, catalogManager, catalogDBAdaptorFactory, ioManagerFactory, configuration); this.userManager = catalogManager.getUserManager(); this.studyManager = catalogManager.getStudyManager(); }
CohortManager(AuthorizationManager authorizationManager, AuditManager auditManager, CatalogManager catalogManager, DBAdaptorFactory catalogDBAdaptorFactory, CatalogIOManagerFactory ioManagerFactory, Configuration configuration) { super(authorizationManager, auditManager, catalogManager, catalogDBAdaptorFactory, ioManagerFactory, configuration); this.userManager = catalogManager.getUserManager(); this.studyManager = catalogManager.getStudyManager(); }