public CatalogManager getCatalogManager() { return catalogManagerExternalResource.getCatalogManager(); }
@Before public void setUp() throws IOException, CatalogException { catalogManager = catalogManagerResource.getCatalogManager(); setUpCatalogManager(catalogManager); }
@Before public void setUp() throws IOException, CatalogException { catalogManager = catalogManagerResource.getCatalogManager(); setUpCatalogManager(catalogManager); }
@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, URISyntaxException { catalogManager = catalogManagerExternalResource.getCatalogManager(); catalogManager.getUserManager().create("user", "User Name", "mail@ebi.ac.uk", PASSWORD, "", null, Account.FULL, null, null); sessionIdUser = catalogManager.getUserManager().login("user", PASSWORD); project = catalogManager.getProjectManager().create("1000G", "Project about some genomes", "", "ACME", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), sessionIdUser).first(); study = catalogManager.getStudyManager().create(project.getId(), "phase1", null, "Phase 1", Study.Type.TRIO, null, "Done", null, null, null, null, null, null, null, null, sessionIdUser).first(); folder = catalogManager.getFileManager().createFolder(study.getId(), Paths.get("data/vcf/").toString(), null, true, null, QueryOptions.empty(), sessionIdUser).first(); Path vcfPath = catalogManagerExternalResource.getOpencgaHome().resolve(VCF_FILE_NAME); Files.copy(this.getClass().getClassLoader().getResourceAsStream("biofiles/" + VCF_FILE_NAME), vcfPath, StandardCopyOption.REPLACE_EXISTING); vcfFileUri = vcfPath.toUri(); Path bamPath = catalogManagerExternalResource.getOpencgaHome().resolve(BAM_FILE_NAME); Files.copy(this.getClass().getClassLoader().getResourceAsStream("biofiles/" + BAM_FILE_NAME), bamPath, StandardCopyOption.REPLACE_EXISTING); bamFileUri = bamPath.toUri(); }
@Before public void setUp() throws IOException, CatalogException { catalogManager = catalogManagerResource.getCatalogManager(); panelManager = catalogManager.getPanelManager(); setUpCatalogManager(catalogManager); adminToken = catalogManager.getUserManager().login("admin", "admin"); }
@Before public void setUp() throws IOException, CatalogException { catalogManager = catalogManagerExternalResource.getCatalogManager(); catalogManager.getUserManager().create("user", "User Name", "mail@ebi.ac.uk", PASSWORD, "", null, Account.FULL, null, null); sessionIdUser = catalogManager.getUserManager().login("user", PASSWORD); project = catalogManager.getProjectManager().create("1000G", "Project about some genomes", "", "ACME", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), sessionIdUser).first(); study = catalogManager.getStudyManager().create(project.getId(), "phase1", null, "Phase 1", Study.Type.TRIO, null, "Done", null, null, null, null, null, null, null, null, sessionIdUser).first(); folder = catalogManager.getFileManager().createFolder(study.getId(), Paths.get("data/test/folder/").toString(), null, true, null, QueryOptions.empty(), sessionIdUser).first(); directory = catalogManagerExternalResource.getOpencgaHome().resolve("catalog_scan_test_folder").toAbsolutePath(); if (directory.toFile().exists()) { IOUtils.deleteDirectory(directory); } Files.createDirectory(directory); }
catalogManager = catalogManagerExternalResource.getCatalogManager(); fileMetadataReader = FileMetadataReader.get(catalogManager); catalogFileUtils = new FileUtils(catalogManager);
@BeforeClass public static void setUp() throws Exception { catalog = catalogManagerExternalResource.getCatalogManager();