@After public void tearDown() throws Exception { DummyProjectMetadataAdaptor.writeAndClear(catalogManagerExternalResource.getOpencgaHome()); DummyStudyConfigurationAdaptor.writeAndClear(catalogManagerExternalResource.getOpencgaHome()); }
public Path isolateOpenCGA() throws IOException { Path opencgaHome = catalogManagerExternalResource.getOpencgaHome(); Path userHome = opencgaHome.resolve("user_home"); Path conf = opencgaHome.resolve("conf");
@Test public void testCreateFileInLinkedFolder() throws Exception { // Create an empty folder Path dir = catalogManagerResource.getOpencgaHome().resolve("folder_to_link"); Files.createDirectory(dir); URI uri = dir.toUri(); // Link the folder in the root link(uri, "", studyFqn, new ObjectMap(), sessionIdUser); File file = catalogManager.getFileManager().create(studyFqn, File.Type.FILE, File.Format.PLAIN, File.Bioformat .NONE, "folder_to_link/file.txt", null, "", null, 0, -1, null, (long) -1, null, null, false, null, null, sessionIdUser).first(); assertEquals(uri.resolve("file.txt"), file.getUri()); }
@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 = 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); }
sessionIdUser2); Path myStudy = Files.createDirectory(catalogManagerResource.getOpencgaHome().resolve("myStudy")); String newStudy = catalogManager.getStudyManager().create(project2, "alias", null, "name", Study.Type.CASE_CONTROL, "", "", null, null, null, myStudy.toUri(), null, null, null, null, sessionIdUser2).first().getFqn();