} catch (CatalogException e) { logger.warn("'{}' does not exist. Trying to create the output directory.", outDirPath); QueryResult<File> folder = createFolder(studyStr, outDirPath, new File.FileStatus(), true, "", new QueryOptions(), sessionId); outDir = folder.first();
StopWatch watch = StopWatch.createStarted(); String currentStatus = file.getStatus().getName(); if (File.FileStatus.DELETED.equals(currentStatus)) { throw new CatalogException("The file was already deleted");
description, new File.FileStatus(File.FileStatus.READY), true, size, null, new Experiment(), Collections.emptyList(), new Job(), Collections.emptyList(), null, catalogManager.getStudyManager().getCurrentRelease(study, userId), Collections.emptyList(), Collections.emptyMap(),
} else { if (file.getType() == File.Type.FILE) { if (file.getStatus().getName().equals(File.FileStatus.MISSING)) { logger.info("File { id:" + file.getUid() + ", path:\"" + file.getPath() + "\" } recover tracking from file " + uri); logger.debug("Set status to " + File.FileStatus.READY);
file.setModificationDate(file.getCreationDate()); if (file.getType() == File.Type.FILE) { file.setStatus(ParamUtils.defaultObject(file.getStatus(), new File.FileStatus(File.FileStatus.STAGE))); } else { file.setStatus(ParamUtils.defaultObject(file.getStatus(), new File.FileStatus(File.FileStatus.READY))); newParent = true; File parentFile = new File(File.Type.DIRECTORY, File.Format.NONE, File.Bioformat.NONE, parentPath, "", new File.FileStatus(File.FileStatus.READY), 0, file.getSamples(), -1, null, Collections.emptyMap(), Collections.emptyMap()); parentFileId = register(study, parentFile, parents, options, sessionId).first().getUid();
throw new CatalogException("Cannot check file status for deletion"); if (File.FileStatus.STAGE.equals(fileAux.getStatus().getName()) || File.FileStatus.MISSING.equals(fileAux.getStatus().getName())) { throw new CatalogException("Cannot delete file: " + fileAux.getName() + ". The status is " + fileAux.getStatus().getName());
} else { try { outDir = catalogManager.getFileManager().createFolder(studyStr, outputDir, new File.FileStatus(), true, "", QueryOptions.empty(), userToken).first(); parameters.append(JobDBAdaptor.QueryParams.OUT_DIR.key(), outDir);
new File.FileStatus(File.FileStatus.READY), 0, project.getCurrentRelease()); rootFile.setUuid(UUIDUtils.generateOpenCGAUUID(UUIDUtils.Entity.FILE)); files.add(rootFile);
Arrays.asList( new File("data/", File.Type.DIRECTORY, File.Format.PLAIN, File.Bioformat.NONE, "data/", "", new File.FileStatus(File.FileStatus.READY), 1000, 1), new File("file.vcf", File.Type.FILE, File.Format.PLAIN, File.Bioformat.NONE, "data/file.vcf", "", new File.FileStatus(File.FileStatus.READY), 1000, 1) ), Collections.emptyList(), new LinkedList<>(), new LinkedList<>(), new LinkedList<>(), new LinkedList<>(), Collections.emptyList(), new LinkedList<>(), null, null, null, 1, Collections.emptyMap(), Arrays.asList(new Group("@members", Collections.emptyList())), null, Arrays.asList( new File("data/", File.Type.DIRECTORY, File.Format.UNKNOWN, File.Bioformat.NONE, "data/", "Description", new File.FileStatus(File.FileStatus.READY), 10, 1), new File("file1.txt", File.Type.FILE, File.Format.COMMA_SEPARATED_VALUES, File.Bioformat.NONE, "data/file1.txt", "Description", new File.FileStatus(File.FileStatus.READY), 100, 1), new File("file2.txt", File.Type.FILE, File.Format.COMMA_SEPARATED_VALUES, File.Bioformat.NONE, "data/file2.txt", "Description2", new File.FileStatus(File.FileStatus.READY), 100, 1), new File("alignment.bam", File.Type.FILE, File.Format.BAM, File.Bioformat.ALIGNMENT, "data/alignment.bam", "Tophat alignment file", new File.FileStatus(File.FileStatus.READY), 5000, 1) ), Collections.emptyList(), new LinkedList<>(), new LinkedList<>(), new LinkedList<>(), new LinkedList<>(), Collections.emptyList(), new LinkedList<>(), null, null, null, 1, Arrays.asList( new File("data/", File.Type.DIRECTORY, File.Format.UNKNOWN, File.Bioformat.NONE, "data/", "Description", new File.FileStatus(File.FileStatus.READY), 10, 1), new File("m_file1.txt", File.Type.FILE, File.Format.COMMA_SEPARATED_VALUES, File.Bioformat.NONE, "data/file1.txt", "Description", new File.FileStatus(File.FileStatus.READY), 100, 1),
stringPath, null, TimeUtils.getTime(), TimeUtils.getTime(), "", new File.FileStatus(File.FileStatus.READY), false, 0, null, new Experiment(), Collections.emptyList(), new Job(), Collections.emptyList(), null, catalogManager.getStudyManager().getCurrentRelease(study, userId), Collections.emptyList(), null, null);
new File.FileStatus(), true, "", QueryOptions.empty(), sessionId);
switch (file.getStatus().getName()) { case File.FileStatus.READY: case File.FileStatus.MISSING: { if (!catalogManager.getCatalogIOManagerFactory().get(fileUri).exists(fileUri)) { logger.warn("File { id:" + file.getPath() + ", path:\"" + file.getPath() + "\" } lost tracking from file " + fileUri); if (!file.getStatus().getName().equals(File.FileStatus.MISSING)) { logger.info("Set status to " + File.FileStatus.MISSING); catalogManager.getFileManager().setStatus(studyStr, file.getPath(), File.FileStatus.MISSING, null, sessionId); modifiedFile = catalogManager.getFileManager().get(studyStr, file.getPath(), null, sessionId).first(); } else if (file.getStatus().getName().equals(File.FileStatus.MISSING)) { logger.info("File { path:\"" + file.getPath() + "\" } recover tracking from file " + fileUri); logger.info("Set status to " + File.FileStatus.READY);
TimeUtils.getTime(), description, new File.FileStatus(File.FileStatus.READY), true, size, null, new Experiment(), Collections.emptyList(), new Job(), Collections.emptyList(), null, catalogManager.getStudyManager().getCurrentRelease(study, userId), Collections.emptyList(),
assertEquals(File.FileStatus.MISSING, returnedFile.getStatus().getName()); returnedFile = catalogFileUtils.checkFile(studyFqn, file, true, userSessionId); assertEquals("Should not modify the still MISSING file, so should return the same file.", file.getStatus().getName(), returnedFile.getStatus().getName()); assertEquals(File.FileStatus.READY, returnedFile.getStatus().getName()); assertEquals(File.FileStatus.TRASHED, returnedFile.getStatus().getName()); assertEquals(File.FileStatus.TRASHED, returnedFile.getStatus().getName());
QueryResult<File> queryResult = catalogManager.getFileManager().create(studyFqn, new File().setPath("data/" + fileName), false, StringUtils.randomString(200), null, sessionIdUser); assertTrue("", queryResult.first().getStatus().getName().equals(File.FileStatus.READY)); assertTrue("", queryResult.first().getSize() == 200);
if (file.getStatus().getName().equals(File.FileStatus.READY) && file.getFormat().equals(File.Format.VCF)) { String indexStatus; if (file.getIndex() != null && file.getIndex().getStatus() != null && file.getIndex().getStatus().getName() != null) {
fileSolrModel.setCreationDay(localDate.getDayOfMonth()); fileSolrModel.setCreationDayOfWeek(localDate.getDayOfWeek().toString()); fileSolrModel.setStatus(file.getStatus().getName()); fileSolrModel.setStatus(file.getStatus().getName()); fileSolrModel.setExternal(file.isExternal()); fileSolrModel.setSize(file.getSize());
TimeUtils.getTime(), description, new File.FileStatus(File.FileStatus.READY), true, 0, null, new Experiment(), Collections.emptyList(), new Job(), Collections.emptyList(), null, catalogManager.getStudyManager().getCurrentRelease(study, userId), Collections.emptyList(),
File file = files.get(0); assertTrue(file.getSize() > 0); assertEquals(File.FileStatus.READY, file.getStatus().getName()); assertTrue(StringUtils.isNotEmpty(file.getChecksum())); assertEquals(File.FileStatus.MISSING, files.get(0).getStatus().getName()); String originalChecksum = files.get(0).getChecksum(); assertEquals(File.FileStatus.READY, files.get(0).getStatus().getName()); String newChecksum = files.get(0).getChecksum(); assertNotEquals(originalChecksum, newChecksum); assertEquals(File.FileStatus.MISSING, files.get(0).getStatus().getName()); originalChecksum = files.get(0).getChecksum(); assertEquals(File.FileStatus.READY, files.get(0).getStatus().getName()); newChecksum = files.get(0).getChecksum(); assertNotEquals(originalChecksum, newChecksum);