@Test public void updateInputAndOutputFiles() throws Exception { Job job = new Job() .setOutDir(new File().setUid(5)) .setStatus(new Job.JobStatus()); long studyId = user3.getProjects().get(0).getStudies().get(0).getUid(); job.setName("jobName1"); QueryResult<Job> insert = catalogJobDBAdaptor.insert(job, studyId, null); List<File> fileInput = Arrays.asList( new File().setUid(5L).setName("file1").setStatus(new File.FileStatus()), new File().setUid(6L).setName("file2").setStatus(new File.FileStatus()), new File().setUid(7L).setName("file3").setStatus(new File.FileStatus()) ); List<File> fileOutput = Arrays.asList( new File().setUid(15L).setName("file1").setStatus(new File.FileStatus()), new File().setUid(16L).setName("file2").setStatus(new File.FileStatus()), new File().setUid(17L).setName("file3").setStatus(new File.FileStatus()) ); ObjectMap params = new ObjectMap() .append(JobDBAdaptor.QueryParams.INPUT.key(), fileInput) .append(JobDBAdaptor.QueryParams.OUTPUT.key(), fileOutput); QueryResult<Job> update = catalogJobDBAdaptor.update(insert.first().getUid(), params, QueryOptions.empty()); assertEquals(3, update.first().getInput().size()); assertEquals(3, update.first().getOutput().size()); assertTrue(Arrays.asList(5L, 6L, 7L).containsAll(update.first().getInput().stream().map(File::getUid).collect(Collectors.toList()))); assertTrue(Arrays.asList(15L, 16L, 17L) .containsAll(update.first().getOutput().stream().map(File::getUid).collect(Collectors.toList()))); }
/** * Job methods * *************************** */ @Test public void testCreateJob() throws CatalogException, IOException { Query query = new Query(StudyDBAdaptor.QueryParams.OWNER.key(), "user"); String studyId = catalogManager.getStudyManager().get(query, null, sessionIdUser).first().getId(); File outDir = catalogManager.getFileManager().createFolder(studyId, Paths.get("jobs", "myJob").toString(), null, true, null, QueryOptions.empty(), sessionIdUser).first(); catalogManager.getJobManager().create(studyId,new Job().setId("myJob").setToolId("samtool").setDescription("description") .setOutDir(outDir).setExecution("echo \"Hello world!\"").setStatus(new Job.JobStatus(Job.JobStatus.PREPARED)), null, sessionIdUser); catalogManager.getJobManager().create(studyId, new Job().setId("myReadyJob").setToolId("samtool").setDescription("description") .setOutDir(outDir).setExecution("echo \"Hello world!\"").setStatus(new Job.JobStatus(Job.JobStatus.READY)), null, sessionIdUser); catalogManager.getJobManager().create(studyId, new Job().setId("myQueuedJob").setToolId("samtool").setDescription("description") .setOutDir(outDir).setExecution("echo \"Hello world!\"").setStatus(new Job.JobStatus(Job.JobStatus.QUEUED)), null, sessionIdUser); catalogManager.getJobManager().create(studyId, new Job().setId("myErrorJob").setToolId("samtool").setDescription("description") .setOutDir(outDir).setExecution("echo \"Hello world!\"").setStatus(new Job.JobStatus(Job.JobStatus.ERROR)), null, sessionIdUser); query = new Query() .append(JobDBAdaptor.QueryParams.STATUS_NAME.key(), Arrays.asList(Job.JobStatus.PREPARED, Job.JobStatus.QUEUED, Job.JobStatus.RUNNING, Job.JobStatus.DONE)); QueryResult<Job> unfinishedJobs = catalogManager.getJobManager().get(String.valueOf(studyId), query, null, sessionIdUser); assertEquals(2, unfinishedJobs.getNumResults()); QueryResult<Job> allJobs = catalogManager.getJobManager().get(String.valueOf(studyId), (Query) null, null, sessionIdUser); assertEquals(4, allJobs.getNumResults()); }
@Test public void getAllJobs() throws CatalogException { Job job = new Job() .setId("job1") .setToolId("toolId") .setOutDir(new File().setPath(data_d1_d2)); long job1 = catalogManager.getJobManager().create(studyFqn, job, null, ownerSessionId).first().getUid(); job.setId("job2"); long job2 = catalogManager.getJobManager().create(studyFqn, job, null, ownerSessionId).first().getUid(); job.setId("job3"); long job3 = catalogManager.getJobManager().create(studyFqn, job, null, ownerSessionId).first().getUid(); job.setId("job4"); long job4 = catalogManager.getJobManager().create(studyFqn, job, null, ownerSessionId).first().getUid(); checkGetAllJobs(Arrays.asList(job1, job2, job3, job4), ownerSessionId); //Owner can see everything checkGetAllJobs(Collections.emptyList(), externalSessionId); //Can't see inside data_d1_d2_d3 }