public QueryResult<Job> get(long jobId, QueryOptions options, String sessionId) throws CatalogException { return get(null, String.valueOf(jobId), options, sessionId); }
Job job = jobManager.get(null, query, QueryOptions.empty(), sessionId).first(); long studyUid = jobManager.getStudyId(jobId);
public List<QueryResult<Job>> get(List<String> jobIds, QueryOptions options, boolean silent, String sessionId) throws CatalogException { return get(null, jobIds, new Query(), options, silent, sessionId); }
return catalogManager.getJobManager().get(job.getUid(), new QueryOptions(), sessionId);
return catalogManager.getJobManager().get(job.getUid(), new QueryOptions(), sessionId);
throw new AnalysisExecutionException(e.getCause()); jobQueryResult = catalogManager.getJobManager().get(job.getUid(), null, sessionId);
private void checkGetAllJobs(Collection<Long> expectedJobs, String sessionId) throws CatalogException { QueryResult<Job> allJobs = catalogManager.getJobManager().get(studyFqn, (Query) null, null, sessionId); assertEquals(expectedJobs.size(), allJobs.getNumResults()); allJobs.getResult().forEach(job -> assertTrue(expectedJobs + " does not contain job " + job.getName(), expectedJobs.contains(job .getUid()))); }
public static Job runStorageJob(CatalogManager catalogManager, Job job, Logger logger, String sessionId) throws CatalogException, IOException { try { ExecutorManager.execute(catalogManager, job, sessionId); } catch (ExecutionException e) { throw new IOException(e.getCause()); } return catalogManager.getJobManager().get(job.getUid(), null, sessionId).first(); }
@Test public void testGetAllJobs() throws CatalogException { Query query = new Query(StudyDBAdaptor.QueryParams.OWNER.key(), "user"); String studyId = catalogManager.getStudyManager().get(query, null, sessionIdUser).first().getId(); catalogManager.getJobManager().create(studyId, new Job().setId("myErrorJob").setToolId("samtools"), null, sessionIdUser); QueryResult<Job> allJobs = catalogManager.getJobManager().get(studyId, (Query) null, null, sessionIdUser); assertEquals(1, allJobs.getNumTotalResults()); assertEquals(1, allJobs.getNumResults()); }
/** * 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()); }