Examples with AnalysisSubmission ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission used on opensource projects

Example 31 with AnalysisSubmission

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission in project irida by phac-nml.

the class AnalysisExecutionServiceGalaxyTest method testCleanupCompletedSubmissionSuccess.

/**
 * Tests successfully executing the cleanup method on a completed
 * submission.
 *
 * @throws ExecutionManagerException
 * @throws ExecutionException
 * @throws InterruptedException
 */
@Test
public void testCleanupCompletedSubmissionSuccess() throws ExecutionManagerException, InterruptedException, ExecutionException {
    when(analysisSubmissionService.update(analysisCompleted)).thenReturn(analysisCompletedCleaning);
    when(analysisSubmissionService.update(analysisCompletedCleaning)).thenReturn(analysisCompletedCleaned);
    Future<AnalysisSubmission> cleaningSubmissionFuture = workflowManagement.cleanupSubmission(analysisCompleted);
    AnalysisSubmission cleaningSubmission = cleaningSubmissionFuture.get();
    assertEquals(AnalysisCleanedState.CLEANED, cleaningSubmission.getAnalysisCleanedState());
    verify(galaxyHistoriesService).deleteHistory(ANALYSIS_ID);
    verify(galaxyLibrariesService).deleteLibrary(LIBRARY_ID);
    verify(galaxyWorkflowService).deleteWorkflow(REMOTE_WORKFLOW_ID);
}

Example 32 with AnalysisSubmission

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission in project irida by phac-nml.

the class AnalysisExecutionServiceGalaxyTest method testCleanupErrorSubmissionSuccess.

/**
 * Tests successfully executing the cleanup method on a error submission.
 *
 * @throws ExecutionManagerException
 * @throws ExecutionException
 * @throws InterruptedException
 */
@Test
public void testCleanupErrorSubmissionSuccess() throws ExecutionManagerException, InterruptedException, ExecutionException {
    when(analysisSubmissionService.update(analysisError)).thenReturn(analysisErrorCleaning);
    when(analysisSubmissionService.update(analysisErrorCleaning)).thenReturn(analysisErrorCleaned);
    Future<AnalysisSubmission> cleaningSubmissionFuture = workflowManagement.cleanupSubmission(analysisError);
    AnalysisSubmission cleaningSubmission = cleaningSubmissionFuture.get();
    assertEquals(AnalysisCleanedState.CLEANED, cleaningSubmission.getAnalysisCleanedState());
    verify(galaxyHistoriesService, never()).deleteHistory(ANALYSIS_ID);
    verify(galaxyLibrariesService, never()).deleteLibrary(LIBRARY_ID);
    verify(galaxyWorkflowService).deleteWorkflow(REMOTE_WORKFLOW_ID);
}

Example 33 with AnalysisSubmission

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission in project irida by phac-nml.

the class AnalysisWorkspaceServiceGalaxyIT method testPrepareAnalysisFilesParametersFailInvalidParameter.

/**
 * Tests out failing to prepare paired workflow input files for execution
 * with parameters due to an invalid parameter passed.
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IOException
 * @throws IridaWorkflowException
 */
@Test(expected = IridaWorkflowParameterException.class)
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testPrepareAnalysisFilesParametersFailInvalidParameter() throws InterruptedException, ExecutionManagerException, IOException, IridaWorkflowException {
    History history = new History();
    history.setName("testPrepareAnalysisFilesParametersFailInvalidParameter");
    HistoriesClient historiesClient = localGalaxy.getGalaxyInstanceAdmin().getHistoriesClient();
    WorkflowsClient workflowsClient = localGalaxy.getGalaxyInstanceAdmin().getWorkflowsClient();
    History createdHistory = historiesClient.create(history);
    IridaWorkflow iridaWorkflow = iridaWorkflowsService.getIridaWorkflow(validWorkflowIdPairedWithParameters);
    Path workflowPath = iridaWorkflow.getWorkflowStructure().getWorkflowFile();
    String workflowString = new String(Files.readAllBytes(workflowPath), StandardCharsets.UTF_8);
    Workflow galaxyWorkflow = workflowsClient.importWorkflow(workflowString);
    Map<String, String> parameters = ImmutableMap.of("invalid", "20");
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupPairSubmissionInDatabase(1L, pairSequenceFiles1A, pairSequenceFiles2A, referenceFilePath, parameters, validWorkflowIdPairedWithParameters);
    analysisSubmission.setRemoteAnalysisId(createdHistory.getId());
    analysisSubmission.setRemoteWorkflowId(galaxyWorkflow.getId());
    analysisWorkspaceService.prepareAnalysisFiles(analysisSubmission);
}

Example 34 with AnalysisSubmission

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission in project irida by phac-nml.

the class AnalysisWorkspaceServiceGalaxyIT method testPrepareAnalysisFilesFail.

/**
 * Tests out failure to prepare workflow input files for execution.
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IOException
 * @throws IridaWorkflowException
 */
@Test(expected = WorkflowException.class)
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testPrepareAnalysisFilesFail() throws InterruptedException, ExecutionManagerException, IOException, IridaWorkflowException {
    History history = new History();
    history.setName("testPrepareAnalysisFilesFail");
    HistoriesClient historiesClient = localGalaxy.getGalaxyInstanceAdmin().getHistoriesClient();
    History createdHistory = historiesClient.create(history);
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupSubmissionInDatabase(1L, sequenceFilePathA, referenceFilePath, validWorkflowIdSingle, false);
    analysisSubmission.setRemoteAnalysisId(createdHistory.getId());
    analysisSubmission.setRemoteWorkflowId("invalid");
    analysisWorkspaceService.prepareAnalysisFiles(analysisSubmission);
}

Example 35 with AnalysisSubmission

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission in project irida by phac-nml.

the class AnalysisWorkspaceServiceGalaxyIT method testPrepareAnalysisFilesSinglePairSuccess.

/**
 * Tests out successfully preparing paired and single workflow input files
 * for execution.
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IOException
 * @throws IridaWorkflowException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testPrepareAnalysisFilesSinglePairSuccess() throws InterruptedException, ExecutionManagerException, IOException, IridaWorkflowException {
    History history = new History();
    history.setName("testPrepareAnalysisFilesPairSuccess");
    HistoriesClient historiesClient = localGalaxy.getGalaxyInstanceAdmin().getHistoriesClient();
    WorkflowsClient workflowsClient = localGalaxy.getGalaxyInstanceAdmin().getWorkflowsClient();
    History createdHistory = historiesClient.create(history);
    IridaWorkflow iridaWorkflow = iridaWorkflowsService.getIridaWorkflow(validWorkflowIdSinglePaired);
    Path workflowPath = iridaWorkflow.getWorkflowStructure().getWorkflowFile();
    String workflowString = new String(Files.readAllBytes(workflowPath), StandardCharsets.UTF_8);
    Workflow galaxyWorkflow = workflowsClient.importWorkflow(workflowString);
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupSinglePairSubmissionInDatabaseDifferentSample(1L, 2L, pairSequenceFiles1A, pairSequenceFiles2A, sequenceFilePath3, referenceFilePath, validWorkflowIdSinglePaired);
    analysisSubmission.setRemoteAnalysisId(createdHistory.getId());
    analysisSubmission.setRemoteWorkflowId(galaxyWorkflow.getId());
    PreparedWorkflowGalaxy preparedWorkflow = analysisWorkspaceService.prepareAnalysisFiles(analysisSubmission);
    assertEquals("the response history id should match the input history id", createdHistory.getId(), preparedWorkflow.getRemoteAnalysisId());
    WorkflowInputsGalaxy workflowInputsGalaxy = preparedWorkflow.getWorkflowInputs();
    assertNotNull("the returned workflow inputs should not be null", workflowInputsGalaxy);
    // verify correct files have been uploaded
    List<HistoryContents> historyContents = historiesClient.showHistoryContents(createdHistory.getId());
    assertEquals("the created history has an invalid number of elements", 6, historyContents.size());
    Map<String, HistoryContents> contentsMap = historyContentsAsMap(historyContents);
    assertTrue("the created history should contain the file " + sequenceFilePathA.toFile().getName(), contentsMap.containsKey(sequenceFilePathA.toFile().getName()));
    assertTrue("the created history should contain the file " + sequenceFilePath2A.toFile().getName(), contentsMap.containsKey(sequenceFilePath2A.toFile().getName()));
    assertTrue("the created history should contain the file " + sequenceFilePath3.toFile().getName(), contentsMap.containsKey(sequenceFilePath3.toFile().getName()));
    assertTrue("the created history should contain the file " + referenceFilePath.toFile().getName(), contentsMap.containsKey(referenceFilePath.toFile().getName()));
    assertTrue("the created history should contain a dataset collection with the name " + INPUTS_SINGLE_NAME, contentsMap.containsKey(INPUTS_SINGLE_NAME));
    assertTrue("the created history should contain a dataset collection with the name " + INPUTS_PAIRED_NAME, contentsMap.containsKey(INPUTS_PAIRED_NAME));
    // make sure workflow inputs contains correct information
    Map<String, WorkflowInput> workflowInputsMap = preparedWorkflow.getWorkflowInputs().getInputsObject().getInputs();
    assertEquals("the created workflow inputs has an invalid number of elements", 3, workflowInputsMap.size());
}