Examples with HistoryContents com.github.jmchilton.blend4j.galaxy.beans.HistoryContents used on opensource projects

Example 1 with HistoryContents

use of com.github.jmchilton.blend4j.galaxy.beans.HistoryContents 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());
}

Example 2 with HistoryContents

use of com.github.jmchilton.blend4j.galaxy.beans.HistoryContents in project irida by phac-nml.

the class AnalysisWorkspaceServiceGalaxyIT method testPrepareAnalysisFilesParametersSuccess.

/**
 * Tests out successfully preparing paired workflow input files for
 * execution with parameters.
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IOException
 * @throws IridaWorkflowException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testPrepareAnalysisFilesParametersSuccess() throws InterruptedException, ExecutionManagerException, IOException, IridaWorkflowException {
    History history = new History();
    history.setName("testPrepareAnalysisFilesParametersSuccess");
    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("coverage", "20");
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupPairSubmissionInDatabase(1L, pairSequenceFiles1A, pairSequenceFiles2A, referenceFilePath, parameters, validWorkflowIdPairedWithParameters);
    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);
    assertNotNull("the returned library id should not be null", preparedWorkflow.getRemoteDataId());
    // verify correct files have been uploaded
    List<HistoryContents> historyContents = historiesClient.showHistoryContents(createdHistory.getId());
    assertEquals("the created history has an invalid number of elements", 4, historyContents.size());
    WorkflowInputs workflowInputs = preparedWorkflow.getWorkflowInputs().getInputsObject();
    assertNotNull("created workflowInputs is null", workflowInputs);
    Map<String, Object> toolParameters = workflowInputs.getParameters().get("core_pipeline_outputs_paired_with_parameters");
    assertNotNull("toolParameters is null", toolParameters);
    String coverageMinValue = (String) toolParameters.get("coverageMin");
    assertEquals("coverageMinValue should have been changed", "20", coverageMinValue);
    assertEquals("coverageMidValue should have been changed", ImmutableMap.of("coverageMid", "20"), toolParameters.get("conditional"));
    String coverageMaxValue = (String) toolParameters.get("coverageMin");
    assertEquals("coverageMaxValue should have been changed", "20", coverageMaxValue);
}

Example 3 with HistoryContents

use of com.github.jmchilton.blend4j.galaxy.beans.HistoryContents in project irida by phac-nml.

the class AnalysisProvenanceServiceGalaxyTest method testShowProvenanceFailureTooManyCooks.

@Test(expected = ExecutionManagerException.class)
public void testShowProvenanceFailureTooManyCooks() throws ExecutionManagerException {
    final HistoryContents hc1 = new HistoryContents();
    hc1.setName(FILENAME);
    final HistoryContents hc2 = new HistoryContents();
    hc2.setName(FILENAME);
    when(galaxyHistoriesService.showHistoryContents(any(String.class))).thenReturn(Lists.newArrayList(hc1, hc2));
    provenanceService.buildToolExecutionForOutputFile(analysisSubmission(), analysisOutputFile());
}

Example 4 with HistoryContents

use of com.github.jmchilton.blend4j.galaxy.beans.HistoryContents in project irida by phac-nml.

the class AnalysisProvenanceServiceGalaxyTest method testBuildSingleStepToolExecutionStrangeDataStructureDoToString.

@Test
public void testBuildSingleStepToolExecutionStrangeDataStructureDoToString() throws ExecutionManagerException {
    final HistoryContents hc = new HistoryContents();
    hc.setName(FILENAME);
    final HistoryContentsProvenance hcp = new HistoryContentsProvenance();
    hcp.setParameters(ImmutableMap.of("akey", "[[\"avalue\"]]"));
    final JobDetails jd = new JobDetails();
    jd.setCommandLine("");
    when(galaxyHistoriesService.showHistoryContents(any(String.class))).thenReturn(Lists.newArrayList(hc));
    when(galaxyHistoriesService.showProvenance(any(String.class), any(String.class))).thenReturn(hcp);
    when(toolsClient.showTool(any(String.class))).thenReturn(new Tool());
    when(jobsClient.showJob(any(String.class))).thenReturn(jd);
    final ToolExecution toolExecution = provenanceService.buildToolExecutionForOutputFile(analysisSubmission(), analysisOutputFile());
    assertTrue("tool execution should have the specified parameter.", toolExecution.getExecutionTimeParameters().containsKey("akey"));
    assertEquals("tool execution parameter should be specified value.", "[[\"avalue\"]]", toolExecution.getExecutionTimeParameters().get("akey"));
}

Example 5 with HistoryContents

use of com.github.jmchilton.blend4j.galaxy.beans.HistoryContents in project irida by phac-nml.

the class AnalysisProvenanceServiceGalaxyTest method testCantFindTools.

@Test(expected = ExecutionManagerException.class)
public void testCantFindTools() throws ExecutionManagerException {
    final HistoryContents hc = new HistoryContents();
    hc.setName(FILENAME);
    when(galaxyHistoriesService.showHistoryContents(any(String.class))).thenReturn(Lists.newArrayList(hc));
    when(galaxyHistoriesService.showProvenance(any(String.class), any(String.class))).thenReturn(new HistoryContentsProvenance());
    when(toolsClient.showTool(any(String.class))).thenThrow(new RuntimeException());
    provenanceService.buildToolExecutionForOutputFile(analysisSubmission(), analysisOutputFile());
}