Examples with Analysis ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis used on opensource projects

Example 16 with Analysis

use of ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis in project irida by phac-nml.

the class AnalysisWorkspaceServiceGalaxyIT method testGetAnalysisResultsTestAnalysisPairedSuccess.

/**
 * Tests out successfully getting results for an analysis (TestAnalysis)
 * consisting only of paired sequence reads.
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IridaWorkflowNotFoundException
 * @throws IOException
 * @throws IridaWorkflowAnalysisTypeException
 * @throws TimeoutException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testGetAnalysisResultsTestAnalysisPairedSuccess() throws InterruptedException, ExecutionManagerException, IridaWorkflowNotFoundException, IOException, IridaWorkflowAnalysisTypeException, TimeoutException {
    History history = new History();
    history.setName("testGetAnalysisResultsTestAnalysisPairedSuccess");
    HistoriesClient historiesClient = localGalaxy.getGalaxyInstanceAdmin().getHistoriesClient();
    WorkflowsClient workflowsClient = localGalaxy.getGalaxyInstanceAdmin().getWorkflowsClient();
    ToolsClient toolsClient = localGalaxy.getGalaxyInstanceAdmin().getToolsClient();
    History createdHistory = historiesClient.create(history);
    // upload test outputs
    uploadFileToHistory(sequenceFilePathA, OUTPUT1_NAME, createdHistory.getId(), toolsClient);
    uploadFileToHistory(sequenceFilePathA, OUTPUT2_NAME, createdHistory.getId(), toolsClient);
    // wait for history
    Util.waitUntilHistoryComplete(createdHistory.getId(), galaxyHistoriesService, 60);
    IridaWorkflow iridaWorkflow = iridaWorkflowsService.getIridaWorkflow(validWorkflowIdPaired);
    Path workflowPath = iridaWorkflow.getWorkflowStructure().getWorkflowFile();
    String workflowString = new String(Files.readAllBytes(workflowPath), StandardCharsets.UTF_8);
    Workflow galaxyWorkflow = workflowsClient.importWorkflow(workflowString);
    List<Path> paths1 = new ArrayList<>();
    paths1.add(sequenceFilePathA);
    List<Path> paths2 = new ArrayList<>();
    paths2.add(sequenceFilePath2A);
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupPairSubmissionInDatabase(1L, paths1, paths2, referenceFilePath, validWorkflowIdPaired, false);
    Set<SingleEndSequenceFile> submittedSingleFiles = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SingleEndSequenceFile.class);
    Set<SequenceFilePair> pairedFiles = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SequenceFilePair.class);
    assertEquals("the created submission should have no single input files", 0, submittedSingleFiles.size());
    assertEquals("the created submission has an invalid number of paired input files", 1, pairedFiles.size());
    SequenceFilePair submittedSp = pairedFiles.iterator().next();
    Set<SequenceFile> submittedSf = submittedSp.getFiles();
    assertEquals("the paired input should have 2 files", 2, submittedSf.size());
    analysisSubmission.setRemoteAnalysisId(createdHistory.getId());
    analysisSubmission.setRemoteWorkflowId(galaxyWorkflow.getId());
    analysisSubmission.setAnalysisState(AnalysisState.COMPLETING);
    analysisSubmissionRepository.save(analysisSubmission);
    Analysis analysis = analysisWorkspaceService.getAnalysisResults(analysisSubmission);
    assertNotNull("the analysis results were not properly created", analysis);
    assertEquals("the Analysis results class is invalid", Analysis.class, analysis.getClass());
    assertEquals("the analysis results has an invalid number of output files", 2, analysis.getAnalysisOutputFiles().size());
    assertEquals("the analysis results output file has an invalid name", Paths.get(OUTPUT1_NAME), analysis.getAnalysisOutputFile(OUTPUT1_KEY).getFile().getFileName());
    assertEquals("the analysis results output file has an invalid label", OUTPUT1_NAME, analysis.getAnalysisOutputFile(OUTPUT1_KEY).getLabel());
    assertEquals("the analysis results output file has an invalid name", Paths.get(OUTPUT2_NAME), analysis.getAnalysisOutputFile(OUTPUT2_KEY).getFile().getFileName());
    assertEquals("the analysis results output file has an invalid label", OUTPUT2_NAME, analysis.getAnalysisOutputFile(OUTPUT2_KEY).getLabel());
}

Example 17 with Analysis

use of ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis in project irida by phac-nml.

the class AnalysisServiceTest method testCreateAnalysisWithMultipleOutputFile.

@Test
public void testCreateAnalysisWithMultipleOutputFile() throws IOException {
    Path outputFile1 = Files.createTempFile(null, null);
    Path outputFile2 = Files.createTempFile(null, null);
    Path outputFile3 = Files.createTempFile(null, null);
    AnalysisOutputFile report1 = new AnalysisOutputFile(outputFile1, "", "", null);
    AnalysisOutputFile report2 = new AnalysisOutputFile(outputFile2, "", "", null);
    AnalysisOutputFile report3 = new AnalysisOutputFile(outputFile3, "", "", null);
    Map<String, AnalysisOutputFile> analysisOutputFiles = new ImmutableMap.Builder<String, AnalysisOutputFile>().put("tree", report1).put("matrix", report2).put("table", report3).build();
    Analysis analysis = new Analysis("something", analysisOutputFiles, AnalysisType.PHYLOGENOMICS);
    analysisService.create(analysis);
    verify(analysisOutputFileRepository, times(3)).save(any(AnalysisOutputFile.class));
    verify(analysisRepository).save(analysis);
}

Example 18 with Analysis

use of ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis in project irida by phac-nml.

the class AnalysisServiceImplIT method testCreatePhylogenomicsAnalysis.

@Test
@WithMockUser(username = "admin", roles = "ADMIN")
public void testCreatePhylogenomicsAnalysis() throws IOException {
    Path treePath = Files.createTempFile(null, null);
    Path tablePath = Files.createTempFile(null, null);
    Path matrixPath = Files.createTempFile(null, null);
    Map<String, String> params = new HashMap<>();
    params.put("param", "value");
    ToolExecution toolExecutionTree = new ToolExecution(null, "ls", "1.0", "executionManagerId", params, "/bin/ls -lrth");
    ToolExecution toolExecutionTable = new ToolExecution(null, "ls", "1.0", "executionManagerId", params, "/bin/ls -lrth");
    ToolExecution toolExecutionMatrix = new ToolExecution(null, "ls", "1.0", "executionManagerId", params, "/bin/ls -lrth");
    AnalysisOutputFile tree = new AnalysisOutputFile(treePath, "internal-galaxy-tree-identifier", "", toolExecutionTree);
    AnalysisOutputFile table = new AnalysisOutputFile(tablePath, "internal-galaxy-table-identifier", "", toolExecutionTable);
    AnalysisOutputFile matrix = new AnalysisOutputFile(matrixPath, "internal-galaxy-matrix-identifier", "", toolExecutionMatrix);
    Map<String, AnalysisOutputFile> analysisOutputFiles = new ImmutableMap.Builder<String, AnalysisOutputFile>().put("tree", tree).put("matrix", matrix).put("table", table).build();
    Analysis pipeline = new Analysis(EXECUTION_MANAGER_ID, analysisOutputFiles, AnalysisType.PHYLOGENOMICS);
    // make sure that we're not falsely putting the files into the correct
    // directory in the first place.
    assertFalse("file was stored in the wrong directory.", pipeline.getAnalysisOutputFile(TREE_KEY).getFile().startsWith(outputFileBaseDirectory));
    assertFalse("file was stored in the wrong directory.", pipeline.getAnalysisOutputFile(MATRIX_KEY).getFile().startsWith(outputFileBaseDirectory));
    assertFalse("file was stored in the wrong directory.", pipeline.getAnalysisOutputFile(TABLE_KEY).getFile().startsWith(outputFileBaseDirectory));
    Analysis analysis = analysisService.create(pipeline);
    // make sure that we put the analysis output files into the correct
    // directory.
    assertEquals("returned analysis was of the wrong type.", AnalysisType.PHYLOGENOMICS, analysis.getAnalysisType());
    assertTrue("file was stored in the wrong directory.", analysis.getAnalysisOutputFile(TREE_KEY).getFile().startsWith(outputFileBaseDirectory));
    assertTrue("file was stored in the wrong directory.", analysis.getAnalysisOutputFile(MATRIX_KEY).getFile().startsWith(outputFileBaseDirectory));
    assertTrue("file was stored in the wrong directory.", analysis.getAnalysisOutputFile(TABLE_KEY).getFile().startsWith(outputFileBaseDirectory));
}

Example 19 with Analysis

use of ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis in project irida by phac-nml.

the class AnalysisWorkspaceServiceGalaxy method getAnalysisResults.

/**
 * {@inheritDoc}
 */
@Override
public Analysis getAnalysisResults(AnalysisSubmission analysisSubmission) throws ExecutionManagerException, IridaWorkflowNotFoundException, IOException, IridaWorkflowAnalysisTypeException {
    checkNotNull(analysisSubmission, "analysisSubmission is null");
    checkNotNull(analysisSubmission.getWorkflowId(), "workflowId is null");
    checkNotNull(analysisSubmission.getRemoteWorkflowId(), "remoteWorkflowId is null");
    Path outputDirectory = Files.createTempDirectory("analysis-output");
    logger.trace("Created temporary directory " + outputDirectory + " for analysis output files");
    IridaWorkflow iridaWorkflow = iridaWorkflowsService.getIridaWorkflow(analysisSubmission.getWorkflowId());
    String analysisId = analysisSubmission.getRemoteAnalysisId();
    Map<String, IridaWorkflowOutput> outputsMap = iridaWorkflow.getWorkflowDescription().getOutputsMap();
    String labelPrefix = getLabelPrefix(analysisSubmission, iridaWorkflow);
    Map<String, AnalysisOutputFile> analysisOutputFiles = Maps.newHashMap();
    for (String analysisOutputName : outputsMap.keySet()) {
        String outputFileName = outputsMap.get(analysisOutputName).getFileName();
        Dataset outputDataset = galaxyHistoriesService.getDatasetForFileInHistory(outputFileName, analysisId);
        AnalysisOutputFile analysisOutput = buildOutputFile(analysisId, labelPrefix, outputDataset, outputDirectory);
        analysisOutputFiles.put(analysisOutputName, analysisOutput);
    }
    AnalysisType analysisType = iridaWorkflow.getWorkflowDescription().getAnalysisType();
    return new Analysis(analysisId, analysisOutputFiles, analysisType);
}

Example 20 with Analysis

use of ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis in project irida by phac-nml.

the class AnalysisSubmissionSampleProcessorImpl method updateSamples.

/**
 * {@inheritDoc}
 */
@Override
@RunAsUser("#analysisSubmission.getSubmitter()")
@Transactional(propagation = Propagation.REQUIRES_NEW)
@PreAuthorize("hasPermission(#analysisSubmission, 'canUpdateSamplesFromAnalysisSubmission')")
public void updateSamples(AnalysisSubmission analysisSubmission) throws PostProcessingException {
    if (!analysisSubmission.getUpdateSamples()) {
        logger.trace("Will not update samples from results for submission=" + analysisSubmission);
    } else {
        logger.debug("Updating sample from results for submission=" + analysisSubmission);
        Set<Sample> samples = sampleRepository.findSamplesForAnalysisSubmission(analysisSubmission);
        Analysis analysis = analysisSubmission.getAnalysis();
        checkNotNull(analysis, "No analysis associated with submission " + analysisSubmission);
        checkNotNull(samples, "No samples associated with submission " + analysisSubmission);
        AnalysisSampleUpdater analysisSampleUpdaterService = analysisSampleUpdaterMap.get(analysis.getAnalysisType());
        if (analysisSampleUpdaterService != null) {
            // re-reading submission to ensure file paths are correct
            analysisSubmission = analysisSubmissionService.read(analysisSubmission.getId());
            analysisSampleUpdaterService.update(samples, analysisSubmission);
        } else {
            logger.debug("No associated object for updating samples for analysis of type " + analysis.getAnalysisType());
        }
    }
}