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

Example 11 with Analysis

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

the class SISTRSampleUpdaterTest method testUpdaterNoFile.

@Test(expected = PostProcessingException.class)
public void testUpdaterNoFile() throws PostProcessingException, AnalysisAlreadySetException {
    ImmutableMap<String, String> expectedResults = ImmutableMap.of("SISTR serovar", "Enteritidis", "SISTR cgMLST Subspecies", "enterica", "SISTR QC Status", "PASS");
    Path outputPath = Paths.get("src/test/resources/files/not_really_a_file.txt");
    AnalysisOutputFile outputFile = new AnalysisOutputFile(outputPath, null, null, null);
    Analysis analysis = new Analysis(null, ImmutableMap.of("sistr-predictions", outputFile), null, null);
    AnalysisSubmission submission = AnalysisSubmission.builder(UUID.randomUUID()).inputFiles(ImmutableSet.of(new SingleEndSequenceFile(null))).build();
    submission.setAnalysis(analysis);
    Sample sample = new Sample();
    sample.setId(1L);
    updater.update(Lists.newArrayList(sample), submission);
}

Example 12 with Analysis

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

the class AnalysisExecutionServiceGalaxyIT method testTransferAnalysisResultsSuccessPhylogenomicsPairedNoParameters.

/**
 * Tests out getting analysis results successfully for phylogenomics
 * pipeline (paired test version with no parameters, using defaults).
 *
 * @throws Exception
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testTransferAnalysisResultsSuccessPhylogenomicsPairedNoParameters() throws Exception {
    String validCoverageFromProvenance = "\"10\"";
    String validMidCoverageFromProvenance = "10";
    // I verify parameters were set
    String validTreeFile = "10 10 10";
    // correctly by checking output file
    // (where parameters were printed).
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupPairSubmissionInDatabase(1L, pairedPaths1, pairedPaths2, referenceFilePath, iridaPhylogenomicsPairedParametersWorkflowId, false);
    Future<AnalysisSubmission> analysisSubmittedFuture = analysisExecutionService.prepareSubmission(analysisSubmission);
    AnalysisSubmission analysisSubmitted = analysisSubmittedFuture.get();
    Future<AnalysisSubmission> analysisExecutionFuture = analysisExecutionService.executeAnalysis(analysisSubmitted);
    AnalysisSubmission analysisExecuted = analysisExecutionFuture.get();
    analysisExecutionGalaxyITService.waitUntilSubmissionComplete(analysisExecuted);
    analysisExecuted.setAnalysisState(AnalysisState.FINISHED_RUNNING);
    Future<AnalysisSubmission> analysisSubmissionCompletedFuture = analysisExecutionService.transferAnalysisResults(analysisExecuted);
    analysisSubmissionCompletedFuture.get();
    AnalysisSubmission analysisSubmissionCompletedDatabase = analysisSubmissionService.read(analysisSubmission.getId());
    assertEquals("analysis state is not completed", AnalysisState.COMPLETED, analysisSubmissionCompletedDatabase.getAnalysisState());
    Analysis analysisResults = analysisSubmissionCompletedDatabase.getAnalysis();
    assertEquals("analysis results is an invalid class", AnalysisType.PHYLOGENOMICS, analysisResults.getAnalysisType());
    assertEquals("invalid number of output files", 3, analysisResults.getAnalysisOutputFiles().size());
    AnalysisOutputFile phylogeneticTree = analysisResults.getAnalysisOutputFile(TREE_KEY);
    AnalysisOutputFile snpMatrix = analysisResults.getAnalysisOutputFile(MATRIX_KEY);
    AnalysisOutputFile snpTable = analysisResults.getAnalysisOutputFile(TABLE_KEY);
    // verify parameters were set properly by checking contents of file
    @SuppressWarnings("resource") String treeContent = new Scanner(phylogeneticTree.getFile().toFile()).useDelimiter("\\Z").next();
    assertEquals("phylogenetic trees containing the parameters should be equal", validTreeFile, treeContent);
    // phy tree
    final ToolExecution phyTreeCoreInputs = phylogeneticTree.getCreatedByTool();
    assertEquals("The first tool execution should be by core_pipeline_outputs_paired_with_parameters v0.1.0", "core_pipeline_outputs_paired_with_parameters", phyTreeCoreInputs.getToolName());
    assertEquals("The first tool execution should be by core_pipeline_outputs_paired_with_parameters v0.1.0", "0.1.0", phyTreeCoreInputs.getToolVersion());
    Map<String, String> phyTreeCoreParameters = phyTreeCoreInputs.getExecutionTimeParameters();
    assertEquals("incorrect number of non-file parameters", 4, phyTreeCoreParameters.size());
    assertEquals("parameter coverageMin set incorrectly", validCoverageFromProvenance, phyTreeCoreParameters.get("coverageMin"));
    assertEquals("parameter coverageMid set incorrectly", validMidCoverageFromProvenance, phyTreeCoreParameters.get("conditional.coverageMid"));
    assertEquals("parameter coverageMax set incorrectly", validCoverageFromProvenance, phyTreeCoreParameters.get("coverageMax"));
    assertEquals("parameter conditional_select set incorrectly", "all", phyTreeCoreParameters.get("conditional.conditional_select"));
    Set<ToolExecution> phyTreeCorePreviousSteps = phyTreeCoreInputs.getPreviousSteps();
    assertEquals("there should exist 2 previous steps", 2, phyTreeCorePreviousSteps.size());
    Set<String> uploadedFileTypesPhy = Sets.newHashSet();
    for (ToolExecution previousStep : phyTreeCorePreviousSteps) {
        assertTrue("previous steps should be input tools.", previousStep.isInputTool());
        uploadedFileTypesPhy.add(previousStep.getExecutionTimeParameters().get("file_type"));
    }
    assertEquals("uploaded files should have correct types", Sets.newHashSet("\"fastqsanger\"", "\"fasta\""), uploadedFileTypesPhy);
    // snp matrix
    final ToolExecution matrixCoreInputs = snpMatrix.getCreatedByTool();
    assertEquals("The first tool execution should be by core_pipeline_outputs_paired_with_parameters v0.1.0", "core_pipeline_outputs_paired_with_parameters", matrixCoreInputs.getToolName());
    assertEquals("The first tool execution should be by core_pipeline_outputs_paired_with_parameters v0.1.0", "0.1.0", matrixCoreInputs.getToolVersion());
    Map<String, String> matrixCoreParameters = matrixCoreInputs.getExecutionTimeParameters();
    assertEquals("incorrect number of non-file parameters", 4, matrixCoreParameters.size());
    assertEquals("parameter coverageMin set incorrectly", validCoverageFromProvenance, matrixCoreParameters.get("coverageMin"));
    assertEquals("parameter coverageMid set incorrectly", validMidCoverageFromProvenance, phyTreeCoreParameters.get("conditional.coverageMid"));
    assertEquals("parameter coverageMax set incorrectly", validCoverageFromProvenance, matrixCoreParameters.get("coverageMax"));
    assertEquals("parameter conditional_select set incorrectly", "all", phyTreeCoreParameters.get("conditional.conditional_select"));
    Set<ToolExecution> matrixCorePreviousSteps = matrixCoreInputs.getPreviousSteps();
    assertEquals("there should exist 2 previous steps", 2, matrixCorePreviousSteps.size());
    Set<String> uploadedFileTypesMatrix = Sets.newHashSet();
    for (ToolExecution previousStep : matrixCorePreviousSteps) {
        assertTrue("previous steps should be input tools.", previousStep.isInputTool());
        uploadedFileTypesMatrix.add(previousStep.getExecutionTimeParameters().get("file_type"));
    }
    assertEquals("uploaded files should have correct types", Sets.newHashSet("\"fastqsanger\"", "\"fasta\""), uploadedFileTypesMatrix);
    // snp table
    final ToolExecution tableCoreInputs = snpTable.getCreatedByTool();
    assertEquals("The first tool execution should be by core_pipeline_outputs_paired_with_parameters v0.1.0", "core_pipeline_outputs_paired_with_parameters", tableCoreInputs.getToolName());
    assertEquals("The first tool execution should be by core_pipeline_outputs_paired_with_parameters v0.1.0", "0.1.0", tableCoreInputs.getToolVersion());
    Map<String, String> tableCoreParameters = tableCoreInputs.getExecutionTimeParameters();
    assertEquals("incorrect number of non-file parameters", 4, tableCoreParameters.size());
    assertEquals("parameter coverageMin set incorrectly", validCoverageFromProvenance, tableCoreParameters.get("coverageMin"));
    assertEquals("parameter coverageMid set incorrectly", validMidCoverageFromProvenance, phyTreeCoreParameters.get("conditional.coverageMid"));
    assertEquals("parameter coverageMax set incorrectly", validCoverageFromProvenance, tableCoreParameters.get("coverageMax"));
    assertEquals("parameter conditional_select set incorrectly", "all", phyTreeCoreParameters.get("conditional.conditional_select"));
    Set<ToolExecution> tablePreviousSteps = tableCoreInputs.getPreviousSteps();
    assertEquals("there should exist 2 previous steps", 2, tablePreviousSteps.size());
    Set<String> uploadedFileTypesTable = Sets.newHashSet();
    for (ToolExecution previousStep : tablePreviousSteps) {
        assertTrue("previous steps should be input tools.", previousStep.isInputTool());
        uploadedFileTypesTable.add(previousStep.getExecutionTimeParameters().get("file_type"));
    }
    assertEquals("uploaded files should have correct types", Sets.newHashSet("\"fastqsanger\"", "\"fasta\""), uploadedFileTypesTable);
}

Example 13 with Analysis

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

the class AnalysisWorkspaceServiceGalaxyIT method testGetAnalysisResultsTestAnalysisSingleSingleSampleSuccess.

/**
 * Tests out successfully getting results for an analysis (TestAnalysis)
 * consisting only of single end sequence reads (for workflow accepting single sample).
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IridaWorkflowNotFoundException
 * @throws IOException
 * @throws IridaWorkflowAnalysisTypeException
 * @throws TimeoutException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testGetAnalysisResultsTestAnalysisSingleSingleSampleSuccess() throws InterruptedException, ExecutionManagerException, IridaWorkflowNotFoundException, IOException, IridaWorkflowAnalysisTypeException, TimeoutException {
    History history = new History();
    history.setName("testGetAnalysisResultsTestAnalysisSingleSuccess");
    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(validWorkflowIdSingleSingleSample);
    Path workflowPath = iridaWorkflow.getWorkflowStructure().getWorkflowFile();
    String workflowString = new String(Files.readAllBytes(workflowPath), StandardCharsets.UTF_8);
    Workflow galaxyWorkflow = workflowsClient.importWorkflow(workflowString);
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupSubmissionInDatabase(1L, sequenceFilePathA, referenceFilePath, validWorkflowIdSingleSingleSample, false);
    Set<SingleEndSequenceFile> submittedSf = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SingleEndSequenceFile.class);
    Set<SequenceFilePair> pairedFiles = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SequenceFilePair.class);
    assertEquals("the created submission should have no paired input files", 0, pairedFiles.size());
    assertEquals("the created submission should have 1 single input file", 1, 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", SAMPLE1_NAME + '-' + 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", SAMPLE1_NAME + '-' + OUTPUT2_NAME, analysis.getAnalysisOutputFile(OUTPUT2_KEY).getLabel());
}

Example 14 with Analysis

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

the class AnalysisWorkspaceServiceGalaxyIT method testGetAnalysisResultsTestAnalysisSingleSuccess.

/**
 * Tests out successfully getting results for an analysis (TestAnalysis)
 * consisting only of single end sequence reads.
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IridaWorkflowNotFoundException
 * @throws IOException
 * @throws IridaWorkflowAnalysisTypeException
 * @throws TimeoutException
 * @throws IridaWorkflowAnalysisLabelException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testGetAnalysisResultsTestAnalysisSingleSuccess() throws InterruptedException, ExecutionManagerException, IridaWorkflowNotFoundException, IOException, IridaWorkflowAnalysisTypeException, TimeoutException {
    History history = new History();
    history.setName("testGetAnalysisResultsTestAnalysisSingleSuccess");
    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(validWorkflowIdSingle);
    Path workflowPath = iridaWorkflow.getWorkflowStructure().getWorkflowFile();
    String workflowString = new String(Files.readAllBytes(workflowPath), StandardCharsets.UTF_8);
    Workflow galaxyWorkflow = workflowsClient.importWorkflow(workflowString);
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupSubmissionInDatabase(1L, sequenceFilePathA, referenceFilePath, validWorkflowIdSingle, false);
    Set<SingleEndSequenceFile> submittedSf = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SingleEndSequenceFile.class);
    Set<SequenceFilePair> pairedFiles = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SequenceFilePair.class);
    assertEquals("the created submission should have no paired input files", 0, pairedFiles.size());
    assertEquals("the created submission should have 1 single input file", 1, 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 15 with Analysis

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

the class AnalysisWorkspaceServiceGalaxyIT method testGetAnalysisResultsTestAnalysisPairedSingleSampleSuccess.

/**
 * 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 testGetAnalysisResultsTestAnalysisPairedSingleSampleSuccess() throws InterruptedException, ExecutionManagerException, IridaWorkflowNotFoundException, IOException, IridaWorkflowAnalysisTypeException, TimeoutException {
    History history = new History();
    history.setName("testGetAnalysisResultsTestAnalysisPairedSingleSampleSuccess");
    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(validWorkflowIdPairedSingleSample);
    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, validWorkflowIdPairedSingleSample, 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", SAMPLE1_NAME + "-" + 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", SAMPLE1_NAME + "-" + OUTPUT2_NAME, analysis.getAnalysisOutputFile(OUTPUT2_KEY).getLabel());
}