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

Example 26 with AnalysisSubmission

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission 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 27 with AnalysisSubmission

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

the class AnalysisExecutionServiceGalaxyIT method testCleanupErrorAnalysisFailGalaxy.

/**
 * Tests out cleaning up an analysis in error and failing due to an error in
 * Galaxy.
 *
 * @throws Throwable
 */
@Test(expected = ExecutionManagerException.class)
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testCleanupErrorAnalysisFailGalaxy() throws Throwable {
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupSubmissionInDatabase(1L, sequenceFilePath, referenceFilePath, iridaTestAnalysisWorkflowId, AnalysisState.NEW, false);
    Future<AnalysisSubmission> analysisSubmittedFuture = analysisExecutionService.prepareSubmission(analysisSubmission);
    AnalysisSubmission analysisSubmitted = analysisSubmittedFuture.get();
    analysisSubmitted.setAnalysisState(AnalysisState.ERROR);
    analysisSubmitted.setRemoteWorkflowId("invalid");
    analysisSubmissionRepository.save(analysisSubmitted);
    // Once analysis is complete, attempt to clean up
    Future<AnalysisSubmission> analysisSubmissionCleanedFuture = analysisExecutionService.cleanupSubmission(analysisSubmitted);
    try {
        analysisSubmissionCleanedFuture.get();
        fail("No exception thrown");
    } catch (ExecutionException e) {
        assertEquals("The AnalysisState was changed from ERROR", AnalysisState.ERROR, analysisSubmissionService.read(analysisSubmission.getId()).getAnalysisState());
        assertEquals("The AnalysisCleanedState was not changed to error", AnalysisCleanedState.CLEANING_ERROR, analysisSubmissionService.read(analysisSubmission.getId()).getAnalysisCleanedState());
        // pull out real exception
        throw e.getCause();
    }
}

Example 28 with AnalysisSubmission

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

the class AnalysisExecutionServiceGalaxyIT method testExecuteAnalysisFailRemoteWorkflowId.

/**
 * Tests out attempting to execute an analysis with an invalid remote
 * workflow id.
 *
 * @throws Throwable
 */
@Test(expected = WorkflowException.class)
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testExecuteAnalysisFailRemoteWorkflowId() throws Throwable {
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupSubmissionInDatabase(1L, sequenceFilePath, referenceFilePath, validIridaWorkflowId, false);
    Future<AnalysisSubmission> analysisSubmittedFuture = analysisExecutionService.prepareSubmission(analysisSubmission);
    AnalysisSubmission analysisSubmitted = analysisSubmittedFuture.get();
    analysisSubmitted.setRemoteWorkflowId(localGalaxy.getInvalidWorkflowId());
    analysisSubmissionService.update(analysisSubmitted);
    Future<AnalysisSubmission> analysisExecutedFuture = analysisExecutionService.executeAnalysis(analysisSubmitted);
    try {
        analysisExecutedFuture.get();
    } catch (ExecutionException e) {
        // check to make sure the submission is in the error state
        AnalysisSubmission savedSubmission = analysisSubmissionRepository.findOne(analysisSubmitted.getId());
        assertEquals(AnalysisState.ERROR, savedSubmission.getAnalysisState());
        throw e.getCause();
    }
}

Example 29 with AnalysisSubmission

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

the class AnalysisExecutionServiceGalaxyIT method testCleanupCleanedAnalysisError.

/**
 * Tests out cleaning up an analysis that's already been cleaned and
 * failing.
 *
 * @throws Exception
 */
@Test(expected = IllegalArgumentException.class)
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testCleanupCleanedAnalysisError() throws Exception {
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupSubmissionInDatabase(1L, sequenceFilePath, referenceFilePath, iridaTestAnalysisWorkflowId, false);
    Future<AnalysisSubmission> analysisSubmittedFuture = analysisExecutionService.prepareSubmission(analysisSubmission);
    AnalysisSubmission analysisSubmitted = analysisSubmittedFuture.get();
    analysisSubmitted.setAnalysisState(AnalysisState.ERROR);
    analysisSubmissionRepository.save(analysisSubmitted);
    Future<AnalysisSubmission> analysisSubmissionCleanedFuture = analysisExecutionService.cleanupSubmission(analysisSubmitted);
    AnalysisSubmission cleanedSubmission = analysisSubmissionCleanedFuture.get();
    analysisExecutionService.cleanupSubmission(cleanedSubmission);
}

Example 30 with AnalysisSubmission

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

the class AnalysisExecutionServiceGalaxyIT method testTransferAnalysisResultsFailTestAnalysisMissingOutput.

/**
 * Tests failure to get analysis results due to a missing output file.
 * @throws Throwable
 */
@Test(expected = GalaxyDatasetNotFoundException.class)
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testTransferAnalysisResultsFailTestAnalysisMissingOutput() throws Throwable {
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupSubmissionInDatabase(1L, sequenceFilePath, referenceFilePath, iridaTestAnalysisWorkflowIdMissingOutput, 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);
    try {
        analysisSubmissionCompletedFuture.get();
    } catch (ExecutionException e) {
        logger.debug("Submission on exception=" + analysisSubmissionService.read(analysisSubmission.getId()));
        assertEquals(AnalysisState.ERROR, analysisSubmissionService.read(analysisSubmission.getId()).getAnalysisState());
        // pull out real exception
        throw e.getCause();
    }
}