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

Example 11 with ToolExecution

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

the class AnalysisExecutionServiceGalaxyIT method testTransferAnalysisResultsSuccessPhylogenomicsPairedParametersIgnoreDefaultValues.

/**
 * Tests out getting analysis results successfully for phylogenomics
 * pipeline (paired test version and ignoring default parameters).
 *
 * @throws Exception
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testTransferAnalysisResultsSuccessPhylogenomicsPairedParametersIgnoreDefaultValues() throws Exception {
    String validMinCoverageFromProvenance = "\"5\"";
    String validMidCoverageFromProvenance = "15";
    String validMaxCoverageFromProvenance = "\"20\"";
    Map<String, String> parameters = ImmutableMap.of("coverage", IridaWorkflowParameter.IGNORE_DEFAULT_VALUE);
    // I verify parameters were set
    String validTreeFile = "5 15 20";
    // correctly by checking output file
    // (where parameters were printed).
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupPairSubmissionInDatabase(1L, pairedPaths1, pairedPaths2, referenceFilePath, parameters, iridaPhylogenomicsPairedParametersWorkflowId);
    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", validMinCoverageFromProvenance, phyTreeCoreParameters.get("coverageMin"));
    assertEquals("parameter coverageMid set incorrectly", validMidCoverageFromProvenance, phyTreeCoreParameters.get("conditional.coverageMid"));
    assertEquals("parameter coverageMax set incorrectly", validMaxCoverageFromProvenance, 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", validMinCoverageFromProvenance, matrixCoreParameters.get("coverageMin"));
    assertEquals("parameter coverageMid set incorrectly", validMidCoverageFromProvenance, phyTreeCoreParameters.get("conditional.coverageMid"));
    assertEquals("parameter coverageMax set incorrectly", validMaxCoverageFromProvenance, 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", validMinCoverageFromProvenance, tableCoreParameters.get("coverageMin"));
    assertEquals("parameter coverageMid set incorrectly", validMidCoverageFromProvenance, phyTreeCoreParameters.get("conditional.coverageMid"));
    assertEquals("parameter coverageMax set incorrectly", validMaxCoverageFromProvenance, 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 12 with ToolExecution

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

the class AnalysisExecutionServiceGalaxyIT method testTransferAnalysisResultsSuccessPhylogenomicsPairedParameters.

/**
 * Tests out getting analysis results successfully for phylogenomics
 * pipeline (paired test version with parameters).
 *
 * @throws Exception
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testTransferAnalysisResultsSuccessPhylogenomicsPairedParameters() throws Exception {
    String validCoverage = "20";
    // coverage from
    String validCoverageFromProvenance = "\"20\"";
    // provenance has quotes
    // this value does not have quotes around it in final results.
    String validMidCoverageFromProvenance = "20";
    Map<String, String> parameters = ImmutableMap.of("coverage", validCoverage);
    // I verify parameters were set
    String validTreeFile = "20 20 20";
    // correctly by checking output file
    // (where parameters were printed).
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupPairSubmissionInDatabase(1L, pairedPaths1, pairedPaths2, referenceFilePath, parameters, iridaPhylogenomicsPairedParametersWorkflowId);
    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 ToolExecution

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

the class AnalysisExecutionServiceGalaxyIT method testTransferAnalysisResultsSuccessPhylogenomicsPaired.

/**
 * Tests out getting analysis results successfully for phylogenomics
 * pipeline (paired test version).
 *
 * @throws Exception
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testTransferAnalysisResultsSuccessPhylogenomicsPaired() throws Exception {
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupPairSubmissionInDatabase(1L, pairedPaths1, pairedPaths2, referenceFilePath, iridaPhylogenomicsPairedWorkflowId, 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);
    AnalysisSubmission analysisSubmissionCompleted = analysisSubmissionCompletedFuture.get();
    AnalysisSubmission analysisSubmissionCompletedDatabase = analysisSubmissionService.read(analysisSubmission.getId());
    assertEquals("analysis state is not completed", AnalysisState.COMPLETED, analysisSubmissionCompletedDatabase.getAnalysisState());
    assertEquals("analysis state is not completed", AnalysisState.COMPLETED, analysisSubmissionCompleted.getAnalysisState());
    Analysis analysisResults = analysisSubmissionCompleted.getAnalysis();
    Analysis analysisResultsDatabase = analysisSubmissionCompletedDatabase.getAnalysis();
    assertEquals("analysis results in returned submission and from database should be the same", analysisResults.getId(), analysisResultsDatabase.getId());
    assertEquals(AnalysisType.PHYLOGENOMICS, analysisResults.getAnalysisType());
    String analysisId = analysisExecuted.getRemoteAnalysisId();
    assertEquals("id should be set properly for analysis", analysisId, analysisResultsDatabase.getExecutionManagerAnalysisId());
    assertEquals("invalid number of output files", 3, analysisResultsDatabase.getAnalysisOutputFiles().size());
    AnalysisOutputFile phylogeneticTree = analysisResultsDatabase.getAnalysisOutputFile(TREE_KEY);
    AnalysisOutputFile snpMatrix = analysisResultsDatabase.getAnalysisOutputFile(MATRIX_KEY);
    AnalysisOutputFile snpTable = analysisResultsDatabase.getAnalysisOutputFile(TABLE_KEY);
    assertTrue("phylogenetic trees should be equal", com.google.common.io.Files.equal(expectedTree.toFile(), phylogeneticTree.getFile().toFile()));
    assertEquals("invalid file name for snp tree", expectedTree.getFileName(), phylogeneticTree.getFile().getFileName());
    assertTrue("command line (" + phylogeneticTree.getCreatedByTool().getCommandLine() + ") should match the defined pattern (" + CMD_LINE_PATTERN + ") (phylogenetic tree).", phylogeneticTree.getCreatedByTool().getCommandLine().matches(CMD_LINE_PATTERN));
    final ToolExecution phyTreeCoreInputs = phylogeneticTree.getCreatedByTool();
    assertEquals("The first tool execution should be by core_pipeline_outputs_paired v0.1.0", "core_pipeline_outputs_paired", phyTreeCoreInputs.getToolName());
    assertEquals("The first tool execution should be by core_pipeline_outputs_paired v0.1.0", "0.1.0", phyTreeCoreInputs.getToolVersion());
    final ToolExecution phyTreeCoreUpload = phyTreeCoreInputs.getPreviousSteps().iterator().next();
    assertTrue("Second step should be input tool.", phyTreeCoreUpload.isInputTool());
    assertTrue("snp matrices should be correct", com.google.common.io.Files.equal(expectedSnpMatrix.toFile(), snpMatrix.getFile().toFile()));
    assertEquals("invalid file name for snp matrix", expectedSnpMatrix.getFileName(), snpMatrix.getFile().getFileName());
    assertTrue("command line (" + snpMatrix.getCreatedByTool().getCommandLine() + ") should match the defined pattern (" + CMD_LINE_PATTERN + ") (snp matrix).", snpMatrix.getCreatedByTool().getCommandLine().matches(CMD_LINE_PATTERN));
    final ToolExecution snpMatrixCoreInputs = snpMatrix.getCreatedByTool();
    assertEquals("The first tool execution should be by core_pipeline_outputs_paired v0.1.0", "core_pipeline_outputs_paired", snpMatrixCoreInputs.getToolName());
    assertEquals("The first tool execution should be by core_pipeline_outputs_paired v0.1.0", "0.1.0", snpMatrixCoreInputs.getToolVersion());
    final ToolExecution snpMatrixCoreUpload = snpMatrixCoreInputs.getPreviousSteps().iterator().next();
    assertTrue("Second step should be input tool.", snpMatrixCoreUpload.isInputTool());
    assertTrue("snpTable should be correct", com.google.common.io.Files.equal(expectedSnpTable.toFile(), snpTable.getFile().toFile()));
    assertEquals("invalid file name for snp table", expectedSnpTable.getFileName(), snpTable.getFile().getFileName());
    assertTrue("command line (" + snpTable.getCreatedByTool().getCommandLine() + ") should match the defined pattern (" + CMD_LINE_PATTERN + ") (snp table).", snpTable.getCreatedByTool().getCommandLine().matches(CMD_LINE_PATTERN));
    final ToolExecution snpTableCoreInputs = snpTable.getCreatedByTool();
    assertEquals("The first tool execution should be by core_pipeline_outputs_paired v0.1.0", "core_pipeline_outputs_paired", snpTableCoreInputs.getToolName());
    assertEquals("The first tool execution should be by core_pipeline_outputs_paired v0.1.0", "0.1.0", snpTableCoreInputs.getToolVersion());
    final ToolExecution snpTableCoreUpload = snpTableCoreInputs.getPreviousSteps().iterator().next();
    assertTrue("Second step should be input tool.", snpTableCoreUpload.isInputTool());
    AnalysisSubmission finalSubmission = analysisSubmissionRepository.findOne(analysisExecuted.getId());
    Analysis analysis = finalSubmission.getAnalysis();
    assertNotNull("analysis should not be null in submission", analysis);
    Analysis savedAnalysisFromDatabase = analysisService.read(analysisResultsDatabase.getId());
    assertEquals("saved analysis in submission is not correct class", AnalysisType.PHYLOGENOMICS, savedAnalysisFromDatabase.getAnalysisType());
    assertEquals("Analysis from submission and from database should be the same", savedAnalysisFromDatabase.getId(), analysis.getId());
    assertEquals("analysis results from database and from submission should have correct id", analysisResultsDatabase.getId(), savedAnalysisFromDatabase.getId());
    assertEquals("analysis results from database and from submission should have correct tree output file", analysisResultsDatabase.getAnalysisOutputFile(TREE_KEY).getFile(), savedAnalysisFromDatabase.getAnalysisOutputFile(TREE_KEY).getFile());
    assertEquals("analysis results from database and from submission should have correct matrix output file", analysisResultsDatabase.getAnalysisOutputFile(MATRIX_KEY).getFile(), savedAnalysisFromDatabase.getAnalysisOutputFile(MATRIX_KEY).getFile());
    assertEquals("analysis results from database and from submission should have correct table output file", analysisResultsDatabase.getAnalysisOutputFile(MATRIX_KEY).getFile(), savedAnalysisFromDatabase.getAnalysisOutputFile(MATRIX_KEY).getFile());
}

Example 14 with ToolExecution

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

the class AnalysisExecutionServiceGalaxyIT method testTransferAnalysisResultsSuccessPhylogenomicsPairedMultiLeveledParameters.

/**
 * Tests out getting analysis results successfully for phylogenomics
 * pipeline (paired test version with multiple levels of parameters).
 *
 * @throws Exception
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testTransferAnalysisResultsSuccessPhylogenomicsPairedMultiLeveledParameters() throws Exception {
    String validCoverage = "20";
    // coverage from
    String validCoverageFromProvenance = "\"20\"";
    // provenance has quotes
    // this value does not have quotes around it in final results.
    String validMidCoverageFromProvenance = "20";
    String validParameterValueFromProvenance = "20";
    Map<String, String> parameters = ImmutableMap.of("coverage", validCoverage);
    // I verify parameters were set
    String validTreeFile = "20 20 20 20";
    // correctly by checking output file
    // (where parameters were printed).
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupPairSubmissionInDatabase(1L, pairedPaths1, pairedPaths2, referenceFilePath, parameters, iridaPhylogenomicsPairedMultiLeveledParametersWorkflowId);
    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);
    // 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_multi_level_parameters v0.1.0", "core_pipeline_outputs_paired_with_multi_level_parameters", phyTreeCoreInputs.getToolName());
    assertEquals("The first tool execution should be by core_pipeline_outputs_paired_with_multi_level_parameters v0.1.0", "0.1.0", phyTreeCoreInputs.getToolVersion());
    Map<String, String> phyTreeCoreParameters = phyTreeCoreInputs.getExecutionTimeParameters();
    assertEquals("incorrect number of non-file parameters", 6, phyTreeCoreParameters.size());
    assertEquals("parameter coverageMin set incorrectly", validCoverageFromProvenance, phyTreeCoreParameters.get("coverageMin"));
    assertEquals("parameter coverageMid set incorrectly", validMidCoverageFromProvenance, phyTreeCoreParameters.get("conditional.coverageMid"));
    assertEquals("parameter 'parameter' set incorrectly", validParameterValueFromProvenance, phyTreeCoreParameters.get("conditional.level2.parameter"));
    assertEquals("parameter coverageMax set incorrectly", validCoverageFromProvenance, phyTreeCoreParameters.get("coverageMax"));
    assertEquals("parameter conditional_select set incorrectly", "all", phyTreeCoreParameters.get("conditional.conditional_select"));
    assertEquals("parameter conditional_select set incorrectly", "all2", phyTreeCoreParameters.get("conditional.level2.level2_select"));
}

Example 15 with ToolExecution

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

the class AnalysisProvenanceServiceGalaxyTest method testBuildSingleStepToolExecutionListParameters.

@Test
public void testBuildSingleStepToolExecutionListParameters() throws ExecutionManagerException {
    final HistoryContents hc = new HistoryContents();
    hc.setName(FILENAME);
    final HistoryContentsProvenance hcp = new HistoryContentsProvenance();
    hcp.setParameters(ImmutableMap.<String, Object>builder().put("akey", "[\"avalue\"]").put("akey2", Lists.newArrayList("avalue2")).put("akey3", "[]").put("akey4", Lists.newArrayList()).put("akey5", "[\"avalue5.1\", \"avalue5.2\"]").put("akey6", Lists.newArrayList("avalue6.1", "avalue6.2")).build());
    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"));
    assertTrue("tool execution should have the specified parameter.", toolExecution.getExecutionTimeParameters().containsKey("akey2"));
    assertEquals("tool execution parameter should be specified value.", "[avalue2]", toolExecution.getExecutionTimeParameters().get("akey2"));
    assertEquals("tool execution parameter should be specified value.", "[]", toolExecution.getExecutionTimeParameters().get("akey3"));
    assertEquals("tool execution parameter should be specified value.", "[]", toolExecution.getExecutionTimeParameters().get("akey4"));
    assertEquals("tool execution parameter should be specified value.", "[avalue5.1, avalue5.2]", toolExecution.getExecutionTimeParameters().get("akey5"));
    assertEquals("tool execution parameter should be specified value.", "[avalue6.1, avalue6.2]", toolExecution.getExecutionTimeParameters().get("akey6"));
    assertTrue("Tool execution should be considered input step, no predecessors.", toolExecution.isInputTool());
}