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

Example 11 with AnalysisSubmission

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

the class ReadAnalysisPermission method customPermissionAllowed.

/**
 * {@inheritDoc}
 */
@Override
protected boolean customPermissionAllowed(final Authentication authentication, final Analysis analysis) {
    logger.trace("Testing permission for [" + authentication + "] on analysis  [" + analysis + "]");
    final User u = userRepository.loadUserByUsername(authentication.getName());
    final AnalysisSubmission analysisSubmission = analysisSubmissionRepository.findByAnalysis(analysis);
    if (analysisSubmission.getSubmitter().equals(u)) {
        logger.trace("Permission GRANTED for [" + authentication + "] on analysis submission [" + analysisSubmission + "]");
        return true;
    }
    logger.trace("Permission DENIED for [" + authentication + "] on analysis submission [" + analysisSubmission + "]");
    return false;
}

Example 12 with AnalysisSubmission

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

the class AssemblyPipelinePageIT method testShareResultsWithSamples.

@Test
public void testShareResultsWithSamples() {
    addSamplesToCartManager();
    String analysisName = AssemblyPipelinePageIT.class.getName() + ".testShareResultsWithSamples";
    page.setNameForAnalysisPipeline(analysisName);
    assertTrue("Share Results with Samples checkbox should exist", page.existsShareResultsWithSamples());
    page.clickShareResultsWithSamples();
    page.clickLaunchPipelineBtn();
    assertTrue("Message should be displayed once the pipeline finished submitting", page.isPipelineSubmittedSuccessMessageShown());
    AnalysisSubmission submission = findAnalysisSubmissionWithName(analysisName + "_sample1");
    assertNotNull("Analysis Submission is null", submission);
    assertTrue("updateSamples should be true", submission.getUpdateSamples());
}

Example 13 with AnalysisSubmission

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

the class AssemblyPipelinePageIT method testUserNoShareResultsWithSamples.

@Test
public void testUserNoShareResultsWithSamples() {
    addSamplesToCartUser();
    String analysisName = AssemblyPipelinePageIT.class.getName() + ".testUserNoShareResultsWithSamples";
    page.setNameForAnalysisPipeline(analysisName);
    assertFalse("Share Results with Samples checkbox should not exist", page.existsShareResultsWithSamples());
    page.clickLaunchPipelineBtn();
    assertTrue("Message should be displayed once the pipeline finished submitting", page.isPipelineSubmittedSuccessMessageShown());
    AnalysisSubmission submission = findAnalysisSubmissionWithName(analysisName + "_sample1");
    assertNotNull("Analysis Submission is null", submission);
    assertFalse("updateSamples should be false", submission.getUpdateSamples());
}

Example 14 with AnalysisSubmission

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

the class SNVPhylAnalysisIT method testSNVPhylSuccessHigherSNVReadProportion.

/**
 * Tests out successfully executing the SNVPhyl pipeline and passing a higher value for fraction of reads to call a SNP.
 *
 * @throws Exception
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testSNVPhylSuccessHigherSNVReadProportion() throws Exception {
    SequenceFilePair sequenceFilePairA = databaseSetupGalaxyITService.setupSampleSequenceFileInDatabase(1L, sequenceFilePathsA1List, sequenceFilePathsA2List).get(0);
    SequenceFilePair sequenceFilePairB = databaseSetupGalaxyITService.setupSampleSequenceFileInDatabase(2L, sequenceFilePathsB1List, sequenceFilePathsB2List).get(0);
    SequenceFilePair sequenceFilePairC = databaseSetupGalaxyITService.setupSampleSequenceFileInDatabase(3L, sequenceFilePathsC1List, sequenceFilePathsC2List).get(0);
    waitForFilesToSettle(sequenceFilePairA, sequenceFilePairB, sequenceFilePairC);
    Map<String, String> parameters = ImmutableMap.<String, String>builder().put("snv-abundance-ratio", "0.90").put("minimum-read-coverage", "2").put("minimum-percent-coverage", "75").put("minimum-mean-mapping-quality", "20").put("filter-density-threshold", "3").put("filter-density-window-size", "30").build();
    AnalysisSubmission submission = databaseSetupGalaxyITService.setupPairSubmissionInDatabase(Sets.newHashSet(sequenceFilePairA, sequenceFilePairB, sequenceFilePairC), referenceFilePath, parameters, snvPhylWorkflow.getWorkflowIdentifier());
    completeSubmittedAnalyses(submission.getId());
    submission = analysisSubmissionRepository.findOne(submission.getId());
    assertEquals("analysis state should be completed.", AnalysisState.COMPLETED, submission.getAnalysisState());
    Analysis analysisPhylogenomics = submission.getAnalysis();
    assertEquals("Should have generated a phylogenomics pipeline analysis type.", AnalysisType.PHYLOGENOMICS, analysisPhylogenomics.getAnalysisType());
    assertEquals("the phylogenomics pipeline should have 8 output files.", 8, analysisPhylogenomics.getAnalysisOutputFiles().size());
    @SuppressWarnings("resource") String matrixContent = new Scanner(analysisPhylogenomics.getAnalysisOutputFile(MATRIX_KEY).getFile().toFile()).useDelimiter("\\Z").next();
    assertTrue("snpMatrix should be the same but is \"" + matrixContent + "\"", com.google.common.io.Files.equal(outputSnvMatrix2.toFile(), analysisPhylogenomics.getAnalysisOutputFile(MATRIX_KEY).getFile().toFile()));
    assertNotNull("file should have tool provenance attached.", analysisPhylogenomics.getAnalysisOutputFile(MATRIX_KEY).getCreatedByTool());
    @SuppressWarnings("resource") String snpTableContent = new Scanner(analysisPhylogenomics.getAnalysisOutputFile(TABLE_KEY).getFile().toFile()).useDelimiter("\\Z").next();
    assertTrue("snpTable should be the same but is \"" + snpTableContent + "\"", com.google.common.io.Files.equal(outputSnvTable2.toFile(), analysisPhylogenomics.getAnalysisOutputFile(TABLE_KEY).getFile().toFile()));
    assertNotNull("file should have tool provenance attached.", analysisPhylogenomics.getAnalysisOutputFile(TABLE_KEY).getCreatedByTool());
    @SuppressWarnings("resource") String vcf2coreContent = new Scanner(analysisPhylogenomics.getAnalysisOutputFile(CORE_KEY).getFile().toFile()).useDelimiter("\\Z").next();
    assertTrue("vcf2core should be the same but is \"" + vcf2coreContent + "\"", com.google.common.io.Files.equal(vcf2core2.toFile(), analysisPhylogenomics.getAnalysisOutputFile(CORE_KEY).getFile().toFile()));
    assertNotNull("file should have tool provenance attached.", analysisPhylogenomics.getAnalysisOutputFile(CORE_KEY).getCreatedByTool());
    // only check size of mapping quality file due to samples output in random order
    assertTrue("the mapping quality file should not be empty.", Files.size(analysisPhylogenomics.getAnalysisOutputFile(QUALITY_KEY).getFile()) > 0);
    @SuppressWarnings("resource") String filterStatsContent = new Scanner(analysisPhylogenomics.getAnalysisOutputFile(STATS_KEY).getFile().toFile()).useDelimiter("\\Z").next();
    assertTrue("filterStats should be the same but is \"" + filterStatsContent + "\"", com.google.common.io.Files.equal(filterStats2.toFile(), analysisPhylogenomics.getAnalysisOutputFile(STATS_KEY).getFile().toFile()));
    assertNotNull("file should have tool provenance attached.", analysisPhylogenomics.getAnalysisOutputFile(STATS_KEY).getCreatedByTool());
    @SuppressWarnings("resource") String snvAlignContent = new Scanner(analysisPhylogenomics.getAnalysisOutputFile(ALIGN_KEY).getFile().toFile()).useDelimiter("\\Z").next();
    assertTrue("snvAlign should be the same but is \"" + snvAlignContent + "\"", com.google.common.io.Files.equal(snvAlign2.toFile(), analysisPhylogenomics.getAnalysisOutputFile(ALIGN_KEY).getFile().toFile()));
    assertNotNull("file should have tool provenance attached.", analysisPhylogenomics.getAnalysisOutputFile(ALIGN_KEY).getCreatedByTool());
    // only test to make sure the files have a valid size since PhyML uses a
    // random seed to generate the tree (and so changes results)
    assertTrue("the phylogenetic tree file should not be empty.", Files.size(analysisPhylogenomics.getAnalysisOutputFile(TREE_KEY).getFile()) > 0);
    assertTrue("the phylogenetic tree stats file should not be empty.", Files.size(analysisPhylogenomics.getAnalysisOutputFile(TREE_KEY).getFile()) > 0);
    // try to follow the phylogenomics provenance all the way back to the
    // upload tools
    List<ToolExecution> toolsToVisit = Lists.newArrayList(analysisPhylogenomics.getAnalysisOutputFile(TREE_KEY).getCreatedByTool());
    assertFalse("file should have tool provenance attached.", toolsToVisit.isEmpty());
    String minVcf2AlignCov = null;
    String altAlleleFraction = null;
    String minimumPercentCoverage = null;
    String minimumDepthVerify = null;
    String filterDensityThreshold = null;
    String filterDensityWindowSize = null;
    // one where you upload the reads.
    while (!toolsToVisit.isEmpty()) {
        final ToolExecution ex = toolsToVisit.remove(0);
        toolsToVisit.addAll(ex.getPreviousSteps());
        if (ex.getToolName().contains("Consolidate VCFs")) {
            final Map<String, String> params = ex.getExecutionTimeParameters();
            minVcf2AlignCov = params.get("coverage");
            altAlleleFraction = params.get("snv_abundance_ratio");
            filterDensityThreshold = params.get("use_density_filter.threshold");
            filterDensityWindowSize = params.get("use_density_filter.window_size");
            break;
        }
    }
    // try to follow the mapping quality provenance all the way back to the
    // upload tools
    toolsToVisit = Lists.newArrayList(analysisPhylogenomics.getAnalysisOutputFile(QUALITY_KEY).getCreatedByTool());
    assertFalse("file should have tool provenance attached.", toolsToVisit.isEmpty());
    while (!toolsToVisit.isEmpty()) {
        final ToolExecution ex = toolsToVisit.remove(0);
        toolsToVisit.addAll(ex.getPreviousSteps());
        if (ex.getToolName().contains("Verify Mapping Quality")) {
            final Map<String, String> params = ex.getExecutionTimeParameters();
            minimumPercentCoverage = params.get("minmap");
            minimumDepthVerify = params.get("mindepth");
        }
    }
    assertEquals("incorrect minimum vcf 2 align coverage", "\"2\"", minVcf2AlignCov);
    assertEquals("incorrect alternative allele fraction", "\"0.90\"", altAlleleFraction);
    assertEquals("incorrect minimum depth for verify map", "\"2\"", minimumDepthVerify);
    assertEquals("incorrect min percent coverage for verify map", "\"75\"", minimumPercentCoverage);
    assertEquals("incorrect filter density threshold", "3", filterDensityThreshold);
    assertEquals("incorrect filter density window size", "30", filterDensityWindowSize);
}

Example 15 with AnalysisSubmission

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

the class AnalysisSubmissionTest method testIndividualInputParameter.

@Test
public void testIndividualInputParameter() {
    AnalysisSubmission submission = AnalysisSubmission.builder(workflowId).name("name").referenceFile(referenceFile).inputFiles(Sets.newHashSet(singleEndFile)).inputParameter("name", "value").inputParameter("name2", "value2").build();
    assertEquals("input parameter \"name\" not correct", "value", submission.getInputParameters().get("name"));
    assertEquals("input parameter \"name2\" not correct", "value2", submission.getInputParameters().get("name2"));
}