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

Example 21 with Analysis

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

the class SNVPhylAnalysisIT method testSNVPhylSuccess.

/**
 * Tests out successfully executing the SNVPhyl pipeline.
 *
 * @throws Exception
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testSNVPhylSuccess() 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);
    Map<String, String> parameters = ImmutableMap.of("snv-abundance-ratio", "0.75", "minimum-read-coverage", "2", "filter-density-threshold", "2", "filter-density-window-size", "3");
    waitForFilesToSettle(sequenceFilePairA, sequenceFilePairB, sequenceFilePairC);
    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(outputSnvMatrix1.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(outputSnvTable1.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(vcf2core1.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(filterStats1.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(snvAlign1.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
    final List<ToolExecution> toolsToVisit = Lists.newArrayList(analysisPhylogenomics.getAnalysisOutputFile(TREE_KEY).getCreatedByTool());
    assertFalse("file should have tool provenance attached.", toolsToVisit.isEmpty());
    boolean foundReadsInputTool = false;
    boolean foundReferenceInputTool = false;
    // one where you upload the reads.
    while (!toolsToVisit.isEmpty()) {
        final ToolExecution ex = toolsToVisit.remove(0);
        toolsToVisit.addAll(ex.getPreviousSteps());
        if (ex.isInputTool()) {
            final Map<String, String> params = ex.getExecutionTimeParameters();
            logger.debug("Input tool has " + params);
            foundReferenceInputTool |= params.containsKey("files.NAME") && params.get("files.NAME").contains("reference") && params.get("file_type").contains("fasta");
            foundReadsInputTool |= params.get("file_type").contains("fastq");
        }
    }
    assertTrue("Should have found both reads and reference input tools.", foundReadsInputTool && foundReferenceInputTool);
}

Example 22 with Analysis

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

the class SNVPhylAnalysisIT method testSNVPhylSuccessRemoveSNVDensity.

/**
 * Tests out successfully executing the SNVPhyl pipeline and passing a lower value for SNV density threshold to filter out SNVs.
 *
 * @throws Exception
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testSNVPhylSuccessRemoveSNVDensity() 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);
    Map<String, String> parameters = ImmutableMap.of("snv-abundance-ratio", "0.75", "minimum-read-coverage", "2", "filter-density-threshold", "2", "filter-density-window-size", "4");
    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(outputSnvMatrix3.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(outputSnvTable3.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(vcf2core3.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(filterStats3.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(snvAlign3.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", "\"0.75\"", altAlleleFraction);
    assertEquals("incorrect minimum depth for verify map", "\"2\"", minimumDepthVerify);
    assertEquals("incorrect min percent coverage for verify map", "\"80\"", minimumPercentCoverage);
    assertEquals("incorrect filter density threshold", "2", filterDensityThreshold);
    assertEquals("incorrect filter density window size", "4", filterDensityWindowSize);
}

Example 23 with Analysis

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

the class RESTAnalysisSubmissionController method getAnalysisForSubmission.

/**
 * Get the {@link Analysis} for an {@link AnalysisSubmission}.
 *
 * @param identifier
 *            {@link AnalysisSubmission} identifier to read
 * @return ModelMap containing the {@link Analysis}
 */
@RequestMapping("/{identifier}/analysis")
public ModelMap getAnalysisForSubmission(@PathVariable Long identifier) {
    ModelMap model = new ModelMap();
    AnalysisSubmission read = analysisSubmissionService.read(identifier);
    if (read.getAnalysisState() != AnalysisState.COMPLETED) {
        throw new EntityNotFoundException("Analysis is not completed");
    }
    Analysis analysis = read.getAnalysis();
    analysis.add(linkTo(methodOn(RESTAnalysisSubmissionController.class).getAnalysisForSubmission(identifier)).withSelfRel());
    /*
		 * Add links to the available files
		 */
    for (String name : analysis.getAnalysisOutputFileNames()) {
        analysis.add(linkTo(methodOn(RESTAnalysisSubmissionController.class).getAnalysisOutputFile(identifier, name)).withRel(FILE_REL + "/" + name));
    }
    model.addAttribute(RESOURCE_NAME, analysis);
    return model;
}

Example 24 with Analysis

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

the class AnalysisExecutionServiceGalaxyIT method testTransferAnalysisResultsSuccessAssemblyAnnotation.

/**
 * Tests out getting analysis results successfully for assembly and annotation pipeline (test version).
 *
 * @throws Exception
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testTransferAnalysisResultsSuccessAssemblyAnnotation() throws Exception {
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupPairSubmissionInDatabase(1L, pairedPaths1, pairedPaths2, iridaAssemblyAnnotationWorkflowId);
    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());
    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 contigs = analysisResultsDatabase.getAnalysisOutputFile("contigs");
    AnalysisOutputFile annotations = analysisResultsDatabase.getAnalysisOutputFile("annotations-genbank");
    AnalysisOutputFile prokkaLog = analysisResultsDatabase.getAnalysisOutputFile("annotations-log");
    assertTrue("contigs should be equal", com.google.common.io.Files.equal(expectedContigs.toFile(), contigs.getFile().toFile()));
    assertEquals("invalid file name for contigs", expectedContigs.getFileName(), contigs.getFile().getFileName());
    assertTrue("annotations should be correct", com.google.common.io.Files.equal(expectedAnnotations.toFile(), annotations.getFile().toFile()));
    assertEquals("invalid file name for annotations", expectedAnnotations.getFileName(), annotations.getFile().getFileName());
    assertTrue("annotations log should be correct", com.google.common.io.Files.equal(expectedAnnotationsLog.toFile(), prokkaLog.getFile().toFile()));
    assertEquals("invalid file name for annotations log", expectedAnnotationsLog.getFileName(), prokkaLog.getFile().getFileName());
}

Example 25 with Analysis

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

the class AnalysisExecutionServiceGalaxyIT method testTransferAnalysisResultsSuccessPhylogenomics.

/**
 * Tests out getting analysis results successfully.
 *
 * @throws Exception
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testTransferAnalysisResultsSuccessPhylogenomics() throws Exception {
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupSubmissionInDatabase(1L, sequenceFilePath, referenceFilePath, iridaPhylogenomicsWorkflowId, false);
    Future<AnalysisSubmission> analysisSubmittedFuture = analysisExecutionService.prepareSubmission(analysisSubmission);
    AnalysisSubmission analysisSubmitted = analysisSubmittedFuture.get();
    float percentComplete = analysisSubmissionService.getPercentCompleteForAnalysisSubmission(analysisSubmitted.getId());
    assertEquals("percent complete is incorrect", 11.0f, percentComplete, DELTA);
    Future<AnalysisSubmission> analysisExecutionFuture = analysisExecutionService.executeAnalysis(analysisSubmitted);
    AnalysisSubmission analysisExecuted = analysisExecutionFuture.get();
    assertNotNull("remoteInputDataId is null", analysisExecuted.getRemoteInputDataId());
    String remoteInputDataId = analysisExecuted.getRemoteInputDataId();
    percentComplete = analysisSubmissionService.getPercentCompleteForAnalysisSubmission(analysisSubmitted.getId());
    assertTrue("percent complete is incorrect", 10.0f <= percentComplete && percentComplete <= 90.0f);
    analysisExecutionGalaxyITService.waitUntilSubmissionComplete(analysisExecuted);
    percentComplete = analysisSubmissionService.getPercentCompleteForAnalysisSubmission(analysisSubmitted.getId());
    assertEquals("percent complete is incorrect", 90.0f, percentComplete, DELTA);
    analysisExecuted.setAnalysisState(AnalysisState.FINISHED_RUNNING);
    percentComplete = analysisSubmissionService.getPercentCompleteForAnalysisSubmission(analysisSubmitted.getId());
    assertEquals("percent complete is incorrect", 90.0f, percentComplete, DELTA);
    Future<AnalysisSubmission> analysisSubmissionCompletedFuture = analysisExecutionService.transferAnalysisResults(analysisExecuted);
    AnalysisSubmission analysisSubmissionCompleted = analysisSubmissionCompletedFuture.get();
    AnalysisSubmission analysisSubmissionCompletedDatabase = analysisSubmissionService.read(analysisSubmission.getId());
    assertEquals(AnalysisState.COMPLETED, analysisSubmissionCompletedDatabase.getAnalysisState());
    assertEquals(AnalysisState.COMPLETED, analysisSubmissionCompleted.getAnalysisState());
    assertEquals("remoteInputDataId should be unchanged in the completed analysis", remoteInputDataId, analysisSubmissionCompletedDatabase.getRemoteInputDataId());
    percentComplete = analysisSubmissionService.getPercentCompleteForAnalysisSubmission(analysisSubmitted.getId());
    assertEquals("percent complete is incorrect", 100.0f, percentComplete, DELTA);
    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(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(expectedTree.getFileName(), phylogeneticTree.getFile().getFileName());
    assertTrue("snp matrices should be correct", com.google.common.io.Files.equal(expectedSnpMatrix.toFile(), snpMatrix.getFile().toFile()));
    assertEquals(expectedSnpMatrix.getFileName(), snpMatrix.getFile().getFileName());
    assertTrue("snpTable should be correct", com.google.common.io.Files.equal(expectedSnpTable.toFile(), snpTable.getFile().toFile()));
    assertEquals(expectedSnpTable.getFileName(), snpTable.getFile().getFileName());
    AnalysisSubmission finalSubmission = analysisSubmissionRepository.findOne(analysisExecuted.getId());
    Analysis analysis = finalSubmission.getAnalysis();
    assertNotNull(analysis);
    Analysis savedAnalysisFromDatabase = analysisService.read(analysisResultsDatabase.getId());
    assertEquals(AnalysisType.PHYLOGENOMICS, savedAnalysisFromDatabase.getAnalysisType());
    assertEquals("Analysis from submission and from database should be the same", savedAnalysisFromDatabase.getId(), analysis.getId());
    assertEquals(analysisResultsDatabase.getId(), savedAnalysisFromDatabase.getId());
    assertEquals(analysisResultsDatabase.getAnalysisOutputFile(TREE_KEY).getFile(), savedAnalysisFromDatabase.getAnalysisOutputFile(TREE_KEY).getFile());
    assertEquals(analysisResultsDatabase.getAnalysisOutputFile(MATRIX_KEY).getFile(), savedAnalysisFromDatabase.getAnalysisOutputFile(MATRIX_KEY).getFile());
    assertEquals(analysisResultsDatabase.getAnalysisOutputFile(TABLE_KEY).getFile(), savedAnalysisFromDatabase.getAnalysisOutputFile(TABLE_KEY).getFile());
}