Examples with SingleEndSequenceFile ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile used on opensource projects

Example 26 with SingleEndSequenceFile

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile in project irida by phac-nml.

the class AnalysisWorkspaceServiceGalaxyIT method testGetAnalysisResultsTestAnalysisPairedSuccess.

/**
 * 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 testGetAnalysisResultsTestAnalysisPairedSuccess() throws InterruptedException, ExecutionManagerException, IridaWorkflowNotFoundException, IOException, IridaWorkflowAnalysisTypeException, TimeoutException {
    History history = new History();
    history.setName("testGetAnalysisResultsTestAnalysisPairedSuccess");
    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(validWorkflowIdPaired);
    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, validWorkflowIdPaired, 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", 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 27 with SingleEndSequenceFile

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile in project irida by phac-nml.

the class AnalysisWorkspaceServiceGalaxyTest method setup.

/**
 * Sets up variables for testing.
 *
 * @throws IOException
 * @throws GalaxyDatasetException
 * @throws UploadException
 */
@Before
public void setup() throws IOException, UploadException, GalaxyDatasetException {
    MockitoAnnotations.initMocks(this);
    sFileA = new SequenceFile(createTempFile("fileA", "fastq"));
    sFileB = new SequenceFile(createTempFile("fileB", "fastq"));
    sFileC = new SequenceFile(createTempFile("fileC", "fastq"));
    sObjA = new SingleEndSequenceFile(sFileA);
    sObjB = new SingleEndSequenceFile(sFileB);
    sObjC = new SingleEndSequenceFile(sFileC);
    sequenceFilePair = new SequenceFilePair(sFileB, sFileC);
    singleEndSequenceFile = sObjA;
    Sample sampleA = new Sample();
    sampleA.setSampleName("SampleA");
    Sample sampleB = new Sample();
    sampleB.setSampleName("SampleB");
    Sample sampleC = new Sample();
    sampleC.setSampleName("SampleC");
    sampleSingleSequenceFileMap = ImmutableMap.of(sampleA, singleEndSequenceFile);
    sampleSequenceFilePairMap = ImmutableMap.of(sampleB, sequenceFilePair);
    sampleSequenceFilePairMapSampleA = ImmutableMap.of(sampleA, sequenceFilePair);
    refFile = createTempFile("reference", "fasta");
    referenceFile = new ReferenceFile(refFile);
    inputFiles = new HashSet<>();
    inputFiles.addAll(Arrays.asList(sObjA, sObjB, sObjC));
    submission = AnalysisSubmission.builder(workflowId).name("my analysis").inputFiles(inputFiles).referenceFile(referenceFile).build();
    workflowHistory = new History();
    workflowHistory.setId(HISTORY_ID);
    workflowLibrary = new Library();
    workflowLibrary.setId(LIBRARY_ID);
    workflowDetails = new WorkflowDetails();
    workflowDetails.setId(WORKFLOW_ID);
    workflowPreparation = new AnalysisWorkspaceServiceGalaxy(galaxyHistoriesService, galaxyWorkflowService, galaxyLibrariesService, iridaWorkflowsService, analysisCollectionServiceGalaxy, analysisProvenanceServiceGalaxy, analysisParameterServiceGalaxy, sequencingObjectService);
    output1Dataset = new Dataset();
    output1Dataset.setId("1");
    output1Dataset.setName("output1.txt");
    output2Dataset = new Dataset();
    output2Dataset.setId("2");
    output2Dataset.setName("output2.txt");
    collectionResponseSingle = new CollectionResponse();
    collectionResponseSingle.setId(COLLECTION_SINGLE_ID);
    collectionResponsePaired = new CollectionResponse();
    collectionResponsePaired.setId(COLLECTION_PAIRED_ID);
    singleInputFiles = Sets.newHashSet(singleEndSequenceFile);
    pairedInputFiles = Sets.newHashSet(sequenceFilePair);
}

Example 28 with SingleEndSequenceFile

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile in project irida by phac-nml.

the class SequencingObjectServiceImplIT method testCreateNotCompressedSequenceFile.

@Test
@WithMockUser(username = "fbristow", roles = "SEQUENCER")
public void testCreateNotCompressedSequenceFile() throws IOException, InterruptedException {
    final Long expectedRevisionNumber = 1L;
    SequenceFile sf = createSequenceFile("file1");
    Path sequenceFile = sf.getFile();
    SingleEndSequenceFile singleEndSequenceFile = new SingleEndSequenceFile(sf);
    logger.trace("About to save the file.");
    SequencingObject sequencingObject = asRole(Role.ROLE_SEQUENCER, "fbristow").objectService.create(singleEndSequenceFile);
    logger.trace("Finished saving the file.");
    assertNotNull("ID wasn't assigned.", sequencingObject.getId());
    // Sleeping for a bit to let file processing run
    Thread.sleep(10000);
    // figure out what the version number of the sequence file is (should be
    // 1; the file wasn't gzipped, but fastqc will have modified it.)
    SequencingObject readObject = null;
    do {
        readObject = asRole(Role.ROLE_ADMIN, "admin").objectService.read(sequencingObject.getId());
        sf = readObject.getFiles().iterator().next();
        if (sf.getFileRevisionNumber() < expectedRevisionNumber) {
            logger.info("Still waiting on thread to finish, having a bit of a sleep.");
            Thread.sleep(1000);
        }
    } while (sf.getFileRevisionNumber() < expectedRevisionNumber);
    assertEquals("Wrong version number after processing.", expectedRevisionNumber, sf.getFileRevisionNumber());
    // verify the file checksum was taken properly
    assertEquals("checksum should be equal", CHECKSUM, sf.getUploadSha256());
    AnalysisFastQC analysis = asRole(Role.ROLE_ADMIN, "admin").analysisService.getFastQCAnalysisForSequenceFile(readObject, sf.getId());
    assertNotNull("FastQCAnalysis should have been created for the file.", analysis);
    Set<OverrepresentedSequence> overrepresentedSequences = analysis.getOverrepresentedSequences();
    assertNotNull("No overrepresented sequences were found.", overrepresentedSequences);
    assertEquals("Wrong number of overrepresented sequences were found.", 1, overrepresentedSequences.size());
    OverrepresentedSequence overrepresentedSequence = overrepresentedSequences.iterator().next();
    assertEquals("Sequence was not the correct sequence.", SEQUENCE, overrepresentedSequence.getSequence());
    assertEquals("The count was not correct.", 2, overrepresentedSequence.getOverrepresentedSequenceCount());
    assertEquals("The percent was not correct.", new BigDecimal("100.00"), overrepresentedSequence.getPercentage());
    // confirm that the file structure is correct
    Path idDirectory = baseDirectory.resolve(Paths.get(sf.getId().toString()));
    assertTrue("Revision directory doesn't exist.", Files.exists(idDirectory.resolve(Paths.get(sf.getFileRevisionNumber().toString(), sequenceFile.getFileName().toString()))));
    // no other files or directories should be beneath the ID directory
    int fileCount = 0;
    Iterator<Path> dir = Files.newDirectoryStream(idDirectory).iterator();
    while (dir.hasNext()) {
        dir.next();
        fileCount++;
    }
    assertEquals("Wrong number of directories beneath the id directory", 1, fileCount);
}

Example 29 with SingleEndSequenceFile

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile in project irida by phac-nml.

the class SequencingObjectServiceImplIT method testCoverage.

@Test
@WithMockUser(username = "admin", roles = "ADMIN")
public void testCoverage() throws IOException, InterruptedException {
    Project project = projectService.read(1L);
    project.setGenomeSize(3L);
    project.setMinimumCoverage(2);
    project = projectService.update(project);
    Sample s = sampleService.read(1L);
    SequenceFile sf = new SequenceFile();
    Path sequenceFile = Files.createTempFile("TEMPORARY-SEQUENCE-FILE", ".gz");
    OutputStream gzOut = new GZIPOutputStream(Files.newOutputStream(sequenceFile));
    gzOut.write(FASTQ_FILE_CONTENTS);
    gzOut.close();
    sf.setFile(sequenceFile);
    SingleEndSequenceFile so = new SingleEndSequenceFile(sf);
    objectService.createSequencingObjectInSample(so, s);
    SequencingRun mr = sequencingRunService.read(1L);
    sequencingRunService.addSequencingObjectToSequencingRun(mr, so);
    // Wait 10 seconds. file processing should have run by then.
    Thread.sleep(10000);
    Sample readSample = sampleService.read(s.getId());
    List<QCEntry> qcEntries = sampleService.getQCEntriesForSample(readSample);
    assertEquals("should be one qc entry", 1, qcEntries.size());
    QCEntry qcEntry = qcEntries.iterator().next();
    qcEntry.addProjectSettings(project);
    assertTrue("should be coverage entry", qcEntry instanceof CoverageQCEntry);
    assertEquals("qc should have passed", QCEntryStatus.POSITIVE, qcEntry.getStatus());
    assertEquals("should be 6x coverage", "6x", qcEntry.getMessage());
    project.setMinimumCoverage(10);
    project = projectService.update(project);
    // Wait 10 seconds. file processing should have run by then.
    Thread.sleep(10000);
    qcEntries = sampleService.getQCEntriesForSample(readSample);
    assertEquals("should be one qc entry", 1, qcEntries.size());
    qcEntry = qcEntries.iterator().next();
    qcEntry.addProjectSettings(project);
    assertTrue("should be coverage entry", qcEntry instanceof CoverageQCEntry);
    assertEquals("qc should have failed", QCEntryStatus.NEGATIVE, qcEntry.getStatus());
}

Example 30 with SingleEndSequenceFile

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile in project irida by phac-nml.

the class SequencingRunServiceImplIT method testAddDetachedRunToSequenceFile.

/**
 * This test simulates a bug that happens from the REST API when uploading
 * sequence files to samples, where a new sequence file is created, then
 * detached from a transaction.
 *
 * @throws IOException
 * @throws InterruptedException
 */
@Test
@WithMockUser(username = "fbristow", password = "password1", roles = "ADMIN")
public void testAddDetachedRunToSequenceFile() throws IOException, InterruptedException {
    final String SEQUENCE = "ACGTACGTN";
    final byte[] FASTQ_FILE_CONTENTS = ("@testread\n" + SEQUENCE + "\n+\n?????????\n@testread2\n" + SEQUENCE + "\n+\n?????????").getBytes();
    Path p = Files.createTempFile(null, null);
    Files.write(p, FASTQ_FILE_CONTENTS);
    SequenceFile sf = new SequenceFile();
    sf.setFile(p);
    SingleEndSequenceFile so = new SingleEndSequenceFile(sf);
    Sample sample = sampleService.read(1L);
    SequencingRun run = miseqRunService.read(2L);
    objectService.createSequencingObjectInSample(so, sample);
    miseqRunService.addSequencingObjectToSequencingRun(run, so);
    AnalysisFastQC analysis = null;
    do {
        try {
            analysis = analysisService.getFastQCAnalysisForSequenceFile(so, sf.getId());
        } catch (final EntityNotFoundException e) {
            logger.info("Fastqc still isn't finished, sleeping a bit.");
            Thread.sleep(1000);
        }
    } while (analysis == null);
    assertNotNull("FastQC analysis should have been created for sequence file.", analysis);
}