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

Example 11 with AnalysisFastQC

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

the class RESTSampleSequenceFilesController method readQCForSequenceFile.

/**
 * Get the fastqc metrics for a {@link SequenceFile}
 *
 * @param sampleId
 *            {@link Sample} id of the file
 * @param objectType
 *            type of {@link SequencingObject}
 * @param objectId
 *            id of the {@link SequencingObject}
 * @param fileId
 *            id of the {@link SequenceFile}
 * @return an {@link AnalysisFastQC} for the file
 */
@RequestMapping(value = "/api/samples/{sampleId}/{objectType}/{objectId}/files/{fileId}/qc", method = RequestMethod.GET)
public ModelMap readQCForSequenceFile(@PathVariable Long sampleId, @PathVariable String objectType, @PathVariable Long objectId, @PathVariable Long fileId) {
    ModelMap modelMap = new ModelMap();
    Sample sample = sampleService.read(sampleId);
    SequencingObject readSequencingObjectForSample = sequencingObjectService.readSequencingObjectForSample(sample, objectId);
    AnalysisFastQC fastQCAnalysisForSequenceFile = analysisService.getFastQCAnalysisForSequenceFile(readSequencingObjectForSample, fileId);
    if (fastQCAnalysisForSequenceFile == null) {
        throw new EntityNotFoundException("No QC data for file");
    }
    fastQCAnalysisForSequenceFile.add(linkTo(methodOn(RESTSampleSequenceFilesController.class).readSequenceFileForSequencingObject(sampleId, objectType, objectId, fileId)).withRel(REL_QC_SEQFILE));
    fastQCAnalysisForSequenceFile.add(linkTo(methodOn(RESTSampleSequenceFilesController.class).readQCForSequenceFile(sampleId, objectType, objectId, fileId)).withSelfRel());
    modelMap.addAttribute(RESTGenericController.RESOURCE_NAME, fastQCAnalysisForSequenceFile);
    return modelMap;
}

Example 12 with AnalysisFastQC

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

the class SequencingObjectServiceImplIT method testCreateCompressedSequenceFile.

@Test
@WithMockUser(username = "fbristow", roles = "SEQUENCER")
public void testCreateCompressedSequenceFile() throws IOException, InterruptedException {
    final Long expectedRevisionNumber = 2L;
    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 singleEndSequenceFile = new SingleEndSequenceFile(sf);
    logger.trace("About to save the file.");
    SequencingObject sequencingObject = 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
    // 2; the file was gzipped)
    // get the MOST RECENT version of the sequence file from the database
    // (it will have been modified outside of the create method.)
    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());
    assertFalse("File name is still gzipped.", sf.getFile().getFileName().toString().endsWith(".gz"));
    AnalysisFastQC analysis = asRole(Role.ROLE_ADMIN, "admin").analysisService.getFastQCAnalysisForSequenceFile(readObject, sf.getId());
    // verify the file checksum was taken properly
    assertEquals("checksum should be equal", ZIPPED_CHECKSUM, sf.getUploadSha256());
    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
    String filename = sequenceFile.getFileName().toString();
    filename = filename.substring(0, filename.lastIndexOf('.'));
    Path idDirectory = baseDirectory.resolve(Paths.get(sf.getId().toString()));
    assertTrue("Revision directory doesn't exist.", Files.exists(idDirectory.resolve(Paths.get(sf.getFileRevisionNumber().toString(), filename))));
    // 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", 2, fileCount);
}

Example 13 with AnalysisFastQC

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

the class SequencingRunServiceImplIT method testAddSequenceFileToMiseqRun.

private void testAddSequenceFileToMiseqRun() throws IOException, InterruptedException {
    SequencingRun miseqRun = miseqRunService.read(1L);
    // we can't actually know a file name in the XML file that we use to
    // populate the database for these tests, so the files don't exist
    // anywhere. Create a new temp file and update that in the database
    // prior to adding a file to a miseq run so that we have something there
    // that we can link to.
    Path sequenceFile = Files.createTempFile(null, null);
    Files.write(sequenceFile, FASTQ_FILE_CONTENTS);
    SequenceFile sf = new SequenceFile(sequenceFile);
    SequencingObject so = new SingleEndSequenceFile(sf);
    so = objectService.create(so);
    miseqRunService.addSequencingObjectToSequencingRun(miseqRun, so);
    SequencingRun saved = miseqRunService.read(1L);
    SequencingObject readObject = objectService.read(so.getId());
    Set<SequencingObject> sequencingObjectsForSequencingRun = objectService.getSequencingObjectsForSequencingRun(saved);
    assertTrue("Saved miseq run should have seqence file", sequencingObjectsForSequencingRun.contains(so));
    if (SecurityContextHolder.getContext().getAuthentication().getAuthorities().stream().anyMatch(auth -> auth.getAuthority().equals("ROLE_ADMIN"))) {
        AnalysisFastQC analysis = null;
        do {
            try {
                readObject = objectService.read(so.getId());
                SequenceFile readFile = readObject.getFiles().iterator().next();
                analysis = analysisService.getFastQCAnalysisForSequenceFile(readObject, readFile.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 uploaded file.", analysis);
    }
}

Example 14 with AnalysisFastQC

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

the class SampleServiceImplTest method testGetTotalBasesForSampleSuccessTwo.

/**
 * Tests out successfully getting the total bases from a sample with two
 * sequence files.
 *
 * @throws SequenceFileAnalysisException
 * @throws AnalysisAlreadySetException
 */
@Test
public void testGetTotalBasesForSampleSuccessTwo() throws SequenceFileAnalysisException, AnalysisAlreadySetException {
    Sample s1 = new Sample();
    s1.setId(1L);
    SequenceFile sf1 = new SequenceFile();
    sf1.setId(2222L);
    SequenceFile sf2 = new SequenceFile();
    sf1.setId(3333L);
    SampleSequencingObjectJoin join1 = new SampleSequencingObjectJoin(s1, new SingleEndSequenceFile(sf1));
    SampleSequencingObjectJoin join2 = new SampleSequencingObjectJoin(s1, new SingleEndSequenceFile(sf2));
    AnalysisFastQC analysisFastQC1 = AnalysisFastQC.sloppyBuilder().executionManagerAnalysisId("id").totalBases(1000L).build();
    sf1.setFastQCAnalysis(analysisFastQC1);
    AnalysisFastQC analysisFastQC2 = AnalysisFastQC.sloppyBuilder().executionManagerAnalysisId("id2").totalBases(1000L).build();
    sf2.setFastQCAnalysis(analysisFastQC2);
    when(ssoRepository.getSequencesForSample(s1)).thenReturn(Arrays.asList(join1, join2));
    when(analysisRepository.findFastqcAnalysisForSequenceFile(sf1)).thenReturn(analysisFastQC1);
    when(analysisRepository.findFastqcAnalysisForSequenceFile(sf2)).thenReturn(analysisFastQC2);
    long actualBases = sampleService.getTotalBasesForSample(s1);
    assertEquals(2000, actualBases);
}

Example 15 with AnalysisFastQC

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

the class AnalysisServiceTest method testCreateAnalysisWithOneOutputFile.

@Test
public void testCreateAnalysisWithOneOutputFile() throws IOException {
    Path outputFile = Files.createTempFile(null, null);
    AnalysisOutputFile report = new AnalysisOutputFile(outputFile, "", "", null);
    AnalysisFastQC analysis = AnalysisFastQC.sloppyBuilder().description("something").fastQCReport(report).build();
    analysisService.create(analysis);
    verify(analysisOutputFileRepository).save(report);
    verify(analysisRepository).save(analysis);
}