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

Example 26 with SequencingObject

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

the class CoverageFileProcessor method process.

@Override
public void process(SequencingObject sequencingObject) {
    logger.trace("Counting coverage for file " + sequencingObject);
    if (sequencingObject.getQcEntries() != null) {
        // remove any existing coverage entries
        sequencingObject.getQcEntries().stream().filter(q -> q instanceof CoverageQCEntry).forEach(q -> qcEntryRepository.delete(q));
    }
    // count the total bases
    long totalBases = sequencingObject.getFiles().stream().mapToLong(f -> {
        AnalysisFastQC fastqc = analysisRepository.findFastqcAnalysisForSequenceFile(f);
        return fastqc.getTotalBases();
    }).sum();
    // save the entry
    CoverageQCEntry coverageQCEntry = new CoverageQCEntry(sequencingObject, totalBases);
    qcEntryRepository.save(coverageQCEntry);
}

Example 27 with SequencingObject

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

the class DefaultFileProcessingChain method getSettledSequencingObject.

/**
 * Checks the {@link SequenceFile}s for the given {@link SequencingObject}
 * to see if it's files are in the place they should be. Since there's lots
 * of saves going on during the {@link FileProcessingChain} the transaction
 * might not be complete in the time the file is first read.
 *
 * @param sequencingObjectId
 *            the id of the {@link SequencingObject} to check
 * @return the settled {@link SequencingObject}
 * @throws FileProcessorTimeoutException
 *             if the files don't settle in the configured timeout
 */
private SequencingObject getSettledSequencingObject(Long sequencingObjectId) throws FileProcessorTimeoutException {
    boolean filesNotSettled = true;
    Integer waiting = 0;
    SequencingObject sequencingObject;
    do {
        if (waiting > timeout) {
            throw new FileProcessorTimeoutException("Waiting for longer than " + sleepDuration * timeout + "ms, bailing out.  File id " + sequencingObjectId);
        }
        waiting++;
        try {
            Thread.sleep(sleepDuration);
        } catch (InterruptedException e) {
        }
        sequencingObject = sequencingObjectRepository.findOne(sequencingObjectId);
        Set<SequenceFile> files = sequencingObject.getFiles();
        filesNotSettled = files.stream().anyMatch(f -> {
            return !Files.exists(f.getFile());
        });
    } while (filesNotSettled);
    return sequencingObject;
}

Example 28 with SequencingObject

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

the class SistrTypingFileProcessor method shouldTypeWithSISTR.

/**
 * Check whether any {@link Project} associated with the
 * {@link SequencingObject} is set to type with SISTR.
 *
 * @param object {@link SequencingObject} to check to type with SISTR.
 * @return true if it should type with SISTR, false otherwise
 */
private Project.AutomatedSISTRSetting shouldTypeWithSISTR(SequencingObject object) {
    Project.AutomatedSISTRSetting type = Project.AutomatedSISTRSetting.OFF;
    SampleSequencingObjectJoin sampleForSequencingObject = ssoRepository.getSampleForSequencingObject(object);
    /*
		 * This is something that should only ever happen in tests, but added
		 * check with a warning
		 */
    if (sampleForSequencingObject != null) {
        List<Join<Project, Sample>> projectForSample = psjRepository.getProjectForSample(sampleForSequencingObject.getSubject());
        Set<Project.AutomatedSISTRSetting> sistrOptions = projectForSample.stream().map(j -> j.getSubject().getSistrTypingUploads()).collect(Collectors.toSet());
        if (sistrOptions.contains(Project.AutomatedSISTRSetting.AUTO_METADATA)) {
            return Project.AutomatedSISTRSetting.AUTO_METADATA;
        } else if (sistrOptions.contains(Project.AutomatedSISTRSetting.AUTO))
            return Project.AutomatedSISTRSetting.AUTO;
    } else {
        logger.warn("Cannot find sample for sequencing object.  Not typing with SISTR");
    }
    return type;
}

Example 29 with SequencingObject

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

the class SequenceFilePairConcatenator method concatenateFiles.

/**
 * {@inheritDoc}
 */
@Override
public SequenceFilePair concatenateFiles(List<? extends SequencingObject> toConcatenate, String filename) throws ConcatenateException {
    // create the filenames with F/R for the forward and reverse files
    String forwardName = filename + "_R1.fastq";
    String reverseName = filename + "_R2.fastq";
    Path forwardFile;
    Path reverseFile;
    try {
        // create a temp directory for the new files
        Path tempDirectory = Files.createTempDirectory(null);
        forwardFile = tempDirectory.resolve(forwardName);
        reverseFile = tempDirectory.resolve(reverseName);
        // create temp files
        forwardFile = Files.createFile(forwardFile);
        reverseFile = Files.createFile(reverseFile);
    } catch (IOException e) {
        throw new ConcatenateException("Could not create temporary files", e);
    }
    // for each file concatenate the forward and reverse files
    for (SequencingObject f : toConcatenate) {
        SequenceFilePair pair = (SequenceFilePair) f;
        SequenceFile forwardSequenceFile = pair.getForwardSequenceFile();
        SequenceFile reverseSequenceFile = pair.getReverseSequenceFile();
        appendToFile(forwardFile, forwardSequenceFile);
        appendToFile(reverseFile, reverseSequenceFile);
    }
    // create new SequenceFiles
    SequenceFile forward = new SequenceFile(forwardFile);
    SequenceFile reverse = new SequenceFile(reverseFile);
    // create the new pair
    SequenceFilePair sequenceFilePair = new SequenceFilePair(forward, reverse);
    return sequenceFilePair;
}

Example 30 with SequencingObject

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

the class SingleEndSequenceFileConcatenator method concatenateFiles.

/**
 * {@inheritDoc}
 */
@Override
public SingleEndSequenceFile concatenateFiles(List<? extends SequencingObject> toConcatenate, String filename) throws ConcatenateException {
    Path tempFile;
    // create the filename with extension
    filename = filename + ".fastq";
    try {
        // create a temp directory and temp file
        Path tempDirectory = Files.createTempDirectory(null);
        tempFile = tempDirectory.resolve(filename);
        tempFile = Files.createFile(tempFile);
    } catch (IOException e) {
        throw new ConcatenateException("Could not create temporary files", e);
    }
    // for each file concatenate the file
    for (SequencingObject f : toConcatenate) {
        SingleEndSequenceFile single = (SingleEndSequenceFile) f;
        SequenceFile forwardSequenceFile = single.getSequenceFile();
        appendToFile(tempFile, forwardSequenceFile);
    }
    // create the new sequencefile and object
    SequenceFile forward = new SequenceFile(tempFile);
    SingleEndSequenceFile seqObject = new SingleEndSequenceFile(forward);
    return seqObject;
}