Examples with FileProcessorErrorQCEntry ca.corefacility.bioinformatics.irida.model.sample.FileProcessorErrorQCEntry used on opensource projects

Example 1 with FileProcessorErrorQCEntry

use of ca.corefacility.bioinformatics.irida.model.sample.FileProcessorErrorQCEntry in project irida by phac-nml.

the class DefaultFileProcessingChain method launchChain.

/**
 * {@inheritDoc}
 */
@Override
public List<Exception> launchChain(Long sequencingObjectId) throws FileProcessorTimeoutException {
    List<Exception> ignoredExceptions = new ArrayList<>();
    Integer waiting = 0;
    // file has been persisted in the database.
    while (!sequencingObjectRepository.exists(sequencingObjectId)) {
        if (waiting > timeout) {
            throw new FileProcessorTimeoutException("Waiting for longer than " + sleepDuration * timeout + "ms, bailing out.");
        }
        waiting++;
        try {
            Thread.sleep(sleepDuration);
        } catch (InterruptedException e) {
        }
    }
    for (FileProcessor fileProcessor : fileProcessors) {
        try {
            if (fileProcessor.shouldProcessFile(sequencingObjectId)) {
                SequencingObject settledSequencingObject = getSettledSequencingObject(sequencingObjectId);
                fileProcessor.process(settledSequencingObject);
            }
        } catch (FileProcessorException e) {
            SequencingObject sequencingObject = sequencingObjectRepository.findOne(sequencingObjectId);
            qcRepository.save(new FileProcessorErrorQCEntry(sequencingObject));
            // execution (show the error, but proceed).
            if (fileProcessor.modifiesFile() || fastFail) {
                throw e;
            } else {
                ignoredExceptions.add(e);
                logger.error("File processor [" + fileProcessor.getClass() + "] failed to process [" + sequencingObjectId + "], but proceeding with the remaining processors because the " + "file would not be modified by the processor. Stack trace follows.", e);
            }
        }
    }
    return ignoredExceptions;
}

Example 2 with FileProcessorErrorQCEntry

use of ca.corefacility.bioinformatics.irida.model.sample.FileProcessorErrorQCEntry in project irida by phac-nml.

the class SequencingObjectServiceImplIT method testCreateCorruptSequenceFileInSample.

@Test
@WithMockUser(username = "fbristow", roles = "SEQUENCER")
public void testCreateCorruptSequenceFileInSample() throws IOException, InterruptedException {
    Sample s = sampleService.read(1L);
    SequenceFile sf = new SequenceFile();
    Path sequenceFile = Files.createTempFile("TEMPORARY-SEQUENCE-FILE", ".gz");
    OutputStream gzOut = Files.newOutputStream(sequenceFile);
    gzOut.write("not a file".getBytes());
    gzOut.close();
    sf.setFile(sequenceFile);
    SingleEndSequenceFile so = new SingleEndSequenceFile(sf);
    objectService.createSequencingObjectInSample(so, s);
    // Wait 5 seconds. file processing should have failed by then.
    Thread.sleep(5000);
    Sample readSample = sampleService.read(s.getId());
    List<QCEntry> qcEntries = sampleService.getQCEntriesForSample(readSample);
    assertFalse("should be a qc entry", qcEntries.isEmpty());
    QCEntry qc = qcEntries.iterator().next();
    assertTrue("should be a FileProcessorErrorQCEntry", qc instanceof FileProcessorErrorQCEntry);
}