Examples with FileProcessorException ca.corefacility.bioinformatics.irida.processing.FileProcessorException used on opensource projects

Example 6 with FileProcessorException

use of ca.corefacility.bioinformatics.irida.processing.FileProcessorException in project irida by phac-nml.

the class GzipFileProcessor method processSingleFile.

/**
 * Process a single {@link SequenceFile}
 *
 * @param sequenceFile
 *            file to process
 * @throws FileProcessorException
 *             if an error occurs while processing
 */
public void processSingleFile(SequenceFile sequenceFile) throws FileProcessorException {
    Path file = sequenceFile.getFile();
    String nameWithoutExtension = file.getFileName().toString();
    // strip the extension from the filename (if necessary)
    if (nameWithoutExtension.endsWith(GZIP_EXTENSION)) {
        nameWithoutExtension = nameWithoutExtension.substring(0, nameWithoutExtension.lastIndexOf(GZIP_EXTENSION));
    }
    try {
        logger.trace("About to try handling a gzip file.");
        if (isCompressed(file)) {
            file = addExtensionToFilename(file, GZIP_EXTENSION);
            try (GZIPInputStream zippedInputStream = new GZIPInputStream(Files.newInputStream(file))) {
                logger.trace("Handling gzip compressed file.");
                Path targetDirectory = Files.createTempDirectory(null);
                Path target = targetDirectory.resolve(nameWithoutExtension);
                logger.debug("Target directory is [" + targetDirectory + "]");
                logger.debug("Writing uncompressed file to [" + target + "]");
                Files.copy(zippedInputStream, target);
                sequenceFile.setFile(target);
                sequenceFile = sequenceFileRepository.save(sequenceFile);
                if (removeCompressedFile) {
                    logger.debug("Removing original compressed files [file.processing.decompress.remove.compressed.file=true]");
                    try {
                        Files.delete(file);
                    } catch (final Exception e) {
                        logger.error("Failed to remove the original compressed file.", e);
                        // outer try/catch block:
                        throw e;
                    }
                }
            }
        }
    } catch (Exception e) {
        logger.error("Failed to process the input file [" + sequenceFile + "]; stack trace follows.", e);
        throw new FileProcessorException("Failed to process input file [" + sequenceFile + "].");
    }
}

Example 7 with FileProcessorException

use of ca.corefacility.bioinformatics.irida.processing.FileProcessorException in project irida by phac-nml.

the class DefaultFileProcessingChainTest method testFailWithContinueChain.

@Test
public void testFailWithContinueChain() throws FileProcessorTimeoutException {
    FileProcessingChain fileProcessingChain = new DefaultFileProcessingChain(objectRepository, qcRepository, new FailingFileProcessor());
    when(objectRepository.exists(objectId)).thenReturn(true);
    List<Exception> exceptions = fileProcessingChain.launchChain(1L);
    // exceptions should be ignored in this test
    assertEquals("exactly one exception should have been ignored.", 1, exceptions.size());
    assertTrue("ignored exception should be of type FileProcessorException.", exceptions.iterator().next() instanceof FileProcessorException);
}

Example 8 with FileProcessorException

use of ca.corefacility.bioinformatics.irida.processing.FileProcessorException in project irida by phac-nml.

the class DefaultFileProcessingChainTest method testFailWriteQCEntry.

@Test
public void testFailWriteQCEntry() throws FileProcessorTimeoutException {
    FileProcessingChain fileProcessingChain = new DefaultFileProcessingChain(objectRepository, qcRepository, new FailingFileProcessorNoContinue());
    when(objectRepository.exists(objectId)).thenReturn(true);
    boolean exceptionCaught = false;
    try {
        fileProcessingChain.launchChain(1L);
    } catch (FileProcessorException e) {
        exceptionCaught = true;
    }
    assertTrue("File process should have thrown exception", exceptionCaught);
    ArgumentCaptor<QCEntry> captor = ArgumentCaptor.forClass(QCEntry.class);
    verify(qcRepository).save(captor.capture());
    QCEntry qcEntry = captor.getValue();
    assertEquals("should have saved qc entry for sample", seqObject, qcEntry.getSequencingObject());
}