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

Example 6 with FileProcessingChain

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

the class DefaultFileProcessingChainTest method testProcessEmptyChain.

@Test
public void testProcessEmptyChain() throws FileProcessorTimeoutException {
    FileProcessingChain fileProcessingChain = new DefaultFileProcessingChain(objectRepository, qcRepository);
    when(objectRepository.exists(objectId)).thenReturn(true);
    fileProcessingChain.launchChain(objectId);
}

Example 7 with FileProcessingChain

use of ca.corefacility.bioinformatics.irida.processing.FileProcessingChain 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());
}

Example 8 with FileProcessingChain

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

the class DefaultFileProcessingChainTest method testFailOnProcessorChain.

@Test(expected = FileProcessorException.class)
public void testFailOnProcessorChain() throws FileProcessorTimeoutException {
    FileProcessingChain fileProcessingChain = new DefaultFileProcessingChain(objectRepository, qcRepository, new FailingFileProcessorNoContinue());
    when(objectRepository.exists(objectId)).thenReturn(true);
    fileProcessingChain.launchChain(1L);
}