Examples with SequenceFileRepository ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequenceFileRepository used on opensource projects

Example 1 with SequenceFileRepository

use of ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequenceFileRepository in project irida by phac-nml.

the class GzipFileProcessorTest method setUp.

@Before
public void setUp() {
    sequenceFileRepository = mock(SequenceFileRepository.class);
    fileProcessor = new GzipFileProcessor(sequenceFileRepository, Boolean.FALSE);
}

Example 2 with SequenceFileRepository

use of ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequenceFileRepository in project irida by phac-nml.

the class SequencingObjectServiceTest method setUp.

@Before
public void setUp() {
    repository = mock(SequencingObjectRepository.class);
    sequenceFileRepository = mock(SequenceFileRepository.class);
    ssoRepository = mock(SampleSequencingObjectJoinRepository.class);
    executor = mock(TaskExecutor.class);
    fileProcessingChain = mock(FileProcessingChain.class);
    concatenationRepository = mock(SequenceConcatenationRepository.class);
    service = new SequencingObjectServiceImpl(repository, sequenceFileRepository, ssoRepository, concatenationRepository, executor, fileProcessingChain, validator);
}

Example 3 with SequenceFileRepository

use of ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequenceFileRepository in project irida by phac-nml.

the class ChecksumFileProcessorTest method setUp.

@Before
public void setUp() {
    sequenceFileRepository = mock(SequenceFileRepository.class);
    fileProcessor = new ChecksumFileProcessor(sequenceFileRepository);
}

Example 4 with SequenceFileRepository

use of ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequenceFileRepository in project irida by phac-nml.

the class FastqcFileProcessorTest method setUp.

@Before
public void setUp() {
    messageSource = mock(MessageSource.class);
    sequenceFileRepository = mock(SequenceFileRepository.class);
    fileProcessor = new FastqcFileProcessor(messageSource, sequenceFileRepository);
}