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

Example 11 with SingleEndSequenceFile

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

the class SISTRSampleUpdaterTest method testUpdaterNoFile.

@Test(expected = PostProcessingException.class)
public void testUpdaterNoFile() throws PostProcessingException, AnalysisAlreadySetException {
    ImmutableMap<String, String> expectedResults = ImmutableMap.of("SISTR serovar", "Enteritidis", "SISTR cgMLST Subspecies", "enterica", "SISTR QC Status", "PASS");
    Path outputPath = Paths.get("src/test/resources/files/not_really_a_file.txt");
    AnalysisOutputFile outputFile = new AnalysisOutputFile(outputPath, null, null, null);
    Analysis analysis = new Analysis(null, ImmutableMap.of("sistr-predictions", outputFile), null, null);
    AnalysisSubmission submission = AnalysisSubmission.builder(UUID.randomUUID()).inputFiles(ImmutableSet.of(new SingleEndSequenceFile(null))).build();
    submission.setAnalysis(analysis);
    Sample sample = new Sample();
    sample.setId(1L);
    updater.update(Lists.newArrayList(sample), submission);
}

Example 12 with SingleEndSequenceFile

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

the class SingleEndSequenceFileConcatenatorTest method testConcatenateFiles.

@Test
public void testConcatenateFiles() throws IOException, ConcatenateException {
    String newFileName = "newFile";
    SequenceFile original1 = createSequenceFile("testFile");
    SequenceFile original2 = createSequenceFile("testFile2");
    long originalLength = original1.getFile().toFile().length();
    SingleEndSequenceFile f1 = new SingleEndSequenceFile(original1);
    SingleEndSequenceFile f2 = new SingleEndSequenceFile(original2);
    SingleEndSequenceFile concatenateFiles = concat.concatenateFiles(Lists.newArrayList(f1, f2), newFileName);
    SequenceFile newSeqFile = concatenateFiles.getSequenceFile();
    assertTrue("file exists", Files.exists(newSeqFile.getFile()));
    long newFileSize = newSeqFile.getFile().toFile().length();
    assertEquals("new file should be 2x size of originals", originalLength * 2, newFileSize);
}

Example 13 with SingleEndSequenceFile

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

the class ChecksumFileProcessorTest method testChecksumCreated.

@Test
public void testChecksumCreated() throws IOException {
    final SequenceFile sf = constructSequenceFile();
    SingleEndSequenceFile so = new SingleEndSequenceFile(sf);
    fileProcessor.process(so);
    ArgumentCaptor<SequenceFile> fileCaptor = ArgumentCaptor.forClass(SequenceFile.class);
    verify(sequenceFileRepository).saveMetadata(fileCaptor.capture());
    SequenceFile file = fileCaptor.getValue();
    assertEquals("checksums should be equal", CHECKSUM, file.getUploadSha256());
}

Example 14 with SingleEndSequenceFile

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

the class ChecksumFileProcessorTest method testFileNotExists.

@Test(expected = FileProcessorException.class)
public void testFileNotExists() throws IOException {
    final SequenceFile sf = new SequenceFile(Paths.get("/reallyfakefile"));
    SingleEndSequenceFile so = new SingleEndSequenceFile(sf);
    fileProcessor.process(so);
}

Example 15 with SingleEndSequenceFile

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

the class CoverageFileProcessorTest method testBadCoverage.

@Test
public void testBadCoverage() {
    Project p = new Project();
    p.setGenomeSize(100L);
    p.setMinimumCoverage(5);
    SequenceFile file = new SequenceFile();
    SequencingObject o = new SingleEndSequenceFile(file);
    AnalysisFastQC fqc = mock(AnalysisFastQC.class);
    Long baseCount = 300L;
    when(analysisRepository.findFastqcAnalysisForSequenceFile(file)).thenReturn(fqc);
    when(fqc.getTotalBases()).thenReturn(baseCount);
    processor.process(o);
    ArgumentCaptor<CoverageQCEntry> qcCaptor = ArgumentCaptor.forClass(CoverageQCEntry.class);
    verify(qcEntryRepository, times(0)).delete(any(QCEntry.class));
    verify(qcEntryRepository).save(qcCaptor.capture());
    CoverageQCEntry qc = qcCaptor.getValue();
    qc.addProjectSettings(p);
    assertEquals("should show 3 times coverage", 3, qc.getCoverage());
    assertEquals("should be bad coverage", QCEntryStatus.NEGATIVE, qc.getStatus());
}