Examples with Project ca.corefacility.bioinformatics.irida.model.project.Project used on opensource projects

Example 71 with Project

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

the class ProjectEventHandler method handleSampleRemovedEvent.

/**
 * Create {@link SampleRemovedProjectEvent}s for any {@link Sample}s removed
 * from a {@link Project}
 *
 * @param event
 *            the {@link MethodEvent} containing params from the method call
 * @return a collectino of {@link SampleRemovedProjectEvent}s
 */
private Collection<SampleRemovedProjectEvent> handleSampleRemovedEvent(MethodEvent event) {
    Collection<SampleRemovedProjectEvent> events = new ArrayList<>();
    Optional<Object> projectOpt = Arrays.stream(event.getArgs()).filter(e -> e instanceof Project).findAny();
    Optional<Object> sampleOpt = Arrays.stream(event.getArgs()).filter(e -> e instanceof Sample).findAny();
    Optional<Object> sampleListOpt = Arrays.stream(event.getArgs()).filter(e -> e instanceof Iterable).findAny();
    if (projectOpt.isPresent()) {
        Project project = (Project) projectOpt.get();
        if (sampleOpt.isPresent()) {
            Sample sample = (Sample) sampleOpt.get();
            events.add(eventRepository.save(new SampleRemovedProjectEvent(project, sample.getSampleName())));
        } else if (sampleListOpt.isPresent()) {
            @SuppressWarnings("unchecked") Iterable<Sample> samples = (Iterable<Sample>) sampleListOpt.get();
            for (Sample sample : samples) {
                events.add(eventRepository.save(new SampleRemovedProjectEvent(project, sample.getSampleName())));
            }
        }
    }
    return events;
}

Example 72 with Project

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

the class ProjectEventHandler method handleIndividualSequenceFileAddedEvent.

/**
 * Create {@link DataAddedToSampleProjectEvent} for all {@link Project}s a
 * {@link Sample} belongs to
 *
 * @param join
 *            a {@link SampleSequencingObjectJoin} to turn into a
 *            {@link DataAddedToSampleProjectEvent}
 */
private Collection<DataAddedToSampleProjectEvent> handleIndividualSequenceFileAddedEvent(SampleSequencingObjectJoin join) {
    Sample subject = join.getSubject();
    Collection<DataAddedToSampleProjectEvent> events = new ArrayList<>();
    List<Join<Project, Sample>> projectForSample = psjRepository.getProjectForSample(subject);
    for (Join<Project, Sample> psj : projectForSample) {
        events.add(eventRepository.save(new DataAddedToSampleProjectEvent(psj.getSubject(), subject)));
    }
    return events;
}

Example 73 with Project

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

the class AssemblyFileProcessorTest method testAssembleFile.

@Test
public void testAssembleFile() {
    Long sequenceFileId = 1L;
    SequenceFilePair pair = new SequenceFilePair(new SequenceFile(Paths.get("file_R1_1.fastq.gz")), new SequenceFile(Paths.get("file_R2_1.fastq.gz")));
    Sample sample = new Sample();
    Project project = new Project();
    project.setAssembleUploads(true);
    when(objectRepository.findOne(sequenceFileId)).thenReturn(pair);
    when(ssoRepository.getSampleForSequencingObject(pair)).thenReturn(new SampleSequencingObjectJoin(sample, pair));
    when(psjRepository.getProjectForSample(sample)).thenReturn(ImmutableList.of(new ProjectSampleJoin(project, sample, true)));
    assertTrue("should want to assemble file", processor.shouldProcessFile(sequenceFileId));
    processor.process(pair);
    verify(submissionRepository).save(any(AnalysisSubmission.class));
}

Example 74 with Project

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

the class AssemblyFileProcessorTest method testOneProjectEnabled.

@Test
public void testOneProjectEnabled() {
    SequenceFilePair pair = new SequenceFilePair(new SequenceFile(Paths.get("file_R1_1.fastq.gz")), new SequenceFile(Paths.get("file_R2_1.fastq.gz")));
    Sample sample = new Sample();
    Project project = new Project();
    project.setAssembleUploads(true);
    Project disabledProject = new Project();
    disabledProject.setAssembleUploads(false);
    when(ssoRepository.getSampleForSequencingObject(pair)).thenReturn(new SampleSequencingObjectJoin(sample, pair));
    when(psjRepository.getProjectForSample(sample)).thenReturn(ImmutableList.of(new ProjectSampleJoin(disabledProject, sample, true), new ProjectSampleJoin(project, sample, true)));
    processor.process(pair);
    verify(submissionRepository).save(any(AnalysisSubmission.class));
}

Example 75 with Project

use of ca.corefacility.bioinformatics.irida.model.project.Project 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());
}