Examples with Sample ca.corefacility.bioinformatics.irida.model.sample.Sample used on opensource projects

Example 41 with Sample

use of ca.corefacility.bioinformatics.irida.model.sample.Sample 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 42 with Sample

use of ca.corefacility.bioinformatics.irida.model.sample.Sample 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 43 with Sample

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

the class AssemblySampleUpdaterIT method testUpdateSuccess.

@Test
@WithMockUser(username = "fbristow", roles = "USER")
public void testUpdateSuccess() {
    AnalysisSubmission a = analysisSubmissionRepository.findOne(1L);
    Sample s = sampleRepository.findOne(2L);
    assertEquals("Should be no join between sample and assembly", 0, sampleGenomeAssemblyJoinRepository.count());
    assemblySampleUpdater.update(Sets.newHashSet(s), a);
    assertEquals("Should exist a join between sample and assembly", 1, sampleGenomeAssemblyJoinRepository.count());
    SampleGenomeAssemblyJoin j = sampleGenomeAssemblyJoinRepository.findAll().iterator().next();
    assertEquals("Should have joined sample 2L", (Long) 2L, j.getSubject().getId());
    assertNotNull("Should have joined an assembly", j.getObject().getId());
}

Example 44 with Sample

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

the class SISTRSampleUpdaterTest method testUpdaterPassed.

@SuppressWarnings("unchecked")
@Test
public void testUpdaterPassed() 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/sistr-predictions-pass.json");
    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);
    ImmutableMap<MetadataTemplateField, MetadataEntry> metadataMap = ImmutableMap.of(new MetadataTemplateField("SISTR Field", "text"), new MetadataEntry("Value1", "text"));
    when(metadataTemplateService.getMetadataMap(any(Map.class))).thenReturn(metadataMap);
    updater.update(Lists.newArrayList(sample), submission);
    ArgumentCaptor<Map> mapCaptor = ArgumentCaptor.forClass(Map.class);
    // this is the important bit.  Ensures the correct values got pulled from the file
    verify(metadataTemplateService).getMetadataMap(mapCaptor.capture());
    Map<String, MetadataEntry> metadata = mapCaptor.getValue();
    int found = 0;
    for (Map.Entry<String, MetadataEntry> e : metadata.entrySet()) {
        if (expectedResults.containsKey(e.getKey())) {
            String expected = expectedResults.get(e.getKey());
            MetadataEntry value = e.getValue();
            assertEquals("metadata values should match", expected, value.getValue());
            found++;
        }
    }
    assertEquals("should have found the same number of results", expectedResults.keySet().size(), found);
    // this bit just ensures the merged data got saved
    verify(sampleService).updateFields(eq(sample.getId()), mapCaptor.capture());
    Map<MetadataTemplateField, MetadataEntry> value = (Map<MetadataTemplateField, MetadataEntry>) mapCaptor.getValue().get("metadata");
    assertEquals(metadataMap.keySet().iterator().next(), value.keySet().iterator().next());
}

Example 45 with Sample

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

the class SISTRSampleUpdaterTest method testUpdaterBadFile.

@Test(expected = PostProcessingException.class)
public void testUpdaterBadFile() 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/snp_tree.tree");
    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);
}