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Example 16 with SingleEndSequenceFile

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

the class CoverageFileProcessorTest method testRemoveExistingEntry.

@Test
public void testRemoveExistingEntry() {
    Project p = new Project();
    p.setGenomeSize(100L);
    p.setMinimumCoverage(2);
    SequenceFile file = new SequenceFile();
    SequencingObject o = new SingleEndSequenceFile(file);
    AnalysisFastQC fqc = mock(AnalysisFastQC.class);
    Long baseCount = 300L;
    QCEntry existingQc = new CoverageQCEntry();
    o.setQcEntries(Sets.newHashSet(existingQc));
    when(analysisRepository.findFastqcAnalysisForSequenceFile(file)).thenReturn(fqc);
    when(fqc.getTotalBases()).thenReturn(baseCount);
    processor.process(o);
    ArgumentCaptor<CoverageQCEntry> qcCaptor = ArgumentCaptor.forClass(CoverageQCEntry.class);
    verify(qcEntryRepository).delete(existingQc);
    verify(qcEntryRepository).save(qcCaptor.capture());
    CoverageQCEntry qc = qcCaptor.getValue();
    qc.addProjectSettings(p);
    assertEquals("should show 3 times coverage", 3, qc.getCoverage());
    assertEquals("should be positive coverage", QCEntryStatus.POSITIVE, qc.getStatus());
}
Also used : Project(ca.corefacility.bioinformatics.irida.model.project.Project) SequencingObject(ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject) CoverageQCEntry(ca.corefacility.bioinformatics.irida.model.sample.CoverageQCEntry) SequenceFile(ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile) SingleEndSequenceFile(ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile) CoverageQCEntry(ca.corefacility.bioinformatics.irida.model.sample.CoverageQCEntry) QCEntry(ca.corefacility.bioinformatics.irida.model.sample.QCEntry) SingleEndSequenceFile(ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile) AnalysisFastQC(ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC) Test(org.junit.Test)

Example 17 with SingleEndSequenceFile

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

the class CoverageFileProcessorTest method testGoodCoverage.

@Test
public void testGoodCoverage() {
    Project p = new Project();
    p.setGenomeSize(100L);
    p.setMinimumCoverage(2);
    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 positive coverage", QCEntryStatus.POSITIVE, qc.getStatus());
}
Also used : Project(ca.corefacility.bioinformatics.irida.model.project.Project) SequencingObject(ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject) CoverageQCEntry(ca.corefacility.bioinformatics.irida.model.sample.CoverageQCEntry) SequenceFile(ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile) SingleEndSequenceFile(ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile) CoverageQCEntry(ca.corefacility.bioinformatics.irida.model.sample.CoverageQCEntry) QCEntry(ca.corefacility.bioinformatics.irida.model.sample.QCEntry) SingleEndSequenceFile(ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile) AnalysisFastQC(ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC) Test(org.junit.Test)

Example 18 with SingleEndSequenceFile

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

the class GzipFileProcessorTest method handleCompressedFileWithoutGzExtension.

@Test
public void handleCompressedFileWithoutGzExtension() throws IOException {
    // the file processor should decompress the file, then update the
    // sequence file in the database.
    SequenceFile sf = constructSequenceFile();
    SequenceFile sfUpdated = new SequenceFile();
    sfUpdated.setFile(sf.getFile());
    final Long id = 1L;
    sf.setId(id);
    // compress the file, update the sequence file reference
    Path uncompressed = sf.getFile();
    Path compressed = Files.createTempFile(null, null);
    GZIPOutputStream out = new GZIPOutputStream(Files.newOutputStream(compressed));
    Files.copy(uncompressed, out);
    out.close();
    sf.setFile(compressed);
    SingleEndSequenceFile so = new SingleEndSequenceFile(sf);
    fileProcessor.process(so);
    ArgumentCaptor<SequenceFile> argument = ArgumentCaptor.forClass(SequenceFile.class);
    verify(sequenceFileRepository).save(argument.capture());
    SequenceFile modified = argument.getValue();
    String uncompressedFileContents = new String(Files.readAllBytes(modified.getFile()));
    assertEquals("uncompressed file and file in database should be the same.", FILE_CONTENTS, uncompressedFileContents);
    Files.delete(uncompressed);
    if (Files.exists(compressed)) {
        Files.delete(compressed);
    }
}
Also used : Path(java.nio.file.Path) SequenceFile(ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile) SingleEndSequenceFile(ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile) GZIPOutputStream(java.util.zip.GZIPOutputStream) SingleEndSequenceFile(ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile) Test(org.junit.Test)

Example 19 with SingleEndSequenceFile

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

the class ProjectEventHandlerTest method testHandleSequenceFileAddedEventMultipleReturn.

@SuppressWarnings("unchecked")
@Test
public void testHandleSequenceFileAddedEventMultipleReturn() {
    Class<? extends ProjectEvent> clazz = DataAddedToSampleProjectEvent.class;
    Project project = new Project();
    Sample sample = new Sample();
    SequenceFile file = new SequenceFile();
    SingleEndSequenceFile seqObj1 = new SingleEndSequenceFile(file);
    SingleEndSequenceFile seqObj2 = new SingleEndSequenceFile(file);
    SampleSequencingObjectJoin join1 = new SampleSequencingObjectJoin(sample, seqObj1);
    SampleSequencingObjectJoin join2 = new SampleSequencingObjectJoin(sample, seqObj2);
    when(psjRepository.getProjectForSample(sample)).thenReturn(Lists.newArrayList(new ProjectSampleJoin(project, sample, true)));
    when(eventRepository.save(any(ProjectEvent.class))).thenReturn(new DataAddedToSampleProjectEvent(project, sample));
    Object[] args = {};
    MethodEvent methodEvent = new MethodEvent(clazz, Lists.newArrayList(join1, join2), args);
    handler.delegate(methodEvent);
    ArgumentCaptor<ProjectEvent> captor = ArgumentCaptor.forClass(ProjectEvent.class);
    verify(eventRepository).save(captor.capture());
    ProjectEvent event = captor.getValue();
    assertTrue(event instanceof DataAddedToSampleProjectEvent);
    verify(projectRepository).save(any(Project.class));
    verify(sampleRepository).save(any(Sample.class));
}
Also used : Sample(ca.corefacility.bioinformatics.irida.model.sample.Sample) SingleEndSequenceFile(ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile) ProjectSampleJoin(ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin) Project(ca.corefacility.bioinformatics.irida.model.project.Project) SequenceFile(ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile) SingleEndSequenceFile(ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile) DataAddedToSampleProjectEvent(ca.corefacility.bioinformatics.irida.model.event.DataAddedToSampleProjectEvent) SampleSequencingObjectJoin(ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin) UserRoleSetProjectEvent(ca.corefacility.bioinformatics.irida.model.event.UserRoleSetProjectEvent) UserRemovedProjectEvent(ca.corefacility.bioinformatics.irida.model.event.UserRemovedProjectEvent) DataAddedToSampleProjectEvent(ca.corefacility.bioinformatics.irida.model.event.DataAddedToSampleProjectEvent) ProjectEvent(ca.corefacility.bioinformatics.irida.model.event.ProjectEvent) SampleAddedProjectEvent(ca.corefacility.bioinformatics.irida.model.event.SampleAddedProjectEvent) Test(org.junit.Test)

Example 20 with SingleEndSequenceFile

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

the class GzipFileProcessorTest method handleUncompressedFile.

@Test
public void handleUncompressedFile() throws IOException {
    // the file processor just shouldn't do *anything*.
    SequenceFile sf = constructSequenceFile();
    Path original = sf.getFile();
    SingleEndSequenceFile so = new SingleEndSequenceFile(sf);
    fileProcessor.process(so);
    verify(sequenceFileRepository, times(0)).save(any(SequenceFile.class));
    Files.deleteIfExists(sf.getFile());
    Files.deleteIfExists(original);
}
Also used : Path(java.nio.file.Path) SequenceFile(ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile) SingleEndSequenceFile(ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile) SingleEndSequenceFile(ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile) Test(org.junit.Test)

Aggregations

SingleEndSequenceFile (ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile)99 Test (org.junit.Test)72 SequenceFile (ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile)61 Sample (ca.corefacility.bioinformatics.irida.model.sample.Sample)44 Path (java.nio.file.Path)33 SampleSequencingObjectJoin (ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin)24 SequencingObject (ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject)22 SequenceFilePair (ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair)20 WithMockUser (org.springframework.security.test.context.support.WithMockUser)18 Project (ca.corefacility.bioinformatics.irida.model.project.Project)17 AnalysisSubmission (ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission)17 AnalysisFastQC (ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC)12 Analysis (ca.corefacility.bioinformatics.irida.model.workflow.analysis.Analysis)11 IridaWorkflow (ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow)10 ArrayList (java.util.ArrayList)10 SequencingRun (ca.corefacility.bioinformatics.irida.model.run.SequencingRun)8 HistoriesClient (com.github.jmchilton.blend4j.galaxy.HistoriesClient)8 History (com.github.jmchilton.blend4j.galaxy.beans.History)8 GZIPOutputStream (java.util.zip.GZIPOutputStream)8 ModelMap (org.springframework.ui.ModelMap)8