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Example 26 with SequenceFile

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

the class ChecksumFileProcessorTest method constructSequenceFile.

private SequenceFile constructSequenceFile() throws IOException {
    SequenceFile sf = new SequenceFile();
    Path sequenceFile = Files.createTempFile(null, null);
    Files.write(sequenceFile, FILE_CONTENTS.getBytes());
    sf.setFile(sequenceFile);
    return sf;
}
Also used : Path(java.nio.file.Path) SequenceFile(ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile) SingleEndSequenceFile(ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile)

Example 27 with SequenceFile

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile 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);
}
Also used : 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)

Example 28 with SequenceFile

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile 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());
}
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 29 with SequenceFile

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile 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 30 with SequenceFile

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile 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)

Aggregations

SequenceFile (ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile)111 SingleEndSequenceFile (ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile)84 Test (org.junit.Test)61 Path (java.nio.file.Path)50 Sample (ca.corefacility.bioinformatics.irida.model.sample.Sample)39 SampleSequencingObjectJoin (ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin)31 SequencingObject (ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject)25 SequenceFilePair (ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair)20 Project (ca.corefacility.bioinformatics.irida.model.project.Project)15 AnalysisFastQC (ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisFastQC)15 WithMockUser (org.springframework.security.test.context.support.WithMockUser)13 IOException (java.io.IOException)11 SequencingRun (ca.corefacility.bioinformatics.irida.model.run.SequencingRun)9 ArrayList (java.util.ArrayList)9 ProjectSampleJoin (ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin)8 GZIPOutputStream (java.util.zip.GZIPOutputStream)8 Link (org.springframework.hateoas.Link)8 AnalysisSubmission (ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission)7 OutputStream (java.io.OutputStream)7 Before (org.junit.Before)7