private GeneLocationConfiguration createGeneLocationConfiguration(
List<SegmentData> segmentDatas) {
GeneLocationConfiguration configuration = new GeneLocationConfiguration();
for (SegmentData segmentData : segmentDatas) {
ChromosomalLocation location = segmentData.getLocation();
GeneChromosomalLocation geneLocation = new GeneChromosomalLocation();
geneLocation.setLocation(location);
configuration.getGeneLocations().add(geneLocation);
}
return configuration;
}
/**
* Unit test setup.
*
* @throws Exception on error
*/
@Before
public void setUp() throws Exception {
Platform platform = dao.getPlatform("platformName");
ReporterList reporterList =
platform.addReporterList("reporterList", ReporterTypeEnum.DNA_ANALYSIS_REPORTER);
study = new Study();
query = new Query();
query.setCopyNumberPlatform(platform);
StudySubscription subscription = new StudySubscription();
subscription.setStudy(study);
query.setSubscription(subscription);
StudySubjectAssignment assignment = new StudySubjectAssignment();
study.getAssignmentCollection().add(assignment);
SampleAcquisition acquisition = new SampleAcquisition();
Sample sample = new Sample();
Array array = new Array();
array.setPlatform(platform);
ArrayData arrayData = new ArrayData();
arrayData.setStudy(study);
arrayData.setArray(array);
arrayData.getReporterLists().add(reporterList);
reporterList.getArrayDatas().add(arrayData);
arrayData.setSample(sample);
sample.getSampleAcquisitions().add(acquisition);
sample.getArrayDataCollection().add(arrayData);
segmentData = new SegmentData();
arrayData.getSegmentDatas().add(segmentData);
segmentData.setArrayData(arrayData);
acquisition.setSample(sample);
assignment.getSampleAcquisitionCollection().add(acquisition);
StudyConfiguration studyConfiguration = new StudyConfiguration();
studyConfiguration.getGenomicDataSources().add(new GenomicDataSourceConfiguration());
study.setStudyConfiguration(studyConfiguration);
when(dao.findMatchingSegmentDatas(
any(CopyNumberAlterationCriterion.class), any(Study.class), any(Platform.class)))
.thenReturn(Arrays.asList(segmentData));
when(dao.findMatchingSegmentDatasByLocation(
anyListOf(SegmentData.class), any(Study.class), any(Platform.class)))
.thenReturn(Arrays.asList(segmentData));
}
private List<SegmentData> createSegmentDatas() {
List<SegmentData> dataSet = new ArrayList<SegmentData>();
SegmentData result = new SegmentData();
result.setArrayData(new ArrayData());
result.getArrayData().setSample(new Sample());
result.getArrayData().getSample().setName("Sample 1");
result.setLocation(new ChromosomalLocation());
result.getLocation().setChromosome("1");
result.getLocation().setStartPosition(Integer.valueOf(1));
result.getLocation().setEndPosition(Integer.valueOf(5));
result.setSegmentValue(Float.valueOf("0.1"));
dataSet.add(result);
result = new SegmentData();
result.setArrayData(new ArrayData());
result.getArrayData().setSample(new Sample());
result.getArrayData().getSample().setName("Sample 2");
result.setLocation(new ChromosomalLocation());
result.getLocation().setChromosome("2");
result.getLocation().setStartPosition(Integer.valueOf(6));
result.getLocation().setEndPosition(Integer.valueOf(9));
result.setSegmentValue(Float.valueOf("0.2"));
dataSet.add(result);
return dataSet;
}