@Before
public void setUp() throws DaoException {
DaoCancerStudy.reCacheAll();
DaoGeneOptimized.getInstance().reCache();
ProgressMonitor.resetWarnings();
studyId = DaoCancerStudy.getCancerStudyByStableId("study_tcga_pub").getInternalId();
GeneticProfile newGeneticProfile = new GeneticProfile();
newGeneticProfile.setCancerStudyId(studyId);
newGeneticProfile.setGeneticAlterationType(GeneticAlterationType.COPY_NUMBER_ALTERATION);
newGeneticProfile.setStableId("study_tcga_pub_test");
newGeneticProfile.setProfileName("Barry CNA Results");
newGeneticProfile.setDatatype("test");
DaoGeneticProfile.addGeneticProfile(newGeneticProfile);
geneticProfileId =
DaoGeneticProfile.getGeneticProfileByStableId("study_tcga_pub_test").getGeneticProfileId();
sample1 =
DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-A1-A0SB-01").getInternalId();
sample2 =
DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-A1-A0SD-01").getInternalId();
sample3 =
DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-A1-A0SE-01").getInternalId();
sample4 =
DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-A1-A0SF-01").getInternalId();
sample5 =
DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-A1-A0SG-01").getInternalId();
}
