/**
* Test importing of Clinical Data File.
*
* @throws DaoException Database Access Error.
* @throws IOException IO Error.
*/
@Test
@Ignore("To be fixed")
public void testImportClinicalDataSlice() throws Exception {
// TBD: change this to use getResourceAsStream()
File clinicalFile = new File("target/test-classes/clinical_data.txt");
ImportClinicalData importClinicalData = new ImportClinicalData(study, clinicalFile);
importClinicalData.importData();
List<ClinicalParameterMap> slice =
DaoClinicalData.getDataSlice(study.getInternalId(), Arrays.asList("PLATINUMSTATUS"));
assertTrue(slice.size() >= 1);
ClinicalParameterMap paramMap = slice.get(0);
assertEquals("PLATINUMSTATUS", paramMap.getName());
assertEquals("Sensitive", paramMap.getValue("TCGA-A1-A0SD"));
assertEquals("NA", paramMap.getValue("TCGA-A1-A0SE"));
assertEquals(2, paramMap.getDistinctCategories().size());
}
