/**
* Grabs the appropriate stuff from a request and returns a list of case_ids
*
* @param request
* @return
* @throws ProtocolException
* @throws DaoException
*/
public static ArrayList<String> getSampleIds(HttpServletRequest request)
throws ProtocolException, DaoException {
String samples = request.getParameter(WebService.CASE_LIST);
String sampleSetId = request.getParameter(WebService.CASE_SET_ID);
String sampleIdsKey = request.getParameter(WebService.CASE_IDS_KEY);
if (sampleIdsKey != null) {
samples = SampleSetUtil.getSampleIds(sampleIdsKey);
}
ArrayList<String> sampleList = new ArrayList<String>();
if (sampleSetId != null && !(sampleSetId.equals("-1"))) {
DaoSampleList dao = new DaoSampleList();
SampleList selectedSampleList = dao.getSampleListByStableId(sampleSetId);
if (selectedSampleList == null) {
throw new ProtocolException(
"Invalid " + WebService.CASE_SET_ID + ": " + sampleSetId + ".");
}
sampleList = selectedSampleList.getSampleList();
} else if (samples != null) {
for (String _sample : samples.split("[\\s,]+")) {
_sample = _sample.trim();
if (_sample.length() == 0) continue;
sampleList.add(_sample);
}
} else if (samples != null) { // todo: this is a hack, samples is just another word for patients
return new ArrayList(Arrays.asList(samples.split(" ")));
} else {
throw new ProtocolException(
WebService.CASE_SET_ID + " or " + WebService.CASE_LIST + " must be specified.");
}
return sampleList;
}
/**
* 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());
}