@Test(expected = InvalidReferenceException.class)
public void testExportMageTab_badRef() throws Exception {
logForSilverCompatibility(TEST_NAME, "testExportMageTab_badRef");
String qtid = "URN:LSID:gov.nih.nci.caarray.external.v1_0.data.QuantitationType:1";
CaArrayEntityReference badRef = new CaArrayEntityReference(qtid);
service.exportMageTab(badRef);
}
@Test(expected = InvalidReferenceException.class)
public void testStreamFileContents_BadRef() throws Exception {
logForSilverCompatibility(TEST_NAME, "testStreamFileContents_BadRef");
String dfid = "URN:LSID:caarray.nci.nih.gov:gov.nih.nci.caarray.external.v1_0.data.File:0";
CaArrayEntityReference fileRef = new CaArrayEntityReference(dfid);
service.streamFileContents(fileRef, true);
}
@Test
public void testExportMageTab_1Ex() throws Exception {
logForSilverCompatibility(TEST_NAME, "testExportMageTab_1Ex");
String type = gov.nih.nci.caarray.external.v1_0.experiment.Experiment.class.getName();
String eid = "URN:LSID:" + type + ":1";
CaArrayEntityReference ref = new CaArrayEntityReference(eid);
MageTabFileSet df = service.exportMageTab(ref);
logForSilverCompatibility(
TEST_OUTPUT, "exteriment has " + df.getDataFiles().size() + " data files");
assertEquals(19, df.getDataFiles().size());
assertEquals("admin-00001.idf", df.getIdf().getMetadata().getName());
assertEquals("admin-00001.sdrf", df.getSdrf().getMetadata().getName());
Map<String, String> expected = new HashMap<String, String>();
expected.put("8kNew111_14v1p4m12.gpr", "84823097c0db8d62028cfaa896a14ff9");
expected.put("8kNew111_14_4601_m84.gpr", "a563783e47fe4ef352f82ac1731f848b");
expected.put("8kNew111_17m12701m36.gpr", "3aaeb9ef790bf2867750913070008f7a");
expected.put("8kNew111_17_4601_m82.gpr", "9879a28ea8d11698d7c7ed27b9ef7f73");
expected.put("8kNewPr111_14v1p4m11.gpr", "97df92ef864ff3edb04fffb418ea842b");
expected.put("8kNewPr111_14v1p4m13.gpr", "2b2bb27b31c19d7a60c809148f807bb5");
expected.put("8kNewPr111_14v1p4m14.gpr", "15b6a2d3dbb0bb01e3d3c7fc50a7e331");
expected.put("8kNewPr111_1712701m37.gpr", "b081876b46410e6bdd9749fa9bd82bbe");
expected.put("8kPr111_17M62103100p1090600.gpr", "cb481dadbcf00e73ab6ed9566e8a95fb");
expected.put("8KReverNewC2_111_4601_m86.gpr", "5a38e79b403e3d0dad8053e9eda7c19c");
expected.put("8kReversNew17_111_4601_m83.gpr", "111722aa71d45af97810f82b5715c745");
expected.put("G_New8k111C131501m73.gpr", "eedecb1b0ea2cdfe7e6fa9a3dcf335d1");
expected.put("New8kPr111_C221601m29.gpr", "738385806286014ae5081eb0267b70fd");
expected.put("New8kPr111_C221601m30.gpr", "85176edd715c326005c0a2721261550c");
expected.put("New8kPr111_C221601m31.gpr", "8954bf4a8b6dee62eab34b6eb5262ebf");
expected.put("VG_1New8k111_C14401m78.gpr", "a2532abf56b767231492224c1ff0616f");
expected.put("VG_8k1New111_C14401m79.gpr", "56c72116692e5888f3737991b5b41bef");
expected.put("VG_8k3New111_C14401m80.gpr", "cedff2aa6707bc8518578d0b177cd0a5");
expected.put("VG_8k4New111_C14401m81.gpr", "f528f00fc219062a641cff653d08456");
for (File f : df.getDataFiles()) {
String exHash = expected.get(f.getMetadata().getName());
assertNotNull(exHash);
FileStreamableContents fsContents = service.streamFileContents(f.getReference(), true);
InputStream is = RemoteInputStreamClient.wrap(fsContents.getContentStream());
GZIPInputStream zin = new GZIPInputStream(is);
byte[] b = md5(zin);
String hash = toHex(b);
assertEquals(exHash, hash);
}
}
@Test
public void testExportMageTab_2Ex() throws Exception {
logForSilverCompatibility(TEST_NAME, "testStreamMageTab_2Ex");
String type = gov.nih.nci.caarray.external.v1_0.experiment.Experiment.class.getName();
String eid = "URN:LSID:" + type + ":2";
CaArrayEntityReference ref = new CaArrayEntityReference(eid);
MageTabFileSet df = service.exportMageTab(ref);
assertEquals(0, df.getDataFiles().size());
assertEquals("admin-00002.idf", df.getIdf().getMetadata().getName());
assertEquals("admin-00002.sdrf", df.getSdrf().getMetadata().getName());
}
@Test(expected = java.io.IOException.class)
public void testStreamFileContents_UnCompressed() throws Exception {
logForSilverCompatibility(TEST_NAME, "testStreamFileContents_UnCompressed");
String dfid = "URN:LSID:caarray.nci.nih.gov:gov.nih.nci.caarray.external.v1_0.data.File:1";
CaArrayEntityReference fileRef = new CaArrayEntityReference(dfid);
FileStreamableContents fsContents = service.streamFileContents(fileRef, false);
InputStream is = RemoteInputStreamClient.wrap(fsContents.getContentStream());
GZIPInputStream zin = new GZIPInputStream(is);
zin.read();
logForSilverCompatibility(TEST_OUTPUT, "data was gziped");
fail("zipped");
}
@Test
public void testStreamFileContents_Compressed() throws Exception {
logForSilverCompatibility(TEST_NAME, "testStreamFileContents_Compressed");
String dfid = "URN:LSID:caarray.nci.nih.gov:gov.nih.nci.caarray.external.v1_0.data.File:1";
CaArrayEntityReference fileRef = new CaArrayEntityReference(dfid);
FileStreamableContents fsContents = service.streamFileContents(fileRef, true);
InputStream is = RemoteInputStreamClient.wrap(fsContents.getContentStream());
GZIPInputStream zin = new GZIPInputStream(is);
byte[] b = md5(zin);
String hash = toHex(b);
logForSilverCompatibility(TEST_OUTPUT, dfid + "MD5 hash :" + hash);
assertEquals("7d875adfcee0e18b0cc28b1311db40ae", hash);
}
@Test(expected = gov.nih.nci.caarray.services.external.v1_0.IncorrectEntityTypeException.class)
public void testGetDataSet_NonDataFile() throws Exception {
logForSilverCompatibility(TEST_NAME, "testGetDataSet_NonDataFile");
Class<?> c = gov.nih.nci.caarray.external.v1_0.vocabulary.Term.class;
assertFalse(c.isAssignableFrom(CaArrayFile.class));
DataSetRequest dataRequest = new DataSetRequest();
String dfid = "URN:LSID:" + c.getName() + ":1";
dataRequest.setDataFiles(Collections.singleton(new CaArrayEntityReference(dfid)));
String qtid = "URN:LSID:gov.nih.nci.caarray.external.v1_0.data.QuantitationType:1";
dataRequest.setQuantitationTypes(Collections.singleton(new CaArrayEntityReference(qtid)));
service.getDataSet(dataRequest);
fail("expected an IncorrectEntityTypeException");
}
@Test
public void testGetDataSet_Hybridizations1() throws Exception {
logForSilverCompatibility(TEST_NAME, "testGetDataSet_Hybridizations1");
DataSetRequest dataRequest = new DataSetRequest();
String hid =
"URN:LSID:caarray.nci.nih.gov:gov.nih.nci.caarray.external.v1_0.sample.Hybridization:1";
dataRequest.setHybridizations(Collections.singleton(new CaArrayEntityReference(hid)));
String qtid =
"URN:LSID:caarray.nci.nih.gov:gov.nih.nci.caarray.external.v1_0.data.QuantitationType:24";
dataRequest.setQuantitationTypes(Collections.singleton(new CaArrayEntityReference(qtid)));
DataSet ds = service.getDataSet(dataRequest);
List<HybridizationData> l = ds.getDatas();
assertEquals(1, l.size());
HybridizationData hd = l.get(0);
assertEquals(1, hd.getDataColumns().size());
assertEquals(qtid, hd.getDataColumns().get(0).getQuantitationType().getId());
String resultId = hd.getHybridization().getId();
assertEquals(hid, resultId);
}
@Test
public void testGetDataSet_checkRequest() throws Exception {
logForSilverCompatibility(TEST_NAME, "testGetDataSet_checkRequest");
logForSilverCompatibility(TEST_OUTPUT, "Null");
DataSetRequest dataRequest = null;
try {
service.getDataSet(dataRequest);
logForSilverCompatibility(TEST_OUTPUT, "unexpected validation outcome");
fail("Expected an InvalidInputException");
} catch (InvalidInputException e) {
logForSilverCompatibility(TEST_OUTPUT, "null validation :" + e);
}
logForSilverCompatibility(TEST_OUTPUT, "Empty");
dataRequest = new DataSetRequest();
try {
service.getDataSet(dataRequest);
logForSilverCompatibility(TEST_OUTPUT, "unexpected validation outcome");
fail("Expected an InvalidInputException");
} catch (InvalidInputException e) {
logForSilverCompatibility(TEST_OUTPUT, "validation :" + e);
}
logForSilverCompatibility(TEST_OUTPUT, "BadHib");
dataRequest = new DataSetRequest();
String qtid =
"URN:LSID:caarray.nci.nih.gov:gov.nih.nci.caarray.external.v1_0.data.QuantitationType:24";
dataRequest.setQuantitationTypes(Collections.singleton(new CaArrayEntityReference(qtid)));
try {
dataRequest.setHybridizations(Collections.singleton(new CaArrayEntityReference("foo hib")));
service.getDataSet(dataRequest);
logForSilverCompatibility(TEST_OUTPUT, "unexpected validation outcome");
fail("Expected an InvalidReferenceException");
} catch (InvalidReferenceException e) {
logForSilverCompatibility(TEST_OUTPUT, "validation :" + e);
}
logForSilverCompatibility(TEST_OUTPUT, "BadDataFiles");
dataRequest = new DataSetRequest();
dataRequest.setQuantitationTypes(Collections.singleton(new CaArrayEntityReference(qtid)));
try {
dataRequest.setDataFiles(Collections.singleton(new CaArrayEntityReference("foo df")));
service.getDataSet(dataRequest);
logForSilverCompatibility(TEST_OUTPUT, "unexpected validation outcome");
fail("Expected an InvalidReferenceException");
} catch (InvalidReferenceException e) {
logForSilverCompatibility(TEST_OUTPUT, "validation :" + e);
}
logForSilverCompatibility(TEST_OUTPUT, "BadQuantitationTypes");
dataRequest = new DataSetRequest();
String hid =
"URN:LSID:caarray.nci.nih.gov:gov.nih.nci.caarray.external.v1_0.sample.Hybridization:1";
dataRequest.setHybridizations(Collections.singleton(new CaArrayEntityReference(hid)));
try {
dataRequest.setQuantitationTypes(Collections.singleton(new CaArrayEntityReference("foo qt")));
service.getDataSet(dataRequest);
logForSilverCompatibility(TEST_OUTPUT, "unexpected validation outcome");
fail("Expected an InvalidReferenceException");
} catch (InvalidReferenceException e) {
logForSilverCompatibility(TEST_OUTPUT, "validation :" + e);
}
}