void CDFFileReaderTest::BadFilenameTest()
{
CDFData data;
CDFFileReader reader;
data.SetFilename("CDFMetaDataBad");
CPPUNIT_ASSERT_THROW(reader.Read(data, CDFFileReader::ReadSequential), affymetrix_calvin_exceptions::FileNotFoundException);
}
void CDFFileReaderTest::UnknownQCProbeSetNameTest()
{
CDFData data;
CDFFileReader reader;
reader.SetFilename(SMALL_QCCDF_FILE);
reader.Read(data, CDFFileReader::ReadByProbeSetName);
CDFQCProbeSetInformation info;
CPPUNIT_ASSERT_THROW(data.GetQCProbeSetInformation(L"hello", info), ProbeSetNotFoundException);
}
void CDFFileReaderTest::GetQCProbeSetInformationWithProbeSetNumberOutOfBoundsTest()
{
CDFData data;
CDFFileReader reader;
reader.SetFilename(SMALL_QCCDF_FILE);
reader.Read(data, CDFFileReader::ReadByProbeSetNumber);
CDFQCProbeSetInformation info;
CPPUNIT_ASSERT_THROW(data.GetQCProbeSetInformation(11, info), ProbeSetNotFoundException);
}
void CDFFileReaderTest::ReadQCCDFProbeSetInformationOpenProbeNameModeInWrongMode()
{
CDFData data;
CDFFileReader reader;
reader.SetFilename(SMALL_QCCDF_FILE);
reader.Read(data, CDFFileReader::ReadByProbeSetName);
CDFQCProbeSetInformation info;
CPPUNIT_ASSERT_THROW(data.GetQCProbeSetInformation(3, info), CDFAccessNotSupportedByModeException);
}
void CDFFileReaderTest::ReadCDFProbeSetInformationOpenProbeIndexModeInWrongMode()
{
CDFData data;
CDFFileReader reader;
reader.SetFilename(SMALL_CDF_FILE);
reader.Read(data, CDFFileReader::ReadByProbeSetNumber);
CDFProbeSetInformation info;
CPPUNIT_ASSERT_THROW(data.GetProbeSetInformation(L"hello", info), CDFAccessNotSupportedByModeException);
}
void CDFFileReaderTest::UseGetProbeSEtInformationTOReadQCCDFFileTest()
{
CDFData data;
CDFFileReader reader;
reader.SetFilename(SMALL_QCCDF_FILE);
reader.Read(data, CDFFileReader::ReadByProbeSetNumber);
CDFProbeSetInformation info;
CPPUNIT_ASSERT_THROW(data.GetProbeSetInformation(0, info), ProbeSetNotFoundException);
CPPUNIT_ASSERT_THROW(data.GetProbeSetInformation(L"hello", info), ProbeSetNotFoundException);
}
void CDFFileReaderTest::ReadSmallCDFFileBasicTest()
{
CDFData data;
CDFFileReader reader;
CPPUNIT_ASSERT_NO_THROW(reader.SetFilename(SMALL_CDF_FILE));
CPPUNIT_ASSERT_NO_THROW(reader.Read(data));
CPPUNIT_ASSERT(data.GetFilename() == SMALL_CDF_FILE);
FileHeader* fh = data.GetFileHeader();
u_int32_t pos = fh->GetFirstDataGroupFilePos();
CPPUNIT_ASSERT(pos == 0x1BD);
CPPUNIT_ASSERT(data.GetProbeSetCnt() == 10);
CPPUNIT_ASSERT(data.GetArrayRows() == 10*2);
CPPUNIT_ASSERT(data.GetArrayCols() == 11);
}
void CDFFileReaderTest::ReadSmallCDFFileSeqModeTest()
{
CDFData data;
CDFFileReader reader;
CPPUNIT_ASSERT_NO_THROW(reader.SetFilename(SMALL_CDF_FILE));
CPPUNIT_ASSERT_NO_THROW(reader.Read(data, CDFFileReader::ReadSequential));
int32_t probeSetCnt = data.GetProbeSetCnt();
for (int32_t i = 0; i < probeSetCnt; ++i)
{
CDFProbeSetInformation info;
data.GetProbeSetInformation(i, info);
CheckSmallCDFProbeSetInformation(i, info);
}
CheckGetProbeSetName(data);
}
void CDFFileReaderTest::ReadSmallCDFFileProbeSetNumberModeTest()
{
CDFData data;
CDFFileReader reader;
CPPUNIT_ASSERT_NO_THROW(reader.SetFilename(SMALL_CDF_FILE));
CPPUNIT_ASSERT_NO_THROW(reader.Read(data, CDFFileReader::ReadByProbeSetNumber));
int32_t probeSetCnt = data.GetProbeSetCnt();
// go backwards
for (int32_t i = probeSetCnt-1; i >= 0; --i)
{
CDFProbeSetInformation info;
data.GetProbeSetInformation(i, info);
CheckSmallCDFProbeSetInformation(i, info);
}
CheckGetProbeSetName(data);
}
/*
* Read the header of the file only. Read a calvin file in its entirety - this really
* reads the header until the data groups are opened.
*/
bool FusionCDFData::ReadHeader()
{
CreateObject();
if (gcosData)
{
gcosData->SetFileName(fileName.c_str());
return gcosData->ReadHeader();
}
else
{
CDFFileReader reader;
reader.SetFilename(fileName);
try
{
reader.Read(*calvinData);
}
catch(...)
{
return false;
}
return true;
}
}
void CDFFileReaderTest::ReadSmallQCCDFFileProbeSetNameModeTest()
{
CDFData data;
CDFFileReader reader;
CPPUNIT_ASSERT_NO_THROW(reader.SetFilename(SMALL_QCCDF_FILE));
CPPUNIT_ASSERT_NO_THROW(reader.Read(data, CDFFileReader::ReadByProbeSetName));
int32_t probeSetCnt = data.GetProbeSetCnt();
// go backwards
for (int32_t i = probeSetCnt-1; i >= 0; --i)
{
wchar_t name[100];
FormatString1(name, 100, L"control_%d", i);
CDFQCProbeSetInformation info;
data.GetQCProbeSetInformation(name, info);
CheckSmallQCCDFProbeSetInformation(i, info);
}
CheckQCGetProbeSetName(data);
}
