void ArrayDataTest::testproperty_UserAttributes()
{
ArrayData array;
ParameterNameValueDefaultRequiredTypeList ¶ms = array.UserAttributes();
ParameterNameValueDefaultRequiredType vparam;
vparam.SetName(L"user-att-name-1");
vparam.SetValueAscii("user-att-value-1");
vparam.SetDefaultValueAscii("user-att-defaultvalue-1");
vparam.RequiredFlag() = false;
vparam.ControlledVocabulary().clear() ;
params.push_back(vparam);
vparam.SetName(L"user-att-name-2");
vparam.SetValueText(L"user-att-value-2");
vparam.SetDefaultValueText(L"user-att-defaultvalue-2");
vparam.RequiredFlag() = true;
vparam.ControlledVocabulary().clear() ;
params.push_back(vparam);
vparam.SetName(L"user-att-name-3");
vparam.SetValueText(L"user-att-value-3");
vparam.SetDefaultValueText(L"user-att-defaultvalue-3");
vparam.RequiredFlag() = false;
vparam.ControlledVocabulary().push_back(L"control1");
vparam.ControlledVocabulary().push_back(L"control2");
params.push_back(vparam);
CPPUNIT_ASSERT( array.UserAttributes().size() == 3 );
ParameterNameValueDefaultRequiredTypeList::iterator it = array.UserAttributes().begin();
CPPUNIT_ASSERT( (*it).GetName() == L"user-att-name-1" );
CPPUNIT_ASSERT( (*it).GetValueAscii() == "user-att-value-1" );
CPPUNIT_ASSERT( (*it).GetDefaultValueAscii() == "user-att-defaultvalue-1" );
CPPUNIT_ASSERT( (*it).ControlledVocabulary().size() == 0 );
CPPUNIT_ASSERT( (*it).RequiredFlag() == false);
++it;
CPPUNIT_ASSERT( (*it).GetName() == L"user-att-name-2" );
CPPUNIT_ASSERT( (*it).GetValueText() == L"user-att-value-2" );
CPPUNIT_ASSERT( (*it).GetDefaultValueText() == L"user-att-defaultvalue-2" );
CPPUNIT_ASSERT( (*it).ControlledVocabulary().size() == 0 );
CPPUNIT_ASSERT( (*it).RequiredFlag() == true);
++it;
CPPUNIT_ASSERT( (*it).GetName() == L"user-att-name-3" );
CPPUNIT_ASSERT( (*it).GetValueText() == L"user-att-value-3" );
CPPUNIT_ASSERT( (*it).GetDefaultValueText() == L"user-att-defaultvalue-3" );
CPPUNIT_ASSERT( (*it).ControlledVocabulary().size() == 2 );
CPPUNIT_ASSERT( (*it).RequiredFlag() == false);
std::list<std::wstring>::iterator controllIt = (*it).ControlledVocabulary().begin();
CPPUNIT_ASSERT( (*controllIt) == L"control1" );
++controllIt;
CPPUNIT_ASSERT( (*controllIt) == L"control2" );
++it;
CPPUNIT_ASSERT (it == array.UserAttributes().end() );
}
/*! Test the ability to read an Data Transfer Tool formated array file. */
void FusionArrayFileReaderTest::testmethod_Read_dtt_array_file()
{
FusionArrayFileReader reader;
ArrayData data;
CPPUNIT_ASSERT( reader.Read(MAGE_FILE, data) == true);
CPPUNIT_ASSERT( data.ArraySetFileIdentifier() == std::string(""));
CPPUNIT_ASSERT( data.PhysicalArraysAttributes().size() == 1);
CPPUNIT_ASSERT( data.PhysicalArraysAttributes()[0].Identifier() == "");
const ParameterNameValuePairVector &arrayParams = data.PhysicalArraysAttributes()[0].Attributes();
CPPUNIT_ASSERT( arrayParams.size() == 1 );
ParameterNameValuePairVector::const_iterator arrayIt = arrayParams.begin();
CPPUNIT_ASSERT( (*arrayIt).Name == L"Probe Array Type" );
CPPUNIT_ASSERT( (*arrayIt).Value == L"Test3" );
ParameterNameValueDefaultRequiredTypeList &userParams = data.UserAttributes();
CPPUNIT_ASSERT( userParams.size() == 33 );
ParameterNameValueDefaultRequiredTypeList::iterator userIt = userParams.begin();
CPPUNIT_ASSERT( (*userIt).GetName() == L"GCOS Sample Name" );
CPPUNIT_ASSERT( (*userIt).GetValueText() == L"Sample_with_Sample_Template" );
CPPUNIT_ASSERT( (*userIt).ControlledVocabulary().size() == 0 );
++userIt;
CPPUNIT_ASSERT( (*userIt).GetName() == L"Sample Template Name" );
CPPUNIT_ASSERT( (*userIt).GetValueText() == L"MIAME Sample Information" );
CPPUNIT_ASSERT( (*userIt).ControlledVocabulary().size() == 0 );
userIt = userParams.end();
--userIt;
CPPUNIT_ASSERT( (*userIt).GetName() == L"Grid Alignment Passed" );
CPPUNIT_ASSERT( (*userIt).GetValueText() == L"" );
CPPUNIT_ASSERT( (*userIt).ControlledVocabulary().size() == 0 );
}
/*! Test the handling of attempting to read an array file that does not exist. */
void FusionArrayFileReaderTest::testmethod_Read_missing_file()
{
FusionArrayFileReader reader;
ArrayData data;
CPPUNIT_ASSERT( reader.Read("no_file", data) == false);
CPPUNIT_ASSERT( data.ArraySetFileIdentifier() == "");
CPPUNIT_ASSERT( data.DataTypeIdentifier() == "");
CPPUNIT_ASSERT( data.PhysicalArraysAttributes().size() == 0);
CPPUNIT_ASSERT( data.UserAttributes().size() == 0);
}
/*! Test the ability to read an Micro Array Suit formated array file (EXP). */
void FusionArrayFileReaderTest::testmethod_Read_mas_array_file()
{
FusionArrayFileReader reader;
ArrayData data;
CPPUNIT_ASSERT( reader.Read(EXP_FILE, data) == true);
CPPUNIT_ASSERT( data.ArraySetFileIdentifier() == std::string(""));
CPPUNIT_ASSERT( data.PhysicalArraysAttributes().size() == 1);
CPPUNIT_ASSERT( data.PhysicalArraysAttributes()[0].Identifier() == "");
const ParameterNameValuePairVector &arrayParams = data.PhysicalArraysAttributes()[0].Attributes();
CPPUNIT_ASSERT( arrayParams.size() == 1 );
ParameterNameValuePairVector::const_iterator arrayIt = arrayParams.begin();
CPPUNIT_ASSERT( (*arrayIt).Name == L"Probe Array Type" );
CPPUNIT_ASSERT( (*arrayIt).Value == L"Test3" );
ParameterNameValueDefaultRequiredTypeList &userParams = data.UserAttributes();
CPPUNIT_ASSERT( userParams.size() == 8 );
ParameterNameValueDefaultRequiredTypeList::iterator userIt = userParams.begin();
CPPUNIT_ASSERT( (*userIt).GetName() == L"Chip Lot" );
CPPUNIT_ASSERT( (*userIt).GetValueText() == L"123" );
CPPUNIT_ASSERT( (*userIt).ControlledVocabulary().size() == 0 );
++userIt;
CPPUNIT_ASSERT( (*userIt).GetName() == L"Operator" );
CPPUNIT_ASSERT( (*userIt).GetValueText() == L"ljevon" );
CPPUNIT_ASSERT( (*userIt).ControlledVocabulary().size() == 0 );
++userIt;
CPPUNIT_ASSERT( (*userIt).GetName() == L"Sample Type" );
CPPUNIT_ASSERT( (*userIt).GetValueText() == L"s_type" );
CPPUNIT_ASSERT( (*userIt).ControlledVocabulary().size() == 0 );
++userIt;
CPPUNIT_ASSERT( (*userIt).GetName() == L"Description" );
CPPUNIT_ASSERT( (*userIt).GetValueText() == L"Demo data" );
CPPUNIT_ASSERT( (*userIt).ControlledVocabulary().size() == 0 );
++userIt;
CPPUNIT_ASSERT( (*userIt).GetName() == L"Project" );
CPPUNIT_ASSERT( (*userIt).GetValueText() == L"s_proj" );
CPPUNIT_ASSERT( (*userIt).ControlledVocabulary().size() == 0 );
++userIt;
CPPUNIT_ASSERT( (*userIt).GetName() == L"Comments" );
CPPUNIT_ASSERT( (*userIt).GetValueText() == L"None" );
CPPUNIT_ASSERT( (*userIt).ControlledVocabulary().size() == 0 );
++userIt;
CPPUNIT_ASSERT( (*userIt).GetName() == L"Solution Type" );
CPPUNIT_ASSERT( (*userIt).GetValueText() == L"sol type" );
CPPUNIT_ASSERT( (*userIt).ControlledVocabulary().size() == 0 );
++userIt;
CPPUNIT_ASSERT( (*userIt).GetName() == L"Solution Lot" );
CPPUNIT_ASSERT( (*userIt).GetValueText() == L"123123" );
CPPUNIT_ASSERT( (*userIt).ControlledVocabulary().size() == 0 );
++userIt;
}
void ArrayDataTest::testmethod_Clear()
{
string id = "file_id";
ArrayData array;
array.ArraySetFileIdentifier() = id;
array.PhysicalArraysAttributes().resize(2);
array.UserAttributes().resize(4);
array.DataTypeIdentifier() = "affymetrix-calvin-arraysetfile";
array.CreatedStep() = ArrayRegistrationStep;
array.InitialProject() = L"none";
array.CreationDateTime() = L"now";
array.CreatedBy() = L"me";
array.Clear();
CPPUNIT_ASSERT(array.ArraySetFileIdentifier() == "");
CPPUNIT_ASSERT(array.PhysicalArraysAttributes().size() == 0);
CPPUNIT_ASSERT(array.UserAttributes().size() == 0);
CPPUNIT_ASSERT(array.DataTypeIdentifier() == "");
CPPUNIT_ASSERT(array.CreatedStep() == NoStep);
CPPUNIT_ASSERT(array.InitialProject() == L"");
CPPUNIT_ASSERT(array.CreationDateTime() == L"");
CPPUNIT_ASSERT(array.CreatedBy() == L"");
}
/*! Test the ability to read a valid Calvin array file. */
void FusionArrayFileReaderTest::testmethod_Read_calvin_array_file()
{
FusionArrayFileReader reader;
ArrayData array;
CPPUNIT_ASSERT( reader.Read(CALVIN_FILE, array) == true);
CPPUNIT_ASSERT( array.DataTypeIdentifier() == ARRAY_SET_FILE_TYPE_IDENTIFIER );
CPPUNIT_ASSERT( array.ArraySetFileIdentifier() == std::string("432-432-432-432"));
CPPUNIT_ASSERT( array.CreatedStep() == ArrayRegistrationStep);
CPPUNIT_ASSERT( array.InitialProject() == L"my_project");
CPPUNIT_ASSERT( array.CreationDateTime() == L"8/12/2005 9:00AM");
CPPUNIT_ASSERT( array.CreatedBy() == L"ljevon");
CPPUNIT_ASSERT( array.PhysicalArraysAttributes().size() == 1);
ArrayAttributes &atts = array.PhysicalArraysAttributes()[0];
CPPUNIT_ASSERT( atts.Identifier() == "123-123-123-123");
CPPUNIT_ASSERT( atts.ArrayName() == "mychip");
CPPUNIT_ASSERT( atts.ArrayBarcode() == "@1234567890");
CPPUNIT_ASSERT( atts.Media() == PlateOrStripMedia);
CPPUNIT_ASSERT( atts.MediaRow() == 1);
CPPUNIT_ASSERT( atts.MediaCol() == 12);
CPPUNIT_ASSERT( atts.MasterFile() == "Test3.master");
CPPUNIT_ASSERT( atts.MasterFileId() == "123-123-123-123");
CPPUNIT_ASSERT( atts.PatAssignment() == AffyBarcodeAssignment);
CPPUNIT_ASSERT( atts.CreationDateTime() == L"8/12/2005 10:00AM");
CPPUNIT_ASSERT( atts.CreatedBy() == L"ljevon");
CPPUNIT_ASSERT( atts.CreatedStep() == ScanningStep);
CPPUNIT_ASSERT( atts.Comment() == L"here is a comment");
ParameterNameValuePairVector ¶ms = atts.Attributes();
ParameterNameValuePairVector::iterator paramIt = params.begin();
CPPUNIT_ASSERT( params.size() == 2);
CPPUNIT_ASSERT( (*paramIt).Name == L"SampleID");
CPPUNIT_ASSERT( (*paramIt).Value == L"433232");
++paramIt;
CPPUNIT_ASSERT( (*paramIt).Name == L"LIMS System");
CPPUNIT_ASSERT( (*paramIt).Value == L"Nautilis");
ParameterNameValueDefaultRequiredTypeList &userParams = array.UserAttributes();
CPPUNIT_ASSERT( userParams.size() == 6 );
ParameterNameValueDefaultRequiredTypeList::iterator userIt = userParams.begin();
CPPUNIT_ASSERT( (*userIt).GetName() == L"Species" );
CPPUNIT_ASSERT( (*userIt).GetValueText() == L"H**o Sapien" );
CPPUNIT_ASSERT( (*userIt).RequiredFlag() == true );
CPPUNIT_ASSERT( (*userIt).ControlledVocabulary().size() == 0 );
CPPUNIT_ASSERT( (*userIt).ValueType() == ParameterNameValueDefaultRequiredType::TextParameterType);
++userIt;
CPPUNIT_ASSERT( (*userIt).GetName() == L"Individual" );
CPPUNIT_ASSERT( (*userIt).GetValueText() == L"me" );
CPPUNIT_ASSERT( (*userIt).RequiredFlag() == false );
CPPUNIT_ASSERT( (*userIt).ControlledVocabulary().size() == 0 );
CPPUNIT_ASSERT( (*userIt).ValueType() == ParameterNameValueDefaultRequiredType::TextParameterType);
++userIt;
CPPUNIT_ASSERT( (*userIt).GetName() == L"When" );
CPPUNIT_ASSERT( (*userIt).GetValueText() == L"now" );
CPPUNIT_ASSERT( (*userIt).RequiredFlag() == false );
CPPUNIT_ASSERT( (*userIt).ControlledVocabulary().size() == 0 );
CPPUNIT_ASSERT( (*userIt).ValueType() == ParameterNameValueDefaultRequiredType::TimeParameterType);
++userIt;
CPPUNIT_ASSERT( (*userIt).GetName() == L"How much" );
const double eps = 1e-5;
CPPUNIT_ASSERT_DOUBLES_EQUAL( (*userIt).GetValueFloat(), 1.0, eps);
CPPUNIT_ASSERT( (*userIt).RequiredFlag() == false );
CPPUNIT_ASSERT( (*userIt).ControlledVocabulary().size() == 0 );
CPPUNIT_ASSERT( (*userIt).ValueType() == ParameterNameValueDefaultRequiredType::FloatParameterType);
++userIt;
CPPUNIT_ASSERT( (*userIt).GetName() == L"Sex" );
CPPUNIT_ASSERT( (*userIt).GetValueText() == L"" );
CPPUNIT_ASSERT( (*userIt).RequiredFlag() == false );
CPPUNIT_ASSERT( (*userIt).ValueType() == ParameterNameValueDefaultRequiredType::ControlMultiParameterType);
std::list<std::wstring>::iterator cit = (*userIt).ControlMultiValues().begin();
CPPUNIT_ASSERT( (*cit) == L"Male" );
++cit;
CPPUNIT_ASSERT( (*cit) == L"Other" );
CPPUNIT_ASSERT( (*userIt).ControlledVocabulary().size() == 4 );
cit = (*userIt).ControlledVocabulary().begin();
CPPUNIT_ASSERT( (*cit) == L"Male" );
++cit;
CPPUNIT_ASSERT( (*cit) == L"Female" );
++cit;
CPPUNIT_ASSERT( (*cit) == L"Unknown" );
++cit;
CPPUNIT_ASSERT( (*cit) == L"Other" );
++userIt;
CPPUNIT_ASSERT( (*userIt).GetName() == L"Age" );
CPPUNIT_ASSERT( (*userIt).GetValueText() == L"30 something" );
CPPUNIT_ASSERT( (*userIt).RequiredFlag() == false );
CPPUNIT_ASSERT( (*userIt).ValueType() == ParameterNameValueDefaultRequiredType::TextParameterType);
CPPUNIT_ASSERT( (*userIt).ControlledVocabulary().size() == 0 );
++userIt;
CPPUNIT_ASSERT (userIt == userParams.end() );
}
