public static SdtmMedDRADescriptors GetSdtmMedDRADescriptors(Dataset dataset)
{
var meddraDescriptors = new SdtmMedDRADescriptors();
meddraDescriptors.LowesLevelTerm_variable = dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == "AELLT")?.VariableDefinition;
meddraDescriptors.LowestLevelTermCode_variable = dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == "AELLTCD")?.VariableDefinition;
meddraDescriptors.PreferredTerm_variable = dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == "AEDECOD")?.VariableDefinition;
meddraDescriptors.PreferredTermCode_variable = dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == "AEPTCD")?.VariableDefinition;
meddraDescriptors.HighLevelTerm_variable = dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == "AEHLT")?.VariableDefinition;
meddraDescriptors.HighLevelTermCode_variable = dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == "AEHLTCD")?.VariableDefinition;
meddraDescriptors.HighLevelGroupTerm_variable = dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == "AEHLGT")?.VariableDefinition;
meddraDescriptors.HighLevelGroupTermCode_variable = dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == "AEHLGTCD")?.VariableDefinition;
meddraDescriptors.SystemOrganClass_variable = dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == "AESOC")?.VariableDefinition;
meddraDescriptors.SystemOrganClassCode_variable = dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == "AESOCCD")?.VariableDefinition;
return(meddraDescriptors);
}
//public Dictionary<string, VariableDefinition> name2variable { get; set; }
public static SdtmRowDescriptor GetSdtmRowDescriptor(Dataset dataset)
{
var descriptor = new SdtmRowDescriptor();
descriptor.Class = dataset.Template.Class;
descriptor.Domain = dataset.Template.Domain;
descriptor.DomainCode = dataset.Template.Code;
descriptor.ObsIsAFinding = descriptor.Class.ToUpper() == ("FINDINGS");
descriptor.ObsIsAnEvent = descriptor.Class.ToUpper() == "EVENTS";
//IDENTIFIERS
descriptor.StudyIdentifierVariable =
dataset.Variables.Single(v => v.VariableDefinition.Name == "STUDYID").VariableDefinition;
descriptor.DomainVariable =
dataset.Variables.Single(v => v.VariableDefinition.Name == "DOMAIN").VariableDefinition;
descriptor.SubjIdVariable =
dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == "SUBJID")?.VariableDefinition;
descriptor.UniqueSubjIdVariable =
dataset.Variables.Single(v => v.VariableDefinition.Name == "USUBJID").VariableDefinition;
descriptor.SampleIdVariable =
dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name.EndsWith("REFID"))?.VariableDefinition;
//TOPIC DESCRIPTORS
descriptor.TopicVariable = dataset.Variables
.Select(l => l.VariableDefinition).FirstOrDefault(v => v.RoleId == "CL-Role-T-2");
descriptor.TopicCVtermVariable = dataset.Variables
.Select(l => l.VariableDefinition).FirstOrDefault(v => v.Name == descriptor.DomainCode + "DECOD");
if (dataset.Template.Class.ToLower().Equals("findings"))
{
descriptor.TopicCVtermVariable = dataset.Variables
.Select(l => l.VariableDefinition).FirstOrDefault(v => v.Name == descriptor.DomainCode + "LOINC");
}
descriptor.TopicSynonymVariable = dataset.Variables
.Select(l => l.VariableDefinition).FirstOrDefault(v => v.Name == descriptor.DomainCode + "MODIFY");
if (dataset.Template.Class.ToLower().Equals("findings") || dataset.Template.Code.ToLower().Equals("bs"))
{
descriptor.TopicSynonymVariable = dataset.Variables
.Select(l => l.VariableDefinition).FirstOrDefault(v => v.Name == descriptor.DomainCode + "TEST");
}
//GROUP DESCRIPTORS
descriptor.GroupVariable = dataset.Variables
.Select(l => l.VariableDefinition).FirstOrDefault(v => v.Name == descriptor.DomainCode + "CAT");
descriptor.SubgroupVariable = dataset.Variables
.Select(l => l.VariableDefinition).FirstOrDefault(v => v.Name == descriptor.DomainCode + "SCAT");
//QUALIFIERS
descriptor.QualifierVariables = dataset.Variables
.Select(l => l.VariableDefinition)
.Where(v => v.RoleId == "CL-Role-T-3")
.ToList();
descriptor.SynonymVariables = dataset.Variables
.Select(l => l.VariableDefinition)
.Where(v => v.RoleId == "CL-Role-T-4")
.ToList();
descriptor.VariableQualifierVariables = dataset.Variables
.Select(l => l.VariableDefinition)
.Where(v => v.RoleId == "CL-Role-T-5")
.ToList();
descriptor.ResultVariables = dataset.Variables
.Select(l => l.VariableDefinition)
.Where(v => v.RoleId == "CL-Role-T-8")
.ToList();
descriptor.TimeVariables = dataset.Variables
.Select(l => l.VariableDefinition)
.Where(v => v.RoleId == "CL-Role-T-6")
.ToList();
//MedDRAVariables
if (descriptor.ObsIsAnEvent)
{
descriptor.MedDRAvariables = SdtmMedDRADescriptors.GetSdtmMedDRADescriptors(dataset);
// descriptor.ObsIsMedDRAcoded = SdtmMedDRADescriptors.
}
//VISIT
descriptor.VisitNameVariable =
dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == "VISIT")?.VariableDefinition;
descriptor.VisitNumVariable =
dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == "VISITNUM")?.VariableDefinition;
descriptor.VisitPlannedStudyDay =
dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == "VISITDY")?.VariableDefinition;
//DATETIME
descriptor.DateTimeVariable =
dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == descriptor.DomainCode + "DTC")?.VariableDefinition;
//STUDYDAY
descriptor.StudyDayVariable =
dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == descriptor.DomainCode + "DY")?.VariableDefinition;
//TIMEPOINT
descriptor.TimePointNameVariable =
dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == descriptor.DomainCode + "TPT")?.VariableDefinition;
descriptor.TimePointNumberVariable =
dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == descriptor.DomainCode + "TPTNUM")?.VariableDefinition;
//DURATION (Collected NOT derived)
descriptor.DurationVariable =
dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == descriptor.DomainCode + "DUR")?.VariableDefinition;
//START DATETIME
descriptor.StartDateTimeVariable =
dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == descriptor.DomainCode + "STDTC")?.VariableDefinition;
//END DATETIME
descriptor.EndDateTimeVariable =
dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == descriptor.DomainCode + "ENDTC")?.VariableDefinition;
//START STUDY DAY
descriptor.StartStudyDayVariable =
dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == descriptor.DomainCode + "STDY")?.VariableDefinition;
//END STUDY DAY
descriptor.EndStudyDayVariable =
dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == descriptor.DomainCode + "ENDY")?.VariableDefinition;
////DEMOGRAPHICS SPECIFIC VARIABLES
////ARM
//descriptor.ArmVariable = dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == "ARM")?.VariableDefinition;
////ARMCODE
//descriptor.ArmCodeVariable = dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == "ARMCD")?.VariableDefinition;
////Subject Reference Start Date
//descriptor.RefStartDate = dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == "RFSTDTC")?.VariableDefinition;
////Reference End Date
//descriptor.RefEndDate = dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == "RFENDTC")?.VariableDefinition;
////SITE ID
//descriptor.SiteIdVariable = dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name == "SITEID")?.VariableDefinition;
return(descriptor);
}
