private Observation CreateObsCVterms(SdtmRow sdtmRow, SdtmRowDescriptor sdtmDescriptor, out Observation ob)
{
//const string AESOCvar = "AESOC";
//const string AEHG
throw new NotImplementedException();
}
private List <SdtmRow> GetFakeAEoccurN(List <string> subjectIds, SdtmRow yAE)
{
return(subjectIds.Select(subj => new SdtmRow()
{
USubjId = subj,
//StudyId = subj.Study.Name,
//Topic = obsreq.O3,
//DBTopicId = termId,//obsreq.TermIds[0],
//Id = Guid.NewGuid(),
ActivityId = yAE.ActivityId,
DatasetId = yAE.DatasetId,
DatafileId = yAE.DatafileId,
ProjectId = yAE.ProjectId,
ProjectAccession = yAE.ProjectAccession,
Class = yAE.Class,
Group = yAE.Group,
TopicControlledTerm = yAE.TopicControlledTerm,
QualifierQualifiers = yAE.QualifierQualifiers,
Qualifiers = new Dictionary <string, string>()
{
{ "AEOCCUR", "N" }
}
}).ToList());
}
public static DataRow WriteSDTMrow(SdtmRow sdtmrow, DataTable datatable, SdtmRowDescriptor descriptor)
{
var row = datatable.NewRow();
foreach (DataColumn column in datatable.Columns)
{
var colName = column.ColumnName;
//var value = tableRow[column].ToString();
if (colName == descriptor.StudyIdentifierVariable.Name)
{
//"STUDYID":
row[column] = sdtmrow.StudyId ?? "";
}
else if (colName == descriptor.DomainVariable.Name)
{
//DOMAIN
row[column] = sdtmrow.DomainCode ?? "";
}
else if (colName == descriptor.SubjIdVariable?.Name)
{
//SUBJID
row[column] = sdtmrow.SubjectId ?? "";
}
else if (colName == descriptor.UniqueSubjIdVariable.Name)
{
//USUBJID
row[column] = sdtmrow.USubjId ?? "";
}
else if (colName == descriptor.SampleIdVariable?.Name)
{
//--REFID
row[column] = sdtmrow.SampleId ?? "";
}
else if (colName == descriptor.TopicVariable?.Name)
{
//--TESTCD // --TERM // --TRT
row[column] = sdtmrow.Topic ?? "";
}
else if (colName == descriptor.TopicSynonymVariable?.Name)
{
//--TEST // --MODIFY
row[column] = sdtmrow.TopicSynonym ?? "";
}
else if (colName == descriptor.TopicCVtermVariable?.Name)
{
//--LOINC --DECODE
row[column] = sdtmrow.TopicControlledTerm ?? "";
}
else if (colName == descriptor.GroupVariable?.Name)
{
//--CAT
row[column] = sdtmrow.Group ?? "";
}
else if (colName == descriptor.SubgroupVariable?.Name)
{
//--SCAT
row[column] = sdtmrow.Subgroup ?? "";
}
else if (descriptor.QualifierVariables.Select(v => v.Name).Contains(colName))
{
//RECORD QUALIFIERS
var val = sdtmrow.Qualifiers.FirstOrDefault(c => c.Key == colName).Value;
row[column] = val ?? "";
}
else if (descriptor.ResultVariables.Select(v => v.Name).Contains(colName))
{
//RESULT QUALIFIERS
var val = sdtmrow.ResultQualifiers.FirstOrDefault(c => c.Key == colName).Value;
row[column] = val ?? "";
}
else if (descriptor.SynonymVariables.Select(v => v.Name).Contains(colName))
{
//SYNOYMS
var val = sdtmrow.QualifierSynonyms.FirstOrDefault(c => c.Key == colName).Value;
row[column] = val ?? "";
}
else if (descriptor.VariableQualifierVariables.Select(v => v.Name).Contains(colName))
{
//VARIABLE QUALIFIERS
var val = sdtmrow.QualifierQualifiers.FirstOrDefault(c => c.Key == colName).Value;
row[column] = val ?? "";
}
else if (descriptor.TimeVariables.Select(v => v.Name).Contains(colName))
{
//VISIT
var val = sdtmrow.TimingQualifiers.FirstOrDefault(c => c.Key == colName).Value;
row[column] = val ?? "";
}
else if (descriptor.DurationVariable?.Name == colName)
{
//--DUR
row[column] = sdtmrow.Duration;
}
else if (sdtmrow.Leftovers.ContainsKey(colName))
{
var val = sdtmrow.Leftovers.FirstOrDefault(c => c.Key == colName).Value;
row[column] = val ?? "";
}
else
{
row[column] = "";
}
//TODO: else if(column is not mandatory add it and set null)
//else throw new Exception("Unknown column. Cannot find value for it.");column in descriptor
}
return(row);
}
public static SdtmRow readSDTMrow(DataRow tableRow, DataTable dataTable, SdtmRowDescriptor descriptor)
{
var sdtmrow = new SdtmRow();
sdtmrow.Class = descriptor.Class;
foreach (DataColumn column in dataTable.Columns)
{
var colName = column.ColumnName;
var value = tableRow[column].ToString();
if (colName == descriptor.StudyIdentifierVariable.Name)
{
//"STUDYID":
sdtmrow.StudyId = value;
}
else if (colName == descriptor.DomainVariable.Name)
{
//DOMAIN
sdtmrow.DomainCode = value;
}
else if (colName == descriptor.SubjIdVariable?.Name)
{
//SUBJID
sdtmrow.SubjectId = value;
}
else if (colName == descriptor.UniqueSubjIdVariable.Name)
{
//USUBJID
sdtmrow.USubjId = value;
}
else if (colName == descriptor.SampleIdVariable?.Name)
{
//--REFID
sdtmrow.SampleId = value;
}
else if (colName == descriptor.TopicVariable?.Name)
{
//--TESTCD // --TERM // --TRT
sdtmrow.Topic = value;
}
else if (colName == descriptor.TopicSynonymVariable?.Name)
{
//--TEST // --MODIFY
sdtmrow.TopicSynonym = value;
}
else if (colName == descriptor.TopicCVtermVariable?.Name)
{
//--LOINC --DECODE
sdtmrow.TopicControlledTerm = value;
}
else if (colName == descriptor.GroupVariable?.Name)
{
//--CAT
sdtmrow.Group = value;
}
else if (colName == descriptor.SubgroupVariable?.Name)
{
//--SCAT
sdtmrow.Subgroup = value;
}
else if (descriptor.QualifierVariables.Select(v => v.Name).Contains(colName))
{
//RECORD QUALIFIERS
sdtmrow.Qualifiers.Add(colName, value);
}
else if (descriptor.ResultVariables.Select(v => v.Name).Contains(colName))
{
//RESULT QUALIFIERS
sdtmrow.ResultQualifiers.Add(colName, value);
}
else if (descriptor.SynonymVariables.Select(v => v.Name).Contains(colName))
{
//SYNOYMS
sdtmrow.QualifierSynonyms.Add(colName, value);
}
else if (descriptor.VariableQualifierVariables.Select(v => v.Name).Contains(colName))
{
//VARIABLE QUALIFIERS
sdtmrow.QualifierQualifiers.Add(colName, value);
}
else if (descriptor.VisitNameVariable?.Name == colName)
{
//VISIT
sdtmrow.VisitName = value;
sdtmrow.TimingQualifiers.Add(colName, value);
}
else if (descriptor.VisitNumVariable?.Name == colName)
{
//VISITNUM
int num;
if (!int.TryParse(value, out num))
{
continue;
}
sdtmrow.VisitNum = int.Parse(value);
sdtmrow.TimingQualifiers.Add(colName, value);
}
else if (descriptor.VisitPlannedStudyDay?.Name == colName)
{
//VISITNUM
int num;
if (!int.TryParse(value, out num))
{
continue;
}
sdtmrow.VisitPlannedStudyDay = int.Parse(value);
sdtmrow.TimingQualifiers.Add(colName, value);
}
else if (descriptor.DateTimeVariable?.Name == colName)
{
//DTC
DateTime DT;
if (!DateTime.TryParse(value, out DT))
{
continue;
}
if (sdtmrow.CollectionDateTime == null)
{
sdtmrow.CollectionDateTime = new AbsoluteTimePoint();
}
sdtmrow.CollectionDateTime.DateTime = DT;
sdtmrow.TimingQualifiers.Add(colName, value);
}
else if (descriptor.StudyDayVariable?.Name == colName)
{
//--DY
int num;
if (!int.TryParse(value, out num))
{
continue;
}
if (sdtmrow.CollectionStudyDay == null)
{
sdtmrow.CollectionStudyDay = new RelativeTimePoint();
}
sdtmrow.CollectionStudyDay.Number = num;
sdtmrow.TimingQualifiers.Add(colName, value);
}
else if (descriptor.TimePointNameVariable?.Name == colName)
{
//--TPT
if (sdtmrow.CollectionStudyTimePoint == null)
{
sdtmrow.CollectionStudyTimePoint = new RelativeTimePoint();
}
sdtmrow.CollectionStudyTimePoint.Name = value;
sdtmrow.TimingQualifiers.Add(colName, value);
}
else if (descriptor.TimePointNameVariable?.Name == colName)
{
//--TPTNUM
int num;
if (!int.TryParse(value, out num))
{
continue;
}
if (sdtmrow.CollectionStudyTimePoint == null)
{
sdtmrow.CollectionStudyTimePoint = new RelativeTimePoint();
}
sdtmrow.CollectionStudyTimePoint.Number = num;
sdtmrow.TimingQualifiers.Add(colName, value);
}
else if (descriptor.DurationVariable?.Name == colName)
{
//--DUR
sdtmrow.Duration = value;
}
else if (descriptor.StartDateTimeVariable?.Name == colName)
{
//--STDTC
DateTime dt;
if (!DateTime.TryParse(value, out dt))
{
continue;
}
if (sdtmrow.DateTimeInterval == null)
{
sdtmrow.DateTimeInterval = new TimeInterval();
}
sdtmrow.DateTimeInterval.Start = new AbsoluteTimePoint();
((AbsoluteTimePoint)sdtmrow.DateTimeInterval.Start).DateTime = dt;
sdtmrow.TimingQualifiers.Add(colName, value);
}
else if (descriptor.EndDateTimeVariable?.Name == colName)
{
//--ENDTC
DateTime dt;
if (!DateTime.TryParse(value, out dt))
{
continue;
}
if (sdtmrow.DateTimeInterval == null)
{
sdtmrow.DateTimeInterval = new TimeInterval();
}
sdtmrow.DateTimeInterval.End = new AbsoluteTimePoint();
((AbsoluteTimePoint)sdtmrow.DateTimeInterval.End).DateTime = dt;
sdtmrow.TimingQualifiers.Add(colName, value);
}
else if (descriptor.StartStudyDayVariable?.Name == colName)
{
//--STDY
int val;
if (!int.TryParse(value, out val))
{
continue;
}
if (sdtmrow.StudyDayInterval == null)
{
sdtmrow.StudyDayInterval = new TimeInterval();
}
sdtmrow.StudyDayInterval.Start = new RelativeTimePoint();
((RelativeTimePoint)sdtmrow.StudyDayInterval.Start).Number = val;
sdtmrow.TimingQualifiers.Add(colName, value);
}
else if (descriptor.EndStudyDayVariable?.Name == colName)
{
//--ENDY
int val;
if (!int.TryParse(value, out val))
{
continue;
}
if (sdtmrow.StudyDayInterval == null)
{
sdtmrow.StudyDayInterval = new TimeInterval();
}
sdtmrow.StudyDayInterval.End = new RelativeTimePoint();
((RelativeTimePoint)sdtmrow.StudyDayInterval.End).Number = val;
sdtmrow.TimingQualifiers.Add(colName, value);
}
else
{
sdtmrow.Leftovers.Add(colName, value);
}
}
return(sdtmrow);
}
private string ComputeValue(SdtmRow obs, VariableDefinition var)
{
//NO VALIDATIONS AND NO CHECKING WATSOEVA!
var expressionList = var.ComputedVarExpression.Split(',');
if (expressionList[0] == "CASE")
{
var sourceVarAcc = expressionList[1];
var varDef = _variableDefinitionRepository.FindSingle(v => v.Accession == sourceVarAcc && v.ProjectId == var.ProjectId);
var oriVal = obs.Qualifiers[varDef.Name];
var mappings = new Dictionary <string, string>();
var i = 2;
//IT's assumed that the expression has already been validated
while (i < expressionList.Length - 1)
{
mappings.Add(expressionList[i + 1], expressionList[i + 3]);
i += 4;
}
string mappedVal = null;
if (mappings.TryGetValue(oriVal, out mappedVal))
{
return(mappedVal);
}
}
//VERY TEMP ...need to define variable type (rpw vs qggregate
else if (expressionList.Contains("-") || expressionList.Contains("+") || expressionList.Contains("\\") || expressionList.Contains("*"))
{
var left = expressionList[0];
var right = expressionList[2];
var leftOperandVar = _variableDefinitionRepository.FindSingle(
v => v.Accession == left && v.ProjectId == var.ProjectId);
var rightOperandVar = _variableDefinitionRepository.FindSingle(
v => v.Accession == right && v.ProjectId == var.ProjectId);
var op = expressionList[1];
//FOR DATES
if (leftOperandVar.Name.EndsWith("ENDTC") && rightOperandVar.Name.EndsWith("STDTC") && op == "-")
{
TimeSpan?res = ((AbsoluteTimePoint)obs.DateTimeInterval?.End)?.DateTime -
((AbsoluteTimePoint)obs.DateTimeInterval?.Start)?.DateTime;
return(res != null?Math.Round(((TimeSpan)res).TotalDays).ToString() : "");
}
var leftOperandValStr = obs.Qualifiers[leftOperandVar?.Name];
var rightOperandValStr = obs.Qualifiers[rightOperandVar?.Name];
int leftOperandVal, rightOperandVal;
if (int.TryParse(leftOperandValStr, out leftOperandVal) && int.TryParse(rightOperandValStr, out rightOperandVal))
{
return(Evaluate(leftOperandVal, rightOperandVal, op).ToString());
}
}
else if (expressionList[0] == "SUM")
{
}
else if (expressionList[0] == "MAX")
{
}
//if case
//then parse the expression
//get the source variable
//for each when then create a dictionary where the key is the when and the value is the then
//retrieve the value of the source variable from the qualifiers of subjobservation, compare it to dictionary key, if found add to qualifiers new var with value from dictionary value
return("");
}
private async Task <DataTable> ExportSubjectClinicalTable(DataExportObject exportData, ExportFileDefinition fileDefinition) // FEATURE BY FEATURE MAIN QUICK
{
return(await Task.Factory.StartNew(() =>
{
#region Create Table Columns
var datatable = new DataTable();
datatable.TableName = fileDefinition.Name;
foreach (var field in fileDefinition.Fields)
{
datatable.Columns.Add(field.ColumnHeader.ToLower());
}
#endregion
//var subjGroupedObservations = exportData.Observations.GroupBy(ob => new { subjId = ob.USubjId });
var fieldsByO3Id = fileDefinition.Fields.FindAll(f => f.QueryObjectType == nameof(SdtmRow)).GroupBy(f => f.QueryObject.QueryObjectName).ToList();
var subjPropertiesFields = fileDefinition.Fields.FindAll(f => f.QueryObjectType != nameof(SdtmRow)).ToList();
foreach (var subject in exportData.Subjects)
{
var uniqSubjectId = subject.UniqueSubjectId;
var subjectObservations = exportData.Observations.FindAll(o => o.USubjId == uniqSubjectId).ToList();
var subjectCharacteristics = exportData.SubjChars.FindAll(sc => sc.SubjectId == subject.Id).ToList();
var firstRow = true;
while (subjectObservations.Any() || firstRow)
{
var row = datatable.NewRow();
firstRow = false;
#region Design Elements
// row["studyid"] = subject.Study.Name;
#endregion
#region Subject Properties
foreach (var subjPropField in subjPropertiesFields)
{
var charVal = _queryService.GetSubjectOrSampleProperty(subject, subjPropField.QueryObject);
if (charVal != null)
{
row[subjPropField.ColumnHeader.ToLower()] = charVal;
}
}
#endregion
#region WRITE CLINICAL OBSERVATIONS
foreach (var fieldgrp in fieldsByO3Id)//HEADACHE //BMI (EVENTS AND FINDINGS TOGETHER)//NOTE .. TIMEING ARE NOT synchronized YET
{
SdtmRow obs = null;
foreach (var field in fieldgrp) //AEOCCUR / AESEV
{
//ONTOLOGY TERM REQUEST
var query = (ObservationQuery)field.QueryObject;
if (query.IsOntologyEntry)
{
obs = subjectObservations.FirstOrDefault(
o => o.QualifierQualifiers.ContainsKey(query.TermCategory) &&
((ObservationQuery)field.QueryObject).TermId.ToString() == o.QualifierQualifiers[query.TermCategory]);
}
//GROUP OF OBSERVATIONS
else if (field.QueryObject.GetType() == typeof(GroupedObservationsQuery))
{
//ASSUMPTION: GROUPS AREONLY COMPOSED OF ONTOLOGY ENTRY
//ASSUMPTION:
string v;
foreach (var obsQuery in ((GroupedObservationsQuery)field.QueryObject).GroupedObservations)
{
obs = subjectObservations.FirstOrDefault(
o => o.QualifierQualifiers.TryGetValue(obsQuery.TermCategory, out v) &&
obsQuery.TermId.ToString() == o.QualifierQualifiers[obsQuery.TermCategory]);
if (obs != null)
{
break;
}
}
}
//SINGLE OBSERVATION OBJECT TERM REQUEST
else
{
obs = subjectObservations.FirstOrDefault(
o => ((ObservationQuery)field.QueryObject).TermId == o.DBTopicId);
}
string val = "";
//WRITE OBSERVATION INSTANCE TO ROW
obs?.Qualifiers.TryGetValue(((ObservationQuery)field.QueryObject).PropertyName, out val);
if (val == null)
{
obs?.ResultQualifiers.TryGetValue(((ObservationQuery)field.QueryObject).PropertyName, out val);
}
//Write
//if (val == null)
//if (((ObservationQuery)field.QueryObject).PropertyName.ToLower().Equals("visit"))
//val = obs.VisitName;
//if (val==null && ((ObservationQuery)field.QueryObject).PropertyName.EndsWith("DY") && obs.CollectionStudyDay.Number!=null)
//{
// val = obs.CollectionStudyDay.Number.HasValue ? obs.CollectionStudyDay.Number.ToString() : "";
// //row[field.ColumnHeader.ToLower()] = val;
//}
row[field.ColumnHeader.ToLower()] = val ?? "";
}
var visitField = fileDefinition.Fields.Find(f => f.QueryObjectType == nameof(Visit));
if (visitField != null && obs != null)
{
row[visitField.ColumnHeader.ToLower()] = obs?.VisitName ?? "";
}
var timepointField = fileDefinition.Fields.FirstOrDefault(f => f.QueryObject.QueryFor != null &&
f.QueryObject.QueryFor.Equals(nameof(SdtmRow.CollectionStudyTimePoint)));
if (timepointField != null && obs != null)
{
row[timepointField.ColumnHeader.ToLower()] = obs?.CollectionStudyTimePoint?.Name ?? "";
}
subjectObservations.Remove(obs);
}
#endregion
#region Write Timing Variables
#endregion
datatable.Rows.Add(row);
}
}
return datatable;
}));
}