private ExportFileDefinition GetSampleFileDefinition(CombinedQuery query)
{
AssayPanelQuery assayPanelQuery = query.AssayPanels.Single();
// This is for the subject to sample mapping
var assaySampleDataset = new ExportFileDefinition
{
ProjectId = query.ProjectId,
ContentType = "BIOSAMPLES",
Name = assayPanelQuery.AssayName + " Samples",
QueryId = query.Id
};
//CREATE DATAFIELDS
// 1. ADD SubjectId Field
assaySampleDataset.Fields.Add(CreateSubjectIdField());
// 2.ADD sample Id Field
assaySampleDataset.Fields.Add(CreateSampleIdField());
// 3. ADD Study Id
assaySampleDataset.Fields.Add(CreateStudyIdField());
// 4. ADD Sample characteristics
assaySampleDataset.Fields.AddRange(assayPanelQuery.SampleQueries.Select(qObj => new DatasetField()
{
QueryObjectType = nameof(SampleCharacteristic),
QueryObject = qObj,
ColumnHeader = qObj.QueryObjectName
}));
return(assaySampleDataset);
}
private ExportFileDefinition GetAssayDataFileDefinition(CombinedQuery query)
{
AssayPanelQuery assayPanelQuery = query.AssayPanels.Single();
var assayPanelDataset = new ExportFileDefinition
{
ProjectId = query.ProjectId,
ContentType = "ASSAY",
Name = assayPanelQuery.AssayName + " Data File",
QueryId = query.Id
};
return(assayPanelDataset);
}
private async Task <FileInfo> ExportAssayTable(DataExportObject exportData, ExportFileDefinition fileDefinition, string filePath) // FEATURE BY FEATURE MAIN QUICK
{
return(await Task.Factory.StartNew(() =>
{
var projectId = fileDefinition.ProjectId;
var activityId = exportData.Samples.First().AssayId;
// GET sampleIds, observations, and features
var sampleIds = exportData.Samples.OrderBy(o => o.BiosampleStudyId).Select(s => s.BiosampleStudyId).ToList();
var assayObservations = _queryService.GetAssayObservations(projectId, activityId, sampleIds);
var orderObservations = assayObservations.OrderBy(o => o.FeatureName).ThenBy(o => o.SubjectOfObservationName);
//////var features = orderObservations.Select(a => a.FeatureName).Distinct().ToList();
//////var values = orderObservations.Select(c => ((NumericalValue)c.ObservedValue).Value);
var features = orderObservations.Select(a => a.FeatureName).Distinct().ToList();
var values = orderObservations.Select(a => a.Value).ToList();
var samples = orderObservations.Select(a => a.SubjectOfObservationName).Distinct().ToList();
StreamWriter writer = File.CreateText(filePath);
// First write the header (which are samples' Ids)
writer.WriteLine("features" + "," + string.Join(",", samples));
var sb = new StringBuilder();
var i = 0;
var j = 0;
foreach (var value in values)
{
i++;
sb.Append(value + ",");
if (i == exportData.Samples.Count)
{
writer.WriteLine(features[j] + "," + sb);
sb.Clear();
i = 0;
writer.Flush();
j++;
}
}
writer.Dispose();
return new FileInfo(filePath);
}));
}
private ExportFileDefinition GetSubjectFileDefinition(CombinedQuery query)
{
var phenoDataset = new ExportFileDefinition()
{
ProjectId = query.ProjectId,
ContentType = "PHENO",
Name = "Subjects",
QueryId = query.Id
};
bool _hasLongitudinalData = false, _hasTpt = false;
//ADD SUBJECTID & STUDYID DATAFIELD
phenoDataset.Fields.Add(CreateSubjectIdField());
phenoDataset.Fields.Add(CreateStudyIdField());
//ADD DESIGN ELEMENT FIELDS (STUDY, VISIT, ARM...etc)
phenoDataset.Fields.AddRange(query.DesignElements.Select(qObj => new DatasetField()
{
QueryObject = qObj,
QueryObjectType = qObj.QueryFor,
ColumnHeader = qObj.QueryObjectName
}));
//ADD SUBJECT CHARACTERISTICS (AGE, RACE, SEX ...etc)
phenoDataset.Fields.AddRange(query.SubjectCharacteristics.Select(qObj => new DatasetField()
{
QueryObject = qObj,
QueryObjectType = nameof(SubjectCharacteristic),
ColumnHeader = qObj.QueryObjectName//.ObservationName
}));
//ADD CLINICAL OBSERVATIONS
foreach (var co in query.ClinicalObservations)
{
phenoDataset.Fields.Add(new DatasetField()
{
QueryObject = co,
QueryObjectType = nameof(SdtmRow),
ColumnHeader = co.ObservationName
});
if (co.HasLongitudinalData)
{
_hasLongitudinalData = true;
}
if (co.HasTPT)
{
_hasTpt = true;
}
}
//ADD GROUPED CLINICAL OBSERVATIONS
phenoDataset.Fields.AddRange(query.GroupedObservations.Select(gObs => new DatasetField()
{
QueryObject = gObs,
QueryObjectType = nameof(SdtmRow),
ColumnHeader = gObs.ObservationName
}));
//ADD longitudinal data columns
if (_hasLongitudinalData && !phenoDataset.Fields.Exists(f => f.ColumnHeader == "visit"))
{
phenoDataset.Fields.Add(new DatasetField()
{
QueryObject = new Query()
{
QueryFor = nameof(Visit), QueryFrom = nameof(SdtmRow), QuerySelectProperty = "Name"
},
QueryObjectType = nameof(Visit),
ColumnHeader = "visit"
});
}
if (_hasTpt && !phenoDataset.Fields.Exists(f => f.ColumnHeader == "timepoint"))
{
phenoDataset.Fields.Add(new DatasetField()
{
QueryObject = new Query()
{
QueryFor = nameof(SdtmRow.CollectionStudyTimePoint), QueryFrom = nameof(SdtmRow), QuerySelectProperty = "Name"
},
QueryObjectType = nameof(RelativeTimePoint),
ColumnHeader = "timepoint"
});
}
return(phenoDataset);
}
private async Task <DataTable> ExportSampleTable(DataExportObject exportData, ExportFileDefinition fileDefinition) // FEATURE BY FEATURE MAIN QUICK
{
return(await Task.Factory.StartNew(() =>
{
var datatable = new DataTable();
datatable.TableName = fileDefinition.Name;
foreach (var field in fileDefinition.Fields)
{
datatable.Columns.Add(field.ColumnHeader.ToLower());
}
foreach (var biosample in exportData.Samples)
{
var row = datatable.NewRow();
row["subjectid"] = biosample.Subject.UniqueSubjectId;
row["sampleid"] = biosample.BiosampleStudyId;
foreach (var samplePropField in fileDefinition.Fields)
{
var charVal = _queryService.GetSubjectOrSampleProperty(biosample, samplePropField.QueryObject);
if (charVal != null)
{
row[samplePropField.ColumnHeader.ToLower()] = charVal;
}
}
datatable.Rows.Add(row);
}
return datatable;
}));
}
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;
}));
}