public async Task ProcessBundles()
{
var optionsBuilder = new DbContextOptionsBuilder <AgsContext>();
optionsBuilder.UseSqlServer(AgsDbConnection);
using (var context = new AgsContext(optionsBuilder.Options)) {
if (Attributes == null)
{
var attributeList = await context.Agsattributes.ToListAsync();
Attributes = new Dictionary <int, string>(attributeList.Count);
attributeList.ForEach(x => Attributes.Add(x.AttributeId, x.Name));
}
ProcessDiagnosticReports(context);
}
}
private void ProcessDiagnosticReports(AgsContext context)
{
var client = new FhirClient(this.FhirBaseUrl);
var reports = (Bundle)client.Get("DiagnosticReport");
int reportCounter = 0;
while (reports != null)
{
if (reports.Entry == null || reports.Entry.Count == 0)
{
Console.WriteLine("Null or empty list of DiagnosticReport resources returned by FHIR server");
return;
}
Console.WriteLine("Processing bundle of {0} reports", reports.Entry.Count);
foreach (var entry in reports.Entry)
{
var resource = entry.Resource;
var reportResource = resource as DiagnosticReport;
if (resource.ResourceType != ResourceType.DiagnosticReport)
{
throw new FHIRGenomicsException(string.Format("We received a {0} resource where we expected a DiagnosticReport", resource.ResourceType));
}
else if (reportResource == null)
{
throw new FHIRGenomicsException(string.Format("Unable to cast resource ID {0} as a DiagnosticReport", resource.Id));
}
if (!ResourceHasProfile(reportResource, Constants.GenomicsProfile.DiagnosticReport))
{
throw new FHIRGenomicsException("The expected FHIR profile was not specified for the DiagnosticReport");
}
ProcessDiagnosticReport(reportResource, context);
reportCounter++;
}
reports = (Bundle)client.Continue(reports);
}
context.SaveChanges();
Console.WriteLine("Processed {0} reports", reportCounter);
}
//private async Task ProcessPatients(AgsContext context)
//{
// var patients = await GetAllResources("Patient");
// if (patients == null || patients.Entry == null || patients.Entry.Count == 0) {
// Console.WriteLine("Null or empty list of Patient resources returned by FHIR server");
// return;
// }
// Console.WriteLine("PROCESSING {0} PATIENTS", patients.Entry.Count);
// Console.WriteLine("-----------------------");
// foreach (var entry in patients.Entry) {
// var resource = entry.Resource;
// var patientResource = resource as Patient;
// if (resource.ResourceType != ResourceType.Patient) {
// throw new FHIRGenomicsException(string.Format("We received a {0} resource where we expected a Patient", resource.ResourceType));
// } else if (patientResource == null) {
// throw new FHIRGenomicsException(string.Format("Unable to cast resource ID {0} as a Patient", resource.Id));
// }
// ProcessPatient(patientResource, context);
// }
//}
private void ProcessPatient(Patient patientResource, AgsContext context)
{
var firstName = "";
var lastName = "";
if (patientResource.Name == null || patientResource.Name.Count == 0)
{
Console.WriteLine("{0} has no Name entries - using default of 'Patient {0}'",
patientResource.Id);
firstName = "Patient";
lastName = patientResource.Id;
}
else
{
if (patientResource.Name.Count > 1)
{
Console.WriteLine("{0} has {1} Name entries - using the first entry only",
patientResource.Id, patientResource.Name.Count);
}
HumanName name = patientResource.Name[0];
firstName = string.Join(" ", name.Given);
lastName = name.Family;
}
var gender = "U";
var genderElement = patientResource.Extension.Find(x => x.Url.Equals("http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex", StringComparison.CurrentCultureIgnoreCase));
if (genderElement != null)
{
gender = genderElement.Value.ToString();
}
DateTime?dateOfBirth = null;
if (patientResource.BirthDateElement == null)
{
Console.WriteLine("No DOB for Patient {0}", patientResource.Id);
}
else
{
#pragma warning disable CS0618 // Type or member is obsolete
dateOfBirth = patientResource.BirthDateElement.ToDateTime();
#pragma warning restore CS0618 // Type or member is obsolete
}
var mrn = "";
if (patientResource.Identifier == null || patientResource.Identifier.Count == 0)
{
Console.WriteLine("Patinet {0} has no identifier entries", patientResource.Id);
}
else
{
Identifier id = patientResource.Identifier.Find(x => x.System.Equals("https://emerge.mc.vanderbilt.edu/", StringComparison.CurrentCultureIgnoreCase));
if (patientResource.Identifier.Count > 1)
{
Console.WriteLine("Patient {0} had {1} identifiers. We will use the first eMERGE associated entry of {2}",
patientResource.Id, patientResource.Identifier.Count, id.Value);
}
mrn = id.Value;
}
var patient = new Agspatients();
patient.FirstName = firstName;
patient.LastName = lastName;
patient.BirthDate = dateOfBirth;
patient.Gender = gender;
patient.Mrn = mrn;
context.Agspatients.Add(patient);
}
private void ProcessDiagnosticReport(DiagnosticReport report, AgsContext context)
{
var client = new FhirClient(this.FhirBaseUrl);
// The result collection contains observations, including a Grouper type observation that will hold PGx results.
// There can be >1 Grouper, so we need to do a little more investigation (peeking at the first observation type)
// to see if it's really the one we want.
var pgxObservations = new List <Observation>();
foreach (var result in report.Result)
{
var observation = client.Read <Observation>(result.Url);
if (!ResourceHasProfile(observation, Constants.GenomicsProfile.Grouper))
{
continue;
}
foreach (var member in observation.HasMember)
{
var memberResource = client.Read <Observation>(member.Url);
if (memberResource == null ||
!ResourceHasProfile(memberResource, PgxObservationProfiles))
{
pgxObservations.Clear();
break;
}
pgxObservations.Add(memberResource);
}
// If we have any PGx observations at this point, we must have found the right grouper. We can stop
// processing since we have found what we're looking for.
if (pgxObservations.Count > 0)
{
break;
}
}
// Now that we're out of the loop, confirm or refute the assumption that all of our results should have
// a PGx grouper that contains PGx results. If we didn't find one, halt the program.
if (pgxObservations.Count == 0)
{
throw new FHIRGenomicsException("No grouper containing PGx-related Observation resources was found");
}
// Get the patient
Patient patient = client.Read <Patient>(report.Subject.Url);
if (patient == null)
{
throw new FHIRGenomicsException("Unable to find the patient associated with this DiagnosticReport");
}
ProcessPatient(patient, context);
AgsresultMessages message = new AgsresultMessages {
Sender = "HGSC",
Format = "FHIR",
ReceivedOn = DateTime.Now,
ProcessedOn = DateTime.Now,
Status = "Processed"
};
context.AgsresultMessages.Add(message);
AgsresultAttributes sample = NewResultAttribute(Constants.Attribute.Sample);
sample.Value = string.Empty;
message.AgsresultAttributes.Add(sample);
context.SaveChanges();
if (report.Status.HasValue)
{
AgsresultAttributes status = NewResultAttribute(Constants.Attribute.Status, sample.ResultAttributeId);
status.Value = report.Status.Value.ToString();
message.AgsresultAttributes.Add(status);
}
AgsresultAttributes createdOn = NewResultAttribute(Constants.Attribute.CreatedOn, sample.ResultAttributeId);
createdOn.Value = DateTime.Now.ToShortDateString();
message.AgsresultAttributes.Add(createdOn);
var specimens = report.Specimen;
if (specimens == null || specimens.Count == 0)
{
throw new FHIRGenomicsException("No specimen was found for this DiagnosticReport");
}
else if (specimens.Count != 1)
{
throw new FHIRGenomicsException(string.Format("We are expecting exactly 1 specimen for this DiagnosticReport, but found {0}", specimens.Count));
}
var specimen = (Specimen)client.Get(specimens[0].Url);
AgsresultAttributes sampleType = NewResultAttribute(Constants.Attribute.SampleType, sample.ResultAttributeId);
sampleType.Value = specimen.Type.Coding[0].Display;
message.AgsresultAttributes.Add(sampleType);
AgsresultAttributes accession = NewResultAttribute(Constants.Attribute.LabAccession, sample.ResultAttributeId);
accession.Value = report.Identifier.Find(x => x.System.Equals(Constants.CodeSystem.HGSC)).Value;
message.AgsresultAttributes.Add(accession);
var interpreters = report.ResultsInterpreter;
if (interpreters == null || interpreters.Count == 0)
{
throw new FHIRGenomicsException("We expected at least one signer (ResultsInterpreter) for this DiagnosticReport, but found 0");
}
foreach (var interpreter in interpreters)
{
AgsresultAttributes interpreterAttr = NewResultAttribute(Constants.Attribute.SignedBy, sample.ResultAttributeId);
var role = (PractitionerRole)client.Get(interpreter.Url);
var practitioner = (Practitioner)client.Get(role.Practitioner.Url);
interpreterAttr.Value = FormatName(practitioner.Name);
message.AgsresultAttributes.Add(interpreterAttr);
}
var serviceRequest = (ServiceRequest)client.Get(report.BasedOn[0].Url);
if (!ResourceHasProfile(serviceRequest, Constants.GenomicsProfile.ServiceRequest))
{
throw new FHIRGenomicsException("The ServiceRequest profile did not match the Genomics IG profile");
}
Coding indicationCoding = null;
foreach (var reasonCode in serviceRequest.ReasonCode)
{
indicationCoding = reasonCode.Coding.Find(x => x.System.Equals(Constants.CodeSystem.GeneInsight));
if (indicationCoding != null)
{
break;
}
}
if (indicationCoding == null)
{
throw new FHIRGenomicsException("Unable to find a valid reason for testing within the ServiceRequest");
}
AgsresultAttributes testIndication = NewResultAttribute(Constants.Attribute.TestIndication, sample.ResultAttributeId);
testIndication.Value = indicationCoding.Display;
message.AgsresultAttributes.Add(testIndication);
Coding requestCoding = serviceRequest.Code.Coding.Find(x => x.System.Equals(Constants.CodeSystem.BaylorLabTestCodes));
if (requestCoding == null)
{
throw new FHIRGenomicsException("Unable to find a valid code for the ServiceRequest");
}
AgsresultAttributes assayTest = NewResultAttribute(Constants.Attribute.AssayTestCode, sample.ResultAttributeId);
assayTest.Value = requestCoding.Display;
message.AgsresultAttributes.Add(assayTest);
AgsresultAttributes observedOn = NewResultAttribute(Constants.Attribute.ObservedOn, sample.ResultAttributeId);
observedOn.Value = serviceRequest.AuthoredOn;
message.AgsresultAttributes.Add(observedOn);
AgsresultAttributes receivedOn = NewResultAttribute(Constants.Attribute.ReceivedOn, sample.ResultAttributeId);
receivedOn.Value = specimen.ReceivedTime;
message.AgsresultAttributes.Add(receivedOn);
AgsresultAttributes collectedOn = NewResultAttribute(Constants.Attribute.CollectionDate, sample.ResultAttributeId);
collectedOn.Value = ((FhirDateTime)specimen.Collection.Collected).ToString();
message.AgsresultAttributes.Add(collectedOn);
//var tmp = client.SearchById("PlanDefinition", serviceRequest.InstantiatesCanonical.First());
//var tmp2 = client.SearchById("PlanDefinition", serviceRequest.InstantiatesCanonical.First().Replace("urn:uuid:", ""));
//var planDefinition = (PlanDefinition)client.Get(serviceRequest.InstantiatesCanonical.First());
//if (planDefinition == null) {
// throw new FHIRGenomicsException("Failed to retrieve a PlanDefinition resource from the ServiceRequest");
//}
//var methodBuilder = new StringBuilder();
//foreach (var action in planDefinition.Action) {
// methodBuilder.AppendLine(action.Description);
//}
//AgsresultAttributes method = NewResultAttribute(Constants.Attribute.MethodDescription, sample.ResultAttributeId);
//method.Value = methodBuilder.ToString();
//message.AgsresultAttributes.Add(method);
context.SaveChanges();
foreach (var pgxObservation in pgxObservations)
{
AgsresultAttributes pgxResult = NewResultAttribute(Constants.Attribute.PGxResult, sample.ResultAttributeId);
pgxResult.Value = string.Empty;
message.AgsresultAttributes.Add(pgxResult);
context.SaveChanges();
if (pgxObservation.DerivedFrom == null)
{
throw new FHIRGenomicsException("Expected exactly one DerivedFrom entry, but none were found");
}
foreach (var geneDerivation in pgxObservation.DerivedFrom)
{
var geneObservation = (Observation)client.Get(geneDerivation.Url);
AgsresultAttributes gene = NewResultAttribute(Constants.Attribute.GeneSymbol, pgxResult.ResultAttributeId);
gene.Value = ((CodeableConcept)geneObservation.Component[0].Value).Coding[0].Display;
message.AgsresultAttributes.Add(gene);
AgsresultAttributes diplotype = NewResultAttribute(Constants.Attribute.PGxDiplotype, pgxResult.ResultAttributeId);
diplotype.Value = ((CodeableConcept)geneObservation.Value).Text;
message.AgsresultAttributes.Add(diplotype);
}
AgsresultAttributes phenotype = NewResultAttribute(Constants.Attribute.PGxPhenotype, pgxResult.ResultAttributeId);
var pgxPhenotypeConcept = ((CodeableConcept)pgxObservation.Value);
if (((CodeableConcept)pgxObservation.Value).Coding.Count == 0)
{
phenotype.Value = pgxPhenotypeConcept.Text;
}
else
{
phenotype.Value = pgxPhenotypeConcept.Coding[0].Display;
}
message.AgsresultAttributes.Add(phenotype);
AgsresultAttributes variantInterpretation = NewResultAttribute(Constants.Attribute.VariantInterpretation, pgxResult.ResultAttributeId);
variantInterpretation.Value = pgxObservation.GetExtensionValue <Element>(Constants.HGSCExtension.InterpretationSummaryText).ToString();
message.AgsresultAttributes.Add(variantInterpretation);
foreach (var pgxMed in pgxObservation.Component)
{
AgsresultAttributes pgxMedication = NewResultAttribute(Constants.Attribute.PGxAssociatedMedication, pgxResult.ResultAttributeId);
pgxMedication.Value = ((CodeableConcept)pgxMed.Value).Coding[0].Display;
message.AgsresultAttributes.Add(pgxMedication);
context.SaveChanges();
AgsresultAttributes pgxRecommendation = NewResultAttribute(Constants.Attribute.PGxAssociatedRecommendation, pgxMedication.ResultAttributeId);
pgxRecommendation.Value = pgxMed.GetExtensionValue <RelatedArtifact>(Constants.HGSCExtension.RelatedArtifact).Url;
message.AgsresultAttributes.Add(pgxRecommendation);
}
context.SaveChanges();
}
}
