public ActionResult <string> GetPatient()
{
FhirClient fhirClient = _client.ConfigureBasicClient("http://fhir.hl7fundamentals.org/r4/");
Resource patientResource = fhirClient.Get("Patient/50672");
return(Ok(patientResource.ToJson()));
}
public void TestWithParam()
{
var client = new FhirClient(testEndpoint);
var res = client.Get("ValueSet/patient-contact-relationship/$validate-code?system=http://hl7.org/fhir/patient-contact-relationship&code=emergency");
Assert.IsNotNull(res);
}
public IActionResult Read(string type, string id, string version = null)
{
FhirClient client = new FhirClient(url);
String text = FhirSerializer.SerializeResourceToJson(client.Get(ResourceIdentity.Build(type, id, version)));
JsonTextModel m = new JsonTextModel(type, id, version, text);
m.Status_ = JsonTextModel.READING;
return(View(m));
}
public static bool TryGetSmartUrls(
FhirClient fhirClient,
out string authorizeUrl,
out string tokenUrl
)
{
authorizeUrl = string.Empty;
tokenUrl = string.Empty;
CapabilityStatement capabilities = (CapabilityStatement)fhirClient.Get("metadata");
foreach (CapabilityStatement.RestComponent restComponent in capabilities.Rest)
{
if (restComponent.Security == null)
{
continue;
}
foreach (Extension securityExt in restComponent.Security.Extension)
{
if (securityExt.Url != "http://fhir-registry.smarthealthit.org/StructureDefinition/oauth-uris")
{
continue;
}
if ((securityExt.Extension == null) || (securityExt.Extension.Count == 0))
{
continue;
}
foreach (Extension smartExt in securityExt.Extension)
{
switch (smartExt.Url)
{
case "authorize":
authorizeUrl = ((FhirUri)smartExt.Value).Value.ToString();
break;
case "token":
tokenUrl = ((FhirUri)smartExt.Value).Value.ToString();
break;
}
}
}
}
if (string.IsNullOrEmpty(authorizeUrl) || string.IsNullOrEmpty(tokenUrl))
{
return(false);
}
return(true);
}
private IList <PatientProfile> GetPendingPatients()
{
List <PatientProfile> listPending = new List <PatientProfile>();
try
{
MongoDBWrapper dbwrapper = new MongoDBWrapper(NoIDMongoDBAddress, SparkMongoDBAddress);
List <SessionQueue> pendingSessionList = dbwrapper.GetPendingPatients();
FhirClient client = new FhirClient(sparkEndpointAddress);
foreach (var pending in pendingSessionList)
{
string sparkAddress = sparkEndpointAddress.ToString() + "/Patient/" + pending.SparkReference;
Patient pendingPatient = (Patient)client.Get(sparkAddress);
PatientProfile patientProfile = new PatientProfile(pendingPatient, true);
patientProfile.SessionID = pending._id;
patientProfile.LocalNoID = pending.LocalReference;
patientProfile.NoIDStatus = pending.ApprovalStatus;
patientProfile.NoIDType = pending.PatientStatus;
patientProfile.CheckinDateTime = FHIRUtilities.DateTimeToFHIRString(pending.SubmitDate);
listPending.Add(patientProfile);
}
/*
* string gtDateFormat = "gt" + FHIRUtilities.DateToFHIRString(DateTime.UtcNow.AddDays(-2));
* client.PreferredFormat = ResourceFormat.Json;
* Uri uriTwoDays = new Uri(sparkEndpointAddress.ToString() + "/Patient?_lastUpdated=" + gtDateFormat);
* Bundle patientBundle = (Bundle)client.Get(uriTwoDays);
* foreach (Bundle.EntryComponent entry in patientBundle.Entry)
* {
* string ptURL = entry.FullUrl.ToString().Replace("http://localhost:49911/fhir", sparkEndpointAddress.ToString());
* Patient pt = (Patient)client.Get(ptURL);
* if (pt.Meta.Extension.Count > 0)
* {
* Extension ext = pt.Meta.Extension[0];
* if (ext.Value.ToString().ToLower().Contains("pending") == true)
* {
* PatientProfile patientProfile = new PatientProfile(pt, false);
* listPending.Add(patientProfile);
* }
* }
* }
*/
}
catch (Exception ex)
{
throw ex;
}
return(listPending);
}
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);
}
public void DiscoverExtensionsOnFhirServer()
{
string sourcePath = Configuration.GetValue <string>("sourcePath");
string outputPath = Configuration.GetValue <string>("outputPath");
string canonicalBase = Configuration.GetValue <string>("defaults:baseurl");
string publisher = Configuration.GetValue <string>("defaults:publisher");
ScanResources processor = new ScanResources(sourcePath, outputPath,
canonicalBase, publisher);
var settings = Configuration.GetSection("scanserver").Get <ScanServerSettings>();
var server = new FhirClient(settings.baseurl, new FhirClientSettings()
{
VerifyFhirVersion = false
});
int createdResources = 0;
foreach (var query in settings.queries)
{
try
{
Bundle batch = server.Get(server.Endpoint + query) as Bundle;
do
{
foreach (var entry in batch.Entry.Select(e => e.Resource))
{
if (entry != null)
{
System.Diagnostics.Trace.WriteLine($" -->{entry.TypeName}/{entry.Id}");
processor.ScanForExtensions(null, entry.ToTypedElement(), null);
createdResources++;
}
}
// if (batch.NextLink == null)
break;
batch = server.Continue(batch);
}while (true);
}
catch (FhirOperationException ex)
{
DebugDumpOutputXml(ex.Outcome);
}
}
}
static void Main(string[] args)
{
//One of the test endpoints
string adhaPDEndpoint = "https://sandbox.digitalhealth.gov.au/FhirServerSTU3-PDA/fhir";
//New up a FHIR client to make the request
FhirClient client = new FhirClient(adhaPDEndpoint);
// Load certificate used to sign the client request
X509Certificate2 signingCert = GetCertificate(
"06fba6",
X509FindType.FindBySerialNumber,
StoreName.My,
StoreLocation.CurrentUser,
true);
//Add the certificate to the FHIR client request
client.OnBeforeRequest += (object sender, BeforeRequestEventArgs e) =>
{
e.RawRequest.ClientCertificates.Add(signingCert);
};
//Make the request to GET all PractitionerRole resources
Resource responseResource = client.Get("/PractitionerRole");
if (responseResource is Bundle bundle)
{
Console.WriteLine($"Recived a {bundle.TypeName} resource containing a collection of resources as follows:");
int counter = 1;
foreach (var entry in bundle.Entry)
{
Console.WriteLine($"Resource {counter.ToString()} is a {entry.Resource.TypeName} resource.");
counter++;
}
}
else
{
Console.WriteLine($"Not the response we were expecting!");
}
Console.ReadKey();
}
public static string GetIndividualResourceFromBundle(Bundle bundle)
{
LogToFile("Get Individual Resource From Bundle:");
string patientId = string.Empty;
foreach (var entryItem in bundle.Entry)
{
Uri uri = new Uri(FhirClientEndPoint + entryItem.Response.Location);
FhirClient fhirClient = new FhirClient(FhirClientEndPoint);
var resource = fhirClient.Get(uri);
var resourceXml = FhirSerializer.SerializeResourceToXml(resource);
LogToFile(XDocument.Parse(resourceXml).ToString());
if (resource.ResourceType == ResourceType.Patient)
{
patientId = resource.Id;
}
}
return(patientId);
}
public void TestWithParam()
{
var client = new FhirClient(testEndpoint);
var res = client.Get("ValueSet/101/$validate?system=http://hl7.org/fhir/patient-contact-relationship&code=emergency");
Assert.IsNotNull(res);
}
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();
}
}
public void ProcessRequest(HttpContext context)
{
context.Response.ContentType = "text/plain";
try
{
foreach (String key in context.Request.QueryString.AllKeys)
{
switch (key.ToLower())
{
case "localnoid":
_localNoID = context.Request.QueryString[key];
break;
case "fieldname":
_confirmFieldName = context.Request.QueryString[key];
break;
case "confirmreponse":
_confirmReponse = context.Request.QueryString[key];
break;
case "computername":
_computerName = context.Request.QueryString[key];
break;
case "clinicarea":
_clinicArea = context.Request.QueryString[key];
break;
}
}
MongoDBWrapper dbwrapper = new MongoDBWrapper(NoIDMongoDBAddress, SparkMongoDBAddress);
FhirClient client = new FhirClient(sparkEndpointAddress);
string sparkReference = dbwrapper.GetSparkID(_localNoID);
string sparkAddress = sparkEndpointAddress.ToString() + "/Patient/" + sparkReference;
Patient pendingPatient = (Patient)client.Get(sparkAddress);
if (pendingPatient != null)
{
if (_confirmFieldName == "birthdate")
{
if (pendingPatient.BirthDate != null && _confirmReponse == pendingPatient.BirthDate)
{
SessionQueue seq = Utilities.PatientToSessionQueue(pendingPatient, sparkReference, _localNoID, "return", "pending");
seq.SubmitDate = DateTime.UtcNow;
seq._id = StringUtilities.SHA256(DomainName + Guid.NewGuid().ToString() + NodeSalt);
seq.SessionComputerName = _computerName;
seq.ClinicArea = _clinicArea;
dbwrapper.AddPendingPatient(seq);
context.Response.Write("yes");
}
else
{
context.Response.Write("no");
}
}
else if (_confirmFieldName == "lastname")
{
//TODO: implement lastname, use metaphone or just accept exact matches?
context.Response.Write("Error occurred. " + _confirmFieldName + " is not implemented yet!");
}
else if (_confirmFieldName == "firstname")
{
//TODO: implement firstname, use root or just accept exact matches?
context.Response.Write("Error occurred. " + _confirmFieldName + " is not implemented yet!");
}
else if (_confirmFieldName == "failedchallenge")
{
SessionQueue seq = Utilities.PatientToSessionQueue(pendingPatient, sparkReference, _localNoID, "return**", "pending");
seq.SubmitDate = DateTime.UtcNow;
seq._id = StringUtilities.SHA256(DomainName + Guid.NewGuid().ToString() + NodeSalt);
seq.SessionComputerName = _computerName;
seq.ClinicArea = _clinicArea;
dbwrapper.AddPendingPatient(seq);
context.Response.Write("yes");
}
}
}
catch (Exception ex)
{
context.Response.Write("no. Error occured for LocalNoID = " + _localNoID + ". UpdatePendingStatus::ProcessRequest: " + ex.Message);
}
context.Response.End();
}