public async Task <ActionResult <IEnumerable <CustomDiagnostic> > > GetDiagnosticsAsync()
{
List <CustomDiagnostic> diagnostics = new List <CustomDiagnostic>();
var filterParams = new SearchParams()
.Where("identifier=UPTValue");
Bundle result = await _client.SearchAsync <DiagnosticReport>(filterParams);
while (result != null)
{
foreach (var item in result.Entry)
{
var diagnosticReceived = (DiagnosticReport)item.Resource;
var customDiagnostic = new CustomDiagnostic
{
Id = diagnosticReceived.Id,
PatientRef = diagnosticReceived.Performer.FirstOrDefault().ToString(),
PractitionerRef = diagnosticReceived.Subject.ToString(),
IssueDate = diagnosticReceived.Issued.Value
};
diagnostics.Add(customDiagnostic);
}
result = _client.Continue(result, PageDirection.Next);
}
return(Ok(diagnostics));
}
public async Task SearchWithCriteria_SyncContinue_SearchReturned()
{
var client = new FhirClient(_endpoint)
{
PreferredFormat = ResourceFormat.Json,
ReturnFullResource = true
};
var result1 = await client.SearchAsync <Patient>(new[] { "family=clark" });
Assert.IsTrue(result1.Entry.Count >= 1);
while (result1 != null)
{
foreach (var e in result1.Entry)
{
Patient p = (Patient)e.Resource;
if (p.Name.Any())
{
Console.WriteLine(
$"NAME: {p.Name[0].Given.FirstOrDefault()} {p.Name[0].Family.FirstOrDefault()}");
}
}
result1 = client.Continue(result1, PageDirection.Next);
}
Console.WriteLine("Test Completed");
}
/// <summary>
/// Executes the specified arguments.
/// </summary>
/// <param name="arguments">The arguments.</param>
/// <returns>System.Int32.</returns>
/// <remarks>N/A</remarks>
public override int Execute(Arguments arguments)
{
// Get us the needed parameters first
//
var url = arguments["url"];
var text = new [] { "name=" + arguments["text"] };
// Query FHIR server for a list of matching patient resources
//
try
{
var client = new FhirClient(url);
var result = client.SearchAsync("Patient", text).Result;
if (result.Entries.Count == 0)
{
Console.WriteLine("Server {0} returned not results for search criteria [{1}]", url, text[0]);
return(1);
}
foreach (var entry in result.Entries)
{
var rid = new ResourceIdentity(entry.Id);
Console.WriteLine("Found patient {0} that matches {1} on {2}", rid.Id, text[0], url);
}
return(0);
}
catch (Exception e)
{
Console.WriteLine(e.Message);
return(1);
}
}
public async Task SearchUsingPostWithCriteria_AsyncContinue_SearchReturned()
{
var client = new FhirClient(_endpointSupportingSearchUsingPost)
{
PreferredFormat = ResourceFormat.Json,
ReturnFullResource = true
};
var result1 = await client.SearchAsync <Patient>(new[] { "family=Chalmers" }, null, 1);
Assert.IsTrue(result1.Entry.Count >= 1);
while (result1 != null)
{
foreach (var e in result1.Entry)
{
Patient p = (Patient)e.Resource;
if (p.Name.Any())
{
Console.WriteLine(
$"NAME: {p.Name[0].Given.FirstOrDefault()} {p.Name[0].Family.FirstOrDefault()}");
}
}
Console.WriteLine("Fetching more results...");
result1 = await client.ContinueAsync(result1);
}
Console.WriteLine("Test Completed");
}
public async Task <ActionResult <IEnumerable <CustomPatient> > > GetPatientsAsync()
{
List <CustomPatient> patientList = new List <CustomPatient>();
var filterParams = new SearchParams()
.Where("identifier=UPTValue");
Bundle result = await _client.SearchAsync <Patient>(filterParams);
while (result != null)
{
foreach (var item in result.Entry)
{
var patientRetrieved = (Patient)item.Resource;
var customPatient = new CustomPatient()
{
Name = patientRetrieved.Name.FirstOrDefault().Family,
FirstNames = patientRetrieved.Name.FirstOrDefault().Given.ToList(),
Id = patientRetrieved.Id
};
patientList.Add(customPatient);
}
result = _client.Continue(result, PageDirection.Next);
}
return(Ok(patientList));
}
protected virtual async Task <Model.Observation> GetObservationFromServerAsync(Model.Identifier identifier)
{
var searchParams = identifier.ToSearchParams();
var result = await _client.SearchAsync <Model.Observation>(searchParams).ConfigureAwait(false);
return(await result.ReadOneFromBundleWithContinuationAsync <Model.Observation>(_client));
}
public override async Task <FhirHealthCheckStatus> CheckHealth(CancellationToken token = default)
{
try
{
while (!token.IsCancellationRequested)
{
SearchParams search = new SearchParams().SetCount(1);
Hl7.Fhir.Model.Bundle result = await _client.SearchAsync <Hl7.Fhir.Model.StructureDefinition>(search);
return(await Task.FromResult(new FhirHealthCheckStatus(string.Empty, 200)));
}
token.ThrowIfCancellationRequested();
return(await Task.FromResult(new FhirHealthCheckStatus(token.ToString(), 500)));
}
catch (FhirOperationException ex)
{
return(await Task.FromResult(new FhirHealthCheckStatus(ex.Message, (int)ex.Status)));
}
catch (IdentityModel.Clients.ActiveDirectory.AdalServiceException ex)
{
return(await Task.FromResult(new FhirHealthCheckStatus(ex.Message, ex.StatusCode)));
}
#pragma warning disable CA1031
catch (Exception ex)
#pragma warning restore CA1031
{
return(await Task.FromResult(new FhirHealthCheckStatus(ex.Message, 500)));
}
}
public async Task Search_UsingSearchParams_SearchReturned()
{
var client = new FhirClient(_endpoint)
{
PreferredFormat = ResourceFormat.Json,
ReturnFullResource = true
};
var srch = new SearchParams()
.Where("name=Daniel")
.LimitTo(10)
.SummaryOnly()
.OrderBy("birthdate",
SortOrder.Descending);
var result1 = await client.SearchAsync <Patient>(srch);
Assert.IsTrue(result1.Entry.Count >= 1);
while (result1 != null)
{
foreach (var e in result1.Entry)
{
Patient p = (Patient)e.Resource;
Console.WriteLine(
$"NAME: {p.Name[0].Given.FirstOrDefault()} {p.Name[0].Family.FirstOrDefault()}");
}
result1 = client.Continue(result1, PageDirection.Next);
}
Console.WriteLine("Test Completed");
}
/// <summary>
/// Get Practitioner by ID
/// </summary>
/// <param name="practitionerId"> ID of practitioner to be fetched </param>
/// <returns> Practitioner </returns>
public static async Task <Models.Practitioner> GetPractitioner(string practitionerId)
{
Models.Practitioner practitioner = null;
Hl7.Fhir.Model.Practitioner fhirPractitioner = null;
try
{
// limit to 1 to avoid huge response Bundle
var PractitionerQuery = new SearchParams()
.Where("identifier=http://hl7.org/fhir/sid/us-npi|" + practitionerId)
.LimitTo(1);
Bundle PractitionerResult = await Client.SearchAsync <Hl7.Fhir.Model.Practitioner>(PractitionerQuery);
if (PractitionerResult.Entry.Count > 0)
{
// Map the FHIR Practitioner object to App's Practitioner object
fhirPractitioner = (Hl7.Fhir.Model.Practitioner)PractitionerResult.Entry[0].Resource;
PractitionerMapper mapper = new PractitionerMapper();
practitioner = mapper.Map(fhirPractitioner);
}
}
catch (FhirOperationException FhirException)
{
System.Diagnostics.Debug.WriteLine("Fhir error message: " + FhirException.Message);
}
catch (Exception GeneralException)
{
System.Diagnostics.Debug.WriteLine("General error message: " + GeneralException.Message);
}
return(practitioner);
}
/// <summary>
/// Gets Patient's hemoglobin observations
/// </summary>
/// <param name="patientId">Patient resource Id</param>
/// <returns>List of hemoglobin observations</returns>
public async Task <List <Observation> > GetHemoglobinObservationsForPatientAsync(string patientId)
{
List <Observation> result = new List <Observation>();
var searchParameters = new SearchParams();
searchParameters.Parameters.Add(new Tuple <string, string>("patient", patientId));
var responsBundle = await _fhirClient.SearchAsync <Observation>(searchParameters).ConfigureAwait(false);
foreach (var entry in responsBundle.Entry)
{
var observation = (Observation)entry.Resource;
if (observation.Code.Coding.Exists(coding => coding.Code == Hemoglobin.CODE))
{
result.Add(observation);
}
}
return(result);
}
public static async Task <IEnumerable <TResource> > SearchWithContinuationAsync <TResource>(this FhirClient fhirClient, SearchParams searchParams)
where TResource : Resource
{
EnsureArg.IsNotNull(fhirClient, nameof(fhirClient));
EnsureArg.IsNotNull(searchParams, nameof(searchParams));
var result = await fhirClient.SearchAsync <TResource>(searchParams).ConfigureAwait(false);
return(await result.ReadFromBundleWithContinuationAsync <TResource>(fhirClient, searchParams.Count).ConfigureAwait(false));
}
protected static async Task <TResource> GetResourceByIdentityAsync <TResource>(FhirClient client, Model.Identifier identifier)
where TResource : Model.Resource, new()
{
EnsureArg.IsNotNull(client, nameof(client));
EnsureArg.IsNotNull(identifier, nameof(identifier));
var searchParams = identifier.ToSearchParams();
var result = await client.SearchAsync <TResource>(searchParams).ConfigureAwait(false);
return(await result.ReadOneFromBundleWithContinuationAsync <TResource>(client));
}
/// <summary>
/// Get Organization by identifier
/// </summary>
/// <param name="identifier"></param>
/// <returns>Organization</returns>
public async Task <Organization> SearchByIdentifierAsync(string identifier)
{
Organization result = null;
var bundle = await _fhirClient.SearchAsync <Organization>(new[] { $"identifier={identifier}" }).ConfigureAwait(false);
if (bundle.Entry.Any())
{
result = (Organization)bundle.Entry.First().Resource;
}
return(result);
}
public void SearchAsync()
{
FhirClient client = new FhirClient(testEndpoint);
Bundle result;
result = client.SearchAsync <DiagnosticReport>().Result;
Assert.IsNotNull(result);
Assert.IsTrue(result.Entry.Count() > 10, "Test should use testdata with more than 10 reports");
result = client.SearchAsync <DiagnosticReport>(pageSize: 10).Result;
Assert.IsNotNull(result);
Assert.IsTrue(result.Entry.Count <= 10);
var withSubject =
result.Entry.ByResourceType <DiagnosticReport>().FirstOrDefault(dr => dr.Resource.Subject != null);
Assert.IsNotNull(withSubject, "Test should use testdata with a report with a subject");
ResourceIdentity ri = new ResourceIdentity(withSubject.Id);
result = client.SearchByIdAsync <DiagnosticReport>(ri.Id,
includes: new string[] { "DiagnosticReport.subject" }).Result;
Assert.IsNotNull(result);
Assert.AreEqual(2, result.Entry.Count); // should have subject too
Assert.IsNotNull(result.Entry.Single(entry => new ResourceIdentity(entry.Id).Collection ==
typeof(DiagnosticReport).GetCollectionName()));
Assert.IsNotNull(result.Entry.Single(entry => new ResourceIdentity(entry.Id).Collection ==
typeof(Patient).GetCollectionName()));
result = client.SearchAsync <Patient>(new string[] { "name=Everywoman", "name=Eve" }).Result;
Assert.IsNotNull(result);
Assert.IsTrue(result.Entry.Count > 0);
}
public async Task <GetPatientList.Model> Handle(GetPatientList.Query request, CancellationToken cancellationToken)
{
var paramsList = new List <string>();
var queryNames = new SearchParams();
if (!string.IsNullOrEmpty(request.FirstName))
{
request.FirstName = request.FirstName?.ToLower();
request.FirstName = request.FirstName?.Trim();
queryNames.Where($"given={request.FirstName}").SummaryOnly(SummaryType.Text);
paramsList.Add($"given:contains={request.FirstName}");
// queryNames.Where($"given={request.FirstName}").SummaryOnly(SummaryType.Count);
//use this for a execute batch but for Medicaions
}
if (!string.IsNullOrEmpty(request.LastName))
{
request.LastName = request.LastName?.ToLower();
request.LastName = request.LastName?.Trim();
queryNames.Where($"family={request.LastName}").SummaryOnly(SummaryType.Text);
//var p = queryNames.ToParameters().;
paramsList.Add($"name:contains={request.LastName}");
}
// var trans = new TransactionBuilder(client.Endpoint);
// trans = trans.Search(q, "MedicationRequest").Search(t, "MedicationStatement");
// //var result = await _client.SearchAsync<MedicationRequest>(q);
// var tResult = _client.TransactionAsync(trans.ToBundle());
// var result =
// PatientList
// .Where(x =>
// x.GivenNames.Select(n=> n.ToLower()).Contains(term) ||
// x.LastName.ToLower().Contains(term)
// )
// .ToList();
//these shpuld be identical
// var pats = await client.SearchAsync<Patient>(paramsList.ToArray(), default, 10/*, SummaryType.Text*/);
var pats = await client.SearchAsync <Patient>(queryNames.LimitTo(10));
return(new GetPatientList.Model()
{
Patients = pats
});
}
private async Task <List <Organization> > GetOrganizationsFromFHIRAsync()
{
List <Organization> organizations = new List <Organization>();
var result = await _client.SearchAsync <Organization>().ConfigureAwait(false);
while (result != null)
{
if (result.Entry != null)
{
foreach (var e in result.Entry)
{
organizations.Add((Organization)e.Resource);
}
}
// get the next page of results
result = _client.Continue(result);
}
return(organizations);
}
public async virtual Task <List <Patient> > Search(string term = null)
{
if (!string.IsNullOrEmpty(term))
{
term = term.ToLower();
term = term.Trim();
// var trans = new TransactionBuilder(client.Endpoint);
// trans = trans.Search(q, "MedicationRequest").Search(t, "MedicationStatement");
// //var result = await _client.SearchAsync<MedicationRequest>(q);
// var tResult = _client.TransactionAsync(trans.ToBundle());
// var result =
// PatientList
// .Where(x =>
// x.GivenNames.Select(n=> n.ToLower()).Contains(term) ||
// x.LastName.ToLower().Contains(term)
// )
// .ToList();
var queryNames = new SearchParams()
.Where($"given={term}")
.Where($"last={term}")
.LimitTo(50);
var searchCall = await client.SearchAsync <Patient>(queryNames);
List <Patient> patients = new List <Patient>();
while (searchCall != null)
{
foreach (var e in searchCall.Entry)
{
Patient p = (Patient)e.Resource;
patients.Add(p);
}
searchCall = client.Continue(searchCall, PageDirection.Next);
}
return(patients);
}
return(PatientList);
}
/// <summary>
/// Get patient's medications
/// </summary>
/// <param name="patientId">Patient id</param>
/// <returns>List of medications</returns>
public async Task <List <Medication> > GetMedicationDataForPatientAsync(string patientId)
{
List <Medication> result;
var searchParameters = new SearchParams();
searchParameters.Parameters.Add(new Tuple <string, string>("patient", patientId));
try
{
// https://fhir.cerner.com/millennium/r4/medications/medication-request/#example
var searchResultResponse = await _client.SearchAsync <MedicationRequest>(searchParameters);
result = searchResultResponse.Entry.AsParallel() // As parallel since we are making network requests
.Select(entry =>
{
var medOrders = _client.Read <MedicationRequest>("MedicationRequest/" + entry.Resource.Id);
var safeCast = (medOrders?.Medication as ResourceReference)?.Reference;
if (string.IsNullOrWhiteSpace(safeCast))
{
return(null);
}
;
return(_client.Read <Medication>(safeCast));
})
.Where(med => med != null).ToList();
}
catch (AggregateException ex)
{
throw ex.Flatten();
}
catch (FhirOperationException)
{
// Error 404 - no medication orders
result = new List <Medication>();
}
return(result);
}
/// <summary>
///
/// </summary>Get Patients page
/// <param name="pageSize">Page size (default 10)</param>
/// <returns>List of Patients</returns>
public async Task <IEnumerable <Patient> > GetPatientsAsync(int pageSize = 10)
{
var result = await _fhirClient.SearchAsync <Patient>(pageSize : pageSize).ConfigureAwait(false);
return(result.Entry.Select(x => (Patient)x.Resource));
}
public void SearchAsync()
{
FhirClient client = new FhirClient(testEndpoint);
Bundle result;
result = client.SearchAsync<DiagnosticReport>().Result;
Assert.IsNotNull(result);
Assert.IsTrue(result.Entry.Count() > 10, "Test should use testdata with more than 10 reports");
result = client.SearchAsync<DiagnosticReport>(pageSize: 10).Result;
Assert.IsNotNull(result);
Assert.IsTrue(result.Entry.Count <= 10);
var withSubject =
result.Entry.ByResourceType<DiagnosticReport>().FirstOrDefault(dr => dr.Resource.Subject != null);
Assert.IsNotNull(withSubject, "Test should use testdata with a report with a subject");
ResourceIdentity ri = new ResourceIdentity(withSubject.Id);
result = client.SearchByIdAsync<DiagnosticReport>(ri.Id,
includes: new string[] { "DiagnosticReport.subject" }).Result;
Assert.IsNotNull(result);
Assert.AreEqual(2, result.Entry.Count); // should have subject too
Assert.IsNotNull(result.Entry.Single(entry => new ResourceIdentity(entry.Id).Collection ==
typeof(DiagnosticReport).GetCollectionName()));
Assert.IsNotNull(result.Entry.Single(entry => new ResourceIdentity(entry.Id).Collection ==
typeof(Patient).GetCollectionName()));
result = client.SearchAsync<Patient>(new string[] { "name=Everywoman", "name=Eve" }).Result;
Assert.IsNotNull(result);
Assert.IsTrue(result.Entry.Count > 0);
}
protected override async Task ExecuteAsync(CancellationToken stoppingToken)
{
var port = config.GetValue <int>("MetricsPort");
var fetchInterval = TimeSpan.FromSeconds(config.GetValue <int>("FetchIntervalSeconds"));
using var server = new MetricServer(port: port);
server.Start();
log.LogInformation(
"FHIR Server Prometheus Exporter running on port {port} for {fhirServerUrl}",
port,
fhirClient.Endpoint);
while (!stoppingToken.IsCancellationRequested)
{
fhirClient.RequestHeaders.Authorization = await authHeaderProvider.GetAuthHeaderAsync(stoppingToken);
using (FetchResourceCountDuration.WithLabels(fhirServerName).NewTimer())
{
foreach (var customMetric in customMetrics)
{
log.LogInformation("Querying custom metric {name} using {query}", customMetric.Name, customMetric.Query);
var resourceTypeAndFilters = customMetric.Query.Split("?");
if (resourceTypeAndFilters.Length < 2)
{
log.LogWarning("Parsing custom metric query string failed. " +
"Should look like: <resourceType>?<name>=<value>&...");
continue;
}
var resourceType = resourceTypeAndFilters[0];
var kv = HttpUtility.ParseQueryString(resourceTypeAndFilters[1]);
var paramList = kv.AllKeys.Select(key => Tuple.Create(key, kv[key]));
var sp = SearchParams.FromUriParamList(paramList);
sp.Summary = SummaryType.Count;
var result = await fhirClient.SearchAsync(sp, resourceType);
if (result.Total.HasValue)
{
customGauges[customMetric.Name]
.WithLabels(resourceType, fhirServerName)
.Set(result.Total.Value);
}
else
{
log.LogWarning("No 'total' returned for {query}", customMetric.Query);
}
}
foreach (var resourceType in resourceTypes)
{
await UpdateResourceCountAsync(resourceType);
}
}
await Task.Delay(fetchInterval, stoppingToken);
}
await server.StopAsync();
}
