/// <summary>
/// Gets back a resource from a xml sample file.
/// </summary>
/// <param name="fileName">The XML filename, omit the extension</param>
public static Resource GetXmlSample(string fileName)
{
var fhirSource = GetXml(fileName);
var parser = new Hl7.Fhir.Serialization.FhirXmlParser();
return(parser.Parse <Resource>(fhirSource));
}
public List <AuDefinition> GetResourceList()
{
List <AuDefinition> AuDefinitionList = new List <AuDefinition>();
HttpClient downloader = new HttpClient();
Stream stream = null;
stream = downloader.GetStreamAsync(definitionUrl).Result;
using (ZipInputStream s = new ZipInputStream(stream))
{
ZipEntry entry;
while ((entry = s.GetNextEntry()) != null)
{
if (entry.Name.EndsWith(".xml", StringComparison.CurrentCultureIgnoreCase))
{
//Console.WriteLine($"Modified: {entry.DateTime.ToShortDateString()} {entry.DateTime.ToShortTimeString()}");
if (entry.IsFile)
{
var buffer = new MemoryStream();
s.CopyTo(buffer);
buffer.Seek(0, SeekOrigin.Begin);
var sr = SerializationUtil.XmlReaderFromStream(buffer);
Resource resource = new Hl7.Fhir.Serialization.FhirXmlParser().Parse <Resource>(sr);
AuDefinition AuDef = new AuDefinition();
AuDef.FileName = entry.Name;
AuDef.FhirId = resource.Id;
AuDef.ResourceType = resource.ResourceType;
AuDef.Resource = resource;
AuDefinitionList.Add(AuDef);
Console.WriteLine("Resource File Name : {0}", entry.Name);
}
}
}
// Close can be ommitted as the using statement will do it automatically
// but leaving it here reminds you that is should be done.
s.Close();
}
return(AuDefinitionList);
}
protected void ParseResponseBody()
{
var tpXml = this.Body;
Patient Patient = null;
if (this.Format == FhirApi.FhirFormat.Xml)
{
var parser = new Hl7.Fhir.Serialization.FhirXmlParser();
Patient = parser.Parse <Patient>(tpXml);
}
else
{
var parser = new Hl7.Fhir.Serialization.FhirJsonParser();
Patient = parser.Parse <Patient>(tpXml);
}
IElementNavigator PocoPatient = new PocoNavigator(Patient);
this.ApiPatient = new ApiPatient(PocoPatient);
}
public PatientFixture()
{
var parser = new Hl7.Fhir.Serialization.FhirXmlParser();
var tpXml = TestData.ReadTextFile("fp-test-patient.xml");
var patient = parser.Parse <Patient>(tpXml);
TestInput = new PocoNavigator(patient);
tpXml = TestData.ReadTextFile("questionnaire-example.xml");
var quest = parser.Parse <Questionnaire>(tpXml);
Questionnaire = new PocoNavigator(quest);
tpXml = TestData.ReadTextFile("uuid.profile.xml");
var uuid = parser.Parse <StructureDefinition>(tpXml);
UuidProfile = new PocoNavigator(uuid);
Xdoc = new XDocument(new XElement("group", new XAttribute("name", "CSharpTests")));
}
protected void ParseResponseBody()
{
var tpXml = this.Body;
Bundle Bundle = null;
if (this.Format == FhirApi.FhirFormat.Xml)
{
var parser = new Hl7.Fhir.Serialization.FhirXmlParser();
Bundle = parser.Parse <Bundle>(tpXml);
}
else
{
var parser = new Hl7.Fhir.Serialization.FhirJsonParser();
Bundle = parser.Parse <Bundle>(tpXml);
}
IElementNavigator PocoBundel = new PocoNavigator(Bundle);
foreach (var RelatedPerson in PocoBundel.Select(@"Bundle.entry.select(resource as RelatedPerson)"))
{
ApiRelatedPerson ApiRelatedPerson = new ApiRelatedPerson(RelatedPerson);
ApiRelatedPersonList.Add(ApiRelatedPerson);
}
}
private Resource DeSerializeFromXml(System.Xml.XmlReader XmlReader)
{
Hl7.Fhir.Serialization.FhirXmlParser FhirXmlParser = new Hl7.Fhir.Serialization.FhirXmlParser();
return(FhirXmlParser.Parse <Resource>(XmlReader));
}
// Process request and craft response.
public override CefReturnValue ProcessRequestAsync(IRequest request, ICallback callback)
{
if (request.Method == "OPTIONS")
{
// This is the CORS request, and that's good
base.StatusCode = 200;
// base.Headers.Add("Access-Control-Allow-Origin", "*");
base.Headers.Add("Access-Control-Allow-Methods", "GET,POST,PUT,OPTIONS");
base.Headers.Add("Access-Control-Allow-Headers", "Content-Type, Accept, authorization");
callback.Continue();
return(CefReturnValue.Continue);
}
var uri = new Uri(request.Url);
Console.WriteLine($"-----------------\r\n{request.Url}");
// Check the bearer header
if (!string.IsNullOrEmpty(_launchContext.Bearer))
{
string bearer = request.GetHeaderByName("authorization");
if (bearer != "Bearer " + _launchContext.Bearer)
{
base.StatusCode = (int)HttpStatusCode.Unauthorized;
callback.Continue();
return(CefReturnValue.Continue);
}
}
try
{
// This is a regular request
Hl7.Fhir.Rest.FhirClient server = new Hl7.Fhir.Rest.FhirClient("http://localhost:4178");
server.OnAfterResponse += (sender, args) =>
{
base.Charset = args.RawResponse.CharacterSet;
foreach (string header in args.RawResponse.Headers.AllKeys)
{
base.Headers.Add(header, args.RawResponse.Headers[header]);
}
};
server.PreferredFormat = Hl7.Fhir.Rest.ResourceFormat.Json;
string redirectedUrl = server.Endpoint.OriginalString.TrimEnd('/') + uri.PathAndQuery;
System.Diagnostics.Trace.WriteLine($"{redirectedUrl}");
var headers = new List <KeyValuePair <string, IEnumerable <string> > >();
ModelBaseInputs <IServiceProvider> requestDetails = new ModelBaseInputs <IServiceProvider>(null, null, request.Method, uri, new Uri($"https://{AuthProtocolSchemeHandlerFactory.FhirFacadeAddress(_launchContext)}"), null, headers, null);
if (request.Method == "GET")
{
if (uri.LocalPath == "/metadata")
{
_facade.GetConformance(requestDetails, Rest.SummaryType.False).ContinueWith <CapabilityStatement>(r =>
{
if (r.Exception != null)
{
System.Diagnostics.Trace.WriteLine($"Error: {r.Exception.Message}");
if (r.Exception.InnerException is Hl7.Fhir.Rest.FhirOperationException fe)
{
base.StatusCode = (int)fe.Status;
if (fe.Outcome != null)
{
base.Stream = new MemoryStream(new Hl7.Fhir.Serialization.FhirJsonSerializer(new Hl7.Fhir.Serialization.SerializerSettings()
{
Pretty = true
}).SerializeToBytes(fe.Outcome));
base.MimeType = "application/fhir+json";
}
callback.Continue();
System.Diagnostics.Trace.WriteLine($"Error (inner): {fe.Message}");
return(null);
}
}
base.StatusCode = 200;
// As per the documentation http://hl7.org/fhir/smart-app-launch/conformance/index.html
CapabilityStatement cs = r.Result;
// Update the security node with our internal security node
if (cs.Rest[0].Security == null)
{
cs.Rest[0].Security = new Hl7.Fhir.Model.CapabilityStatement.SecurityComponent();
}
Hl7.Fhir.Model.CapabilityStatement.SecurityComponent security = cs.Rest[0].Security;
if (!security.Service.Any(cc => cc.Coding.Any(c => c.System == "http://hl7.org/fhir/restful-security-service" && c.Code == "SMART-on-FHIR")))
{
security.Service.Add(new Hl7.Fhir.Model.CodeableConcept("http://hl7.org/fhir/restful-security-service", "SMART-on-FHIR"));
}
var extension = security.GetExtension("http://fhir-registry.smarthealthit.org/StructureDefinition/oauth-uris");
if (extension == null)
{
extension = new Extension()
{
Url = "http://fhir-registry.smarthealthit.org/StructureDefinition/oauth-uris"
};
security.Extension.Add(extension);
}
// remove the existing authentications, and put in our own
extension.Extension.Clear();
extension.AddExtension("token", new FhirUri($"https://{AuthProtocolSchemeHandlerFactory.AuthAddress(_launchContext)}/token"));
extension.AddExtension("authorize", new FhirUri($"https://{AuthProtocolSchemeHandlerFactory.AuthAddress(_launchContext)}/authorize"));
base.Stream = new MemoryStream(new Hl7.Fhir.Serialization.FhirJsonSerializer(new Hl7.Fhir.Serialization.SerializerSettings()
{
Pretty = true
}).SerializeToBytes(r.Result));
Console.WriteLine($"Success: {base.Stream.Length}");
base.MimeType = "application/fhir+json";
callback.Continue();
return(r.Result);
});
return(CefReturnValue.ContinueAsync);
}
if (!uri.LocalPath.StartsWith("/$") && !uri.LocalPath.StartsWith("/_") && uri.LocalPath.Length > 2)
{
// This is not an operation or history, so it must be a resource type
string resourceType = uri.LocalPath.Substring(1);
if (resourceType.Contains("/"))
{
resourceType = resourceType.Substring(0, resourceType.IndexOf("/"));
}
var rs = _facade.GetResourceService(requestDetails, resourceType);
if (rs == null)
{
System.Diagnostics.Trace.WriteLine($"Error: resource type not handled {resourceType}");
base.StatusCode = (int)HttpStatusCode.BadRequest;
// base.Stream = new MemoryStream(new Hl7.Fhir.Serialization.FhirJsonSerializer(new Hl7.Fhir.Serialization.SerializerSettings() { Pretty = true }).SerializeToBytes(fe.Outcome));
// base.MimeType = "application/fhir+json";
callback.Continue();
return(CefReturnValue.Continue);
}
// GET for a specific resource
ResourceIdentity ri = new ResourceIdentity(uri);
if (ri.IsRestResourceIdentity())
{
rs.Get(ri.Id, ri.VersionId, SummaryType.False).ContinueWith(r =>
{
if (r.Exception != null)
{
System.Diagnostics.Trace.WriteLine($"Error: {r.Exception.Message}");
if (r.Exception.InnerException is Hl7.Fhir.Rest.FhirOperationException fe)
{
base.StatusCode = (int)fe.Status;
if (fe.Outcome != null)
{
base.Stream = new MemoryStream(new Hl7.Fhir.Serialization.FhirJsonSerializer(new Hl7.Fhir.Serialization.SerializerSettings()
{
Pretty = true
}).SerializeToBytes(fe.Outcome));
base.MimeType = "application/fhir+json";
}
callback.Continue();
System.Diagnostics.Trace.WriteLine($"Error (inner): {fe.Message}");
return(null);
}
}
if (r.Result.HasAnnotation <HttpStatusCode>())
{
base.StatusCode = (int)r.Result.Annotation <HttpStatusCode>();
}
else
{
base.StatusCode = 200;
}
base.Stream = new MemoryStream(new Hl7.Fhir.Serialization.FhirJsonSerializer(new Hl7.Fhir.Serialization.SerializerSettings()
{
Pretty = true
}).SerializeToBytes(r.Result));
Console.WriteLine($"Success: {base.Stream.Length}");
base.MimeType = "application/fhir+json";
callback.Continue();
return(r.Result);
});
return(CefReturnValue.ContinueAsync);
}
// Search for the resource type
var parameters = TupledParameters(uri, SearchQueryParameterNames);
int?pagesize = GetIntParameter(uri, FhirParameter.COUNT);
var summary = GetSummaryParameter(uri);
rs.Search(parameters, pagesize, summary).ContinueWith(r =>
{
if (r.Exception != null)
{
System.Diagnostics.Trace.WriteLine($"Error: {r.Exception.Message}");
if (r.Exception.InnerException is Hl7.Fhir.Rest.FhirOperationException fe)
{
base.StatusCode = (int)fe.Status;
if (fe.Outcome != null)
{
base.Stream = new MemoryStream(new Hl7.Fhir.Serialization.FhirJsonSerializer(new Hl7.Fhir.Serialization.SerializerSettings()
{
Pretty = true
}).SerializeToBytes(fe.Outcome));
base.MimeType = "application/fhir+json";
}
callback.Continue();
System.Diagnostics.Trace.WriteLine($"Error (inner): {fe.Message}");
return(null);
}
}
if (r.Result.HasAnnotation <HttpStatusCode>())
{
base.StatusCode = (int)r.Result.Annotation <HttpStatusCode>();
}
else
{
base.StatusCode = 200;
}
base.Stream = new MemoryStream(new Hl7.Fhir.Serialization.FhirJsonSerializer(new Hl7.Fhir.Serialization.SerializerSettings()
{
Pretty = true
}).SerializeToBytes(r.Result));
Console.WriteLine($"Success: {base.Stream.Length}");
base.MimeType = "application/fhir+json";
callback.Continue();
return(r.Result);
});
return(CefReturnValue.ContinueAsync);
}
System.Threading.Tasks.Task <Hl7.Fhir.Model.Resource> t = server.GetAsync(redirectedUrl).ContinueWith <Hl7.Fhir.Model.Resource>(r =>
{
if (r.Exception != null)
{
System.Diagnostics.Trace.WriteLine($"Error: {r.Exception.Message}");
if (r.Exception.InnerException is Hl7.Fhir.Rest.FhirOperationException fe)
{
base.StatusCode = (int)fe.Status;
if (fe.Outcome != null)
{
base.Stream = new MemoryStream(new Hl7.Fhir.Serialization.FhirJsonSerializer(new Hl7.Fhir.Serialization.SerializerSettings()
{
Pretty = true
}).SerializeToBytes(fe.Outcome));
base.MimeType = "application/fhir+json";
}
callback.Continue();
System.Diagnostics.Trace.WriteLine($"Error (inner): {fe.Message}");
return(null);
}
}
base.StatusCode = 200;
if (r.Result is Hl7.Fhir.Model.CapabilityStatement cs)
{
// As per the documentation http://hl7.org/fhir/smart-app-launch/conformance/index.html
// Update the security node with our internal security node
if (cs.Rest[0].Security == null)
{
cs.Rest[0].Security = new Hl7.Fhir.Model.CapabilityStatement.SecurityComponent();
}
Hl7.Fhir.Model.CapabilityStatement.SecurityComponent security = cs.Rest[0].Security;
if (!security.Service.Any(cc => cc.Coding.Any(c => c.System == "http://hl7.org/fhir/restful-security-service" && c.Code == "SMART-on-FHIR")))
{
security.Service.Add(new Hl7.Fhir.Model.CodeableConcept("http://hl7.org/fhir/restful-security-service", "SMART-on-FHIR"));
}
var extension = security.GetExtension("http://fhir-registry.smarthealthit.org/StructureDefinition/oauth-uris");
if (extension == null)
{
extension = new Extension()
{
Url = "http://fhir-registry.smarthealthit.org/StructureDefinition/oauth-uris"
};
security.Extension.Add(extension);
}
// remove the existing authentications, and put in our own
extension.Extension.Clear();
extension.AddExtension("token", new FhirUri($"https://{AuthProtocolSchemeHandlerFactory.AuthAddress(_launchContext)}/token"));
extension.AddExtension("authorize", new FhirUri($"https://{AuthProtocolSchemeHandlerFactory.AuthAddress(_launchContext)}/authorize"));
}
base.Stream = new MemoryStream(new Hl7.Fhir.Serialization.FhirJsonSerializer(new Hl7.Fhir.Serialization.SerializerSettings()
{
Pretty = true
}).SerializeToBytes(r.Result));
Console.WriteLine($"Success: {base.Stream.Length}");
base.MimeType = "application/fhir+json";
callback.Continue();
return(r.Result);
});
}
if (request.Method == "POST")
{
if (uri.LocalPath == "/")
{
Bundle b = null;
if (request.PostData != null)
{
var data = request.PostData.Elements.FirstOrDefault();
var body = data.GetBody();
if (request.GetHeaderByName("Content-Type").Contains("xml"))
{
b = new Hl7.Fhir.Serialization.FhirXmlParser().Parse <Bundle>(body);
}
else
{
b = new Hl7.Fhir.Serialization.FhirJsonParser().Parse <Bundle>(body);
}
}
_facade.ProcessBatch(requestDetails, b).ContinueWith(r =>
{
if (r.Exception != null)
{
System.Diagnostics.Trace.WriteLine($"Error: {r.Exception.Message}");
if (r.Exception.InnerException is Hl7.Fhir.Rest.FhirOperationException fe)
{
base.StatusCode = (int)fe.Status;
if (fe.Outcome != null)
{
base.Stream = new MemoryStream(new Hl7.Fhir.Serialization.FhirJsonSerializer(new Hl7.Fhir.Serialization.SerializerSettings()
{
Pretty = true
}).SerializeToBytes(fe.Outcome));
base.MimeType = "application/fhir+json";
}
callback.Continue();
System.Diagnostics.Trace.WriteLine($"Error (inner): {fe.Message}");
return(null);
}
}
if (r.Result.HasAnnotation <HttpStatusCode>())
{
base.StatusCode = (int)r.Result.Annotation <HttpStatusCode>();
}
else
{
base.StatusCode = 200;
}
base.Stream = new MemoryStream(new Hl7.Fhir.Serialization.FhirJsonSerializer(new Hl7.Fhir.Serialization.SerializerSettings()
{
Pretty = true
}).SerializeToBytes(r.Result));
Console.WriteLine($"Success: {base.Stream.Length}");
base.MimeType = "application/fhir+json";
callback.Continue();
return(r.Result);
});
return(CefReturnValue.ContinueAsync);
}
System.Net.Http.HttpClient client = new System.Net.Http.HttpClient();
client.DefaultRequestHeaders.Add("Accept", request.GetHeaderByName("Accept"));
// client.DefaultRequestHeaders.Add("Content-Type", request.GetHeaderByName("Content-Type"));
HttpContent content = null;
if (request.PostData != null)
{
var data = request.PostData.Elements.FirstOrDefault();
var body = data.GetBody();
content = new System.Net.Http.StringContent(body, System.Text.Encoding.UTF8, request.GetHeaderByName("Content-Type"));
}
else
{
content = new System.Net.Http.StreamContent(null);
}
client.PostAsync(redirectedUrl, content).ContinueWith((System.Threading.Tasks.Task <HttpResponseMessage> r) =>
{
if (r.Exception != null)
{
Console.WriteLine($"Error: {r.Exception.Message}");
//if (r.Exception.InnerException is Hl7.Fhir.Rest.FhirOperationException fe)
//{
// base.StatusCode = (int)fe.Status;
// if (fe.Outcome != null)
// base.Stream = new MemoryStream(r.Result.Content.ReadAsStringAsync().GetAwaiter().GetResult());
// callback.Continue();
// System.Diagnostics.Trace.WriteLine($"Error (inner): {fe.Message}");
// return;
//}
}
base.StatusCode = (int)r.Result.StatusCode;
base.Stream = r.Result.Content.ReadAsStreamAsync().GetAwaiter().GetResult();
Console.WriteLine($"Success: {base.Stream.Length}");
base.MimeType = r.Result.Content.Headers.ContentType.MediaType;
callback.Continue();
return;
});
}
if (request.Method == "PUT")
{
System.Net.Http.HttpClient client = new System.Net.Http.HttpClient();
client.DefaultRequestHeaders.Add("Accept", request.GetHeaderByName("Accept"));
// client.DefaultRequestHeaders.Add("Content-Type", request.GetHeaderByName("Content-Type"));
HttpContent content = null;
if (request.PostData != null)
{
var data = request.PostData.Elements.FirstOrDefault();
var body = data.GetBody();
content = new System.Net.Http.StringContent(body, System.Text.Encoding.UTF8, request.GetHeaderByName("Content-Type"));
}
else
{
content = new System.Net.Http.StreamContent(null);
}
client.PutAsync(redirectedUrl, content).ContinueWith((System.Threading.Tasks.Task <HttpResponseMessage> r) =>
{
if (r.Exception != null)
{
Console.WriteLine($"Error: {r.Exception.Message}");
//if (r.Exception.InnerException is Hl7.Fhir.Rest.FhirOperationException fe)
//{
// base.StatusCode = (int)fe.Status;
// if (fe.Outcome != null)
// base.Stream = new MemoryStream(r.Result.Content.ReadAsStringAsync().GetAwaiter().GetResult());
// callback.Continue();
// System.Diagnostics.Trace.WriteLine($"Error (inner): {fe.Message}");
// return;
//}
}
base.StatusCode = (int)r.Result.StatusCode;
base.Stream = r.Result.Content.ReadAsStreamAsync().GetAwaiter().GetResult();
Console.WriteLine($"Success: {base.Stream.Length}");
base.MimeType = r.Result.Content.Headers.ContentType.MediaType;
callback.Continue();
return;
});
}
return(CefReturnValue.ContinueAsync);
}
catch (Exception ex)
{
Console.WriteLine($"{ex.Message}");
callback.Dispose();
return(CefReturnValue.Cancel);
}
}
/// <summary>
/// Process the specified excel file into a dataset file
/// </summary>
private static void Main(string[] args)
{
try
{
Console.WriteLine("SanteDB Vocabulary Importer v{0} ({1})", Assembly.GetEntryAssembly().GetName().Version, Assembly.GetEntryAssembly().GetCustomAttribute <AssemblyInformationalVersionAttribute>().InformationalVersion);
Console.WriteLine("Copyright (C) 2015-2022 See NOTICE for contributors");
var parms = new ParameterParser <ConsoleParameters>().Parse(args);
Dataset retVal = new Dataset()
{
Id = parms.Name ?? "Imported Dataset",
Action = new List <DataInstallAction>()
};
// Process a FHIR
if (parms.Fhir || parms.Csv)
{
if (!File.Exists(parms.SourceFile))
{
throw new FileNotFoundException($"{parms.SourceFile} not found");
}
if (parms.Fhir)
{
using (var fhirFileStream = File.OpenRead(parms.SourceFile))
{
using (var xreader = XmlReader.Create(fhirFileStream))
{
var fsz = new Hl7.Fhir.Serialization.FhirXmlParser();
var cs = fsz.Parse <Hl7.Fhir.Model.CodeSystem>(xreader);
retVal.Id = $"Import FHIR Code System {cs.Id}";
var csId = Guid.NewGuid();
retVal.Action.Add(new DataUpdate()
{
InsertIfNotExists = true,
Element = new CodeSystem()
{
Key = csId,
Authority = CamelCase(cs.Name),
Url = cs.Url,
Oid = cs.Identifier.First(i => i.System == "urn:ietf:rfc:3986").Value,
VersionText = cs.Version,
Name = cs.Title
}
});
if (parms.CreateConcept)
{
var setId = Guid.NewGuid();
retVal.Action.Add(new DataUpdate()
{
InsertIfNotExists = true,
Element = new ConceptSet()
{
Key = setId,
Name = cs.Name,
Mnemonic = CamelCase(cs.Name),
Url = cs.Url,
Oid = cs.Identifier.First(i => i.System == "urn:ietf:rfc:3986").Value
}
});
retVal.Action.AddRange(cs.Concept.SelectMany(o => ConvertToReferenceTerm(o, csId, setId, cs.Name)));
}
else
{
retVal.Action.AddRange(cs.Concept.SelectMany(o => ConvertToReferenceTerm(o, csId, null, null)));
}
}
}
}
else if (parms.Csv)
{
// Open excel file stream
using (var excelFileStream = File.OpenRead(parms.SourceFile))
{
using (var importWkb = new XLWorkbook(excelFileStream, new LoadOptions()
{
RecalculateAllFormulas = false
}))
{
retVal.Action = importWkb.Worksheets.SelectMany(o => o.Rows()).SelectMany(o => CreateReferenceTermInstruction(o, parms)).ToList();
}
}
}
if (parms.CreateConcept)
{
retVal.Action.Add(new DataUpdate()
{
InsertIfNotExists = true,
Element = new ConceptSet()
{
ConceptsXml = retVal.Action.Where(o => o.Element is Concept).Select(o => o.Element.Key.Value).ToList(),
Mnemonic = parms.Prefix,
Name = "A new Code System",
Oid = ""
}
});
}
if (parms.OutputFile == "-")
{
new XmlSerializer(typeof(Dataset)).Serialize(Console.Out, retVal);
}
else
{
using (var fs = File.Create(parms.OutputFile))
{
new XmlSerializer(typeof(Dataset)).Serialize(fs, retVal);
}
}
}
else
{
new ParameterParser <ConsoleParameters>().WriteHelp(Console.Out);
}
}
catch (Exception e)
{
Console.Error.WriteLine("Error processing file: {0}", e);
}
}
