/// <summary>
/// Try to deserialize the full resource represented by the specified <see cref="ArtifactSummary"/>.
/// </summary>
/// <param name="info">An <see cref="ArtifactSummary"/> instance.</param>
/// <typeparam name="T">The expected resource type.</typeparam>
/// <returns>A new instance of type <typeparamref name="T"/>, or <c>null</c>.</returns>
private static T getResourceFromScannedSource <T>(ArtifactSummary info)
where T : Resource
{
// File path of the containing resource file (could be a Bundle)
var path = info.Origin;
using (var navStream = DefaultNavigatorStreamFactory.Create(path))
{
// TODO: Handle exceptions & null return values
// e.g. file may have been deleted/renamed since last scan
// Advance stream to the target resource (e.g. specific Bundle entry)
if (navStream != null && navStream.Seek(info.Position))
{
// Create navigator for the target resource
var nav = navStream.Current;
if (nav != null)
{
// Parse target resource from navigator
var parser = new BaseFhirParser();
var result = parser.Parse <T>(nav);
if (result != null)
{
// Add origin annotation
result.SetOrigin(info.Origin);
return(result);
}
}
}
return(null);
}
}
public void TestLoadResourceFromZipStream()
{
// Harvest summaries and load artifact straight from core ZIP archive
// Use XmlNavigatorStream to navigate resources stored inside a zip file
// ZipDeflateStream does not support seeking (forward-only stream)
// Therefore this only works for the XmlNavigatorStream, as the ctor does NOT (need to) call Reset()
// JsonNavigatorStream cannot support zip streams; ctor needs to call Reset after scanning resourceType
ArtifactSummary corePatientSummary;
var corePatientUrl = ModelInfo.CanonicalUriForFhirCoreType(FHIRDefinedType.Patient);
string zipEntryName = "profiles-resources.xml";
// Generate summaries from core ZIP resource definitions (extract in memory)
using (var archive = ZipFile.Open(ZipSource.SpecificationZipFileName, ZipArchiveMode.Read))
{
var entry = archive.Entries.FirstOrDefault(e => e.Name == zipEntryName);
Assert.IsNotNull(entry);
using (var entryStream = entry.Open())
using (var navStream = new XmlNavigatorStream(entryStream))
{
var summaries = ArtifactSummaryGenerator.Default.Generate(navStream);
Assert.IsNotNull(summaries);
corePatientSummary = summaries.FindConformanceResources(corePatientUrl).FirstOrDefault();
}
}
Assert.IsNotNull(corePatientSummary);
Assert.AreEqual(ResourceType.StructureDefinition, corePatientSummary.ResourceType);
Assert.AreEqual(corePatientUrl, corePatientSummary.GetConformanceCanonicalUrl());
// Load core Patient resource from ZIP (extract in memory)
using (var archive = ZipFile.Open(ZipSource.SpecificationZipFileName, ZipArchiveMode.Read))
{
var entry = archive.Entries.FirstOrDefault(e => e.Name == zipEntryName);
using (var entryStream = entry.Open())
using (var navStream = new XmlNavigatorStream(entryStream))
{
var nav = navStream.Current;
if (nav != null)
{
// Parse target resource from navigator
var parser = new BaseFhirParser();
var corePatient = parser.Parse <StructureDefinition>(nav);
Assert.IsNotNull(corePatient);
Assert.AreEqual(corePatientUrl, corePatient.Url);
}
}
}
}
/// <summary>Returns <c>null</c> if the specified <paramref name="summary"/> equals <c>null</c>.</summary>
T loadResourceInternal <T>(ArtifactSummary summary) where T : Resource
{
if (summary == null)
{
return(null);
}
// File path of the containing resource file (could be a Bundle)
var origin = summary.Origin;
if (string.IsNullOrEmpty(origin))
{
throw Error.Argument($"Cannot load resource from summary. The {nameof(ArtifactSummary.Origin)} information is empty or missing.");
}
var pos = summary.Position;
if (string.IsNullOrEmpty(pos))
{
throw Error.Argument($"Cannot load resource from summary. The {nameof(ArtifactSummary.Position)} information is empty or missing.");
}
T result = null;
using (var navStream = DefaultNavigatorStreamFactory.Create(origin))
{
// Handle exceptions & null return values?
// e.g. file may have been deleted/renamed since last scan
// Advance stream to the target resource (e.g. specific Bundle entry)
if (navStream != null && navStream.Seek(pos))
{
// Create navigator for the target resource
var nav = navStream.Current;
if (nav != null)
{
// Parse target resource from navigator
var parser = new BaseFhirParser();
result = parser.Parse <T>(nav);
// Add origin annotation
result?.SetOrigin(origin);
}
}
}
return(result);
}
public FhirClient(HttpClient httpClient, ResourceFormat format)
{
HttpClient = httpClient;
_format = format;
if (format == ResourceFormat.Json)
{
var jsonSerializer = new FhirJsonSerializer();
_serializer = jsonSerializer;
_serialize = (resource, summary) => jsonSerializer.SerializeToString(resource, summary);
var jsonParser = new FhirJsonParser();
_parser = jsonParser;
_deserialize = jsonParser.Parse <Resource>;
_contentType = ContentType.JSON_CONTENT_HEADER;
}
else if (format == ResourceFormat.Xml)
{
var xmlSerializer = new FhirXmlSerializer();
_serializer = xmlSerializer;
_serialize = (resource, summary) => xmlSerializer.SerializeToString(resource, summary);
var xmlParser = new FhirXmlParser();
_parser = xmlParser;
_deserialize = xmlParser.Parse <Resource>;
_contentType = ContentType.XML_CONTENT_HEADER;
}
else
{
throw new InvalidOperationException("Unsupported format.");
}
_mediaType = MediaTypeWithQualityHeaderValue.Parse(_contentType);
SetupAuthenticationAsync(TestApplications.ServiceClient).GetAwaiter().GetResult();
}
private async Task <HttpResponseMessage> Upsert(string resourceType, HttpStatusCode statusCode)
{
try
{
string raw = await Request.Content.ReadAsStringAsync();
BaseFhirParser parser = null;
if (IsContentTypeJSON)
{
parser = jsonparser;
}
else if (IsContentTypeXML)
{
parser = xmlparser;
}
else
{
throw new Exception("Invalid Content-Type must be application/fhir+json or application/fhir+xml");
}
var reader = IsContentTypeJSON ? FhirJsonParser.CreateFhirReader(raw) : FhirXmlParser.CreateFhirReader(raw, false);
var p = (Resource)parser.Parse(reader, FhirHelper.ResourceTypeFromString(resourceType));
ResourceType rt;
Enum.TryParse(resourceType, out rt);
if (p.ResourceType != rt)
{
OperationOutcome oo = new OperationOutcome();
oo.Issue = new System.Collections.Generic.List <OperationOutcome.IssueComponent>();
OperationOutcome.IssueComponent ic = new OperationOutcome.IssueComponent();
ic.Severity = OperationOutcome.IssueSeverity.Error;
ic.Code = OperationOutcome.IssueType.Exception;
ic.Diagnostics = "Resource provide is not of type " + resourceType;
oo.Issue.Add(ic);
var respconf = this.Request.CreateResponse(HttpStatusCode.BadRequest);
respconf.Content = new StringContent(SerializeResponse(oo), Encoding.UTF8, CurrentAcceptType);
return(respconf);
}
//Store resource regardless of type
p = await ProcessSingleResource(p, resourceType, IsMatchVersionId);
var response = this.Request.CreateResponse(statusCode);
response.Headers.Add("Location", Request.RequestUri.AbsoluteUri + "/" + p.Id);
response.Headers.Add("ETag", "W/\"" + p.Meta.VersionId + "\"");
//Extract and Save each Resource in bundle if it's a batch type
if (p.ResourceType == ResourceType.Bundle && ((Bundle)p).Type == Bundle.BundleType.Batch)
{
Bundle source = (Bundle)p;
Bundle results = new Bundle();
results.Id = Guid.NewGuid().ToString();
results.Type = Bundle.BundleType.Searchset;
results.Total = source.Entry.Count();
results.Link = new System.Collections.Generic.List <Bundle.LinkComponent>();
results.Link.Add(new Bundle.LinkComponent()
{
Url = Request.RequestUri.AbsoluteUri, Relation = "original"
});
results.Entry = new System.Collections.Generic.List <Bundle.EntryComponent>();
foreach (Bundle.EntryComponent ec in source.Entry)
{
var rslt = await ProcessSingleResource(ec.Resource, Enum.GetName(typeof(Hl7.Fhir.Model.ResourceType), ec.Resource.ResourceType));
results.Entry.Add(new Bundle.EntryComponent()
{
Resource = rslt
});
}
}
return(response);
}
catch (Exception e)
{
OperationOutcome oo = new OperationOutcome();
oo.Issue = new System.Collections.Generic.List <OperationOutcome.IssueComponent>();
OperationOutcome.IssueComponent ic = new OperationOutcome.IssueComponent();
ic.Severity = OperationOutcome.IssueSeverity.Error;
ic.Code = OperationOutcome.IssueType.Exception;
ic.Diagnostics = e.Message;
oo.Issue.Add(ic);
var response = this.Request.CreateResponse(HttpStatusCode.BadRequest);
response.Content = new StringContent(SerializeResponse(oo), Encoding.UTF8, CurrentAcceptType);
return(response);
}
}
private async Task <HttpResponseMessage> Upsert(string resourceType, string headerid = null)
{
try
{
string raw = await Request.Content.ReadAsStringAsync();
BaseFhirParser parser = null;
if (IsContentTypeJSON)
{
parser = jsonparser;
}
else if (IsContentTypeXML)
{
parser = xmlparser;
}
else
{
throw new Exception("Invalid Content-Type must be application/fhir+json or application/fhir+xml");
}
var reader = IsContentTypeJSON ? FhirJsonParser.CreateFhirReader(raw) : FhirXmlParser.CreateFhirReader(raw, false);
var p = (Resource)parser.Parse(reader, FhirHelper.ResourceTypeFromString(resourceType));
if (p.ResourceType != FhirHelper.GetResourceType(FhirHelper.ValidateResourceType(resourceType)))
{
OperationOutcome oo = new OperationOutcome();
oo.Issue = new System.Collections.Generic.List <OperationOutcome.IssueComponent>();
OperationOutcome.IssueComponent ic = new OperationOutcome.IssueComponent();
ic.Severity = OperationOutcome.IssueSeverity.Error;
ic.Code = OperationOutcome.IssueType.Exception;
ic.Diagnostics = "Resource provided is not of type " + resourceType;
oo.Issue.Add(ic);
var respconf = this.Request.CreateResponse(HttpStatusCode.BadRequest);
respconf.Content = new StringContent(SerializeResponse(oo), Encoding.UTF8);
respconf.Content.Headers.LastModified = DateTimeOffset.Now;
respconf.Headers.TryAddWithoutValidation("Accept", CurrentAcceptType);
respconf.Content.Headers.TryAddWithoutValidation("Content-Type", IsAccceptTypeJSON ? FHIRCONTENTTYPEJSON : FHIRCONTENTTYPEXML);
return(respconf);
}
if (String.IsNullOrEmpty(p.Id) && headerid != null)
{
p.Id = headerid;
}
//Store resource regardless of type
var dbresp = await ProcessSingleResource(p, resourceType, IsMatchVersionId);
p = dbresp.Resource;
var response = this.Request.CreateResponse(dbresp.Response == 1 ? HttpStatusCode.Created : HttpStatusCode.OK);
response.Content = new StringContent("", Encoding.UTF8);
response.Content.Headers.LastModified = p.Meta.LastUpdated;
response.Headers.Add("Location", Request.RequestUri.AbsoluteUri + (headerid == null ? "/" + p.Id :""));
response.Headers.Add("ETag", "W/\"" + p.Meta.VersionId + "\"");
//Extract and Save each Resource in bundle if it's a batch type
if (p.ResourceType == ResourceType.Bundle && (((Bundle)p).Type == Bundle.BundleType.Batch || ((Bundle)p).Type == Bundle.BundleType.Message))
{
Bundle source = (Bundle)p;
/*Bundle results = new Bundle();
* results.Id = Guid.NewGuid().ToString();
* results.Type = Bundle.BundleType.Searchset;
* results.Total = source.Entry.Count();
* results.Link = new System.Collections.Generic.List<Bundle.LinkComponent>();
* results.Link.Add(new Bundle.LinkComponent() { Url = Request.RequestUri.AbsoluteUri, Relation = "original" });
* results.Entry = new System.Collections.Generic.List<Bundle.EntryComponent>();*/
foreach (Bundle.EntryComponent ec in source.Entry)
{
var rslt = await ProcessSingleResource(ec.Resource, Enum.GetName(typeof(Hl7.Fhir.Model.ResourceType), ec.Resource.ResourceType));
//results.Entry.Add(new Bundle.EntryComponent() { Resource = rslt.Resource, FullUrl = FhirHelper.GetFullURL(Request, rslt.Resource) });
}
}
return(response);
}
catch (Exception e)
{
OperationOutcome oo = new OperationOutcome();
oo.Issue = new System.Collections.Generic.List <OperationOutcome.IssueComponent>();
OperationOutcome.IssueComponent ic = new OperationOutcome.IssueComponent();
ic.Severity = OperationOutcome.IssueSeverity.Error;
ic.Code = OperationOutcome.IssueType.Exception;
ic.Diagnostics = e.Message;
oo.Issue.Add(ic);
var response = this.Request.CreateResponse(HttpStatusCode.BadRequest);
response.Headers.TryAddWithoutValidation("Accept", CurrentAcceptType);
response.Content = new StringContent(SerializeResponse(oo), Encoding.UTF8);
response.Content.Headers.TryAddWithoutValidation("Content-Type", IsAccceptTypeJSON ? FHIRCONTENTTYPEJSON : FHIRCONTENTTYPEXML);
response.Content.Headers.LastModified = DateTimeOffset.Now;
return(response);
}
}
