public override Task <object> ReadFromStreamAsync(Type type, Stream readStream, HttpContent content, IFormatterLogger formatterLogger)
{
return(Task.Factory.StartNew(() =>
{
MemoryStream stream = new MemoryStream();
readStream.CopyTo(stream);
IEnumerable <string> xContentHeader;
var success = content.Headers.TryGetValues("X-Content-Type", out xContentHeader);
if (!success)
{
throw new SparkException(System.Net.HttpStatusCode.BadRequest, "POST to binary must provide a Content-Type header");
}
string contentType = xContentHeader.FirstOrDefault();
Binary binary = new Binary();
binary.Content = stream.ToArray();
binary.ContentType = contentType;
ResourceEntry entry = ResourceEntry.Create(binary);
entry.Tags = content.Headers.GetFhirTags();
return (object)entry;
}));
}
internal static ResourceEntry CreateResourceEntryFromResource(Resource resource,
string location, string category = null, string lastModified = null)
{
ResourceEntry result = ResourceEntry.Create(resource);
if (!String.IsNullOrEmpty(location))
{
ResourceIdentity reqId = new ResourceIdentity(location);
result.Id = reqId.WithoutVersion();
if (reqId.VersionId != null)
{
result.SelfLink = reqId;
}
}
if (!String.IsNullOrEmpty(lastModified))
{
result.LastUpdated = DateTimeOffset.Parse(lastModified);
}
if (!String.IsNullOrEmpty(category))
{
result.Tags = ParseCategoryHeader(category);
}
result.Title = "A " + resource.GetType().Name + " resource";
return(result);
}
public override Task <object> ReadFromStreamAsync(Type type, Stream readStream, HttpContent content, IFormatterLogger formatterLogger)
{
return(Task.Factory.StartNew <object>(() =>
{
try
{
var body = base.ReadBodyFromStream(readStream, content);
if (type == typeof(ResourceEntry))
{
Resource resource = FhirParser.ParseResourceFromJson(body);
ResourceEntry entry = ResourceEntry.Create(resource);
entry.Tags = content.Headers.GetFhirTags();
return entry;
}
else if (type == typeof(Bundle))
{
return FhirParser.ParseBundleFromJson(body);
}
else if (type == typeof(TagList))
{
return FhirParser.ParseTagListFromJson(body);
}
else
{
throw new NotSupportedException(String.Format("Cannot read unsupported type {0} from body", type.Name));
}
}
catch (FormatException exc)
{
throw new SparkException(HttpStatusCode.BadRequest, "Body parsing failed: " + exc.Message);
}
}));
}
public static ResourceEntry SingleResourceResponse(string body, byte[] data, string contentType,
string requestUri = null, string location = null,
string category = null, string lastModified = null)
{
Resource resource = null;
if (body != null)
{
resource = parseBody <Resource>(body, contentType,
(b, e) => FhirParser.ParseResourceFromXml(b, e),
(b, e) => FhirParser.ParseResourceFromJson(b, e));
}
else
{
resource = Util.MakeBinary(data, contentType);
}
ResourceEntry result = ResourceEntry.Create(resource);
string versionIdInRequestUri = null;
if (!String.IsNullOrEmpty(requestUri))
{
ResourceLocation reqLoc = new ResourceLocation(requestUri);
versionIdInRequestUri = reqLoc.VersionId;
ResourceLocation idLoc = new ResourceLocation(reqLoc.ServiceUri);
idLoc.Collection = reqLoc.Collection;
idLoc.Id = reqLoc.Id;
result.Id = idLoc.ToUri();
}
if (!String.IsNullOrEmpty(location))
{
result.SelfLink = new Uri(location, UriKind.Absolute);
}
else
{
// Try to get the SelfLink from the requestUri (might contain specific version id)
if (!String.IsNullOrEmpty(versionIdInRequestUri))
{
var rl = new ResourceLocation(result.Id);
rl.VersionId = versionIdInRequestUri;
result.SelfLink = rl.ToUri();
}
}
if (!String.IsNullOrEmpty(lastModified))
{
result.LastUpdated = DateTimeOffset.Parse(lastModified);
}
if (!String.IsNullOrEmpty(category))
{
result.Tags = ParseCategoryHeader(category);
}
result.Title = "A " + resource.GetType().Name + " resource";
return(result);
}
public static Bundle Bundle()
{
Bundle bundle = new Bundle();
Patient p = Test.Patient();
BundleEntry entry = ResourceEntry.Create(p);
bundle.Entries.Add(entry);
return(bundle);
}
internal static ResourceEntry CreateFromResource(Resource resource, Uri id, DateTimeOffset updated, string title = null)
{
var result = ResourceEntry.Create(resource);
initializeResourceEntry(result, id, updated, title);
result.Resource = resource;
return(result);
}
public static ResourceEntry CreateResourceEntryFromId(Uri id)
{
// Figure out the resource type from the id
ResourceIdentity rid = new ResourceIdentity(id);
if (rid.Collection != null)
{
var inspector = SerializationConfig.Inspector;
var classMapping = inspector.FindClassMappingForResource(rid.Collection);
return(ResourceEntry.Create(classMapping.NativeType));
}
else
{
throw Error.Format("BundleEntry's id '{0}' does not specify the type of resource: cannot determine Resource type in parser.", null, id.ToString());
}
}
private ResourceEntry createResourceEntry(string resourceType)
{
Resource resource = null;
if (resourceType == "Binary")
{
resource = makeBinary(Body, ContentType);
}
else
{
resource = parseBody <Resource>(BodyAsString(), ContentType,
b => FhirParser.ParseResourceFromXml(b),
b => FhirParser.ParseResourceFromJson(b));
}
ResourceEntry result = ResourceEntry.Create(resource);
var location = Location ?? ContentLocation ?? ResponseUri.OriginalString;
if (!String.IsNullOrEmpty(location))
{
ResourceIdentity reqId = new ResourceIdentity(location);
// Set the id to the location, without the version specific part
result.Id = reqId.WithoutVersion();
// If the content location has version information, set to SelfLink to it
if (reqId.VersionId != null)
{
result.SelfLink = reqId;
}
}
if (!String.IsNullOrEmpty(LastModified))
{
result.LastUpdated = DateTimeOffset.Parse(LastModified);
}
if (!String.IsNullOrEmpty(Category))
{
result.Tags = HttpUtil.ParseCategoryHeader(Category);
}
result.Title = "A " + resource.GetType().Name + " resource";
return(result);
}
/// <summary>
/// Reinitializes the (database of) the server to its initial state
/// </summary>
/// <returns></returns>
/// <remarks>Quite a destructive operation, mostly useful in debugging situations</remarks>
public OperationOutcome Initialize()
{
//Note: also clears the counters collection, so id generation starts anew and
//clears all stored binaries at Amazon S3.
Stopwatch w = new Stopwatch();
w.Start();
_store.Clean();
//_store.EraseData();
//_store.EnsureIndices();
_index.Clean();
w.Stop();
long cleaning = w.ElapsedMilliseconds;
//Insert our own conformance statement into Conformance collection
ResourceEntry conformanceentry = ResourceEntry.Create(ConformanceBuilder.Build());
_service.Create(ConformanceBuilder.CONFORMANCE_COLLECTION_NAME, conformanceentry, ConformanceBuilder.CONFORMANCE_ID);
//Insert standard examples
w.Restart();
var examples = loadExamples();
var count = examples.Entries.OfType <Condition>().Count();
w.Stop();
long loadex = w.ElapsedMilliseconds;
w.Restart();
_service.Transaction(examples);
w.Stop();
var batch = w.ElapsedMilliseconds;
//Start numbering new resources at an id higher than the examples (we hope)
//EK: I like the convention of examples having id <10000, and new records >10.000, so please retain
_store.EnsureNextSequenceNumberHigherThan(9999);
string message = String.Format("Database was succesfully re-initialized: cleaning {0}, examples {1}, storage {2} ms", cleaning, loadex, batch);
return(new OperationOutcome().Message(message));
}
private static void AddTaggedPatient()
{
IFhirStore store = Spark.Store.MongoStoreFactory.GetMongoFhirStore();
var patient = new Patient();
patient.Id = "Patient/tagged";
patient.Name = new List <HumanName>();
patient.Name.Add(new HumanName()
{
Given = new string[] { "Truus" }, Family = new string[] { "Tagged" }
});
ResourceEntry patientRE = ResourceEntry.Create(patient);
patientRE.Id = new Uri("Patient/tagged", UriKind.Relative);
patientRE.SelfLink = new Uri("Patient/tagged", UriKind.Relative);
patientRE.Tags.Add(new Tag(_otherTag, Tag.FHIRTAGSCHEME_GENERAL, "dummy"));
store.Add(patientRE);
index.Process(patientRE);
}
public override Task <object> ReadFromStreamAsync(Type type, Stream readStream, HttpContent content, IFormatterLogger formatterLogger)
{
return(Task.Factory.StartNew <object>(() =>
{
try
{
var body = base.ReadBodyFromStream(readStream, content);
if (type == typeof(Profile))
{
Profile resource = (Profile)FhirParser.ParseResourceFromXml(body);
return resource;
}
else if (type == typeof(ResourceEntry))
{
Resource resource = FhirParser.ParseResourceFromXml(body);
ResourceEntry entry = ResourceEntry.Create(resource);
return entry;
}
else if (type == typeof(Bundle))
{
if (XmlSignatureHelper.IsSigned(body))
{
if (!XmlSignatureHelper.VerifySignature(body))
{
throw new Exception("Digital signature in body failed verification");
}
}
return FhirParser.ParseBundleFromXml(body);
}
else
{
throw new NotSupportedException(String.Format("Cannot read unsupported type {0} from body", type.Name));
}
}
catch (FormatException exc)
{
throw new Exception("Body parsing failed: " + exc.Message);
}
}));
}
/// <summary>
/// Reinitializes the (database of) the server to its initial state
/// </summary>
/// <returns></returns>
/// <remarks>Quite a destructive operation, mostly useful in debugging situations</remarks>
public string Initialize(bool extract)
{
//Note: also clears the counters collection, so id generation starts anew and
//clears all stored binaries at Amazon S3.
var stopwatch = new Stopwatch();
stopwatch.Start();
store.Clean();
index.Clean();
stopwatch.Stop();
double time_cleaning = stopwatch.Elapsed.Seconds;
//Insert our own conformance statement into Conformance collection
ResourceEntry conformanceentry = ResourceEntry.Create(ConformanceBuilder.Build());
service.Upsert(conformanceentry, ConformanceBuilder.CONFORMANCE_COLLECTION_NAME, ConformanceBuilder.CONFORMANCE_ID);
//Insert standard examples
stopwatch.Restart();
var examples = loadExamples(extract);
stopwatch.Stop();
double time_loading = stopwatch.Elapsed.Seconds;
stopwatch.Restart();
service.Transaction(examples);
stopwatch.Stop();
double time_storing = stopwatch.Elapsed.Seconds;
//Start numbering new resources at an id higher than the examples (we hope)
//EK: I like the convention of examples having id <10000, and new records >10.000, so please retain
//_store.EnsureNextSequenceNumberHigherThan(9999);
string message = String.Format(
"Database was succesfully re-initialized. \nTime spent:" +
"\nCleaning: {0}sec \nLoading examples: {1}sec, \nStoring: {2}sec",
time_cleaning, time_loading, time_storing);
return(message);
}
private void importResource(string filename, Resource resource)
{
Match match = Regex.Match(filename, @"\w+\(([^\)]+)\)\..*");
string id = null;
if (match.Success)
{
id = match.Groups[1].Value;
}
if (id == null)
{
id = Guid.NewGuid().ToString();
}
System.Console.Out.WriteLine(filename + " is a single resource with id " + id);
ResourceEntry newEntry = ResourceEntry.Create(resource);
string collection = resource.GetCollectionName();
// klopt het dat hier een hl7.org uri voor moet?
Uri identity = ResourceIdentity.Build(new Uri("http://hl7.org/fhir"), collection, id);
newEntry.Resource = resource;
newEntry.AuthorName = "(imported from file)";
newEntry.Id = identity;
identity = ResourceIdentity.Build(new Uri("http://hl7.org/fhir"), collection, id, "1");
// identity.VersionId = "1";
newEntry.Links.SelfLink = identity;
newEntry.LastUpdated = File.GetLastWriteTimeUtc(filename);
newEntry.Published = File.GetCreationTimeUtc(filename);
newEntry.Title = String.Format("{0} with id {1}", collection, id);
add(newEntry);
}
private void importResource(string filename, Resource resource)
{
System.Console.Out.WriteLine(filename + " is a single resource form filename: " + filename);
ResourceEntry newEntry = ResourceEntry.Create(resource);
newEntry.Resource = resource;
newEntry.AuthorName = "(imported from file)";
Match match = Regex.Match(filename, @"\w+\(([^\)]+)\)\..*");
string name = match.Groups[1].Value;
string id = (match.Success) ? match.Groups[1].Value : null;
string collection = resource.GetCollectionName();
if (id != null)
{
Uri identity = ResourceIdentity.Build(hl7base, collection, id);
newEntry.Id = identity;
newEntry.Title = String.Format("{0} with id {1}", collection, id);
}
else
{
newEntry.Title = String.Format("{0} from file {1}", collection, filename);
}
//identity = ResourceIdentity.Build(new Uri("http://hl7.org/fhir"), collection, id, "1");
// identity.VersionId = "1";
//newEntry.Links.SelfLink = identity;
//newEntry.LastUpdated = File.GetLastWriteTimeUtc(filename);
newEntry.Published = File.GetCreationTimeUtc(filename);
add(newEntry);
}
private static BundleEntry loadEntry(XElement entry, ErrorList errors)
{
BundleEntry result;
errors.DefaultContext = "An atom entry";
try
{
if (entry.Name == XTOMBSTONE + XATOM_DELETED_ENTRY)
{
result = new DeletedEntry();
result.Id = Util.UriValueOrNull(entry.Attribute(XATOM_DELETED_REF));
if (result.Id != null)
{
errors.DefaultContext = String.Format("Entry '{0}'", result.Id.ToString());
}
}
else
{
XElement content = entry.Element(XATOMNS + XATOM_CONTENT);
var id = Util.UriValueOrNull(entry.Element(XATOMNS + XATOM_ID));
if (id != null)
{
errors.DefaultContext = String.Format("Entry '{0}'", id.ToString());
}
if (content != null)
{
var parsed = getContents(content, errors);
if (parsed != null)
{
result = ResourceEntry.Create(parsed);
}
else
{
return(null);
}
}
else
{
throw new InvalidOperationException("BundleEntry has empty content: cannot determine Resource type in parser.");
}
result.Id = id;
}
result.Links = getLinks(entry.Elements(XATOMNS + XATOM_LINK));
result.Tags = TagListParser.ParseTags(entry.Elements(XATOMNS + XATOM_CATEGORY));
if (result is DeletedEntry)
{
((DeletedEntry)result).When = Util.InstantOrNull(entry.Attribute(XATOM_DELETED_WHEN));
}
else
{
ResourceEntry re = (ResourceEntry)result;
re.Title = Util.StringValueOrNull(entry.Element(XATOMNS + XATOM_TITLE));
re.LastUpdated = Util.InstantOrNull(entry.Element(XATOMNS + XATOM_UPDATED));
re.Published = Util.InstantOrNull(entry.Element(XATOMNS + XATOM_PUBLISHED));
re.AuthorName = entry.Elements(XATOMNS + XATOM_AUTHOR).Count() == 0 ? null :
Util.StringValueOrNull(entry.Element(XATOMNS + XATOM_AUTHOR)
.Element(XATOMNS + XATOM_AUTH_NAME));
re.AuthorUri = entry.Elements(XATOMNS + XATOM_AUTHOR).Count() == 0 ? null :
Util.StringValueOrNull(entry.Element(XATOMNS + XATOM_AUTHOR)
.Element(XATOMNS + XATOM_AUTH_URI));
}
}
catch (Exception exc)
{
errors.Add("Exception while reading entry: " + exc.Message);
return(null);
}
finally
{
errors.DefaultContext = null;
}
return(result);
}
private static BundleEntry loadEntry(XElement entry)
{
BundleEntry result;
try
{
if (entry.Name == XTOMBSTONE + XATOM_DELETED_ENTRY)
{
result = new DeletedEntry();
result.Id = SerializationUtil.UriValueOrNull(entry.Attribute(XATOM_DELETED_REF));
}
else
{
XElement content = entry.Element(XATOMNS + XATOM_CONTENT);
var id = SerializationUtil.UriValueOrNull(entry.Element(XATOMNS + XATOM_ID));
if (content != null)
{
var parsed = getContents(content);
if (parsed != null)
{
result = ResourceEntry.Create(parsed);
}
else
{
throw Error.Format("BundleEntry has a content element without content", XmlDomFhirReader.GetLineInfo(content));
}
}
else
{
result = SerializationUtil.CreateResourceEntryFromId(id);
}
result.Id = id;
}
result.Links = getLinks(entry.Elements(XATOMNS + XATOM_LINK));
result.Tags = TagListParser.ParseTags(entry.Elements(XATOMNS + XATOM_CATEGORY));
if (result is DeletedEntry)
{
((DeletedEntry)result).When = SerializationUtil.InstantOrNull(entry.Attribute(XATOM_DELETED_WHEN));
}
else
{
ResourceEntry re = (ResourceEntry)result;
re.Title = SerializationUtil.StringValueOrNull(entry.Element(XATOMNS + XATOM_TITLE));
re.LastUpdated = SerializationUtil.InstantOrNull(entry.Element(XATOMNS + XATOM_UPDATED));
re.Published = SerializationUtil.InstantOrNull(entry.Element(XATOMNS + XATOM_PUBLISHED));
re.AuthorName = entry.Elements(XATOMNS + XATOM_AUTHOR).Count() == 0 ? null :
SerializationUtil.StringValueOrNull(entry.Element(XATOMNS + XATOM_AUTHOR)
.Element(XATOMNS + XATOM_AUTH_NAME));
re.AuthorUri = entry.Elements(XATOMNS + XATOM_AUTHOR).Count() == 0 ? null :
SerializationUtil.StringValueOrNull(entry.Element(XATOMNS + XATOM_AUTHOR)
.Element(XATOMNS + XATOM_AUTH_URI));
}
}
catch (Exception exc)
{
throw Error.Format("Exception while reading entry: " + exc.Message, XmlDomFhirReader.GetLineInfo(entry));
}
return(result);
}
private static BundleEntry loadEntry(JToken entry, ErrorList errors)
{
BundleEntry result;
errors.DefaultContext = "An atom entry";
try
{
if (entry.Value <DateTimeOffset?>(JATOM_DELETED) != null)
{
result = new DeletedEntry();
}
else
{
var content = entry[BundleXmlParser.XATOM_CONTENT];
if (content != null)
{
var parsed = getContents(content, errors);
if (parsed != null)
{
result = ResourceEntry.Create(parsed);
}
else
{
return(null);
}
}
else
{
throw new InvalidOperationException("BundleEntry has empty content: cannot determine Resource type in parser");
}
}
result.Id = Util.UriValueOrNull(entry[BundleXmlParser.XATOM_ID]);
if (result.Id != null)
{
errors.DefaultContext = String.Format("Entry '{0}'", result.Id.ToString());
}
result.Links = getLinks(entry[BundleXmlParser.XATOM_LINK]);
result.Tags = TagListParser.ParseTags(entry[BundleXmlParser.XATOM_CATEGORY]);
if (result is DeletedEntry)
{
((DeletedEntry)result).When = instantOrNull(entry[JATOM_DELETED]);
}
else
{
var re = (ResourceEntry)result;
re.Title = entry.Value <string>(BundleXmlParser.XATOM_TITLE);
re.LastUpdated = instantOrNull(entry[BundleXmlParser.XATOM_UPDATED]);
re.Published = instantOrNull(entry[BundleXmlParser.XATOM_PUBLISHED]);
re.AuthorName = entry[BundleXmlParser.XATOM_AUTHOR] as JArray != null ?
entry[BundleXmlParser.XATOM_AUTHOR]
.Select(auth => auth.Value <string>(BundleXmlParser.XATOM_AUTH_NAME))
.FirstOrDefault() : null;
re.AuthorUri = entry[BundleXmlParser.XATOM_AUTHOR] as JArray != null ?
entry[BundleXmlParser.XATOM_AUTHOR]
.Select(auth => auth.Value <string>(BundleXmlParser.XATOM_AUTH_URI))
.FirstOrDefault() : null;
}
}
catch (Exception exc)
{
errors.Add("Exception while reading entry: " + exc.Message);
return(null);
}
finally
{
errors.DefaultContext = null;
}
return(result);
}
private static BundleEntry loadEntry(JObject entry)
{
BundleEntry result;
try
{
if (entry[JATOM_DELETED] != null)
{
result = new DeletedEntry();
result.Id = SerializationUtil.UriValueOrNull(entry[BundleXmlParser.XATOM_ID]);
}
else
{
var content = entry[BundleXmlParser.XATOM_CONTENT];
var id = SerializationUtil.UriValueOrNull(entry[BundleXmlParser.XATOM_ID]);
if (id == null)
{
throw Error.Format("BundleEntry found without an id", null);
}
if (content != null)
{
var parsed = getContents(content);
if (parsed != null)
{
result = ResourceEntry.Create(parsed);
}
else
{
throw Error.Format("BundleEntry {0} has a content element without content", null, id);
}
}
else
{
result = SerializationUtil.CreateResourceEntryFromId(id);
}
result.Id = id;
}
result.Links = getLinks(entry[BundleXmlParser.XATOM_LINK]);
result.Tags = TagListParser.ParseTags(entry[BundleXmlParser.XATOM_CATEGORY]);
if (result is DeletedEntry)
{
((DeletedEntry)result).When = instantOrNull(entry[JATOM_DELETED]);
}
else
{
var re = (ResourceEntry)result;
re.Title = entry.Value <string>(BundleXmlParser.XATOM_TITLE);
re.LastUpdated = instantOrNull(entry[BundleXmlParser.XATOM_UPDATED]);
re.Published = instantOrNull(entry[BundleXmlParser.XATOM_PUBLISHED]);
re.AuthorName = entry[BundleXmlParser.XATOM_AUTHOR] as JArray != null ?
entry[BundleXmlParser.XATOM_AUTHOR]
.Select(auth => auth.Value <string>(BundleXmlParser.XATOM_AUTH_NAME))
.FirstOrDefault() : null;
re.AuthorUri = entry[BundleXmlParser.XATOM_AUTHOR] as JArray != null ?
entry[BundleXmlParser.XATOM_AUTHOR]
.Select(auth => auth.Value <string>(BundleXmlParser.XATOM_AUTH_URI))
.FirstOrDefault() : null;
}
}
catch (Exception exc)
{
throw Error.Format("Exception while reading entry: " + exc.Message, null);
}
return(result);
}
