private static void ProcessEncounters(List<TimelineEntry> timeline, Bundle matchingEncounters)
{
foreach (var encounter in matchingEncounters.Entries.Select(x => (ResourceEntry<Encounter>)x))
{
DateTimeOffset? startTime;
DateTimeOffset? endTime;
if (encounter.Resource.Hospitalization != null)
{
startTime = DateTimeOffset.Parse(encounter.Resource.Hospitalization.Period.Start);
endTime = DateTimeOffset.Parse(encounter.Resource.Hospitalization.Period.End);
}
else
{
startTime = encounter.Published;
endTime = encounter.Published;
}
timeline.Add(new TimelineEntry
{
StartTime = startTime,
EndTime = endTime,
TypeOfEntry = TimelineEntryType.Encounter,
Summary = encounter.Resource.Reason.ToString()
});
}
}
public IEnumerable<ValidationResult> Validate(ValidationContext validationContext)
{
var result = new List<ValidationResult>();
if (String.IsNullOrWhiteSpace(Title))
result.Add(new ValidationResult("Feed must contain a title"));
if (!UriHasValue(Id))
result.Add(new ValidationResult("Feed must have an id"));
else
if (!Id.IsAbsoluteUri)
result.Add(new ValidationResult("Feed id must be an absolute URI"));
if (LastUpdated == null)
result.Add(new ValidationResult("Feed must have a updated date"));
if (Links.SearchLink != null)
result.Add(new ValidationResult("Links with rel='search' can only be used on feed entries"));
bool feedHasAuthor = !String.IsNullOrEmpty(this.AuthorName);
if (Entries != null)
{
foreach (var entry in Entries.Where(e => e != null))
{
if (!feedHasAuthor && entry is ResourceEntry && String.IsNullOrEmpty(((ResourceEntry)entry).AuthorName))
result.Add(new ValidationResult("Bundle's author and Entry author cannot both be empty"));
Validator.TryValidateObject(entry, ValidationContextFactory.Create(entry, null), result, true);
}
}
return result;
}
public Import(ILocalhost localhost, IGenerator generator)
{
this.localhost = localhost;
this.generator = generator;
mapper = new Mapper<Key, Key>();
interactions = new List<Interaction>();
}
public static ICollection<Tag> ParseCategoryHeader(string value)
{
if (String.IsNullOrEmpty(value)) return new List<Tag>();
var result = new List<Tag>();
var categories = value.SplitNotInQuotes(',').Where(s => !String.IsNullOrEmpty(s));
foreach (var category in categories)
{
var values = category.SplitNotInQuotes(';').Where(s => !String.IsNullOrEmpty(s));
if (values.Count() >= 1)
{
var term = values.First();
var pars = values.Skip(1).Select( v =>
{
var vsplit = v.Split('=');
var item1 = vsplit[0].Trim();
var item2 = vsplit.Length > 1 ? vsplit[1].Trim() : null;
return new Tuple<string,string>(item1,item2);
});
var scheme = new Uri(pars.Where(t => t.Item1 == "scheme").Select(t => t.Item2.Trim('\"')).FirstOrDefault(), UriKind.RelativeOrAbsolute);
var label = pars.Where(t => t.Item1 == "label").Select(t => t.Item2.Trim('\"')).FirstOrDefault();
result.Add(new Tag(term,scheme,label));
}
}
return result;
}
public void UpdateTagsOnUpdate()
{
if (original == null) TestResult.Skipped();
// Update one tag, add another
var tags = new List<Tag>() {
new Tag(NUTAG, Tag.FHIRTAGNS, "readTagTest2"),
new Tag(OTHERTAG, Tag.FHIRTAGNS, "dummy") };
HttpTests.AssertSuccess(client, () => latest = client.Fetch<Patient>(original.Id));
latest.Tags = tags;
HttpTests.AssertSuccess(client, () => client.Update<Patient>(latest));
var read = client.Fetch<Patient>(latest.Id);
if (read.Tags == null)
TestResult.Fail("fetch after update did not return any tags");
if (read.Tags.Count() != 2)
TestResult.Fail(String.Format("Wrong number of tags after update: {0}, expected 2", read.Tags.Count()));
var nutags = read.Tags.FindByTerm(NUTAG,Tag.FHIRTAGNS);
if (nutags.Count() != 1 || nutags.First().Label != "readTagTest2")
TestResult.Fail("update did not replace value in tag");
var othertags = read.Tags.FindByTerm(OTHERTAG,Tag.FHIRTAGNS);
if(othertags.Count() != 1 || othertags.First().Label != "dummy")
TestResult.Fail("update failed to add new tag");
latest = read;
}
public void TestTagsOnCreateAndRead()
{
var tags = new List<Tag>() { new Tag(NUTAG, Tag.FHIRTAGNS, "readTagTest") };
HttpTests.AssertSuccess(client, () => latest = client.Create<Patient>(DemoData.GetDemoPatient(),tags));
if(latest.Tags == null)
TestResult.Fail("create did not return any tags");
var nutags = latest.Tags.FindByTerm(NUTAG, Tag.FHIRTAGNS);
if (nutags.Count() != 1 || nutags.First().Label != "readTagTest")
TestResult.Fail("create did not return specified tag");
var read = client.Fetch<Patient>(latest.Id);
if (read.Tags == null)
TestResult.Fail("read did not return any tags");
nutags = latest.Tags.FindByTerm(NUTAG, Tag.FHIRTAGNS);
if (nutags.Count() != 1 || nutags.First().Label != "readTagTest")
TestResult.Fail("read did not return specified tag");
var vread = client.Fetch<Patient>(latest.SelfLink);
if (vread.Tags == null)
TestResult.Fail("vread did not return any tags");
nutags = latest.Tags.FindByTerm(NUTAG, Tag.FHIRTAGNS);
if (nutags.Count() != 1 || nutags.First().Label != "readTagTest")
TestResult.Fail("vread did not return specified tag");
original = latest;
}
public SearchParams()
{
Include = new List<string>();
RevInclude = new List<string>();
Sort = new List<Tuple<string, SortOrder>>();
Parameters = new List<Tuple<string, string>>();
}
public IEnumerable<Patient> GetAllPatients()
{
var patients = new List<Patient>();
var patientsExist = true;
var i = 1;
while (patientsExist)
{
try
{
var patient = _client.Read<Patient>(i.ToString());
patients.Add(patient.Resource);
i++;
}
catch (FhirOperationException)
{
patientsExist = false;
}
}
return patients;
}
public static void AddHistoryKeys(this IGenerator generator, List<Interaction> interactions)
{
// PERF: this needs a performance improvement.
foreach (Interaction interaction in interactions)
{
interaction.Key = generator.NextHistoryKey(interaction.Key);
}
}
public InitializeHub(FhirService fhirService, ILocalhost localhost, IFhirStore fhirStore, IFhirIndex fhirIndex)
{
this.localhost = localhost;
this.fhirService = fhirService;
this.fhirStore = fhirStore;
this.fhirIndex = fhirIndex;
this.resources = null;
}
static CustomModelInfo()
{
searchParameters = new List<SearchParamDefinition>
{
new SearchParamDefinition() { Resource = "Practitioner", Name = "roleid", Description = @"Search by role identifier extension", Type = SearchParamType.Token, Path = new string[] { @"Practitioner.practitionerRole.Extension[url=http://hl7.no/fhir/StructureDefinition/practitonerRole-identifier].ValueIdentifier" } }
};
// searchParameters.AddRange(ModelInfo.SearchParameters);
}
public Pager(IFhirStore fhirStore, ISnapshotStore snapshotstore, ILocalhost localhost, Transfer transfer, List<ModelInfo.SearchParamDefinition> searchParameters)
{
this.fhirStore = fhirStore;
this.snapshotstore = snapshotstore;
this.localhost = localhost;
this.transfer = transfer;
this.searchParameters = searchParameters;
}
private IMongoQuery ParametersToQuery(IEnumerable<IParameter> parameters)
{
List<IMongoQuery> queries = new List<IMongoQuery>();
queries.Add(M.Query.EQ(InternalField.LEVEL, 0)); // geindexeerde contained documents overslaan
IEnumerable<IMongoQuery> q = parameters.Select(p => ParameterToQuery(p));
queries.AddRange(q);
return M.Query.And(queries);
}
public static Conformance AddMultipleResourceComponents(this Conformance conformance, List<String> resourcetypes, Boolean readhistory, Boolean updatecreate, Conformance.ResourceVersionPolicy versioning)
{
foreach (var type in resourcetypes)
{
AddSingleResourceComponent(conformance, type, readhistory, updatecreate, versioning);
}
return conformance;
}
public InitializeHub()
{
this.localhost = InfrastructureProvider.Mongo.Localhost;
this.service = InfrastructureProvider.Mongo.CreateService();
this.store = InfrastructureProvider.Mongo.Store;
this.index = InfrastructureProvider.Mongo.Index;
this.resources = null;
}
internal static IMongoQuery ResourceFilter(string resourceType)
{
var queries = new List<IMongoQuery>();
queries.Add(M.Query.EQ(InternalField.LEVEL, 0));
queries.Add(M.Query.EQ(InternalField.RESOURCE, resourceType));
return M.Query.And(queries);
}
public IEnumerable<ValidationResult> Validate(ValidationContext validationContext)
{
var result = new List<ValidationResult>();
foreach (var tag in Category)
result.AddRange(tag.Validate(validationContext));
return result;
}
public IEnumerable<Tuple<string, IFhirReader>> GetMembers()
{
if (_current is XElement)
{
var rootElem = (XElement)_current;
var result = new List<Tuple<string, IFhirReader>>();
// First, any attributes
foreach(var attr in rootElem.Attributes()) //.Where(xattr => xattr.Name.LocalName != "xmlns"))
{
if (attr.Name == XName.Get("xmlns", "")) continue; // skip xmlns declarations
if (attr.Name == XName.Get("{http://www.w3.org/2000/xmlns/}xsi") && !SerializationConfig.EnforceNoXsiAttributesOnRoot ) continue; // skip xmlns:xsi declaration
if (attr.Name == XName.Get("{http://www.w3.org/2001/XMLSchema-instance}schemaLocation") && !SerializationConfig.EnforceNoXsiAttributesOnRoot) continue; // skip schemaLocation
if (attr.Name.NamespaceName == "")
result.Add(Tuple.Create(attr.Name.LocalName, (IFhirReader)new XmlDomFhirReader(attr)));
else
throw Error.Format("Encountered unsupported attribute {0}", this, attr.Name);
}
foreach(var node in rootElem.Nodes())
{
if(node is XText)
{
// A nested text node (the content attribute of a Binary)
result.Add(Tuple.Create(SerializationConfig.BINARY_CONTENT_MEMBER_NAME, (IFhirReader)new XmlDomFhirReader(node)));
}
else if(node is XElement)
{
var elem = (XElement)node;
// All normal elements
if(elem.Name.NamespaceName == SerializationUtil.FHIRNS)
result.Add(Tuple.Create(elem.Name.LocalName, (IFhirReader)new XmlDomFhirReader(elem)));
// The special xhtml div element
else if(elem.Name == XHTMLDIV)
result.Add(Tuple.Create(XHTMLDIV.LocalName,
(IFhirReader)new XmlDomFhirReader(buildDivXText(elem))));
else
throw Error.Format("Encountered element '{0}' from unsupported namespace '{1}'", this, elem.Name.LocalName, elem.Name.NamespaceName);
}
else if(node is XComment)
{
// nothing
}
else
throw Error.Format("Encountered unexpected element member of type {0}", this, node.GetType().Name);
}
return result;
}
else
throw Error.Format("Cannot get members: reader not at an element", this);
}
public override IEnumerable<ValidationResult> Validate(ValidationContext validationContext)
{
var result = new List<ValidationResult>();
result.AddRange(base.Validate(validationContext));
if (!result.Any()) result.Add(ValidationResult.Success);
return result;
}
public Chain(string path)
{
List<string> chain = SplitPath(path);
// Keep the typename separate.
var typeName = chain.First();
chain.RemoveAt(0);
segments = BuildSegments(typeName, chain);
}
public IEnumerable<Patient> GetPatientsByName(string firstName, string lastName)
{
var searchParameters = new SearchParams();
searchParameters.Add("Given", firstName);
searchParameters.Add("Family", lastName);
var matches = new List<Patient>();
var result = _client.Search(searchParameters, ResourceType.Patient.ToString());
return result.Entry.Select(x => (Patient) x.Resource);
}
public static IList<Interaction> GetInteractions(this ILocalhost localhost, Bundle bundle)
{
var interactions = new List<Interaction>();
foreach(var entry in bundle.Entry)
{
Interaction interaction = localhost.ToInteraction(entry);
interaction.SupplementBase(bundle.Base);
interactions.Add(interaction);
}
return interactions;
}
public static void SetBundleType(this Bundle bundle, BundleType type)
{
List<Tag> result = new List<Tag>(bundle.Tags.Exclude(new Tag[] { MESSAGE_TAG, DOCUMENT_TAG }));
if (type == BundleType.Document)
result.Add(DOCUMENT_TAG);
else if (type == BundleType.Message)
result.Add(MESSAGE_TAG);
bundle.Tags = result;
}
public override IEnumerable<ValidationResult> Validate(ValidationContext validationContext)
{
var result = new List<ValidationResult>();
result.AddRange(base.Validate(validationContext));
if (When == null)
result.Add(new ValidationResult("A DeletedEntry must have a non-null deletion time (When)"));
if (!result.Any()) result.Add(ValidationResult.Success);
return result;
}
public IEnumerable<TimelineEntry> GetTimelineForPatient(string patientIdentifier)
{
var timeline = new List<TimelineEntry>();
var matchingEncounters = _client.Search(ResourceType.Encounter, "subject.identifier", patientIdentifier);
var matchingAlerts = _client.Search(ResourceType.Alert, "subject.identifier", patientIdentifier);
ProcessAlerts(timeline, matchingAlerts);
ProcessEncounters(timeline, matchingEncounters);
return timeline.OrderBy(x => x.StartTime).ThenBy(x => x.EndTime);
}
private static IEnumerable<Type> LoadSupportedTypesFromAssembly(Assembly fhirAssembly)
{
var result = new List<Type>();
foreach (Type fhirType in fhirAssembly.GetTypes())
{
if (typeof(Resource).IsAssignableFrom(fhirType) || typeof(Element).IsAssignableFrom(fhirType)) //It is derived of Resource or Element, so we should support it.
{
result.Add(fhirType);
}
}
return result;
}
public RestUrl(Uri url)
{
if (!url.IsAbsoluteUri) throw Error.Argument("url", "Must be an absolute url");
if (url.Scheme != "http")
Error.Argument("uri", "RestUrl must be a http url");
_builder = new UriBuilder(url);
if (!String.IsNullOrEmpty(_builder.Query))
_parameters = new List<Tuple<string,string>>( HttpUtil.SplitParams(_builder.Query) );
}
public override IEnumerable<ValidationResult> Validate(ValidationContext validationContext)
{
var result = new List<ValidationResult>();
result.AddRange(base.Validate(validationContext));
if (Content == null)
result.Add(new ValidationResult("Entry must contain (possibly 0-length) data in Content element"));
if (ContentType == null)
result.Add(new ValidationResult("Entry must contain a ContentType"));
return result;
}
public static Expression ToExpression(this Quantity quantity)
{
quantity = System.Canonical(quantity);
string searchable = quantity.LeftSearchableString();
var values = new List<ValueExpression>();
values.Add(new IndexValue("system", new StringValue(UCUM.Uri.ToString())));
values.Add(new IndexValue("value", new NumberValue(quantity.Value.ToDecimal())));
values.Add(new IndexValue("decimals", new StringValue(searchable)));
values.Add(new IndexValue("unit", new StringValue(quantity.Metric.ToString())));
return new CompositeValue(values);
}
public static void SetTextTag(this BundleEntry entry, string text)
{
var result = new List<Tag>();
if (entry.Tags != null) result.AddRange(entry.Tags);
result.RemoveAll(t => Equals(t.Scheme,Tag.FHIRTAGSCHEME_GENERAL) &&
(t.Term != null && t.Term.StartsWith(TAG_TERM_TEXT)));
result.Add(new Tag(TAG_TERM_TEXT + Uri.EscapeUriString(text), Tag.FHIRTAGSCHEME_GENERAL, text));
entry.Tags = result;
}
public static void SerializeList(Hl7.Fhir.Model.List value, IFhirWriter writer, bool summary)
{
writer.WriteStartRootObject("List");
writer.WriteStartComplexContent();
// Serialize element _id
if (value.LocalIdElement != null)
{
writer.WritePrimitiveContents("_id", value.LocalIdElement, XmlSerializationHint.Attribute);
}
// Serialize element extension
if (value.Extension != null && !summary && value.Extension.Count > 0)
{
writer.WriteStartArrayElement("extension");
foreach (var item in value.Extension)
{
writer.WriteStartArrayMember("extension");
ExtensionSerializer.SerializeExtension(item, writer, summary);
writer.WriteEndArrayMember();
}
writer.WriteEndArrayElement();
}
// Serialize element language
if (value.LanguageElement != null && !summary)
{
writer.WriteStartElement("language");
CodeSerializer.SerializeCode(value.LanguageElement, writer, summary);
writer.WriteEndElement();
}
// Serialize element text
if (value.Text != null && !summary)
{
writer.WriteStartElement("text");
NarrativeSerializer.SerializeNarrative(value.Text, writer, summary);
writer.WriteEndElement();
}
// Serialize element contained
if (value.Contained != null && !summary && value.Contained.Count > 0)
{
writer.WriteStartArrayElement("contained");
foreach (var item in value.Contained)
{
writer.WriteStartArrayMember("contained");
FhirSerializer.SerializeResource(item, writer, summary);
writer.WriteEndArrayMember();
}
writer.WriteEndArrayElement();
}
// Serialize element code
if (value.Code != null && !summary)
{
writer.WriteStartElement("code");
CodeableConceptSerializer.SerializeCodeableConcept(value.Code, writer, summary);
writer.WriteEndElement();
}
// Serialize element source
if (value.Source != null && !summary)
{
writer.WriteStartElement("source");
ResourceReferenceSerializer.SerializeResourceReference(value.Source, writer, summary);
writer.WriteEndElement();
}
// Serialize element date
if (value.DateElement != null && !summary)
{
writer.WriteStartElement("date");
FhirDateTimeSerializer.SerializeFhirDateTime(value.DateElement, writer, summary);
writer.WriteEndElement();
}
// Serialize element ordered
if (value.OrderedElement != null && !summary)
{
writer.WriteStartElement("ordered");
FhirBooleanSerializer.SerializeFhirBoolean(value.OrderedElement, writer, summary);
writer.WriteEndElement();
}
// Serialize element mode
if (value.ModeElement != null && !summary)
{
writer.WriteStartElement("mode");
CodeSerializer.SerializeCode <Hl7.Fhir.Model.List.ListMode>(value.ModeElement, writer, summary);
writer.WriteEndElement();
}
// Serialize element entry
if (value.Entry != null && !summary && value.Entry.Count > 0)
{
writer.WriteStartArrayElement("entry");
foreach (var item in value.Entry)
{
writer.WriteStartArrayMember("entry");
ListSerializer.SerializeListEntryComponent(item, writer, summary);
writer.WriteEndArrayMember();
}
writer.WriteEndArrayElement();
}
// Serialize element emptyReason
if (value.EmptyReason != null && !summary)
{
writer.WriteStartElement("emptyReason");
CodeableConceptSerializer.SerializeCodeableConcept(value.EmptyReason, writer, summary);
writer.WriteEndElement();
}
writer.WriteEndComplexContent();
writer.WriteEndRootObject();
}
/// <summary>
/// Parse List
/// </summary>
public static Hl7.Fhir.Model.List ParseList(IFhirReader reader, ErrorList errors, Hl7.Fhir.Model.List existingInstance = null)
{
Hl7.Fhir.Model.List result = existingInstance != null ? existingInstance : new Hl7.Fhir.Model.List();
string currentElementName = reader.CurrentElementName;
reader.EnterElement();
while (reader.HasMoreElements())
{
var atName = reader.CurrentElementName;
// Parse element extension
if (atName == "extension")
{
result.Extension = new List <Hl7.Fhir.Model.Extension>();
reader.EnterArray();
while (ParserUtils.IsAtArrayElement(reader, "extension"))
{
result.Extension.Add(ExtensionParser.ParseExtension(reader, errors));
}
reader.LeaveArray();
}
// Parse element language
else if (atName == "language")
{
result.LanguageElement = CodeParser.ParseCode(reader, errors);
}
// Parse element text
else if (atName == "text")
{
result.Text = NarrativeParser.ParseNarrative(reader, errors);
}
// Parse element contained
else if (atName == "contained")
{
result.Contained = new List <Hl7.Fhir.Model.Resource>();
reader.EnterArray();
while (ParserUtils.IsAtArrayElement(reader, "contained"))
{
result.Contained.Add(ParserUtils.ParseContainedResource(reader, errors));
}
reader.LeaveArray();
}
// Parse element _id
else if (atName == "_id")
{
result.LocalIdElement = Id.Parse(reader.ReadPrimitiveContents(typeof(Id)));
}
// Parse element code
else if (atName == "code")
{
result.Code = CodeableConceptParser.ParseCodeableConcept(reader, errors);
}
// Parse element source
else if (atName == "source")
{
result.Source = ResourceReferenceParser.ParseResourceReference(reader, errors);
}
// Parse element date
else if (atName == "date")
{
result.DateElement = FhirDateTimeParser.ParseFhirDateTime(reader, errors);
}
// Parse element ordered
else if (atName == "ordered")
{
result.OrderedElement = FhirBooleanParser.ParseFhirBoolean(reader, errors);
}
// Parse element mode
else if (atName == "mode")
{
result.ModeElement = CodeParser.ParseCode <Hl7.Fhir.Model.List.ListMode>(reader, errors);
}
// Parse element entry
else if (atName == "entry")
{
result.Entry = new List <Hl7.Fhir.Model.List.ListEntryComponent>();
reader.EnterArray();
while (ParserUtils.IsAtArrayElement(reader, "entry"))
{
result.Entry.Add(ListParser.ParseListEntryComponent(reader, errors));
}
reader.LeaveArray();
}
// Parse element emptyReason
else if (atName == "emptyReason")
{
result.EmptyReason = CodeableConceptParser.ParseCodeableConcept(reader, errors);
}
else
{
errors.Add(String.Format("Encountered unknown element {0} while parsing {1}", reader.CurrentElementName, currentElementName), reader);
reader.SkipSubElementsFor(currentElementName);
result = null;
}
}
reader.LeaveElement();
return(result);
}