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()
});
}
}
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 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 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 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 override IEnumerable<ValidationResult> Validate(ValidationContext validationContext)
{
var result = new List<ValidationResult>(base.Validate(validationContext));
if (this.Contained != null)
{
if (!Contained.OfType<DomainResource>().All(dr => dr.Text == null))
result.Add(new ValidationResult("Resource has contained resources with narrative"));
if(!Contained.OfType<DomainResource>().All(cr => cr.Contained == null || !cr.Contained.Any()))
result.Add(new ValidationResult("Resource has contained resources with nested contained resources"));
}
return result;
}
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 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 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 static Expression NonUcumIndexedExpression(this FM.Quantity quantity)
{
var values = new List<ValueExpression>();
if (quantity.System != null)
values.Add(new IndexValue("system", new StringValue(quantity.System)));
if (quantity.Unit != null)
values.Add(new IndexValue("unit", new StringValue(quantity.Unit)));
if (quantity.Value.HasValue)
values.Add(new IndexValue("value", new NumberValue(quantity.Value.Value)));
if (values.Any())
return new CompositeValue(values);
return null;
}
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);
}
private void genProfile(List<Row> rows, Profile profile, bool extensionsOnly)
{
if (!extensionsOnly)
{
var r = new Row();
rows.Add(r);
r.setIcon("icon_profile.png");
r.getCells().Add(new Cell(null, null, profile.Name, null, null));
r.getCells().Add(new Cell());
r.getCells().Add(new Cell(null, null, "Profile", null, null));
r.getCells().Add(new Cell(null, null, profile.Description, null, null));
foreach (var s in profile.Structure)
{
var re = new Row();
r.getSubRows().Add(re);
re.setIcon("icon_resource.png");
re.getCells().Add(new Cell(null, null, s.Name, null, null));
re.getCells().Add(new Cell(null, null, "", null, null));
re.getCells().Add(new Cell(null, null, s.Type, null, null));
re.getCells().Add(new Cell(null, null, s.Element[0].Definition.Short, null, null)); // DSTU1
//re.getCells().Add(new Cell(null, null, s.Base, null, null)); // DSTU2
}
}
if (profile.ExtensionDefn.Any() || extensionsOnly)
{
var re = new Row();
rows.Add(re);
re.setIcon("icon_profile.png");
re.getCells().Add(new Cell(null, null, "Extensions", null, null));
re.getCells().Add(new Cell());
re.getCells().Add(new Cell());
re.getCells().Add(new Cell(null, null, "Extensions defined by this profile", null, null)); // DSTU1
//re.getCells().Add(new Cell(null, null, "Extensions defined by the URL \"" + profile.Url + "\"", null, null)); // DSTU2
foreach (var ext in profile.ExtensionDefn)
{
genExtension(re.getSubRows(), ext, true);
}
}
}
public virtual IEnumerable<ValidationResult> Validate(ValidationContext validationContext)
{
var result = new List<ValidationResult>();
if (Id != null && !Id.IsAbsoluteUri)
result.Add(FhirValidator.BuildResult(validationContext, "Entry id must be an absolute URI"));
if (Bundle.UriHasValue(SelfLink) && !SelfLink.IsAbsoluteUri)
result.Add(FhirValidator.BuildResult(validationContext, "Entry selflink must be an absolute URI"));
if (Links.FirstLink != null || Links.LastLink != null || Links.PreviousLink != null || Links.NextLink != null)
result.Add(FhirValidator.BuildResult(validationContext, "Paging links can only be used on feeds, not entries"));
if (Tags != null && validationContext.ValidateRecursively())
FhirValidator.TryValidate(Tags,result,true);
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 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 virtual IEnumerable<ValidationResult> Validate(ValidationContext validationContext)
{
// TODO: Contained resources share the same internal id resolution space as the parent
// resource -> verify id uniqueness
var result = new List<ValidationResult>();
if (Contained != null)
{
foreach (var contained in Contained)
{
if (contained.Contained != null && contained.Contained.Any())
result.Add(new ValidationResult("Contained resources cannot contain nested contained resources"));
if (contained.Text != null)
result.Add(new ValidationResult("Contained resources should not contain narrative"));
}
}
return result;
}
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 virtual IEnumerable<ValidationResult> Validate(ValidationContext validationContext)
{
var result = new List<ValidationResult>();
if (!Bundle.UriHasValue(Id))
result.Add(new ValidationResult("Entry must have an id"));
else
if (!Id.IsAbsoluteUri)
result.Add(new ValidationResult("Entry id must be an absolute URI"));
if (Bundle.UriHasValue(SelfLink) && !SelfLink.IsAbsoluteUri)
result.Add(new ValidationResult("Entry selflink must be an absolute URI"));
if (Links.FirstLink != null || Links.LastLink != null || Links.PreviousLink != null || Links.NextLink != null)
result.Add(new ValidationResult("Paging links can only be used on feeds, not entries"));
if (Tags != null)
result.AddRange(new TagList(Tags).Validate(validationContext));
return result;
}
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 virtual IEnumerable<ValidationResult> Validate(ValidationContext validationContext)
{
// TODO: Contained resources share the same internal id resolution space as the parent
// resource -> verify id uniqueness
var result = new List<ValidationResult>();
// Validate specific invariants for contained items. The content of the contained
// items is validated by the "normal" validation triggered by the FhirElement attribute
if (Contained != null)
{
foreach (var contained in Contained)
{
if (contained.Contained != null && contained.Contained.Any())
result.Add(FhirValidator.BuildResult(validationContext, "Contained resources cannot contain nested contained resources"));
if (contained.Text != null)
result.Add(FhirValidator.BuildResult(validationContext, "Contained resources should not contain narrative"));
}
}
return result;
}
internal static PropertyMapping Create(PropertyInfo prop, out IEnumerable<Type> referredTypes)
{
if (prop == null) throw Error.ArgumentNull("prop");
var foundTypes = new List<Type>();
PropertyMapping result = new PropertyMapping();
#if PORTABLE45
var elementAttr = prop.GetCustomAttribute<FhirElementAttribute>();
#else
var elementAttr = (FhirElementAttribute)Attribute.GetCustomAttribute(prop, typeof(FhirElementAttribute));
#endif
result.Name = determinePropertyName(prop);
result.ReturnType = prop.PropertyType;
result.ElementType = result.ReturnType;
result.InSummary = elementAttr != null ? elementAttr.InSummary : false;
result.Choice = elementAttr != null ? elementAttr.Choice : ChoiceType.None;
if (elementAttr != null)
{
result.SerializationHint = elementAttr.XmlSerialization;
result.Order = elementAttr.Order;
}
foundTypes.Add(result.ElementType);
result.IsCollection = ReflectionHelper.IsTypedCollection(prop.PropertyType) && !prop.PropertyType.IsArray;
// Get to the actual (native) type representing this element
if (result.IsCollection) result.ElementType = ReflectionHelper.GetCollectionItemType(prop.PropertyType);
if (ReflectionHelper.IsNullableType(result.ElementType)) result.ElementType = ReflectionHelper.GetNullableArgument(result.ElementType);
result.IsPrimitive = isAllowedNativeTypeForDataTypeValue(result.ElementType);
// Check wether this property represents a native .NET type
// marked to receive the class' primitive value in the fhir serialization
// (e.g. the value from the Xml 'value' attribute or the Json primitive member value)
if(result.IsPrimitive) result.RepresentsValueElement = isPrimitiveValueElement(prop);
referredTypes = foundTypes;
// May need to generate getters/setters using pre-compiled expression trees for performance.
// See http://weblogs.asp.net/marianor/archive/2009/04/10/using-expression-trees-to-get-property-getter-and-setters.aspx
result._getter = instance => prop.GetValue(instance, null);
result._setter = (instance,value) => prop.SetValue(instance, value, null);
return result;
}
public FhirModel(Dictionary<Type, string> csTypeToFhirTypeNameMapping, IEnumerable<SearchParamDefinition> searchParameters, List<Type> enums)
{
LoadSearchParameters(searchParameters);
_csTypeToFhirTypeName = csTypeToFhirTypeNameMapping;
_fhirTypeNameToCsType = _csTypeToFhirTypeName.ToLookup(pair => pair.Value, pair => pair.Key).ToDictionary(group => group.Key, group => group.FirstOrDefault());
_enumMappings = new List<EnumMapping>();
foreach (var enumType in enums)
{
if (EnumMapping.IsMappableEnum(enumType))
{
_enumMappings.Add(EnumMapping.Create(enumType));
}
}
}
public static IEnumerable<Uri> GetReferences(this BundleEntry entry, string include)
{
Resource resource = (entry as ResourceEntry).Resource;
ElementQuery query = new ElementQuery(include);
var list = new List<Uri>();
query.Visit(resource, element =>
{
if (element is ResourceReference)
{
Uri uri = (element as ResourceReference).Url;
if (uri != null) list.Add(uri);
}
});
return list.Where(u => u != null);
}
private static void ProcessAlerts(List<TimelineEntry> timeline, Bundle matchingAlerts)
{
foreach (var encounter in matchingAlerts.Entries.Select(x => (ResourceEntry<Alert>)x))
{
var startTime = encounter.Published;
var endTime = encounter.Published;
timeline.Add(new TimelineEntry
{
StartTime = startTime,
EndTime = endTime,
TypeOfEntry = TimelineEntryType.Alert,
Summary = encounter.Resource.Note
});
}
}
/// <summary>
/// Rewrites the Path's of the elements in a structure so they are based on the given path: the root
/// of the given structure will become the given path, it's children will be relocated below that path
/// </summary>
/// <param name="root">The structure that will be rebased on the path</param>
/// <param name="path">The path to rebase the structure on</param>
public static void Rebase(this Profile.ProfileStructureComponent root, string path)
{
var nav = new ElementNavigator(root);
if (nav.MoveToFirstChild())
{
var newPaths = new List<string>();
newPaths.Add(path);
rebaseChildren(nav, path, newPaths);
// Can only change the paths after navigating the tree, otherwise the
// navigation functions (which are based on the paths) won't function correctly
for (var i = 0; i < root.Element.Count; i++)
root.Element[i].Path = newPaths[i];
}
}
//internal static IList<Tag> ParseTags(XmlReader xr)
//{
// xr.MoveToContent();
// var taglist = (XElement)XElement.ReadFrom(xr);
// if (taglist.Name == BundleXmlParser.XFHIRNS + TagListSerializer.TAGLIST_TYPE)
// {
// if (taglist.Elements().All(xe => xe.Name == BundleXmlParser.XFHIRNS + BundleXmlParser.XATOM_CATEGORY))
// return ParseTags(taglist.Elements());
// else
// throw Error.Format("TagList contains unexpected child elements");
// }
// else
// throw Error.Format("Unexpected element name {0} found at start of TagList", taglist.Name);
//}
//internal static IList<Tag> ParseTags(JsonReader xr)
//{
// var tagObj = JObject.Load(xr);
// var tagType = tagObj[SerializationConfig.RESOURCETYPE_MEMBER_NAME];
// if(tagType == null || tagType.Value<string>() != TagListSerializer.TAGLIST_TYPE)
// throw Error.Format("TagList should start with a resourceType member TagList");
// var categoryArray = tagObj[BundleXmlParser.XATOM_CATEGORY] as JArray;
// if (categoryArray != null)
// return ParseTags(categoryArray);
// else
// return new List<Tag>();
//}
internal static IList<Tag> ParseTags(IEnumerable<XElement> tags)
{
var result = new List<Tag>();
if (tags != null)
{
foreach (var tag in tags)
{
var scheme = SerializationUtil.StringValueOrNull(tag.Attribute(BundleXmlParser.XATOM_CAT_SCHEME));
var term = SerializationUtil.StringValueOrNull(tag.Attribute(BundleXmlParser.XATOM_CAT_TERM));
var label = SerializationUtil.StringValueOrNull(tag.Attribute(BundleXmlParser.XATOM_CAT_LABEL));
result.Add(new Tag(term,scheme,label));
}
}
return result;
}
public List<Resource> GetExampleData()
{
var list = new List<Resource>();
Bundle data = Examples.ImportEmbeddedZip().LimitPerType(5).ToBundle(localhost.Base);
if (data.Entry != null && data.Entry.Count() != 0)
{
foreach (var entry in data.Entry)
{
if (entry.Resource != null)
{
list.Add((Resource)entry.Resource);
}
}
}
return list;
}
internal static IList<Tag> ParseTags(JToken token)
{
var result = new List<Tag>();
var tags = token as JArray;
if (tags != null)
{
foreach (var tag in tags)
{
var scheme = tag.Value<string>(BundleXmlParser.XATOM_CAT_SCHEME);
var term = tag.Value<string>(BundleXmlParser.XATOM_CAT_TERM);
var label = tag.Value<string>(BundleXmlParser.XATOM_CAT_LABEL);
result.Add(new Tag(term,scheme,label));
}
}
return result;
}
private static void rebaseChildren(BaseElementNavigator nav, string path, List<string> newPaths)
{
var bm = nav.Bookmark();
if (nav.MoveToFirstChild())
{
do
{
var newPath = path + "." + nav.Current.GetNameFromPath();
newPaths.Add(newPath);
if(nav.HasChildren)
rebaseChildren(nav, newPath, newPaths);
}
while (nav.MoveToNext());
nav.ReturnToBookmark(bm);
}
}
