public async Task TestMethod1()
{
var spec = ZipSource.CreateValidationSource();
var sd = await spec.FindStructureDefinitionForCoreTypeAsync("Patient");
Assert.IsNotNull(sd);
var sw = new Stopwatch();
var te = ElementNode.FromElement(sd.ToTypedElement());
sw.Start();
ExpandoObject expando = null;
for (int i=0; i < 1000; i++)
expando = te.ToExpando();
sw.Stop();
Console.WriteLine($"ToExpando() took {sw.ElapsedMilliseconds / 1000.0} ms");
ReadOnlyMemory<byte> memory = null;
sw.Restart();
for(int i=0; i < 1000; i++)
memory = PrimitiveObjectFormatterCore.SerializeToMemory(expando);
sw.Stop();
Console.WriteLine($"Serializing an expando took {sw.ElapsedMilliseconds / 1000.0} ms");
object result = null;
sw.Restart();
for (int i = 0; i < 1000; i++)
result = PrimitiveObjectFormatterCore.Deserialize(memory);
sw.Stop();
Console.WriteLine($"Deserializing to an expando took {sw.ElapsedMilliseconds / 1000.0} ms");
dynamic dyn = result;
Assert.AreEqual("normative", dyn.extension[1].value.value);
}
public void Setup()
{
var assembly = Assembly.GetExecutingAssembly();
var location = new Uri(assembly.GetName().CodeBase);
var directoryInfo = new FileInfo(location.AbsolutePath).Directory;
Debug.Assert(directoryInfo != null, "directoryInfo != null");
Debug.Assert(directoryInfo.FullName != null, "directoryInfo.FullName != null");
var structureDefinitions = directoryInfo.FullName + @"\Resources\StructureDefinitions";
var includeSubDirectories = new DirectorySourceSettings {
IncludeSubDirectories = true
};
var directorySource = new DirectorySource(structureDefinitions, includeSubDirectories);
var cachedResolver = new CachedResolver(directorySource);
var coreSource = new CachedResolver(ZipSource.CreateValidationSource());
var combinedSource = new MultiResolver(cachedResolver, coreSource);
var settings = new ValidationSettings
{
EnableXsdValidation = true,
GenerateSnapshot = true,
Trace = true,
ResourceResolver = combinedSource,
ResolveExteralReferences = true,
SkipConstraintValidation = false
};
var validator = new Validator(settings);
_profileValidator = new ProfileValidator(validator);
}
/// <summary>
/// Creates a default non-cached artifact resolver
/// Default only searches in the executable directory files and the core zip.
/// This non-cached resolver is primary for testing purposes.
/// </summary>
public static IResourceResolver CreateDefault()
{
return(new MultiResolver(new DirectorySource(new DirectorySourceSettings {
IncludeSubDirectories = true
}),
ZipSource.CreateValidationSource(), new WebResolver()));
}
public void TestSourceCaching()
{
var src = new CachedResolver(new MultiResolver(ZipSource.CreateValidationSource(), new WebResolver()));
Stopwatch sw1 = new Stopwatch();
// Ensure looking up a failed endpoint repeatedly does not cost much time
sw1.Start();
src.ResolveByUri("http://some.none.existant.address.nl/fhir/StructureDefinition/bla");
sw1.Stop();
var sw2 = new Stopwatch();
sw2.Start();
src.ResolveByUri("http://some.none.existant.address.nl/fhir/StructureDefinition/bla");
sw2.Stop();
Debug.WriteLine("sw2 {0}, sw1 {1}", sw2.ElapsedMilliseconds, sw1.ElapsedMilliseconds);
Assert.IsTrue(sw2.ElapsedMilliseconds <= sw1.ElapsedMilliseconds && sw2.ElapsedMilliseconds < 100);
// Now try an existing artifact
sw1.Restart();
src.ResolveByUri("http://hl7.org/fhir/ValueSet/v2-0292");
sw1.Stop();
sw2.Restart();
src.ResolveByUri("http://hl7.org/fhir/ValueSet/v2-0292");
sw2.Stop();
Assert.IsTrue(sw2.ElapsedMilliseconds < sw1.ElapsedMilliseconds && sw2.ElapsedMilliseconds < 100);
}
int validate()
{
int returncode = 0;
// Example from https://stackoverflow.com/questions/53399139/fhir-net-api-stu3-validating
// https://www.devdays.com/wp-content/uploads/2019/02/DD18-US-Validation-in-NET-and-Java-Ewout-Kramer-James-Agnew-2018-06-19.pdf
// https://blog.fire.ly/2016/10/27/validation-and-other-new-features-in-the-net-api-stack/
// setup the resolver to use specification.zip, and a folder with custom profiles
var source = new CachedResolver(new MultiResolver(
new DirectorySource(@"C:\Users\dag\source\repos\FhirTool\SfmFhir\Profiles\"),
ZipSource.CreateValidationSource()));
// prepare the settings for the validator
var ctx = new ValidationSettings()
{
ResourceResolver = source,
GenerateSnapshot = true,
Trace = false,
EnableXsdValidation = true,
ResolveExternalReferences = false
};
var validator = new Validator(ctx);
// validate the resource; optionally enter a custom profile url as 2nd parameter
var result = validator.Validate(this);
return(returncode);
}
public void FullRoundtripOfAllExamplesJsonNavSdProvider()
{
var source = new CachedResolver(ZipSource.CreateValidationSource());
FullRoundtripOfAllExamples("examples-json.zip", "FHIRRoundTripTestJson",
"Roundtripping json->xml->json", usingPoco: false, provider: new StructureDefinitionSummaryProvider(source));
}
public SpecZipResourcesFixture()
{
var specSource = ZipSource.CreateValidationSource();
Resources = specSource.FindAll <DataElement>().ToDictionary <DataElement, string>(sd => sd.Url);
//By putting all the url's in a dictionary we can be sure there are no duplicates.
}
/// <summary>
/// Creates an offline non-cached artifact resolver
/// Default only searches in the executable directory files and the core zip.
/// </summary>
public static IResourceResolver CreateOffline()
{
// Making requests to a WebArtifactSource is time consuming. So for performance we have an Offline Resolver.
return(new MultiResolver(new DirectorySource(new DirectorySourceSettings {
IncludeSubDirectories = true
}),
ZipSource.CreateValidationSource()));
}
public void CannotCreateNestedSnapshotSource()
{
var orgSource = ZipSource.CreateValidationSource();
var cachedSource = new CachedResolver(orgSource);
var src = new SnapshotSource(cachedSource);
// Verify that SnapshotSource ctor rejects SnapshotSource arguments
Assert.ThrowsException <ArgumentException>(() => new SnapshotSource(src));
}
public void TestZipSummary()
{
var source = ZipSource.CreateValidationSource();
var summaries = source.ListSummaries().ToList();
Assert.IsNotNull(summaries);
Assert.AreEqual(7155, summaries.FhirResources().Count());
Assert.AreEqual(552, summaries.OfResourceType(ResourceType.StructureDefinition).Count());
Assert.IsTrue(!summaries.Errors().Any());
}
static void InitCoreProfiles()
{
Console.WriteLine("Load FHIR core resource definitions...");
var src = _coreSource = ZipSource.CreateValidationSource();
_cachedCoreSource = new CachedResolver(src);
var profiles = _coreProfiles = src.ListResourceUris(ResourceType.StructureDefinition).ToList();
Console.WriteLine($"Found {profiles.Count} core definitions.");
}
public void ListSummariesExcludingSubdirectories()
{
var zipfile = Path.Combine("TestData", "ResourcesInSubfolder.zip");
var zip = new ZipSource(zipfile, new DirectorySourceSettings()
{
IncludeSubDirectories = false
});
var summaries = zip.ListSummaries();
Assert.IsNotNull(summaries, "Collection of summeries should not be null");
Assert.AreEqual(1, summaries.Count(), "In the zipfile there is 1 resource in the root folder.");
}
public void ListSummariesIncludingSubdirectories()
{
var zipfile = Path.Combine("TestData", "ResourcesInSubfolder.zip");
var zip = new ZipSource(zipfile, new DirectorySourceSettings()
{
IncludeSubDirectories = true
});
var summaries = zip.ListSummaries();
Assert.IsNotNull(summaries, "Collection of summeries should not be null");
Assert.AreEqual(20, summaries.Count(), "In the zipfile there are 20 resources distrubuted over several folders in the zipfile.");
}
public void TestCanonicalUrlConflicts()
{
//const string srcFileName = "extension-definitions.xml";
const string dupFileName = "diagnosticorder-reason-duplicate";
const string url = "http://hl7.org/fhir/StructureDefinition/diagnosticorder-reason";
var za = ZipSource.CreateValidationSource();
// Try to find a core extension
var ext = za.ResolveByCanonicalUri(url);
Assert.IsNotNull(ext);
Assert.IsTrue(ext is StructureDefinition);
// Save back to disk to create a conflicting duplicate
var b = new Bundle();
b.AddResourceEntry(ext, url);
var xml = new FhirXmlSerializer().SerializeToString(b);
var filePath = Path.Combine(DirectorySource.SpecificationDirectory, dupFileName) + ".xml";
var filePath2 = Path.Combine(DirectorySource.SpecificationDirectory, dupFileName) + "2.xml";
File.WriteAllText(filePath, xml);
File.WriteAllText(filePath2, xml);
bool conflictException = false;
try
{
var fa = new DirectorySource();
var res = fa.ResolveByCanonicalUri(url);
}
catch (ResolvingConflictException ex)
{
Debug.WriteLine("{0}:\r\n{1}", ex.GetType().Name, ex.Message);
Assert.IsNotNull(ex.Conflicts);
Assert.AreEqual(1, ex.Conflicts.Length);
var conflict = ex.Conflicts[0];
Assert.AreEqual(url, conflict.Identifier);
Assert.IsTrue(conflict.Origins.Contains(filePath));
Assert.IsTrue(conflict.Origins.Contains(filePath2));
conflictException = true;
}
finally
{
try { File.Delete(filePath); } catch { }
File.Delete(filePath2);
}
Assert.IsTrue(conflictException);
}
public ProfileValidator(IProvideProfilesForValidation profilesResolver, IOptions <ValidateOperationConfiguration> options)
{
EnsureArg.IsNotNull(profilesResolver, nameof(profilesResolver));
EnsureArg.IsNotNull(options?.Value, nameof(options));
try
{
_resolver = new MultiResolver(new CachedResolver(ZipSource.CreateValidationSource(), options.Value.CacheDurationInSeconds), profilesResolver);
}
catch (Exception)
{
// Something went wrong during profile loading, what should we do?
throw;
}
}
public void GetSomeArtifactsById()
{
var fa = ZipSource.CreateValidationSource();
var vs = fa.ResolveByUri("http://hl7.org/fhir/ValueSet/v2-0292");
Assert.IsNotNull(vs);
Assert.IsTrue(vs is ValueSet);
var ci = vs.Annotation <OriginInformation>();
Assert.IsTrue(ci.Origin.EndsWith("v2-tables.xml"));
vs = fa.ResolveByUri("http://hl7.org/fhir/ValueSet/administrative-gender");
Assert.IsNotNull(vs);
Assert.IsTrue(vs is ValueSet);
vs = fa.ResolveByUri("http://hl7.org/fhir/ValueSet/location-status");
Assert.IsNotNull(vs);
Assert.IsTrue(vs is ValueSet);
var rs = fa.ResolveByUri("http://hl7.org/fhir/StructureDefinition/Condition");
Assert.IsNotNull(rs);
Assert.IsTrue(rs is StructureDefinition);
ci = rs.Annotation <OriginInformation>();
Assert.IsTrue(ci.Origin.EndsWith("profiles-resources.xml"));
rs = fa.ResolveByUri("http://hl7.org/fhir/StructureDefinition/ValueSet");
Assert.IsNotNull(rs);
Assert.IsTrue(rs is StructureDefinition);
var dt = fa.ResolveByUri("http://hl7.org/fhir/StructureDefinition/Money");
Assert.IsNotNull(dt);
Assert.IsTrue(dt is StructureDefinition);
// Try to find a core extension
var ext = fa.ResolveByUri("http://hl7.org/fhir/StructureDefinition/diagnosticorder-reason");
Assert.IsNotNull(ext);
Assert.IsTrue(ext is StructureDefinition);
// Try to find an additional US profile (they are distributed with the spec for now)
var us = fa.ResolveByUri("http://hl7.org/fhir/StructureDefinition/uslab-dr");
Assert.IsNotNull(us);
Assert.IsTrue(us is StructureDefinition);
}
public MainForm()
{
InitializeComponent();
btnErrors.Tag = "OFF";
btnWarnings.Tag = "OFF";
btnMessages.Tag = "OFF";
btnError_Click(btnErrors, null);
btnWarning_Click(btnWarnings, null);
btnMessage_Click(btnMessages, null);
// Create a resource resolver that searches for the core resources in 'specification.zip', which comes with the .NET FHIR Specification NuGet package
// We create a source that takes its contents from a ZIP file (in this case the default 'specification.zip'). We decorate that source by encapsulating
// it in a CachedResolver, which speeds up access by caching conformance resources once we got them from the large files in the ZIP.
CoreSource = new CachedResolver(ZipSource.CreateValidationSource());
}
public void TestSetupIsOnce()
{
var fa = ZipSource.CreateValidationSource();
var sw = new Stopwatch();
sw.Start();
var vs = fa.ResolveByCanonicalUri("http://hl7.org/fhir/v2/vs/0292");
sw.Stop();
var sw2 = new Stopwatch();
sw2.Start();
var vs2 = fa.ResolveByCanonicalUri("http://hl7.org/fhir/v2/vs/0292");
sw2.Stop();
Assert.IsTrue(sw2.ElapsedMilliseconds < sw.ElapsedMilliseconds);
Debug.WriteLine(String.Format("First time {0}, second time {1}", sw.ElapsedMilliseconds, sw2.ElapsedMilliseconds));
}
public void Issue474StartdateIs0001_01_01()
{
var json = "{ \"resourceType\": \"Patient\", \"active\": true, \"contact\": [{\"organization\": {\"reference\": \"Organization/1\", \"display\": \"Walt Disney Corporation\" }, \"period\": { \"start\": \"0001-01-01\", \"end\": \"2018\" } } ],}";
var ctx = new ValidationSettings()
{
ResourceResolver = ZipSource.CreateValidationSource(),
};
var validator = new Validator(ctx);
var pat = new FhirJsonParser().Parse <Patient>(json);
var report = validator.Validate(pat);
Assert.IsTrue(report.Success);
}
private FhirStructureDefinitions(String bundleDir)
{
this.bundleDir = bundleDir;
if (Directory.Exists(bundleDir) == false)
{
Directory.CreateDirectory(bundleDir);
}
String specPath = Path.GetFullPath("specification.zip");
if (File.Exists(specPath) == false)
{
throw new Exception($"Missing {specPath}");
}
this.source = new ZipSource(specPath);
FhirStructureDefinitions.Self = this;
}
public void TestZipSourceMask()
{
var zipFile = Path.Combine(Directory.GetCurrentDirectory(), "specification.zip");
Assert.IsTrue(File.Exists(zipFile), "Error! specification.zip is not available.");
var za = new ZipSource(zipFile);
za.Mask = "profiles-types.xml";
var artifacts = za.ListArtifactNames().ToArray();
Assert.AreEqual(1, artifacts.Length);
Assert.AreEqual("profiles-types.xml", artifacts[0]);
var resourceIds = za.ListResourceUris(ResourceType.StructureDefinition).ToArray();
Assert.IsNotNull(resourceIds);
Assert.IsTrue(resourceIds.Length > 0);
Assert.IsTrue(resourceIds.All(url => url.StartsWith("http://hl7.org/fhir/StructureDefinition/")));
// + total number of known FHIR core types
// - total number of known (concrete) resources
// - 1 for abstract type Resource
// - 1 for abstract type DomainResource
// + 1 xhtml (not present as FhirCsType)
// =======================================
// total number of known FHIR (complex & primitive) datatypes
var coreDataTypes = ModelInfo.FhirCsTypeToString.Where(kvp => !ModelInfo.IsKnownResource(kvp.Key) &&
kvp.Value != "Resource" &&
kvp.Value != "DomainResource"
)
.Select(kvp => kvp.Value).Concat(new[] { "xhtml" });
var numCoreDataTypes = coreDataTypes.Count();
Assert.AreEqual(resourceIds.Length, numCoreDataTypes);
// Assert.IsTrue(resourceIds.All(url => ModelInfo.CanonicalUriForFhirCoreType));
var coreTypeUris = coreDataTypes.Select(typeName => ModelInfo.CanonicalUriForFhirCoreType(typeName)).ToArray();
// Boths arrays should contains same urls, possibly in different order
Assert.AreEqual(coreTypeUris.Length, resourceIds.Length);
Assert.IsTrue(coreTypeUris.All(url => resourceIds.Contains(url)));
Assert.IsTrue(resourceIds.All(url => coreTypeUris.Contains(url)));
}
public void TestLoadResourceFromZipSource()
{
// ZipSource extracts core ZIP archive to (temp) folder, then delegates to DirectorySource
// i.e. artifact summaries are harvested from files on disk
var source = ZipSource.CreateValidationSource();
var summaries = source.ListSummaries();
var patientUrl = ModelInfo.CanonicalUriForFhirCoreType(FHIRDefinedType.Patient);
var patientSummary = summaries.FindConformanceResources(patientUrl).FirstOrDefault();
Assert.IsNotNull(patientSummary);
Assert.AreEqual(ResourceType.StructureDefinition, patientSummary.ResourceType);
Assert.AreEqual(patientUrl, patientSummary.GetConformanceCanonicalUrl());
Assert.IsNotNull(patientSummary.Origin);
var patientStructure = source.LoadBySummary <StructureDefinition>(patientSummary);
Assert.IsNotNull(patientStructure);
}
public void GetSomeBundledArtifacts()
{
var za = ZipSource.CreateValidationSource();
using (var a = za.LoadArtifactByName("patient.sch"))
{
Assert.IsNotNull(a);
}
using (var a = za.LoadArtifactByName("v3-codesystems.xml"))
{
Assert.IsNotNull(a);
}
using (var a = za.LoadArtifactByName("patient.xsd"))
{
Assert.IsNotNull(a);
}
}
public void TestCacheInvalidation()
{
var src = new CachedResolver(new MultiResolver(ZipSource.CreateValidationSource()));
CachedResolver.LoadResourceEventArgs eventArgs = null;
CachedResolver.LoadResourceEventHandler handler = (sender, args) => { eventArgs = args; };
src.Load += handler;
// Verify that the Load event is fired on the initial load
const string resourceUri = "http://hl7.org/fhir/ValueSet/v2-0292";
var resource = src.ResolveByUri(resourceUri);
Assert.IsNotNull(eventArgs);
Assert.AreEqual(resourceUri, eventArgs.Url);
Assert.AreEqual(resource, eventArgs.Resource);
// Verify that the Load event is not fired on subsequent load
eventArgs = null;
resource = src.ResolveByUri(resourceUri);
Assert.IsNull(eventArgs);
// Verify that we can remove the cache entry
var result = src.InvalidateByUri(resourceUri);
Assert.IsTrue(result);
// Verify that the cache entry has been removed
result = src.InvalidateByUri(resourceUri);
Assert.IsFalse(result);
// Verify that the Load event is fired again on the next load
var resource2 = src.ResolveByUri(resourceUri);
Assert.IsNotNull(eventArgs);
Assert.AreEqual(resourceUri, eventArgs.Url);
Assert.AreEqual(resource2, eventArgs.Resource);
// Verify that the cache returned a new instance with exact same value
Assert.AreNotEqual(resource2.GetHashCode(), resource.GetHashCode());
Assert.IsTrue(resource.IsExactly(resource2));
}
static void Main(string[] args)
{
var xml = "<Patient xmlns=\"http://hl7.org/fhir\"><identifier>" +
"<use value=\"official\" /></identifier></Patient>";
MemoryStream memStream = new MemoryStream();
byte[] data = Encoding.Default.GetBytes(xml);
memStream.Write(data, 0, data.Length);
memStream.Position = 0;
XmlReader reader = XmlReader.Create(memStream);
reader.Read();
FhirXmlParsingSettings settings = new FhirXmlParsingSettings();
ISourceNode patientNode = FhirXmlNode.Read(reader, settings);
//IResourceResolver Resolver = new TestResourceResolver();
IResourceResolver Resolver = ZipSource.CreateValidationSource();
StructureDefinitionSummaryProvider Provider = new StructureDefinitionSummaryProvider(Resolver);
ITypedElement patientRootElement = patientNode.ToTypedElement(Provider);
var r = patientRootElement.Select("Patient.identifier.use");
string test = (string)r.FirstOrDefault().Value;
//ITypedElement activeElement = patientRootElement.Children("active").First();
//Assert.AreEqual("boolean", activeElement.Type);
//Assert.AreEqual("boolean", activeElement.Type);
//var patientNode = FhirXmlNode.Parse(xml);
//var use = patientNode.Children("identifier").Children("use").First();
//Assert.AreEqual("official", use.Text);
//Assert.AreEqual("Patient.identifier[0].use[0]", use.Location);
}
public ValidationFixture()
{
var zip = ZipSource.CreateValidationSource();
Resolver = new CachedResolver(
new MultiResolver(
new TestProfileArtifactSource(),
new DirectorySource(@"TestData\validation"),
zip
));
var ctx = new ValidationSettings()
{
ResourceResolver = Resolver,
GenerateSnapshot = true,
EnableXsdValidation = true,
Trace = false,
ResolveExteralReferences = true
};
Validator = new Validator(ctx);
}
public Validator GetValidator()
{
if (!IsValidationOn())
{
return(null);
}
var zipSource = ZipSource.CreateValidationSource();
var coreSource = new CachedResolver(zipSource);
var combinedSource = new MultiResolver(GetResourceResolver(), coreSource);
var settings = new ValidationSettings
{
EnableXsdValidation = true,
GenerateSnapshot = true,
Trace = true,
ResourceResolver = combinedSource,
ResolveExteralReferences = true,
SkipConstraintValidation = false
};
return(new Validator(settings));
}
public ProfileValidator(bool validateXsd, bool showTrace, bool reloadValidator, string profileFolder)
{
if (_validator != null && !reloadValidator)
{
return;
}
var coreSource = new CachedResolver(ZipSource.CreateValidationSource());
var cachedResolver = new CachedResolver(new DirectorySource(profileFolder, new DirectorySourceSettings {
IncludeSubDirectories = true
}));
var combinedSource = new MultiResolver(cachedResolver, coreSource);
var settings = new ValidationSettings
{
EnableXsdValidation = validateXsd,
GenerateSnapshot = true,
Trace = showTrace,
ResourceResolver = combinedSource,
ResolveExteralReferences = true,
SkipConstraintValidation = false
};
_validator = new Validator(settings);
}
public static Validator GetValidator()
{
var structureDefinitions = GetStructureDefinitionsPath();
var includeSubDirectories = new DirectorySourceSettings {
IncludeSubDirectories = true
};
var directorySource = new DirectorySource(structureDefinitions, includeSubDirectories);
var cachedResolver = new CachedResolver(directorySource);
var coreSource = new CachedResolver(ZipSource.CreateValidationSource());
var combinedSource = new MultiResolver(cachedResolver, coreSource);
var settings = new ValidationSettings
{
EnableXsdValidation = true,
GenerateSnapshot = true,
Trace = true,
ResourceResolver = combinedSource,
ResolveExternalReferences = true,
SkipConstraintValidation = false
};
var validator = new Validator(settings);
return(validator);
}
public static void SetupSource(TestContext t)
{
source = ZipSource.CreateValidationSource();
}
