/// <summary>
/// Generate snapshots for all StructureDefinitions available to the preprocessor
/// </summary>
/// <returns></returns>
public static OperationOutcome GenerateSnapshots(IEnumerable <StructureDefinition> sds, Action <StructureDefinition> snapshotGenerator, string path)
{
var outcome = new OperationOutcome();
foreach (var sd in sds)
{
if (!sd.HasSnapshot)
{
try
{
snapshotGenerator(sd);
}
catch (Exception e)
{
outcome.AddIssue($"Snapshot generation failed for '{sd.Url}'. Message: {e.Message}",
Issue.UNAVAILABLE_SNAPSHOT_GENERATION_FAILED, path);
}
}
if (!sd.HasSnapshot)
{
outcome.AddIssue($"Profile '{sd.Url}' does not include a snapshot.", Issue.UNAVAILABLE_NEED_SNAPSHOT, path);
}
}
return(outcome);
}
public void Setup()
{
OperationOutcome level0 = new OperationOutcome();
level0.AddIssue(Issue.CONTENT_ELEMENT_HAS_INCORRECT_TYPE.ToIssueComponent("A test error at level 0", "Patient"));
OperationOutcome level1 = new OperationOutcome();
Patient p = new Patient();
p.Active = true;
_location = new PocoNavigator(p);
_location.MoveToFirstChild();
level1.AddIssue(Issue.PROFILE_ELEMENTDEF_CARDINALITY_MISSING.ToIssueComponent("A test warning at level 1", _location));
OperationOutcome level2 = new OperationOutcome();
level2.AddIssue(Issue.UNSUPPORTED_CONSTRAINT_WITHOUT_FHIRPATH.ToIssueComponent("A test warning at level 2", "Patient.active[0].id[0]"));
level2.AddIssue(Issue.CONTENT_ELEMENT_MUST_MATCH_TYPE.ToIssueComponent("Another test error at level 2", "Patient.active[0].id[0]"));
level1.Include(level2);
level0.Include(level1);
level0.AddIssue(Issue.PROFILE_ELEMENTDEF_IS_EMPTY.ToIssueComponent("A test warning at level 0", "Patient"));
_report = level0;
}
private OperationOutcome processResult(string code, string system, string display, Coding coding, CodeableConcept codeableConcept, ValidateCodeResult result)
{
if (result?.Result?.Value == null)
{
throw Error.InvalidOperation($"Terminology service at {Endpoint.Endpoint.ToString()} did not return a result.");
}
var outcome = new OperationOutcome();
if (result?.Result?.Value == false)
{
string message = result?.Message?.Value;
if (message != null)
{
outcome.AddIssue(message, Issue.TERMINOLOGY_CODE_NOT_IN_VALUESET);
}
else
{
if (code != null && coding == null)
{
coding = new Coding(system, code, display);
}
var codeDisplay = codeableConcept != null?FhirSerializer.SerializeToJson(codeableConcept)
: FhirSerializer.SerializeToJson(coding);
outcome.AddIssue($"Validation of '{codeDisplay}' failed, but" +
$"the terminology service at {Endpoint.Endpoint.ToString()} did not provide further details.",
Issue.TERMINOLOGY_CODE_NOT_IN_VALUESET);
}
}
return(outcome);
}
public OperationOutcome ValidateBinding(IElementNavigator instance, ElementDefinition definition)
{
var outcome = new OperationOutcome();
if (definition.Binding != null)
{
var binding = definition.Binding;
if (binding.ValueSet != null)
{
var uri = (binding.ValueSet as FhirUri)?.Value;
// == null, so we check whether this could NOT be casted to a FhirUri, thus is a ValueSet reference
if (uri == null)
{
uri = (binding.ValueSet as ResourceReference).Reference;
var codedType = Validator.DetermineType(definition, instance);
if (codedType != null)
{
if (codedType.Value.IsBindeableFhirType())
{
var bindable = instance.ParseBindable(codedType.Value);
if (bindable is Coding)
{
return(ValidateBinding(bindable as Coding, uri, binding.Strength));
}
else
{
return(ValidateBinding(bindable as CodeableConcept, uri, binding.Strength));
}
}
else
{
outcome.AddIssue($"A binding is given ('{uri}'), but the instance data is of type '{codedType.Value}', which is not bindeable.", Issue.CONTENT_TYPE_NOT_BINDEABLE, instance);
}
}
else
{
outcome.AddIssue($"Cannot determine type of data in instance to extract code/system information", Issue.CONTENT_ELEMENT_CANNOT_DETERMINE_TYPE, instance);
}
}
else
{
outcome.AddIssue($"Binding element references a valueset by uri ({uri}), which cannot be used to validate a binding",
Issue.UNSUPPORTED_URI_BINDING_NOT_SUPPORTED, instance);
}
}
else
{
outcome.AddIssue($"Encountered a binding element without a ValueSet reference", Issue.PROFILE_BINDING_WITHOUT_VALUESET, instance);
}
}
return(outcome);
}
public OperationOutcome ValidateCode(string uri, string code, string system, string display = null, bool abstractAllowed = false)
{
var result = new OperationOutcome();
var vs = _resolver.FindValueSet(uri);
if (vs == null)
{
result.AddIssue($"Cannot retrieve valueset '{uri}'", Issue.UNAVAILABLE_VALUESET);
return(result);
}
// We might have a cached or pre-expanded version brought to us by the _source
if (!vs.HasExpansion)
{
// This will expand te vs - since we do not deepcopy() it, it will change the instance
// as it was passed to us from the source
try
{
_expander.Expand(vs);
}
catch (Exception e)
{
var tooComplex = e is NotSupportedException || e is ValueSetExpansionTooBigException;
result.AddIssue($"ValueSet cannot be expanded: {e.Message}",
tooComplex ? Issue.TERMINOLOGY_VALUESET_TOO_COMPLEX : Issue.TERMINOLOGY_EXPANSION_FAILED);
return(result);
}
}
// No fallback necessary, just do a direct check for now
var component = vs.FindInExpansion(code, system);
var codeLabel = $"Code '{code}' from system '{system}'";
if (component == null)
{
result.AddIssue($"{codeLabel} does not exists in valueset '{uri}'", Issue.TERMINOLOGY_CODE_NOT_IN_VALUESET);
}
else
{
if (component.Abstract == true && !abstractAllowed)
{
result.AddIssue($"{codeLabel} is abstract, which is not allowed here", Issue.TERMINOLOGY_ABSTRACT_CODE_NOT_ALLOWED);
}
if (display != null && component.Display != null && display != component.Display)
{
result.AddIssue($"{codeLabel} has incorrect display '{display}', should be '{component.Display}'", Issue.TERMINOLOGY_INCORRECT_DISPLAY);
}
}
return(result);
}
// This is the one and only main internal entry point for all validations, which in its term
// will call step 1 in the validator, the function validateElement
internal OperationOutcome Validate(ScopedNavigator instance, IEnumerable <ElementDefinitionNavigator> definitions)
{
var outcome = new OperationOutcome();
try
{
List <ElementDefinitionNavigator> allDefinitions = new List <ElementDefinitionNavigator>(definitions);
if (allDefinitions.Count() == 1)
{
outcome.Add(validateElement(allDefinitions.Single(), instance));
}
else
{
var validators = allDefinitions.Select(nav => createValidator(nav, instance));
outcome.Add(this.Combine(BatchValidationMode.All, instance, validators));
}
}
catch (Exception e)
{
outcome.AddIssue($"Internal logic failure: {e.Message}", Issue.PROCESSING_CATASTROPHIC_FAILURE, instance);
}
return(outcome);
}
internal void Trace(OperationOutcome outcome, string message, Issue issue, IElementNavigator location)
{
if (Settings.Trace || issue.Severity != OperationOutcome.IssueSeverity.Information)
{
outcome.AddIssue(message, issue, location);
}
}
public static OperationOutcome.IssueComponent AddIssue(this OperationOutcome outcome, string message, Issue infoIssue, string location = null)
{
var issue = infoIssue.ToIssueComponent(message, location);
outcome.AddIssue(issue);
return(issue);
}
public static OperationOutcome NewOutcomeWithIssue(this Issue infoIssue, string message, string location = null)
{
var outcome = new OperationOutcome();
var issue = infoIssue.ToIssueComponent(message, location);
outcome.AddIssue(issue);
return(outcome);
}
internal OperationOutcome.IssueComponent Trace(OperationOutcome outcome, string message, Issue issue, string location)
{
if (Settings.Trace || issue.Severity != OperationOutcome.IssueSeverity.Information)
{
return(outcome.AddIssue(message, issue, location));
}
return(null);
}
public static void Add(this OperationOutcome outcome, OperationOutcome other)
{
outcome.AddIssue(other.Issue);
//foreach (var issue in other.Issue)
//{
// //var myIssue = (OperationOutcome.IssueComponent)issue.DeepCopy();
// var myIssue = issue;
// outcome.AddIssue(myIssue);
//}
}
internal static OperationOutcome ValidateXml(this Validator me, XDocument instance)
{
var result = new OperationOutcome();
ValidationEventHandler veh = (o, args) => result.AddIssue(ToIssueComponent(args));
instance.Validate(SchemaCollection.ValidationSchemaSet, veh);
return(result);
}
public static void Include(this OperationOutcome outcome, OperationOutcome other)
{
foreach (var issue in other.Issue)
{
// var myIssue = (OperationOutcome.IssueComponent)issue.DeepCopy();
var myIssue = issue;
myIssue.SetHierarchyLevel(myIssue.GetHierarchyLevel() + 1);
outcome.AddIssue(myIssue);
}
}
private static OperationOutcome validateMinMaxValue(Validator me, Element definition, ITypedElement instance,
int comparisonOutcome, string elementName)
{
var outcome = new OperationOutcome();
if (definition != null)
{
// Min/max are only defined for ordered types
if (definition.GetType().IsOrderedFhirType())
{
try
{
var instanceValue = instance.GetComparableValue(definition.GetType());
if (instanceValue != null)
{
if (Compare(instanceValue, definition) == comparisonOutcome)
{
var label = comparisonOutcome == -1 ? "smaller than" :
comparisonOutcome == 0 ? "equal to" :
"larger than";
var issue = comparisonOutcome == -1 ? Issue.CONTENT_ELEMENT_PRIMITIVE_VALUE_TOO_SMALL :
Issue.CONTENT_ELEMENT_PRIMITIVE_VALUE_TOO_LARGE;
outcome.AddIssue($"Instance value '{instanceValue}' is {label} {elementName} '{definition}'", issue, instance);
}
}
}
catch (NotSupportedException ns)
{
outcome.AddIssue($"Comparing the instance against the {elementName} failed: {ns.Message}", Issue.UNSUPPORTED_MIN_MAX_QUANTITY, instance);
}
}
else
{
me.Trace(outcome, $"{elementName} was given in ElementDefinition, but type '{definition.TypeName}' is not an ordered type", Issue.PROFILE_ELEMENTDEF_MIN_MAX_USES_UNORDERED_TYPE, instance);
}
}
return(outcome);
}
private OperationOutcome validateCodeVS(ValueSet vs, string code, string system, string display, bool?abstractAllowed)
{
if (code == null)
{
return(Issue.TERMINOLOGY_NO_CODE_IN_INSTANCE.NewOutcomeWithIssue($"No code supplied."));
}
lock (vs.SyncLock)
{
// We might have a cached or pre-expanded version brought to us by the _source
if (!vs.HasExpansion)
{
// This will expand te vs - since we do not deepcopy() it, it will change the instance
// as it was passed to us from the source
_expander.Expand(vs);
}
}
var component = vs.FindInExpansion(code, system);
var codeLabel = $"Code '{code}' from system '{system}'";
var result = new OperationOutcome();
if (component == null)
{
result.AddIssue($"{codeLabel} does not exist in valueset '{vs.Url}'", Issue.TERMINOLOGY_CODE_NOT_IN_VALUESET);
}
else
{
if (component.Abstract == true && abstractAllowed == false) // will be ignored if abstractAllowed == null
{
result.AddIssue($"{codeLabel} is abstract, which is not allowed here", Issue.TERMINOLOGY_ABSTRACT_CODE_NOT_ALLOWED);
}
if (display != null && component.Display != null && display != component.Display)
{
result.AddIssue($"{codeLabel} has incorrect display '{display}', should be '{component.Display}'", Issue.TERMINOLOGY_INCORRECT_DISPLAY);
}
}
return(result);
}
private OperationOutcome callService(string code, string system, string display, string uri, BindingStrength?strength, string path)
{
var outcome = new OperationOutcome();
OperationOutcome validateResult = _service.ValidateCode(uri, code, system, display, abstractAllowed: false);
var codeLabel = $"Code '{code}' from system '{system}'";
if (display != null)
{
codeLabel += $" with display '{display}'";
}
if (validateResult.Where(type: OperationOutcome.IssueType.NotSupported).Any())
{
if (strength != BindingStrength.Example)
{
outcome.AddIssue($"The terminology service is incapable of validating {codeLabel} (valueset '{uri}').", Issue.UNSUPPORTED_BINDING_NOT_SUPPORTED_BY_SERVICE, path);
validateResult.MakeInformational();
outcome.Include(validateResult);
}
return(outcome);
}
if (!validateResult.Success)
{
if (strength == BindingStrength.Required)
{
outcome.AddIssue($"{codeLabel} is not valid for required binding to valueset '{uri}'", Issue.CONTENT_INVALID_FOR_REQUIRED_BINDING, path);
}
else if (strength != BindingStrength.Example)
{
outcome.AddIssue($"{codeLabel} is not valid for non-required binding to valueset '{uri}'", Issue.CONTENT_INVALID_FOR_NON_REQUIRED_BINDING, path);
}
validateResult.MakeInformational();
}
outcome.Include(validateResult);
return(outcome);
}
/// <summary>
/// Resolves the StructureDefinitions referred to by the given canonicals, and adds them
/// to the list of StructureDefinitions available to the preprocessor
/// </summary>
/// <returns></returns>
public OperationOutcome Resolve()
{
if (_lastResolutionOutcome != null)
{
return(_lastResolutionOutcome);
}
var outcome = new OperationOutcome();
// Go through all entries to find those that don't yet have a StructureDefinition
foreach (var entry in _allEntries.Where(e => e.Unresolved))
{
StructureDefinition structureDefinition = null;
try
{
// Once FindStructureDefinition() gets an overload to resolve multiple at the same time,
// use that one
structureDefinition = _resolver(entry.Reference);
if (structureDefinition == null)
{
outcome.AddIssue($"Unable to resolve reference to profile '{entry.Reference}'", Issue.UNAVAILABLE_REFERENCED_PROFILE, _path);
}
else
{
entry.StructureDefinition = structureDefinition;
}
}
catch (Exception e)
{
outcome.AddIssue($"Resolution of profile at '{entry.Reference}' failed: {e.Message}", Issue.UNAVAILABLE_REFERENCED_PROFILE, _path);
continue;
}
}
_lastResolutionOutcome = outcome;
return(outcome);
}
/// <summary>
/// Generate snapshots for all StructureDefinitions available to the preprocessor
/// </summary>
/// <returns></returns>
public static OperationOutcome GenerateSnapshots(IEnumerable <StructureDefinition> sds, Func <StructureDefinition, OperationOutcome> snapshotGenerator, string path)
{
var outcome = new OperationOutcome();
foreach (var sd in sds)
{
lock (sd.SyncLock)
{
if (!sd.HasSnapshot)
{
try
{
var snapshotOutcome = snapshotGenerator(sd);
// [WMR 20180725] Null outcome also indicates success
if (snapshotOutcome != null && !snapshotOutcome.Success)
{
outcome.AddIssue($"Snapshot generation failed for '{sd.Url}'. Details follow below.",
Issue.UNAVAILABLE_SNAPSHOT_GENERATION_FAILED, path);
outcome.Add(snapshotOutcome);
}
}
catch (Exception e)
{
outcome.AddIssue($"Snapshot generation failed for '{sd.Url}'. Message: {e.Message}",
Issue.UNAVAILABLE_SNAPSHOT_GENERATION_FAILED, path);
}
}
}
if (!sd.HasSnapshot)
{
outcome.AddIssue($"Profile '{sd.Url}' does not include a snapshot.", Issue.UNAVAILABLE_NEED_SNAPSHOT, path);
}
}
return(outcome);
}
OperationOutcome.IssueComponent addIssue(OperationOutcome.IssueComponent component, string profileUrl = null)
{
if (component == null)
{
throw Error.ArgumentNull(nameof(component));
}
if (_outcome == null)
{
_outcome = new OperationOutcome();
}
// Return current profile url in Diagnostics field
component.Diagnostics = profileUrl ?? CurrentProfileUri;
_outcome.AddIssue(component);
return(component);
}
private OperationOutcome callService(string canonical, string code = null, string system = null, string display = null,
Coding coding = null, CodeableConcept cc = null, bool?abstractAllowed = null)
{
var outcome = new OperationOutcome();
try
{
outcome = _service.ValidateCode(canonical: canonical, code: code, system: system, display: display,
coding: coding, codeableConcept: cc, @abstract: abstractAllowed);
foreach (var issue in outcome.Issue)
{
issue.Location = new string[] { _path }
}
;
}
catch (TerminologyServiceException tse)
{
outcome.AddIssue($"Terminology service failed while validating code '{code}' (system '{system}'): {tse.Message}", Issue.TERMINOLOGY_SERVICE_FAILED, _path);
}
return(outcome);
}
public OperationOutcome Process()
{
var outcome = new OperationOutcome();
// Start preprocessing by resolving the references to the profiles (if any)
var resolveOutcome = _profiles.Resolve();
outcome.Add(resolveOutcome);
if (resolveOutcome.Success)
{
// Then, validate consistency of the profile assertions
var validationOutcome = _profiles.Validate();
outcome.Add(validationOutcome);
if (validationOutcome.Success)
{
if (_profiles.MinimalProfiles.Any())
{
// Then, generate snapshots for all sds that we have found
var genSnapshotOutcome = GenerateSnapshots(_profiles.MinimalProfiles, _snapshotGenerator, _path);
outcome.Add(genSnapshotOutcome);
if (genSnapshotOutcome.Success)
{
// Finally, return navigators to the definitions
Result = CreateNavigators(_profiles.MinimalProfiles);
}
}
else
{
outcome.AddIssue("There are no profile and type assertions at this point in the instance, so validation cannot succeed",
Issue.PROFILE_NO_PROFILE_TO_VALIDATE_AGAINST, _path);
}
}
}
return(outcome);
}
internal static OperationOutcome ValidatedParseXml(this Validator me, XmlReader instance, out Resource poco)
{
var result = new OperationOutcome();
try
{
if (me.Settings.EnableXsdValidation)
{
var doc = XDocument.Load(instance, LoadOptions.SetLineInfo);
result.Add(me.ValidateXml(doc));
instance = doc.CreateReader();
}
poco = (Resource)(new FhirXmlParser()).Parse(instance, typeof(Resource));
}
catch (Exception e)
{
result.AddIssue($"Parsing of Xml into a FHIR Poco failed: {e.Message}", Issue.XSD_CONTENT_POCO_PARSING_FAILED, (string)null);
poco = null;
}
return(result);
}
private OperationOutcome validateCodeVS(ValueSet vs, CodeableConcept cc, bool?abstractAllowed)
{
var outcome = new OperationOutcome();
// Maybe just a text, but if there are no codings, that's a positive result
if (!cc.Coding.Any())
{
return(outcome);
}
// If we have just 1 coding, we better handle this using the simpler version of ValidateBinding
if (cc.Coding.Count == 1)
{
return(validateCodeVS(vs, cc.Coding.Single(), abstractAllowed));
}
// Else, look for one succesful match in any of the codes in the CodeableConcept
var callResults = cc.Coding.Select(coding => validateCodeVS(vs, coding, abstractAllowed));
var successOutcome = callResults.Where(r => r.Success).OrderBy(oo => oo.Warnings).FirstOrDefault();
if (successOutcome == null)
{
outcome.AddIssue("None of the Codings in the CodeableConcept were valid for the binding. Details follow.", Issue.CONTENT_INVALID_FOR_REQUIRED_BINDING);
foreach (var cr in callResults)
{
cr.MakeInformational();
outcome.Include(cr);
}
}
else
{
outcome.Add(successOutcome);
}
return(outcome);
}
public static void AddIssue(this OperationOutcome outcome, params OperationOutcome.IssueComponent[] issue)
{
outcome.AddIssue((IEnumerable <OperationOutcome.IssueComponent>)issue);
}
public static OperationOutcome AddError(this OperationOutcome outcome, string message)
{
return(outcome.AddIssue(OperationOutcome.IssueSeverity.Error, message));
}
public static OperationOutcome AddMessage(this OperationOutcome outcome, HttpStatusCode code, string message)
{
return(outcome.AddIssue(IssueSeverityOf(code), message));
}
public static OperationOutcome AddMessage(this OperationOutcome outcome, string message)
{
return(outcome.AddIssue(OperationOutcome.IssueSeverity.Information, message));
}
public static OperationOutcome Combine(this Validator validator, BatchValidationMode mode, ITypedElement instance, IEnumerable <Func <OperationOutcome> > validations)
{
if (validations.Count() == 0)
{
return(new OperationOutcome());
}
if (validations.Count() == 1)
{
// To not pollute the output if there's just a single input, just add it to the output
return(validations.First()());
}
OperationOutcome combinedResult = new OperationOutcome();
var modeLabel = mode == BatchValidationMode.All ? "ALL" : "ANY";
validator.Trace(combinedResult, $"Combination of {validations.Count()} child validation runs, {modeLabel} must succeed", Issue.PROCESSING_PROGRESS, instance);
int failures = 0;
int successes = 0;
List <OperationOutcome> results = new List <OperationOutcome>();
// Run the given validations one by one, short circuiting when ANY success is enough
foreach (var validation in validations)
{
var result = validation();
results.Add(result);
if (result.Success)
{
successes += 1;
}
else
{
failures += 1;
}
if (mode == BatchValidationMode.Any && successes > 0)
{
break; // shortcut evaluation
}
}
// Did we have success overall?
bool success = mode == BatchValidationMode.Any && successes > 0 ||
mode == BatchValidationMode.All && failures == 0 ||
mode == BatchValidationMode.Once && successes == 1;
// Now, build final report
for (var index = 0; index < results.Count; index++)
{
var result = results[index];
validator.Trace(combinedResult, $"Report {index}: {(result.Success ? "SUCCESS" : "FAILURE")}", Issue.PROCESSING_PROGRESS, instance);
if (success)
{
// We'd like to include all results of the combined reports, but if the total result is a success,
// any errors in failing runs should just be informational
if (!result.Success)
{
result.MakeInformational();
}
}
combinedResult.Include(result);
}
if (success)
{
validator.Trace(combinedResult, "Combined validation succeeded", Issue.PROCESSING_PROGRESS, instance);
}
else
{
combinedResult.AddIssue($"Combined {modeLabel} validation failed, {failures} child validation runs failed, {successes} succeeded", Issue.PROCESSING_PROGRESS, instance);
}
return(combinedResult);
}
public static void AddIssue(this OperationOutcome outcome, string message, Issue infoIssue, string location = null)
{
outcome.AddIssue(infoIssue.ToIssueComponent(message, location));
}
public static void AddIssue(this OperationOutcome outcome, string message, Issue infoIssue, IElementNavigator location)
{
outcome.AddIssue(infoIssue.ToIssueComponent(message, location));
}