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Replaced references to SystemIdentifier with SystemUrlAndVersion.

This commit is contained in:
ianmarshall 2020-09-30 22:04:08 -04:00
parent 90f1981817
commit 7899837fe0
1 changed files with 32 additions and 32 deletions
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64
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/InMemoryTerminologyServerValidationSupport.java
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@ -124,12 +124,12 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
@Override @Override
public CodeValidationResult public CodeValidationResult
validateCodeInValueSet(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystemIdentifier, String theCode, String theDisplay, @Nonnull IBaseResource theValueSet) { validateCodeInValueSet(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystemUrlAndVersion, String theCode, String theDisplay, @Nonnull IBaseResource theValueSet) {
org.hl7.fhir.r5.model.ValueSet expansion = expandValueSetToCanonical(theValidationSupportContext, theValueSet, theCodeSystemIdentifier, theCode); org.hl7.fhir.r5.model.ValueSet expansion = expandValueSetToCanonical(theValidationSupportContext, theValueSet, theCodeSystemUrlAndVersion, theCode);
if (expansion == null) { if (expansion == null) {
return null; return null;
} }
return validateCodeInExpandedValueSet(theValidationSupportContext, theOptions, theCodeSystemIdentifier, theCode, theDisplay, expansion); return validateCodeInExpandedValueSet(theValidationSupportContext, theOptions, theCodeSystemUrlAndVersion, theCode, theDisplay, expansion);
} }
@ -208,13 +208,13 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
} }
private CodeValidationResult validateCodeInExpandedValueSet(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystemIdentifierToValidate, String theCodeToValidate, String theDisplayToValidate, IBaseResource theExpansion) { private CodeValidationResult validateCodeInExpandedValueSet(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystemUrlAndVersionToValidate, String theCodeToValidate, String theDisplayToValidate, IBaseResource theExpansion) {
assert theExpansion != null; assert theExpansion != null;
boolean caseSensitive = true; boolean caseSensitive = true;
IBaseResource codeSystemToValidateResource = null; IBaseResource codeSystemToValidateResource = null;
if (!theOptions.isInferSystem() && isNotBlank(theCodeSystemIdentifierToValidate)) { if (!theOptions.isInferSystem() && isNotBlank(theCodeSystemUrlAndVersionToValidate)) {
codeSystemToValidateResource = theValidationSupportContext.getRootValidationSupport().fetchCodeSystem(theCodeSystemIdentifierToValidate); codeSystemToValidateResource = theValidationSupportContext.getRootValidationSupport().fetchCodeSystem(theCodeSystemUrlAndVersionToValidate);
} }
List<FhirVersionIndependentConcept> codes = new ArrayList<>(); List<FhirVersionIndependentConcept> codes = new ArrayList<>();
@ -291,13 +291,13 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
String codeSystemUrlToValidate=null; String codeSystemUrlToValidate=null;
String codeSystemVersionToValidate=null; String codeSystemVersionToValidate=null;
if (theCodeSystemIdentifierToValidate != null) { if (theCodeSystemUrlAndVersionToValidate != null) {
int versionIndex = theCodeSystemIdentifierToValidate.indexOf("|"); int versionIndex = theCodeSystemUrlAndVersionToValidate.indexOf("|");
if (versionIndex > -1) { if (versionIndex > -1) {
codeSystemUrlToValidate = theCodeSystemIdentifierToValidate.substring(0, versionIndex); codeSystemUrlToValidate = theCodeSystemUrlAndVersionToValidate.substring(0, versionIndex);
codeSystemVersionToValidate = theCodeSystemIdentifierToValidate.substring(versionIndex+1); codeSystemVersionToValidate = theCodeSystemUrlAndVersionToValidate.substring(versionIndex+1);
} else { } else {
codeSystemUrlToValidate = theCodeSystemIdentifierToValidate; codeSystemUrlToValidate = theCodeSystemUrlAndVersionToValidate;
} }
} }
for (FhirVersionIndependentConcept nextExpansionCode : codes) { for (FhirVersionIndependentConcept nextExpansionCode : codes) {
@ -332,10 +332,10 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
String message; String message;
if ("fragment".equals(codeSystemResourceContentMode)) { if ("fragment".equals(codeSystemResourceContentMode)) {
severity = ValidationMessage.IssueSeverity.WARNING; severity = ValidationMessage.IssueSeverity.WARNING;
message = "Unknown code in fragment CodeSystem '" + (isNotBlank(theCodeSystemIdentifierToValidate) ? theCodeSystemIdentifierToValidate + "#" : "") + theCodeToValidate + "'"; message = "Unknown code in fragment CodeSystem '" + (isNotBlank(theCodeSystemUrlAndVersionToValidate) ? theCodeSystemUrlAndVersionToValidate + "#" : "") + theCodeToValidate + "'";
} else { } else {
severity = ValidationMessage.IssueSeverity.ERROR; severity = ValidationMessage.IssueSeverity.ERROR;
message = "Unknown code '" + (isNotBlank(theCodeSystemIdentifierToValidate) ? theCodeSystemIdentifierToValidate + "#" : "") + theCodeToValidate + "'"; message = "Unknown code '" + (isNotBlank(theCodeSystemUrlAndVersionToValidate) ? theCodeSystemUrlAndVersionToValidate + "#" : "") + theCodeToValidate + "'";
} }
return new CodeValidationResult() return new CodeValidationResult()
@ -349,7 +349,7 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
} }
@Nullable @Nullable
private org.hl7.fhir.r5.model.ValueSet expandValueSetDstu2Hl7Org(ValidationSupportContext theValidationSupportContext, ValueSet theInput, @Nullable String theWantSystemIdentifier, @Nullable String theWantCode) { private org.hl7.fhir.r5.model.ValueSet expandValueSetDstu2Hl7Org(ValidationSupportContext theValidationSupportContext, ValueSet theInput, @Nullable String theWantSystemUrlAndVersion, @Nullable String theWantCode) {
Function<String, CodeSystem> codeSystemLoader = t -> { Function<String, CodeSystem> codeSystemLoader = t -> {
org.hl7.fhir.dstu2.model.ValueSet codeSystem = (org.hl7.fhir.dstu2.model.ValueSet) theValidationSupportContext.getRootValidationSupport().fetchCodeSystem(t); org.hl7.fhir.dstu2.model.ValueSet codeSystem = (org.hl7.fhir.dstu2.model.ValueSet) theValidationSupportContext.getRootValidationSupport().fetchCodeSystem(t);
CodeSystem retVal = new CodeSystem(); CodeSystem retVal = new CodeSystem();
@ -362,12 +362,12 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
}; };
org.hl7.fhir.r5.model.ValueSet input = ValueSet10_50.convertValueSet(theInput); org.hl7.fhir.r5.model.ValueSet input = ValueSet10_50.convertValueSet(theInput);
org.hl7.fhir.r5.model.ValueSet output = expandValueSetR5(theValidationSupportContext, input, codeSystemLoader, valueSetLoader, theWantSystemIdentifier, theWantCode); org.hl7.fhir.r5.model.ValueSet output = expandValueSetR5(theValidationSupportContext, input, codeSystemLoader, valueSetLoader, theWantSystemUrlAndVersion, theWantCode);
return (output); return (output);
} }
@Nullable @Nullable
private org.hl7.fhir.r5.model.ValueSet expandValueSetDstu2(ValidationSupportContext theValidationSupportContext, ca.uhn.fhir.model.dstu2.resource.ValueSet theInput, @Nullable String theWantSystemIdentifier, @Nullable String theWantCode) { private org.hl7.fhir.r5.model.ValueSet expandValueSetDstu2(ValidationSupportContext theValidationSupportContext, ca.uhn.fhir.model.dstu2.resource.ValueSet theInput, @Nullable String theWantSystemUrlAndVersion, @Nullable String theWantCode) {
IParser parserRi = FhirContext.forCached(FhirVersionEnum.DSTU2_HL7ORG).newJsonParser(); IParser parserRi = FhirContext.forCached(FhirVersionEnum.DSTU2_HL7ORG).newJsonParser();
IParser parserHapi = FhirContext.forCached(FhirVersionEnum.DSTU2).newJsonParser(); IParser parserHapi = FhirContext.forCached(FhirVersionEnum.DSTU2).newJsonParser();
@ -390,7 +390,7 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
org.hl7.fhir.dstu2.model.ValueSet valueSetRi = parserRi.parseResource(org.hl7.fhir.dstu2.model.ValueSet.class, parserHapi.encodeResourceToString(theInput)); org.hl7.fhir.dstu2.model.ValueSet valueSetRi = parserRi.parseResource(org.hl7.fhir.dstu2.model.ValueSet.class, parserHapi.encodeResourceToString(theInput));
org.hl7.fhir.r5.model.ValueSet input = ValueSet10_50.convertValueSet(valueSetRi); org.hl7.fhir.r5.model.ValueSet input = ValueSet10_50.convertValueSet(valueSetRi);
org.hl7.fhir.r5.model.ValueSet output = expandValueSetR5(theValidationSupportContext, input, codeSystemLoader, valueSetLoader, theWantSystemIdentifier, theWantCode); org.hl7.fhir.r5.model.ValueSet output = expandValueSetR5(theValidationSupportContext, input, codeSystemLoader, valueSetLoader, theWantSystemUrlAndVersion, theWantCode);
return (output); return (output);
} }
@ -439,7 +439,7 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
} }
@Nullable @Nullable
private org.hl7.fhir.r5.model.ValueSet expandValueSetDstu3(ValidationSupportContext theValidationSupportContext, org.hl7.fhir.dstu3.model.ValueSet theInput, @Nullable String theWantSystemIdentifier, @Nullable String theWantCode) { private org.hl7.fhir.r5.model.ValueSet expandValueSetDstu3(ValidationSupportContext theValidationSupportContext, org.hl7.fhir.dstu3.model.ValueSet theInput, @Nullable String theWantSystemUrlAndVersion, @Nullable String theWantCode) {
Function<String, org.hl7.fhir.r5.model.CodeSystem> codeSystemLoader = t -> { Function<String, org.hl7.fhir.r5.model.CodeSystem> codeSystemLoader = t -> {
org.hl7.fhir.dstu3.model.CodeSystem codeSystem = (org.hl7.fhir.dstu3.model.CodeSystem) theValidationSupportContext.getRootValidationSupport().fetchCodeSystem(t); org.hl7.fhir.dstu3.model.CodeSystem codeSystem = (org.hl7.fhir.dstu3.model.CodeSystem) theValidationSupportContext.getRootValidationSupport().fetchCodeSystem(t);
return CodeSystem30_50.convertCodeSystem(codeSystem); return CodeSystem30_50.convertCodeSystem(codeSystem);
@ -450,12 +450,12 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
}; };
org.hl7.fhir.r5.model.ValueSet input = ValueSet30_50.convertValueSet(theInput); org.hl7.fhir.r5.model.ValueSet input = ValueSet30_50.convertValueSet(theInput);
org.hl7.fhir.r5.model.ValueSet output = expandValueSetR5(theValidationSupportContext, input, codeSystemLoader, valueSetLoader, theWantSystemIdentifier, theWantCode); org.hl7.fhir.r5.model.ValueSet output = expandValueSetR5(theValidationSupportContext, input, codeSystemLoader, valueSetLoader, theWantSystemUrlAndVersion, theWantCode);
return (output); return (output);
} }
@Nullable @Nullable
private org.hl7.fhir.r5.model.ValueSet expandValueSetR4(ValidationSupportContext theValidationSupportContext, org.hl7.fhir.r4.model.ValueSet theInput, @Nullable String theWantSystemIdentifier, @Nullable String theWantCode) { private org.hl7.fhir.r5.model.ValueSet expandValueSetR4(ValidationSupportContext theValidationSupportContext, org.hl7.fhir.r4.model.ValueSet theInput, @Nullable String theWantSystemUrlAndVersion, @Nullable String theWantCode) {
Function<String, org.hl7.fhir.r5.model.CodeSystem> codeSystemLoader = t -> { Function<String, org.hl7.fhir.r5.model.CodeSystem> codeSystemLoader = t -> {
org.hl7.fhir.r4.model.CodeSystem codeSystem = (org.hl7.fhir.r4.model.CodeSystem) theValidationSupportContext.getRootValidationSupport().fetchCodeSystem(t); org.hl7.fhir.r4.model.CodeSystem codeSystem = (org.hl7.fhir.r4.model.CodeSystem) theValidationSupportContext.getRootValidationSupport().fetchCodeSystem(t);
return CodeSystem40_50.convertCodeSystem(codeSystem); return CodeSystem40_50.convertCodeSystem(codeSystem);
@ -466,7 +466,7 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
}; };
org.hl7.fhir.r5.model.ValueSet input = ValueSet40_50.convertValueSet(theInput); org.hl7.fhir.r5.model.ValueSet input = ValueSet40_50.convertValueSet(theInput);
org.hl7.fhir.r5.model.ValueSet output = expandValueSetR5(theValidationSupportContext, input, codeSystemLoader, valueSetLoader, theWantSystemIdentifier, theWantCode); org.hl7.fhir.r5.model.ValueSet output = expandValueSetR5(theValidationSupportContext, input, codeSystemLoader, valueSetLoader, theWantSystemUrlAndVersion, theWantCode);
return (output); return (output);
} }
@ -479,12 +479,12 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
} }
@Nullable @Nullable
private org.hl7.fhir.r5.model.ValueSet expandValueSetR5(ValidationSupportContext theValidationSupportContext, org.hl7.fhir.r5.model.ValueSet theInput, Function<String, CodeSystem> theCodeSystemLoader, Function<String, org.hl7.fhir.r5.model.ValueSet> theValueSetLoader, @Nullable String theWantSystemIdentifier, @Nullable String theWantCode) { private org.hl7.fhir.r5.model.ValueSet expandValueSetR5(ValidationSupportContext theValidationSupportContext, org.hl7.fhir.r5.model.ValueSet theInput, Function<String, CodeSystem> theCodeSystemLoader, Function<String, org.hl7.fhir.r5.model.ValueSet> theValueSetLoader, @Nullable String theWantSystemUrlAndVersion, @Nullable String theWantCode) {
Set<FhirVersionIndependentConcept> concepts = new HashSet<>(); Set<FhirVersionIndependentConcept> concepts = new HashSet<>();
try { try {
expandValueSetR5IncludeOrExclude(theValidationSupportContext, concepts, theCodeSystemLoader, theValueSetLoader, theInput.getCompose().getInclude(), true, theWantSystemIdentifier, theWantCode); expandValueSetR5IncludeOrExclude(theValidationSupportContext, concepts, theCodeSystemLoader, theValueSetLoader, theInput.getCompose().getInclude(), true, theWantSystemUrlAndVersion, theWantCode);
expandValueSetR5IncludeOrExclude(theValidationSupportContext, concepts, theCodeSystemLoader, theValueSetLoader, theInput.getCompose().getExclude(), false, theWantSystemIdentifier, theWantCode); expandValueSetR5IncludeOrExclude(theValidationSupportContext, concepts, theCodeSystemLoader, theValueSetLoader, theInput.getCompose().getExclude(), false, theWantSystemUrlAndVersion, theWantCode);
} catch (ExpansionCouldNotBeCompletedInternallyException e) { } catch (ExpansionCouldNotBeCompletedInternallyException e) {
return null; return null;
} }
@ -501,16 +501,16 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
return retVal; return retVal;
} }
private void expandValueSetR5IncludeOrExclude(ValidationSupportContext theValidationSupportContext, Set<FhirVersionIndependentConcept> theConcepts, Function<String, CodeSystem> theCodeSystemLoader, Function<String, org.hl7.fhir.r5.model.ValueSet> theValueSetLoader, List<org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent> theComposeList, boolean theComposeListIsInclude, @Nullable String theWantSystemIdentifier, @Nullable String theWantCode) throws ExpansionCouldNotBeCompletedInternallyException { private void expandValueSetR5IncludeOrExclude(ValidationSupportContext theValidationSupportContext, Set<FhirVersionIndependentConcept> theConcepts, Function<String, CodeSystem> theCodeSystemLoader, Function<String, org.hl7.fhir.r5.model.ValueSet> theValueSetLoader, List<org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent> theComposeList, boolean theComposeListIsInclude, @Nullable String theWantSystemUrlAndVersion, @Nullable String theWantCode) throws ExpansionCouldNotBeCompletedInternallyException {
String wantSystemUrl = null; String wantSystemUrl = null;
String wantSystemVersion = null; String wantSystemVersion = null;
if (theWantSystemIdentifier != null) { if (theWantSystemUrlAndVersion != null) {
int versionIndex = theWantSystemIdentifier.indexOf("|"); int versionIndex = theWantSystemUrlAndVersion.indexOf("|");
if (versionIndex > -1) { if (versionIndex > -1) {
wantSystemUrl = theWantSystemIdentifier.substring(0,versionIndex); wantSystemUrl = theWantSystemUrlAndVersion.substring(0,versionIndex);
wantSystemVersion = theWantSystemIdentifier.substring(versionIndex+1); wantSystemVersion = theWantSystemUrlAndVersion.substring(versionIndex+1);
} else { } else {
wantSystemUrl = theWantSystemIdentifier; wantSystemUrl = theWantSystemUrlAndVersion;
} }
} }
@ -572,7 +572,7 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
* enumerate a set of good codes for them is a nice compromise there. * enumerate a set of good codes for them is a nice compromise there.
*/ */
for (org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent next : theComposeList) { for (org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent next : theComposeList) {
if (Objects.equals(next.getSystem(), theWantSystemIdentifier)) { if (Objects.equals(next.getSystem(), theWantSystemUrlAndVersion)) {
Optional<org.hl7.fhir.r5.model.ValueSet.ConceptReferenceComponent> matchingEnumeratedConcept = next.getConcept().stream().filter(t -> Objects.equals(t.getCode(), theWantCode)).findFirst(); Optional<org.hl7.fhir.r5.model.ValueSet.ConceptReferenceComponent> matchingEnumeratedConcept = next.getConcept().stream().filter(t -> Objects.equals(t.getCode(), theWantCode)).findFirst();
if (matchingEnumeratedConcept.isPresent()) { if (matchingEnumeratedConcept.isPresent()) {
CodeSystem.ConceptDefinitionComponent conceptDefinition = new CodeSystem.ConceptDefinitionComponent() CodeSystem.ConceptDefinitionComponent conceptDefinition = new CodeSystem.ConceptDefinitionComponent()
@ -607,7 +607,7 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
for (CanonicalType nextValueSetInclude : nextInclude.getValueSet()) { for (CanonicalType nextValueSetInclude : nextInclude.getValueSet()) {
org.hl7.fhir.r5.model.ValueSet vs = theValueSetLoader.apply(nextValueSetInclude.getValueAsString()); org.hl7.fhir.r5.model.ValueSet vs = theValueSetLoader.apply(nextValueSetInclude.getValueAsString());
if (vs != null) { if (vs != null) {
org.hl7.fhir.r5.model.ValueSet subExpansion = expandValueSetR5(theValidationSupportContext, vs, theCodeSystemLoader, theValueSetLoader, theWantSystemIdentifier, theWantCode); org.hl7.fhir.r5.model.ValueSet subExpansion = expandValueSetR5(theValidationSupportContext, vs, theCodeSystemLoader, theValueSetLoader, theWantSystemUrlAndVersion, theWantCode);
if (subExpansion == null) { if (subExpansion == null) {
throw new ExpansionCouldNotBeCompletedInternallyException(); throw new ExpansionCouldNotBeCompletedInternallyException();
} }