Validate code changes and new tests.
This commit is contained in:
ianmarshall
parent
e5daea17b7
commit
5fe46be41c
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@ -100,7 +100,11 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
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String system;
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if (haveCoding) {
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code = theCoding.getCode();
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if (theCoding.hasVersion()) {
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system = theCoding.getSystem() + "|" + theCoding.getVersion();
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} else {
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system = theCoding.getSystem();
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}
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} else {
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code = theCode.getValue();
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system = theSystem.getValue();
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@ -95,7 +95,11 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
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String system;
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if (haveCoding) {
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code = theCoding.getCode();
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if (theCoding.hasVersion()) {
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system = theCoding.getSystem() + "|" + theCoding.getVersion();
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} else {
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system = theCoding.getSystem();
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}
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} else {
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code = theCode.getValue();
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system = theSystem.getValue();
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@ -97,7 +97,11 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
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String system;
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if (haveCoding) {
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code = theCoding.getCode();
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if (theCoding.hasVersion()) {
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system = theCoding.getSystem() + "|" + theCoding.getVersion();
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} else {
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system = theCoding.getSystem();
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}
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} else {
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code = theCode.getValue();
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system = theSystem.getValue();
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@ -144,8 +144,10 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
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@IdParam(optional = true) IdType theId,
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@OperationParam(name = "identifier", min = 0, max = 1) UriType theValueSetIdentifier,
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@OperationParam(name = "url", min = 0, max = 1) UriType theValueSetUrl,
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@OperationParam(name = "valueSetVersion", min = 0, max = 1) StringType theValueSetVersion,
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@OperationParam(name = "code", min = 0, max = 1) CodeType theCode,
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@OperationParam(name = "system", min = 0, max = 1) UriType theSystem,
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@OperationParam(name = "systemVersion", min = 0, max = 1) StringType theSystemVersion,
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@OperationParam(name = "display", min = 0, max = 1) StringType theDisplay,
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@OperationParam(name = "coding", min = 0, max = 1) Coding theCoding,
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@OperationParam(name = "codeableConcept", min = 0, max = 1) CodeableConcept theCodeableConcept,
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@ -160,7 +162,19 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
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startRequest(theServletRequest);
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try {
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IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> dao = (IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept>) getDao();
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IValidationSupport.CodeValidationResult result = dao.validateCode(url, theId, theCode, theSystem, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
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UriType valueSetIdentifier;
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if (theValueSetVersion != null) {
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valueSetIdentifier = new UriType(theValueSetUrl.getValue() + "|" + theValueSetVersion);
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} else {
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valueSetIdentifier = theValueSetUrl;
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}
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UriType codeSystemIdentifier;
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if (theSystemVersion != null) {
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codeSystemIdentifier = new UriType(theSystem.getValue() + "|" + theSystemVersion);
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} else {
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codeSystemIdentifier = theSystem;
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}
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IValidationSupport.CodeValidationResult result = dao.validateCode(valueSetIdentifier, theId, theCode, codeSystemIdentifier, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
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return (Parameters) BaseJpaResourceProviderValueSetDstu2.toValidateCodeResult(getContext(), result);
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} finally {
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endRequest(theServletRequest);
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@ -66,9 +66,6 @@ public class BaseJpaResourceProviderCodeSystemR4 extends JpaResourceProviderR4<C
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IValidationSupport.LookupCodeResult result;
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if (theVersion != null) {
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result = dao.lookupCode(theCode, new UriType(theSystem.getValue() + "|" + theVersion), theCoding, theRequestDetails);
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} else if (theCoding != null && theCoding.hasVersion()) {
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Coding codingWithVersion = new Coding(theCoding.getSystem() + "|" + theCoding.getVersion(), theCoding.getCode(), theCoding.getDisplay());
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result = dao.lookupCode(theCode, theSystem, codingWithVersion, theRequestDetails);
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} else {
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result = dao.lookupCode(theCode, theSystem, theCoding, theRequestDetails);
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}
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@ -104,12 +101,6 @@ public class BaseJpaResourceProviderCodeSystemR4 extends JpaResourceProviderR4<C
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if (theVersion != null) {
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theSystem = new UriType(theSystem.asStringValue() + "|" + theVersion.toString());
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}
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if (theCodingA != null && theCodingA.hasVersion()) {
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theCodingA.setSystem(theCodingA.getSystemElement().asStringValue() + "|" + theCodingA.getVersion());
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}
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if (theCodingB != null && theCodingB.hasVersion()) {
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theCodingB.setSystem(theCodingB.getSystemElement().asStringValue() + "|" + theCodingB.getVersion());
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}
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result = dao.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theRequestDetails);
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return (Parameters) result.toParameters(theRequestDetails.getFhirContext());
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} finally {
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@ -135,8 +135,10 @@ public class BaseJpaResourceProviderValueSetR4 extends JpaResourceProviderR4<Val
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HttpServletRequest theServletRequest,
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@IdParam(optional = true) IdType theId,
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@OperationParam(name = "url", min = 0, max = 1) UriType theValueSetUrl,
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@OperationParam(name = "valueSetVersion", min = 0, max = 1) StringType theValueSetVersion,
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@OperationParam(name = "code", min = 0, max = 1) CodeType theCode,
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@OperationParam(name = "system", min = 0, max = 1) UriType theSystem,
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@OperationParam(name = "systemVersion", min = 0, max = 1) StringType theSystemVersion,
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@OperationParam(name = "display", min = 0, max = 1) StringType theDisplay,
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@OperationParam(name = "coding", min = 0, max = 1) Coding theCoding,
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@OperationParam(name = "codeableConcept", min = 0, max = 1) CodeableConcept theCodeableConcept,
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@ -146,7 +148,19 @@ public class BaseJpaResourceProviderValueSetR4 extends JpaResourceProviderR4<Val
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startRequest(theServletRequest);
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try {
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IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> dao = (IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept>) getDao();
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IValidationSupport.CodeValidationResult result = dao.validateCode(theValueSetUrl, theId, theCode, theSystem, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
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UriType valueSetIdentifier;
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if (theValueSetVersion != null) {
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valueSetIdentifier = new UriType(theValueSetUrl.getValue() + "|" + theValueSetVersion);
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} else {
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valueSetIdentifier = theValueSetUrl;
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}
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UriType codeSystemIdentifier;
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if (theSystemVersion != null) {
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codeSystemIdentifier = new UriType(theSystem.getValue() + "|" + theSystemVersion);
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} else {
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codeSystemIdentifier = theSystem;
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}
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IValidationSupport.CodeValidationResult result = dao.validateCode(valueSetIdentifier, theId, theCode, codeSystemIdentifier, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
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return (Parameters) BaseJpaResourceProviderValueSetDstu2.toValidateCodeResult(getContext(), result);
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} finally {
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endRequest(theServletRequest);
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@ -66,9 +66,6 @@ public class BaseJpaResourceProviderCodeSystemR5 extends JpaResourceProviderR5<C
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IValidationSupport.LookupCodeResult result;
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if (theVersion != null) {
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result = dao.lookupCode(theCode, new UriType(theSystem.getValue() + "|" + theVersion), theCoding, theRequestDetails);
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} else if (theCoding != null && theCoding.hasVersion()) {
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Coding codingWithVersion = new Coding(theCoding.getSystem() + "|" + theCoding.getVersion(), theCoding.getCode(), theCoding.getDisplay());
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result = dao.lookupCode(theCode, theSystem, codingWithVersion, theRequestDetails);
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} else {
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result = dao.lookupCode(theCode, theSystem, theCoding, theRequestDetails);
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}
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@ -104,12 +101,6 @@ public class BaseJpaResourceProviderCodeSystemR5 extends JpaResourceProviderR5<C
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if (theVersion != null) {
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theSystem = new UriType(theSystem.asStringValue() + "|" + theVersion.toString());
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}
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if (theCodingA != null && theCodingA.hasVersion()) {
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theCodingA.setSystem(theCodingA.getSystemElement().asStringValue() + "|" + theCodingA.getVersion());
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}
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if (theCodingB != null && theCodingB.hasVersion()) {
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theCodingB.setSystem(theCodingB.getSystemElement().asStringValue() + "|" + theCodingB.getVersion());
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}
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result = dao.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theRequestDetails);
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return (Parameters) result.toParameters(theRequestDetails.getFhirContext());
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} finally {
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@ -44,7 +44,7 @@ public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<Val
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@IdParam(optional = true) IdType theId,
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@OperationParam(name = "valueSet", min = 0, max = 1) ValueSet theValueSet,
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@OperationParam(name = "url", min = 0, max = 1) UriType theUrl,
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@OperationParam(name = "valueSetVersion", min = 0, max = 1) org.hl7.fhir.r4.model.StringType theValueSetVersion,
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@OperationParam(name = "valueSetVersion", min = 0, max = 1) StringType theValueSetVersion,
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@OperationParam(name = "filter", min = 0, max = 1) StringType theFilter,
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@OperationParam(name = "offset", min = 0, max = 1) IntegerType theOffset,
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@OperationParam(name = "count", min = 0, max = 1) IntegerType theCount,
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@ -135,8 +135,10 @@ public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<Val
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HttpServletRequest theServletRequest,
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@IdParam(optional = true) IdType theId,
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@OperationParam(name = "url", min = 0, max = 1) UriType theValueSetUrl,
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@OperationParam(name = "valueSetVersion", min = 0, max = 1) StringType theValueSetVersion,
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@OperationParam(name = "code", min = 0, max = 1) CodeType theCode,
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@OperationParam(name = "system", min = 0, max = 1) UriType theSystem,
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@OperationParam(name = "systemVersion", min = 0, max = 1) StringType theSystemVersion,
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@OperationParam(name = "display", min = 0, max = 1) StringType theDisplay,
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@OperationParam(name = "coding", min = 0, max = 1) Coding theCoding,
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@OperationParam(name = "codeableConcept", min = 0, max = 1) CodeableConcept theCodeableConcept,
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@ -146,7 +148,19 @@ public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<Val
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startRequest(theServletRequest);
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try {
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IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> dao = (IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept>) getDao();
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IValidationSupport.CodeValidationResult result = dao.validateCode(theValueSetUrl, theId, theCode, theSystem, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
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UriType valueSetIdentifier;
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if (theValueSetVersion != null) {
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valueSetIdentifier = new UriType(theValueSetUrl.getValue() + "|" + theValueSetVersion);
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} else {
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valueSetIdentifier = theValueSetUrl;
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}
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UriType codeSystemIdentifier;
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if (theSystemVersion != null) {
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codeSystemIdentifier = new UriType(theSystem.getValue() + "|" + theSystemVersion);
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} else {
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codeSystemIdentifier = theSystem;
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}
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IValidationSupport.CodeValidationResult result = dao.validateCode(valueSetIdentifier, theId, theCode, codeSystemIdentifier, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
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return (Parameters) BaseJpaResourceProviderValueSetDstu2.toValidateCodeResult(getContext(), result);
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} finally {
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endRequest(theServletRequest);
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@ -651,22 +651,22 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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*/
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private Boolean expandValueSetHandleIncludeOrExclude(@Nullable ValueSetExpansionOptions theExpansionOptions, IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theIncludeOrExclude, boolean theAdd, AtomicInteger theCodeCounter, int theQueryIndex, VersionIndependentConcept theWantConceptOrNull) {
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String system = theIncludeOrExclude.getSystem();
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boolean hasSystem = isNotBlank(system);
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String includeOrExcludeSystemUrl = theIncludeOrExclude.getSystem();
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boolean hasSystem = isNotBlank(includeOrExcludeSystemUrl);
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boolean hasValueSet = theIncludeOrExclude.getValueSet().size() > 0;
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if (hasSystem) {
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if (theWantConceptOrNull != null && theWantConceptOrNull.getSystem() != null && !system.equals(theWantConceptOrNull.getSystem())) {
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if (theWantConceptOrNull != null && theWantConceptOrNull.getSystem() != null && !includeOrExcludeSystemUrl.equals(theWantConceptOrNull.getSystem())) {
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return false;
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}
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ourLog.debug("Starting {} expansion around CodeSystem: {}", (theAdd ? "inclusion" : "exclusion"), system);
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ourLog.debug("Starting {} expansion around CodeSystem: {}", (theAdd ? "inclusion" : "exclusion"), includeOrExcludeSystemUrl);
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TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(system);
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TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(includeOrExcludeSystemUrl);
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if (cs != null) {
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return expandValueSetHandleIncludeOrExcludeUsingDatabase(theValueSetCodeAccumulator, theAddedCodes, theIncludeOrExclude, theAdd, theCodeCounter, theQueryIndex, theWantConceptOrNull, system, cs);
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return expandValueSetHandleIncludeOrExcludeUsingDatabase(theValueSetCodeAccumulator, theAddedCodes, theIncludeOrExclude, theAdd, theCodeCounter, theQueryIndex, theWantConceptOrNull, includeOrExcludeSystemUrl, cs);
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} else {
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@ -679,7 +679,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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}
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// No CodeSystem matching the URL found in the database.
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CodeSystem codeSystemFromContext = fetchCanonicalCodeSystemFromCompleteContext(system);
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CodeSystem codeSystemFromContext = fetchCanonicalCodeSystemFromCompleteContext(includeOrExcludeSystemUrl);
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if (codeSystemFromContext == null) {
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// This is a last ditch effort.. We don't have a CodeSystem resource for the desired CS, and we don't have
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@ -704,7 +704,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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for (VersionIndependentConcept next : includedConcepts) {
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String nextSystem = next.getSystem();
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if (nextSystem == null) {
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nextSystem = system;
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nextSystem = includeOrExcludeSystemUrl;
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}
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LookupCodeResult lookup = myValidationSupport.lookupCode(new ValidationSupportContext(provideValidationSupport()), nextSystem, next.getCode());
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@ -720,7 +720,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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}
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}
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String msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "expansionRefersToUnknownCs", system);
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String msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "expansionRefersToUnknownCs", includeOrExcludeSystemUrl);
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if (provideExpansionOptions(theExpansionOptions).isFailOnMissingCodeSystem()) {
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throw new PreconditionFailedException(msg);
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} else {
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@ -735,12 +735,12 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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for (ValueSet.ConceptReferenceComponent next : theIncludeOrExclude.getConcept()) {
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String nextCode = next.getCode();
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if (theWantConceptOrNull == null || theWantConceptOrNull.getCode().equals(nextCode)) {
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if (isNoneBlank(system, nextCode) && !theAddedCodes.contains(system + "|" + nextCode)) {
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if (isNoneBlank(includeOrExcludeSystemUrl, nextCode) && !theAddedCodes.contains(includeOrExcludeSystemUrl + "|" + nextCode)) {
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CodeSystem.ConceptDefinitionComponent code = findCode(codeSystemFromContext.getConcept(), nextCode);
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if (code != null) {
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String display = code.getDisplay();
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addOrRemoveCode(theValueSetCodeAccumulator, theAddedCodes, theAdd, system, nextCode, display);
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addOrRemoveCode(theValueSetCodeAccumulator, theAddedCodes, theAdd, includeOrExcludeSystemUrl, nextCode, display);
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}
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}
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@ -748,7 +748,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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}
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} else {
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List<CodeSystem.ConceptDefinitionComponent> concept = codeSystemFromContext.getConcept();
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addConceptsToList(theValueSetCodeAccumulator, theAddedCodes, system, concept, theAdd, theWantConceptOrNull);
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addConceptsToList(theValueSetCodeAccumulator, theAddedCodes, includeOrExcludeSystemUrl, concept, theAdd, theWantConceptOrNull);
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}
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return false;
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@ -841,13 +841,13 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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/*
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* Filters
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*/
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String canonicalSystem;
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String codeSystemIdentifier;
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if (codeSystemVersion != null) {
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canonicalSystem = theSystem + "|" + codeSystemVersion;
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codeSystemIdentifier = theSystem + "|" + codeSystemVersion;
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} else {
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canonicalSystem = theSystem;
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codeSystemIdentifier = theSystem;
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}
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handleFilters(bool, canonicalSystem, qb, theIncludeOrExclude);
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handleFilters(bool, codeSystemIdentifier, qb, theIncludeOrExclude);
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Query luceneQuery = bool.createQuery();
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@ -956,15 +956,15 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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}
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}
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private void handleFilters(BooleanJunction<?> theBool, String theCanonicalSystem, QueryBuilder theQb, ValueSet.ConceptSetComponent theIncludeOrExclude) {
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private void handleFilters(BooleanJunction<?> theBool, String theCodeSystemIdentifier, QueryBuilder theQb, ValueSet.ConceptSetComponent theIncludeOrExclude) {
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if (theIncludeOrExclude.getFilter().size() > 0) {
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for (ValueSet.ConceptSetFilterComponent nextFilter : theIncludeOrExclude.getFilter()) {
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handleFilter(theCanonicalSystem, theQb, theBool, nextFilter);
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handleFilter(theCodeSystemIdentifier, theQb, theBool, nextFilter);
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}
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}
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}
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private void handleFilter(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
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private void handleFilter(String theCodeSystemIdentifier, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
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if (isBlank(theFilter.getValue()) && theFilter.getOp() == null && isBlank(theFilter.getProperty())) {
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return;
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}
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@ -980,23 +980,23 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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break;
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case "concept":
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case "code":
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handleFilterConceptAndCode(theSystem, theQb, theBool, theFilter);
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handleFilterConceptAndCode(theCodeSystemIdentifier, theQb, theBool, theFilter);
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break;
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case "parent":
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case "child":
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isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
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isCodeSystemLoingOrThrowInvalidRequestException(theCodeSystemIdentifier, theFilter.getProperty());
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handleFilterLoincParentChild(theBool, theFilter);
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break;
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case "ancestor":
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isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
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handleFilterLoincAncestor(theSystem, theBool, theFilter);
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isCodeSystemLoingOrThrowInvalidRequestException(theCodeSystemIdentifier, theFilter.getProperty());
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handleFilterLoincAncestor(theCodeSystemIdentifier, theBool, theFilter);
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break;
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case "descendant":
|
||||
isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
|
||||
handleFilterLoincDescendant(theSystem, theBool, theFilter);
|
||||
isCodeSystemLoingOrThrowInvalidRequestException(theCodeSystemIdentifier, theFilter.getProperty());
|
||||
handleFilterLoincDescendant(theCodeSystemIdentifier, theBool, theFilter);
|
||||
break;
|
||||
case "copyright":
|
||||
isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
|
||||
isCodeSystemLoingOrThrowInvalidRequestException(theCodeSystemIdentifier, theFilter.getProperty());
|
||||
handleFilterLoincCopyright(theBool, theFilter);
|
||||
break;
|
||||
default:
|
||||
|
|
@ -1005,8 +1005,8 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
}
|
||||
}
|
||||
|
||||
private void isCodeSystemLoingOrThrowInvalidRequestException(String theSystem, String theProperty) {
|
||||
String systemUrl = getSystemFromCanonicalUrl(theSystem);
|
||||
private void isCodeSystemLoingOrThrowInvalidRequestException(String theSystemIdentifier, String theProperty) {
|
||||
String systemUrl = getUrlFromIdentifier(theSystemIdentifier);
|
||||
if (!isCodeSystemLoinc(systemUrl)) {
|
||||
throw new InvalidRequestException("Invalid filter, property " + theProperty + " is LOINC-specific and cannot be used with system: " + systemUrl);
|
||||
}
|
||||
|
|
@ -1435,12 +1435,12 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
}
|
||||
|
||||
@Nullable
|
||||
private TermCodeSystemVersion getCurrentCodeSystemVersion(String theUri) {
|
||||
String myVersion = getVersionFromCanonicalUrl(theUri);
|
||||
String key = theUri;
|
||||
private TermCodeSystemVersion getCurrentCodeSystemVersion(String theCodeSystemIdentifier) {
|
||||
String myVersion = getVersionFromIdentifier(theCodeSystemIdentifier);
|
||||
String key = theCodeSystemIdentifier;
|
||||
TermCodeSystemVersion retVal = myCodeSystemCurrentVersionCache.get(key.toString(), t -> myTxTemplate.execute(tx -> {
|
||||
TermCodeSystemVersion csv = null;
|
||||
TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(getSystemFromCanonicalUrl(theUri));
|
||||
TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(getUrlFromIdentifier(theCodeSystemIdentifier));
|
||||
if (cs != null) {
|
||||
if (myVersion != null) {
|
||||
csv = myCodeSystemVersionDao.findByCodeSystemPidAndVersion(cs.getPid(), myVersion);
|
||||
|
|
@ -1460,7 +1460,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
return retVal;
|
||||
}
|
||||
|
||||
private String getVersionFromCanonicalUrl(String theUri) {
|
||||
private String getVersionFromIdentifier(String theUri) {
|
||||
String retVal = null;
|
||||
if (StringUtils.isNotEmpty((theUri))) {
|
||||
int versionSeparator = theUri.lastIndexOf('|');
|
||||
|
|
@ -1471,7 +1471,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
return retVal;
|
||||
}
|
||||
|
||||
private String getSystemFromCanonicalUrl(String theUri) {
|
||||
private String getUrlFromIdentifier(String theUri) {
|
||||
String retVal = theUri;
|
||||
if (StringUtils.isNotEmpty((theUri))){
|
||||
int versionSeparator = theUri.lastIndexOf('|');
|
||||
|
|
@ -1777,15 +1777,15 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
}
|
||||
|
||||
@Override
|
||||
public CodeValidationResult validateCode(ConceptValidationOptions theOptions, IIdType theValueSetId, String theValueSetUrl, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
|
||||
public CodeValidationResult validateCode(ConceptValidationOptions theOptions, IIdType theValueSetId, String theValueSetIdentifier, String theCodeSystemIdentifierToValidate, String theCodeToValidate, String theDisplayToValidate, IBaseDatatype theCodingToValidate, IBaseDatatype theCodeableConceptToValidate) {
|
||||
|
||||
CodeableConcept codeableConcept = toCanonicalCodeableConcept(theCodeableConcept);
|
||||
CodeableConcept codeableConcept = toCanonicalCodeableConcept(theCodeableConceptToValidate);
|
||||
boolean haveCodeableConcept = codeableConcept != null && codeableConcept.getCoding().size() > 0;
|
||||
|
||||
Coding coding = toCanonicalCoding(theCoding);
|
||||
boolean haveCoding = coding != null && coding.isEmpty() == false;
|
||||
Coding canonicalCodingToValidate = toCanonicalCoding(theCodingToValidate);
|
||||
boolean haveCoding = canonicalCodingToValidate != null && canonicalCodingToValidate.isEmpty() == false;
|
||||
|
||||
boolean haveCode = theCode != null && theCode.isEmpty() == false;
|
||||
boolean haveCode = theCodeToValidate != null && theCodeToValidate.isEmpty() == false;
|
||||
|
||||
if (!haveCodeableConcept && !haveCoding && !haveCode) {
|
||||
throw new InvalidRequestException("No code, coding, or codeableConcept provided to validate");
|
||||
|
|
@ -1794,38 +1794,54 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
throw new InvalidRequestException("$validate-code can only validate (system AND code) OR (coding) OR (codeableConcept)");
|
||||
}
|
||||
|
||||
boolean haveIdentifierParam = isNotBlank(theValueSetUrl);
|
||||
String valueSetUrl;
|
||||
boolean haveIdentifierParam = isNotBlank(theValueSetIdentifier);
|
||||
String valueSetIdentifier;
|
||||
if (theValueSetId != null) {
|
||||
IBaseResource valueSet = myDaoRegistry.getResourceDao("ValueSet").read(theValueSetId);
|
||||
valueSetUrl = CommonCodeSystemsTerminologyService.getValueSetUrl(valueSet);
|
||||
StringBuilder valueSetIdentifierBuilder = new StringBuilder(CommonCodeSystemsTerminologyService.getValueSetUrl(valueSet));
|
||||
String valueSetVersion = CommonCodeSystemsTerminologyService.getValueSetVersion(valueSet);
|
||||
if (valueSetVersion != null) {
|
||||
valueSetIdentifierBuilder.append("|").append(valueSetVersion);
|
||||
}
|
||||
valueSetIdentifier = valueSetIdentifierBuilder.toString();
|
||||
|
||||
} else if (haveIdentifierParam) {
|
||||
valueSetUrl = theValueSetUrl;
|
||||
valueSetIdentifier = theValueSetIdentifier;
|
||||
} else {
|
||||
throw new InvalidRequestException("Either ValueSet ID or ValueSet identifier or system and code must be provided. Unable to validate.");
|
||||
}
|
||||
|
||||
ValidationSupportContext validationContext = new ValidationSupportContext(provideValidationSupport());
|
||||
|
||||
String code = theCode;
|
||||
String system = theSystem;
|
||||
String display = theDisplay;
|
||||
String codeValueToValidate = theCodeToValidate;
|
||||
String codeSystemIdentifierValueToValidate = theCodeSystemIdentifierToValidate;
|
||||
String codeDisplayValueToValidate = theDisplayToValidate;
|
||||
|
||||
if (haveCodeableConcept) {
|
||||
for (int i = 0; i < codeableConcept.getCoding().size(); i++) {
|
||||
Coding nextCoding = codeableConcept.getCoding().get(i);
|
||||
CodeValidationResult nextValidation = validateCode(validationContext, theOptions, nextCoding.getSystem(), nextCoding.getCode(), nextCoding.getDisplay(), valueSetUrl);
|
||||
String codeSystemIdentifier;
|
||||
if (nextCoding.hasVersion()) {
|
||||
codeSystemIdentifier = nextCoding.getSystem() + "|" + nextCoding.getVersion();
|
||||
} else {
|
||||
codeSystemIdentifier = nextCoding.getSystem();
|
||||
}
|
||||
CodeValidationResult nextValidation = validateCode(validationContext, theOptions, codeSystemIdentifier, nextCoding.getCode(), nextCoding.getDisplay(), valueSetIdentifier);
|
||||
if (nextValidation.isOk() || i == codeableConcept.getCoding().size() - 1) {
|
||||
return nextValidation;
|
||||
}
|
||||
}
|
||||
} else if (haveCoding) {
|
||||
system = coding.getSystem();
|
||||
code = coding.getCode();
|
||||
display = coding.getDisplay();
|
||||
if (canonicalCodingToValidate.hasVersion()) {
|
||||
codeSystemIdentifierValueToValidate = canonicalCodingToValidate.getSystem() + "|" + canonicalCodingToValidate.getVersion();
|
||||
} else {
|
||||
codeSystemIdentifierValueToValidate = canonicalCodingToValidate.getSystem();
|
||||
}
|
||||
codeValueToValidate = canonicalCodingToValidate.getCode();
|
||||
codeDisplayValueToValidate = canonicalCodingToValidate.getDisplay();
|
||||
}
|
||||
|
||||
return validateCode(validationContext, theOptions, system, code, display, valueSetUrl);
|
||||
return validateCode(validationContext, theOptions, codeSystemIdentifierValueToValidate, codeValueToValidate, codeDisplayValueToValidate, valueSetIdentifier);
|
||||
}
|
||||
|
||||
private boolean isNotSafeToPreExpandValueSets() {
|
||||
|
|
@ -1914,22 +1930,22 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
throw new InvalidRequestException("Unable to test subsumption across different code system versions");
|
||||
}
|
||||
|
||||
String codeACanonicalUrl;
|
||||
String codeASystemIdentifier;
|
||||
if (StringUtils.isNotEmpty(conceptA.getSystemVersion())) {
|
||||
codeACanonicalUrl = conceptA.getSystem() + "|" + conceptA.getSystemVersion();
|
||||
codeASystemIdentifier = conceptA.getSystem() + "|" + conceptA.getSystemVersion();
|
||||
} else {
|
||||
codeACanonicalUrl = conceptA.getSystem();
|
||||
codeASystemIdentifier = conceptA.getSystem();
|
||||
}
|
||||
TermConcept codeA = findCode(codeACanonicalUrl, conceptA.getCode())
|
||||
TermConcept codeA = findCode(codeASystemIdentifier, conceptA.getCode())
|
||||
.orElseThrow(() -> new InvalidRequestException("Unknown code: " + conceptA));
|
||||
|
||||
String codeBCanonicalUrl;
|
||||
String codeBSystemIdentifier;
|
||||
if (StringUtils.isNotEmpty(conceptB.getSystemVersion())) {
|
||||
codeBCanonicalUrl = conceptB.getSystem() + "|" + conceptB.getSystemVersion();
|
||||
codeBSystemIdentifier = conceptB.getSystem() + "|" + conceptB.getSystemVersion();
|
||||
} else {
|
||||
codeBCanonicalUrl = conceptB.getSystem();
|
||||
codeBSystemIdentifier = conceptB.getSystem();
|
||||
}
|
||||
TermConcept codeB = findCode(codeBCanonicalUrl, conceptB.getCode())
|
||||
TermConcept codeB = findCode(codeBSystemIdentifier, conceptB.getCode())
|
||||
.orElseThrow(() -> new InvalidRequestException("Unknown code: " + conceptB));
|
||||
|
||||
FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
|
||||
|
|
@ -2405,6 +2421,9 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
@Nullable
|
||||
protected abstract Coding toCanonicalCoding(@Nullable IBaseDatatype theCoding);
|
||||
|
||||
@Nullable
|
||||
protected abstract Coding toCanonicalCoding(@Nullable IBaseCoding theCoding);
|
||||
|
||||
@Nullable
|
||||
protected abstract CodeableConcept toCanonicalCodeableConcept(@Nullable IBaseDatatype theCodeableConcept);
|
||||
|
||||
|
|
@ -2496,14 +2515,15 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
}
|
||||
|
||||
@NotNull
|
||||
private VersionIndependentConcept toConcept(IPrimitiveType<String> theCodeType, IPrimitiveType<String> theSystemType, IBaseCoding theCodingType) {
|
||||
private VersionIndependentConcept toConcept(IPrimitiveType<String> theCodeType, IPrimitiveType<String> theCodeSystemIdentifierType, IBaseCoding theCodingType) {
|
||||
String code = theCodeType != null ? theCodeType.getValueAsString() : null;
|
||||
String system = theSystemType != null ? getSystemFromCanonicalUrl(theSystemType.getValueAsString()): null;
|
||||
String systemVersion = theSystemType != null ? getVersionFromCanonicalUrl(theSystemType.getValueAsString()): null;
|
||||
String system = theCodeSystemIdentifierType != null ? getUrlFromIdentifier(theCodeSystemIdentifierType.getValueAsString()): null;
|
||||
String systemVersion = theCodeSystemIdentifierType != null ? getVersionFromIdentifier(theCodeSystemIdentifierType.getValueAsString()): null;
|
||||
if (theCodingType != null) {
|
||||
code = theCodingType.getCode();
|
||||
system = getSystemFromCanonicalUrl(theCodingType.getSystem());
|
||||
systemVersion = getVersionFromCanonicalUrl(theCodingType.getSystem());
|
||||
Coding canonicalizedCoding = toCanonicalCoding(theCodingType);
|
||||
code = canonicalizedCoding.getCode();
|
||||
system = canonicalizedCoding.getSystem();
|
||||
systemVersion = canonicalizedCoding.getVersion();
|
||||
}
|
||||
return new VersionIndependentConcept(system, code, null, systemVersion);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -27,6 +27,7 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
|||
import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
|
||||
import ca.uhn.fhir.model.dstu2.composite.CodingDt;
|
||||
import ca.uhn.fhir.util.VersionIndependentConcept;
|
||||
import org.hl7.fhir.instance.model.api.IBaseCoding;
|
||||
import org.hl7.fhir.instance.model.api.IBaseDatatype;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.r4.model.CodeSystem;
|
||||
|
|
@ -148,6 +149,17 @@ public class TermReadSvcDstu2 extends BaseTermReadSvcImpl {
|
|||
return retVal;
|
||||
}
|
||||
|
||||
@Nullable
|
||||
@Override
|
||||
protected Coding toCanonicalCoding(@Nullable IBaseCoding theCoding) {
|
||||
Coding retVal = null;
|
||||
if (theCoding != null) {
|
||||
CodingDt coding = (CodingDt) theCoding;
|
||||
retVal = new Coding(coding.getSystem(), coding.getCode(), coding.getDisplay());
|
||||
}
|
||||
return retVal;
|
||||
}
|
||||
|
||||
@Nullable
|
||||
@Override
|
||||
protected CodeableConcept toCanonicalCodeableConcept(@Nullable IBaseDatatype theCodeableConcept) {
|
||||
|
|
@ -157,7 +169,7 @@ public class TermReadSvcDstu2 extends BaseTermReadSvcImpl {
|
|||
CodeableConceptDt cc = (CodeableConceptDt) theCodeableConcept;
|
||||
outcome.setText(cc.getText());
|
||||
for (CodingDt next : cc.getCoding()) {
|
||||
outcome.addCoding(toCanonicalCoding(next));
|
||||
outcome.addCoding(toCanonicalCoding((IBaseDatatype)next));
|
||||
}
|
||||
}
|
||||
return outcome;
|
||||
|
|
|
|||
|
|
@ -20,6 +20,7 @@ import org.hl7.fhir.dstu3.model.CodeableConcept;
|
|||
import org.hl7.fhir.dstu3.model.Coding;
|
||||
import org.hl7.fhir.dstu3.model.ValueSet;
|
||||
import org.hl7.fhir.exceptions.FHIRException;
|
||||
import org.hl7.fhir.instance.model.api.IBaseCoding;
|
||||
import org.hl7.fhir.instance.model.api.IBaseDatatype;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.utilities.validation.ValidationOptions;
|
||||
|
|
@ -112,6 +113,12 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
|
|||
return VersionConvertor_30_40.convertCoding((org.hl7.fhir.dstu3.model.Coding) theCoding);
|
||||
}
|
||||
|
||||
@Override
|
||||
@Nullable
|
||||
protected org.hl7.fhir.r4.model.Coding toCanonicalCoding(IBaseCoding theCoding) {
|
||||
return VersionConvertor_30_40.convertCoding((org.hl7.fhir.dstu3.model.Coding) theCoding);
|
||||
}
|
||||
|
||||
@Override
|
||||
@Nullable
|
||||
protected org.hl7.fhir.r4.model.CodeableConcept toCanonicalCodeableConcept(IBaseDatatype theCoding) {
|
||||
|
|
|
|||
|
|
@ -8,6 +8,7 @@ import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
|
|||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
|
||||
import ca.uhn.fhir.jpa.term.ex.ExpansionTooCostlyException;
|
||||
import org.hl7.fhir.instance.model.api.IBaseCoding;
|
||||
import org.hl7.fhir.instance.model.api.IBaseDatatype;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.r4.model.CodeSystem;
|
||||
|
|
@ -107,6 +108,11 @@ public class TermReadSvcR4 extends BaseTermReadSvcImpl implements ITermReadSvcR4
|
|||
return (Coding) theCoding;
|
||||
}
|
||||
|
||||
@Override
|
||||
protected Coding toCanonicalCoding(IBaseCoding theCoding) {
|
||||
return (Coding) theCoding;
|
||||
}
|
||||
|
||||
@Override
|
||||
protected CodeableConcept toCanonicalCodeableConcept(IBaseDatatype theCodeableConcept) {
|
||||
return (CodeableConcept) theCodeableConcept;
|
||||
|
|
|
|||
|
|
@ -12,6 +12,7 @@ import ca.uhn.fhir.jpa.term.ex.ExpansionTooCostlyException;
|
|||
import ca.uhn.fhir.util.ValidateUtil;
|
||||
import org.hl7.fhir.convertors.VersionConvertor_40_50;
|
||||
import org.hl7.fhir.convertors.conv40_50.CodeSystem40_50;
|
||||
import org.hl7.fhir.instance.model.api.IBaseCoding;
|
||||
import org.hl7.fhir.instance.model.api.IBaseDatatype;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.r5.model.CodeSystem;
|
||||
|
|
@ -111,6 +112,12 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
|
|||
return VersionConvertor_40_50.convertCoding((Coding) theCoding);
|
||||
}
|
||||
|
||||
@Override
|
||||
@Nullable
|
||||
protected org.hl7.fhir.r4.model.Coding toCanonicalCoding(IBaseCoding theCoding) {
|
||||
return VersionConvertor_40_50.convertCoding((Coding) theCoding);
|
||||
}
|
||||
|
||||
@Override
|
||||
@Nullable
|
||||
protected org.hl7.fhir.r4.model.CodeableConcept toCanonicalCodeableConcept(IBaseDatatype theCoding) {
|
||||
|
|
|
|||
|
|
@ -29,6 +29,10 @@ import org.hl7.fhir.dstu3.model.ValueSet;
|
|||
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
|
||||
import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
|
||||
import org.hl7.fhir.dstu3.model.codesystems.HttpVerb;
|
||||
import org.hl7.fhir.dstu3.model.BooleanType;
|
||||
import org.hl7.fhir.dstu3.model.CodeType;
|
||||
import org.hl7.fhir.dstu3.model.CodeableConcept;
|
||||
import org.hl7.fhir.dstu3.model.Coding;
|
||||
import org.junit.jupiter.api.AfterEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.springframework.data.domain.PageRequest;
|
||||
|
|
@ -49,6 +53,7 @@ import static org.hamcrest.Matchers.containsStringIgnoringCase;
|
|||
import static org.hamcrest.Matchers.not;
|
||||
import static org.hamcrest.Matchers.stringContainsInOrder;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertFalse;
|
||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||
import static org.junit.jupiter.api.Assertions.assertSame;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
|
|
@ -116,21 +121,16 @@ public class ResourceProviderDstu3ValueSetVersionedTest extends BaseResourceProv
|
|||
|
||||
private void loadAndPersistValueSet() throws IOException {
|
||||
ValueSet valueSet = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
|
||||
persistTwoVersionsOfValueSet(valueSet, HttpVerb.POST);
|
||||
}
|
||||
|
||||
@SuppressWarnings("EnumSwitchStatementWhichMissesCases")
|
||||
private void persistTwoVersionsOfValueSet(ValueSet theValueSet, HttpVerb theVerb) {
|
||||
theValueSet.setVersion("1");
|
||||
theValueSet.setId("ValueSet/vs1");
|
||||
theValueSet.getCompose().getInclude().get(0).setVersion("1");
|
||||
myExtensionalVsId_v1 = persistSingleValueSet(theValueSet, theVerb);
|
||||
valueSet.setVersion("1");
|
||||
valueSet.setId("ValueSet/vs1");
|
||||
valueSet.getCompose().getInclude().get(0).setVersion("1");
|
||||
myExtensionalVsId_v1 = persistSingleValueSet(valueSet, HttpVerb.POST);
|
||||
myExtensionalVsIdOnResourceTable_v1 = myValueSetDao.readEntity(myExtensionalVsId_v1, null).getId();
|
||||
|
||||
theValueSet.setVersion("2");
|
||||
theValueSet.setId("ValueSet/vs2");
|
||||
theValueSet.getCompose().getInclude().get(0).setVersion("2");
|
||||
myExtensionalVsId_v2 = persistSingleValueSet(theValueSet, theVerb);
|
||||
valueSet.setVersion("2");
|
||||
valueSet.setId("ValueSet/vs2");
|
||||
valueSet.getCompose().getInclude().get(0).setVersion("2");
|
||||
myExtensionalVsId_v2 = persistSingleValueSet(valueSet, HttpVerb.POST);
|
||||
myExtensionalVsIdOnResourceTable_v2 = myValueSetDao.readEntity(myExtensionalVsId_v2, null).getId();
|
||||
|
||||
}
|
||||
|
|
@ -138,6 +138,8 @@ public class ResourceProviderDstu3ValueSetVersionedTest extends BaseResourceProv
|
|||
private IIdType persistSingleValueSet(ValueSet theValueSet, HttpVerb theVerb) {
|
||||
final IIdType[] vsId = new IIdType[1];
|
||||
switch (theVerb) {
|
||||
case GET:
|
||||
break;
|
||||
case POST:
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
|
|
@ -154,6 +156,8 @@ public class ResourceProviderDstu3ValueSetVersionedTest extends BaseResourceProv
|
|||
}
|
||||
});
|
||||
break;
|
||||
case DELETE:
|
||||
case NULL:
|
||||
default:
|
||||
throw new IllegalArgumentException("HTTP verb is not supported: " + theVerb);
|
||||
}
|
||||
|
|
@ -1053,7 +1057,7 @@ public class ResourceProviderDstu3ValueSetVersionedTest extends BaseResourceProv
|
|||
|
||||
TermValueSetConcept concept = termValueSet.getConcepts().get(0);
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("http://acme.org|1", concept.getSystem());
|
||||
assertEquals("8450-9", concept.getCode());
|
||||
assertEquals("Systolic blood pressure--expiration", concept.getDisplay());
|
||||
assertEquals(2, concept.getDesignations().size());
|
||||
|
|
@ -1075,7 +1079,7 @@ public class ResourceProviderDstu3ValueSetVersionedTest extends BaseResourceProv
|
|||
|
||||
concept = termValueSet.getConcepts().get(1);
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("http://acme.org|1", concept.getSystem());
|
||||
assertEquals("11378-7", concept.getCode());
|
||||
assertEquals("Systolic blood pressure at First encounter", concept.getDisplay());
|
||||
assertEquals(0, concept.getDesignations().size());
|
||||
|
|
@ -1085,7 +1089,7 @@ public class ResourceProviderDstu3ValueSetVersionedTest extends BaseResourceProv
|
|||
|
||||
concept = termValueSet.getConcepts().get(22);
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("http://acme.org|1", concept.getSystem());
|
||||
assertEquals("8491-3", concept.getCode());
|
||||
assertEquals("Systolic blood pressure 1 hour minimum", concept.getDisplay());
|
||||
assertEquals(1, concept.getDesignations().size());
|
||||
|
|
@ -1100,7 +1104,7 @@ public class ResourceProviderDstu3ValueSetVersionedTest extends BaseResourceProv
|
|||
|
||||
concept = termValueSet.getConcepts().get(23);
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("http://acme.org|1", concept.getSystem());
|
||||
assertEquals("8492-1", concept.getCode());
|
||||
assertEquals("Systolic blood pressure 8 hour minimum", concept.getDisplay());
|
||||
assertEquals(0, concept.getDesignations().size());
|
||||
|
|
@ -1126,7 +1130,7 @@ public class ResourceProviderDstu3ValueSetVersionedTest extends BaseResourceProv
|
|||
|
||||
TermValueSetConcept concept = termValueSet.getConcepts().get(0);
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("http://acme.org|2", concept.getSystem());
|
||||
assertEquals("8450-9", concept.getCode());
|
||||
assertEquals("Systolic blood pressure--expiration v2", concept.getDisplay());
|
||||
assertEquals(2, concept.getDesignations().size());
|
||||
|
|
@ -1148,7 +1152,7 @@ public class ResourceProviderDstu3ValueSetVersionedTest extends BaseResourceProv
|
|||
|
||||
concept = termValueSet.getConcepts().get(1);
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("http://acme.org|2", concept.getSystem());
|
||||
assertEquals("11378-7", concept.getCode());
|
||||
assertEquals("Systolic blood pressure at First encounter v2", concept.getDisplay());
|
||||
assertEquals(0, concept.getDesignations().size());
|
||||
|
|
@ -1158,7 +1162,7 @@ public class ResourceProviderDstu3ValueSetVersionedTest extends BaseResourceProv
|
|||
|
||||
concept = termValueSet.getConcepts().get(22);
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("http://acme.org|2", concept.getSystem());
|
||||
assertEquals("8491-3", concept.getCode());
|
||||
assertEquals("Systolic blood pressure 1 hour minimum v2", concept.getDisplay());
|
||||
assertEquals(1, concept.getDesignations().size());
|
||||
|
|
@ -1173,161 +1177,16 @@ public class ResourceProviderDstu3ValueSetVersionedTest extends BaseResourceProv
|
|||
|
||||
concept = termValueSet.getConcepts().get(23);
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("http://acme.org|2", concept.getSystem());
|
||||
assertEquals("8492-1", concept.getCode());
|
||||
assertEquals("Systolic blood pressure 8 hour minimum v2", concept.getDisplay());
|
||||
assertEquals(0, concept.getDesignations().size());
|
||||
assertEquals(23, concept.getOrder());
|
||||
});
|
||||
}
|
||||
/*
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemInstance() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet();
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId_v1)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "code", new CodeType("8495-4"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.execute();
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemInstanceOnType() throws IOException {
|
||||
createLocalCs();
|
||||
createLocalVsWithIncludeConcept();
|
||||
|
||||
String url = ourServerBase +
|
||||
"/ValueSet/" + myLocalValueSetId_v1.getIdPart() + "/$validate-code?system=" +
|
||||
UrlUtil.escapeUrlParam(URL_MY_CODE_SYSTEM) +
|
||||
"&code=AA";
|
||||
|
||||
HttpGet request = new HttpGet(url);
|
||||
request.addHeader("Accept", "application/fhir+json");
|
||||
try (CloseableHttpResponse response = ourHttpClient.execute(request)) {
|
||||
String respString = IOUtils.toString(response.getEntity().getContent(), Charsets.UTF_8);
|
||||
ourLog.info(respString);
|
||||
|
||||
Parameters respParam = myFhirCtx.newJsonParser().parseResource(Parameters.class, respString);
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemInstanceOnInstance() throws IOException {
|
||||
createLocalCs();
|
||||
createLocalVsWithIncludeConcept();
|
||||
|
||||
String url = ourServerBase +
|
||||
"/ValueSet/" + myLocalValueSetId_v1.getIdPart() + "/$validate-code?system=" +
|
||||
UrlUtil.escapeUrlParam(URL_MY_CODE_SYSTEM) +
|
||||
"&code=AA";
|
||||
|
||||
ourLog.info("* Requesting: {}", url);
|
||||
|
||||
HttpGet request = new HttpGet(url);
|
||||
request.addHeader("Accept", "application/fhir+json");
|
||||
try (CloseableHttpResponse response = ourHttpClient.execute(request)) {
|
||||
String respString = IOUtils.toString(response.getEntity().getContent(), Charsets.UTF_8);
|
||||
ourLog.info(respString);
|
||||
|
||||
Parameters respParam = myFhirCtx.newJsonParser().parseResource(Parameters.class, respString);
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemType() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet();
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId_v1)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "code", new CodeType("8450-9"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.execute();
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationNoValueSetProvided() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet();
|
||||
|
||||
try {
|
||||
ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "code", new CodeType("8450-9"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.execute();
|
||||
fail();
|
||||
} catch (InvalidRequestException e) {
|
||||
assertEquals("HTTP 400 Bad Request: Either ValueSet ID or ValueSet identifier or system and code must be provided. Unable to validate.", e.getMessage());
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationOnInstanceWithIsAExpansion() throws IOException {
|
||||
CodeSystem cs = new CodeSystem();
|
||||
cs.setUrl("http://mycs");
|
||||
cs.setContent(CodeSystemContentMode.COMPLETE);
|
||||
cs.setHierarchyMeaning(CodeSystem.CodeSystemHierarchyMeaning.ISA);
|
||||
cs.setStatus(Enumerations.PublicationStatus.ACTIVE);
|
||||
ConceptDefinitionComponent parentA = cs.addConcept().setCode("ParentA").setDisplay("Parent A");
|
||||
parentA.addConcept().setCode("ChildAA").setDisplay("Child AA");
|
||||
myCodeSystemDao.create(cs);
|
||||
|
||||
ValueSet vs = new ValueSet();
|
||||
vs.setUrl("http://myvs");
|
||||
vs.getCompose()
|
||||
.addInclude()
|
||||
.setSystem("http://mycs")
|
||||
.addFilter()
|
||||
.setOp(FilterOperator.ISA)
|
||||
.setProperty("concept")
|
||||
.setValue("ParentA");
|
||||
IIdType vsId = myValueSetDao.create(vs).getId().toUnqualifiedVersionless();
|
||||
|
||||
HttpGet expandGet = new HttpGet(ourServerBase + "/ValueSet/" + vsId.getIdPart() + "/$expand?_pretty=true");
|
||||
try (CloseableHttpResponse status = ourHttpClient.execute(expandGet)) {
|
||||
String response = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
|
||||
ourLog.info("Response: {}", response);
|
||||
}
|
||||
|
||||
HttpGet validateCodeGet = new HttpGet(ourServerBase + "/ValueSet/" + vsId.getIdPart() + "/$validate-code?system=http://mycs&code=ChildAA&_pretty=true");
|
||||
try (CloseableHttpResponse status = ourHttpClient.execute(validateCodeGet)) {
|
||||
String response = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
|
||||
ourLog.info("Response: {}", response);
|
||||
Parameters output = myFhirCtx.newXmlParser().parseResource(Parameters.class, response);
|
||||
assertEquals(true, output.getParameterBool("result"));
|
||||
}
|
||||
|
||||
HttpGet validateCodeGet2 = new HttpGet(ourServerBase + "/ValueSet/" + vsId.getIdPart() + "/$validate-code?system=http://mycs&code=FOO&_pretty=true");
|
||||
try (CloseableHttpResponse status = ourHttpClient.execute(validateCodeGet2)) {
|
||||
String response = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
|
||||
ourLog.info("Response: {}", response);
|
||||
Parameters output = myFhirCtx.newXmlParser().parseResource(Parameters.class, response);
|
||||
assertEquals(false, output.getParameterBool("result"));
|
||||
}
|
||||
|
||||
}
|
||||
*/
|
||||
|
||||
@Test
|
||||
public void testCreateDuplicatValueSetVersion() {
|
||||
public void testCreateDuplicateValueSetVersion() {
|
||||
createExternalCsAndLocalVs();
|
||||
try {
|
||||
persistLocalVs(createLocalVs(URL_MY_CODE_SYSTEM, "1"));
|
||||
|
|
@ -1338,6 +1197,284 @@ public class ResourceProviderDstu3ValueSetVersionedTest extends BaseResourceProv
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystem() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet();
|
||||
|
||||
// With correct system version specified. Should pass.
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "code", new CodeType("8495-4"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.andParameter("systemVersion", new StringType("1"))
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("1"))
|
||||
.execute();
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "code", new CodeType("8495-4"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.andParameter("systemVersion", new StringType("2"))
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("2"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
// With incorrect version specified. Should fail.
|
||||
respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "code", new CodeType("8495-4"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.andParameter("systemVersion", new StringType("1"))
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("2"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertFalse(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "code", new CodeType("8495-4"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.andParameter("systemVersion", new StringType("2"))
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("1"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertFalse(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationOnInstanceByCodeAndSystem() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet();
|
||||
|
||||
// With correct system version specified. Should pass.
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId_v1)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "code", new CodeType("8495-4"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.andParameter("systemVersion", new StringType("1"))
|
||||
.execute();
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
respParam = ourClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId_v2)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "code", new CodeType("8495-4"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.andParameter("systemVersion", new StringType("2"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
// With incorrect version specified. Should fail.
|
||||
respParam = ourClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId_v1)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "code", new CodeType("8495-4"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.andParameter("systemVersion", new StringType("2"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertFalse(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
respParam = ourClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId_v2)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "code", new CodeType("8495-4"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.andParameter("systemVersion", new StringType("1"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertFalse(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCoding() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet();
|
||||
|
||||
Coding codingToValidate_v1 = new Coding("http://acme.org", "8495-4", "Systolic blood pressure 24 hour minimum");
|
||||
codingToValidate_v1.setVersion("1");
|
||||
|
||||
Coding codingToValidate_v2 = new Coding("http://acme.org", "8495-4", "Systolic blood pressure 24 hour minimum v2");
|
||||
codingToValidate_v2.setVersion("2");
|
||||
|
||||
// With correct system version specified. Should pass.
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "coding", codingToValidate_v1)
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("1"))
|
||||
.execute();
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "coding", codingToValidate_v2)
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("2"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
// With incorrect version specified. Should fail.
|
||||
respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "coding", codingToValidate_v1)
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("2"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertFalse(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "coding", codingToValidate_v2)
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("1"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertFalse(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeableConcept() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet();
|
||||
|
||||
Coding codingToValidate = new Coding("http://acme.org", "8495-4", "Systolic blood pressure 24 hour minimum");
|
||||
codingToValidate.setVersion("1");
|
||||
CodeableConcept codeableConceptToValidate_v1 = new CodeableConcept(codingToValidate);
|
||||
|
||||
codingToValidate = new Coding("http://acme.org", "8495-4", "Systolic blood pressure 24 hour minimum v2");
|
||||
codingToValidate.setVersion("2");
|
||||
CodeableConcept codeableConceptToValidate_v2 = new CodeableConcept(codingToValidate);
|
||||
|
||||
// With correct system version specified. Should pass.
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "codeableConcept", codeableConceptToValidate_v1)
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("1"))
|
||||
.execute();
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "codeableConcept", codeableConceptToValidate_v2)
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("2"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
// With incorrect version specified. Should fail.
|
||||
respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "codeableConcept", codeableConceptToValidate_v1)
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("2"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertFalse(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "codeableConcept", codeableConceptToValidate_v2)
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("1"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertFalse(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
}
|
||||
|
||||
@AfterEach
|
||||
public void afterResetPreExpansionDefault() {
|
||||
myDaoConfig.setPreExpandValueSets(new DaoConfig().isPreExpandValueSets());
|
||||
|
|
|
|||
|
|
@ -13,12 +13,11 @@ import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
|
|||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
|
||||
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
|
||||
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
|
||||
import ca.uhn.fhir.util.UrlUtil;
|
||||
import org.apache.commons.io.Charsets;
|
||||
import com.google.common.base.Charsets;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.http.client.methods.CloseableHttpResponse;
|
||||
import org.apache.http.client.methods.HttpGet;
|
||||
|
|
@ -29,6 +28,8 @@ import org.hl7.fhir.r4.model.CodeSystem;
|
|||
import org.hl7.fhir.r4.model.CodeSystem.CodeSystemContentMode;
|
||||
import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
|
||||
import org.hl7.fhir.r4.model.CodeType;
|
||||
import org.hl7.fhir.r4.model.CodeableConcept;
|
||||
import org.hl7.fhir.r4.model.Coding;
|
||||
import org.hl7.fhir.r4.model.Enumerations;
|
||||
import org.hl7.fhir.r4.model.IdType;
|
||||
import org.hl7.fhir.r4.model.Parameters;
|
||||
|
|
@ -59,6 +60,7 @@ import static org.hamcrest.Matchers.containsStringIgnoringCase;
|
|||
import static org.hamcrest.Matchers.not;
|
||||
import static org.hamcrest.Matchers.stringContainsInOrder;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertFalse;
|
||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||
import static org.junit.jupiter.api.Assertions.assertSame;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
|
|
@ -126,21 +128,16 @@ public class ResourceProviderR4ValueSetVersionedTest extends BaseResourceProvide
|
|||
|
||||
private void loadAndPersistValueSet() throws IOException {
|
||||
ValueSet valueSet = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
|
||||
persistTwoVersionsOfValueSet(valueSet, HttpVerb.POST);
|
||||
}
|
||||
|
||||
@SuppressWarnings("EnumSwitchStatementWhichMissesCases")
|
||||
private void persistTwoVersionsOfValueSet(ValueSet theValueSet, HttpVerb theVerb) {
|
||||
theValueSet.setVersion("1");
|
||||
theValueSet.setId("ValueSet/vs1");
|
||||
theValueSet.getCompose().getInclude().get(0).setVersion("1");
|
||||
myExtensionalVsId_v1 = persistSingleValueSet(theValueSet, theVerb);
|
||||
valueSet.setVersion("1");
|
||||
valueSet.setId("ValueSet/vs1");
|
||||
valueSet.getCompose().getInclude().get(0).setVersion("1");
|
||||
myExtensionalVsId_v1 = persistSingleValueSet(valueSet, HttpVerb.POST);
|
||||
myExtensionalVsIdOnResourceTable_v1 = myValueSetDao.readEntity(myExtensionalVsId_v1, null).getId();
|
||||
|
||||
theValueSet.setVersion("2");
|
||||
theValueSet.setId("ValueSet/vs2");
|
||||
theValueSet.getCompose().getInclude().get(0).setVersion("2");
|
||||
myExtensionalVsId_v2 = persistSingleValueSet(theValueSet, theVerb);
|
||||
valueSet.setVersion("2");
|
||||
valueSet.setId("ValueSet/vs2");
|
||||
valueSet.getCompose().getInclude().get(0).setVersion("2");
|
||||
myExtensionalVsId_v2 = persistSingleValueSet(valueSet, HttpVerb.POST);
|
||||
myExtensionalVsIdOnResourceTable_v2 = myValueSetDao.readEntity(myExtensionalVsId_v2, null).getId();
|
||||
|
||||
}
|
||||
|
|
@ -148,6 +145,9 @@ public class ResourceProviderR4ValueSetVersionedTest extends BaseResourceProvide
|
|||
private IIdType persistSingleValueSet(ValueSet theValueSet, HttpVerb theVerb) {
|
||||
final IIdType[] vsId = new IIdType[1];
|
||||
switch (theVerb) {
|
||||
case GET:
|
||||
case HEAD:
|
||||
break;
|
||||
case POST:
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
|
|
@ -164,6 +164,9 @@ public class ResourceProviderR4ValueSetVersionedTest extends BaseResourceProvide
|
|||
}
|
||||
});
|
||||
break;
|
||||
case DELETE:
|
||||
case PATCH:
|
||||
case NULL:
|
||||
default:
|
||||
throw new IllegalArgumentException("HTTP verb is not supported: " + theVerb);
|
||||
}
|
||||
|
|
@ -188,12 +191,6 @@ public class ResourceProviderR4ValueSetVersionedTest extends BaseResourceProvide
|
|||
|
||||
}
|
||||
|
||||
// private void createExternalCsAndLocalVsWithUnknownCode() {
|
||||
// String codeSystemUrl = createExternalCs();
|
||||
|
||||
// createLocalVsWithUnknownCode(codeSystemUrl);
|
||||
// }
|
||||
|
||||
private void createLocalCs() {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
|
|
@ -250,27 +247,6 @@ public class ResourceProviderR4ValueSetVersionedTest extends BaseResourceProvide
|
|||
return myValueSetDao.create(theValueSet, mySrd).getId().toUnqualifiedVersionless();
|
||||
}
|
||||
|
||||
private void createLocalVsWithUnknownCode(String codeSystemUrl) {
|
||||
myLocalVs_v1 = new ValueSet();
|
||||
myLocalVs_v1.setUrl(URL_MY_VALUE_SET);
|
||||
myLocalVs_v1.setVersion("1");
|
||||
ConceptSetComponent include = myLocalVs_v1.getCompose().addInclude();
|
||||
include.setSystem(codeSystemUrl);
|
||||
include.setSystem("1");
|
||||
include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("childFOOOOOOO");
|
||||
myLocalValueSetId_v1 = myValueSetDao.create(myLocalVs_v1, mySrd).getId().toUnqualifiedVersionless();
|
||||
|
||||
myLocalVs_v2 = new ValueSet();
|
||||
myLocalVs_v2.setUrl(URL_MY_VALUE_SET);
|
||||
myLocalVs_v2.setVersion("2");
|
||||
include = myLocalVs_v2.getCompose().addInclude();
|
||||
include.setSystem(codeSystemUrl);
|
||||
include.setSystem("2");
|
||||
include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("childFOOOOOOO");
|
||||
myLocalValueSetId_v2 = myValueSetDao.create(myLocalVs_v2, mySrd).getId().toUnqualifiedVersionless();
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandById() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet();
|
||||
|
|
@ -1201,151 +1177,284 @@ public class ResourceProviderR4ValueSetVersionedTest extends BaseResourceProvide
|
|||
assertEquals(23, concept.getOrder());
|
||||
});
|
||||
}
|
||||
/*
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemInstance() throws Exception {
|
||||
public void testValidateCodeOperationByCodeAndSystem() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet();
|
||||
|
||||
// With correct system version specified. Should pass.
|
||||
Parameters respParam = myClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "code", new CodeType("8495-4"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.andParameter("systemVersion", new StringType("1"))
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("1"))
|
||||
.execute();
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
respParam = myClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "code", new CodeType("8495-4"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.andParameter("systemVersion", new StringType("2"))
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("2"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
// With incorrect version specified. Should fail.
|
||||
respParam = myClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "code", new CodeType("8495-4"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.andParameter("systemVersion", new StringType("1"))
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("2"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertFalse(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
respParam = myClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "code", new CodeType("8495-4"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.andParameter("systemVersion", new StringType("2"))
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("1"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertFalse(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationOnInstanceByCodeAndSystem() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet();
|
||||
|
||||
// With correct system version specified. Should pass.
|
||||
Parameters respParam = myClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId_v1)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "code", new CodeType("8495-4"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.andParameter("systemVersion", new StringType("1"))
|
||||
.execute();
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemInstanceOnType() throws IOException {
|
||||
createLocalCs();
|
||||
createLocalVsWithIncludeConcept();
|
||||
|
||||
String url = ourServerBase +
|
||||
"/ValueSet/" + myLocalValueSetId_v1.getIdPart() + "/$validate-code?system=" +
|
||||
UrlUtil.escapeUrlParam(URL_MY_CODE_SYSTEM) +
|
||||
"&code=AA";
|
||||
|
||||
HttpGet request = new HttpGet(url);
|
||||
request.addHeader("Accept", "application/fhir+json");
|
||||
try (CloseableHttpResponse response = ourHttpClient.execute(request)) {
|
||||
String respString = IOUtils.toString(response.getEntity().getContent(), Charsets.UTF_8);
|
||||
ourLog.info(respString);
|
||||
|
||||
Parameters respParam = myFhirCtx.newJsonParser().parseResource(Parameters.class, respString);
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemInstanceOnInstance() throws IOException {
|
||||
createLocalCs();
|
||||
createLocalVsWithIncludeConcept();
|
||||
respParam = myClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId_v2)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "code", new CodeType("8495-4"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.andParameter("systemVersion", new StringType("2"))
|
||||
.execute();
|
||||
|
||||
String url = ourServerBase +
|
||||
"/ValueSet/" + myLocalValueSetId_v1.getIdPart() + "/$validate-code?system=" +
|
||||
UrlUtil.escapeUrlParam(URL_MY_CODE_SYSTEM) +
|
||||
"&code=AA";
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
ourLog.info("* Requesting: {}", url);
|
||||
|
||||
HttpGet request = new HttpGet(url);
|
||||
request.addHeader("Accept", "application/fhir+json");
|
||||
try (CloseableHttpResponse response = ourHttpClient.execute(request)) {
|
||||
String respString = IOUtils.toString(response.getEntity().getContent(), Charsets.UTF_8);
|
||||
ourLog.info(respString);
|
||||
|
||||
Parameters respParam = myFhirCtx.newJsonParser().parseResource(Parameters.class, respString);
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemType() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet();
|
||||
|
||||
Parameters respParam = myClient
|
||||
// With incorrect version specified. Should fail.
|
||||
respParam = myClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId_v1)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "code", new CodeType("8450-9"))
|
||||
.withParameter(Parameters.class, "code", new CodeType("8495-4"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.andParameter("systemVersion", new StringType("2"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertFalse(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
respParam = myClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId_v2)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "code", new CodeType("8495-4"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.andParameter("systemVersion", new StringType("1"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertFalse(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCoding() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet();
|
||||
|
||||
Coding codingToValidate_v1 = new Coding("http://acme.org", "8495-4", "Systolic blood pressure 24 hour minimum");
|
||||
codingToValidate_v1.setVersion("1");
|
||||
|
||||
Coding codingToValidate_v2 = new Coding("http://acme.org", "8495-4", "Systolic blood pressure 24 hour minimum v2");
|
||||
codingToValidate_v2.setVersion("2");
|
||||
|
||||
// With correct system version specified. Should pass.
|
||||
Parameters respParam = myClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "coding", codingToValidate_v1)
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("1"))
|
||||
.execute();
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
}
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationNoValueSetProvided() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet();
|
||||
|
||||
try {
|
||||
myClient
|
||||
respParam = myClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "code", new CodeType("8450-9"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.withParameter(Parameters.class, "coding", codingToValidate_v2)
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("2"))
|
||||
.execute();
|
||||
fail();
|
||||
} catch (InvalidRequestException e) {
|
||||
assertEquals("HTTP 400 Bad Request: Either ValueSet ID or ValueSet identifier or system and code must be provided. Unable to validate.", e.getMessage());
|
||||
}
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
// With incorrect version specified. Should fail.
|
||||
respParam = myClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "coding", codingToValidate_v1)
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("2"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertFalse(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
respParam = myClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "coding", codingToValidate_v2)
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("1"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertFalse(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationOnInstanceWithIsAExpansion() throws IOException {
|
||||
CodeSystem cs = new CodeSystem();
|
||||
cs.setUrl("http://mycs");
|
||||
cs.setContent(CodeSystemContentMode.COMPLETE);
|
||||
cs.setHierarchyMeaning(CodeSystem.CodeSystemHierarchyMeaning.ISA);
|
||||
cs.setStatus(Enumerations.PublicationStatus.ACTIVE);
|
||||
ConceptDefinitionComponent parentA = cs.addConcept().setCode("ParentA").setDisplay("Parent A");
|
||||
parentA.addConcept().setCode("ChildAA").setDisplay("Child AA");
|
||||
myCodeSystemDao.create(cs);
|
||||
public void testValidateCodeOperationByCodeableConcept() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet();
|
||||
|
||||
ValueSet vs = new ValueSet();
|
||||
vs.setUrl("http://myvs");
|
||||
vs.getCompose()
|
||||
.addInclude()
|
||||
.setSystem("http://mycs")
|
||||
.addFilter()
|
||||
.setOp(FilterOperator.ISA)
|
||||
.setProperty("concept")
|
||||
.setValue("ParentA");
|
||||
IIdType vsId = myValueSetDao.create(vs).getId().toUnqualifiedVersionless();
|
||||
Coding codingToValidate = new Coding("http://acme.org", "8495-4", "Systolic blood pressure 24 hour minimum");
|
||||
codingToValidate.setVersion("1");
|
||||
CodeableConcept codeableConceptToValidate_v1 = new CodeableConcept(codingToValidate);
|
||||
|
||||
HttpGet expandGet = new HttpGet(ourServerBase + "/ValueSet/" + vsId.getIdPart() + "/$expand?_pretty=true");
|
||||
try (CloseableHttpResponse status = ourHttpClient.execute(expandGet)) {
|
||||
String response = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
|
||||
ourLog.info("Response: {}", response);
|
||||
}
|
||||
codingToValidate = new Coding("http://acme.org", "8495-4", "Systolic blood pressure 24 hour minimum v2");
|
||||
codingToValidate.setVersion("2");
|
||||
CodeableConcept codeableConceptToValidate_v2 = new CodeableConcept(codingToValidate);
|
||||
|
||||
HttpGet validateCodeGet = new HttpGet(ourServerBase + "/ValueSet/" + vsId.getIdPart() + "/$validate-code?system=http://mycs&code=ChildAA&_pretty=true");
|
||||
try (CloseableHttpResponse status = ourHttpClient.execute(validateCodeGet)) {
|
||||
String response = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
|
||||
ourLog.info("Response: {}", response);
|
||||
Parameters output = myFhirCtx.newXmlParser().parseResource(Parameters.class, response);
|
||||
assertEquals(true, output.getParameterBool("result"));
|
||||
}
|
||||
// With correct system version specified. Should pass.
|
||||
Parameters respParam = myClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "codeableConcept", codeableConceptToValidate_v1)
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("1"))
|
||||
.execute();
|
||||
|
||||
HttpGet validateCodeGet2 = new HttpGet(ourServerBase + "/ValueSet/" + vsId.getIdPart() + "/$validate-code?system=http://mycs&code=FOO&_pretty=true");
|
||||
try (CloseableHttpResponse status = ourHttpClient.execute(validateCodeGet2)) {
|
||||
String response = IOUtils.toString(status.getEntity().getContent(), Charsets.UTF_8);
|
||||
ourLog.info("Response: {}", response);
|
||||
Parameters output = myFhirCtx.newXmlParser().parseResource(Parameters.class, response);
|
||||
assertEquals(false, output.getParameterBool("result"));
|
||||
}
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
respParam = myClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "codeableConcept", codeableConceptToValidate_v2)
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("2"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
// With incorrect version specified. Should fail.
|
||||
respParam = myClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "codeableConcept", codeableConceptToValidate_v1)
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("2"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertFalse(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
respParam = myClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("validate-code")
|
||||
.withParameter(Parameters.class, "codeableConcept", codeableConceptToValidate_v2)
|
||||
.andParameter("url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.andParameter("valueSetVersion", new StringType("1"))
|
||||
.execute();
|
||||
|
||||
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
||||
assertFalse(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
|
||||
}
|
||||
*/
|
||||
|
||||
private boolean clearDeferredStorageQueue() {
|
||||
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
|
|
@ -326,6 +326,30 @@ public class CommonCodeSystemsTerminologyService implements IValidationSupport {
|
|||
return url;
|
||||
}
|
||||
|
||||
public static String getValueSetVersion(@Nonnull IBaseResource theValueSet) {
|
||||
String version;
|
||||
switch (theValueSet.getStructureFhirVersionEnum()) {
|
||||
case DSTU3: {
|
||||
version = ((org.hl7.fhir.dstu3.model.ValueSet) theValueSet).getVersion();
|
||||
break;
|
||||
}
|
||||
case R4: {
|
||||
version = ((org.hl7.fhir.r4.model.ValueSet) theValueSet).getVersion();
|
||||
break;
|
||||
}
|
||||
case R5: {
|
||||
version = ((org.hl7.fhir.r5.model.ValueSet) theValueSet).getVersion();
|
||||
break;
|
||||
}
|
||||
case DSTU2:
|
||||
case DSTU2_HL7ORG:
|
||||
case DSTU2_1:
|
||||
default:
|
||||
throw new IllegalArgumentException("Can not handle version: " + theValueSet.getStructureFhirVersionEnum());
|
||||
}
|
||||
return version;
|
||||
}
|
||||
|
||||
private static HashMap<String, String> buildUspsCodes() {
|
||||
HashMap<String, String> uspsCodes = new HashMap<>();
|
||||
uspsCodes.put("AK", "Alaska");
|
||||
|
|
|
|||
|
|
@ -91,23 +91,23 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
return new ValueSetExpansionOutcome(expansion, null);
|
||||
}
|
||||
|
||||
private org.hl7.fhir.r5.model.ValueSet expandValueSetToCanonical(ValidationSupportContext theValidationSupportContext, IBaseResource theValueSetToExpand, @Nullable String theWantSystem, @Nullable String theWantCode) {
|
||||
private org.hl7.fhir.r5.model.ValueSet expandValueSetToCanonical(ValidationSupportContext theValidationSupportContext, IBaseResource theValueSetToExpand, @Nullable String theWantSystemIdentifier, @Nullable String theWantCode) {
|
||||
org.hl7.fhir.r5.model.ValueSet expansionR5;
|
||||
switch (theValueSetToExpand.getStructureFhirVersionEnum()) {
|
||||
case DSTU2: {
|
||||
expansionR5 = expandValueSetDstu2(theValidationSupportContext, (ca.uhn.fhir.model.dstu2.resource.ValueSet) theValueSetToExpand, theWantSystem, theWantCode);
|
||||
expansionR5 = expandValueSetDstu2(theValidationSupportContext, (ca.uhn.fhir.model.dstu2.resource.ValueSet) theValueSetToExpand, theWantSystemIdentifier, theWantCode);
|
||||
break;
|
||||
}
|
||||
case DSTU2_HL7ORG: {
|
||||
expansionR5 = expandValueSetDstu2Hl7Org(theValidationSupportContext, (ValueSet) theValueSetToExpand, theWantSystem, theWantCode);
|
||||
expansionR5 = expandValueSetDstu2Hl7Org(theValidationSupportContext, (ValueSet) theValueSetToExpand, theWantSystemIdentifier, theWantCode);
|
||||
break;
|
||||
}
|
||||
case DSTU3: {
|
||||
expansionR5 = expandValueSetDstu3(theValidationSupportContext, (org.hl7.fhir.dstu3.model.ValueSet) theValueSetToExpand, theWantSystem, theWantCode);
|
||||
expansionR5 = expandValueSetDstu3(theValidationSupportContext, (org.hl7.fhir.dstu3.model.ValueSet) theValueSetToExpand, theWantSystemIdentifier, theWantCode);
|
||||
break;
|
||||
}
|
||||
case R4: {
|
||||
expansionR5 = expandValueSetR4(theValidationSupportContext, (org.hl7.fhir.r4.model.ValueSet) theValueSetToExpand, theWantSystem, theWantCode);
|
||||
expansionR5 = expandValueSetR4(theValidationSupportContext, (org.hl7.fhir.r4.model.ValueSet) theValueSetToExpand, theWantSystemIdentifier, theWantCode);
|
||||
break;
|
||||
}
|
||||
case R5: {
|
||||
|
|
@ -119,20 +119,17 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
throw new IllegalArgumentException("Can not handle version: " + myCtx.getVersion().getVersion());
|
||||
}
|
||||
|
||||
if (expansionR5 == null) {
|
||||
return null;
|
||||
}
|
||||
return expansionR5;
|
||||
}
|
||||
|
||||
@Override
|
||||
public CodeValidationResult
|
||||
validateCodeInValueSet(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, @Nonnull IBaseResource theValueSet) {
|
||||
org.hl7.fhir.r5.model.ValueSet expansion = expandValueSetToCanonical(theValidationSupportContext, theValueSet, theCodeSystem, theCode);
|
||||
validateCodeInValueSet(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystemIdentifier, String theCode, String theDisplay, @Nonnull IBaseResource theValueSet) {
|
||||
org.hl7.fhir.r5.model.ValueSet expansion = expandValueSetToCanonical(theValidationSupportContext, theValueSet, theCodeSystemIdentifier, theCode);
|
||||
if (expansion == null) {
|
||||
return null;
|
||||
}
|
||||
return validateCodeInExpandedValueSet(theValidationSupportContext, theOptions, theCodeSystem, theCode, theDisplay, expansion);
|
||||
return validateCodeInExpandedValueSet(theValidationSupportContext, theOptions, theCodeSystemIdentifier, theCode, theDisplay, expansion);
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -145,26 +142,59 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
return null;
|
||||
}
|
||||
} else {
|
||||
String codeSystemUrl;
|
||||
String codeSystemVersion = null;
|
||||
int codeSystemVersionIndex = theCodeSystem.indexOf("|");
|
||||
if (codeSystemVersionIndex > -1) {
|
||||
codeSystemUrl = theCodeSystem.substring(0, codeSystemVersionIndex);
|
||||
codeSystemVersion = theCodeSystem.substring(codeSystemVersionIndex + 1);
|
||||
} else {
|
||||
codeSystemUrl = theCodeSystem;
|
||||
}
|
||||
switch (myCtx.getVersion().getVersion()) {
|
||||
case DSTU2_HL7ORG:
|
||||
if (codeSystemVersion != null) {
|
||||
vs = new org.hl7.fhir.dstu2.model.ValueSet()
|
||||
.setCompose(new org.hl7.fhir.dstu2.model.ValueSet.ValueSetComposeComponent()
|
||||
.addInclude(new org.hl7.fhir.dstu2.model.ValueSet.ConceptSetComponent().setSystem(codeSystemUrl).setVersion(codeSystemVersion)));
|
||||
} else {
|
||||
vs = new org.hl7.fhir.dstu2.model.ValueSet()
|
||||
.setCompose(new org.hl7.fhir.dstu2.model.ValueSet.ValueSetComposeComponent()
|
||||
.addInclude(new org.hl7.fhir.dstu2.model.ValueSet.ConceptSetComponent().setSystem(theCodeSystem)));
|
||||
}
|
||||
break;
|
||||
case DSTU3:
|
||||
if (codeSystemVersion != null) {
|
||||
vs = new org.hl7.fhir.dstu3.model.ValueSet()
|
||||
.setCompose(new org.hl7.fhir.dstu3.model.ValueSet.ValueSetComposeComponent()
|
||||
.addInclude(new org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent().setSystem(codeSystemUrl).setVersion(codeSystemVersion)));
|
||||
} else {
|
||||
vs = new org.hl7.fhir.dstu3.model.ValueSet()
|
||||
.setCompose(new org.hl7.fhir.dstu3.model.ValueSet.ValueSetComposeComponent()
|
||||
.addInclude(new org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent().setSystem(theCodeSystem)));
|
||||
}
|
||||
break;
|
||||
case R4:
|
||||
if (codeSystemVersion != null) {
|
||||
vs = new org.hl7.fhir.r4.model.ValueSet()
|
||||
.setCompose(new org.hl7.fhir.r4.model.ValueSet.ValueSetComposeComponent()
|
||||
.addInclude(new org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent().setSystem(codeSystemUrl).setVersion(codeSystemVersion)));
|
||||
} else {
|
||||
vs = new org.hl7.fhir.r4.model.ValueSet()
|
||||
.setCompose(new org.hl7.fhir.r4.model.ValueSet.ValueSetComposeComponent()
|
||||
.addInclude(new org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent().setSystem(theCodeSystem)));
|
||||
}
|
||||
break;
|
||||
case R5:
|
||||
if (codeSystemVersion != null) {
|
||||
vs = new org.hl7.fhir.r5.model.ValueSet()
|
||||
.setCompose(new org.hl7.fhir.r5.model.ValueSet.ValueSetComposeComponent()
|
||||
.addInclude(new org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent().setSystem(codeSystemUrl).setVersion(codeSystemVersion)));
|
||||
} else {
|
||||
vs = new org.hl7.fhir.r5.model.ValueSet()
|
||||
.setCompose(new org.hl7.fhir.r5.model.ValueSet.ValueSetComposeComponent()
|
||||
.addInclude(new org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent().setSystem(theCodeSystem)));
|
||||
}
|
||||
break;
|
||||
case DSTU2:
|
||||
case DSTU2_1:
|
||||
|
|
@ -184,39 +214,39 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
|
||||
}
|
||||
|
||||
private CodeValidationResult validateCodeInExpandedValueSet(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, IBaseResource theExpansion) {
|
||||
private CodeValidationResult validateCodeInExpandedValueSet(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystemIdentifierToValidate, String theCodeToValidate, String theDisplayToValidate, IBaseResource theExpansion) {
|
||||
assert theExpansion != null;
|
||||
|
||||
boolean caseSensitive = true;
|
||||
IBaseResource system = null;
|
||||
if (!theOptions.isInferSystem() && isNotBlank(theCodeSystem)) {
|
||||
system = theValidationSupportContext.getRootValidationSupport().fetchCodeSystem(theCodeSystem);
|
||||
IBaseResource codeSystemToValidateResource = null;
|
||||
if (!theOptions.isInferSystem() && isNotBlank(theCodeSystemIdentifierToValidate)) {
|
||||
codeSystemToValidateResource = theValidationSupportContext.getRootValidationSupport().fetchCodeSystem(theCodeSystemIdentifierToValidate);
|
||||
}
|
||||
|
||||
List<VersionIndependentConcept> codes = new ArrayList<>();
|
||||
List<VersionIndependentConcept> codesInValueSetExpansion = new ArrayList<>();
|
||||
switch (theExpansion.getStructureFhirVersionEnum()) {
|
||||
case DSTU2_HL7ORG: {
|
||||
ValueSet expansionVs = (ValueSet) theExpansion;
|
||||
List<ValueSet.ValueSetExpansionContainsComponent> contains = expansionVs.getExpansion().getContains();
|
||||
flattenAndConvertCodesDstu2(contains, codes);
|
||||
flattenAndConvertCodesDstu2(contains, codesInValueSetExpansion);
|
||||
break;
|
||||
}
|
||||
case DSTU3: {
|
||||
org.hl7.fhir.dstu3.model.ValueSet expansionVs = (org.hl7.fhir.dstu3.model.ValueSet) theExpansion;
|
||||
List<org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent> contains = expansionVs.getExpansion().getContains();
|
||||
flattenAndConvertCodesDstu3(contains, codes);
|
||||
flattenAndConvertCodesDstu3(contains, codesInValueSetExpansion);
|
||||
break;
|
||||
}
|
||||
case R4: {
|
||||
org.hl7.fhir.r4.model.ValueSet expansionVs = (org.hl7.fhir.r4.model.ValueSet) theExpansion;
|
||||
List<org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent> contains = expansionVs.getExpansion().getContains();
|
||||
flattenAndConvertCodesR4(contains, codes);
|
||||
flattenAndConvertCodesR4(contains, codesInValueSetExpansion);
|
||||
break;
|
||||
}
|
||||
case R5: {
|
||||
org.hl7.fhir.r5.model.ValueSet expansionVs = (org.hl7.fhir.r5.model.ValueSet) theExpansion;
|
||||
List<org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent> contains = expansionVs.getExpansion().getContains();
|
||||
flattenAndConvertCodesR5(contains, codes);
|
||||
flattenAndConvertCodesR5(contains, codesInValueSetExpansion);
|
||||
break;
|
||||
}
|
||||
case DSTU2:
|
||||
|
|
@ -225,37 +255,37 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
throw new IllegalArgumentException("Can not handle version: " + myCtx.getVersion().getVersion());
|
||||
}
|
||||
|
||||
String codeSystemName = null;
|
||||
String codeSystemVersion = null;
|
||||
String codeSystemContentMode = null;
|
||||
if (system != null) {
|
||||
switch (system.getStructureFhirVersionEnum()) {
|
||||
String codeSystemResourceName = null;
|
||||
String codeSystemResourceVersion = null;
|
||||
String codeSystemResourceContentMode = null;
|
||||
if (codeSystemToValidateResource != null) {
|
||||
switch (codeSystemToValidateResource.getStructureFhirVersionEnum()) {
|
||||
case DSTU2_HL7ORG: {
|
||||
caseSensitive = true;
|
||||
break;
|
||||
}
|
||||
case DSTU3: {
|
||||
org.hl7.fhir.dstu3.model.CodeSystem systemDstu3 = (org.hl7.fhir.dstu3.model.CodeSystem) system;
|
||||
org.hl7.fhir.dstu3.model.CodeSystem systemDstu3 = (org.hl7.fhir.dstu3.model.CodeSystem) codeSystemToValidateResource;
|
||||
caseSensitive = systemDstu3.getCaseSensitive();
|
||||
codeSystemName = systemDstu3.getName();
|
||||
codeSystemVersion = systemDstu3.getVersion();
|
||||
codeSystemContentMode = systemDstu3.getContentElement().getValueAsString();
|
||||
codeSystemResourceName = systemDstu3.getName();
|
||||
codeSystemResourceVersion = systemDstu3.getVersion();
|
||||
codeSystemResourceContentMode = systemDstu3.getContentElement().getValueAsString();
|
||||
break;
|
||||
}
|
||||
case R4: {
|
||||
org.hl7.fhir.r4.model.CodeSystem systemR4 = (org.hl7.fhir.r4.model.CodeSystem) system;
|
||||
org.hl7.fhir.r4.model.CodeSystem systemR4 = (org.hl7.fhir.r4.model.CodeSystem) codeSystemToValidateResource;
|
||||
caseSensitive = systemR4.getCaseSensitive();
|
||||
codeSystemName = systemR4.getName();
|
||||
codeSystemVersion = systemR4.getVersion();
|
||||
codeSystemContentMode = systemR4.getContentElement().getValueAsString();
|
||||
codeSystemResourceName = systemR4.getName();
|
||||
codeSystemResourceVersion = systemR4.getVersion();
|
||||
codeSystemResourceContentMode = systemR4.getContentElement().getValueAsString();
|
||||
break;
|
||||
}
|
||||
case R5: {
|
||||
CodeSystem systemR5 = (CodeSystem) system;
|
||||
CodeSystem systemR5 = (CodeSystem) codeSystemToValidateResource;
|
||||
caseSensitive = systemR5.getCaseSensitive();
|
||||
codeSystemName = systemR5.getName();
|
||||
codeSystemVersion = systemR5.getVersion();
|
||||
codeSystemContentMode = systemR5.getContentElement().getValueAsString();
|
||||
codeSystemResourceName = systemR5.getName();
|
||||
codeSystemResourceVersion = systemR5.getVersion();
|
||||
codeSystemResourceContentMode = systemR5.getContentElement().getValueAsString();
|
||||
break;
|
||||
}
|
||||
case DSTU2:
|
||||
|
|
@ -265,29 +295,40 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
}
|
||||
}
|
||||
|
||||
for (VersionIndependentConcept nextExpansionCode : codes) {
|
||||
String codeSystemUrlToValidate=null;
|
||||
String codeSystemVersionToValidate=null;
|
||||
if (theCodeSystemIdentifierToValidate != null) {
|
||||
int versionIndex = theCodeSystemIdentifierToValidate.indexOf("|");
|
||||
if (versionIndex > -1) {
|
||||
codeSystemUrlToValidate = theCodeSystemIdentifierToValidate.substring(0, versionIndex);
|
||||
codeSystemVersionToValidate = theCodeSystemIdentifierToValidate.substring(versionIndex+1);
|
||||
} else {
|
||||
codeSystemUrlToValidate = theCodeSystemIdentifierToValidate;
|
||||
}
|
||||
}
|
||||
for (VersionIndependentConcept nextExpansionCode : codesInValueSetExpansion) {
|
||||
|
||||
boolean codeMatches;
|
||||
if (caseSensitive) {
|
||||
codeMatches = defaultString(theCode).equals(nextExpansionCode.getCode());
|
||||
codeMatches = defaultString(theCodeToValidate).equals(nextExpansionCode.getCode());
|
||||
} else {
|
||||
codeMatches = defaultString(theCode).equalsIgnoreCase(nextExpansionCode.getCode());
|
||||
codeMatches = defaultString(theCodeToValidate).equalsIgnoreCase(nextExpansionCode.getCode());
|
||||
}
|
||||
if (codeMatches) {
|
||||
if (theOptions.isInferSystem() || nextExpansionCode.getSystem().equals(theCodeSystem)) {
|
||||
if (!theOptions.isValidateDisplay() || (isBlank(nextExpansionCode.getDisplay()) || isBlank(theDisplay) || nextExpansionCode.getDisplay().equals(theDisplay))) {
|
||||
if (theOptions.isInferSystem() || (nextExpansionCode.getSystem().equals(codeSystemUrlToValidate) && (codeSystemVersionToValidate == null || codeSystemVersionToValidate.equals(nextExpansionCode.getSystemVersion())))) {
|
||||
if (!theOptions.isValidateDisplay() || (isBlank(nextExpansionCode.getDisplay()) || isBlank(theDisplayToValidate) || nextExpansionCode.getDisplay().equals(theDisplayToValidate))) {
|
||||
return new CodeValidationResult()
|
||||
.setCode(theCode)
|
||||
.setCode(theCodeToValidate)
|
||||
.setDisplay(nextExpansionCode.getDisplay())
|
||||
.setCodeSystemName(codeSystemName)
|
||||
.setCodeSystemVersion(codeSystemVersion);
|
||||
.setCodeSystemName(codeSystemResourceName)
|
||||
.setCodeSystemVersion(codeSystemResourceVersion);
|
||||
} else {
|
||||
return new CodeValidationResult()
|
||||
.setSeverity(IssueSeverity.ERROR)
|
||||
.setDisplay(nextExpansionCode.getDisplay())
|
||||
.setMessage("Concept Display \"" + theDisplay + "\" does not match expected \"" + nextExpansionCode.getDisplay() + "\"")
|
||||
.setCodeSystemName(codeSystemName)
|
||||
.setCodeSystemVersion(codeSystemVersion);
|
||||
.setMessage("Concept Display \"" + theDisplayToValidate + "\" does not match expected \"" + nextExpansionCode.getDisplay() + "\"")
|
||||
.setCodeSystemName(codeSystemResourceName)
|
||||
.setCodeSystemVersion(codeSystemResourceVersion);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -295,12 +336,12 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
|
||||
ValidationMessage.IssueSeverity severity;
|
||||
String message;
|
||||
if ("fragment".equals(codeSystemContentMode)) {
|
||||
if ("fragment".equals(codeSystemResourceContentMode)) {
|
||||
severity = ValidationMessage.IssueSeverity.WARNING;
|
||||
message = "Unknown code in fragment CodeSystem '" + (isNotBlank(theCodeSystem) ? theCodeSystem + "#" : "") + theCode + "'";
|
||||
message = "Unknown code in fragment CodeSystem '" + (isNotBlank(theCodeSystemIdentifierToValidate) ? theCodeSystemIdentifierToValidate + "#" : "") + theCodeToValidate + "'";
|
||||
} else {
|
||||
severity = ValidationMessage.IssueSeverity.ERROR;
|
||||
message = "Unknown code '" + (isNotBlank(theCodeSystem) ? theCodeSystem + "#" : "") + theCode + "'";
|
||||
message = "Unknown code '" + (isNotBlank(theCodeSystemIdentifierToValidate) ? theCodeSystemIdentifierToValidate + "#" : "") + theCodeToValidate + "'";
|
||||
}
|
||||
|
||||
return new CodeValidationResult()
|
||||
|
|
@ -314,7 +355,7 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
}
|
||||
|
||||
@Nullable
|
||||
private org.hl7.fhir.r5.model.ValueSet expandValueSetDstu2Hl7Org(ValidationSupportContext theValidationSupportContext, ValueSet theInput, @Nullable String theWantSystem, @Nullable String theWantCode) {
|
||||
private org.hl7.fhir.r5.model.ValueSet expandValueSetDstu2Hl7Org(ValidationSupportContext theValidationSupportContext, ValueSet theInput, @Nullable String theWantSystemIdentifier, @Nullable String theWantCode) {
|
||||
Function<String, CodeSystem> codeSystemLoader = t -> {
|
||||
org.hl7.fhir.dstu2.model.ValueSet codeSystem = (org.hl7.fhir.dstu2.model.ValueSet) theValidationSupportContext.getRootValidationSupport().fetchCodeSystem(t);
|
||||
CodeSystem retVal = new CodeSystem();
|
||||
|
|
@ -327,12 +368,12 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
};
|
||||
|
||||
org.hl7.fhir.r5.model.ValueSet input = ValueSet10_50.convertValueSet(theInput);
|
||||
org.hl7.fhir.r5.model.ValueSet output = expandValueSetR5(theValidationSupportContext, input, codeSystemLoader, valueSetLoader, theWantSystem, theWantCode);
|
||||
org.hl7.fhir.r5.model.ValueSet output = expandValueSetR5(theValidationSupportContext, input, codeSystemLoader, valueSetLoader, theWantSystemIdentifier, theWantCode);
|
||||
return (output);
|
||||
}
|
||||
|
||||
@Nullable
|
||||
private org.hl7.fhir.r5.model.ValueSet expandValueSetDstu2(ValidationSupportContext theValidationSupportContext, ca.uhn.fhir.model.dstu2.resource.ValueSet theInput, @Nullable String theWantSystem, @Nullable String theWantCode) {
|
||||
private org.hl7.fhir.r5.model.ValueSet expandValueSetDstu2(ValidationSupportContext theValidationSupportContext, ca.uhn.fhir.model.dstu2.resource.ValueSet theInput, @Nullable String theWantSystemIdentifier, @Nullable String theWantCode) {
|
||||
IParser parserRi = FhirContext.forCached(FhirVersionEnum.DSTU2_HL7ORG).newJsonParser();
|
||||
IParser parserHapi = FhirContext.forCached(FhirVersionEnum.DSTU2).newJsonParser();
|
||||
|
||||
|
|
@ -355,7 +396,7 @@ 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.r5.model.ValueSet input = ValueSet10_50.convertValueSet(valueSetRi);
|
||||
org.hl7.fhir.r5.model.ValueSet output = expandValueSetR5(theValidationSupportContext, input, codeSystemLoader, valueSetLoader, theWantSystem, theWantCode);
|
||||
org.hl7.fhir.r5.model.ValueSet output = expandValueSetR5(theValidationSupportContext, input, codeSystemLoader, valueSetLoader, theWantSystemIdentifier, theWantCode);
|
||||
return (output);
|
||||
}
|
||||
|
||||
|
|
@ -404,7 +445,7 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
}
|
||||
|
||||
@Nullable
|
||||
private org.hl7.fhir.r5.model.ValueSet expandValueSetDstu3(ValidationSupportContext theValidationSupportContext, org.hl7.fhir.dstu3.model.ValueSet theInput, @Nullable String theWantSystem, @Nullable String theWantCode) {
|
||||
private org.hl7.fhir.r5.model.ValueSet expandValueSetDstu3(ValidationSupportContext theValidationSupportContext, org.hl7.fhir.dstu3.model.ValueSet theInput, @Nullable String theWantSystemIdentifier, @Nullable String theWantCode) {
|
||||
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);
|
||||
return CodeSystem30_50.convertCodeSystem(codeSystem);
|
||||
|
|
@ -415,12 +456,12 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
};
|
||||
|
||||
org.hl7.fhir.r5.model.ValueSet input = ValueSet30_50.convertValueSet(theInput);
|
||||
org.hl7.fhir.r5.model.ValueSet output = expandValueSetR5(theValidationSupportContext, input, codeSystemLoader, valueSetLoader, theWantSystem, theWantCode);
|
||||
org.hl7.fhir.r5.model.ValueSet output = expandValueSetR5(theValidationSupportContext, input, codeSystemLoader, valueSetLoader, theWantSystemIdentifier, theWantCode);
|
||||
return (output);
|
||||
}
|
||||
|
||||
@Nullable
|
||||
private org.hl7.fhir.r5.model.ValueSet expandValueSetR4(ValidationSupportContext theValidationSupportContext, org.hl7.fhir.r4.model.ValueSet theInput, @Nullable String theWantSystem, @Nullable String theWantCode) {
|
||||
private org.hl7.fhir.r5.model.ValueSet expandValueSetR4(ValidationSupportContext theValidationSupportContext, org.hl7.fhir.r4.model.ValueSet theInput, @Nullable String theWantSystemIdentifier, @Nullable String theWantCode) {
|
||||
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);
|
||||
return CodeSystem40_50.convertCodeSystem(codeSystem);
|
||||
|
|
@ -431,7 +472,7 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
};
|
||||
|
||||
org.hl7.fhir.r5.model.ValueSet input = ValueSet40_50.convertValueSet(theInput);
|
||||
org.hl7.fhir.r5.model.ValueSet output = expandValueSetR5(theValidationSupportContext, input, codeSystemLoader, valueSetLoader, theWantSystem, theWantCode);
|
||||
org.hl7.fhir.r5.model.ValueSet output = expandValueSetR5(theValidationSupportContext, input, codeSystemLoader, valueSetLoader, theWantSystemIdentifier, theWantCode);
|
||||
return (output);
|
||||
}
|
||||
|
||||
|
|
@ -444,12 +485,12 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
}
|
||||
|
||||
@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 theWantSystem, @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 theWantSystemIdentifier, @Nullable String theWantCode) {
|
||||
Set<VersionIndependentConcept> concepts = new HashSet<>();
|
||||
|
||||
try {
|
||||
expandValueSetR5IncludeOrExclude(theValidationSupportContext, concepts, theCodeSystemLoader, theValueSetLoader, theInput.getCompose().getInclude(), true, theWantSystem, theWantCode);
|
||||
expandValueSetR5IncludeOrExclude(theValidationSupportContext, concepts, theCodeSystemLoader, theValueSetLoader, theInput.getCompose().getExclude(), false, theWantSystem, theWantCode);
|
||||
expandValueSetR5IncludeOrExclude(theValidationSupportContext, concepts, theCodeSystemLoader, theValueSetLoader, theInput.getCompose().getInclude(), true, theWantSystemIdentifier, theWantCode);
|
||||
expandValueSetR5IncludeOrExclude(theValidationSupportContext, concepts, theCodeSystemLoader, theValueSetLoader, theInput.getCompose().getExclude(), false, theWantSystemIdentifier, theWantCode);
|
||||
} catch (ExpansionCouldNotBeCompletedInternallyException e) {
|
||||
return null;
|
||||
}
|
||||
|
|
@ -460,23 +501,46 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
contains.setSystem(next.getSystem());
|
||||
contains.setCode(next.getCode());
|
||||
contains.setDisplay(next.getDisplay());
|
||||
contains.setVersion(next.getSystemVersion());
|
||||
}
|
||||
|
||||
return retVal;
|
||||
}
|
||||
|
||||
private void expandValueSetR5IncludeOrExclude(ValidationSupportContext theValidationSupportContext, Set<VersionIndependentConcept> 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 theWantSystem, @Nullable String theWantCode) throws ExpansionCouldNotBeCompletedInternallyException {
|
||||
private void expandValueSetR5IncludeOrExclude(ValidationSupportContext theValidationSupportContext, Set<VersionIndependentConcept> 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 {
|
||||
String wantSystemUrl = null;
|
||||
String wantSystemVersion = null;
|
||||
if (theWantSystemIdentifier != null) {
|
||||
int versionIndex = theWantSystemIdentifier.indexOf("|");
|
||||
if (versionIndex > -1) {
|
||||
wantSystemUrl = theWantSystemIdentifier.substring(0,versionIndex);
|
||||
wantSystemVersion = theWantSystemIdentifier.substring(versionIndex+1);
|
||||
} else {
|
||||
wantSystemUrl = theWantSystemIdentifier;
|
||||
}
|
||||
}
|
||||
|
||||
for (org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent nextInclude : theComposeList) {
|
||||
|
||||
List<VersionIndependentConcept> nextCodeList = new ArrayList<>();
|
||||
String system = nextInclude.getSystem();
|
||||
if (isNotBlank(system)) {
|
||||
String includeOrExcludeConceptSystemUrl = nextInclude.getSystem();
|
||||
String includeOrExcludeConceptSystemVersion = nextInclude.getVersion();
|
||||
if (isNotBlank(includeOrExcludeConceptSystemUrl)) {
|
||||
|
||||
if (theWantSystem != null && !theWantSystem.equals(system)) {
|
||||
if (wantSystemUrl != null && !wantSystemUrl.equals(includeOrExcludeConceptSystemUrl)) {
|
||||
continue;
|
||||
}
|
||||
|
||||
CodeSystem codeSystem = theCodeSystemLoader.apply(system);
|
||||
if (wantSystemVersion != null && !wantSystemVersion.equals(includeOrExcludeConceptSystemVersion)) {
|
||||
continue;
|
||||
}
|
||||
|
||||
CodeSystem includeOrExcludeSystemResource;
|
||||
if (includeOrExcludeConceptSystemVersion != null) {
|
||||
includeOrExcludeSystemResource = theCodeSystemLoader.apply(includeOrExcludeConceptSystemUrl + "|" + includeOrExcludeConceptSystemVersion);
|
||||
} else {
|
||||
includeOrExcludeSystemResource = theCodeSystemLoader.apply(includeOrExcludeConceptSystemUrl);
|
||||
}
|
||||
|
||||
Set<String> wantCodes;
|
||||
if (nextInclude.getConcept().isEmpty()) {
|
||||
|
|
@ -488,18 +552,18 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
}
|
||||
|
||||
boolean ableToHandleCode = false;
|
||||
if (codeSystem == null || codeSystem.getContent() == CodeSystem.CodeSystemContentMode.NOTPRESENT) {
|
||||
if (includeOrExcludeSystemResource == null || includeOrExcludeSystemResource.getContent() == CodeSystem.CodeSystemContentMode.NOTPRESENT) {
|
||||
|
||||
if (theWantCode != null) {
|
||||
if (theValidationSupportContext.getRootValidationSupport().isCodeSystemSupported(theValidationSupportContext, system)) {
|
||||
LookupCodeResult lookup = theValidationSupportContext.getRootValidationSupport().lookupCode(theValidationSupportContext, system, theWantCode);
|
||||
if (theValidationSupportContext.getRootValidationSupport().isCodeSystemSupported(theValidationSupportContext, includeOrExcludeConceptSystemUrl)) {
|
||||
LookupCodeResult lookup = theValidationSupportContext.getRootValidationSupport().lookupCode(theValidationSupportContext, includeOrExcludeConceptSystemUrl, theWantCode);
|
||||
if (lookup != null && lookup.isFound()) {
|
||||
CodeSystem.ConceptDefinitionComponent conceptDefinition = new CodeSystem.ConceptDefinitionComponent()
|
||||
.addConcept()
|
||||
.setCode(theWantCode)
|
||||
.setDisplay(lookup.getCodeDisplay());
|
||||
List<CodeSystem.ConceptDefinitionComponent> codesList = Collections.singletonList(conceptDefinition);
|
||||
addCodes(system, codesList, nextCodeList, wantCodes);
|
||||
addCodes(includeOrExcludeConceptSystemUrl, includeOrExcludeConceptSystemVersion, codesList, nextCodeList, wantCodes);
|
||||
ableToHandleCode = true;
|
||||
}
|
||||
} else if (theComposeListIsInclude) {
|
||||
|
|
@ -514,7 +578,7 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
* enumerate a set of good codes for them is a nice compromise there.
|
||||
*/
|
||||
for (org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent next : theComposeList) {
|
||||
if (Objects.equals(next.getSystem(), theWantSystem)) {
|
||||
if (Objects.equals(next.getSystem(), theWantSystemIdentifier)) {
|
||||
Optional<org.hl7.fhir.r5.model.ValueSet.ConceptReferenceComponent> matchingEnumeratedConcept = next.getConcept().stream().filter(t -> Objects.equals(t.getCode(), theWantCode)).findFirst();
|
||||
if (matchingEnumeratedConcept.isPresent()) {
|
||||
CodeSystem.ConceptDefinitionComponent conceptDefinition = new CodeSystem.ConceptDefinitionComponent()
|
||||
|
|
@ -522,7 +586,7 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
.setCode(theWantCode)
|
||||
.setDisplay(matchingEnumeratedConcept.get().getDisplay());
|
||||
List<CodeSystem.ConceptDefinitionComponent> codesList = Collections.singletonList(conceptDefinition);
|
||||
addCodes(system, codesList, nextCodeList, wantCodes);
|
||||
addCodes(includeOrExcludeConceptSystemUrl, includeOrExcludeConceptSystemVersion, codesList, nextCodeList, wantCodes);
|
||||
ableToHandleCode = true;
|
||||
break;
|
||||
}
|
||||
|
|
@ -540,8 +604,8 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
throw new ExpansionCouldNotBeCompletedInternallyException();
|
||||
}
|
||||
|
||||
if (codeSystem != null && codeSystem.getContent() != CodeSystem.CodeSystemContentMode.NOTPRESENT) {
|
||||
addCodes(system, codeSystem.getConcept(), nextCodeList, wantCodes);
|
||||
if (includeOrExcludeSystemResource != null && includeOrExcludeSystemResource.getContent() != CodeSystem.CodeSystemContentMode.NOTPRESENT) {
|
||||
addCodes(includeOrExcludeConceptSystemUrl, includeOrExcludeConceptSystemVersion, includeOrExcludeSystemResource.getConcept(), nextCodeList, wantCodes);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -549,12 +613,12 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
for (CanonicalType nextValueSetInclude : nextInclude.getValueSet()) {
|
||||
org.hl7.fhir.r5.model.ValueSet vs = theValueSetLoader.apply(nextValueSetInclude.getValueAsString());
|
||||
if (vs != null) {
|
||||
org.hl7.fhir.r5.model.ValueSet subExpansion = expandValueSetR5(theValidationSupportContext, vs, theCodeSystemLoader, theValueSetLoader, theWantSystem, theWantCode);
|
||||
org.hl7.fhir.r5.model.ValueSet subExpansion = expandValueSetR5(theValidationSupportContext, vs, theCodeSystemLoader, theValueSetLoader, theWantSystemIdentifier, theWantCode);
|
||||
if (subExpansion == null) {
|
||||
throw new ExpansionCouldNotBeCompletedInternallyException();
|
||||
}
|
||||
for (org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent next : subExpansion.getExpansion().getContains()) {
|
||||
nextCodeList.add(new VersionIndependentConcept(next.getSystem(), next.getCode(), next.getDisplay()));
|
||||
nextCodeList.add(new VersionIndependentConcept(next.getSystem(), next.getCode(), next.getDisplay(), next.getVersion()));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -569,14 +633,14 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
|
||||
}
|
||||
|
||||
private void addCodes(String theSystem, List<CodeSystem.ConceptDefinitionComponent> theSource, List<VersionIndependentConcept> theTarget, Set<String> theCodeFilter) {
|
||||
private void addCodes(String theCodeSystemUrl, String theCodeSystemVersion, List<CodeSystem.ConceptDefinitionComponent> theSource, List<VersionIndependentConcept> theTarget, Set<String> theCodeFilter) {
|
||||
for (CodeSystem.ConceptDefinitionComponent next : theSource) {
|
||||
if (isNotBlank(next.getCode())) {
|
||||
if (theCodeFilter == null || theCodeFilter.contains(next.getCode())) {
|
||||
theTarget.add(new VersionIndependentConcept(theSystem, next.getCode(), next.getDisplay()));
|
||||
theTarget.add(new VersionIndependentConcept(theCodeSystemUrl, next.getCode(), next.getDisplay(), theCodeSystemVersion));
|
||||
}
|
||||
}
|
||||
addCodes(theSystem, next.getConcept(), theTarget, theCodeFilter);
|
||||
addCodes(theCodeSystemUrl, theCodeSystemVersion, next.getConcept(), theTarget, theCodeFilter);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -593,21 +657,21 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
|
|||
|
||||
private static void flattenAndConvertCodesDstu3(List<org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent> theInput, List<VersionIndependentConcept> theVersionIndependentConcepts) {
|
||||
for (org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent next : theInput) {
|
||||
theVersionIndependentConcepts.add(new VersionIndependentConcept(next.getSystem(), next.getCode(), next.getDisplay()));
|
||||
theVersionIndependentConcepts.add(new VersionIndependentConcept(next.getSystem(), next.getCode(), next.getDisplay(), next.getVersion()));
|
||||
flattenAndConvertCodesDstu3(next.getContains(), theVersionIndependentConcepts);
|
||||
}
|
||||
}
|
||||
|
||||
private static void flattenAndConvertCodesR4(List<org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent> theInput, List<VersionIndependentConcept> theVersionIndependentConcepts) {
|
||||
for (org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent next : theInput) {
|
||||
theVersionIndependentConcepts.add(new VersionIndependentConcept(next.getSystem(), next.getCode(), next.getDisplay()));
|
||||
theVersionIndependentConcepts.add(new VersionIndependentConcept(next.getSystem(), next.getCode(), next.getDisplay(), next.getVersion()));
|
||||
flattenAndConvertCodesR4(next.getContains(), theVersionIndependentConcepts);
|
||||
}
|
||||
}
|
||||
|
||||
private static void flattenAndConvertCodesR5(List<org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent> theInput, List<VersionIndependentConcept> theVersionIndependentConcepts) {
|
||||
for (org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent next : theInput) {
|
||||
theVersionIndependentConcepts.add(new VersionIndependentConcept(next.getSystem(), next.getCode(), next.getDisplay()));
|
||||
theVersionIndependentConcepts.add(new VersionIndependentConcept(next.getSystem(), next.getCode(), next.getDisplay(), next.getVersion()));
|
||||
flattenAndConvertCodesR5(next.getContains(), theVersionIndependentConcepts);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue