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Use canonical identifiers for code systems rather than specifying version separately.

This commit is contained in:
ianmarshall 2020-09-23 16:42:29 -04:00
parent b32c4f01a8
commit ceb5ec6384
36 changed files with 300 additions and 465 deletions
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13
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/IValidationSupport.java
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@ -212,19 +212,6 @@ public interface IValidationSupport {
return null;
}
/**
* Look up a code using the system, system version and code value
*
* @param theValidationSupportContext The validation support module will be passed in to this method. This is convenient in cases where the operation needs to make calls to
* other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
* @param theSystem The CodeSystem URL
* @param theCode The code
* @param theSystemVersion The CodeSystem version
*/
default LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theSystemVersion) {
return null;
}
/**
* Returns <code>true</code> if the given valueset can be validated by the given
* validation support module

5
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirResourceDaoCodeSystem.java
View File

@ -42,11 +42,6 @@ public interface IFhirResourceDaoCodeSystem<T extends IBaseResource, CD, CC> ext
SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, CD theCodingA, CD theCodingB, RequestDetails theRequestDetails);
@Nonnull
IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, CD theCoding, IPrimitiveType<String> theVersion, RequestDetails theRequestDetails);
SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, CD theCodingA, CD theCodingB, IPrimitiveType<String> theVersion, RequestDetails theRequestDetails);
class SubsumesResult {
private final ConceptSubsumptionOutcome myOutcome;

4
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirResourceDaoValueSet.java
View File

@ -38,12 +38,8 @@ public interface IFhirResourceDaoValueSet<T extends IBaseResource, CD, CC> exten
T expandByIdentifier(String theUri, String theFilter);
T expandByIdentifier(String theUri, String theValueSetVersion, String theFilter);
T expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount);
T expandByIdentifier(String theUri, String theValueSetVersion, String theFilter, int theOffset, int theCount);
void purgeCaches();
IValidationSupport.CodeValidationResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, CD theCoding, CC theCodeableConcept, RequestDetails theRequestDetails);

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoValueSetDstu2.java
View File

@ -174,21 +174,11 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
return expand(source, theFilter);
}
@Override
public ValueSet expandByIdentifier(String theUri, String theValueSetVersion, String theFilter) {
throw new UnsupportedOperationException();
}
@Override
public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
throw new UnsupportedOperationException();
}
@Override
public ValueSet expandByIdentifier(String theUri, String theValueSetVersion, String theFilter, int theOffset, int theCount) {
throw new UnsupportedOperationException();
}
@Override
public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
if (theSystem != null && theSystem.startsWith("http://hl7.org/fhir/")) {
@ -244,11 +234,6 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
return null;
}
@Override
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, CodingDt theCoding, IPrimitiveType<String> theVersion, RequestDetails theRequestDetails) {
throw new UnsupportedOperationException();
}
@Override
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, CodingDt theCoding, RequestDetails theRequest) {
boolean haveCoding = theCoding != null && isNotBlank(theCoding.getSystem()) && isNotBlank(theCoding.getCode());
@ -294,11 +279,6 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
return myTerminologySvc.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB);
}
@Override
public SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, CodingDt theCodingA, CodingDt theCodingB, IPrimitiveType<String> theVersion, RequestDetails theRequestDetails) {
throw new UnsupportedOperationException();
}
@Override
@PostConstruct
public void postConstruct() {

27
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java
View File

@ -85,12 +85,6 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
@Nonnull
@Override
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, RequestDetails theRequestDetails) {
return lookupCode(theCode, theSystem, theCoding, null, theRequestDetails);
}
@Nonnull
@Override
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, IPrimitiveType<String> theVersion, RequestDetails theRequestDetails) {
boolean haveCoding = theCoding != null && isNotBlank(theCoding.getSystem()) && isNotBlank(theCoding.getCode());
boolean haveCode = theCode != null && theCode.isEmpty() == false;
boolean haveSystem = theSystem != null && theSystem.isEmpty() == false;
@ -104,29 +98,19 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
String code;
String system;
String codeSystemVersion = null;
if (haveCoding) {
code = theCoding.getCode();
system = theCoding.getSystem();
codeSystemVersion = theCoding.getVersion();
} else {
code = theCode.getValue();
system = theSystem.getValue();
if (theVersion != null) {
codeSystemVersion = theVersion.getValue();
}
}
ourLog.debug("Looking up {} / {}, version {}", system, code, codeSystemVersion);
ourLog.debug("Looking up {} / {}", system, code);
if (myValidationSupport.isCodeSystemSupported(new ValidationSupportContext(myValidationSupport), system)) {
ourLog.debug("Code system {} is supported", system);
IValidationSupport.LookupCodeResult result;
if (codeSystemVersion != null) {
result = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code, codeSystemVersion);
} else {
result = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code);
}
IValidationSupport.LookupCodeResult result = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code);
if (result != null) {
return result;
}
@ -136,13 +120,6 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
return IValidationSupport.LookupCodeResult.notFound(system, code);
}
@Override
public SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, Coding theCodingA, Coding theCodingB, IPrimitiveType<String> theVersion, RequestDetails theRequestDetails) {
String codingBVersion = theCodingB != null ? theCodingB.getVersion() : null;
String codingAVersion = theCodingA != null ? theCodingA.getVersion() : null;
return myTerminologySvc.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theVersion, codingAVersion, codingBVersion);
}
@Override
public SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, Coding theCodingA, Coding theCodingB, RequestDetails theRequestDetails) {
return myTerminologySvc.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB);

52
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
View File

@ -113,7 +113,21 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueS
throw new InvalidRequestException("URI must not be blank or missing");
}
return doExpand(createSourceValueSet(theUri, null, theFilter));
ValueSet source = new ValueSet();
source.setUrl(theUri);
source.getCompose().addInclude().addValueSet(theUri);
if (isNotBlank(theFilter)) {
ConceptSetComponent include = source.getCompose().addInclude();
ConceptSetFilterComponent filter = include.addFilter();
filter.setProperty("display");
filter.setOp(FilterOperator.EQUAL);
filter.setValue(theFilter);
}
ValueSet retVal = doExpand(source);
return retVal;
// if (defaultValueSet != null) {
// source = getContext().newJsonParser().parseResource(ValueSet.class, getContext().newJsonParser().encodeResourceToString(defaultValueSet));
@ -129,27 +143,15 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueS
}
@Override
public ValueSet expandByIdentifier(String theUri, String theValueSetVersion, String theFilter) {
public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
if (isBlank(theUri)) {
throw new InvalidRequestException("URI must not be blank or missing");
}
return doExpand(createSourceValueSet(theUri, theValueSetVersion, theFilter));
}
private ValueSet createSourceValueSet(String theUri, String theValueSetVersion, String theFilter) {
ValueSet source = new ValueSet();
source.setUrl(theUri);
if (theValueSetVersion != null) {
source.setVersion(theValueSetVersion);
}
if (theValueSetVersion != null) {
source.getCompose().addInclude().addValueSet(theUri + "|" +theValueSetVersion);
} else {
source.getCompose().addInclude().addValueSet(theUri);
}
source.getCompose().addInclude().addValueSet(theUri);
if (isNotBlank(theFilter)) {
ConceptSetComponent include = source.getCompose().addInclude();
@ -158,25 +160,9 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueS
filter.setOp(FilterOperator.EQUAL);
filter.setValue(theFilter);
}
return source;
}
@Override
public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
if (isBlank(theUri)) {
throw new InvalidRequestException("URI must not be blank or missing");
}
return doExpand(createSourceValueSet(theUri, null, theFilter), theOffset, theCount);
}
@Override
public ValueSet expandByIdentifier(String theUri, String theValueSetVersion, String theFilter, int theOffset, int theCount) {
if (isBlank(theUri)) {
throw new InvalidRequestException("URI must not be blank or missing");
}
return doExpand(createSourceValueSet(theUri, theValueSetVersion, theFilter), theOffset, theCount);
ValueSet retVal = doExpand(source, theOffset, theCount);
return retVal;
}
@Override

27
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java
View File

@ -80,12 +80,6 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
@Nonnull
@Override
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, RequestDetails theRequestDetails) {
return lookupCode(theCode, theSystem, theCoding, null, theRequestDetails);
}
@Nonnull
@Override
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, IPrimitiveType<String> theVersion, RequestDetails theRequestDetails) {
boolean haveCoding = theCoding != null && isNotBlank(theCoding.getSystem()) && isNotBlank(theCoding.getCode());
boolean haveCode = theCode != null && theCode.isEmpty() == false;
boolean haveSystem = theSystem != null && theSystem.isEmpty() == false;
@ -99,30 +93,20 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
String code;
String system;
String codeSystemVersion = null;
if (haveCoding) {
code = theCoding.getCode();
system = theCoding.getSystem();
codeSystemVersion = theCoding.getVersion();
} else {
code = theCode.getValue();
system = theSystem.getValue();
if (theVersion != null) {
codeSystemVersion = theVersion.getValue();
}
}
ourLog.debug("Looking up {} / {}, version {}", system, code, codeSystemVersion);
ourLog.debug("Looking up {} / {}", system, code);
if (myValidationSupport.isCodeSystemSupported(new ValidationSupportContext(myValidationSupport), system)) {
ourLog.debug("Code system {} is supported", system);
IValidationSupport.LookupCodeResult retVal;
if (codeSystemVersion != null) {
retVal = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code, codeSystemVersion);
} else {
retVal = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code);
}
IValidationSupport.LookupCodeResult retVal = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code);
if (retVal != null) {
return retVal;
}
@ -134,13 +118,6 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
}
@Override
public SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, Coding theCodingA, Coding theCodingB, IPrimitiveType<String> theVersion, RequestDetails theRequestDetails) {
String codingBVersion = theCodingB != null ? theCodingB.getVersion() : null;
String codingAVersion = theCodingA != null ? theCodingA.getVersion() : null;
return myTerminologySvc.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theVersion, codingAVersion, codingBVersion);
}
@Override
public SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, Coding theCodingA, Coding theCodingB, RequestDetails theRequestDetails) {
return myTerminologySvc.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB);

49
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
View File

@ -95,7 +95,20 @@ public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet>
throw new InvalidRequestException("URI must not be blank or missing");
}
return doExpand(createSourceValueSet(theUri, null, theFilter));
ValueSet source = new ValueSet();
source.setUrl(theUri);
source.getCompose().addInclude().addValueSet(theUri);
if (isNotBlank(theFilter)) {
ConceptSetComponent include = source.getCompose().addInclude();
ValueSet.ConceptSetFilterComponent filter = include.addFilter();
filter.setProperty("display");
filter.setOp(FilterOperator.EQUAL);
filter.setValue(theFilter);
}
return doExpand(source);
// if (defaultValueSet != null) {
// source = getContext().newJsonParser().parseResource(ValueSet.class, getContext().newJsonParser().encodeResourceToString(defaultValueSet));
@ -111,26 +124,15 @@ public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet>
}
@Override
public ValueSet expandByIdentifier(String theUri, String theValueSetVersion, String theFilter) {
public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
if (isBlank(theUri)) {
throw new InvalidRequestException("URI must not be blank or missing");
}
return doExpand(createSourceValueSet(theUri, theValueSetVersion, theFilter));
}
private ValueSet createSourceValueSet(String theUri, String theValueSetVersion, String theFilter) {
ValueSet source = new ValueSet();
source.setUrl(theUri);
if (theValueSetVersion != null) {
source.setVersion(theValueSetVersion);
}
if (theValueSetVersion != null) {
source.getCompose().addInclude().addValueSet(theUri + "|" +theValueSetVersion);
} else {
source.getCompose().addInclude().addValueSet(theUri);
}
source.getCompose().addInclude().addValueSet(theUri);
if (isNotBlank(theFilter)) {
ValueSet.ConceptSetComponent include = source.getCompose().addInclude();
@ -139,25 +141,8 @@ public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet>
filter.setOp(ValueSet.FilterOperator.EQUAL);
filter.setValue(theFilter);
}
return source;
}
@Override
public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
if (isBlank(theUri)) {
throw new InvalidRequestException("URI must not be blank or missing");
}
return doExpand(createSourceValueSet(theUri,null,theFilter), theOffset, theCount);
}
@Override
public ValueSet expandByIdentifier(String theUri, String theValueSetVersion, String theFilter, int theOffset, int theCount) {
if (isBlank(theUri)) {
throw new InvalidRequestException("URI must not be blank or missing");
}
return doExpand(createSourceValueSet(theUri,theValueSetVersion,theFilter), theOffset, theCount);
return doExpand(source, theOffset, theCount);
}
@Override

29
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCodeSystemR5.java
View File

@ -82,12 +82,6 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
@Nonnull
@Override
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, RequestDetails theRequestDetails) {
return lookupCode(theCode, theSystem, theCoding, null, theRequestDetails);
}
@Nonnull
@Override
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, IPrimitiveType<String> theVersion, RequestDetails theRequestDetails) {
boolean haveCoding = theCoding != null && isNotBlank(theCoding.getSystem()) && isNotBlank(theCoding.getCode());
boolean haveCode = theCode != null && theCode.isEmpty() == false;
boolean haveSystem = theSystem != null && theSystem.isEmpty() == false;
@ -101,30 +95,20 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
String code;
String system;
String codeSystemVersion = null;
if (haveCoding) {
code = theCoding.getCode();
system = theCoding.getSystem();
codeSystemVersion = theCoding.getVersion();
} else {
code = theCode.getValue();
system = theSystem.getValue();
if (theVersion != null) {
codeSystemVersion = theVersion.getValue();
}
}
ourLog.debug("Looking up {} / {}, version {}", system, code, codeSystemVersion);
ourLog.info("Looking up {} / {}", system, code);
if (myValidationSupport.isCodeSystemSupported(new ValidationSupportContext(myValidationSupport), system)) {
ourLog.debug("Code system {} is supported", system);
IValidationSupport.LookupCodeResult retVal;
if (codeSystemVersion != null) {
retVal = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code, codeSystemVersion);
} else {
retVal = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code);
}
ourLog.info("Code system {} is supported", system);
IValidationSupport.LookupCodeResult retVal = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code);
if (retVal != null) {
return retVal;
}
@ -136,13 +120,6 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
}
@Override
public SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, Coding theCodingA, Coding theCodingB, IPrimitiveType<String> theVersion, RequestDetails theRequestDetails) {
String codingBVersion = theCodingB != null ? theCodingB.getVersion() : null;
String codingAVersion = theCodingA != null ? theCodingA.getVersion() : null;
return myTerminologySvc.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theVersion, codingAVersion, codingBVersion);
}
@Override
public SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, Coding theCodingA, Coding theCodingB, RequestDetails theRequestDetails) {
return myTerminologySvc.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB);

50
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
View File

@ -95,7 +95,20 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet>
throw new InvalidRequestException("URI must not be blank or missing");
}
return doExpand(createSourceValueSet(theUri, null, theFilter));
ValueSet source = new ValueSet();
source.setUrl(theUri);
source.getCompose().addInclude().addValueSet(theUri);
if (isNotBlank(theFilter)) {
ConceptSetComponent include = source.getCompose().addInclude();
ValueSet.ConceptSetFilterComponent filter = include.addFilter();
filter.setProperty("display");
filter.setOp(Enumerations.FilterOperator.EQUAL);
filter.setValue(theFilter);
}
return doExpand(source);
// if (defaultValueSet != null) {
// source = getContext().newJsonParser().parseResource(ValueSet.class, getContext().newJsonParser().encodeResourceToString(defaultValueSet));
@ -111,27 +124,15 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet>
}
@Override
public ValueSet expandByIdentifier(String theUri, String theValueSetUri, String theFilter) {
public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
if (isBlank(theUri)) {
throw new InvalidRequestException("URI must not be blank or missing");
}
return doExpand(createSourceValueSet(theUri, theValueSetUri, theFilter));
}
private ValueSet createSourceValueSet(String theUri, String theValueSetVersion, String theFilter) {
ValueSet source = new ValueSet();
source.setUrl(theUri);
if (theValueSetVersion != null) {
source.setVersion(theValueSetVersion);
}
if (theValueSetVersion != null) {
source.getCompose().addInclude().addValueSet(theUri + "|" +theValueSetVersion);
} else {
source.getCompose().addInclude().addValueSet(theUri);
}
source.getCompose().addInclude().addValueSet(theUri);
if (isNotBlank(theFilter)) {
ValueSet.ConceptSetComponent include = source.getCompose().addInclude();
@ -140,25 +141,8 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet>
filter.setOp(Enumerations.FilterOperator.EQUAL);
filter.setValue(theFilter);
}
return source;
}
@Override
public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
if (isBlank(theUri)) {
throw new InvalidRequestException("URI must not be blank or missing");
}
return doExpand(createSourceValueSet(theUri, null, theFilter), theOffset, theCount);
}
@Override
public ValueSet expandByIdentifier(String theUri, String theValueSetVersion, String theFilter, int theOffset, int theCount) {
if (isBlank(theUri)) {
throw new InvalidRequestException("URI must not be blank or missing");
}
return doExpand(createSourceValueSet(theUri, theValueSetVersion, theFilter), theOffset, theCount);
return doExpand(source, theOffset, theCount);
}
@Override

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderCodeSystemDstu3.java
View File

@ -63,7 +63,7 @@ public class BaseJpaResourceProviderCodeSystemDstu3 extends JpaResourceProviderD
IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
IValidationSupport.LookupCodeResult result;
if (theVersion != null) {
result = dao.lookupCode(theCode, theSystem, theCoding, theVersion, theRequestDetails);
result = dao.lookupCode(theCode, new UriType(theSystem.getValue() + "|" + theVersion), theCoding, theRequestDetails);
} else {
result = dao.lookupCode(theCode, theSystem, theCoding, theRequestDetails);
}
@ -98,11 +98,16 @@ public class BaseJpaResourceProviderCodeSystemDstu3 extends JpaResourceProviderD
try {
IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
IFhirResourceDaoCodeSystem.SubsumesResult result;
if (theVersion != null || (theCodingA != null && theCodingA.hasVersion()) || (theCodingB != null &&theCodingB.hasVersion())) {
result = dao.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theVersion, theRequestDetails);
} else {
result = dao.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theRequestDetails);
if (theVersion != null) {
theSystem = new UriType(theSystem.asStringValue() + "|" + theVersion.toString());
}
if (theCodingA != null && theCodingA.hasVersion()) {
theCodingA.setSystem(theCodingA.getSystemElement().asStringValue() + "|" + theCodingA.getVersion());
}
if (theCodingB != null && theCodingB.hasVersion()) {
theCodingB.setSystem(theCodingB.getSystemElement().asStringValue() + "|" + theCodingB.getVersion());
}
result = dao.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theRequestDetails);
return (Parameters) result.toParameters(theRequestDetails.getFhirContext());
} finally {
endRequest(theServletRequest);

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderValueSetDstu3.java
View File

@ -102,7 +102,7 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
return dao.expand(theId, toFilterString(theFilter), offset, count, theRequestDetails);
} else if (haveIdentifier) {
if (haveValueSetVersion) {
return dao.expandByIdentifier(url.getValue(), theValueSetVersion.getValue(), toFilterString(theFilter), offset, count);
return dao.expandByIdentifier(url.getValue() + "|" + theValueSetVersion.getValue(), toFilterString(theFilter), offset, count);
} else {
return dao.expandByIdentifier(url.getValue(), toFilterString(theFilter), offset, count);
}
@ -114,7 +114,7 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
} else if (haveIdentifier) {
if (haveValueSetVersion) {
return dao.expandByIdentifier(url.getValue(), theValueSetVersion.getValue(), toFilterString(theFilter));
return dao.expandByIdentifier(url.getValue() + "|" + theValueSetVersion.getValue(), toFilterString(theFilter));
} else {
return dao.expandByIdentifier(url.getValue(), toFilterString(theFilter));
}

18
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderCodeSystemR4.java
View File

@ -65,7 +65,10 @@ public class BaseJpaResourceProviderCodeSystemR4 extends JpaResourceProviderR4<C
IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
IValidationSupport.LookupCodeResult result;
if (theVersion != null) {
result = dao.lookupCode(theCode, theSystem, theCoding, theVersion, theRequestDetails);
result = dao.lookupCode(theCode, new UriType(theSystem.getValue() + "|" + theVersion), theCoding, theRequestDetails);
} else if (theCoding != null && theCoding.hasVersion()) {
Coding codingWithVersion = new Coding(theCoding.getSystem() + "|" + theCoding.getVersion(), theCoding.getCode(), theCoding.getDisplay());
result = dao.lookupCode(theCode, theSystem, codingWithVersion, theRequestDetails);
} else {
result = dao.lookupCode(theCode, theSystem, theCoding, theRequestDetails);
}
@ -98,11 +101,16 @@ public class BaseJpaResourceProviderCodeSystemR4 extends JpaResourceProviderR4<C
try {
IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
IFhirResourceDaoCodeSystem.SubsumesResult result;
if (theVersion != null || (theCodingA != null && theCodingA.hasVersion()) || (theCodingB != null &&theCodingB.hasVersion())) {
result = dao.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theVersion, theRequestDetails);
} else {
result = dao.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theRequestDetails);
if (theVersion != null) {
theSystem = new UriType(theSystem.asStringValue() + "|" + theVersion.toString());
}
if (theCodingA != null && theCodingA.hasVersion()) {
theCodingA.setSystem(theCodingA.getSystemElement().asStringValue() + "|" + theCodingA.getVersion());
}
if (theCodingB != null && theCodingB.hasVersion()) {
theCodingB.setSystem(theCodingB.getSystemElement().asStringValue() + "|" + theCodingB.getVersion());
}
result = dao.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theRequestDetails);
return (Parameters) result.toParameters(theRequestDetails.getFhirContext());
} finally {
endRequest(theServletRequest);

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderValueSetR4.java
View File

@ -94,7 +94,7 @@ public class BaseJpaResourceProviderValueSetR4 extends JpaResourceProviderR4<Val
return dao.expand(theId, toFilterString(theFilter), offset, count, theRequestDetails);
} else if (haveIdentifier) {
if (haveValueSetVersion) {
return dao.expandByIdentifier(theUrl.getValue(), theValueSetVersion.getValue(), toFilterString(theFilter), offset, count);
return dao.expandByIdentifier(theUrl.getValue() + "|" + theValueSetVersion.getValue(), toFilterString(theFilter), offset, count);
} else {
return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter), offset, count);
}
@ -106,7 +106,7 @@ public class BaseJpaResourceProviderValueSetR4 extends JpaResourceProviderR4<Val
return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
} else if (haveIdentifier) {
if (haveValueSetVersion) {
return dao.expandByIdentifier(theUrl.getValue(), theValueSetVersion.getValue(), toFilterString(theFilter));
return dao.expandByIdentifier(theUrl.getValue() + "|" + theValueSetVersion.getValue(), toFilterString(theFilter));
} else {
return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter));
}

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderCodeSystemR5.java
View File

@ -65,7 +65,7 @@ public class BaseJpaResourceProviderCodeSystemR5 extends JpaResourceProviderR5<C
IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
IValidationSupport.LookupCodeResult result;
if (theVersion != null) {
result = dao.lookupCode(theCode, theSystem, theCoding, theVersion, theRequestDetails);
result = dao.lookupCode(theCode, new UriType(theSystem.getValue() + "|" + theVersion), theCoding, theRequestDetails);
} else {
result = dao.lookupCode(theCode, theSystem, theCoding, theRequestDetails);
}
@ -98,11 +98,16 @@ public class BaseJpaResourceProviderCodeSystemR5 extends JpaResourceProviderR5<C
try {
IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
IFhirResourceDaoCodeSystem.SubsumesResult result;
if (theVersion != null || (theCodingA != null && theCodingA.hasVersion()) || (theCodingB != null &&theCodingB.hasVersion())) {
result = dao.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theVersion, theRequestDetails);
} else {
result = dao.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theRequestDetails);
if (theVersion != null) {
theSystem = new UriType(theSystem.asStringValue() + "|" + theVersion.toString());
}
if (theCodingA != null && theCodingA.hasVersion()) {
theCodingA.setSystem(theCodingA.getSystemElement().asStringValue() + "|" + theCodingA.getVersion());
}
if (theCodingB != null && theCodingB.hasVersion()) {
theCodingB.setSystem(theCodingB.getSystemElement().asStringValue() + "|" + theCodingB.getVersion());
}
result = dao.subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, theRequestDetails);
return (Parameters) result.toParameters(theRequestDetails.getFhirContext());
} finally {
endRequest(theServletRequest);

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderValueSetR5.java
View File

@ -94,7 +94,7 @@ public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<Val
return dao.expand(theId, toFilterString(theFilter), offset, count, theRequestDetails);
} else if (haveIdentifier) {
if (haveValueSetVersion) {
return dao.expandByIdentifier(theUrl.getValue(), theValueSetVersion.getValue(), toFilterString(theFilter), offset, count);
return dao.expandByIdentifier(theUrl.getValue() + "|" + theValueSetVersion.getValue(), toFilterString(theFilter), offset, count);
} else {
return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter), offset, count);
}
@ -106,7 +106,7 @@ public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<Val
return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
} else if (haveIdentifier) {
if (haveValueSetVersion) {
return dao.expandByIdentifier(theUrl.getValue(), theValueSetVersion.getValue(), toFilterString(theFilter));
return dao.expandByIdentifier(theUrl.getValue() + "|" + theValueSetVersion.getValue(), toFilterString(theFilter));
} else {
return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter));
}

182
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
View File

@ -240,7 +240,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
@Override
public boolean isCodeSystemSupported(ValidationSupportContext theValidationSupportContext, String theSystem) {
TermCodeSystemVersion cs = getCurrentCodeSystemVersion(theSystem,null);
TermCodeSystemVersion cs = getCurrentCodeSystemVersion(theSystem);
return cs != null;
}
@ -251,21 +251,33 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
String display = theConcept.getDisplay();
Collection<TermConceptDesignation> designations = theConcept.getDesignations();
if (StringUtils.isNotEmpty(codeSystemVersion)) {
addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, designations, theAdd, theCodeCounter, codeSystem, codeSystemVersion, code, display);
addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, designations, theAdd, theCodeCounter, codeSystem + "|" + codeSystemVersion, code, display);
} else {
addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, designations, theAdd, theCodeCounter, codeSystem, code, display);
}
}
private void addCodeIfNotAlreadyAdded(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, Collection<TermConceptDesignation> theDesignations, boolean theAdd, AtomicInteger theCodeCounter, String theCodeSystem, String theCodeSystemVersion, String theCode, String theDisplay) {
if (isNoneBlank(theCodeSystem, theCode)) {
if (theAdd && theAddedCodes.add(theCodeSystem + "|" + theCode + "|" + theCodeSystemVersion)) {
theValueSetCodeAccumulator.includeConceptWithDesignations(theCodeSystem, theCodeSystemVersion, theCode, theDisplay, theDesignations);
if (StringUtils.isNotEmpty(theCodeSystemVersion)) {
if (isNoneBlank(theCodeSystem, theCode)) {
if (theAdd && theAddedCodes.add(theCodeSystem + "|" + theCode + "|" + theCodeSystemVersion)) {
theValueSetCodeAccumulator.includeConceptWithDesignations(theCodeSystem + "|" + theCodeSystemVersion, theCode, theDisplay, theDesignations);
theCodeCounter.incrementAndGet();
}
if (!theAdd && theAddedCodes.remove(theCodeSystem + "|" + theCode + "|" + theCodeSystemVersion)) {
theValueSetCodeAccumulator.excludeConcept(theCodeSystem + "|" + theCodeSystemVersion, theCode);
theCodeCounter.decrementAndGet();
}
}
} else {
if (theAdd && theAddedCodes.add(theCodeSystem + "|" + theCode)) {
theValueSetCodeAccumulator.includeConceptWithDesignations(theCodeSystem, theCode, theDisplay, theDesignations);
theCodeCounter.incrementAndGet();
}
if (!theAdd && theAddedCodes.remove(theCodeSystem + "|" + theCode + "|" + theCodeSystemVersion)) {
theValueSetCodeAccumulator.excludeConcept(theCodeSystem, theCodeSystemVersion, theCode);
if (!theAdd && theAddedCodes.remove(theCodeSystem + "|" + theCode)) {
theValueSetCodeAccumulator.excludeConcept(theCodeSystem, theCode);
theCodeCounter.decrementAndGet();
}
}
@ -829,7 +841,13 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
/*
* Filters
*/
handleFilters(bool, theSystem, codeSystemVersion, qb, theIncludeOrExclude);
String canonicalSystem;
if (codeSystemVersion != null) {
canonicalSystem = theSystem + "|" + codeSystemVersion;
} else {
canonicalSystem = theSystem;
}
handleFilters(bool, canonicalSystem, qb, theIncludeOrExclude);
Query luceneQuery = bool.createQuery();
@ -938,15 +956,15 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
}
}
private void handleFilters(BooleanJunction<?> theBool, String theSystem, String theSystemVersion, QueryBuilder theQb, ValueSet.ConceptSetComponent theIncludeOrExclude) {
private void handleFilters(BooleanJunction<?> theBool, String theCanonicalSystem, QueryBuilder theQb, ValueSet.ConceptSetComponent theIncludeOrExclude) {
if (theIncludeOrExclude.getFilter().size() > 0) {
for (ValueSet.ConceptSetFilterComponent nextFilter : theIncludeOrExclude.getFilter()) {
handleFilter(theSystem, theSystemVersion, theQb, theBool, nextFilter);
handleFilter(theCanonicalSystem, theQb, theBool, nextFilter);
}
}
}
private void handleFilter(String theSystem, String theSystemVersion, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
private void handleFilter(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
if (isBlank(theFilter.getValue()) && theFilter.getOp() == null && isBlank(theFilter.getProperty())) {
return;
}
@ -962,7 +980,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
break;
case "concept":
case "code":
handleFilterConceptAndCode(theSystem, theSystemVersion, theQb, theBool, theFilter);
handleFilterConceptAndCode(theSystem, theQb, theBool, theFilter);
break;
case "parent":
case "child":
@ -971,11 +989,11 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
break;
case "ancestor":
isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
handleFilterLoincAncestor(theSystem, theSystemVersion, theBool, theFilter);
handleFilterLoincAncestor(theSystem, theBool, theFilter);
break;
case "descendant":
isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
handleFilterLoincDescendant(theSystem, theSystemVersion, theBool, theFilter);
handleFilterLoincDescendant(theSystem, theBool, theFilter);
break;
case "copyright":
isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
@ -988,8 +1006,9 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
}
private void isCodeSystemLoingOrThrowInvalidRequestException(String theSystem, String theProperty) {
if (!isCodeSystemLoinc(theSystem)) {
throw new InvalidRequestException("Invalid filter, property " + theProperty + " is LOINC-specific and cannot be used with system: " + theSystem);
String systemUrl = getSystemFromCanonicalUrl(theSystem);
if (!isCodeSystemLoinc(systemUrl)) {
throw new InvalidRequestException("Invalid filter, property " + theProperty + " is LOINC-specific and cannot be used with system: " + systemUrl);
}
}
@ -1025,8 +1044,8 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
bool.must(textQuery);
}
private void handleFilterConceptAndCode(String theSystem, String theSystemVersion, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
TermConcept code = findCode(theSystem, theFilter.getValue(), theSystemVersion)
private void handleFilterConceptAndCode(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
TermConcept code = findCode(theSystem, theFilter.getValue())
.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + Constants.codeSystemWithDefaultDescription(theSystem) + "}" + theFilter.getValue()));
if (theFilter.getOp() == ValueSet.FilterOperator.ISA) {
@ -1071,41 +1090,41 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
}
@SuppressWarnings("EnumSwitchStatementWhichMissesCases")
private void handleFilterLoincAncestor(String theSystem, String theSystemVersion, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
private void handleFilterLoincAncestor(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
switch (theFilter.getOp()) {
case EQUAL:
addLoincFilterAncestorEqual(theSystem, theSystemVersion, theBool, theFilter);
addLoincFilterAncestorEqual(theSystem, theBool, theFilter);
break;
case IN:
addLoincFilterAncestorIn(theSystem, theSystemVersion, theBool, theFilter);
addLoincFilterAncestorIn(theSystem, theBool, theFilter);
break;
default:
throw new InvalidRequestException("Don't know how to handle op=" + theFilter.getOp() + " on property " + theFilter.getProperty());
}
}
private void addLoincFilterAncestorEqual(String theSystem, String theSystemVersion, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
addLoincFilterAncestorEqual(theSystem, theSystemVersion, theBool, theFilter.getProperty(), theFilter.getValue());
private void addLoincFilterAncestorEqual(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
addLoincFilterAncestorEqual(theSystem, theBool, theFilter.getProperty(), theFilter.getValue());
}
private void addLoincFilterAncestorEqual(String theSystem, String theSystemVersion, BooleanJunction<?> theBool, String theProperty, String theValue) {
List<Term> terms = getAncestorTerms(theSystem, theSystemVersion, theProperty, theValue);
private void addLoincFilterAncestorEqual(String theSystem, BooleanJunction<?> theBool, String theProperty, String theValue) {
List<Term> terms = getAncestorTerms(theSystem, theProperty, theValue);
theBool.must(new TermsQuery(terms));
}
private void addLoincFilterAncestorIn(String theSystem, String theSystemVersion, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
private void addLoincFilterAncestorIn(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
String[] values = theFilter.getValue().split(",");
List<Term> terms = new ArrayList<>();
for (String value : values) {
terms.addAll(getAncestorTerms(theSystem, theSystemVersion, theFilter.getProperty(), value));
terms.addAll(getAncestorTerms(theSystem, theFilter.getProperty(), value));
}
theBool.must(new TermsQuery(terms));
}
private List<Term> getAncestorTerms(String theSystem, String theSystemVersion, String theProperty, String theValue) {
private List<Term> getAncestorTerms(String theSystem, String theProperty, String theValue) {
List<Term> retVal = new ArrayList<>();
TermConcept code = findCode(theSystem, theValue, theSystemVersion)
TermConcept code = findCode(theSystem, theValue)
.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + Constants.codeSystemWithDefaultDescription(theSystem) + "}" + theValue));
retVal.add(new Term("myParentPids", "" + code.getId()));
@ -1115,41 +1134,41 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
}
@SuppressWarnings("EnumSwitchStatementWhichMissesCases")
private void handleFilterLoincDescendant(String theSystem, String theSystemVersion, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
private void handleFilterLoincDescendant(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
switch (theFilter.getOp()) {
case EQUAL:
addLoincFilterDescendantEqual(theSystem, theSystemVersion, theBool, theFilter);
addLoincFilterDescendantEqual(theSystem, theBool, theFilter);
break;
case IN:
addLoincFilterDescendantIn(theSystem, theSystemVersion, theBool, theFilter);
addLoincFilterDescendantIn(theSystem, theBool, theFilter);
break;
default:
throw new InvalidRequestException("Don't know how to handle op=" + theFilter.getOp() + " on property " + theFilter.getProperty());
}
}
private void addLoincFilterDescendantEqual(String theSystem, String theSystemVersion, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
addLoincFilterDescendantEqual(theSystem, theSystemVersion, theBool, theFilter.getProperty(), theFilter.getValue());
private void addLoincFilterDescendantEqual(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
addLoincFilterDescendantEqual(theSystem, theBool, theFilter.getProperty(), theFilter.getValue());
}
private void addLoincFilterDescendantEqual(String theSystem, String theSystemVersion, BooleanJunction<?> theBool, String theProperty, String theValue) {
List<Term> terms = getDescendantTerms(theSystem, theSystemVersion, theProperty, theValue);
private void addLoincFilterDescendantEqual(String theSystem, BooleanJunction<?> theBool, String theProperty, String theValue) {
List<Term> terms = getDescendantTerms(theSystem, theProperty, theValue);
theBool.must(new TermsQuery(terms));
}
private void addLoincFilterDescendantIn(String theSystem, String theSystemVersion, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
private void addLoincFilterDescendantIn(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
String[] values = theFilter.getValue().split(",");
List<Term> terms = new ArrayList<>();
for (String value : values) {
terms.addAll(getDescendantTerms(theSystem, theSystemVersion, theFilter.getProperty(), value));
terms.addAll(getDescendantTerms(theSystem, theFilter.getProperty(), value));
}
theBool.must(new TermsQuery(terms));
}
private List<Term> getDescendantTerms(String theSystem, String theSystemVersion, String theProperty, String theValue) {
private List<Term> getDescendantTerms(String theSystem, String theProperty, String theValue) {
List<Term> retVal = new ArrayList<>();
TermConcept code = findCode(theSystem, theValue, theSystemVersion)
TermConcept code = findCode(theSystem, theValue)
.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + Constants.codeSystemWithDefaultDescription(theSystem) + "}" + theValue));
String[] parentPids = code.getParentPidsAsString().split(" ");
@ -1398,11 +1417,6 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
@Override
public Optional<TermConcept> findCode(String theCodeSystem, String theCode) {
return findCode(theCodeSystem, theCode, null);
}
@Override
public Optional<TermConcept> findCode(String theCodeSystem, String theCode, String theVersion) {
/*
* Loading concepts without a transaction causes issues later on some
* platforms (e.g. PSQL) so this transactiontemplate is here to make
@ -1410,8 +1424,9 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
*/
TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_MANDATORY);
return txTemplate.execute(t -> {
TermCodeSystemVersion csv = getCurrentCodeSystemVersion(theCodeSystem, theVersion);
TermCodeSystemVersion csv = getCurrentCodeSystemVersion(theCodeSystem);
if (csv == null) {
return Optional.empty();
}
@ -1420,17 +1435,15 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
}
@Nullable
private TermCodeSystemVersion getCurrentCodeSystemVersion(String theUri, String theVersion) {
StringBuilder key = new StringBuilder(theUri);
if (theVersion != null) {
key.append("|").append(theVersion);
}
private TermCodeSystemVersion getCurrentCodeSystemVersion(String theUri) {
String myVersion = getVersionFromCanonicalUrl(theUri);
String key = theUri;
TermCodeSystemVersion retVal = myCodeSystemCurrentVersionCache.get(key.toString(), t -> myTxTemplate.execute(tx -> {
TermCodeSystemVersion csv = null;
TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(theUri);
TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(getSystemFromCanonicalUrl(theUri));
if (cs != null) {
if (theVersion != null) {
csv = myCodeSystemVersionDao.findByCodeSystemPidAndVersion(cs.getPid(), theVersion);
if (myVersion != null) {
csv = myCodeSystemVersionDao.findByCodeSystemPidAndVersion(cs.getPid(), myVersion);
} else if (cs.getCurrentVersion() != null) {
csv = cs.getCurrentVersion();
}
@ -1447,6 +1460,27 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
return retVal;
}
private String getVersionFromCanonicalUrl(String theUri) {
String retVal = null;
if (StringUtils.isNotEmpty((theUri))) {
int versionSeparator = theUri.lastIndexOf('|');
if (versionSeparator != -1) {
retVal = theUri.substring(versionSeparator + 1);
}
}
return retVal;
}
private String getSystemFromCanonicalUrl(String theUri) {
String retVal = theUri;
if (StringUtils.isNotEmpty((theUri))){
int versionSeparator = theUri.lastIndexOf('|');
if (versionSeparator != -1) {
retVal = theUri.substring(0, versionSeparator);
}
}
return retVal;
}
@Transactional(propagation = Propagation.REQUIRED)
@Override
@ -1869,14 +1903,8 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
@Transactional
public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB,
IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB) {
return subsumes(theCodeA, theCodeB, theSystem, theCodingA, theCodingB, null, null, null);
}
@Override
@Transactional
public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB, IPrimitiveType<String> theSystemVersion, String theCodingAVersion, String theCodingBVersion) {
VersionIndependentConcept conceptA = toConcept(theCodeA, theSystem, theCodingA, theSystemVersion, theCodingAVersion);
VersionIndependentConcept conceptB = toConcept(theCodeB, theSystem, theCodingB, theSystemVersion, theCodingBVersion);
VersionIndependentConcept conceptA = toConcept(theCodeA, theSystem, theCodingA);
VersionIndependentConcept conceptB = toConcept(theCodeB, theSystem, theCodingB);
if (!StringUtils.equals(conceptA.getSystem(), conceptB.getSystem())) {
throw new InvalidRequestException("Unable to test subsumption across different code systems");
@ -1886,10 +1914,22 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
throw new InvalidRequestException("Unable to test subsumption across different code system versions");
}
TermConcept codeA = findCode(conceptA.getSystem(), conceptA.getCode(), conceptA.getSystemVersion())
String codeACanonicalUrl;
if (StringUtils.isNotEmpty(conceptA.getSystemVersion())) {
codeACanonicalUrl = conceptA.getSystem() + "|" + conceptA.getSystemVersion();
} else {
codeACanonicalUrl = conceptA.getSystem();
}
TermConcept codeA = findCode(codeACanonicalUrl, conceptA.getCode())
.orElseThrow(() -> new InvalidRequestException("Unknown code: " + conceptA));
TermConcept codeB = findCode(conceptB.getSystem(), conceptB.getCode(), conceptB.getSystemVersion())
String codeBCanonicalUrl;
if (StringUtils.isNotEmpty(conceptB.getSystemVersion())) {
codeBCanonicalUrl = conceptB.getSystem() + "|" + conceptB.getSystemVersion();
} else {
codeBCanonicalUrl = conceptB.getSystem();
}
TermConcept codeB = findCode(codeBCanonicalUrl, conceptB.getCode())
.orElseThrow(() -> new InvalidRequestException("Unknown code: " + conceptB));
FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
@ -1908,10 +1948,10 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
protected abstract ValueSet toCanonicalValueSet(IBaseResource theValueSet);
protected IValidationSupport.LookupCodeResult lookupCode(String theSystem, String theCode, String theVersion) {
protected IValidationSupport.LookupCodeResult lookupCode(String theSystem, String theCode) {
TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
return txTemplate.execute(t -> {
Optional<TermConcept> codeOpt = findCode(theSystem, theCode, theVersion);
Optional<TermConcept> codeOpt = findCode(theSystem, theCode);
if (codeOpt.isPresent()) {
TermConcept code = codeOpt.get();
@ -2456,14 +2496,14 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
}
@NotNull
private VersionIndependentConcept toConcept(IPrimitiveType<String> theCodeType, IPrimitiveType<String> theSystemType, IBaseCoding theCodingType, IPrimitiveType<String> theSystemVersionType, String theCodingVersionType) {
private VersionIndependentConcept toConcept(IPrimitiveType<String> theCodeType, IPrimitiveType<String> theSystemType, IBaseCoding theCodingType) {
String code = theCodeType != null ? theCodeType.getValueAsString() : null;
String system = theSystemType != null ? theSystemType.getValueAsString() : null;
String systemVersion = theSystemVersionType != null ? theSystemVersionType.getValueAsString() : null;
String system = theSystemType != null ? getSystemFromCanonicalUrl(theSystemType.getValueAsString()): null;
String systemVersion = theSystemType != null ? getVersionFromCanonicalUrl(theSystemType.getValueAsString()): null;
if (theCodingType != null) {
code = theCodingType.getCode();
system = theCodingType.getSystem();
systemVersion = theCodingVersionType;
system = getSystemFromCanonicalUrl(theCodingType.getSystem());
systemVersion = getVersionFromCanonicalUrl(theCodingType.getSystem());
}
return new VersionIndependentConcept(system, code, null, systemVersion);
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IValueSetConceptAccumulator.java
View File

@ -33,11 +33,11 @@ public interface IValueSetConceptAccumulator {
void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, @Nullable Collection<TermConceptDesignation> theDesignations);
void includeConceptWithDesignations(String theSystem, String theSystemVersion, String theCode, String theDisplay, @Nullable Collection<TermConceptDesignation> theDesignations);
// void includeConceptWithDesignations(String theSystem, String theSystemVersion, String theCode, String theDisplay, @Nullable Collection<TermConceptDesignation> theDesignations);
void excludeConcept(String theSystem, String theCode);
void excludeConcept(String theSystem, String theSystemVersion, String theCode);
// void excludeConcept(String theSystem, String theSystemVersion, String theCode);
@Nullable
default Integer getCapacityRemaining() {

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcDstu3.java
View File

@ -149,12 +149,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
return super.lookupCode(theSystem, theCode, null);
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theVersion) {
return super.lookupCode(theSystem, theCode, theVersion);
return super.lookupCode(theSystem, theCode);
}
@Override

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcR4.java
View File

@ -89,14 +89,9 @@ public class TermReadSvcR4 extends BaseTermReadSvcImpl implements ITermReadSvcR4
return (CodeSystem) theCodeSystem;
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theVersion) {
return super.lookupCode(theSystem, theCode, theVersion);
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
return super.lookupCode(theSystem, theCode, null);
return super.lookupCode(theSystem, theCode);
}
@Override

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetConceptAccumulator.java
View File

@ -71,7 +71,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
}
@Override
public void includeConceptWithDesignations(String theSystem, String theSystemVersion, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations) {
public void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations) {
TermValueSetConcept concept = saveConcept(theSystem, theCode, theDisplay);
if (theDesignations != null) {
for (TermConceptDesignation designation : theDesignations) {
@ -80,18 +80,8 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
}
}
@Override
public void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations) {
includeConceptWithDesignations(theSystem, null, theCode, theDisplay, theDesignations);
}
@Override
public void excludeConcept(String theSystem, String theCode) {
excludeConcept(theSystem, null, theCode);
}
@Override
public void excludeConcept(String theSystem, String theSystemVersion, String theCode) {
if (isAnyBlank(theSystem, theCode)) {
return;
}

63
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetExpansionComponentWithConceptAccumulator.java
View File

@ -26,6 +26,7 @@ import ca.uhn.fhir.jpa.term.ex.ExpansionTooCostlyException;
import ca.uhn.fhir.model.api.annotation.Block;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.HapiExtensions;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.ValueSet;
@ -67,21 +68,18 @@ public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.V
public void includeConcept(String theSystem, String theCode, String theDisplay) {
incrementConceptsCount();
ValueSet.ValueSetExpansionContainsComponent contains = this.addContains();
contains.setSystem(theSystem);
setSystemAndVersion(theSystem, contains);
contains.setCode(theCode);
contains.setDisplay(theDisplay);
}
@Override
public void includeConceptWithDesignations(String theSystem, String theSystemVersion, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations) {
public void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations) {
incrementConceptsCount();
ValueSet.ValueSetExpansionContainsComponent contains = this.addContains();
contains.setSystem(theSystem);
setSystemAndVersion(theSystem, contains);
contains.setCode(theCode);
contains.setDisplay(theDisplay);
if (theSystemVersion != null) {
contains.setVersion(theSystemVersion);
}
if (theDesignations != null) {
for (TermConceptDesignation termConceptDesignation : theDesignations) {
contains
@ -96,28 +94,28 @@ public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.V
}
}
@Override
public void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations) {
this.includeConceptWithDesignations(theSystem, null, theCode, theDisplay, theDesignations);
}
@Override
public void excludeConcept(String theSystem, String theSystemVersion, String theCode) {
this
.getContains()
.removeIf(t ->
theSystem.equals(t.getSystem()) &&
theCode.equals(t.getCode()) &&
theSystemVersion.equals(t.getVersion()));
}
@Override
public void excludeConcept(String theSystem, String theCode) {
this
.getContains()
.removeIf(t ->
theSystem.equals(t.getSystem()) &&
theCode.equals(t.getCode()));
String excludeSystem;
String excludeSystemVersion;
int versionSeparator = theSystem.indexOf("|");
if(versionSeparator > -1) {
excludeSystemVersion = theSystem.substring(versionSeparator + 1);
excludeSystem = theSystem.substring(0, versionSeparator);
} else {
excludeSystem = theSystem;
excludeSystemVersion = null;
}
if (excludeSystemVersion != null) {
this.getContains().removeIf(t ->
excludeSystem.equals(t.getSystem()) &&
theCode.equals(t.getCode()) &&
excludeSystemVersion.equals(t.getVersion()));
} else {
this.getContains().removeIf(t ->
theSystem.equals(t.getSystem()) &&
theCode.equals(t.getCode()));
}
}
private void incrementConceptsCount() {
@ -126,4 +124,17 @@ public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.V
throw new ExpansionTooCostlyException(msg);
}
}
private void setSystemAndVersion(String theSystemAndVersion, ValueSet.ValueSetExpansionContainsComponent myComponent) {
if (StringUtils.isNotEmpty((theSystemAndVersion))) {
int versionSeparator = theSystemAndVersion.lastIndexOf('|');
if (versionSeparator != -1) {
myComponent.setVersion(theSystemAndVersion.substring(versionSeparator + 1));
myComponent.setSystem(theSystemAndVersion.substring(0,versionSeparator));
} else {
myComponent.setSystem(theSystemAndVersion);
}
}
}
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermReadSvc.java
View File

@ -73,8 +73,6 @@ public interface ITermReadSvc extends IValidationSupport {
List<VersionIndependentConcept> expandValueSet(ValueSetExpansionOptions theExpansionOptions, String theValueSet);
Optional<TermConcept> findCode(String theCodeSystem, String theCode, String theVersion);
Optional<TermConcept> findCode(String theCodeSystem, String theCode);
Set<TermConcept> findCodesAbove(Long theCodeSystemResourcePid, Long theCodeSystemResourceVersionPid, String theCode);
@ -105,8 +103,6 @@ public interface ITermReadSvc extends IValidationSupport {
IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB);
IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB, IPrimitiveType<String> theSystemVersion, String theCodingAVersion, String theCodingBVersion);
void preExpandDeferredValueSetsToTerminologyTables();
/**

22
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoValueSetDstu2Test.java
View File

@ -233,26 +233,4 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
assertThat(resp, not(containsString("<code value=\"8450-9\"/>")));
}
@Test
public void unsupportedMethodsThrowException() {
IFhirResourceDaoCodeSystem<ValueSet, CodingDt, CodeableConceptDt> testFhirResourceDaoValueSet = new FhirResourceDaoValueSetDstu2();
// Multi-version lookupCode method
try {
testFhirResourceDaoValueSet.lookupCode(null, null, null, null, null);
fail();
} catch (UnsupportedOperationException theE) {
// Success
}
// Multi-version subsumes method
try {
testFhirResourceDaoValueSet.subsumes(null, null, null, null, null, null, null);
fail();
} catch (UnsupportedOperationException theE) {
// Success
}
}
}

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
View File

@ -524,7 +524,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
myTerminologyDeferredStorageSvc.saveDeferred();
myTerminologyDeferredStorageSvc.saveDeferred();
IValidationSupport.LookupCodeResult lookupResults = myCodeSystemDao.lookupCode(new StringType("childAA"), new StringType(URL_MY_CODE_SYSTEM), null,null, mySrd);
IValidationSupport.LookupCodeResult lookupResults = myCodeSystemDao.lookupCode(new StringType("childAA"), new StringType(URL_MY_CODE_SYSTEM), null, mySrd);
assertEquals(true, lookupResults.isFound());
ValueSet vs = new ValueSet();
@ -715,7 +715,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
StringType code = new StringType("ParentA");
StringType system = new StringType("http://snomed.info/sct");
IValidationSupport.LookupCodeResult outcome = myCodeSystemDao.lookupCode(code, system, null,null, mySrd);
IValidationSupport.LookupCodeResult outcome = myCodeSystemDao.lookupCode(code, system, null, mySrd);
assertEquals(true, outcome.isFound());
}

17
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetTest.java
View File

@ -56,6 +56,7 @@ import java.util.Optional;
import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest.URL_MY_CODE_SYSTEM;
import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest.URL_MY_VALUE_SET;
import static org.awaitility.Awaitility.await;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.containsStringIgnoringCase;
@ -246,6 +247,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet();
await().until(() -> clearDeferredStorageQueue());
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
Slice<TermValueSet> page = myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED);
assertEquals(1, page.getContent().size());
@ -300,6 +302,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet();
await().until(() -> clearDeferredStorageQueue());
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
Slice<TermValueSet> page = myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED);
assertEquals(1, page.getContent().size());
@ -361,6 +364,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet();
await().until(() -> clearDeferredStorageQueue());
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
Slice<TermValueSet> page = myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED);
assertEquals(1, page.getContent().size());
@ -745,6 +749,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
String initialValueSetName = valueSet.getName();
validateTermValueSetNotExpanded(initialValueSetName);
await().until(() -> clearDeferredStorageQueue());
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
validateTermValueSetExpandedAndChildren(initialValueSetName, codeSystem);
@ -774,6 +779,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
String initialValueSetName = valueSet.getName();
validateTermValueSetNotExpanded(initialValueSetName);
await().until(() -> clearDeferredStorageQueue());
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
validateTermValueSetExpandedAndChildren(initialValueSetName, codeSystem);
@ -1059,6 +1065,17 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
}
private boolean clearDeferredStorageQueue() {
if(!myTerminologyDeferredStorageSvc.isStorageQueueEmpty()) {
myTerminologyDeferredStorageSvc.saveAllDeferred();
return false;
} else {
return true;
}
}
@AfterEach
public void afterResetPreExpansionDefault() {
myDaoConfig.setPreExpandValueSets(new DaoConfig().isPreExpandValueSets());

33
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetVersionedTest.java
View File

@ -52,6 +52,7 @@ import java.util.Optional;
import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest.URL_MY_CODE_SYSTEM;
import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest.URL_MY_VALUE_SET;
import static org.awaitility.Awaitility.await;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.containsStringIgnoringCase;
@ -331,6 +332,7 @@ public class ResourceProviderR4ValueSetVersionedTest extends BaseResourceProvide
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet();
await().until(() -> clearDeferredStorageQueue());
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
Slice<TermValueSet> page = myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED);
assertEquals(2, page.getContent().size());
@ -426,6 +428,7 @@ public class ResourceProviderR4ValueSetVersionedTest extends BaseResourceProvide
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet();
await().until(() -> clearDeferredStorageQueue());
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
Slice<TermValueSet> page = myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED);
@ -538,6 +541,7 @@ public class ResourceProviderR4ValueSetVersionedTest extends BaseResourceProvide
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet();
await().until(() -> clearDeferredStorageQueue());
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
Slice<TermValueSet> page = myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED);
@ -930,6 +934,7 @@ public class ResourceProviderR4ValueSetVersionedTest extends BaseResourceProvide
validateTermValueSetNotExpanded(initialValueSetName_v1, "1", myExtensionalVsIdOnResourceTable_v1);
String initialValueSetName_v2 = valueSet_v2.getName();
validateTermValueSetNotExpanded(initialValueSetName_v2, "2", myExtensionalVsIdOnResourceTable_v2);
await().until(() -> clearDeferredStorageQueue());
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
validateTermValueSetExpandedAndChildrenV1(initialValueSetName_v1, codeSystem_v1);
validateTermValueSetExpandedAndChildrenV2(initialValueSetName_v2, codeSystem_v2);
@ -979,6 +984,7 @@ public class ResourceProviderR4ValueSetVersionedTest extends BaseResourceProvide
String initialValueSetName_v2 = valueSet_v2.getName();
validateTermValueSetNotExpanded(initialValueSetName_v2, "2", myExtensionalVsIdOnResourceTable_v2);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
await().until(() -> clearDeferredStorageQueue());
validateTermValueSetExpandedAndChildrenV1(initialValueSetName_v1, codeSystem_v1);
validateTermValueSetExpandedAndChildrenV2(initialValueSetName_v2, codeSystem_v2);
@ -1068,7 +1074,7 @@ public class ResourceProviderR4ValueSetVersionedTest extends BaseResourceProvide
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());
@ -1090,7 +1096,7 @@ public class ResourceProviderR4ValueSetVersionedTest extends BaseResourceProvide
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());
@ -1100,7 +1106,7 @@ public class ResourceProviderR4ValueSetVersionedTest extends BaseResourceProvide
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());
@ -1115,7 +1121,7 @@ public class ResourceProviderR4ValueSetVersionedTest extends BaseResourceProvide
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());
@ -1141,7 +1147,7 @@ public class ResourceProviderR4ValueSetVersionedTest extends BaseResourceProvide
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());
@ -1163,7 +1169,7 @@ public class ResourceProviderR4ValueSetVersionedTest extends BaseResourceProvide
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());
@ -1173,7 +1179,7 @@ public class ResourceProviderR4ValueSetVersionedTest extends BaseResourceProvide
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());
@ -1188,7 +1194,7 @@ public class ResourceProviderR4ValueSetVersionedTest extends BaseResourceProvide
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());
@ -1341,6 +1347,17 @@ public class ResourceProviderR4ValueSetVersionedTest extends BaseResourceProvide
}
*/
private boolean clearDeferredStorageQueue() {
if(!myTerminologyDeferredStorageSvc.isStorageQueueEmpty()) {
myTerminologyDeferredStorageSvc.saveAllDeferred();
return false;
} else {
return true;
}
}
@Test
public void testCreateDuplicatValueSetVersion() {
createExternalCsAndLocalVs();

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java
View File

@ -63,7 +63,6 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
codeSystem.setUrl(CS_URL);
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
codeSystem.setName("SYSTEM NAME");
codeSystem.setVersion("SYSTEM VERSION");
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalArgumentException::new);
@ -107,7 +106,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
TermConcept parentB = new TermConcept(cs, "ParentB");
cs.getConcepts().add(parentB);
myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), CS_URL, "SYSTEM NAME", null, cs, table);
myTerminologyDeferredStorageSvc.saveAllDeferred();

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4ElasticsearchIT.java
View File

@ -195,7 +195,7 @@ public class ValueSetExpansionR4ElasticsearchIT extends BaseJpaTest {
include.setSystem(CS_URL);
myTermSvc.expandValueSet(null, vs, myValueSetCodeAccumulator);
verify(myValueSetCodeAccumulator, times(9)).includeConceptWithDesignations(anyString(), anyString(), anyString(), nullable(String.class), anyCollection());
verify(myValueSetCodeAccumulator, times(9)).includeConceptWithDesignations(anyString(), anyString(), nullable(String.class), anyCollection());
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4Test.java
View File

@ -904,7 +904,7 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test {
include.setSystem(CS_URL);
myTermSvc.expandValueSet(null, vs, myValueSetCodeAccumulator);
verify(myValueSetCodeAccumulator, times(9)).includeConceptWithDesignations(anyString(), anyString(), anyString(), nullable(String.class), anyCollection());
verify(myValueSetCodeAccumulator, times(9)).includeConceptWithDesignations(anyString(), anyString(), nullable(String.class), anyCollection());
}
@Test

5
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/BaseValidationSupportWrapper.java
View File

@ -58,11 +58,6 @@ public class BaseValidationSupportWrapper extends BaseValidationSupport {
return myWrap.validateCode(theValidationSupportContext, theOptions, theCodeSystem, theCode, theDisplay, theValueSetUrl);
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theVersion) {
return myWrap.lookupCode(theValidationSupportContext, theSystem, theCode, theVersion);
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
return myWrap.lookupCode(theValidationSupportContext, theSystem, theCode);

6
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/CachingValidationSupport.java
View File

@ -83,12 +83,6 @@ public class CachingValidationSupport extends BaseValidationSupportWrapper imple
return loadFromCache(myValidateCodeCache, key, t -> super.validateCode(theValidationSupportContext, theOptions, theCodeSystem, theCode, theDisplay, theValueSetUrl));
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theVersion) {
String key = "lookupCode " + theSystem + " " + theCode + " " + theVersion;
return loadFromCache(myLookupCodeCache, key, t -> super.lookupCode(theValidationSupportContext, theSystem, theCode, theVersion));
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
String key = "lookupCode " + theSystem + " " + theCode;

6
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/CommonCodeSystemsTerminologyService.java
View File

@ -145,12 +145,6 @@ public class CommonCodeSystemsTerminologyService implements IValidationSupport {
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theVersion) {
// For now Common Code Systems will not be versioned.
return lookupCode(theValidationSupportContext, theSystem, theCode);
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {

38
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/InMemoryTerminologyServerValidationSupport.java
View File

@ -308,44 +308,6 @@ public class InMemoryTerminologyServerValidationSupport implements IValidationSu
.setMessage(message);
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theVersion) {
// The following code mostly duplicates the validateCode method, differing in that it includes the code system version in the generated ValueSet resource.
IBaseResource vs;
switch (myCtx.getVersion().getVersion()) {
case DSTU3:
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(theSystem).setVersion(theVersion)));
break;
case R4:
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(theSystem).setVersion(theVersion)));
break;
case R5:
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(theSystem).setVersion(theVersion)));
break;
case DSTU2_HL7ORG:
case DSTU2:
case DSTU2_1:
default:
throw new IllegalArgumentException("Can not handle version: " + myCtx.getVersion().getVersion());
}
ValueSetExpansionOutcome valueSetExpansionOutcome = expandValueSet(theValidationSupportContext, null, vs);
if (valueSetExpansionOutcome == null) {
return null;
}
IBaseResource expansion = valueSetExpansionOutcome.getValueSet();
return validateCodeInExpandedValueSet(theValidationSupportContext, new ConceptValidationOptions(), theSystem, theCode, null, expansion).asLookupCodeResult(theSystem, theCode);
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
return validateCode(theValidationSupportContext, new ConceptValidationOptions(), theSystem, theCode, null, null).asLookupCodeResult(theSystem, theCode);

10
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationSupportChain.java
View File

@ -257,16 +257,6 @@ public class ValidationSupportChain implements IValidationSupport {
return null;
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theVersion) {
for (IValidationSupport next : myChain) {
if (next.isCodeSystemSupported(theValidationSupportContext, theSystem)) {
return next.lookupCode(theValidationSupportContext, theSystem, theCode, theVersion);
}
}
return null;
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
for (IValidationSupport next : myChain) {

2
hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java
View File

@ -254,7 +254,7 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
return retVal;
}
});
when(mockSupport.lookupCode(any(), any(), any(), any())).thenAnswer(t -> {
when(mockSupport.lookupCode(any(), any(), any())).thenAnswer(t -> {
String system = t.getArgument(1, String.class);
String code = t.getArgument(2, String.class);
if (myValidConcepts.contains(system + "___" + code)) {