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validate-code operation now works with client-assigned IDs; added a bunch of failing tests to work on tomorrow.

This commit is contained in:
Diederik Muylwyk 2019-08-28 18:49:18 -04:00
parent 5650bc9baa
commit e67a750c4f
5 changed files with 981 additions and 103 deletions
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4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetConceptDao.java
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@ -47,8 +47,8 @@ public interface ITermValueSetConceptDao extends JpaRepository<TermValueSetConce
Optional<TermValueSetConcept> findByTermValueSetIdSystemAndCode(@Param("pid") Long theValueSetId, @Param("system_url") String theSystem, @Param("codeval") String theCode); Optional<TermValueSetConcept> findByTermValueSetIdSystemAndCode(@Param("pid") Long theValueSetId, @Param("system_url") String theSystem, @Param("codeval") String theCode);
@Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myResourcePid = :resource_pid AND vsc.myCode = :codeval") @Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myResourcePid = :resource_pid AND vsc.myCode = :codeval")
List<TermValueSetConcept> findOneByValueSetIdAndCode(@Param("resource_pid") Long theValueSetId, @Param("codeval") String theCode); List<TermValueSetConcept> findByValueSetResourcePidAndCode(@Param("resource_pid") Long theValueSetId, @Param("codeval") String theCode);
@Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myResourcePid = :resource_pid AND vsc.mySystem = :system_url AND vsc.myCode = :codeval") @Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myResourcePid = :resource_pid AND vsc.mySystem = :system_url AND vsc.myCode = :codeval")
List<TermValueSetConcept> findOneByValueSetIdSystemAndCode(@Param("resource_pid") Long theValueSetId, @Param("system_url") String theSystem, @Param("codeval") String theCode); Optional<TermValueSetConcept> findByValueSetResourcePidSystemAndCode(@Param("resource_pid") Long theValueSetId, @Param("system_url") String theSystem, @Param("codeval") String theCode);
} }

23
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
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@ -145,6 +145,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
@Autowired @Autowired
private PlatformTransactionManager myTransactionMgr; private PlatformTransactionManager myTransactionMgr;
private IFhirResourceDaoCodeSystem<?, ?, ?> myCodeSystemResourceDao; private IFhirResourceDaoCodeSystem<?, ?, ?> myCodeSystemResourceDao;
private IFhirResourceDaoValueSet<?, ?, ?> myValueSetResourceDao;
private Cache<TranslationQuery, List<TermConceptMapGroupElementTarget>> myTranslationCache; private Cache<TranslationQuery, List<TermConceptMapGroupElementTarget>> myTranslationCache;
private Cache<TranslationQuery, List<TermConceptMapGroupElement>> myTranslationWithReverseCache; private Cache<TranslationQuery, List<TermConceptMapGroupElement>> myTranslationWithReverseCache;
private int myFetchSize = DEFAULT_FETCH_SIZE; private int myFetchSize = DEFAULT_FETCH_SIZE;
@ -964,24 +965,24 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
ValueSet theValueSet, String theSystem, String theCode, String theDisplay, Coding theCoding, CodeableConcept theCodeableConcept) { ValueSet theValueSet, String theSystem, String theCode, String theDisplay, Coding theCoding, CodeableConcept theCodeableConcept) {
ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet.hasId(), "ValueSet.id is required"); ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet.hasId(), "ValueSet.id is required");
ResourceTable resource = (ResourceTable) myValueSetResourceDao.readEntity(theValueSet.getIdElement(), null);
Long valueSetId = theValueSet.getIdElement().toUnqualifiedVersionless().getIdPartAsLong(); Long resourcePid = resource.getId();
List<TermValueSetConcept> concepts = new ArrayList<>(); List<TermValueSetConcept> concepts = new ArrayList<>();
if (isNotBlank(theCode)) { if (isNotBlank(theCode)) {
if (isNotBlank(theSystem)) { if (isNotBlank(theSystem)) {
concepts = myValueSetConceptDao.findOneByValueSetIdSystemAndCode(valueSetId, theSystem, theCode); concepts.addAll(findByValueSetResourcePidSystemAndCode(resourcePid, theSystem, theCode));
} else { } else {
concepts = myValueSetConceptDao.findOneByValueSetIdAndCode(valueSetId, theCode); concepts.addAll(myValueSetConceptDao.findByValueSetResourcePidAndCode(resourcePid, theCode));
} }
} else if (theCoding != null) { } else if (theCoding != null) {
if (theCoding.hasSystem() && theCoding.hasCode()) { if (theCoding.hasSystem() && theCoding.hasCode()) {
concepts = myValueSetConceptDao.findOneByValueSetIdSystemAndCode(valueSetId, theCoding.getSystem(), theCoding.getCode()); concepts.addAll(findByValueSetResourcePidSystemAndCode(resourcePid, theCoding.getSystem(), theCoding.getCode()));
} }
} else if (theCodeableConcept != null){ } else if (theCodeableConcept != null){
for (Coding coding : theCodeableConcept.getCoding()) { for (Coding coding : theCodeableConcept.getCoding()) {
if (coding.hasSystem() && coding.hasCode()) { if (coding.hasSystem() && coding.hasCode()) {
concepts = myValueSetConceptDao.findOneByValueSetIdSystemAndCode(valueSetId, coding.getSystem(), coding.getCode()); concepts.addAll(findByValueSetResourcePidSystemAndCode(resourcePid, coding.getSystem(), coding.getCode()));
if (!concepts.isEmpty()) { if (!concepts.isEmpty()) {
break; break;
} }
@ -1002,6 +1003,15 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
return null; return null;
} }
private List<TermValueSetConcept> findByValueSetResourcePidSystemAndCode(Long theResourcePid, String theSystem, String theCode) {
List<TermValueSetConcept> retVal = new ArrayList<>();
Optional<TermValueSetConcept> optionalTermValueSetConcept = myValueSetConceptDao.findByValueSetResourcePidSystemAndCode(theResourcePid, theSystem, theCode);
if (optionalTermValueSetConcept.isPresent()) {
retVal.add(optionalTermValueSetConcept.get());
}
return retVal;
}
private void fetchChildren(TermConcept theConcept, Set<TermConcept> theSetToPopulate) { private void fetchChildren(TermConcept theConcept, Set<TermConcept> theSetToPopulate) {
for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) { for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) {
TermConcept nextChild = nextChildLink.getChild(); TermConcept nextChild = nextChildLink.getChild();
@ -1467,6 +1477,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
@PostConstruct @PostConstruct
public void start() { public void start() {
myCodeSystemResourceDao = myApplicationContext.getBean(IFhirResourceDaoCodeSystem.class); myCodeSystemResourceDao = myApplicationContext.getBean(IFhirResourceDaoCodeSystem.class);
myValueSetResourceDao = myApplicationContext.getBean(IFhirResourceDaoValueSet.class);
myTxTemplate = new TransactionTemplate(myTransactionManager); myTxTemplate = new TransactionTemplate(myTransactionManager);
} }

24
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java
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@ -365,23 +365,17 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implemen
@Override @Override
public ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) { public ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
ValueSet valueSet = (ValueSet) theValueSet; ValueSet valueSet = (ValueSet) theValueSet;
org.hl7.fhir.r4.model.ValueSet valueSetR4 = VersionConvertor_30_40.convertValueSet(valueSet);
Coding coding = (Coding) theCoding; Coding coding = (Coding) theCoding;
org.hl7.fhir.r4.model.Coding codingR4 = new org.hl7.fhir.r4.model.Coding(coding.getSystem(), coding.getCode(), coding.getDisplay());
CodeableConcept codeableConcept = (CodeableConcept) theCodeableConcept; CodeableConcept codeableConcept = (CodeableConcept) theCodeableConcept;
org.hl7.fhir.r4.model.CodeableConcept codeableConceptR4 = new org.hl7.fhir.r4.model.CodeableConcept();
try { for (Coding nestedCoding : codeableConcept.getCoding()) {
org.hl7.fhir.r4.model.ValueSet valueSetR4; codeableConceptR4.addCoding(new org.hl7.fhir.r4.model.Coding(nestedCoding.getSystem(), nestedCoding.getCode(), nestedCoding.getDisplay()));
valueSetR4 = VersionConvertor_30_40.convertValueSet(valueSet);
org.hl7.fhir.r4.model.Coding codingR4 = new org.hl7.fhir.r4.model.Coding(coding.getSystem(), coding.getCode(), coding.getDisplay());
org.hl7.fhir.r4.model.CodeableConcept codeableConceptR4 = new org.hl7.fhir.r4.model.CodeableConcept();
for (Coding nestedCoding : codeableConcept.getCoding()) {
codeableConceptR4.addCoding(new org.hl7.fhir.r4.model.Coding(nestedCoding.getSystem(), nestedCoding.getCode(), nestedCoding.getDisplay()));
}
return super.validateCodeIsInPreExpandedValueSet(valueSetR4, theSystem, theCode, theDisplay, codingR4, codeableConceptR4);
} catch (FHIRException e) {
throw new InternalErrorException(e);
} }
return super.validateCodeIsInPreExpandedValueSet(valueSetR4, theSystem, theCode, theDisplay, codingR4, codeableConceptR4);
} }
} }

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR5.java
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@ -10,8 +10,8 @@ import ca.uhn.fhir.util.UrlUtil;
import org.hl7.fhir.instance.model.api.IBaseDatatype; import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType; import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.hapi.ctx.IValidationSupport; import org.hl7.fhir.r5.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent; import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent; import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.terminologies.ValueSetExpander; import org.hl7.fhir.r5.terminologies.ValueSetExpander;
@ -291,7 +291,8 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
@Override @Override
public ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) { public ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
org.hl7.fhir.r4.model.ValueSet valueSetR4 = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet((ValueSet) theValueSet); ValueSet valueSet = (ValueSet) theValueSet;
org.hl7.fhir.r4.model.ValueSet valueSetR4 = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSet);
Coding coding = (Coding) theCoding; Coding coding = (Coding) theCoding;
org.hl7.fhir.r4.model.Coding codingR4 = new org.hl7.fhir.r4.model.Coding(coding.getSystem(), coding.getCode(), coding.getDisplay()); org.hl7.fhir.r4.model.Coding codingR4 = new org.hl7.fhir.r4.model.Coding(coding.getSystem(), coding.getCode(), coding.getDisplay());

1028
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java
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