Changes to support multi-versioning in ValueSet $expand operation.
This commit is contained in:
parent
b2b63cbb02
commit
302bbca8fd
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@ -28,6 +28,7 @@ import org.apache.commons.lang3.builder.HashCodeBuilder;
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public class VersionIndependentConcept implements Comparable<VersionIndependentConcept> {
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private final String mySystem;
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private final String mySystemVersion;
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private final String myCode;
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private final String myDisplay;
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private int myHashCode;
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@ -40,7 +41,12 @@ public class VersionIndependentConcept implements Comparable<VersionIndependentC
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}
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public VersionIndependentConcept(String theSystem, String theCode, String theDisplay) {
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this(theSystem, theCode, theDisplay, null);
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}
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public VersionIndependentConcept(String theSystem, String theCode, String theDisplay, String theSystemVersion) {
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mySystem = theSystem;
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mySystemVersion = theSystemVersion;
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myCode = theCode;
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myDisplay = theDisplay;
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myHashCode = new HashCodeBuilder(17, 37)
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@ -57,6 +63,9 @@ public class VersionIndependentConcept implements Comparable<VersionIndependentC
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return mySystem;
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}
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public String getSystemVersion() {
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return mySystemVersion;
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}
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public String getCode() {
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return myCode;
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@ -142,7 +142,6 @@ ca.uhn.fhir.jpa.binstore.BinaryAccessProvider.unknownType=Content in resource of
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ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateCodeSystemUrl=Can not create multiple CodeSystem resources with CodeSystem.url "{0}", already have one with resource ID: {1}
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ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateCodeSystemUrlAndVersion=Can not create multiple CodeSystem resources with CodeSystem.url "{0}" and CodeSystem.version "{1}", already have one with resource ID: {2}
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ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotUpdateUrlOrVersionForCodeSystemResource=Cannot update URL or version for CodeSystem resource. Existing CodeSystem resource with resource ID {0} found with CodeSystem.url "{1}" and CodeSystem.version "{2}"
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ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateConceptMapUrl=Can not create multiple ConceptMap resources with ConceptMap.url "{0}", already have one with resource ID: {1}
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ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateValueSetUrl=Can not create multiple ValueSet resources with ValueSet.url "{0}", already have one with resource ID: {1}
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ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
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@ -38,8 +38,12 @@ public interface IFhirResourceDaoValueSet<T extends IBaseResource, CD, CC> exten
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T expandByIdentifier(String theUri, String theFilter);
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T expandByIdentifier(String theUri, String theValueSetVersion, String theFilter);
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T expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount);
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T expandByIdentifier(String theUri, String theValueSetVersion, String theFilter, int theOffset, int theCount);
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void purgeCaches();
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IValidationSupport.CodeValidationResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, CD theCoding, CC theCodeableConcept, RequestDetails theRequestDetails);
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@ -174,11 +174,21 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
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return expand(source, theFilter);
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}
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@Override
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public ValueSet expandByIdentifier(String theUri, String theValueSetVersion, String theFilter) {
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throw new UnsupportedOperationException();
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}
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@Override
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public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
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throw new UnsupportedOperationException();
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}
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@Override
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public ValueSet expandByIdentifier(String theUri, String theValueSetVersion, String theFilter, int theOffset, int theCount) {
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throw new UnsupportedOperationException();
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}
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@Override
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public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
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if (theSystem != null && theSystem.startsWith("http://hl7.org/fhir/")) {
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@ -25,8 +25,11 @@ import ca.uhn.fhir.context.FhirVersionEnum;
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import ca.uhn.fhir.context.support.IValidationSupport;
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import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import ca.uhn.fhir.rest.api.SortOrderEnum;
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import ca.uhn.fhir.rest.api.SortSpec;
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import ca.uhn.fhir.rest.api.server.IBundleProvider;
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import ca.uhn.fhir.rest.param.StringParam;
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import ca.uhn.fhir.rest.param.TokenParam;
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import ca.uhn.fhir.rest.param.UriParam;
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import com.github.benmanes.caffeine.cache.Cache;
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import com.github.benmanes.caffeine.cache.Caffeine;
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@ -121,18 +124,25 @@ public class JpaPersistedResourceValidationSupport implements IValidationSupport
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SearchParameterMap params = new SearchParameterMap();
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params.setLoadSynchronousUpTo(1);
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params.add(IAnyResource.SP_RES_ID, new StringParam(theUri));
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search = myDaoRegistry.getResourceDao("ValueSet").search(params);
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search = myDaoRegistry.getResourceDao(resourceName).search(params);
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if (search.size() == 0) {
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params = new SearchParameterMap();
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params.setLoadSynchronousUpTo(1);
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params.add(ValueSet.SP_URL, new UriParam(theUri));
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search = myDaoRegistry.getResourceDao("ValueSet").search(params);
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search = myDaoRegistry.getResourceDao(resourceName).search(params);
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}
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} else {
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int versionSeparator = theUri.lastIndexOf('|');
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SearchParameterMap params = new SearchParameterMap();
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params.setLoadSynchronousUpTo(1);
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params.add(ValueSet.SP_URL, new UriParam(theUri));
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search = myDaoRegistry.getResourceDao("ValueSet").search(params);
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if (versionSeparator != -1) {
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params.add(ValueSet.SP_VERSION, new TokenParam(theUri.substring(versionSeparator + 1)));
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params.add(ValueSet.SP_URL, new UriParam(theUri.substring(0,versionSeparator)));
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} else {
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params.add(ValueSet.SP_URL, new UriParam(theUri));
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}
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params.setSort(new SortSpec("_lastUpdated").setOrder(SortOrderEnum.DESC));
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search = myDaoRegistry.getResourceDao(resourceName).search(params);
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}
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} else if ("StructureDefinition".equals(resourceName)) {
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// Don't allow the core FHIR definitions to be overwritten
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@ -156,9 +166,16 @@ public class JpaPersistedResourceValidationSupport implements IValidationSupport
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}
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search = myDaoRegistry.getResourceDao("Questionnaire").search(params);
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} else if ("CodeSystem".equals(resourceName)) {
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int versionSeparator = theUri.lastIndexOf('|');
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SearchParameterMap params = new SearchParameterMap();
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params.setLoadSynchronousUpTo(1);
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params.add(CodeSystem.SP_URL, new UriParam(theUri));
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if (versionSeparator != -1) {
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params.add(CodeSystem.SP_VERSION, new TokenParam(theUri.substring(versionSeparator + 1)));
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params.add(CodeSystem.SP_URL, new UriParam(theUri.substring(0,versionSeparator)));
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} else {
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params.add(CodeSystem.SP_URL, new UriParam(theUri));
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}
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params.setSort(new SortSpec("_lastUpdated").setOrder(SortOrderEnum.DESC));
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search = myDaoRegistry.getResourceDao(resourceName).search(params);
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} else if ("ImplementationGuide".equals(resourceName)) {
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SearchParameterMap params = new SearchParameterMap();
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@ -49,7 +49,7 @@ public interface ITermCodeSystemVersionDao extends JpaRepository<TermCodeSystemV
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TermCodeSystemVersion findByCodeSystemPidVersionIsNull(@Param("codesystem_pid") Long theCodeSystemPid);
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@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myResourcePid = :resource_id")
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TermCodeSystemVersion findByCodeSystemResourcePid(@Param("resource_id") Long theCodeSystemResourcePid);
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List<TermCodeSystemVersion> findByCodeSystemResourcePid(@Param("resource_id") Long theCodeSystemResourcePid);
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@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myCodeSystemHavingThisVersionAsCurrentVersionIfAny.myResource.myId = :resource_id")
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TermCodeSystemVersion findCurrentVersionForCodeSystemResourcePid(@Param("resource_id") Long theCodeSystemResourcePid);
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@ -36,6 +36,7 @@ public interface ITermValueSetDao extends JpaRepository<TermValueSet, Long> {
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@Query("SELECT vs FROM TermValueSet vs WHERE vs.myResourcePid = :resource_pid")
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Optional<TermValueSet> findByResourcePid(@Param("resource_pid") Long theResourcePid);
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@Deprecated
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@Query("SELECT vs FROM TermValueSet vs WHERE vs.myUrl = :url")
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Optional<TermValueSet> findByUrl(@Param("url") String theUrl);
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@ -21,22 +21,18 @@ package ca.uhn.fhir.jpa.dao.dstu3;
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*/
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import ca.uhn.fhir.context.support.ConceptValidationOptions;
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import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
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import ca.uhn.fhir.context.support.IValidationSupport;
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import ca.uhn.fhir.context.support.ValidationSupportContext;
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import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
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import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
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import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
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import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
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import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
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import ca.uhn.fhir.jpa.model.entity.ResourceTable;
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import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
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import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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import ca.uhn.fhir.util.ElementUtil;
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import org.hl7.fhir.dstu3.model.CodeSystem;
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import org.hl7.fhir.dstu3.model.CodeableConcept;
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import org.hl7.fhir.dstu3.model.Coding;
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import org.hl7.fhir.dstu3.model.IntegerType;
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@ -49,9 +45,6 @@ import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.instance.model.api.IPrimitiveType;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import java.util.Date;
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import java.util.List;
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@ -63,16 +56,9 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
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import static org.hl7.fhir.convertors.conv30_40.ValueSet30_40.convertValueSet;
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public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
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private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoValueSetDstu3.class);
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@Autowired
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private DefaultProfileValidationSupport myDefaultProfileValidationSupport;
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private IValidationSupport myValidationSupport;
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@Autowired
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private IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> myCodeSystemDao;
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@Override
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public void start() {
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super.start();
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@ -127,21 +113,7 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueS
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throw new InvalidRequestException("URI must not be blank or missing");
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}
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ValueSet source = new ValueSet();
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source.setUrl(theUri);
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source.getCompose().addInclude().addValueSet(theUri);
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if (isNotBlank(theFilter)) {
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ConceptSetComponent include = source.getCompose().addInclude();
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ConceptSetFilterComponent filter = include.addFilter();
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filter.setProperty("display");
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filter.setOp(FilterOperator.EQUAL);
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filter.setValue(theFilter);
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}
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ValueSet retVal = doExpand(source);
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return retVal;
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return doExpand(createSourceValueSet(theUri, null, theFilter));
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// if (defaultValueSet != null) {
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// source = getContext().newJsonParser().parseResource(ValueSet.class, getContext().newJsonParser().encodeResourceToString(defaultValueSet));
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@ -157,15 +129,27 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueS
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}
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@Override
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public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
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public ValueSet expandByIdentifier(String theUri, String theValueSetVersion, String theFilter) {
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if (isBlank(theUri)) {
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throw new InvalidRequestException("URI must not be blank or missing");
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}
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return doExpand(createSourceValueSet(theUri, theValueSetVersion, theFilter));
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}
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private ValueSet createSourceValueSet(String theUri, String theValueSetVersion, String theFilter) {
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ValueSet source = new ValueSet();
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source.setUrl(theUri);
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if (theValueSetVersion != null) {
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source.setVersion(theValueSetVersion);
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}
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source.getCompose().addInclude().addValueSet(theUri);
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if (theValueSetVersion != null) {
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source.getCompose().addInclude().addValueSet(theUri + "|" +theValueSetVersion);
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} else {
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source.getCompose().addInclude().addValueSet(theUri);
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}
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if (isNotBlank(theFilter)) {
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ConceptSetComponent include = source.getCompose().addInclude();
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@ -174,9 +158,25 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueS
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filter.setOp(FilterOperator.EQUAL);
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filter.setValue(theFilter);
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}
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return source;
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}
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ValueSet retVal = doExpand(source, theOffset, theCount);
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return retVal;
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@Override
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public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
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if (isBlank(theUri)) {
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throw new InvalidRequestException("URI must not be blank or missing");
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}
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return doExpand(createSourceValueSet(theUri, null, theFilter), theOffset, theCount);
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}
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@Override
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public ValueSet expandByIdentifier(String theUri, String theValueSetVersion, String theFilter, int theOffset, int theCount) {
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if (isBlank(theUri)) {
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throw new InvalidRequestException("URI must not be blank or missing");
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}
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return doExpand(createSourceValueSet(theUri, theValueSetVersion, theFilter), theOffset, theCount);
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}
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@Override
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@ -214,6 +214,9 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueS
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ValueSet toExpand = new ValueSet();
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toExpand.setId(theSource.getId());
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toExpand.setUrl(theSource.getUrl());
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if (theSource.getVersion() != null) {
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toExpand.setVersion(theSource.getVersion());
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}
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for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
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toExpand.getCompose().addInclude(next);
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@ -20,35 +20,28 @@ package ca.uhn.fhir.jpa.dao.r4;
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* #L%
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*/
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import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
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import ca.uhn.fhir.context.support.IValidationSupport;
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import ca.uhn.fhir.context.support.ValidationSupportContext;
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import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
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import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
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import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
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import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
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import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
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import ca.uhn.fhir.jpa.model.entity.ResourceTable;
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import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
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import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
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import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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import ca.uhn.fhir.util.ElementUtil;
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import org.apache.commons.codec.binary.StringUtils;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.instance.model.api.IPrimitiveType;
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import org.hl7.fhir.r4.model.CodeSystem;
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import org.hl7.fhir.r4.model.CodeableConcept;
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import org.hl7.fhir.r4.model.Coding;
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import org.hl7.fhir.r4.model.IntegerType;
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import org.hl7.fhir.r4.model.ValueSet;
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import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
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import org.hl7.fhir.r4.model.ValueSet.ConceptSetFilterComponent;
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import org.hl7.fhir.r4.model.ValueSet.FilterOperator;
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import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent;
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import org.springframework.beans.factory.annotation.Autowired;
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import java.util.Date;
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import java.util.List;
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@ -60,12 +53,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
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public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
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@Autowired
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private DefaultProfileValidationSupport myDefaultProfileValidationSupport;
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private IValidationSupport myValidationSupport;
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@Autowired
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private IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> myCodeSystemDao;
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@Override
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public void start() {
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@ -107,21 +95,7 @@ public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet>
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throw new InvalidRequestException("URI must not be blank or missing");
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}
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ValueSet source = new ValueSet();
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source.setUrl(theUri);
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source.getCompose().addInclude().addValueSet(theUri);
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if (isNotBlank(theFilter)) {
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ConceptSetComponent include = source.getCompose().addInclude();
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ConceptSetFilterComponent filter = include.addFilter();
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filter.setProperty("display");
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filter.setOp(FilterOperator.EQUAL);
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filter.setValue(theFilter);
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}
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ValueSet retVal = doExpand(source);
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return retVal;
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return doExpand(createSourceValueSet(theUri, null, theFilter));
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// if (defaultValueSet != null) {
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// source = getContext().newJsonParser().parseResource(ValueSet.class, getContext().newJsonParser().encodeResourceToString(defaultValueSet));
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@ -136,27 +110,54 @@ public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet>
|
|||
// return expand(defaultValueSet, theFilter);
|
||||
}
|
||||
|
||||
@Override
|
||||
public ValueSet expandByIdentifier(String theUri, String theValueSetVersion, String theFilter) {
|
||||
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);
|
||||
}
|
||||
|
||||
if (isNotBlank(theFilter)) {
|
||||
ValueSet.ConceptSetComponent include = source.getCompose().addInclude();
|
||||
ValueSet.ConceptSetFilterComponent filter = include.addFilter();
|
||||
filter.setProperty("display");
|
||||
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");
|
||||
}
|
||||
|
||||
ValueSet source = new ValueSet();
|
||||
source.setUrl(theUri);
|
||||
return doExpand(createSourceValueSet(theUri,null,theFilter), theOffset, theCount);
|
||||
}
|
||||
|
||||
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);
|
||||
@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");
|
||||
}
|
||||
|
||||
ValueSet retVal = doExpand(source, theOffset, theCount);
|
||||
return retVal;
|
||||
return doExpand(createSourceValueSet(theUri,theValueSetVersion,theFilter), theOffset, theCount);
|
||||
}
|
||||
|
||||
@Override
|
||||
|
@ -194,6 +195,9 @@ public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet>
|
|||
ValueSet toExpand = new ValueSet();
|
||||
toExpand.setId(theSource.getId());
|
||||
toExpand.setUrl(theSource.getUrl());
|
||||
if (theSource.getVersion() != null) {
|
||||
toExpand.setVersion(theSource.getVersion());
|
||||
}
|
||||
|
||||
for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
|
||||
toExpand.getCompose().addInclude(next);
|
||||
|
|
|
@ -20,39 +20,28 @@ package ca.uhn.fhir.jpa.dao.r5;
|
|||
* #L%
|
||||
*/
|
||||
|
||||
import ca.uhn.fhir.context.support.ConceptValidationOptions;
|
||||
import ca.uhn.fhir.context.support.IValidationSupport;
|
||||
import ca.uhn.fhir.context.support.ValidationSupportContext;
|
||||
import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
|
||||
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
|
||||
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
|
||||
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
|
||||
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
|
||||
import ca.uhn.fhir.jpa.util.LogicUtil;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.util.ElementUtil;
|
||||
import org.apache.commons.codec.binary.StringUtils;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.instance.model.api.IPrimitiveType;
|
||||
import org.hl7.fhir.r5.model.CodeSystem;
|
||||
import org.hl7.fhir.r5.model.CodeableConcept;
|
||||
import org.hl7.fhir.r5.model.Coding;
|
||||
import org.hl7.fhir.r5.model.Enumerations;
|
||||
import org.hl7.fhir.r5.model.IntegerType;
|
||||
import org.hl7.fhir.r5.model.ValueSet;
|
||||
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
|
||||
import org.hl7.fhir.r5.model.ValueSet.ConceptSetFilterComponent;
|
||||
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
|
||||
import org.hl7.fhir.utilities.validation.ValidationOptions;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.beans.factory.annotation.Qualifier;
|
||||
|
||||
import java.util.Collections;
|
||||
import java.util.Date;
|
||||
import java.util.List;
|
||||
|
||||
|
@ -64,15 +53,8 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
|||
|
||||
public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
|
||||
|
||||
@Autowired
|
||||
@Qualifier("myDefaultProfileValidationSupport")
|
||||
private IValidationSupport myDefaultProfileValidationSupport;
|
||||
|
||||
private IValidationSupport myValidationSupport;
|
||||
|
||||
@Autowired
|
||||
private IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> myCodeSystemDao;
|
||||
|
||||
@Override
|
||||
public void start() {
|
||||
super.start();
|
||||
|
@ -113,21 +95,7 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet>
|
|||
throw new InvalidRequestException("URI must not be blank or missing");
|
||||
}
|
||||
|
||||
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(Enumerations.FilterOperator.EQUAL);
|
||||
filter.setValue(theFilter);
|
||||
}
|
||||
|
||||
ValueSet retVal = doExpand(source);
|
||||
return retVal;
|
||||
return doExpand(createSourceValueSet(theUri, null, theFilter));
|
||||
|
||||
// if (defaultValueSet != null) {
|
||||
// source = getContext().newJsonParser().parseResource(ValueSet.class, getContext().newJsonParser().encodeResourceToString(defaultValueSet));
|
||||
|
@ -142,27 +110,55 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet>
|
|||
// return expand(defaultValueSet, theFilter);
|
||||
}
|
||||
|
||||
@Override
|
||||
public ValueSet expandByIdentifier(String theUri, String theValueSetUri, String theFilter) {
|
||||
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);
|
||||
}
|
||||
|
||||
if (isNotBlank(theFilter)) {
|
||||
ValueSet.ConceptSetComponent include = source.getCompose().addInclude();
|
||||
ValueSet.ConceptSetFilterComponent filter = include.addFilter();
|
||||
filter.setProperty("display");
|
||||
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");
|
||||
}
|
||||
|
||||
ValueSet source = new ValueSet();
|
||||
source.setUrl(theUri);
|
||||
return doExpand(createSourceValueSet(theUri, null, theFilter), theOffset, theCount);
|
||||
}
|
||||
|
||||
source.getCompose().addInclude().addValueSet(theUri);
|
||||
|
||||
if (isNotBlank(theFilter)) {
|
||||
ConceptSetComponent include = source.getCompose().addInclude();
|
||||
ConceptSetFilterComponent filter = include.addFilter();
|
||||
filter.setProperty("display");
|
||||
filter.setOp(Enumerations.FilterOperator.EQUAL);
|
||||
filter.setValue(theFilter);
|
||||
@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");
|
||||
}
|
||||
|
||||
ValueSet retVal = doExpand(source, theOffset, theCount);
|
||||
return retVal;
|
||||
return doExpand(createSourceValueSet(theUri, theValueSetVersion, theFilter), theOffset, theCount);
|
||||
}
|
||||
|
||||
@Override
|
||||
|
@ -200,6 +196,9 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet>
|
|||
ValueSet toExpand = new ValueSet();
|
||||
toExpand.setId(theSource.getId());
|
||||
toExpand.setUrl(theSource.getUrl());
|
||||
if (theSource.getVersion() != null) {
|
||||
toExpand.setVersion(theSource.getVersion());
|
||||
}
|
||||
|
||||
for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
|
||||
toExpand.getCompose().addInclude(next);
|
||||
|
|
|
@ -46,6 +46,7 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
|
|||
// Note: url is correct and identifier is not, but identifier was only added as
|
||||
// of 3.1.0 so we'll leave url for now. See: https://groups.google.com/d/msgid/hapi-fhir/CAN2Cfy8kW%2BAOkgC6VjPsU3gRCpExCNZBmJdi-k5R_TWeyWH4tA%40mail.gmail.com?utm_medium=email&utm_source=footer
|
||||
@OperationParam(name = "url", min = 0, max = 1) UriType theUrl,
|
||||
@OperationParam(name = "valueSetVersion", min = 0, max = 1) org.hl7.fhir.r4.model.StringType theValueSetVersion,
|
||||
@OperationParam(name = "identifier", min = 0, max = 1) UriType theIdentifier,
|
||||
@OperationParam(name = "filter", min = 0, max = 1) StringType theFilter,
|
||||
@OperationParam(name = "offset", min = 0, max = 1) IntegerType theOffset,
|
||||
|
@ -60,6 +61,7 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
|
|||
|
||||
boolean haveIdentifier = url != null && isNotBlank(url.getValue());
|
||||
boolean haveValueSet = theValueSet != null && !theValueSet.isEmpty();
|
||||
boolean haveValueSetVersion = theValueSetVersion != null && !theValueSetVersion.isEmpty();
|
||||
|
||||
if (!haveId && !haveIdentifier && !haveValueSet) {
|
||||
throw new InvalidRequestException("$expand operation at the type level (no ID specified) requires an identifier or a valueSet as a part of the request.");
|
||||
|
@ -99,7 +101,11 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
|
|||
if (haveId) {
|
||||
return dao.expand(theId, toFilterString(theFilter), offset, count, theRequestDetails);
|
||||
} else if (haveIdentifier) {
|
||||
return dao.expandByIdentifier(url.getValue(), toFilterString(theFilter), offset, count);
|
||||
if (haveValueSetVersion) {
|
||||
return dao.expandByIdentifier(url.getValue(), theValueSetVersion.getValue(), toFilterString(theFilter), offset, count);
|
||||
} else {
|
||||
return dao.expandByIdentifier(url.getValue(), toFilterString(theFilter), offset, count);
|
||||
}
|
||||
} else {
|
||||
return dao.expand(theValueSet, toFilterString(theFilter), offset, count);
|
||||
}
|
||||
|
@ -107,7 +113,11 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
|
|||
if (haveId) {
|
||||
return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
|
||||
} else if (haveIdentifier) {
|
||||
return dao.expandByIdentifier(url.getValue(), toFilterString(theFilter));
|
||||
if (haveValueSetVersion) {
|
||||
return dao.expandByIdentifier(url.getValue(), theValueSetVersion.getValue(), toFilterString(theFilter));
|
||||
} else {
|
||||
return dao.expandByIdentifier(url.getValue(), toFilterString(theFilter));
|
||||
}
|
||||
} else {
|
||||
return dao.expand(theValueSet, toFilterString(theFilter));
|
||||
}
|
||||
|
|
|
@ -44,6 +44,7 @@ public class BaseJpaResourceProviderValueSetR4 extends JpaResourceProviderR4<Val
|
|||
@IdParam(optional = true) IdType theId,
|
||||
@OperationParam(name = "valueSet", min = 0, max = 1) ValueSet theValueSet,
|
||||
@OperationParam(name = "url", min = 0, max = 1) UriType theUrl,
|
||||
@OperationParam(name = "valueSetVersion", min = 0, max = 1) StringType theValueSetVersion,
|
||||
@OperationParam(name = "filter", min = 0, max = 1) StringType theFilter,
|
||||
@OperationParam(name = "offset", min = 0, max = 1) IntegerType theOffset,
|
||||
@OperationParam(name = "count", min = 0, max = 1) IntegerType theCount,
|
||||
|
@ -52,6 +53,7 @@ public class BaseJpaResourceProviderValueSetR4 extends JpaResourceProviderR4<Val
|
|||
boolean haveId = theId != null && theId.hasIdPart();
|
||||
boolean haveIdentifier = theUrl != null && isNotBlank(theUrl.getValue());
|
||||
boolean haveValueSet = theValueSet != null && !theValueSet.isEmpty();
|
||||
boolean haveValueSetVersion = theValueSetVersion != null && !theValueSetVersion.isEmpty();
|
||||
|
||||
if (!haveId && !haveIdentifier && !haveValueSet) {
|
||||
throw new InvalidRequestException("$expand operation at the type level (no ID specified) requires a url or a valueSet as a part of the request.");
|
||||
|
@ -91,7 +93,11 @@ public class BaseJpaResourceProviderValueSetR4 extends JpaResourceProviderR4<Val
|
|||
if (haveId) {
|
||||
return dao.expand(theId, toFilterString(theFilter), offset, count, theRequestDetails);
|
||||
} else if (haveIdentifier) {
|
||||
return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter), offset, count);
|
||||
if (haveValueSetVersion) {
|
||||
return dao.expandByIdentifier(theUrl.getValue(), theValueSetVersion.getValue(), toFilterString(theFilter), offset, count);
|
||||
} else {
|
||||
return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter), offset, count);
|
||||
}
|
||||
} else {
|
||||
return dao.expand(theValueSet, toFilterString(theFilter), offset, count);
|
||||
}
|
||||
|
@ -99,7 +105,11 @@ public class BaseJpaResourceProviderValueSetR4 extends JpaResourceProviderR4<Val
|
|||
if (haveId) {
|
||||
return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
|
||||
} else if (haveIdentifier) {
|
||||
return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter));
|
||||
if (haveValueSetVersion) {
|
||||
return dao.expandByIdentifier(theUrl.getValue(), theValueSetVersion.getValue(), toFilterString(theFilter));
|
||||
} else {
|
||||
return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter));
|
||||
}
|
||||
} else {
|
||||
return dao.expand(theValueSet, toFilterString(theFilter));
|
||||
}
|
||||
|
|
|
@ -44,6 +44,7 @@ public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<Val
|
|||
@IdParam(optional = true) IdType theId,
|
||||
@OperationParam(name = "valueSet", min = 0, max = 1) ValueSet theValueSet,
|
||||
@OperationParam(name = "url", min = 0, max = 1) UriType theUrl,
|
||||
@OperationParam(name = "valueSetVersion", min = 0, max = 1) org.hl7.fhir.r4.model.StringType theValueSetVersion,
|
||||
@OperationParam(name = "filter", min = 0, max = 1) StringType theFilter,
|
||||
@OperationParam(name = "offset", min = 0, max = 1) IntegerType theOffset,
|
||||
@OperationParam(name = "count", min = 0, max = 1) IntegerType theCount,
|
||||
|
@ -52,6 +53,7 @@ public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<Val
|
|||
boolean haveId = theId != null && theId.hasIdPart();
|
||||
boolean haveIdentifier = theUrl != null && isNotBlank(theUrl.getValue());
|
||||
boolean haveValueSet = theValueSet != null && !theValueSet.isEmpty();
|
||||
boolean haveValueSetVersion = theValueSetVersion != null && !theValueSetVersion.isEmpty();
|
||||
|
||||
if (!haveId && !haveIdentifier && !haveValueSet) {
|
||||
throw new InvalidRequestException("$expand operation at the type level (no ID specified) requires a url or a valueSet as a part of the request.");
|
||||
|
@ -91,7 +93,11 @@ public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<Val
|
|||
if (haveId) {
|
||||
return dao.expand(theId, toFilterString(theFilter), offset, count, theRequestDetails);
|
||||
} else if (haveIdentifier) {
|
||||
return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter), offset, count);
|
||||
if (haveValueSetVersion) {
|
||||
return dao.expandByIdentifier(theUrl.getValue(), theValueSetVersion.getValue(), toFilterString(theFilter), offset, count);
|
||||
} else {
|
||||
return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter), offset, count);
|
||||
}
|
||||
} else {
|
||||
return dao.expand(theValueSet, toFilterString(theFilter), offset, count);
|
||||
}
|
||||
|
@ -99,7 +105,11 @@ public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<Val
|
|||
if (haveId) {
|
||||
return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
|
||||
} else if (haveIdentifier) {
|
||||
return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter));
|
||||
if (haveValueSetVersion) {
|
||||
return dao.expandByIdentifier(theUrl.getValue(), theValueSetVersion.getValue(), toFilterString(theFilter));
|
||||
} else {
|
||||
return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter));
|
||||
}
|
||||
} else {
|
||||
return dao.expand(theValueSet, toFilterString(theFilter));
|
||||
}
|
||||
|
|
|
@ -170,6 +170,7 @@ import java.util.stream.Collectors;
|
|||
|
||||
import static org.apache.commons.lang3.StringUtils.defaultString;
|
||||
import static org.apache.commons.lang3.StringUtils.isBlank;
|
||||
import static org.apache.commons.lang3.StringUtils.isEmpty;
|
||||
import static org.apache.commons.lang3.StringUtils.isNoneBlank;
|
||||
import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
||||
|
||||
|
@ -245,10 +246,25 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
|
||||
private void addCodeIfNotAlreadyAdded(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, TermConcept theConcept, boolean theAdd, AtomicInteger theCodeCounter) {
|
||||
String codeSystem = theConcept.getCodeSystemVersion().getCodeSystem().getCodeSystemUri();
|
||||
String codeSystemVersion = theConcept.getCodeSystemVersion().getCodeSystemVersionId();
|
||||
String code = theConcept.getCode();
|
||||
String display = theConcept.getDisplay();
|
||||
Collection<TermConceptDesignation> designations = theConcept.getDesignations();
|
||||
addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, designations, theAdd, theCodeCounter, codeSystem, code, display);
|
||||
addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, designations, theAdd, theCodeCounter, codeSystem, codeSystemVersion, 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);
|
||||
theCodeCounter.incrementAndGet();
|
||||
}
|
||||
|
||||
if (!theAdd && theAddedCodes.remove(theCodeSystem + "|" + theCode + "|" + theCodeSystemVersion)) {
|
||||
theValueSetCodeAccumulator.excludeConcept(theCodeSystem, theCodeSystemVersion, theCode);
|
||||
theCodeCounter.decrementAndGet();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private void addCodeIfNotAlreadyAdded(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, Collection<TermConceptDesignation> theDesignations, boolean theAdd, AtomicInteger theCodeCounter, String theCodeSystem, String theCode, String theDisplay) {
|
||||
|
@ -609,7 +625,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
|
||||
ArrayList<VersionIndependentConcept> retVal = new ArrayList<>();
|
||||
for (org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent nextContains : expandedR4.getContains()) {
|
||||
retVal.add(new VersionIndependentConcept(nextContains.getSystem(), nextContains.getCode(), nextContains.getDisplay()));
|
||||
retVal.add(new VersionIndependentConcept(nextContains.getSystem(), nextContains.getCode(), nextContains.getDisplay(), nextContains.getVersion()));
|
||||
}
|
||||
return retVal;
|
||||
}
|
||||
|
@ -740,8 +756,14 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
|
||||
TermCodeSystem codeSystem = uriToCodeSystem.get(nextConcept.getSystem());
|
||||
if (codeSystem != null) {
|
||||
TermCodeSystemVersion termCodeSystemVersion;
|
||||
if (nextConcept.getSystemVersion() != null) {
|
||||
termCodeSystemVersion = myCodeSystemVersionDao.findByCodeSystemPidAndVersion(codeSystem.getPid(), nextConcept.getSystemVersion());
|
||||
} else {
|
||||
termCodeSystemVersion = codeSystem.getCurrentVersion();
|
||||
}
|
||||
myConceptDao
|
||||
.findByCodeSystemAndCode(codeSystem.getCurrentVersion(), nextConcept.getCode())
|
||||
.findByCodeSystemAndCode(termCodeSystemVersion, nextConcept.getCode())
|
||||
.ifPresent(concept ->
|
||||
addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, concept, theAdd, theCodeCounter)
|
||||
);
|
||||
|
@ -770,7 +792,13 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
|
||||
@Nonnull
|
||||
private Boolean expandValueSetHandleIncludeOrExcludeUsingDatabase(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theIncludeOrExclude, boolean theAdd, AtomicInteger theCodeCounter, int theQueryIndex, VersionIndependentConcept theWantConceptOrNull, String theSystem, TermCodeSystem theCs) {
|
||||
TermCodeSystemVersion csv = theCs.getCurrentVersion();
|
||||
String codeSystemVersion = theIncludeOrExclude.getVersion();
|
||||
TermCodeSystemVersion csv;
|
||||
if (isEmpty(codeSystemVersion)) {
|
||||
csv = theCs.getCurrentVersion();
|
||||
} else {
|
||||
csv = myCodeSystemVersionDao.findByCodeSystemPidAndVersion(theCs.getPid(), codeSystemVersion);
|
||||
}
|
||||
FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
|
||||
|
||||
/*
|
||||
|
@ -797,7 +825,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
/*
|
||||
* Filters
|
||||
*/
|
||||
handleFilters(bool, theSystem, qb, theIncludeOrExclude);
|
||||
handleFilters(bool, theSystem, codeSystemVersion, qb, theIncludeOrExclude);
|
||||
|
||||
Query luceneQuery = bool.createQuery();
|
||||
|
||||
|
@ -906,15 +934,15 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
}
|
||||
}
|
||||
|
||||
private void handleFilters(BooleanJunction<?> theBool, String theSystem, QueryBuilder theQb, ValueSet.ConceptSetComponent theIncludeOrExclude) {
|
||||
private void handleFilters(BooleanJunction<?> theBool, String theSystem, String theSystemVersion, QueryBuilder theQb, ValueSet.ConceptSetComponent theIncludeOrExclude) {
|
||||
if (theIncludeOrExclude.getFilter().size() > 0) {
|
||||
for (ValueSet.ConceptSetFilterComponent nextFilter : theIncludeOrExclude.getFilter()) {
|
||||
handleFilter(theSystem, theQb, theBool, nextFilter);
|
||||
handleFilter(theSystem, theSystemVersion, theQb, theBool, nextFilter);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private void handleFilter(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
|
||||
private void handleFilter(String theSystem, String theSystemVersion, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
|
||||
if (isBlank(theFilter.getValue()) && theFilter.getOp() == null && isBlank(theFilter.getProperty())) {
|
||||
return;
|
||||
}
|
||||
|
@ -930,7 +958,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
break;
|
||||
case "concept":
|
||||
case "code":
|
||||
handleFilterConceptAndCode(theSystem, theQb, theBool, theFilter);
|
||||
handleFilterConceptAndCode(theSystem, theSystemVersion, theQb, theBool, theFilter);
|
||||
break;
|
||||
case "parent":
|
||||
case "child":
|
||||
|
@ -939,11 +967,11 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
break;
|
||||
case "ancestor":
|
||||
isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
|
||||
handleFilterLoincAncestor(theSystem, theBool, theFilter);
|
||||
handleFilterLoincAncestor(theSystem, theSystemVersion, theBool, theFilter);
|
||||
break;
|
||||
case "descendant":
|
||||
isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
|
||||
handleFilterLoincDescendant(theSystem, theBool, theFilter);
|
||||
handleFilterLoincDescendant(theSystem, theSystemVersion, theBool, theFilter);
|
||||
break;
|
||||
case "copyright":
|
||||
isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
|
||||
|
@ -993,8 +1021,8 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
bool.must(textQuery);
|
||||
}
|
||||
|
||||
private void handleFilterConceptAndCode(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
|
||||
TermConcept code = findCode(theSystem, theFilter.getValue())
|
||||
private void handleFilterConceptAndCode(String theSystem, String theSystemVersion, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
|
||||
TermConcept code = findCode(theSystem, theFilter.getValue(), theSystemVersion)
|
||||
.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + Constants.codeSystemWithDefaultDescription(theSystem) + "}" + theFilter.getValue()));
|
||||
|
||||
if (theFilter.getOp() == ValueSet.FilterOperator.ISA) {
|
||||
|
@ -1039,41 +1067,41 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
}
|
||||
|
||||
@SuppressWarnings("EnumSwitchStatementWhichMissesCases")
|
||||
private void handleFilterLoincAncestor(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
|
||||
private void handleFilterLoincAncestor(String theSystem, String theSystemVersion, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
|
||||
switch (theFilter.getOp()) {
|
||||
case EQUAL:
|
||||
addLoincFilterAncestorEqual(theSystem, theBool, theFilter);
|
||||
addLoincFilterAncestorEqual(theSystem, theSystemVersion, theBool, theFilter);
|
||||
break;
|
||||
case IN:
|
||||
addLoincFilterAncestorIn(theSystem, theBool, theFilter);
|
||||
addLoincFilterAncestorIn(theSystem, theSystemVersion, 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, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
|
||||
addLoincFilterAncestorEqual(theSystem, theBool, theFilter.getProperty(), theFilter.getValue());
|
||||
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, String theProperty, String theValue) {
|
||||
List<Term> terms = getAncestorTerms(theSystem, theProperty, theValue);
|
||||
private void addLoincFilterAncestorEqual(String theSystem, String theSystemVersion, BooleanJunction<?> theBool, String theProperty, String theValue) {
|
||||
List<Term> terms = getAncestorTerms(theSystem, theSystemVersion, theProperty, theValue);
|
||||
theBool.must(new TermsQuery(terms));
|
||||
}
|
||||
|
||||
private void addLoincFilterAncestorIn(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
|
||||
private void addLoincFilterAncestorIn(String theSystem, String theSystemVersion, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
|
||||
String[] values = theFilter.getValue().split(",");
|
||||
List<Term> terms = new ArrayList<>();
|
||||
for (String value : values) {
|
||||
terms.addAll(getAncestorTerms(theSystem, theFilter.getProperty(), value));
|
||||
terms.addAll(getAncestorTerms(theSystem, theSystemVersion, theFilter.getProperty(), value));
|
||||
}
|
||||
theBool.must(new TermsQuery(terms));
|
||||
}
|
||||
|
||||
private List<Term> getAncestorTerms(String theSystem, String theProperty, String theValue) {
|
||||
private List<Term> getAncestorTerms(String theSystem, String theSystemVersion, String theProperty, String theValue) {
|
||||
List<Term> retVal = new ArrayList<>();
|
||||
|
||||
TermConcept code = findCode(theSystem, theValue)
|
||||
TermConcept code = findCode(theSystem, theValue, theSystemVersion)
|
||||
.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + Constants.codeSystemWithDefaultDescription(theSystem) + "}" + theValue));
|
||||
|
||||
retVal.add(new Term("myParentPids", "" + code.getId()));
|
||||
|
@ -1083,41 +1111,41 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
}
|
||||
|
||||
@SuppressWarnings("EnumSwitchStatementWhichMissesCases")
|
||||
private void handleFilterLoincDescendant(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
|
||||
private void handleFilterLoincDescendant(String theSystem, String theSystemVersion, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
|
||||
switch (theFilter.getOp()) {
|
||||
case EQUAL:
|
||||
addLoincFilterDescendantEqual(theSystem, theBool, theFilter);
|
||||
addLoincFilterDescendantEqual(theSystem, theSystemVersion, theBool, theFilter);
|
||||
break;
|
||||
case IN:
|
||||
addLoincFilterDescendantIn(theSystem, theBool, theFilter);
|
||||
addLoincFilterDescendantIn(theSystem, theSystemVersion, 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, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
|
||||
addLoincFilterDescendantEqual(theSystem, theBool, theFilter.getProperty(), theFilter.getValue());
|
||||
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, String theProperty, String theValue) {
|
||||
List<Term> terms = getDescendantTerms(theSystem, theProperty, theValue);
|
||||
private void addLoincFilterDescendantEqual(String theSystem, String theSystemVersion, BooleanJunction<?> theBool, String theProperty, String theValue) {
|
||||
List<Term> terms = getDescendantTerms(theSystem, theSystemVersion, theProperty, theValue);
|
||||
theBool.must(new TermsQuery(terms));
|
||||
}
|
||||
|
||||
private void addLoincFilterDescendantIn(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
|
||||
private void addLoincFilterDescendantIn(String theSystem, String theSystemVersion, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
|
||||
String[] values = theFilter.getValue().split(",");
|
||||
List<Term> terms = new ArrayList<>();
|
||||
for (String value : values) {
|
||||
terms.addAll(getDescendantTerms(theSystem, theFilter.getProperty(), value));
|
||||
terms.addAll(getDescendantTerms(theSystem, theSystemVersion, theFilter.getProperty(), value));
|
||||
}
|
||||
theBool.must(new TermsQuery(terms));
|
||||
}
|
||||
|
||||
private List<Term> getDescendantTerms(String theSystem, String theProperty, String theValue) {
|
||||
private List<Term> getDescendantTerms(String theSystem, String theSystemVersion, String theProperty, String theValue) {
|
||||
List<Term> retVal = new ArrayList<>();
|
||||
|
||||
TermConcept code = findCode(theSystem, theValue)
|
||||
TermConcept code = findCode(theSystem, theValue, theSystemVersion)
|
||||
.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + Constants.codeSystemWithDefaultDescription(theSystem) + "}" + theValue));
|
||||
|
||||
String[] parentPids = code.getParentPidsAsString().split(" ");
|
||||
|
@ -1391,7 +1419,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
private TermCodeSystemVersion getCurrentCodeSystemVersion(String theUri, String theVersion) {
|
||||
StringBuilder key = new StringBuilder(theUri);
|
||||
if (theVersion != null) {
|
||||
key.append("_").append(theVersion);
|
||||
key.append("|").append(theVersion);
|
||||
}
|
||||
TermCodeSystemVersion retVal = myCodeSystemCurrentVersionCache.get(key.toString(), t -> myTxTemplate.execute(tx -> {
|
||||
TermCodeSystemVersion csv = null;
|
||||
|
@ -1842,21 +1870,21 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
@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) {
|
||||
VersionIndependentConceptWithSystemVersion conceptA = toConcept(theCodeA, theSystem, theCodingA, theSystemVersion, theCodingAVersion);
|
||||
VersionIndependentConceptWithSystemVersion conceptB = toConcept(theCodeB, theSystem, theCodingB, theSystemVersion, theCodingBVersion);
|
||||
VersionIndependentConcept conceptA = toConcept(theCodeA, theSystem, theCodingA, theSystemVersion, theCodingAVersion);
|
||||
VersionIndependentConcept conceptB = toConcept(theCodeB, theSystem, theCodingB, theSystemVersion, theCodingBVersion);
|
||||
|
||||
if (!StringUtils.equals(conceptA.getSystem(), conceptB.getSystem())) {
|
||||
throw new InvalidRequestException("Unable to test subsumption across different code systems");
|
||||
}
|
||||
|
||||
if (!StringUtils.equals(conceptA.getCodeSystemVersion(), conceptB.getCodeSystemVersion())) {
|
||||
if (!StringUtils.equals(conceptA.getSystemVersion(), conceptB.getSystemVersion())) {
|
||||
throw new InvalidRequestException("Unable to test subsumption across different code system versions");
|
||||
}
|
||||
|
||||
TermConcept codeA = findCode(conceptA.getSystem(), conceptA.getCode(), conceptA.getCodeSystemVersion())
|
||||
TermConcept codeA = findCode(conceptA.getSystem(), conceptA.getCode(), conceptA.getSystemVersion())
|
||||
.orElseThrow(() -> new InvalidRequestException("Unknown code: " + conceptA));
|
||||
|
||||
TermConcept codeB = findCode(conceptB.getSystem(), conceptB.getCode(), conceptB.getCodeSystemVersion())
|
||||
TermConcept codeB = findCode(conceptB.getSystem(), conceptB.getCode(), conceptB.getSystemVersion())
|
||||
.orElseThrow(() -> new InvalidRequestException("Unknown code: " + conceptB));
|
||||
|
||||
FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
|
||||
|
@ -2214,7 +2242,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
}
|
||||
|
||||
@Override
|
||||
public CodeSystem fetchCanonicalCodeSystemFromCompleteContext(String theSystem) {
|
||||
public CodeSystem fetchCanonicalCodeSystemFromCompleteContext(String theSystem) {
|
||||
IValidationSupport validationSupport = provideValidationSupport();
|
||||
IBaseResource codeSystem = validationSupport.fetchCodeSystem(theSystem);
|
||||
if (codeSystem != null) {
|
||||
|
@ -2423,7 +2451,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
}
|
||||
|
||||
@NotNull
|
||||
private VersionIndependentConceptWithSystemVersion 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, IPrimitiveType<String> theSystemVersionType, String theCodingVersionType) {
|
||||
String code = theCodeType != null ? theCodeType.getValueAsString() : null;
|
||||
String system = theSystemType != null ? theSystemType.getValueAsString() : null;
|
||||
String systemVersion = theSystemVersionType != null ? theSystemVersionType.getValueAsString() : null;
|
||||
|
@ -2432,10 +2460,10 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
system = theCodingType.getSystem();
|
||||
systemVersion = theCodingVersionType;
|
||||
}
|
||||
return new VersionIndependentConceptWithSystemVersion(system, code, systemVersion);
|
||||
return new VersionIndependentConcept(system, code, null, systemVersion);
|
||||
}
|
||||
|
||||
private static class VersionIndependentConceptWithSystemVersion extends VersionIndependentConcept {
|
||||
/* private static class VersionIndependentConceptWithSystemVersion extends VersionIndependentConcept {
|
||||
|
||||
String myCodeSystemVersion;
|
||||
|
||||
|
@ -2449,7 +2477,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
}
|
||||
|
||||
}
|
||||
|
||||
*/
|
||||
/**
|
||||
* This method is present only for unit tests, do not call from client code
|
||||
*/
|
||||
|
|
|
@ -33,8 +33,12 @@ 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 excludeConcept(String theSystem, String theCode);
|
||||
|
||||
void excludeConcept(String theSystem, String theSystemVersion, String theCode);
|
||||
|
||||
@Nullable
|
||||
default Integer getCapacityRemaining() {
|
||||
return null;
|
||||
|
|
|
@ -351,32 +351,23 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
|
|||
ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystemUri, "No system URI supplied");
|
||||
|
||||
// Grab the existing version so we can delete it
|
||||
TermCodeSystem existingCodeSystem = myCodeSystemDao.findByCodeSystemUri(theSystemUri);
|
||||
TermCodeSystemVersion existing = null;
|
||||
if (existingCodeSystem != null) {
|
||||
existing = getExistingTermCodeSystemVersion(existingCodeSystem.getPid(), theSystemVersionId);
|
||||
}
|
||||
|
||||
/*
|
||||
* Get CodeSystem and validate CodeSystemVersion
|
||||
*/
|
||||
TermCodeSystem codeSystem = getOrCreateDistinctTermCodeSystem(theCodeSystemResourcePid, theSystemUri, theSystemName, theSystemVersionId, theCodeSystemResourceTable);
|
||||
List<TermCodeSystemVersion> existing = myCodeSystemVersionDao.findByCodeSystemResourcePid(theCodeSystemResourcePid.getIdAsLong());
|
||||
|
||||
/*
|
||||
* Delete version being replaced.
|
||||
*/
|
||||
|
||||
if(existing != null) {
|
||||
ourLog.info("Deleting old code system version {}", existing.getPid());
|
||||
Long codeSystemVersionPid = existing.getPid();
|
||||
for (TermCodeSystemVersion next : existing) {
|
||||
ourLog.info("Deleting old code system version {}", next.getPid());
|
||||
Long codeSystemVersionPid = next.getPid();
|
||||
deleteCodeSystemVersion(codeSystemVersionPid);
|
||||
|
||||
}
|
||||
|
||||
/*
|
||||
* Do the upload
|
||||
*/
|
||||
|
||||
TermCodeSystem codeSystem = getOrCreateDistinctTermCodeSystem(theCodeSystemResourcePid, theSystemUri, theSystemName, theSystemVersionId, theCodeSystemResourceTable);
|
||||
theCodeSystemVersion.setCodeSystem(codeSystem);
|
||||
|
||||
theCodeSystemVersion.setCodeSystemDisplayName(theSystemName);
|
||||
|
@ -687,13 +678,14 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
|
|||
if (codeSystem == null) {
|
||||
codeSystem = new TermCodeSystem();
|
||||
}
|
||||
} else {
|
||||
checkForCodeSystemVersionDuplicate(codeSystem, theSystemUri, theSystemVersionId, theCodeSystemResourceTable);
|
||||
}
|
||||
|
||||
codeSystem.setResource(theCodeSystemResourceTable);
|
||||
codeSystem.setCodeSystemUri(theSystemUri);
|
||||
codeSystem.setName(theSystemName);
|
||||
codeSystem = myCodeSystemDao.save(codeSystem);
|
||||
checkForCodeSystemVersionDuplicate(codeSystem,theSystemUri, theSystemVersionId, theCodeSystemResourceTable);
|
||||
return codeSystem;
|
||||
}
|
||||
|
||||
|
@ -711,13 +703,6 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
|
|||
codeSystemVersionEntity = myCodeSystemVersionDao.findByCodeSystemPidAndVersion(theCodeSystem.getPid(), theSystemVersionId);
|
||||
if (codeSystemVersionEntity != null) {
|
||||
msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "cannotCreateDuplicateCodeSystemUrlAndVersion", theSystemUri, theSystemVersionId, codeSystemVersionEntity.getResource().getIdDt().toUnqualifiedVersionless().getValue());
|
||||
} else {
|
||||
// Check if a TermCodeSystemVersion entity already exists for this CodeSystem resource (i.e. with a different version or URL)
|
||||
codeSystemVersionEntity = myCodeSystemVersionDao.findByCodeSystemResourcePid(theCodeSystemResourceTable.getId());
|
||||
if (codeSystemVersionEntity != null) {
|
||||
msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "cannotUpdateUrlOrVersionForCodeSystemResource", codeSystemVersionEntity.getResource().getIdDt().toUnqualifiedVersionless().getValue(), theSystemUri, theSystemVersionId);
|
||||
throw new UnprocessableEntityException(msg);
|
||||
}
|
||||
}
|
||||
}
|
||||
// Throw exception if the TermCodeSystemVersion is being duplicated.
|
||||
|
|
|
@ -20,7 +20,6 @@ package ca.uhn.fhir.jpa.term;
|
|||
* #L%
|
||||
*/
|
||||
|
||||
import ca.uhn.fhir.jpa.api.config.DaoConfig;
|
||||
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
|
||||
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
|
||||
import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
|
||||
|
@ -69,14 +68,12 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
|
|||
@Autowired
|
||||
protected PlatformTransactionManager myTransactionMgr;
|
||||
private boolean myProcessDeferred = true;
|
||||
private List<TermCodeSystem> myDefferedCodeSystemsDeletions = Collections.synchronizedList(new ArrayList<>());
|
||||
private List<TermCodeSystemVersion> myDefferedCodeSystemVersionsDeletions = Collections.synchronizedList(new ArrayList<>());
|
||||
private List<TermConcept> myDeferredConcepts = Collections.synchronizedList(new ArrayList<>());
|
||||
private List<ValueSet> myDeferredValueSets = Collections.synchronizedList(new ArrayList<>());
|
||||
private List<ConceptMap> myDeferredConceptMaps = Collections.synchronizedList(new ArrayList<>());
|
||||
private List<TermConceptParentChildLink> myConceptLinksToSaveLater = Collections.synchronizedList(new ArrayList<>());
|
||||
@Autowired
|
||||
private DaoConfig myDaoConfig;
|
||||
final private List<TermCodeSystem> myDefferedCodeSystemsDeletions = Collections.synchronizedList(new ArrayList<>());
|
||||
final private List<TermCodeSystemVersion> myDefferedCodeSystemVersionsDeletions = Collections.synchronizedList(new ArrayList<>());
|
||||
final private List<TermConcept> myDeferredConcepts = Collections.synchronizedList(new ArrayList<>());
|
||||
final private List<ValueSet> myDeferredValueSets = Collections.synchronizedList(new ArrayList<>());
|
||||
final private List<ConceptMap> myDeferredConceptMaps = Collections.synchronizedList(new ArrayList<>());
|
||||
final private List<TermConceptParentChildLink> myConceptLinksToSaveLater = Collections.synchronizedList(new ArrayList<>());
|
||||
@Autowired
|
||||
private ITermConceptParentChildLinkDao myConceptParentChildLinkDao;
|
||||
@Autowired
|
||||
|
@ -121,9 +118,11 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
|
|||
@Override
|
||||
@Transactional
|
||||
public void deleteCodeSystemForResource(ResourceTable theCodeSystemToDelete) {
|
||||
TermCodeSystemVersion codeSystemVersionToDelete = myCodeSystemVersionDao.findByCodeSystemResourcePid(theCodeSystemToDelete.getResourceId());
|
||||
if (codeSystemVersionToDelete != null) {
|
||||
myDefferedCodeSystemVersionsDeletions.add(codeSystemVersionToDelete);
|
||||
List<TermCodeSystemVersion> codeSystemVersionsToDelete = myCodeSystemVersionDao.findByCodeSystemResourcePid(theCodeSystemToDelete.getResourceId());
|
||||
for (TermCodeSystemVersion codeSystemVersionToDelete : codeSystemVersionsToDelete){
|
||||
if (codeSystemVersionToDelete != null) {
|
||||
myDefferedCodeSystemVersionsDeletions.add(codeSystemVersionToDelete);
|
||||
}
|
||||
}
|
||||
TermCodeSystem codeSystemToDelete = myCodeSystemDao.findByResourcePid(theCodeSystemToDelete.getResourceId());
|
||||
if (codeSystemToDelete != null) {
|
||||
|
@ -297,8 +296,7 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
|
|||
|
||||
@Override
|
||||
public boolean isStorageQueueEmpty() {
|
||||
boolean retVal = true;
|
||||
retVal &= !isProcessDeferredPaused();
|
||||
boolean retVal = !isProcessDeferredPaused();
|
||||
retVal &= !isDeferredConcepts();
|
||||
retVal &= !isConceptLinksToSaveLater();
|
||||
retVal &= !isDeferredValueSets();
|
||||
|
@ -368,11 +366,6 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
|
|||
myTransactionMgr = theTxManager;
|
||||
}
|
||||
|
||||
@VisibleForTesting
|
||||
void setDaoConfigForUnitTest(DaoConfig theDaoConfig) {
|
||||
myDaoConfig = theDaoConfig;
|
||||
}
|
||||
|
||||
@VisibleForTesting
|
||||
void setCodeSystemStorageSvcForUnitTest(ITermCodeSystemStorageSvc theCodeSystemStorageSvc) {
|
||||
myCodeSystemStorageSvc = theCodeSystemStorageSvc;
|
||||
|
|
|
@ -71,7 +71,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
|
|||
}
|
||||
|
||||
@Override
|
||||
public void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations) {
|
||||
public void includeConceptWithDesignations(String theSystem, String theSystemVersion, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations) {
|
||||
TermValueSetConcept concept = saveConcept(theSystem, theCode, theDisplay);
|
||||
if (theDesignations != null) {
|
||||
for (TermConceptDesignation designation : theDesignations) {
|
||||
|
@ -80,8 +80,18 @@ 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;
|
||||
}
|
||||
|
|
|
@ -73,12 +73,15 @@ public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.V
|
|||
}
|
||||
|
||||
@Override
|
||||
public void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations) {
|
||||
public void includeConceptWithDesignations(String theSystem, String theSystemVersion, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations) {
|
||||
incrementConceptsCount();
|
||||
ValueSet.ValueSetExpansionContainsComponent contains = this.addContains();
|
||||
contains.setSystem(theSystem);
|
||||
contains.setCode(theCode);
|
||||
contains.setDisplay(theDisplay);
|
||||
if (theSystemVersion != null) {
|
||||
contains.setVersion(theSystemVersion);
|
||||
}
|
||||
if (theDesignations != null) {
|
||||
for (TermConceptDesignation termConceptDesignation : theDesignations) {
|
||||
contains
|
||||
|
@ -93,6 +96,21 @@ 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
|
||||
|
|
|
@ -0,0 +1,222 @@
|
|||
package ca.uhn.fhir.jpa.dao.dstu3;
|
||||
|
||||
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
|
||||
import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDao;
|
||||
import ca.uhn.fhir.jpa.entity.TermValueSet;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import org.hl7.fhir.dstu3.model.CodeSystem;
|
||||
import org.hl7.fhir.dstu3.model.ValueSet;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.data.domain.PageRequest;
|
||||
|
||||
import java.util.HashMap;
|
||||
import java.util.HashSet;
|
||||
import java.util.Map;
|
||||
import java.util.Optional;
|
||||
import java.util.Set;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
import static org.junit.jupiter.api.Assertions.fail;
|
||||
|
||||
public class FhirResourceDaoDstu3ValueSetMultiVersionTest extends BaseJpaDstu3Test {
|
||||
|
||||
public static final String URL_MY_VALUE_SET = "http://example.com/my_value_set";
|
||||
public static final String URL_MY_CODE_SYSTEM = "http://example.com/my_code_system";
|
||||
|
||||
private enum ValueSetVersions { NULL, V1, V2 }
|
||||
|
||||
@Autowired
|
||||
protected ITermValueSetConceptDao myTermValueSetConceptDao;
|
||||
|
||||
private DaoMethodOutcome createLocalCsAndVs(String theVersion, Set<String> theCodeSystemCodes) {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setVersion(theVersion);
|
||||
codeSystem.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
|
||||
for (String codeSystemCode : theCodeSystemCodes) {
|
||||
codeSystem.addConcept().setCode(codeSystemCode);
|
||||
}
|
||||
myCodeSystemDao.create(codeSystem, mySrd);
|
||||
|
||||
return createLocalVs(codeSystem, theVersion);
|
||||
|
||||
}
|
||||
|
||||
private DaoMethodOutcome createLocalVs(CodeSystem theCodeSystem, String theVersion) {
|
||||
ValueSet valueSet = new ValueSet();
|
||||
valueSet.setUrl(URL_MY_VALUE_SET);
|
||||
valueSet.setVersion(theVersion);
|
||||
if (theVersion == null) {
|
||||
valueSet.setName("ValueSet_noVersion");
|
||||
} else {
|
||||
valueSet.setName("ValueSet_"+theVersion);
|
||||
}
|
||||
valueSet.getCompose().addInclude().setSystem(theCodeSystem.getUrl());
|
||||
return myValueSetDao.create(valueSet, mySrd);
|
||||
}
|
||||
|
||||
private Map<ValueSetVersions, DaoMethodOutcome> createVersionedValueSets() {
|
||||
|
||||
HashMap<ValueSetVersions, DaoMethodOutcome> valueSets = new HashMap<>();
|
||||
|
||||
Set<String> valueSetConcepts_noVersion = new HashSet<>();
|
||||
valueSetConcepts_noVersion.add("hello");
|
||||
valueSetConcepts_noVersion.add("goodbye");
|
||||
valueSets.put(ValueSetVersions.NULL, createLocalCsAndVs(null, valueSetConcepts_noVersion));
|
||||
|
||||
Set<String> valueSetConcepts_v1 = new HashSet<>(valueSetConcepts_noVersion);
|
||||
valueSetConcepts_v1.add("hi");
|
||||
valueSets.put(ValueSetVersions.V1, createLocalCsAndVs("v1", valueSetConcepts_v1));
|
||||
|
||||
Set<String> valueSetConcepts_v2 = new HashSet<>(valueSetConcepts_v1);
|
||||
valueSetConcepts_v2.add("so-long");
|
||||
valueSets.put(ValueSetVersions.V2, createLocalCsAndVs("v2", valueSetConcepts_v2));
|
||||
|
||||
return valueSets;
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testCreateVersionedValueSets() {
|
||||
Map<ValueSetVersions, DaoMethodOutcome> myValueSets = createVersionedValueSets();
|
||||
|
||||
assertEquals(3, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
|
||||
Optional<TermValueSet> optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET);
|
||||
assertTrue(optionalTermValueSet.isPresent());
|
||||
Long nullVersion_resid = ((ResourceTable)myValueSets.get(ValueSetVersions.NULL).getEntity()).getId();
|
||||
assertNotNull(nullVersion_resid);
|
||||
assertNotNull(optionalTermValueSet.get().getResource());
|
||||
assertEquals(nullVersion_resid, optionalTermValueSet.get().getResource().getId());
|
||||
assertEquals("ValueSet_noVersion", optionalTermValueSet.get().getName());
|
||||
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1");
|
||||
assertTrue(optionalTermValueSet.isPresent());
|
||||
Long v1Version_resid = ((ResourceTable)myValueSets.get(ValueSetVersions.V1).getEntity()).getId();
|
||||
assertNotNull(v1Version_resid);
|
||||
assertNotNull(optionalTermValueSet.get().getResource());
|
||||
assertEquals(v1Version_resid, optionalTermValueSet.get().getResource().getId());
|
||||
assertEquals("ValueSet_v1", optionalTermValueSet.get().getName());
|
||||
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2");
|
||||
assertTrue(optionalTermValueSet.isPresent());
|
||||
Long v2Version_resid = ((ResourceTable)myValueSets.get(ValueSetVersions.V2).getEntity()).getId();
|
||||
assertNotNull(v2Version_resid);
|
||||
assertNotNull(optionalTermValueSet.get().getResource());
|
||||
assertEquals(v2Version_resid, optionalTermValueSet.get().getResource().getId());
|
||||
assertEquals("ValueSet_v2", optionalTermValueSet.get().getName());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testUpdateVersionedValueSets() {
|
||||
Map<ValueSetVersions, DaoMethodOutcome> myValueSets = createVersionedValueSets();
|
||||
|
||||
assertEquals(3, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
|
||||
TermValueSet termValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version"));
|
||||
assertEquals("ValueSet_noVersion", termValueSet.getName());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1"));
|
||||
assertEquals("ValueSet_v1", termValueSet.getName());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
|
||||
assertEquals("ValueSet_v2", termValueSet.getName());
|
||||
|
||||
// Update ValueSets
|
||||
ValueSet updated = (ValueSet)myValueSets.get(ValueSetVersions.NULL).getResource();
|
||||
updated.setName("ValueSet_noVersion_updated");
|
||||
DaoMethodOutcome nullVersion_update_outcome = myValueSetDao.update(updated);
|
||||
Long nullVersion_resid = ((ResourceTable)nullVersion_update_outcome.getEntity()).getId();
|
||||
|
||||
updated = (ValueSet)myValueSets.get(ValueSetVersions.V1).getResource();
|
||||
updated.setName("ValueSet_v1_updated");
|
||||
DaoMethodOutcome v1Version_update_outcome = myValueSetDao.update(updated);
|
||||
Long v1Version_resid = ((ResourceTable)v1Version_update_outcome.getEntity()).getId();
|
||||
|
||||
updated = (ValueSet)myValueSets.get(ValueSetVersions.V2).getResource();
|
||||
updated.setName("ValueSet_v2_updated");
|
||||
DaoMethodOutcome v2Version_update_outcome = myValueSetDao.update(updated);
|
||||
Long v2Version_resid = ((ResourceTable)v2Version_update_outcome.getEntity()).getId();
|
||||
|
||||
// Verify that ValueSets were updated.
|
||||
assertEquals(3, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version"));
|
||||
assertNotNull(nullVersion_resid);
|
||||
assertNotNull(termValueSet.getResource());
|
||||
assertEquals(nullVersion_resid, termValueSet.getResource().getId());
|
||||
assertEquals("ValueSet_noVersion_updated", termValueSet.getName());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1"));
|
||||
assertNotNull(v1Version_resid);
|
||||
assertNotNull(termValueSet.getResource());
|
||||
assertEquals(v1Version_resid, termValueSet.getResource().getId());
|
||||
assertEquals("ValueSet_v1_updated", termValueSet.getName());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
|
||||
assertNotNull(v2Version_resid);
|
||||
assertNotNull(termValueSet.getResource());
|
||||
assertEquals(v2Version_resid, termValueSet.getResource().getId());
|
||||
assertEquals("ValueSet_v2_updated", termValueSet.getName());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testDeleteVersionedValueSets() {
|
||||
Map<ValueSetVersions, DaoMethodOutcome> myValueSets = createVersionedValueSets();
|
||||
|
||||
assertEquals(3, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
|
||||
TermValueSet termValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version"));
|
||||
assertEquals("ValueSet_noVersion", termValueSet.getName());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1"));
|
||||
assertEquals("ValueSet_v1", termValueSet.getName());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
|
||||
assertEquals("ValueSet_v2", termValueSet.getName());
|
||||
|
||||
// Delete ValueSets
|
||||
myValueSetDao.delete(myValueSets.get(ValueSetVersions.NULL).getResource().getIdElement());
|
||||
assertEquals(2, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
Optional<TermValueSet> optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET);
|
||||
if (optionalTermValueSet.isPresent()) {
|
||||
fail();
|
||||
}
|
||||
myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1"));
|
||||
myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
|
||||
|
||||
myValueSetDao.delete(myValueSets.get(ValueSetVersions.V1).getResource().getIdElement());
|
||||
assertEquals(1, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET);
|
||||
if (optionalTermValueSet.isPresent()) {
|
||||
fail();
|
||||
}
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1");
|
||||
if (optionalTermValueSet.isPresent()) {
|
||||
fail();
|
||||
}
|
||||
myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
|
||||
|
||||
myValueSetDao.delete(myValueSets.get(ValueSetVersions.V2).getResource().getIdElement());
|
||||
assertEquals(0, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET);
|
||||
if (optionalTermValueSet.isPresent()) {
|
||||
fail();
|
||||
}
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1");
|
||||
if (optionalTermValueSet.isPresent()) {
|
||||
fail();
|
||||
}
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2");
|
||||
if (optionalTermValueSet.isPresent()) {
|
||||
fail();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
|
@ -235,6 +235,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
|
||||
@Test
|
||||
public void testCodeSystemCreateDuplicateFails() {
|
||||
// No version.
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setContent(CodeSystemContentMode.COMPLETE);
|
||||
|
@ -249,6 +250,25 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
} catch (UnprocessableEntityException e) {
|
||||
assertEquals("Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/" + id.getIdPart(), e.getMessage());
|
||||
}
|
||||
|
||||
// With version.
|
||||
codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setVersion("1");
|
||||
codeSystem.setContent(CodeSystemContentMode.COMPLETE);
|
||||
id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
|
||||
|
||||
codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setVersion("1");
|
||||
codeSystem.setContent(CodeSystemContentMode.COMPLETE);
|
||||
try {
|
||||
myCodeSystemDao.create(codeSystem, mySrd);
|
||||
fail();
|
||||
} catch (UnprocessableEntityException e) {
|
||||
assertEquals("Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\" and CodeSystem.version \"1\", already have one with resource ID: CodeSystem/" + id.getIdPart(), e.getMessage());
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
|
@ -0,0 +1,222 @@
|
|||
package ca.uhn.fhir.jpa.dao.r4;
|
||||
|
||||
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
|
||||
import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDao;
|
||||
import ca.uhn.fhir.jpa.entity.TermValueSet;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import org.hl7.fhir.r4.model.CodeSystem;
|
||||
import org.hl7.fhir.r4.model.ValueSet;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.data.domain.PageRequest;
|
||||
|
||||
import java.util.HashMap;
|
||||
import java.util.HashSet;
|
||||
import java.util.Map;
|
||||
import java.util.Optional;
|
||||
import java.util.Set;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
import static org.junit.jupiter.api.Assertions.fail;
|
||||
|
||||
public class FhirResourceDaoR4ValueSetMultiVersionTest extends BaseJpaR4Test {
|
||||
|
||||
public static final String URL_MY_VALUE_SET = "http://example.com/my_value_set";
|
||||
public static final String URL_MY_CODE_SYSTEM = "http://example.com/my_code_system";
|
||||
|
||||
private enum ValueSetVersions { NULL, V1, V2 }
|
||||
|
||||
@Autowired
|
||||
protected ITermValueSetConceptDao myTermValueSetConceptDao;
|
||||
|
||||
private DaoMethodOutcome createLocalCsAndVs(String theVersion, Set<String> theCodeSystemCodes) {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setVersion(theVersion);
|
||||
codeSystem.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
|
||||
for (String codeSystemCode : theCodeSystemCodes) {
|
||||
codeSystem.addConcept().setCode(codeSystemCode);
|
||||
}
|
||||
myCodeSystemDao.create(codeSystem, mySrd);
|
||||
|
||||
return createLocalVs(codeSystem, theVersion);
|
||||
|
||||
}
|
||||
|
||||
private DaoMethodOutcome createLocalVs(CodeSystem theCodeSystem, String theVersion) {
|
||||
ValueSet valueSet = new ValueSet();
|
||||
valueSet.setUrl(URL_MY_VALUE_SET);
|
||||
valueSet.setVersion(theVersion);
|
||||
if (theVersion == null) {
|
||||
valueSet.setName("ValueSet_noVersion");
|
||||
} else {
|
||||
valueSet.setName("ValueSet_"+theVersion);
|
||||
}
|
||||
valueSet.getCompose().addInclude().setSystem(theCodeSystem.getUrl());
|
||||
return myValueSetDao.create(valueSet, mySrd);
|
||||
}
|
||||
|
||||
private Map<ValueSetVersions, DaoMethodOutcome> createVersionedValueSets() {
|
||||
|
||||
HashMap<ValueSetVersions, DaoMethodOutcome> valueSets = new HashMap<>();
|
||||
|
||||
Set<String> valueSetConcepts_noVersion = new HashSet<>();
|
||||
valueSetConcepts_noVersion.add("hello");
|
||||
valueSetConcepts_noVersion.add("goodbye");
|
||||
valueSets.put(ValueSetVersions.NULL, createLocalCsAndVs(null, valueSetConcepts_noVersion));
|
||||
|
||||
Set<String> valueSetConcepts_v1 = new HashSet<>(valueSetConcepts_noVersion);
|
||||
valueSetConcepts_v1.add("hi");
|
||||
valueSets.put(ValueSetVersions.V1, createLocalCsAndVs("v1", valueSetConcepts_v1));
|
||||
|
||||
Set<String> valueSetConcepts_v2 = new HashSet<>(valueSetConcepts_v1);
|
||||
valueSetConcepts_v2.add("so-long");
|
||||
valueSets.put(ValueSetVersions.V2, createLocalCsAndVs("v2", valueSetConcepts_v2));
|
||||
|
||||
return valueSets;
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testCreateVersionedValueSets() {
|
||||
Map<ValueSetVersions, DaoMethodOutcome> myValueSets = createVersionedValueSets();
|
||||
|
||||
assertEquals(3, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
|
||||
Optional<TermValueSet> optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET);
|
||||
assertTrue(optionalTermValueSet.isPresent());
|
||||
Long nullVersion_resid = ((ResourceTable)myValueSets.get(ValueSetVersions.NULL).getEntity()).getId();
|
||||
assertNotNull(nullVersion_resid);
|
||||
assertNotNull(optionalTermValueSet.get().getResource());
|
||||
assertEquals(nullVersion_resid, optionalTermValueSet.get().getResource().getId());
|
||||
assertEquals("ValueSet_noVersion", optionalTermValueSet.get().getName());
|
||||
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1");
|
||||
assertTrue(optionalTermValueSet.isPresent());
|
||||
Long v1Version_resid = ((ResourceTable)myValueSets.get(ValueSetVersions.V1).getEntity()).getId();
|
||||
assertNotNull(v1Version_resid);
|
||||
assertNotNull(optionalTermValueSet.get().getResource());
|
||||
assertEquals(v1Version_resid, optionalTermValueSet.get().getResource().getId());
|
||||
assertEquals("ValueSet_v1", optionalTermValueSet.get().getName());
|
||||
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2");
|
||||
assertTrue(optionalTermValueSet.isPresent());
|
||||
Long v2Version_resid = ((ResourceTable)myValueSets.get(ValueSetVersions.V2).getEntity()).getId();
|
||||
assertNotNull(v2Version_resid);
|
||||
assertNotNull(optionalTermValueSet.get().getResource());
|
||||
assertEquals(v2Version_resid, optionalTermValueSet.get().getResource().getId());
|
||||
assertEquals("ValueSet_v2", optionalTermValueSet.get().getName());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testUpdateVersionedValueSets() {
|
||||
Map<ValueSetVersions, DaoMethodOutcome> myValueSets = createVersionedValueSets();
|
||||
|
||||
assertEquals(3, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
|
||||
TermValueSet termValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version"));
|
||||
assertEquals("ValueSet_noVersion", termValueSet.getName());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1"));
|
||||
assertEquals("ValueSet_v1", termValueSet.getName());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
|
||||
assertEquals("ValueSet_v2", termValueSet.getName());
|
||||
|
||||
// Update ValueSets
|
||||
ValueSet updated = (ValueSet)myValueSets.get(ValueSetVersions.NULL).getResource();
|
||||
updated.setName("ValueSet_noVersion_updated");
|
||||
DaoMethodOutcome nullVersion_update_outcome = myValueSetDao.update(updated);
|
||||
Long nullVersion_resid = ((ResourceTable)nullVersion_update_outcome.getEntity()).getId();
|
||||
|
||||
updated = (ValueSet)myValueSets.get(ValueSetVersions.V1).getResource();
|
||||
updated.setName("ValueSet_v1_updated");
|
||||
DaoMethodOutcome v1Version_update_outcome = myValueSetDao.update(updated);
|
||||
Long v1Version_resid = ((ResourceTable)v1Version_update_outcome.getEntity()).getId();
|
||||
|
||||
updated = (ValueSet)myValueSets.get(ValueSetVersions.V2).getResource();
|
||||
updated.setName("ValueSet_v2_updated");
|
||||
DaoMethodOutcome v2Version_update_outcome = myValueSetDao.update(updated);
|
||||
Long v2Version_resid = ((ResourceTable)v2Version_update_outcome.getEntity()).getId();
|
||||
|
||||
// Verify that ValueSets were updated.
|
||||
assertEquals(3, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version"));
|
||||
assertNotNull(nullVersion_resid);
|
||||
assertNotNull(termValueSet.getResource());
|
||||
assertEquals(nullVersion_resid, termValueSet.getResource().getId());
|
||||
assertEquals("ValueSet_noVersion_updated", termValueSet.getName());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1"));
|
||||
assertNotNull(v1Version_resid);
|
||||
assertNotNull(termValueSet.getResource());
|
||||
assertEquals(v1Version_resid, termValueSet.getResource().getId());
|
||||
assertEquals("ValueSet_v1_updated", termValueSet.getName());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
|
||||
assertNotNull(v2Version_resid);
|
||||
assertNotNull(termValueSet.getResource());
|
||||
assertEquals(v2Version_resid, termValueSet.getResource().getId());
|
||||
assertEquals("ValueSet_v2_updated", termValueSet.getName());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testDeleteVersionedValueSets() {
|
||||
Map<ValueSetVersions, DaoMethodOutcome> myValueSets = createVersionedValueSets();
|
||||
|
||||
assertEquals(3, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
|
||||
TermValueSet termValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version"));
|
||||
assertEquals("ValueSet_noVersion", termValueSet.getName());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1"));
|
||||
assertEquals("ValueSet_v1", termValueSet.getName());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
|
||||
assertEquals("ValueSet_v2", termValueSet.getName());
|
||||
|
||||
// Delete ValueSets
|
||||
myValueSetDao.delete(myValueSets.get(ValueSetVersions.NULL).getResource().getIdElement());
|
||||
assertEquals(2, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
Optional<TermValueSet> optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET);
|
||||
if (optionalTermValueSet.isPresent()) {
|
||||
fail();
|
||||
}
|
||||
myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1"));
|
||||
myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
|
||||
|
||||
myValueSetDao.delete(myValueSets.get(ValueSetVersions.V1).getResource().getIdElement());
|
||||
assertEquals(1, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET);
|
||||
if (optionalTermValueSet.isPresent()) {
|
||||
fail();
|
||||
}
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1");
|
||||
if (optionalTermValueSet.isPresent()) {
|
||||
fail();
|
||||
}
|
||||
myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
|
||||
|
||||
myValueSetDao.delete(myValueSets.get(ValueSetVersions.V2).getResource().getIdElement());
|
||||
assertEquals(0, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET);
|
||||
if (optionalTermValueSet.isPresent()) {
|
||||
fail();
|
||||
}
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1");
|
||||
if (optionalTermValueSet.isPresent()) {
|
||||
fail();
|
||||
}
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2");
|
||||
if (optionalTermValueSet.isPresent()) {
|
||||
fail();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
|
@ -0,0 +1,222 @@
|
|||
package ca.uhn.fhir.jpa.dao.r5;
|
||||
|
||||
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
|
||||
import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDao;
|
||||
import ca.uhn.fhir.jpa.entity.TermValueSet;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import org.hl7.fhir.r5.model.CodeSystem;
|
||||
import org.hl7.fhir.r5.model.ValueSet;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.data.domain.PageRequest;
|
||||
|
||||
import java.util.HashMap;
|
||||
import java.util.HashSet;
|
||||
import java.util.Map;
|
||||
import java.util.Optional;
|
||||
import java.util.Set;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
import static org.junit.jupiter.api.Assertions.fail;
|
||||
|
||||
public class FhirResourceDaoR5ValueSetMultiVersionTest extends BaseJpaR5Test {
|
||||
|
||||
public static final String URL_MY_VALUE_SET = "http://example.com/my_value_set";
|
||||
public static final String URL_MY_CODE_SYSTEM = "http://example.com/my_code_system";
|
||||
|
||||
private enum ValueSetVersions { NULL, V1, V2 }
|
||||
|
||||
@Autowired
|
||||
protected ITermValueSetConceptDao myTermValueSetConceptDao;
|
||||
|
||||
private DaoMethodOutcome createLocalCsAndVs(String theVersion, Set<String> theCodeSystemCodes) {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setVersion(theVersion);
|
||||
codeSystem.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
|
||||
for (String codeSystemCode : theCodeSystemCodes) {
|
||||
codeSystem.addConcept().setCode(codeSystemCode);
|
||||
}
|
||||
myCodeSystemDao.create(codeSystem, mySrd);
|
||||
|
||||
return createLocalVs(codeSystem, theVersion);
|
||||
|
||||
}
|
||||
|
||||
private DaoMethodOutcome createLocalVs(CodeSystem theCodeSystem, String theVersion) {
|
||||
ValueSet valueSet = new ValueSet();
|
||||
valueSet.setUrl(URL_MY_VALUE_SET);
|
||||
valueSet.setVersion(theVersion);
|
||||
if (theVersion == null) {
|
||||
valueSet.setName("ValueSet_noVersion");
|
||||
} else {
|
||||
valueSet.setName("ValueSet_"+theVersion);
|
||||
}
|
||||
valueSet.getCompose().addInclude().setSystem(theCodeSystem.getUrl());
|
||||
return myValueSetDao.create(valueSet, mySrd);
|
||||
}
|
||||
|
||||
private Map<ValueSetVersions, DaoMethodOutcome> createVersionedValueSets() {
|
||||
|
||||
HashMap<ValueSetVersions, DaoMethodOutcome> valueSets = new HashMap<>();
|
||||
|
||||
Set<String> valueSetConcepts_noVersion = new HashSet<>();
|
||||
valueSetConcepts_noVersion.add("hello");
|
||||
valueSetConcepts_noVersion.add("goodbye");
|
||||
valueSets.put(ValueSetVersions.NULL, createLocalCsAndVs(null, valueSetConcepts_noVersion));
|
||||
|
||||
Set<String> valueSetConcepts_v1 = new HashSet<>(valueSetConcepts_noVersion);
|
||||
valueSetConcepts_v1.add("hi");
|
||||
valueSets.put(ValueSetVersions.V1, createLocalCsAndVs("v1", valueSetConcepts_v1));
|
||||
|
||||
Set<String> valueSetConcepts_v2 = new HashSet<>(valueSetConcepts_v1);
|
||||
valueSetConcepts_v2.add("so-long");
|
||||
valueSets.put(ValueSetVersions.V2, createLocalCsAndVs("v2", valueSetConcepts_v2));
|
||||
|
||||
return valueSets;
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testCreateVersionedValueSets() {
|
||||
Map<ValueSetVersions, DaoMethodOutcome> myValueSets = createVersionedValueSets();
|
||||
|
||||
assertEquals(3, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
|
||||
Optional<TermValueSet> optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET);
|
||||
assertTrue(optionalTermValueSet.isPresent());
|
||||
Long nullVersion_resid = ((ResourceTable)myValueSets.get(ValueSetVersions.NULL).getEntity()).getId();
|
||||
assertNotNull(nullVersion_resid);
|
||||
assertNotNull(optionalTermValueSet.get().getResource());
|
||||
assertEquals(nullVersion_resid, optionalTermValueSet.get().getResource().getId());
|
||||
assertEquals("ValueSet_noVersion", optionalTermValueSet.get().getName());
|
||||
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1");
|
||||
assertTrue(optionalTermValueSet.isPresent());
|
||||
Long v1Version_resid = ((ResourceTable)myValueSets.get(ValueSetVersions.V1).getEntity()).getId();
|
||||
assertNotNull(v1Version_resid);
|
||||
assertNotNull(optionalTermValueSet.get().getResource());
|
||||
assertEquals(v1Version_resid, optionalTermValueSet.get().getResource().getId());
|
||||
assertEquals("ValueSet_v1", optionalTermValueSet.get().getName());
|
||||
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2");
|
||||
assertTrue(optionalTermValueSet.isPresent());
|
||||
Long v2Version_resid = ((ResourceTable)myValueSets.get(ValueSetVersions.V2).getEntity()).getId();
|
||||
assertNotNull(v2Version_resid);
|
||||
assertNotNull(optionalTermValueSet.get().getResource());
|
||||
assertEquals(v2Version_resid, optionalTermValueSet.get().getResource().getId());
|
||||
assertEquals("ValueSet_v2", optionalTermValueSet.get().getName());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testUpdateVersionedValueSets() {
|
||||
Map<ValueSetVersions, DaoMethodOutcome> myValueSets = createVersionedValueSets();
|
||||
|
||||
assertEquals(3, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
|
||||
TermValueSet termValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version"));
|
||||
assertEquals("ValueSet_noVersion", termValueSet.getName());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1"));
|
||||
assertEquals("ValueSet_v1", termValueSet.getName());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
|
||||
assertEquals("ValueSet_v2", termValueSet.getName());
|
||||
|
||||
// Update ValueSets
|
||||
ValueSet updated = (ValueSet)myValueSets.get(ValueSetVersions.NULL).getResource();
|
||||
updated.setName("ValueSet_noVersion_updated");
|
||||
DaoMethodOutcome nullVersion_update_outcome = myValueSetDao.update(updated);
|
||||
Long nullVersion_resid = ((ResourceTable)nullVersion_update_outcome.getEntity()).getId();
|
||||
|
||||
updated = (ValueSet)myValueSets.get(ValueSetVersions.V1).getResource();
|
||||
updated.setName("ValueSet_v1_updated");
|
||||
DaoMethodOutcome v1Version_update_outcome = myValueSetDao.update(updated);
|
||||
Long v1Version_resid = ((ResourceTable)v1Version_update_outcome.getEntity()).getId();
|
||||
|
||||
updated = (ValueSet)myValueSets.get(ValueSetVersions.V2).getResource();
|
||||
updated.setName("ValueSet_v2_updated");
|
||||
DaoMethodOutcome v2Version_update_outcome = myValueSetDao.update(updated);
|
||||
Long v2Version_resid = ((ResourceTable)v2Version_update_outcome.getEntity()).getId();
|
||||
|
||||
// Verify that ValueSets were updated.
|
||||
assertEquals(3, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version"));
|
||||
assertNotNull(nullVersion_resid);
|
||||
assertNotNull(termValueSet.getResource());
|
||||
assertEquals(nullVersion_resid, termValueSet.getResource().getId());
|
||||
assertEquals("ValueSet_noVersion_updated", termValueSet.getName());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1"));
|
||||
assertNotNull(v1Version_resid);
|
||||
assertNotNull(termValueSet.getResource());
|
||||
assertEquals(v1Version_resid, termValueSet.getResource().getId());
|
||||
assertEquals("ValueSet_v1_updated", termValueSet.getName());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
|
||||
assertNotNull(v2Version_resid);
|
||||
assertNotNull(termValueSet.getResource());
|
||||
assertEquals(v2Version_resid, termValueSet.getResource().getId());
|
||||
assertEquals("ValueSet_v2_updated", termValueSet.getName());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testDeleteVersionedValueSets() {
|
||||
Map<ValueSetVersions, DaoMethodOutcome> myValueSets = createVersionedValueSets();
|
||||
|
||||
assertEquals(3, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
|
||||
TermValueSet termValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET).orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " with null version"));
|
||||
assertEquals("ValueSet_noVersion", termValueSet.getName());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1"));
|
||||
assertEquals("ValueSet_v1", termValueSet.getName());
|
||||
|
||||
termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
|
||||
assertEquals("ValueSet_v2", termValueSet.getName());
|
||||
|
||||
// Delete ValueSets
|
||||
myValueSetDao.delete(myValueSets.get(ValueSetVersions.NULL).getResource().getIdElement());
|
||||
assertEquals(2, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
Optional<TermValueSet> optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET);
|
||||
if (optionalTermValueSet.isPresent()) {
|
||||
fail();
|
||||
}
|
||||
myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v1"));
|
||||
myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
|
||||
|
||||
myValueSetDao.delete(myValueSets.get(ValueSetVersions.V1).getResource().getIdElement());
|
||||
assertEquals(1, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET);
|
||||
if (optionalTermValueSet.isPresent()) {
|
||||
fail();
|
||||
}
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1");
|
||||
if (optionalTermValueSet.isPresent()) {
|
||||
fail();
|
||||
}
|
||||
myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2").orElseThrow(() -> new IllegalArgumentException("No TerValueSet found for " + URL_MY_VALUE_SET + " version v2"));
|
||||
|
||||
myValueSetDao.delete(myValueSets.get(ValueSetVersions.V2).getResource().getIdElement());
|
||||
assertEquals(0, myTermValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 10), URL_MY_VALUE_SET).size());
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(URL_MY_VALUE_SET);
|
||||
if (optionalTermValueSet.isPresent()) {
|
||||
fail();
|
||||
}
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v1");
|
||||
if (optionalTermValueSet.isPresent()) {
|
||||
fail();
|
||||
}
|
||||
optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(URL_MY_VALUE_SET, "v2");
|
||||
if (optionalTermValueSet.isPresent()) {
|
||||
fail();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
|
@ -1,9 +1,16 @@
|
|||
package ca.uhn.fhir.jpa.provider.r4;
|
||||
|
||||
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
|
||||
import ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.model.util.JpaConstants;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.http.client.methods.CloseableHttpResponse;
|
||||
import org.apache.http.client.methods.HttpPut;
|
||||
import org.apache.http.entity.ContentType;
|
||||
import org.apache.http.entity.StringEntity;
|
||||
import org.hl7.fhir.r4.model.*;
|
||||
import org.hl7.fhir.r4.model.codesystems.ConceptSubsumptionOutcome;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
|
@ -18,6 +25,7 @@ public class ResourceProviderR4CodeSystemTest extends BaseResourceProviderR4Test
|
|||
|
||||
private static final String SYSTEM_PARENTCHILD = "http://parentchild";
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderR4CodeSystemTest.class);
|
||||
private Long parentChildCsId;
|
||||
|
||||
@BeforeEach
|
||||
@Transactional
|
||||
|
@ -27,6 +35,7 @@ public class ResourceProviderR4CodeSystemTest extends BaseResourceProviderR4Test
|
|||
|
||||
CodeSystem parentChildCs = new CodeSystem();
|
||||
parentChildCs.setUrl(SYSTEM_PARENTCHILD);
|
||||
parentChildCs.setName("Parent Child CodeSystem");
|
||||
parentChildCs.setStatus(Enumerations.PublicationStatus.ACTIVE);
|
||||
parentChildCs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
|
||||
parentChildCs.setHierarchyMeaning(CodeSystem.CodeSystemHierarchyMeaning.ISA);
|
||||
|
@ -35,7 +44,8 @@ public class ResourceProviderR4CodeSystemTest extends BaseResourceProviderR4Test
|
|||
parentA.addConcept().setCode("ChildAA").setDisplay("Child AA");
|
||||
parentChildCs.addConcept().setCode("ParentB").setDisplay("Parent B");
|
||||
|
||||
myCodeSystemDao.create(parentChildCs);
|
||||
DaoMethodOutcome parentChildCsOutcome = myCodeSystemDao.create(parentChildCs);
|
||||
parentChildCsId = ((ResourceTable)parentChildCsOutcome.getEntity()).getId();
|
||||
|
||||
}
|
||||
|
||||
|
@ -416,5 +426,25 @@ public class ResourceProviderR4CodeSystemTest extends BaseResourceProviderR4Test
|
|||
assertEquals(ConceptSubsumptionOutcome.NOTSUBSUMED.toCode(), ((CodeType) respParam.getParameter().get(0).getValue()).getValue());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testUpdateCodeSystemName() throws IOException {
|
||||
|
||||
CodeSystem initialCodeSystem = myClient.read().resource(CodeSystem.class).withId(parentChildCsId).execute();
|
||||
assertEquals("Parent Child CodeSystem", initialCodeSystem.getName());
|
||||
initialCodeSystem.setName("Updated Parent Child CodeSystem");
|
||||
String encoded = myFhirCtx.newJsonParser().encodeResourceToString(initialCodeSystem);
|
||||
HttpPut putRequest = new HttpPut(ourServerBase + "/CodeSystem/" + parentChildCsId);
|
||||
putRequest.setEntity(new StringEntity(encoded, ContentType.parse("application/json+fhir")));
|
||||
CloseableHttpResponse resp = ourHttpClient.execute(putRequest);
|
||||
try {
|
||||
assertEquals(200, resp.getStatusLine().getStatusCode());
|
||||
} finally {
|
||||
IOUtils.closeQuietly(resp);
|
||||
}
|
||||
|
||||
CodeSystem updatedCodeSystem = myClient.read().resource(CodeSystem.class).withId(parentChildCsId).execute();
|
||||
assertEquals("Updated Parent Child CodeSystem", updatedCodeSystem.getName());
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
|
@ -1,9 +1,16 @@
|
|||
package ca.uhn.fhir.jpa.provider.r4;
|
||||
|
||||
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
|
||||
import ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.model.util.JpaConstants;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.http.client.methods.CloseableHttpResponse;
|
||||
import org.apache.http.client.methods.HttpPut;
|
||||
import org.apache.http.entity.ContentType;
|
||||
import org.apache.http.entity.StringEntity;
|
||||
import org.hl7.fhir.r4.model.BooleanType;
|
||||
import org.hl7.fhir.r4.model.CodeSystem;
|
||||
import org.hl7.fhir.r4.model.CodeType;
|
||||
|
@ -12,7 +19,6 @@ import org.hl7.fhir.r4.model.Enumerations;
|
|||
import org.hl7.fhir.r4.model.Parameters;
|
||||
import org.hl7.fhir.r4.model.StringType;
|
||||
import org.hl7.fhir.r4.model.UriType;
|
||||
import org.hl7.fhir.r4.model.ValueSet;
|
||||
import org.hl7.fhir.r4.model.codesystems.ConceptSubsumptionOutcome;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
|
@ -27,6 +33,8 @@ public class ResourceProviderR4CodeSystemVersionedTest extends BaseResourceProvi
|
|||
|
||||
private static final String SYSTEM_PARENTCHILD = "http://parentchild";
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderR4CodeSystemVersionedTest.class);
|
||||
private long parentChildCs1Id;
|
||||
private long parentChildCs2Id;
|
||||
|
||||
@BeforeEach
|
||||
@Transactional
|
||||
|
@ -48,6 +56,7 @@ public class ResourceProviderR4CodeSystemVersionedTest extends BaseResourceProvi
|
|||
CodeSystem parentChildCs = new CodeSystem();
|
||||
parentChildCs.setUrl(SYSTEM_PARENTCHILD);
|
||||
parentChildCs.setVersion("1");
|
||||
parentChildCs.setName("Parent Child CodeSystem 1");
|
||||
parentChildCs.setStatus(Enumerations.PublicationStatus.ACTIVE);
|
||||
parentChildCs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
|
||||
parentChildCs.setHierarchyMeaning(CodeSystem.CodeSystemHierarchyMeaning.ISA);
|
||||
|
@ -57,10 +66,12 @@ public class ResourceProviderR4CodeSystemVersionedTest extends BaseResourceProvi
|
|||
parentA.addConcept().setCode("ParentC").setDisplay("Parent C");
|
||||
parentChildCs.addConcept().setCode("ParentB").setDisplay("Parent B");
|
||||
|
||||
myCodeSystemDao.create(parentChildCs);
|
||||
DaoMethodOutcome parentChildCsOutcome = myCodeSystemDao.create(parentChildCs);
|
||||
parentChildCs1Id = ((ResourceTable)parentChildCsOutcome.getEntity()).getId();
|
||||
|
||||
parentChildCs = new CodeSystem();
|
||||
parentChildCs.setVersion("2");
|
||||
parentChildCs.setName("Parent Child CodeSystem 2");
|
||||
parentChildCs.setUrl(SYSTEM_PARENTCHILD);
|
||||
parentChildCs.setStatus(Enumerations.PublicationStatus.ACTIVE);
|
||||
parentChildCs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
|
||||
|
@ -71,7 +82,8 @@ public class ResourceProviderR4CodeSystemVersionedTest extends BaseResourceProvi
|
|||
parentA.addConcept().setCode("ParentB").setDisplay("Parent B v2");
|
||||
parentChildCs.addConcept().setCode("ParentC").setDisplay("Parent C v2");
|
||||
|
||||
myCodeSystemDao.create(parentChildCs);
|
||||
parentChildCsOutcome = myCodeSystemDao.create(parentChildCs);
|
||||
parentChildCs2Id = ((ResourceTable)parentChildCsOutcome.getEntity()).getId();
|
||||
|
||||
}
|
||||
|
||||
|
@ -770,5 +782,41 @@ public class ResourceProviderR4CodeSystemVersionedTest extends BaseResourceProvi
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testUpdateCodeSystemName() throws IOException {
|
||||
|
||||
CodeSystem initialCodeSystem = myClient.read().resource(CodeSystem.class).withId(parentChildCs1Id).execute();
|
||||
assertEquals("Parent Child CodeSystem 1", initialCodeSystem.getName());
|
||||
initialCodeSystem.setName("Updated Parent Child CodeSystem 1");
|
||||
String encoded = myFhirCtx.newJsonParser().encodeResourceToString(initialCodeSystem);
|
||||
HttpPut putRequest = new HttpPut(ourServerBase + "/CodeSystem/" + parentChildCs1Id);
|
||||
putRequest.setEntity(new StringEntity(encoded, ContentType.parse("application/json+fhir")));
|
||||
CloseableHttpResponse resp = ourHttpClient.execute(putRequest);
|
||||
try {
|
||||
assertEquals(200, resp.getStatusLine().getStatusCode());
|
||||
} finally {
|
||||
IOUtils.closeQuietly(resp);
|
||||
}
|
||||
|
||||
CodeSystem updatedCodeSystem = myClient.read().resource(CodeSystem.class).withId(parentChildCs1Id).execute();
|
||||
assertEquals("Updated Parent Child CodeSystem 1", updatedCodeSystem.getName());
|
||||
|
||||
initialCodeSystem = myClient.read().resource(CodeSystem.class).withId(parentChildCs2Id).execute();
|
||||
assertEquals("Parent Child CodeSystem 2", initialCodeSystem.getName());
|
||||
initialCodeSystem.setName("Updated Parent Child CodeSystem 2");
|
||||
encoded = myFhirCtx.newJsonParser().encodeResourceToString(initialCodeSystem);
|
||||
putRequest = new HttpPut(ourServerBase + "/CodeSystem/" + parentChildCs2Id);
|
||||
putRequest.setEntity(new StringEntity(encoded, ContentType.parse("application/json+fhir")));
|
||||
resp = ourHttpClient.execute(putRequest);
|
||||
try {
|
||||
assertEquals(200, resp.getStatusLine().getStatusCode());
|
||||
} finally {
|
||||
IOUtils.closeQuietly(resp);
|
||||
}
|
||||
|
||||
updatedCodeSystem = myClient.read().resource(CodeSystem.class).withId(parentChildCs2Id).execute();
|
||||
assertEquals("Updated Parent Child CodeSystem 2", updatedCodeSystem.getName());
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
|
@ -43,6 +43,8 @@ import org.hl7.fhir.r4.model.ValueSet.FilterOperator;
|
|||
import org.hl7.fhir.r4.model.codesystems.HttpVerb;
|
||||
import org.junit.jupiter.api.AfterEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.springframework.data.domain.PageRequest;
|
||||
import org.springframework.data.domain.Slice;
|
||||
import org.springframework.transaction.TransactionStatus;
|
||||
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
|
||||
import org.springframework.transaction.support.TransactionTemplate;
|
||||
|
@ -245,6 +247,8 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
|
||||
loadAndPersistCodeSystemAndValueSet();
|
||||
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
Slice<TermValueSet> page = myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED);
|
||||
assertEquals(1, page.getContent().size());
|
||||
|
||||
Parameters respParam = myClient
|
||||
.operation()
|
||||
|
@ -297,6 +301,8 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
|
||||
loadAndPersistCodeSystemAndValueSet();
|
||||
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
Slice<TermValueSet> page = myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED);
|
||||
assertEquals(1, page.getContent().size());
|
||||
|
||||
Parameters respParam = myClient
|
||||
.operation()
|
||||
|
@ -356,6 +362,8 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
|
||||
loadAndPersistCodeSystemAndValueSet();
|
||||
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
Slice<TermValueSet> page = myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 10), TermValueSetPreExpansionStatusEnum.EXPANDED);
|
||||
assertEquals(1, page.getContent().size());
|
||||
|
||||
Parameters respParam = myClient
|
||||
.operation()
|
||||
|
@ -1093,7 +1101,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
public static CodeSystem createExternalCs(IFhirResourceDao<CodeSystem> theCodeSystemDao, IResourceTableDao theResourceTableDao, ITermCodeSystemStorageSvc theTermCodeSystemStorageSvc, ServletRequestDetails theRequestDetails, String theCodeSystemVersion) {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
codeSystem.setVersion(theCodeSystemVersion);
|
||||
IIdType id = theCodeSystemDao.create(codeSystem, theRequestDetails).getId().toUnqualified();
|
||||
|
|
File diff suppressed because it is too large
Load Diff
|
@ -1,6 +1,5 @@
|
|||
package ca.uhn.fhir.jpa.term;
|
||||
|
||||
import ca.uhn.fhir.jpa.api.config.DaoConfig;
|
||||
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
|
||||
import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
|
||||
|
@ -54,7 +53,6 @@ public class TermDeferredStorageSvcImplTest {
|
|||
TermDeferredStorageSvcImpl svc = new TermDeferredStorageSvcImpl();
|
||||
svc.setTransactionManagerForUnitTest(myTxManager);
|
||||
svc.setCodeSystemStorageSvcForUnitTest(myTermConceptStorageSvc);
|
||||
svc.setDaoConfigForUnitTest(new DaoConfig());
|
||||
|
||||
when(myTermCodeSystemVersionDao.findById(anyLong())).thenReturn(Optional.of(myTermCodeSystemVersion));
|
||||
svc.setCodeSystemVersionDaoForUnitTest(myTermCodeSystemVersionDao);
|
||||
|
@ -78,7 +76,6 @@ public class TermDeferredStorageSvcImplTest {
|
|||
TermDeferredStorageSvcImpl svc = new TermDeferredStorageSvcImpl();
|
||||
svc.setTransactionManagerForUnitTest(myTxManager);
|
||||
svc.setCodeSystemStorageSvcForUnitTest(myTermConceptStorageSvc);
|
||||
svc.setDaoConfigForUnitTest(new DaoConfig());
|
||||
|
||||
when(myTermCodeSystemVersionDao.findById(anyLong())).thenReturn(Optional.empty());
|
||||
svc.setCodeSystemVersionDaoForUnitTest(myTermCodeSystemVersionDao);
|
||||
|
@ -104,7 +101,6 @@ public class TermDeferredStorageSvcImplTest {
|
|||
TermDeferredStorageSvcImpl svc = new TermDeferredStorageSvcImpl();
|
||||
svc.setTransactionManagerForUnitTest(myTxManager);
|
||||
svc.setCodeSystemStorageSvcForUnitTest(myTermConceptStorageSvc);
|
||||
svc.setDaoConfigForUnitTest(new DaoConfig());
|
||||
|
||||
// Simulate the case where an exception is thrown despite a valid code system version.
|
||||
when(myTermCodeSystemVersionDao.findById(anyLong())).thenReturn(Optional.of(myTermCodeSystemVersion));
|
||||
|
@ -129,7 +125,6 @@ public class TermDeferredStorageSvcImplTest {
|
|||
svc.setTransactionManagerForUnitTest(myTxManager);
|
||||
svc.setCodeSystemStorageSvcForUnitTest(myTermConceptStorageSvc);
|
||||
svc.setConceptDaoForUnitTest(myConceptDao);
|
||||
svc.setDaoConfigForUnitTest(new DaoConfig());
|
||||
svc.setProcessDeferred(true);
|
||||
svc.addConceptLinkToStorageQueue(conceptLink);
|
||||
svc.saveDeferred();
|
||||
|
|
|
@ -1942,6 +1942,58 @@ public class TerminologySvcImplR4Test extends BaseTermR4Test {
|
|||
});
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testUpdateCodeSystemUrlAndVersion() {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(CS_URL);
|
||||
codeSystem.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
|
||||
codeSystem
|
||||
.addConcept().setCode("A").setDisplay("Code A");
|
||||
codeSystem
|
||||
.addConcept().setCode("B").setDisplay("Code A");
|
||||
|
||||
codeSystem.setVersion("1");
|
||||
|
||||
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
|
||||
|
||||
Set<TermConcept> codes = myTermSvc.findCodesBelow(id.getIdPartAsLong(), id.getVersionIdPartAsLong(), "A");
|
||||
assertThat(toCodes(codes), containsInAnyOrder("A"));
|
||||
|
||||
codes = myTermSvc.findCodesBelow(id.getIdPartAsLong(), id.getVersionIdPartAsLong(), "B");
|
||||
assertThat(toCodes(codes), containsInAnyOrder("B"));
|
||||
|
||||
runInTransaction(() -> {
|
||||
List<TermCodeSystemVersion> termCodeSystemVersions = myTermCodeSystemVersionDao.findAll();
|
||||
assertEquals(termCodeSystemVersions.size(), 1);
|
||||
TermCodeSystemVersion termCodeSystemVersion_1 = termCodeSystemVersions.get(0);
|
||||
assertEquals(termCodeSystemVersion_1.getConcepts().size(), 2);
|
||||
Set<TermConcept> termConcepts = new HashSet<>(termCodeSystemVersion_1.getConcepts());
|
||||
assertThat(toCodes(termConcepts), containsInAnyOrder("A", "B"));
|
||||
|
||||
TermCodeSystem termCodeSystem = myTermCodeSystemDao.findByResourcePid(id.getIdPartAsLong());
|
||||
assertEquals("1", termCodeSystem.getCurrentVersion().getCodeSystemVersionId());
|
||||
|
||||
});
|
||||
|
||||
codeSystem.setVersion("2");
|
||||
codeSystem.setUrl(CS_URL_2);
|
||||
|
||||
IIdType id_v2 = myCodeSystemDao.update(codeSystem, mySrd).getId().toUnqualified();
|
||||
|
||||
runInTransaction(() -> {
|
||||
List<TermCodeSystemVersion> termCodeSystemVersions_updated = myTermCodeSystemVersionDao.findAll();
|
||||
assertEquals(termCodeSystemVersions_updated.size(), 1);
|
||||
TermCodeSystemVersion termCodeSystemVersion_2 = termCodeSystemVersions_updated.get(0);
|
||||
assertEquals(termCodeSystemVersion_2.getConcepts().size(), 2);
|
||||
Set<TermConcept> termConcepts_updated = new HashSet<>(termCodeSystemVersion_2.getConcepts());
|
||||
assertThat(toCodes(termConcepts_updated), containsInAnyOrder("A", "B"));
|
||||
|
||||
TermCodeSystem termCodeSystem = myTermCodeSystemDao.findByResourcePid(id_v2.getIdPartAsLong());
|
||||
assertEquals("2", termCodeSystem.getCurrentVersion().getCodeSystemVersionId());
|
||||
assertEquals(CS_URL_2, termCodeSystem.getCodeSystemUri());
|
||||
});
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testUpdateCodeSystemContentModeNotPresent() {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
|
|
|
@ -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(), nullable(String.class), anyCollection());
|
||||
verify(myValueSetCodeAccumulator, times(9)).includeConceptWithDesignations(anyString(), anyString(), anyString(), nullable(String.class), anyCollection());
|
||||
}
|
||||
|
||||
|
||||
|
|
|
@ -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(), nullable(String.class), anyCollection());
|
||||
verify(myValueSetCodeAccumulator, times(9)).includeConceptWithDesignations(anyString(), anyString(), anyString(), nullable(String.class), anyCollection());
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
|
@ -141,6 +141,11 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
|
|||
|
||||
//EMPI Target Type
|
||||
empiLink.addColumn("20200727.1","TARGET_TYPE").nullable().type(ColumnTypeEnum.STRING, EmpiLink.TARGET_TYPE_LENGTH);
|
||||
|
||||
//Term CodeSystem Version
|
||||
Builder.BuilderWithTableName trmCodeSystemVer = version.onTable("TRM_CODESYSTEM_VER");
|
||||
trmCodeSystemVer.addIndex("20200916.1", "IDX_CODESYSTEM_AND_VER").unique(true).withColumns("CODESYSTEM_PID", "CS_VERSION_ID");
|
||||
|
||||
}
|
||||
|
||||
protected void init510_20200725() {
|
||||
|
|
Loading…
Reference in New Issue