Merge remote-tracking branch 'remotes/origin/im_20200728_term_multi_version_support' into feature_2020_09_02_term_multi_version_support
This commit is contained in:
commit
3add1320b7
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@ -144,11 +144,13 @@ 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.cannotUpdateVersionForExistingCodeSystemVersion=Updated CodeSystem has wrong version id. Existing CodeSystem resource has 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.cannotCreateDuplicateConceptMapUrlAndVersion=Can not create multiple ConceptMap resources with ConceptMap.url "{0}", ConceptMap.version "{1}", already have one with resource ID: {2}
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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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ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateValueSetUrlAndVersion=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.cannotUpdateUrlOrVersionForValueSetResource=Cannot update URL or version for ValueSet resource. Existing ValueSet resource with resource ID {0} found with ValueSet.url "{1}" and ValueSet.version "{2}"
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ca.uhn.fhir.jpa.patch.JsonPatchUtils.failedToApplyPatch=Failed to apply JSON patch to {0}: {1}
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@ -1,28 +0,0 @@
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package ca.uhn.fhir.jpa.dao;
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import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
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import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
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import ca.uhn.fhir.jpa.entity.TermCodeSystem;
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import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
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import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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public class HapiFhirResourceDaoCodeSystemUtil {
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static public void deleteCodeSystemEntities(ITermCodeSystemDao theCsDao, ITermCodeSystemVersionDao theCsvDao,
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ITermDeferredStorageSvc theTermDeferredStorageSvc, String theCodeSystemUrl,
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String theCodeSystemVersion) {
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if (isNotBlank(theCodeSystemUrl)) {
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TermCodeSystem persCs = theCsDao.findByCodeSystemUri(theCodeSystemUrl);
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if (persCs != null) {
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if (theCodeSystemVersion != null) {
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TermCodeSystemVersion persCsVersion = theCsvDao.findByCodeSystemPidAndVersion(persCs.getPid(), theCodeSystemVersion);
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theTermDeferredStorageSvc.deleteCodeSystemVersion(persCsVersion);
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} else {
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theTermDeferredStorageSvc.deleteCodeSystem(persCs);
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}
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}
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}
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}
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}
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@ -28,6 +28,7 @@ import org.springframework.data.jpa.repository.JpaRepository;
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import org.springframework.data.jpa.repository.Query;
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import org.springframework.data.repository.query.Param;
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import java.util.List;
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import java.util.Optional;
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public interface ITermValueSetDao extends JpaRepository<TermValueSet, Long> {
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@ -41,4 +42,14 @@ public interface ITermValueSetDao extends JpaRepository<TermValueSet, Long> {
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@Query("SELECT vs FROM TermValueSet vs WHERE vs.myExpansionStatus = :expansion_status")
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Slice<TermValueSet> findByExpansionStatus(Pageable pageable, @Param("expansion_status") TermValueSetPreExpansionStatusEnum theExpansionStatus);
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@Query(value="SELECT vs FROM TermValueSet vs INNER JOIN ResourceTable r ON r.myId = vs.myResourcePid WHERE vs.myUrl = :url ORDER BY r.myUpdated DESC")
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List<TermValueSet> findTermValueSetByUrl(Pageable thePage, @Param("url") String theUrl);
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@Query("SELECT vs FROM TermValueSet vs WHERE vs.myUrl = :url AND vs.myVersion IS NULL")
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Optional<TermValueSet> findTermValueSetByUrlAndNullVersion(@Param("url") String theUrl);
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@Query("SELECT vs FROM TermValueSet vs WHERE vs.myUrl = :url AND vs.myVersion = :version")
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Optional<TermValueSet> findTermValueSetByUrlAndVersion(@Param("url") String theUrl, @Param("version") String theVersion);
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}
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@ -25,10 +25,6 @@ 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.jpa.api.dao.IFhirResourceDaoCodeSystem;
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import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
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import ca.uhn.fhir.jpa.dao.HapiFhirResourceDaoCodeSystemUtil;
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import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
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import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
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import ca.uhn.fhir.jpa.entity.TermCodeSystem;
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import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
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import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
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import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
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@ -67,10 +63,6 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
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@Autowired
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protected ITermDeferredStorageSvc myTermDeferredStorageSvc;
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@Autowired
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private ITermCodeSystemDao myCsDao;
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@Autowired
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private ITermCodeSystemVersionDao myCsvDao;
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@Autowired
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private IValidationSupport myValidationSupport;
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@Autowired
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private FhirContext myFhirContext;
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@ -155,8 +147,7 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
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protected void preDelete(CodeSystem theResourceToDelete, ResourceTable theEntityToDelete) {
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super.preDelete(theResourceToDelete, theEntityToDelete);
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HapiFhirResourceDaoCodeSystemUtil.deleteCodeSystemEntities(myCsDao, myCsvDao, myTermDeferredStorageSvc, theResourceToDelete.getUrl(),
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theResourceToDelete.getVersion());
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myTermDeferredStorageSvc.deleteCodeSystemForResource(theEntityToDelete);
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}
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@ -65,9 +65,6 @@ 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 ITermReadSvc myHapiTerminologySvc;
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@Autowired
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private DefaultProfileValidationSupport myDefaultProfileValidationSupport;
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@ -283,12 +280,12 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueS
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try {
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ValueSet valueSet = (ValueSet) theResource;
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org.hl7.fhir.r4.model.ValueSet converted = convertValueSet(valueSet);
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myHapiTerminologySvc.storeTermValueSet(retVal, converted);
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myTerminologySvc.storeTermValueSet(retVal, converted);
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} catch (FHIRException fe) {
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throw new InternalErrorException(fe);
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}
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} else {
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myHapiTerminologySvc.deleteValueSetAndChildren(retVal);
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myTerminologySvc.deleteValueSetAndChildren(retVal);
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}
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}
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@ -25,10 +25,6 @@ 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.jpa.api.dao.IFhirResourceDaoCodeSystem;
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import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
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import ca.uhn.fhir.jpa.dao.HapiFhirResourceDaoCodeSystemUtil;
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import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
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import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
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import ca.uhn.fhir.jpa.entity.TermCodeSystem;
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import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
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import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
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import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
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@ -60,10 +56,6 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoCodeSystemR4.class);
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@Autowired
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private ITermCodeSystemDao myCsDao;
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@Autowired
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private ITermCodeSystemVersionDao myCsvDao;
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@Autowired
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private IValidationSupport myValidationSupport;
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@Autowired
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@ -153,8 +145,7 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
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protected void preDelete(CodeSystem theResourceToDelete, ResourceTable theEntityToDelete) {
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super.preDelete(theResourceToDelete, theEntityToDelete);
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HapiFhirResourceDaoCodeSystemUtil.deleteCodeSystemEntities(myCsDao, myCsvDao, myTermDeferredStorageSvc, theResourceToDelete.getUrl(),
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theResourceToDelete.getVersion());
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myTermDeferredStorageSvc.deleteCodeSystemForResource(theEntityToDelete);
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}
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@ -60,9 +60,6 @@ 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 ITermReadSvc myHapiTerminologySvc;
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@Autowired
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private DefaultProfileValidationSupport myDefaultProfileValidationSupport;
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@ -113,17 +110,14 @@ public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet>
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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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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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ConceptSetFilterComponent filter = source.getCompose().addInclude().addValueSet(theUri).addFilter();
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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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} else {
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source.getCompose().addInclude().addValueSet(theUri);
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}
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ValueSet retVal = doExpand(source);
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@ -151,17 +145,14 @@ public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet>
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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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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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ConceptSetFilterComponent filter = source.getCompose().addInclude().addValueSet(theUri).addFilter();
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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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} else {
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source.getCompose().addInclude().addValueSet(theUri);
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}
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ValueSet retVal = doExpand(source, theOffset, theCount);
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@ -268,9 +259,9 @@ public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet>
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if (myDaoConfig.isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
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if (retVal.getDeleted() == null) {
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ValueSet valueSet = (ValueSet) theResource;
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myHapiTerminologySvc.storeTermValueSet(retVal, valueSet);
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myTerminologySvc.storeTermValueSet(retVal, valueSet);
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} else {
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myHapiTerminologySvc.deleteValueSetAndChildren(retVal);
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myTerminologySvc.deleteValueSetAndChildren(retVal);
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}
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}
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@ -25,11 +25,7 @@ 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.jpa.api.dao.IFhirResourceDaoCodeSystem;
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import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
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import ca.uhn.fhir.jpa.dao.HapiFhirResourceDaoCodeSystemUtil;
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import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
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import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
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import ca.uhn.fhir.jpa.dao.index.IdHelperService;
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import ca.uhn.fhir.jpa.entity.TermCodeSystem;
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import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
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import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
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import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
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@ -65,10 +61,6 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
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@Autowired
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protected IdHelperService myIdHelperService;
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@Autowired
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private ITermCodeSystemDao myCsDao;
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@Autowired
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private ITermCodeSystemVersionDao myCsvDao;
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@Autowired
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private IValidationSupport myValidationSupport;
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@Autowired
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private FhirContext myFhirContext;
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@ -155,8 +147,7 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
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protected void preDelete(CodeSystem theResourceToDelete, ResourceTable theEntityToDelete) {
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super.preDelete(theResourceToDelete, theEntityToDelete);
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HapiFhirResourceDaoCodeSystemUtil.deleteCodeSystemEntities(myCsDao, myCsvDao, myTermDeferredStorageSvc, theResourceToDelete.getUrl(),
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theResourceToDelete.getVersion());
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myTermDeferredStorageSvc.deleteCodeSystemForResource(theEntityToDelete);
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}
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|
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@ -64,9 +64,6 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
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public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
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@Autowired
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private ITermReadSvc myHapiTerminologySvc;
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@Autowired
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@Qualifier("myDefaultProfileValidationSupport")
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private IValidationSupport myDefaultProfileValidationSupport;
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|
@ -267,9 +264,9 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet>
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if (myDaoConfig.isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
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if (retVal.getDeleted() == null) {
|
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ValueSet valueSet = (ValueSet) theResource;
|
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myHapiTerminologySvc.storeTermValueSet(retVal, org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSet));
|
||||
myTerminologySvc.storeTermValueSet(retVal, org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSet));
|
||||
} else {
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myHapiTerminologySvc.deleteValueSetAndChildren(retVal);
|
||||
myTerminologySvc.deleteValueSetAndChildren(retVal);
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||||
}
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}
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||||
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||||
|
|
|
@ -37,7 +37,7 @@ import static org.apache.commons.lang3.StringUtils.left;
|
|||
import static org.apache.commons.lang3.StringUtils.length;
|
||||
|
||||
@Table(name = "TRM_VALUESET", uniqueConstraints = {
|
||||
@UniqueConstraint(name = "IDX_VALUESET_URL", columnNames = {"URL"})
|
||||
@UniqueConstraint(name = "IDX_VALUESET_URL", columnNames = {"URL", "VER"})
|
||||
})
|
||||
@Entity()
|
||||
public class TermValueSet implements Serializable {
|
||||
|
@ -46,6 +46,7 @@ public class TermValueSet implements Serializable {
|
|||
public static final int MAX_EXPANSION_STATUS_LENGTH = 50;
|
||||
public static final int MAX_NAME_LENGTH = 200;
|
||||
public static final int MAX_URL_LENGTH = 200;
|
||||
static final int MAX_VER_LENGTH = 200;
|
||||
|
||||
@Id()
|
||||
@SequenceGenerator(name = "SEQ_VALUESET_PID", sequenceName = "SEQ_VALUESET_PID")
|
||||
|
@ -56,6 +57,9 @@ public class TermValueSet implements Serializable {
|
|||
@Column(name = "URL", nullable = false, length = MAX_URL_LENGTH)
|
||||
private String myUrl;
|
||||
|
||||
@Column(name = "VER", nullable = true, length = MAX_VER_LENGTH)
|
||||
private String myVersion;
|
||||
|
||||
@OneToOne()
|
||||
@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_TRMVALUESET_RES"))
|
||||
private ResourceTable myResource;
|
||||
|
@ -183,6 +187,17 @@ public class TermValueSet implements Serializable {
|
|||
myExpansionStatus = theExpansionStatus;
|
||||
}
|
||||
|
||||
public String getVersion() {
|
||||
return myVersion;
|
||||
}
|
||||
|
||||
public TermValueSet setVersion(String theVersion) {
|
||||
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theVersion, MAX_VER_LENGTH,
|
||||
"Version exceeds maximum length (" + MAX_VER_LENGTH + "): " + length(theVersion));
|
||||
myVersion = theVersion;
|
||||
return this;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean equals(Object theO) {
|
||||
if (this == theO) return true;
|
||||
|
|
|
@ -332,7 +332,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
deleteConceptMap(theResourceTable);
|
||||
}
|
||||
|
||||
public void deleteValueSet(ResourceTable theResourceTable) {
|
||||
public void deleteValueSetForResource(ResourceTable theResourceTable) {
|
||||
// Get existing entity so it can be deleted.
|
||||
Optional<TermValueSet> optionalExistingTermValueSetById = myValueSetDao.findByResourcePid(theResourceTable.getId());
|
||||
|
||||
|
@ -350,7 +350,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
@Override
|
||||
@Transactional
|
||||
public void deleteValueSetAndChildren(ResourceTable theResourceTable) {
|
||||
deleteValueSet(theResourceTable);
|
||||
deleteValueSetForResource(theResourceTable);
|
||||
}
|
||||
|
||||
private ValueSet expandValueSetInMemory(ValueSetExpansionOptions theExpansionOptions, ValueSet theValueSetToExpand, VersionIndependentConcept theWantConceptOrNull) {
|
||||
|
@ -392,7 +392,12 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
|
||||
Optional<TermValueSet> optionalTermValueSet;
|
||||
if (theValueSetToExpand.hasUrl()) {
|
||||
optionalTermValueSet = myValueSetDao.findByUrl(theValueSetToExpand.getUrl());
|
||||
if (theValueSetToExpand.hasVersion()) {
|
||||
optionalTermValueSet = myValueSetDao.findTermValueSetByUrlAndVersion(theValueSetToExpand.getUrl(), theValueSetToExpand.getVersion());
|
||||
} else {
|
||||
List<TermValueSet> termValueSets = myValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 1), theValueSetToExpand.getUrl());
|
||||
optionalTermValueSet = Optional.of(termValueSets.get(0));
|
||||
}
|
||||
} else {
|
||||
optionalTermValueSet = Optional.empty();
|
||||
}
|
||||
|
@ -1795,38 +1800,52 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
ValidateUtil.isTrueOrThrowInvalidRequest(theResourceTable != null, "No resource supplied");
|
||||
ValidateUtil.isNotBlankOrThrowUnprocessableEntity(theValueSet.getUrl(), "ValueSet has no value for ValueSet.url");
|
||||
|
||||
/*
|
||||
* Get CodeSystem and validate CodeSystemVersion
|
||||
*/
|
||||
TermValueSet termValueSet = new TermValueSet();
|
||||
termValueSet.setResource(theResourceTable);
|
||||
termValueSet.setUrl(theValueSet.getUrl());
|
||||
termValueSet.setVersion(theValueSet.getVersion());
|
||||
termValueSet.setName(theValueSet.hasName() ? theValueSet.getName() : null);
|
||||
|
||||
// We delete old versions; we don't support versioned ValueSets.
|
||||
deleteValueSet(theResourceTable);
|
||||
// Delete version being replaced
|
||||
deleteValueSetForResource(theResourceTable);
|
||||
|
||||
/*
|
||||
* Do the upload.
|
||||
*/
|
||||
String url = termValueSet.getUrl();
|
||||
Optional<TermValueSet> optionalExistingTermValueSetByUrl = myValueSetDao.findByUrl(url);
|
||||
String version = termValueSet.getVersion();
|
||||
Optional<TermValueSet> optionalExistingTermValueSetByUrl;
|
||||
if (version != null) {
|
||||
optionalExistingTermValueSetByUrl = myValueSetDao.findTermValueSetByUrlAndVersion(url, version);
|
||||
} else {
|
||||
optionalExistingTermValueSetByUrl = myValueSetDao.findTermValueSetByUrlAndNullVersion(url);
|
||||
}
|
||||
if (!optionalExistingTermValueSetByUrl.isPresent()) {
|
||||
|
||||
termValueSet = myValueSetDao.save(termValueSet);
|
||||
myValueSetDao.save(termValueSet);
|
||||
|
||||
} else {
|
||||
TermValueSet existingTermValueSet = optionalExistingTermValueSetByUrl.get();
|
||||
|
||||
String msg = myContext.getLocalizer().getMessage(
|
||||
String msg;
|
||||
if (version != null) {
|
||||
msg = myContext.getLocalizer().getMessage(
|
||||
BaseTermReadSvcImpl.class,
|
||||
"cannotCreateDuplicateValueSetUrlAndVersion",
|
||||
url, version, existingTermValueSet.getResource().getIdDt().toUnqualifiedVersionless().getValue());
|
||||
} else {
|
||||
msg = myContext.getLocalizer().getMessage(
|
||||
BaseTermReadSvcImpl.class,
|
||||
"cannotCreateDuplicateValueSetUrl",
|
||||
url,
|
||||
existingTermValueSet.getResource().getIdDt().toUnqualifiedVersionless().getValue());
|
||||
|
||||
url, existingTermValueSet.getResource().getIdDt().toUnqualifiedVersionless().getValue());
|
||||
}
|
||||
throw new UnprocessableEntityException(msg);
|
||||
}
|
||||
|
||||
ourLog.info("Done storing TermValueSet[{}] for {}", termValueSet.getId(), theValueSet.getIdElement().toVersionless().getValueAsString());
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB,
|
||||
IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB) {
|
||||
|
|
|
@ -238,17 +238,6 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
|
|||
ourLog.info(" * Deleting code system version {}", theCodeSystemVersion.getCodeSystemVersionId());
|
||||
deleteCodeSystemVersion(theCodeSystemVersion.getPid());
|
||||
|
||||
// Check if the version deleted is the current version. If so, delete TermCodeSystem as well.
|
||||
TermCodeSystem termCodeSystem = theCodeSystemVersion.getCodeSystem();
|
||||
TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
|
||||
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
|
||||
txTemplate.executeWithoutResult(t -> {
|
||||
if (myCodeSystemVersionDao.findByCodeSystemPid(termCodeSystem.getPid()).size() == 0) {
|
||||
ourLog.info(" * Deleting code system {}", termCodeSystem.getPid());
|
||||
deleteCodeSystem(termCodeSystem);
|
||||
}
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
|
@ -709,27 +698,29 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
|
|||
}
|
||||
|
||||
private void checkForCodeSystemVersionDuplicate(TermCodeSystem theCodeSystem, String theSystemUri, String theSystemVersionId, ResourceTable theCodeSystemResourceTable) {
|
||||
// Check if CodeSystemVersion entity already exists.
|
||||
TermCodeSystemVersion codeSystemVersionEntity;
|
||||
String msg = null;
|
||||
if (theSystemVersionId == null) {
|
||||
// Check if a non-versioned TermCodeSystemVersion entity already exists for this TermCodeSystem.
|
||||
codeSystemVersionEntity = myCodeSystemVersionDao.findByCodeSystemPidVersionIsNull(theCodeSystem.getPid());
|
||||
if (codeSystemVersionEntity != null) {
|
||||
msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "cannotCreateDuplicateCodeSystemUrl", theSystemUri, codeSystemVersionEntity.getResource().getIdDt().toUnqualifiedVersionless().getValue());
|
||||
}
|
||||
} else {
|
||||
// Check if a TermCodeSystemVersion entity already exists for this TermCodeSystem and version.
|
||||
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, "cannotCreateDuplicateCodeSystemUrlAndVersion", theSystemUri, theSystemVersionId, codeSystemVersionEntity.getResource().getIdDt().toUnqualifiedVersionless().getValue());
|
||||
msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "cannotUpdateUrlOrVersionForCodeSystemResource", codeSystemVersionEntity.getResource().getIdDt().toUnqualifiedVersionless().getValue(), theSystemUri, theSystemVersionId);
|
||||
throw new UnprocessableEntityException(msg);
|
||||
}
|
||||
}
|
||||
}
|
||||
// Throw exception if the CodeSystemVersion is being duplicated.
|
||||
// Throw exception if the TermCodeSystemVersion is being duplicated.
|
||||
if (codeSystemVersionEntity != null) {
|
||||
if (!ObjectUtil.equals(codeSystemVersionEntity.getResource().getId(), theCodeSystemResourceTable.getId())) {
|
||||
throw new UnprocessableEntityException(msg);
|
||||
|
|
|
@ -29,6 +29,7 @@ import ca.uhn.fhir.jpa.entity.TermCodeSystem;
|
|||
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
|
||||
import ca.uhn.fhir.jpa.entity.TermConcept;
|
||||
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.model.sched.HapiJob;
|
||||
import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
|
||||
import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
|
||||
|
@ -119,8 +120,15 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
|
|||
|
||||
@Override
|
||||
@Transactional
|
||||
public void deleteCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
|
||||
myDefferedCodeSystemVersionsDeletions.add(theCodeSystemVersion);
|
||||
public void deleteCodeSystemForResource(ResourceTable theCodeSystemToDelete) {
|
||||
TermCodeSystemVersion codeSystemVersionToDelete = myCodeSystemVersionDao.findByCodeSystemResourcePid(theCodeSystemToDelete.getResourceId());
|
||||
if (codeSystemVersionToDelete != null) {
|
||||
myDefferedCodeSystemVersionsDeletions.add(codeSystemVersionToDelete);
|
||||
}
|
||||
TermCodeSystem codeSystemToDelete = myCodeSystemDao.findByResourcePid(theCodeSystemToDelete.getResourceId());
|
||||
if (codeSystemToDelete != null) {
|
||||
deleteCodeSystem(codeSystemToDelete);
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
|
@ -219,6 +227,7 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
|
|||
myDeferredConceptMaps.clear();
|
||||
myDeferredConcepts.clear();
|
||||
myDefferedCodeSystemsDeletions.clear();
|
||||
myConceptLinksToSaveLater.clear();
|
||||
}
|
||||
|
||||
@Transactional(propagation = Propagation.NEVER)
|
||||
|
|
|
@ -381,6 +381,7 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
|
|||
String codeSystemVersionId = theUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
|
||||
if (codeSystemVersionId != null) {
|
||||
loincCs.setVersion(codeSystemVersionId);
|
||||
loincCs.setId(loincCs.getId() + "-" + codeSystemVersionId);
|
||||
}
|
||||
} catch (IOException e) {
|
||||
throw new InternalErrorException("Failed to load loinc.xml", e);
|
||||
|
|
|
@ -42,13 +42,12 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
|
|||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ValueSetConceptAccumulator.class);
|
||||
|
||||
private TermValueSet myTermValueSet;
|
||||
private ITermValueSetDao myValueSetDao;
|
||||
private ITermValueSetConceptDao myValueSetConceptDao;
|
||||
private ITermValueSetConceptDesignationDao myValueSetConceptDesignationDao;
|
||||
final private ITermValueSetDao myValueSetDao;
|
||||
final private ITermValueSetConceptDao myValueSetConceptDao;
|
||||
final private ITermValueSetConceptDesignationDao myValueSetConceptDesignationDao;
|
||||
private int myConceptsSaved;
|
||||
private int myDesignationsSaved;
|
||||
private int myConceptsExcluded;
|
||||
private int myCount;
|
||||
|
||||
public ValueSetConceptAccumulator(@Nonnull TermValueSet theTermValueSet, @Nonnull ITermValueSetDao theValueSetDao, @Nonnull ITermValueSetConceptDao theValueSetConceptDao, @Nonnull ITermValueSetConceptDesignationDao theValueSetConceptDesignationDao) {
|
||||
myTermValueSet = theTermValueSet;
|
||||
|
|
|
@ -24,6 +24,7 @@ import ca.uhn.fhir.jpa.entity.TermCodeSystem;
|
|||
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
|
||||
import ca.uhn.fhir.jpa.entity.TermConcept;
|
||||
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import org.hl7.fhir.r4.model.ConceptMap;
|
||||
import org.hl7.fhir.r4.model.ValueSet;
|
||||
|
||||
|
@ -55,7 +56,7 @@ public interface ITermDeferredStorageSvc {
|
|||
|
||||
void deleteCodeSystem(TermCodeSystem theCodeSystem);
|
||||
|
||||
void deleteCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion);
|
||||
void deleteCodeSystemForResource(ResourceTable theCodeSystemResourceToDelete);
|
||||
|
||||
/**
|
||||
* This is mostly here for unit tests - Saves any and all deferred concepts and links
|
||||
|
|
|
@ -52,7 +52,6 @@ import ca.uhn.fhir.rest.api.Constants;
|
|||
import ca.uhn.fhir.rest.api.EncodingEnum;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
import ca.uhn.fhir.util.UrlUtil;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.hibernate.search.jpa.FullTextEntityManager;
|
||||
|
|
|
@ -80,6 +80,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
|
|||
private CodeSystem createExternalCs() {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
codeSystem.setName("ACME Codes");
|
||||
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
|
||||
|
@ -124,6 +125,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
|
|||
private void createExternalCsLarge() {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
|
||||
|
||||
|
@ -165,6 +167,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
|
|||
private CodeSystem createExternalCsDogs() {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
|
||||
|
||||
|
@ -698,6 +701,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
|
|||
public void testLookupSnomed() {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl("http://snomed.info/sct");
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
|
||||
|
||||
|
|
|
@ -22,6 +22,7 @@ import org.springframework.transaction.annotation.Transactional;
|
|||
|
||||
import java.io.IOException;
|
||||
|
||||
import static org.awaitility.Awaitility.await;
|
||||
import static org.hamcrest.MatcherAssert.assertThat;
|
||||
import static org.hamcrest.Matchers.containsString;
|
||||
import static org.hamcrest.Matchers.not;
|
||||
|
@ -76,6 +77,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
|
|||
validationOutcome = myValueSetDao.validateCode(vsIdentifier, null, code, system, null, null, null, mySrd);
|
||||
assertEquals(false, validationOutcome.isOk());
|
||||
|
||||
await().until(() -> clearDeferredStorageQueue());
|
||||
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
|
||||
runInTransaction(() -> {
|
||||
|
@ -95,6 +97,16 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
|
|||
|
||||
}
|
||||
|
||||
private boolean clearDeferredStorageQueue() {
|
||||
|
||||
if(!myTerminologyDeferredStorageSvc.isStorageQueueEmpty()) {
|
||||
myTerminologyDeferredStorageSvc.saveAllDeferred();
|
||||
return false;
|
||||
} else {
|
||||
return true;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
@Disabled
|
||||
|
|
|
@ -64,7 +64,6 @@ import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
|
|||
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
|
||||
import ca.uhn.fhir.jpa.search.warm.ICacheWarmingSvc;
|
||||
import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryImpl;
|
||||
import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionRegistry;
|
||||
import ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl;
|
||||
import ca.uhn.fhir.jpa.term.TermDeferredStorageSvcImpl;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
|
||||
|
@ -81,7 +80,6 @@ import ca.uhn.fhir.rest.server.BasePagingProvider;
|
|||
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
|
||||
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
|
||||
import ca.uhn.fhir.test.utilities.ITestDataBuilder;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
import ca.uhn.fhir.util.UrlUtil;
|
||||
import ca.uhn.fhir.validation.FhirValidator;
|
||||
import ca.uhn.fhir.validation.ValidationResult;
|
||||
|
|
|
@ -136,10 +136,10 @@ public class FhirResourceDaoR4CodeSystemTest extends BaseJpaR4Test {
|
|||
// Attempt to delete second version
|
||||
myCodeSystemDao.delete(id_second, mySrd);
|
||||
|
||||
// Only the resource will be deleted initially
|
||||
// Only the resource will be deleted initially, but the URL for the TermCodeSystem will be cleared and not searchable.
|
||||
runInTransaction(() -> {
|
||||
assertEquals(1, myTermCodeSystemDao.count());
|
||||
assertNotNull(myTermCodeSystemDao.findByCodeSystemUri("http://foo"));
|
||||
assertNull(myTermCodeSystemDao.findByCodeSystemUri("http://foo"));
|
||||
assertEquals(1, myTermCodeSystemVersionDao.count());
|
||||
assertEquals(222, myTermConceptDao.count());
|
||||
List<ResourceTable> resourceList = myResourceTableDao.findAll();
|
||||
|
|
|
@ -209,6 +209,7 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest {
|
|||
private CodeSystem createExternalCs() {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
|
||||
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
|
||||
|
||||
|
|
|
@ -85,6 +85,7 @@ public class FhirResourceDaoR4TerminologyElasticsearchIT extends BaseJpaTest {
|
|||
public void testExpandWithIncludeContainingDashesInInclude() {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
|
||||
|
||||
|
|
|
@ -80,6 +80,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
private CodeSystem createExternalCs() {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
|
||||
|
||||
|
@ -129,6 +130,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
private CodeSystem createExternalCsDogs() {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
|
||||
|
||||
|
@ -159,6 +161,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
private void createExternalCsLarge() {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
|
||||
|
||||
|
@ -473,6 +476,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
public void testExpandWithIncludeContainingDashesInInclude() {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
|
||||
|
||||
|
@ -815,6 +819,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
public void testLookupSnomed() {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl("http://snomed.info/sct");
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
|
||||
|
||||
|
@ -828,7 +833,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
|
||||
StringType code = new StringType("ParentA");
|
||||
StringType system = new StringType("http://snomed.info/sct");
|
||||
IValidationSupport.LookupCodeResult outcome = myCodeSystemDao.lookupCode(code, system, null,null, mySrd);
|
||||
IValidationSupport.LookupCodeResult outcome = myCodeSystemDao.lookupCode(code, system, null, mySrd);
|
||||
assertEquals(true, outcome.isFound());
|
||||
}
|
||||
|
||||
|
|
|
@ -9,8 +9,6 @@ import ca.uhn.fhir.jpa.entity.TermValueSet;
|
|||
import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl;
|
||||
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcLoincTest;
|
||||
import ca.uhn.fhir.jpa.term.ZipCollectionBuilder;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
|
||||
|
@ -80,7 +78,6 @@ import static org.hamcrest.Matchers.containsString;
|
|||
import static org.hamcrest.Matchers.not;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertFalse;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
import static org.junit.jupiter.api.Assertions.fail;
|
||||
import static org.mockito.ArgumentMatchers.any;
|
||||
import static org.mockito.Mockito.mock;
|
||||
|
|
|
@ -69,7 +69,6 @@ import ca.uhn.fhir.rest.api.EncodingEnum;
|
|||
import ca.uhn.fhir.rest.server.BasePagingProvider;
|
||||
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
|
||||
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
import ca.uhn.fhir.util.UrlUtil;
|
||||
import ca.uhn.fhir.validation.FhirValidator;
|
||||
import ca.uhn.fhir.validation.ValidationResult;
|
||||
|
|
|
@ -13,7 +13,6 @@ import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
|
|||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
import ca.uhn.fhir.util.UrlUtil;
|
||||
import com.google.common.base.Charsets;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
|
@ -37,7 +36,6 @@ import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
|
|||
import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.junit.jupiter.api.AfterEach;
|
||||
import org.junit.jupiter.api.AfterAll;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.springframework.transaction.TransactionStatus;
|
||||
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
|
||||
|
@ -137,6 +135,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
runInTransaction(() -> {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(CS_URL);
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
|
||||
|
||||
|
@ -823,7 +822,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
codeSystem.setName("ACME Codes");
|
||||
codeSystem.setVersion("1.2.3.4");
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
IIdType id = theCodeSystemDao.create(codeSystem, theRequestDetails).getId().toUnqualified();
|
||||
|
||||
ResourceTable table = theResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalStateException::new);
|
||||
|
|
|
@ -25,9 +25,6 @@ public class ResourceProviderR4CodeSystemTest extends BaseResourceProviderR4Test
|
|||
CodeSystem cs = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
|
||||
myCodeSystemDao.create(cs, mySrd);
|
||||
|
||||
ValueSet upload = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
|
||||
myValueSetDao.create(upload, mySrd).getId().toUnqualifiedVersionless();
|
||||
|
||||
CodeSystem parentChildCs = new CodeSystem();
|
||||
parentChildCs.setUrl(SYSTEM_PARENTCHILD);
|
||||
parentChildCs.setStatus(Enumerations.PublicationStatus.ACTIVE);
|
||||
|
|
|
@ -37,9 +37,6 @@ public class ResourceProviderR4CodeSystemVersionedTest extends BaseResourceProvi
|
|||
cs = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs-v2.xml");
|
||||
myCodeSystemDao.create(cs, mySrd);
|
||||
|
||||
ValueSet upload = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
|
||||
myValueSetDao.create(upload, mySrd).getId().toUnqualifiedVersionless();
|
||||
|
||||
CodeSystem parentChildCs = new CodeSystem();
|
||||
parentChildCs.setUrl(SYSTEM_PARENTCHILD);
|
||||
parentChildCs.setVersion("1");
|
||||
|
|
|
@ -16,7 +16,6 @@ import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
|
|||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
|
||||
import ca.uhn.fhir.util.ParametersUtil;
|
||||
import ca.uhn.fhir.util.UrlUtil;
|
||||
import com.google.common.base.Charsets;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
|
@ -1060,6 +1059,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
public static CodeSystem createExternalCs(IFhirResourceDao<CodeSystem> theCodeSystemDao, IResourceTableDao theResourceTableDao, ITermCodeSystemStorageSvc theTermCodeSystemStorageSvc, ServletRequestDetails theRequestDetails) {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
IIdType id = theCodeSystemDao.create(codeSystem, theRequestDetails).getId().toUnqualified();
|
||||
|
||||
|
@ -1093,6 +1093,7 @@ 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();
|
||||
|
|
|
@ -106,7 +106,7 @@ public class TerminologyUploaderProviderR4Test extends BaseResourceProviderR4Tes
|
|||
ourLog.info(resp);
|
||||
|
||||
assertThat(((IntegerType) respParam.getParameter().get(1).getValue()).getValue(), greaterThan(1));
|
||||
assertThat(((Reference) respParam.getParameter().get(2).getValue()).getReference(), matchesPattern("CodeSystem\\/[a-zA-Z0-9]+"));
|
||||
assertThat(((Reference) respParam.getParameter().get(2).getValue()).getReference(), matchesPattern("CodeSystem\\/[a-zA-Z0-9\\.\\-]+"));
|
||||
|
||||
/*
|
||||
* Try uploading a second time
|
||||
|
|
|
@ -1405,6 +1405,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
|
|||
public static CodeSystem createExternalCs(IFhirResourceDao<CodeSystem> theCodeSystemDao, IResourceTableDao theResourceTableDao, ITermCodeSystemStorageSvc theTermCodeSystemStorageSvc, ServletRequestDetails theRequestDetails) {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
IIdType id = theCodeSystemDao.create(codeSystem, theRequestDetails).getId().toUnqualified();
|
||||
|
||||
|
|
|
@ -41,6 +41,8 @@ public class TerminologyLoaderSvcLoincIntegratedTest extends BaseJpaR4Test {
|
|||
TermCodeSystemVersion myTermCodeSystemVersion = myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), "2.67");
|
||||
assertEquals(myTermCodeSystem.getCurrentVersion().getPid(), myTermCodeSystemVersion.getPid());
|
||||
assertEquals(myTermCodeSystem.getResource().getId(), myTermCodeSystemVersion.getResource().getId());
|
||||
|
||||
assertEquals(1, myResourceTableDao.count());
|
||||
});
|
||||
|
||||
// Update LOINC marked as version 2.67
|
||||
|
@ -56,6 +58,8 @@ public class TerminologyLoaderSvcLoincIntegratedTest extends BaseJpaR4Test {
|
|||
TermCodeSystemVersion myTermCodeSystemVersion = myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), "2.67");
|
||||
assertEquals(myTermCodeSystem.getCurrentVersion().getPid(), myTermCodeSystemVersion.getPid());
|
||||
assertEquals(myTermCodeSystem.getResource().getId(), myTermCodeSystemVersion.getResource().getId());
|
||||
|
||||
assertEquals(1, myResourceTableDao.count());
|
||||
});
|
||||
|
||||
|
||||
|
@ -72,6 +76,8 @@ public class TerminologyLoaderSvcLoincIntegratedTest extends BaseJpaR4Test {
|
|||
TermCodeSystemVersion mySecondTermCodeSystemVersion = myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), "2.68");
|
||||
assertEquals(myTermCodeSystem.getCurrentVersion().getPid(), mySecondTermCodeSystemVersion.getPid());
|
||||
assertEquals(myTermCodeSystem.getResource().getId(), mySecondTermCodeSystemVersion.getResource().getId());
|
||||
|
||||
assertEquals(2, myResourceTableDao.count());
|
||||
});
|
||||
|
||||
}
|
||||
|
|
|
@ -184,7 +184,7 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
|
|||
assertEquals(2, outcome.getUpdatedConceptCount());
|
||||
|
||||
runInTransaction(() -> {
|
||||
TermConcept concept = myTermSvc.findCode("http://foo/cs", "ChildAA", null).orElseThrow(() -> new IllegalStateException());
|
||||
TermConcept concept = myTermSvc.findCode("http://foo/cs", "ChildAA").orElseThrow(() -> new IllegalStateException());
|
||||
assertEquals(2, concept.getParents().size());
|
||||
assertThat(concept.getParentPidsAsString(), matchesPattern("^[0-9]+ [0-9]+$"));
|
||||
});
|
||||
|
|
|
@ -63,6 +63,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
|
|||
codeSystem.setUrl(CS_URL);
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
codeSystem.setName("SYSTEM NAME");
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
|
||||
|
||||
ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalArgumentException::new);
|
||||
|
@ -116,6 +117,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
|
|||
private void createCodeSystem2() {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(CS_URL_2);
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
|
||||
|
||||
|
@ -135,6 +137,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
|
|||
runInTransaction(() -> {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(LOINC_URI);
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
|
||||
|
||||
|
@ -204,6 +207,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
|
|||
public void testCreateDuplicateCodeSystemUri() {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(CS_URL);
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
|
||||
|
||||
|
@ -226,12 +230,13 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
|
|||
// Try to update to a different resource
|
||||
codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(CS_URL);
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
try {
|
||||
myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
|
||||
fail();
|
||||
} catch (UnprocessableEntityException e) {
|
||||
assertThat(e.getMessage(), containsString("Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/"));
|
||||
assertThat(e.getMessage(), containsString("Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\" and CodeSystem.version \"SYSTEM VERSION\", already have one with resource ID: CodeSystem/"));
|
||||
}
|
||||
|
||||
}
|
||||
|
@ -1813,6 +1818,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
|
|||
public void testStoreCodeSystemInvalidCyclicLoop() {
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(CS_URL);
|
||||
codeSystem.setVersion("SYSTEM VERSION");
|
||||
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
|
||||
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
|
||||
|
||||
|
@ -1834,7 +1840,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
|
|||
child.addChild(parent, RelationshipTypeEnum.ISA);
|
||||
|
||||
try {
|
||||
myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getPersistentId(), "http://foo", "SYSTEM NAME", "SYSTEM VERSION", cs, table);
|
||||
myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(table.getPersistentId(), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
|
||||
fail();
|
||||
} catch (InvalidRequestException e) {
|
||||
assertEquals("CodeSystem contains circular reference around code parent", e.getMessage());
|
||||
|
@ -1948,6 +1954,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
|
|||
|
||||
CodeSystem cs = new CodeSystem();
|
||||
cs.setUrl("http://codesystems-r-us");
|
||||
cs.setVersion("SYSTEM VERSION");
|
||||
cs.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
|
||||
IIdType csId = myCodeSystemDao.create(cs).getId().toUnqualifiedVersionless();
|
||||
|
||||
|
|
Loading…
Reference in New Issue