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Merge remote-tracking branch 'origin/feature_2020_09_02_term_multi_version_support' into im_20200728_term_multi_version_support 

# Conflicts:
#	hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirResourceDaoCodeSystem.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandler.java
#	hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincIeeeMedicalDeviceCodeHandler.java
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
#	hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/CommonCodeSystemsTerminologyService.java
This commit is contained in:
ianmarshall 2020-09-25 09:10:07 -04:00
parent 2bceacd9a6 6f9874468a
commit 47244c54dc
35 changed files with 2339 additions and 75 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
View File

@ -125,6 +125,8 @@ ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoConceptMapDstu3.matchesFound=Matches fo
ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoConceptMapDstu3.noMatchesFound=No matches found!
ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoConceptMapR4.matchesFound=Matches found!
ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoConceptMapR4.noMatchesFound=No matches found!
ca.uhn.fhir.jpa.dao.r5.FhirResourceDaoConceptMapR5.matchesFound=Matches found!
ca.uhn.fhir.jpa.dao.r5.FhirResourceDaoConceptMapR5.noMatchesFound=No matches found!
ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoSearchParameterR4.invalidSearchParamExpression=The expression "{0}" can not be evaluated and may be invalid: {1}
ca.uhn.fhir.jpa.dao.predicate.PredicateBuilderToken.textModifierDisabledForSearchParam=The :text modifier is disabled for this search parameter
@ -143,6 +145,7 @@ ca.uhn.fhir.jpa.binstore.BinaryAccessProvider.unknownType=Content in resource of
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateCodeSystemUrl=Can not create multiple CodeSystem resources with CodeSystem.url "{0}", already have one with resource ID: {1}
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}
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateConceptMapUrl=Can not create multiple ConceptMap resources with ConceptMap.url "{0}", already have one with resource ID: {1}
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}
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateValueSetUrl=Can not create multiple ValueSet resources with ValueSet.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateValueSetUrlAndVersion=Can not create multiple ValueSet resources with ValueSet.url "{0}" and ValueSet.version "{1}", already have one with resource ID: {2}

33
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/model/TranslationQuery.java
View File

@ -23,11 +23,14 @@ package ca.uhn.fhir.jpa.api.model;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
public class TranslationQuery {
private Coding myCoding;
private Long myResourceId;
private UriType myUrl;
private StringType myConceptMapVersion;
private UriType mySource;
private UriType myTarget;
private UriType myTargetSystem;
@ -58,6 +61,32 @@ public class TranslationQuery {
myResourceId = theResourceId;
}
//-- url
public boolean hasUrl() {
return myUrl != null && myUrl.hasValue();
}
public UriType getUrl() {
return myUrl;
}
public void setUrl(UriType theUrl) {
myUrl = theUrl;
}
//-- ConceptMapVersion
public boolean hasConceptMapVersion() {
return myConceptMapVersion != null && myConceptMapVersion.hasValue();
}
public StringType getConceptMapVersion() {
return myConceptMapVersion;
}
public void setConceptMapVersion(StringType theConceptMapVersion) {
myConceptMapVersion = theConceptMapVersion;
}
public boolean hasSource() {
return mySource != null && mySource.hasValue();
}
@ -107,6 +136,8 @@ public class TranslationQuery {
.append(getCoding().getSystem(), that.getCoding().getSystem())
.append(getCoding().getVersion(), that.getCoding().getVersion())
.append(getResourceId(), that.getResourceId())
.append(getUrl(), that.getUrl())
.append(getConceptMapVersion(), that.getConceptMapVersion())
.append(getSource(), that.getSource())
.append(getTarget(), that.getTarget())
.append(getTargetSystem(), that.getTargetSystem())
@ -120,6 +151,8 @@ public class TranslationQuery {
.append(getCoding().getSystem())
.append(getCoding().getVersion())
.append(getResourceId())
.append(getUrl())
.append(getConceptMapVersion())
.append(getSource())
.append(getTarget())
.append(getTargetSystem())

43
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/model/TranslationRequest.java
View File

@ -1,5 +1,8 @@
package ca.uhn.fhir.jpa.api.model;
import java.util.ArrayList;
import java.util.List;
/*
* #%L
* HAPI FHIR JPA API
@ -24,15 +27,15 @@ import org.apache.commons.lang3.Validate;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
import java.util.ArrayList;
import java.util.List;
public class TranslationRequest {
private CodeableConcept myCodeableConcept;
private Long myResourceId;
private BooleanType myReverse;
private UriType myUrl;
private StringType myConceptMapVersion;
private UriType mySource;
private UriType myTarget;
private UriType myTargetSystem;
@ -90,6 +93,24 @@ public class TranslationRequest {
return false;
}
public UriType getUrl() {
return myUrl;
}
public TranslationRequest setUrl(UriType theUrl) {
myUrl = theUrl;
return this;
}
public StringType getConceptMapVersion() {
return myConceptMapVersion;
}
public TranslationRequest setConceptMapVersion(StringType theConceptMapVersion) {
myConceptMapVersion = theConceptMapVersion;
return this;
}
public UriType getSource() {
return mySource;
}
@ -130,6 +151,14 @@ public class TranslationRequest {
translationQuery.setResourceId(this.getResourceId());
}
if (this.hasUrl()) {
translationQuery.setUrl(this.getUrl());
}
if (this.hasConceptMapVersion()) {
translationQuery.setConceptMapVersion(this.getConceptMapVersion());
}
if (this.hasSource()) {
translationQuery.setSource(this.getSource());
}
@ -156,6 +185,14 @@ public class TranslationRequest {
return myReverse != null;
}
public boolean hasUrl() {
return myUrl != null && myUrl.hasValue();
}
public boolean hasConceptMapVersion() {
return myConceptMapVersion != null && myConceptMapVersion.hasValue();
}
public boolean hasSource() {
return mySource != null && mySource.hasValue();
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoValueSetDstu2.java
View File

@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
@ -56,6 +57,7 @@ import java.util.Collections;
import java.util.List;
import java.util.Set;
import static ca.uhn.fhir.jpa.dao.FhirResourceDaoValueSetDstu2.toStringOrNull;
import static ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoValueSetDstu3.vsValidateCodeOptions;
import static ca.uhn.fhir.jpa.util.LogicUtil.multiXor;
import static org.apache.commons.lang3.StringUtils.isBlank;
@ -302,4 +304,10 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
return myTerminologySvc.validateCode(vsValidateCodeOptions(), theId, toStringOrNull(theValueSetIdentifier), toStringOrNull(theSystem), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
}
@Override
public CodeValidationResult validateCode(IIdType theCodeSystemId, IPrimitiveType<String> theCodeSystemUrl, IPrimitiveType<String> theVersion, IPrimitiveType<String> theCode,
IPrimitiveType<String> theDisplay, CodingDt theCoding, CodeableConceptDt theCodeableConcept, RequestDetails theRequestDetails) {
throw new UnsupportedOperationException();
}
}

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermConceptMapDao.java
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@ -1,12 +1,15 @@
package ca.uhn.fhir.jpa.dao.data;
import ca.uhn.fhir.jpa.entity.TermConceptMap;
import java.util.List;
import java.util.Optional;
import org.springframework.data.domain.Pageable;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Modifying;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
import java.util.Optional;
import ca.uhn.fhir.jpa.entity.TermConceptMap;
/*
* #%L
@ -36,6 +39,17 @@ public interface ITermConceptMapDao extends JpaRepository<TermConceptMap, Long>
@Query("SELECT cm FROM TermConceptMap cm WHERE cm.myResourcePid = :resource_pid")
Optional<TermConceptMap> findTermConceptMapByResourcePid(@Param("resource_pid") Long theResourcePid);
@Query("SELECT cm FROM TermConceptMap cm WHERE cm.myUrl = :url")
// Keep backwards compatibility, recommend to use findTermConceptMapByUrlAndNullVersion instead
@Deprecated
@Query("SELECT cm FROM TermConceptMap cm WHERE cm.myUrl = :url and cm.myVersion is null")
Optional<TermConceptMap> findTermConceptMapByUrl(@Param("url") String theUrl);
@Query("SELECT cm FROM TermConceptMap cm WHERE cm.myUrl = :url and cm.myVersion is null")
Optional<TermConceptMap> findTermConceptMapByUrlAndNullVersion(@Param("url") String theUrl);
@Query(value="SELECT cm FROM TermConceptMap cm INNER JOIN ResourceTable r ON r.myId = cm.myResourcePid WHERE cm.myUrl = :url ORDER BY r.myUpdated DESC")
List<TermConceptMap> getTermConceptMapEntitiesByUrlOrderByVersion(Pageable thePage, @Param("url") String theUrl);
@Query("SELECT cm FROM TermConceptMap cm WHERE cm.myUrl = :url AND cm.myVersion = :version")
Optional<TermConceptMap> findTermConceptMapByUrlAndVersion(@Param("url") String theUrl, @Param("version") String theVersion);
}

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java
View File

@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
@ -155,4 +156,10 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
return retVal;
}
@Override
public CodeValidationResult validateCode(IIdType theCodeSystemId, IPrimitiveType<String> theCodeSystemUrl, IPrimitiveType<String> theVersion, IPrimitiveType<String> theCode,
IPrimitiveType<String> theDisplay, Coding theCoding, CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
throw new UnsupportedOperationException();
}
}

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java
View File

@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
@ -50,6 +51,8 @@ import java.util.Date;
import java.util.List;
import java.util.Set;
import static ca.uhn.fhir.jpa.dao.FhirResourceDaoValueSetDstu2.toStringOrNull;
import static ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoValueSetDstu3.vsValidateCodeOptions;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSystem> implements IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> {
@ -150,5 +153,13 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
return retVal;
}
@Override
public CodeValidationResult validateCode(IIdType theCodeSystemId, IPrimitiveType<String> theCodeSystemUrl,
IPrimitiveType<String> theVersion, IPrimitiveType<String> theCode, IPrimitiveType<String> theDisplay,
Coding theCoding, CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
return myTerminologySvc.codeSystemValidateCode(theCodeSystemId, toStringOrNull(theCodeSystemUrl), toStringOrNull(theVersion), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
}
}

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoConceptMapR4.java
View File

@ -32,6 +32,8 @@ 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.rest.api.server.RequestDetails;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeType;
@ -39,6 +41,7 @@ import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.Date;
@ -152,7 +155,11 @@ public class FhirResourceDaoConceptMapR4 extends BaseHapiFhirResourceDao<Concept
translationMatch.setSource(new UriType(element.getConceptMapUrl()));
if (element.getConceptMapGroupElementTargets().size() == 1) {
translationMatch.setEquivalence(new CodeType(element.getConceptMapGroupElementTargets().get(0).getEquivalence().toCode()));
ConceptMapEquivalence eq = element.getConceptMapGroupElementTargets().get(0).getEquivalence();
if (eq != null) {
translationMatch.setEquivalence(new CodeType(eq.toCode()));
}
}
retVal.addMatch(translationMatch);

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCodeSystemR5.java
View File

@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.dao.r5;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
@ -51,6 +52,8 @@ import java.util.Date;
import java.util.List;
import java.util.Set;
import static ca.uhn.fhir.jpa.dao.FhirResourceDaoValueSetDstu2.toStringOrNull;
import static ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoValueSetDstu3.vsValidateCodeOptions;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSystem> implements IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> {
@ -152,5 +155,11 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
return retVal;
}
@Override
public CodeValidationResult validateCode(IIdType theCodeSystemId, IPrimitiveType<String> theCodeSystemUrl,
IPrimitiveType<String> theVersion, IPrimitiveType<String> theCode, IPrimitiveType<String> theDisplay,
Coding theCoding, CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
return myTerminologySvc.codeSystemValidateCode(theCodeSystemId, toStringOrNull(theCodeSystemUrl), toStringOrNull(theVersion), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
}
}

38
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoConceptMapR5.java
View File

@ -1,5 +1,21 @@
package ca.uhn.fhir.jpa.dao.r5;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.ConceptMap;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.UriType;
import org.springframework.beans.factory.annotation.Autowired;
/*
* #%L
* HAPI FHIR JPA Server
@ -29,23 +45,9 @@ import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
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.rest.api.server.RequestDetails;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.ConceptMap;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.UriType;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
public class FhirResourceDaoConceptMapR5 extends BaseHapiFhirResourceDao<ConceptMap> implements IFhirResourceDaoConceptMap<ConceptMap> {
@Autowired
@ -153,7 +155,11 @@ public class FhirResourceDaoConceptMapR5 extends BaseHapiFhirResourceDao<Concept
translationMatch.setSource(VersionConvertor_40_50.convertUri(new UriType(element.getConceptMapUrl())));
if (element.getConceptMapGroupElementTargets().size() == 1) {
translationMatch.setEquivalence(VersionConvertor_40_50.convertCode(new CodeType(element.getConceptMapGroupElementTargets().get(0).getEquivalence().toCode())));
ConceptMapEquivalence eq = element.getConceptMapGroupElementTargets().get(0).getEquivalence();
if (eq != null) {
translationMatch.setEquivalence(VersionConvertor_40_50.convertCode(new CodeType(eq.toCode())));
}
}
retVal.addMatch(translationMatch);

18
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptMap.java
View File

@ -35,12 +35,13 @@ import static org.apache.commons.lang3.StringUtils.length;
@Entity
@Table(name = "TRM_CONCEPT_MAP", uniqueConstraints = {
@UniqueConstraint(name = "IDX_CONCEPT_MAP_URL", columnNames = {"URL"})
@UniqueConstraint(name = "IDX_CONCEPT_MAP_URL", columnNames = {"URL", "VER"})
})
public class TermConceptMap implements Serializable {
private static final long serialVersionUID = 1L;
static final int MAX_URL_LENGTH = 200;
public static final int MAX_VER_LENGTH = 200;
@Id()
@SequenceGenerator(name = "SEQ_CONCEPT_MAP_PID", sequenceName = "SEQ_CONCEPT_MAP_PID")
@ -64,6 +65,9 @@ public class TermConceptMap 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;
@OneToMany(mappedBy = "myConceptMap")
private List<TermConceptMapGroup> myConceptMapGroups;
@ -131,6 +135,17 @@ public class TermConceptMap implements Serializable {
return this;
}
public String getVersion() {
return myVersion;
}
public TermConceptMap setVersion(String theVersion) {
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theVersion, MAX_VER_LENGTH,
"Version exceeds maximum length (" + MAX_VER_LENGTH + "): " + length(theVersion));
myVersion = theVersion;
return this;
}
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
@ -140,6 +155,7 @@ public class TermConceptMap implements Serializable {
.append("mySource", mySource)
.append("myTarget", myTarget)
.append("myUrl", myUrl)
.append("myVersion", myVersion)
.append(myConceptMapGroups != null ? ("myConceptMapGroups - size=" + myConceptMapGroups.size()) : ("myConceptMapGroups=(null)"))
.toString();
}

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderConceptMapDstu3.java
View File

@ -54,6 +54,8 @@ public class BaseJpaResourceProviderConceptMapDstu3 extends JpaResourceProviderD
public Parameters translate(
HttpServletRequest theServletRequest,
@IdParam(optional = true) IdType theId,
@OperationParam(name = "url", min = 0, max = 1) UriType theUrl,
@OperationParam(name = "conceptMapVersion", min = 0, max = 1) StringType theConceptMapVersion,
@OperationParam(name = "code", min = 0, max = 1) CodeType theSourceCode,
@OperationParam(name = "system", min = 0, max = 1) UriType theSourceCodeSystem,
@OperationParam(name = "version", min = 0, max = 1) StringType theSourceCodeSystemVersion,
@ -65,6 +67,10 @@ public class BaseJpaResourceProviderConceptMapDstu3 extends JpaResourceProviderD
@OperationParam(name = "reverse", min = 0, max = 1) BooleanType theReverse,
RequestDetails theRequestDetails
) {
boolean haveUrl = theUrl != null
&& theUrl.hasValue();
boolean haveConceptMapVersion = theConceptMapVersion != null
&& theConceptMapVersion.hasValue();
boolean haveSourceCode = theSourceCode != null
&& theSourceCode.hasValue();
boolean haveSourceCodeSystem = theSourceCodeSystem != null
@ -93,6 +99,15 @@ public class BaseJpaResourceProviderConceptMapDstu3 extends JpaResourceProviderD
TranslationRequest translationRequest = new TranslationRequest();
try {
if (haveUrl) {
translationRequest.setUrl(VersionConvertor_30_40.convertUri(theUrl));
}
if (haveConceptMapVersion) {
translationRequest.setConceptMapVersion(VersionConvertor_30_40.convertString(theConceptMapVersion));
}
// Convert from DSTU3 to R4
if (haveSourceCode) {
translationRequest.getCodeableConcept().addCoding().setCodeElement(VersionConvertor_30_40.convertCode(theSourceCode));

59
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderCodeSystemR4.java
View File

@ -1,5 +1,19 @@
package ca.uhn.fhir.jpa.provider.r4;
import java.util.List;
import javax.servlet.http.HttpServletRequest;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
/*
* #%L
* HAPI FHIR JPA Server
@ -23,20 +37,11 @@ package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.provider.BaseJpaResourceProviderValueSetDstu2;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
import javax.servlet.http.HttpServletRequest;
import java.util.List;
public class BaseJpaResourceProviderCodeSystemR4 extends JpaResourceProviderR4<CodeSystem> {
@ -107,4 +112,36 @@ public class BaseJpaResourceProviderCodeSystemR4 extends JpaResourceProviderR4<C
endRequest(theServletRequest);
}
}
/**
* $validate-code operation
*/
@SuppressWarnings("unchecked")
@Operation(name = JpaConstants.OPERATION_VALIDATE_CODE, idempotent = true, returnParameters = {
@OperationParam(name = "result", type = BooleanType.class, min = 1),
@OperationParam(name = "message", type = StringType.class),
@OperationParam(name = "display", type = StringType.class)
})
public Parameters validateCode(
HttpServletRequest theServletRequest,
@IdParam(optional = true) IdType theId,
@OperationParam(name = "url", min = 0, max = 1) UriType theCodeSystemUrl,
@OperationParam(name = "version", min = 0, max = 1) StringType theVersion,
@OperationParam(name = "code", min = 0, max = 1) CodeType theCode,
@OperationParam(name = "display", min = 0, max = 1) StringType theDisplay,
@OperationParam(name = "coding", min = 0, max = 1) Coding theCoding,
@OperationParam(name = "codeableConcept", min = 0, max = 1) CodeableConcept theCodeableConcept,
RequestDetails theRequestDetails
) {
startRequest(theServletRequest);
try {
IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
IValidationSupport.CodeValidationResult result = dao.validateCode(theId, theCodeSystemUrl, theVersion, theCode, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
return (Parameters) BaseJpaResourceProviderValueSetDstu2.toValidateCodeResult(getContext(), result);
} finally {
endRequest(theServletRequest);
}
}
}

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderConceptMapR4.java
View File

@ -49,6 +49,8 @@ public class BaseJpaResourceProviderConceptMapR4 extends JpaResourceProviderR4<C
public Parameters translate(
HttpServletRequest theServletRequest,
@IdParam(optional = true) IdType theId,
@OperationParam(name = "url", min = 0, max = 1) UriType theUrl,
@OperationParam(name = "conceptMapVersion", min = 0, max = 1) StringType theConceptMapVersion,
@OperationParam(name = "code", min = 0, max = 1) CodeType theSourceCode,
@OperationParam(name = "system", min = 0, max = 1) UriType theSourceCodeSystem,
@OperationParam(name = "version", min = 0, max = 1) StringType theSourceCodeSystemVersion,
@ -60,6 +62,10 @@ public class BaseJpaResourceProviderConceptMapR4 extends JpaResourceProviderR4<C
@OperationParam(name = "reverse", min = 0, max = 1) BooleanType theReverse,
RequestDetails theRequestDetails
) {
boolean haveUrl = theUrl != null
&& theUrl.hasValue();
boolean haveConceptMapVersion = theConceptMapVersion != null
&& theConceptMapVersion.hasValue();
boolean haveSourceCode = theSourceCode != null
&& theSourceCode.hasCode();
boolean haveSourceCodeSystem = theSourceCodeSystem != null
@ -88,6 +94,14 @@ public class BaseJpaResourceProviderConceptMapR4 extends JpaResourceProviderR4<C
TranslationRequest translationRequest = new TranslationRequest();
if (haveUrl) {
translationRequest.setUrl(theUrl);
}
if (haveConceptMapVersion) {
translationRequest.setConceptMapVersion(theConceptMapVersion);
}
if (haveSourceCode) {
translationRequest.getCodeableConcept().addCoding().setCodeElement(theSourceCode);

36
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderCodeSystemR5.java
View File

@ -23,9 +23,13 @@ package ca.uhn.fhir.jpa.provider.r5;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.provider.BaseJpaResourceProviderValueSetDstu2;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.r5.model.IdType;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CodeType;
@ -107,4 +111,36 @@ public class BaseJpaResourceProviderCodeSystemR5 extends JpaResourceProviderR5<C
endRequest(theServletRequest);
}
}
/**
* $validate-code operation
*/
@SuppressWarnings("unchecked")
@Operation(name = JpaConstants.OPERATION_VALIDATE_CODE, idempotent = true, returnParameters = {
@OperationParam(name = "result", type = BooleanType.class, min = 1),
@OperationParam(name = "message", type = StringType.class),
@OperationParam(name = "display", type = StringType.class)
})
public Parameters validateCode(
HttpServletRequest theServletRequest,
@IdParam(optional = true) IdType theId,
@OperationParam(name = "url", min = 0, max = 1) UriType theCodeSystemUrl,
@OperationParam(name = "version", min = 0, max = 1) StringType theVersion,
@OperationParam(name = "code", min = 0, max = 1) CodeType theCode,
@OperationParam(name = "display", min = 0, max = 1) StringType theDisplay,
@OperationParam(name = "coding", min = 0, max = 1) Coding theCoding,
@OperationParam(name = "codeableConcept", min = 0, max = 1) CodeableConcept theCodeableConcept,
RequestDetails theRequestDetails
) {
startRequest(theServletRequest);
try {
IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
IValidationSupport.CodeValidationResult result = dao.validateCode(theId, theCodeSystemUrl, theVersion, theCode, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
return (Parameters) BaseJpaResourceProviderValueSetDstu2.toValidateCodeResult(getContext(), result);
} finally {
endRequest(theServletRequest);
}
}
}

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderConceptMapR5.java
View File

@ -50,6 +50,8 @@ public class BaseJpaResourceProviderConceptMapR5 extends JpaResourceProviderR5<C
public Parameters translate(
HttpServletRequest theServletRequest,
@IdParam(optional = true) IdType theId,
@OperationParam(name = "url", min = 0, max = 1) UriType theUrl,
@OperationParam(name = "conceptMapVersion", min = 0, max = 1) StringType theConceptMapVersion,
@OperationParam(name = "code", min = 0, max = 1) CodeType theSourceCode,
@OperationParam(name = "system", min = 0, max = 1) UriType theSourceCodeSystem,
@OperationParam(name = "version", min = 0, max = 1) StringType theSourceCodeSystemVersion,
@ -61,6 +63,10 @@ public class BaseJpaResourceProviderConceptMapR5 extends JpaResourceProviderR5<C
@OperationParam(name = "reverse", min = 0, max = 1) BooleanType theReverse,
RequestDetails theRequestDetails
) {
boolean haveUrl = theUrl != null
&& theUrl.hasValue();
boolean haveConceptMapVersion = theConceptMapVersion != null
&& theConceptMapVersion.hasValue();
boolean haveSourceCode = theSourceCode != null
&& theSourceCode.hasCode();
boolean haveSourceCodeSystem = theSourceCodeSystem != null
@ -89,6 +95,14 @@ public class BaseJpaResourceProviderConceptMapR5 extends JpaResourceProviderR5<C
TranslationRequest translationRequest = new TranslationRequest();
if (haveUrl) {
translationRequest.setUrl(VersionConvertor_40_50.convertUri(theUrl));
}
if (haveConceptMapVersion) {
translationRequest.setConceptMapVersion(VersionConvertor_40_50.convertString(theConceptMapVersion));
}
if (haveSourceCode) {
translationRequest.getCodeableConcept().addCoding().setCodeElement(VersionConvertor_40_50.convertCode(theSourceCode));

202
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
View File

@ -176,6 +176,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
public static final int DEFAULT_FETCH_SIZE = 250;
private static final int SINGLE_FETCH_SIZE = 1;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseTermReadSvcImpl.class);
private static final ValueSetExpansionOptions DEFAULT_EXPANSION_OPTIONS = new ValueSetExpansionOptions();
private static final TermCodeSystemVersion NO_CURRENT_VERSION = new TermCodeSystemVersion().setId(-1L);
@ -1596,6 +1597,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
TermConceptMap termConceptMap = new TermConceptMap();
termConceptMap.setResource(theResourceTable);
termConceptMap.setUrl(theConceptMap.getUrl());
termConceptMap.setVersion(theConceptMap.getVersion());
String source = theConceptMap.hasSourceUriType() ? theConceptMap.getSourceUriType().getValueAsString() : null;
String target = theConceptMap.hasTargetUriType() ? theConceptMap.getTargetUriType().getValueAsString() : null;
@ -1629,7 +1631,13 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
* Do the upload.
*/
String conceptMapUrl = termConceptMap.getUrl();
Optional<TermConceptMap> optionalExistingTermConceptMapByUrl = myConceptMapDao.findTermConceptMapByUrl(conceptMapUrl);
String conceptMapVersion = termConceptMap.getVersion();
Optional<TermConceptMap> optionalExistingTermConceptMapByUrl = null;
if (isBlank(conceptMapVersion)) {
optionalExistingTermConceptMapByUrl = myConceptMapDao.findTermConceptMapByUrlAndNullVersion(conceptMapUrl);
} else {
optionalExistingTermConceptMapByUrl = myConceptMapDao.findTermConceptMapByUrlAndVersion(conceptMapUrl, conceptMapVersion);
}
if (!optionalExistingTermConceptMapByUrl.isPresent()) {
try {
if (isNotBlank(source)) {
@ -1710,13 +1718,22 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
} else {
TermConceptMap existingTermConceptMap = optionalExistingTermConceptMapByUrl.get();
String msg = myContext.getLocalizer().getMessage(
BaseTermReadSvcImpl.class,
"cannotCreateDuplicateConceptMapUrl",
conceptMapUrl,
existingTermConceptMap.getResource().getIdDt().toUnqualifiedVersionless().getValue());
if (isBlank(conceptMapVersion)) {
String msg = myContext.getLocalizer().getMessage(
BaseTermReadSvcImpl.class,
"cannotCreateDuplicateConceptMapUrl",
conceptMapUrl,
existingTermConceptMap.getResource().getIdDt().toUnqualifiedVersionless().getValue());
throw new UnprocessableEntityException(msg);
throw new UnprocessableEntityException(msg);
} else {
String msg = myContext.getLocalizer().getMessage(
BaseTermReadSvcImpl.class,
"cannotCreateDuplicateConceptMapUrlAndVersion",
conceptMapUrl, conceptMapVersion,
existingTermConceptMap.getResource().getIdDt().toUnqualifiedVersionless().getValue());
throw new UnprocessableEntityException(msg);
}
}
ourLog.info("Done storing TermConceptMap[{}] for {}", termConceptMap.getId(), theConceptMap.getIdElement().toVersionless().getValueAsString());
@ -2049,6 +2066,12 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
List<TermConceptMapGroupElementTarget> cachedTargets;
ArrayList<Predicate> predicates;
Coding coding;
//-- get the latest ConceptMapVersion if theTranslationRequest has url, but ConceptMapVersion
String latestConceptMapVersion = null;
if (theTranslationRequest.hasUrl() && !theTranslationRequest.hasConceptMapVersion())
latestConceptMapVersion = getLatestConceptMapVersion(theTranslationRequest);
for (TranslationQuery translationQuery : translationQueries) {
cachedTargets = myTranslationCache.getIfPresent(translationQuery);
if (cachedTargets == null) {
@ -2075,6 +2098,21 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
predicates.add(criteriaBuilder.equal(groupJoin.get("myTarget"), translationQuery.getTargetSystem().getValueAsString()));
}
if (translationQuery.hasUrl()) {
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myUrl"), translationQuery.getUrl().getValueAsString()));
if (translationQuery.hasConceptMapVersion()) {
// both url and conceptMapVersion
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myVersion"), translationQuery.getConceptMapVersion().getValueAsString()));
} else {
if (StringUtils.isNotBlank(latestConceptMapVersion)) {
// only url and use latestConceptMapVersion
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myVersion"), latestConceptMapVersion));
} else {
predicates.add(criteriaBuilder.isNull(conceptMapJoin.get("myVersion")));
}
}
}
if (translationQuery.hasSource()) {
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("mySource"), translationQuery.getSource().getValueAsString()));
}
@ -2132,6 +2170,12 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
List<TermConceptMapGroupElement> cachedElements;
ArrayList<Predicate> predicates;
Coding coding;
//-- get the latest ConceptMapVersion if theTranslationRequest has url, but ConceptMapVersion
String latestConceptMapVersion = null;
if (theTranslationRequest.hasUrl() && !theTranslationRequest.hasConceptMapVersion())
latestConceptMapVersion = getLatestConceptMapVersion(theTranslationRequest);
for (TranslationQuery translationQuery : translationQueries) {
cachedElements = myTranslationWithReverseCache.getIfPresent(translationQuery);
if (cachedElements == null) {
@ -2158,6 +2202,21 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
predicates.add(criteriaBuilder.equal(groupJoin.get("myTargetVersion"), coding.getVersion()));
}
if (translationQuery.hasUrl()) {
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myUrl"), translationQuery.getUrl().getValueAsString()));
if (translationQuery.hasConceptMapVersion()) {
// both url and conceptMapVersion
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myVersion"), translationQuery.getConceptMapVersion().getValueAsString()));
} else {
if (StringUtils.isNotBlank(latestConceptMapVersion)) {
// only url and use latestConceptMapVersion
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myVersion"), latestConceptMapVersion));
} else {
predicates.add(criteriaBuilder.isNull(conceptMapJoin.get("myVersion")));
}
}
}
if (translationQuery.hasTargetSystem()) {
predicates.add(criteriaBuilder.equal(groupJoin.get("mySource"), translationQuery.getTargetSystem().getValueAsString()));
}
@ -2224,6 +2283,20 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
throw new ResourceNotFoundException("Unknown ValueSet: " + UrlUtil.escapeUrlParam(theValueSet));
}
// Special case for the translate operation with url and without
// conceptMapVersion, find the latest conecptMapVersion
private String getLatestConceptMapVersion(TranslationRequest theTranslationRequest) {
Pageable page = PageRequest.of(0, 1);
List<TermConceptMap> theConceptMapList = myConceptMapDao.getTermConceptMapEntitiesByUrlOrderByVersion(page,
theTranslationRequest.getUrl().asStringValue());
if (!theConceptMapList.isEmpty()) {
return theConceptMapList.get(0).getVersion();
}
return null;
}
@Override
@Transactional
public CodeValidationResult validateCodeInValueSet(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, @Nonnull IBaseResource theValueSet) {
@ -2560,5 +2633,120 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
return ourLastResultsFromTranslationWithReverseCache;
}
@Override
@Transactional
public CodeValidationResult codeSystemValidateCode(IIdType theCodeSystemId, String theCodeSystemUrl, String theVersion, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
CodeableConcept codeableConcept = toCanonicalCodeableConcept(theCodeableConcept);
boolean haveCodeableConcept = codeableConcept != null && codeableConcept.getCoding().size() > 0;
Coding coding = toCanonicalCoding(theCoding);
boolean haveCoding = coding != null && coding.isEmpty() == false;
boolean haveCode = theCode != null && theCode.isEmpty() == false;
if (!haveCodeableConcept && !haveCoding && !haveCode) {
throw new InvalidRequestException("No code, coding, or codeableConcept provided to validate.");
}
if (!LogicUtil.multiXor(haveCodeableConcept, haveCoding, haveCode)) {
throw new InvalidRequestException("$validate-code can only validate (code) OR (coding) OR (codeableConcept)");
}
boolean haveIdentifierParam = isNotBlank(theCodeSystemUrl);
String codeSystemUrl;
if (theCodeSystemId != null) {
IBaseResource codeSystem = myDaoRegistry.getResourceDao("CodeSystem").read(theCodeSystemId);
codeSystemUrl = CommonCodeSystemsTerminologyService.getCodeSystemUrl(codeSystem);
} else if (haveIdentifierParam) {
codeSystemUrl = theCodeSystemUrl;
} else {
throw new InvalidRequestException("Either CodeSystem ID or CodeSystem identifier must be provided. Unable to validate.");
}
String code = theCode;
String version = theVersion;
String display = theDisplay;
if (haveCodeableConcept) {
for (int i = 0; i < codeableConcept.getCoding().size(); i++) {
Coding nextCoding = codeableConcept.getCoding().get(i);
if (nextCoding.hasSystem()) {
if (!codeSystemUrl.equalsIgnoreCase(nextCoding.getSystem())) {
throw new InvalidRequestException("Coding.system '" + nextCoding.getSystem() + "' does not equal with CodeSystem.url '" + theCodeSystemUrl + "'. Unable to validate.");
}
codeSystemUrl = nextCoding.getSystem();
}
code = nextCoding.getCode();
display = nextCoding.getDisplay();
CodeValidationResult nextValidation = codeSystemValidateCode(codeSystemUrl, version, code, display);
if (nextValidation.isOk() || i == codeableConcept.getCoding().size() - 1) {
return nextValidation;
}
}
} else if (haveCoding) {
if (coding.hasSystem()) {
if (!codeSystemUrl.equalsIgnoreCase(coding.getSystem())) {
throw new InvalidRequestException("Coding.system '" + coding.getSystem() + "' does not equal with CodeSystem.url '" + theCodeSystemUrl + "'. Unable to validate.");
}
codeSystemUrl = coding.getSystem();
}
code = coding.getCode();
display = coding.getDisplay();
}
return codeSystemValidateCode(codeSystemUrl, version, code, display);
}
@SuppressWarnings("unchecked")
private CodeValidationResult codeSystemValidateCode(String theCodeSystemUrl, String theCodeSystemVersion, String theCode, String theDisplay) {
CriteriaBuilder criteriaBuilder = myEntityManager.getCriteriaBuilder();
CriteriaQuery<TermConcept> query = criteriaBuilder.createQuery(TermConcept.class);
Root<TermConcept> root = query.from(TermConcept.class);
Fetch<TermCodeSystemVersion, TermConcept> systemVersionFetch = root.fetch("myCodeSystem", JoinType.INNER);
Join<TermCodeSystemVersion, TermConcept> systemVersionJoin = (Join<TermCodeSystemVersion, TermConcept>)systemVersionFetch;
Fetch<TermCodeSystem, TermCodeSystemVersion> systemFetch = systemVersionFetch.fetch("myCodeSystem", JoinType.INNER);
Join<TermCodeSystem, TermCodeSystemVersion> systemJoin = (Join<TermCodeSystem, TermCodeSystemVersion>)systemFetch;
ArrayList<Predicate> predicates = new ArrayList<>();
if (isNotBlank(theCode)) {
predicates.add(criteriaBuilder.equal(root.get("myCode"), theCode));
}
if (isNotBlank(theDisplay)) {
predicates.add(criteriaBuilder.equal(root.get("myDisplay"), theDisplay));
}
if (isNoneBlank(theCodeSystemUrl)) {
predicates.add(criteriaBuilder.equal(systemJoin.get("myCodeSystemUri"), theCodeSystemUrl));
}
if (isNoneBlank(theCodeSystemVersion)) {
predicates.add(criteriaBuilder.equal(systemVersionJoin.get("myCodeSystemVersionId"), theCodeSystemVersion));
} else {
query.orderBy(criteriaBuilder.desc(root.get("myUpdated")));
}
Predicate outerPredicate = criteriaBuilder.and(predicates.toArray(new Predicate[0]));
query.where(outerPredicate);
final TypedQuery<TermConcept> typedQuery = myEntityManager.createQuery(query.select(root));
org.hibernate.query.Query<TermConcept> hibernateQuery = (org.hibernate.query.Query<TermConcept>) typedQuery;
hibernateQuery.setFetchSize(SINGLE_FETCH_SIZE);
List<TermConcept> resultsList = hibernateQuery.getResultList();
if (!resultsList.isEmpty()) {
TermConcept concept = resultsList.get(0);
return new CodeValidationResult().setCode(concept.getCode()).setDisplay(concept.getDisplay());
}
if (isBlank(theDisplay))
return createFailureCodeValidationResult(theCodeSystemUrl, theCode);
else
return createFailureCodeValidationResult(theCodeSystemUrl, theCode, " - Concept Display : " + theDisplay);
}
}

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermReadSvc.java
View File

@ -122,4 +122,9 @@ public interface ITermReadSvc extends IValidationSupport {
*/
boolean isValueSetPreExpandedForCodeValidation(IBaseResource theValueSet);
/**
* Version independent
*/
CodeValidationResult codeSystemValidateCode(IIdType theCodeSystemId, String theValueSetUrl, String theVersion, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept);
}

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandler.java
View File

@ -52,7 +52,7 @@ public abstract class BaseLoincHandler implements IRecordHandler {
private final List<ValueSet> myValueSets;
private final Map<String, ValueSet> myIdToValueSet = new HashMap<>();
private final Map<String, TermConcept> myCode2Concept;
final Properties myUploadProperties;
protected final Properties myUploadProperties;
BaseLoincHandler(Map<String, TermConcept> theCode2Concept, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps, Properties theUploadProperties) {
myValueSets = theValueSets;
@ -115,7 +115,7 @@ public abstract class BaseLoincHandler implements IRecordHandler {
conceptMap.setId(theMapping.getConceptMapId());
conceptMap.setUrl(theMapping.getConceptMapUri());
conceptMap.setName(theMapping.getConceptMapName());
conceptMap.setVersion(myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode()));
conceptMap.setVersion(theMapping.getConceptMapVersion());
conceptMap.setPublisher(REGENSTRIEF_INSTITUTE_INC);
conceptMap.addContact()
.setName(REGENSTRIEF_INSTITUTE_INC)
@ -228,6 +228,7 @@ public abstract class BaseLoincHandler implements IRecordHandler {
private String myCopyright;
private String myConceptMapId;
private String myConceptMapUri;
private String myConceptMapVersion;
private String myConceptMapName;
private String mySourceCodeSystem;
private String mySourceCode;
@ -265,6 +266,15 @@ public abstract class BaseLoincHandler implements IRecordHandler {
return this;
}
String getConceptMapVersion() {
return myConceptMapVersion;
}
ConceptMapping setConceptMapVersion(String theConceptMapVersion) {
myConceptMapVersion = theConceptMapVersion;
return this;
}
String getCopyright() {
return myCopyright;
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincIeeeMedicalDeviceCodeHandler.java
View File

@ -52,6 +52,7 @@ public class LoincIeeeMedicalDeviceCodeHandler extends BaseLoincHandler implemen
@Override
public void accept(CSVRecord theRecord) {
String loincIeeeCmVersion = myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode());
String loincNumber = trim(theRecord.get("LOINC_NUM"));
String longCommonName = trim(theRecord.get("LOINC_LONG_COMMON_NAME"));
String ieeeCode = trim(theRecord.get("IEEE_CF_CODE10"));
@ -64,6 +65,7 @@ public class LoincIeeeMedicalDeviceCodeHandler extends BaseLoincHandler implemen
new ConceptMapping()
.setConceptMapId(LOINC_IEEE_CM_ID + "-" + myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode()))
.setConceptMapUri(LOINC_IEEE_CM_URI)
.setConceptMapVersion(loincIeeeCmVersion)
.setConceptMapName(LOINC_IEEE_CM_NAME)
.setSourceCodeSystem(sourceCodeSystemUri)
.setSourceCode(loincNumber)

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

@ -76,6 +76,9 @@ public class LoincPartRelatedCodeMappingHandler extends BaseLoincHandler impleme
String extCodeSystemVersion = trim(theRecord.get("ExtCodeSystemVersion"));
String extCodeSystemCopyrightNotice = trim(theRecord.get("ExtCodeSystemCopyrightNotice"));
// ConceptMap version from properties files
String loincPartMapVersion = myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode());
Enumerations.ConceptMapEquivalence equivalence;
switch (trim(defaultString(mapType))) {
case "":
@ -131,6 +134,7 @@ public class LoincPartRelatedCodeMappingHandler extends BaseLoincHandler impleme
new ConceptMapping()
.setConceptMapId(loincPartMapId + "-" + myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode()))
.setConceptMapUri(loincPartMapUri)
.setConceptMapVersion(loincPartMapVersion)
.setConceptMapName(loincPartMapName)
.setSourceCodeSystem(ITermLoaderSvc.LOINC_URI)
.setSourceCode(partNumber)

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincRsnaPlaybookHandler.java
View File

@ -81,6 +81,9 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
String rpid = trim(theRecord.get("RPID"));
String longName = trim(theRecord.get("LongName"));
// ConceptMap version from properties files
String loincRsnaCmVersion = myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode());
// RSNA Codes VS
ValueSet vs;
if (!myIdToValueSet.containsKey(RSNA_CODES_VS_ID)) {
@ -177,6 +180,7 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
new ConceptMapping()
.setConceptMapId(LoincPartRelatedCodeMappingHandler.LOINC_PART_TO_RID_PART_MAP_ID + "-" + myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode()))
.setConceptMapUri(LoincPartRelatedCodeMappingHandler.LOINC_PART_TO_RID_PART_MAP_URI)
.setConceptMapVersion(loincRsnaCmVersion)
.setConceptMapName(LoincPartRelatedCodeMappingHandler.LOINC_PART_TO_RID_PART_MAP_NAME)
.setSourceCodeSystem(ITermLoaderSvc.LOINC_URI)
.setSourceCode(partNumber)
@ -194,6 +198,7 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
new ConceptMapping()
.setConceptMapId(LoincPartRelatedCodeMappingHandler.LOINC_TERM_TO_RPID_PART_MAP_ID + "-" + myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode()))
.setConceptMapUri(LoincPartRelatedCodeMappingHandler.LOINC_TERM_TO_RPID_PART_MAP_URI)
.setConceptMapVersion(loincRsnaCmVersion)
.setConceptMapName(LoincPartRelatedCodeMappingHandler.LOINC_TERM_TO_RPID_PART_MAP_NAME)
.setSourceCodeSystem(ITermLoaderSvc.LOINC_URI)
.setSourceCode(loincNumber)

91
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ConceptMapTest.java
View File

@ -1,23 +1,32 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.jpa.api.model.TranslationMatch;
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
import ca.uhn.fhir.jpa.api.model.TranslationResult;
import ca.uhn.fhir.util.TestUtil;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import java.util.List;
import java.util.Optional;
import org.hl7.fhir.dstu3.model.ConceptMap;
import org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.UriType;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Pageable;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import static org.junit.jupiter.api.Assertions.*;
import ca.uhn.fhir.jpa.api.model.TranslationMatch;
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
import ca.uhn.fhir.jpa.api.model.TranslationResult;
import ca.uhn.fhir.jpa.entity.TermConceptMap;
public class FhirResourceDaoDstu3ConceptMapTest extends BaseJpaDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3ConceptMapTest.class);
@ -98,4 +107,74 @@ public class FhirResourceDaoDstu3ConceptMapTest extends BaseJpaDstu3Test {
});
}
@Test
public void testConcaptMapFindTermConceptMapByUrl() {
Pageable page = PageRequest.of(0, 1);
List<TermConceptMap> theExpConceptMapList = myTermConceptMapDao.getTermConceptMapEntitiesByUrlOrderByVersion(page, CM_URL);
assertEquals(1, theExpConceptMapList.size());
assertEquals(CM_URL, theExpConceptMapList.get(0).getUrl());
}
@Test
public void testConcaptMapTwoConceptMapWithSameUrlDifferentVersion() {
String theUrl = "http://loinc.org/property/analyte-suffix";
ConceptMap theConceptMap1 = new ConceptMap();
ConceptMap theConceptMap2 = new ConceptMap();
theConceptMap1.setUrl(theUrl).setStatus(PublicationStatus.ACTIVE).setName("name1").setVersion("v1");
theConceptMap2.setUrl(theUrl).setStatus(PublicationStatus.ACTIVE).setName("name2").setVersion("v2");
myConceptMapDao.create(theConceptMap1);
myConceptMapDao.create(theConceptMap2);
Optional<TermConceptMap> theExpConceptMapV1 = myTermConceptMapDao.findTermConceptMapByUrlAndVersion(theUrl, "v1");
Optional<TermConceptMap> theExpConceptMapV2 = myTermConceptMapDao.findTermConceptMapByUrlAndVersion(theUrl, "v2");
assertTrue(theExpConceptMapV1.isPresent());
assertEquals(theUrl, theExpConceptMapV1.get().getUrl());
assertEquals("v1", theExpConceptMapV1.get().getVersion());
assertTrue(theExpConceptMapV2.isPresent());
assertEquals(theUrl, theExpConceptMapV2.get().getUrl());
assertEquals("v2", theExpConceptMapV2.get().getVersion());
// should return the latest one which is v2
Pageable page = PageRequest.of(0, 1);
List<TermConceptMap> theExpSecondOne = myTermConceptMapDao.getTermConceptMapEntitiesByUrlOrderByVersion(page, theUrl);
assertEquals(1, theExpSecondOne.size());
assertEquals(theUrl, theExpSecondOne.get(0).getUrl());
assertEquals("v2", theExpSecondOne.get(0).getVersion());
}
@Test
public void testConcaptMapTwoConceptMapWithSameUrlOneWithoutVersion() {
String theUrl = "http://loinc.org/property/analyte-suffix";
ConceptMap theConceptMap1 = new ConceptMap();
ConceptMap theConceptMap2 = new ConceptMap();
theConceptMap1.setUrl(theUrl).setStatus(PublicationStatus.ACTIVE).setName("name1").setVersion("v1");
theConceptMap2.setUrl(theUrl).setStatus(PublicationStatus.ACTIVE).setName("name2");
myConceptMapDao.create(theConceptMap1);
myConceptMapDao.create(theConceptMap2);
Optional<TermConceptMap> theExpConceptMapV1 = myTermConceptMapDao.findTermConceptMapByUrlAndVersion(theUrl, "v1");
assertTrue(theExpConceptMapV1.isPresent());
assertEquals(theUrl, theExpConceptMapV1.get().getUrl());
assertEquals("v1", theExpConceptMapV1.get().getVersion());
// should return the latest one which in this case is not versioned
Pageable page = PageRequest.of(0, 1);
List<TermConceptMap> theExpSecondOne = myTermConceptMapDao.getTermConceptMapEntitiesByUrlOrderByVersion(page, theUrl);
assertEquals(1, theExpSecondOne.size());
assertEquals(theUrl, theExpSecondOne.get(0).getUrl());
assertNull(theExpSecondOne.get(0).getVersion());
}
}

95
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConceptMapTest.java
View File

@ -1,31 +1,37 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.api.model.TranslationMatch;
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
import ca.uhn.fhir.jpa.api.model.TranslationResult;
import ca.uhn.fhir.util.TestUtil;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import java.io.IOException;
import java.util.List;
import java.util.Optional;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CanonicalType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r4.model.UriType;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Pageable;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import java.io.IOException;
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 ca.uhn.fhir.jpa.api.model.TranslationMatch;
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
import ca.uhn.fhir.jpa.api.model.TranslationResult;
import ca.uhn.fhir.jpa.entity.TermConceptMap;
public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoR4ConceptMapTest.class);
@ -1148,5 +1154,74 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
assertEquals("S52.209A", outcome.getMatches().get(0).getConcept().getCode());
}
@Test
public void testConcaptMapFindTermConceptMapByUrl() {
Pageable page = PageRequest.of(0, 1);
List<TermConceptMap> theExpConceptMapList = myTermConceptMapDao.getTermConceptMapEntitiesByUrlOrderByVersion(page, CM_URL);
assertEquals(1, theExpConceptMapList.size());
assertEquals(CM_URL, theExpConceptMapList.get(0).getUrl());
}
@Test
public void testConcaptMapTwoConceptMapWithSameUrlDifferentVersion() {
String theUrl = "http://loinc.org/property/analyte-suffix";
ConceptMap theConceptMap1 = new ConceptMap();
ConceptMap theConceptMap2 = new ConceptMap();
theConceptMap1.setUrl(theUrl).setStatus(PublicationStatus.ACTIVE).setName("name1").setVersion("v1");
theConceptMap2.setUrl(theUrl).setStatus(PublicationStatus.ACTIVE).setName("name2").setVersion("v2");
myConceptMapDao.create(theConceptMap1);
myConceptMapDao.create(theConceptMap2);
Optional<TermConceptMap> theExpConceptMapV1 = myTermConceptMapDao.findTermConceptMapByUrlAndVersion(theUrl, "v1");
Optional<TermConceptMap> theExpConceptMapV2 = myTermConceptMapDao.findTermConceptMapByUrlAndVersion(theUrl, "v2");
assertTrue(theExpConceptMapV1.isPresent());
assertEquals(theUrl, theExpConceptMapV1.get().getUrl());
assertEquals("v1", theExpConceptMapV1.get().getVersion());
assertTrue(theExpConceptMapV2.isPresent());
assertEquals(theUrl, theExpConceptMapV2.get().getUrl());
assertEquals("v2", theExpConceptMapV2.get().getVersion());
// should return the latest one which is v2
Pageable page = PageRequest.of(0, 1);
List<TermConceptMap> theExpSecondOne = myTermConceptMapDao.getTermConceptMapEntitiesByUrlOrderByVersion(page, theUrl);
assertEquals(1, theExpSecondOne.size());
assertEquals(theUrl, theExpSecondOne.get(0).getUrl());
assertEquals("v2", theExpSecondOne.get(0).getVersion());
}
@Test
public void testConcaptMapTwoConceptMapWithSameUrlOneWithoutVersion() {
String theUrl = "http://loinc.org/property/analyte-suffix";
ConceptMap theConceptMap1 = new ConceptMap();
ConceptMap theConceptMap2 = new ConceptMap();
theConceptMap1.setUrl(theUrl).setStatus(PublicationStatus.ACTIVE).setName("name1").setVersion("v1");
theConceptMap2.setUrl(theUrl).setStatus(PublicationStatus.ACTIVE).setName("name2");
myConceptMapDao.create(theConceptMap1);
myConceptMapDao.create(theConceptMap2);
Optional<TermConceptMap> theExpConceptMapV1 = myTermConceptMapDao.findTermConceptMapByUrlAndVersion(theUrl, "v1");
assertTrue(theExpConceptMapV1.isPresent());
assertEquals(theUrl, theExpConceptMapV1.get().getUrl());
assertEquals("v1", theExpConceptMapV1.get().getVersion());
// should return the latest one which is v2
Pageable page = PageRequest.of(0, 1);
List<TermConceptMap> theExpSecondOne = myTermConceptMapDao.getTermConceptMapEntitiesByUrlOrderByVersion(page, theUrl);
assertEquals(1, theExpSecondOne.size());
assertEquals(theUrl, theExpSecondOne.get(0).getUrl());
assertNull(theExpSecondOne.get(0).getVersion());
}
}

13
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3CodeSystemTest.java
View File

@ -330,6 +330,19 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
return ourCtx.newJsonParser().parseResource(theType, loadResource(theFilename));
}
@Test
public void testValidateCodeOperation() {
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType("https://url"));
inParams.addParameter().setName("code").setValue(new CodeType("1"));
try {
ourClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: Invalid request: The FHIR endpoint on this server does not know how to handle POST operation[CodeSystem/$validate-code] with parameters [[]]", e.getMessage());
}
}
}

568
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ConceptMapTest.java
View File

@ -1,18 +1,30 @@
package ca.uhn.fhir.jpa.provider.dstu3;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.dstu3.model.*;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import org.hl7.fhir.dstu3.model.BooleanType;
import org.hl7.fhir.dstu3.model.CodeType;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.ConceptMap;
import org.hl7.fhir.dstu3.model.ConceptMap.ConceptMapGroupComponent;
import org.hl7.fhir.dstu3.model.ConceptMap.SourceElementComponent;
import org.hl7.fhir.dstu3.model.ConceptMap.TargetElementComponent;
import org.hl7.fhir.dstu3.model.Enumerations.ConceptMapEquivalence;
import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.dstu3.model.UriType;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.transaction.annotation.Transactional;
import static org.junit.jupiter.api.Assertions.*;
import ca.uhn.fhir.rest.api.MethodOutcome;
public class ResourceProviderDstu3ConceptMapTest extends BaseResourceProviderDstu3Test {
private static final Logger ourLog = LoggerFactory.getLogger(ResourceProviderDstu3ConceptMapTest.class);
@ -114,4 +126,550 @@ public class ResourceProviderDstu3ConceptMapTest extends BaseResourceProviderDst
part = getPartByName(param, "source");
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateWithConceptMapUrlAndVersion() {
String url = "http://url";
createConceptMap(url, "v1", "12222", "Target Code 12222");
createConceptMap(url, "v2", "13333", "Target Code 13333");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(url));
inParams.addParameter().setName("conceptMapVersion").setValue(new StringType("v2"));
inParams.addParameter().setName("system").setValue(new UriType(CS_URL));
inParams.addParameter().setName("targetsystem").setValue(new UriType(CS_URL_2));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = ourClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertTrue(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("Matches found!", ((StringType) param.getValue()).getValueAsString());
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParametersByName(respParams, "match").get(0);
assertEquals(3, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "equivalence");
assertEquals("equal", ((CodeType) part.getValue()).getValueAsString());
part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
assertEquals("13333", coding.getCode());
assertEquals("Target Code 13333", coding.getDisplay());
assertFalse(coding.getUserSelected());
assertEquals(CS_URL_2, coding.getSystem());
assertEquals("Version 2", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(url, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateWithVersionedConcaptMapUrl_v2() {
String url = "http://url";
createConceptMap(url, "v1", "12222", "Target Code 12222");
createConceptMap(url, "v2", "13333", "Target Code 13333");
// Call translate with ConceptMap v2.
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(url));
inParams.addParameter().setName("conceptMapVersion").setValue(new StringType("v2"));
inParams.addParameter().setName("system").setValue(new UriType(CS_URL));
inParams.addParameter().setName("targetsystem").setValue(new UriType(CS_URL_2));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = ourClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
// Should return v2 since v2 specified.
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertTrue(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("Matches found!", ((StringType) param.getValue()).getValueAsString());
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParametersByName(respParams, "match").get(0);
assertEquals(3, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "equivalence");
assertEquals("equal", ((CodeType) part.getValue()).getValueAsString());
part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
assertEquals("13333", coding.getCode());
assertEquals("Target Code 13333", coding.getDisplay());
assertFalse(coding.getUserSelected());
assertEquals(CS_URL_2, coding.getSystem());
assertEquals("Version 2", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(url, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateWithVersionedConcaptMapUrl_v1() {
String url = "http://url";
createConceptMap(url, "v1", "12222", "Target Code 12222");
createConceptMap(url, "v2", "13333", "Target Code 13333");
// Call translate with ConceptMap v1.
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(url));
inParams.addParameter().setName("conceptMapVersion").setValue(new StringType("v1"));
inParams.addParameter().setName("system").setValue(new UriType(CS_URL));
inParams.addParameter().setName("targetsystem").setValue(new UriType(CS_URL_2));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = ourClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
// Should return v1 since v1 specified.
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertTrue(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("Matches found!", ((StringType) param.getValue()).getValueAsString());
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParametersByName(respParams, "match").get(0);
assertEquals(3, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "equivalence");
assertEquals("equal", ((CodeType) part.getValue()).getValueAsString());
part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
assertEquals("12222", coding.getCode());
assertEquals("Target Code 12222", coding.getDisplay());
assertFalse(coding.getUserSelected());
assertEquals(CS_URL_2, coding.getSystem());
assertEquals("Version 2", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(url, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateWithVersionedConcaptMapUrl_NoVersion() {
String url = "http://url";
createConceptMap(url, "v1", "12222", "Target Code 12222");
createConceptMap(url, "v2", "13333", "Target Code 13333");
// Call translate with no ConceptMap version.
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(url));
inParams.addParameter().setName("system").setValue(new UriType(CS_URL));
inParams.addParameter().setName("targetsystem").setValue(new UriType(CS_URL_2));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = ourClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
// Should return v2 since v2 is the most recently updated version.
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertTrue(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("Matches found!", ((StringType) param.getValue()).getValueAsString());
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParametersByName(respParams, "match").get(0);
assertEquals(3, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "equivalence");
assertEquals("equal", ((CodeType) part.getValue()).getValueAsString());
part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
assertEquals("13333", coding.getCode());
assertEquals("Target Code 13333", coding.getDisplay());
assertFalse(coding.getUserSelected());
assertEquals(CS_URL_2, coding.getSystem());
assertEquals("Version 2", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(url, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateWithVersionedConcaptMapUrl_NoVersion_null_v1() {
String url = "http://url";
createConceptMap(url, null, "12222", "Target Code 12222"); // first version is null
createConceptMap(url, "v2", "13333", "Target Code 13333");
// Call translate with no ConceptMap version.
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(url));
inParams.addParameter().setName("system").setValue(new UriType(CS_URL));
inParams.addParameter().setName("targetsystem").setValue(new UriType(CS_URL_2));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = ourClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
// Should return v2 since v2 is the most recently updated version.
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertTrue(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("Matches found!", ((StringType) param.getValue()).getValueAsString());
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParametersByName(respParams, "match").get(0);
assertEquals(3, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "equivalence");
assertEquals("equal", ((CodeType) part.getValue()).getValueAsString());
part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
assertEquals("13333", coding.getCode());
assertEquals("Target Code 13333", coding.getDisplay());
assertFalse(coding.getUserSelected());
assertEquals(CS_URL_2, coding.getSystem());
assertEquals("Version 2", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(url, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateWithVersionedConcaptMapUrl_NoVersion_null_v2() {
String url = "http://url";
createConceptMap(url, "v1", "12222", "Target Code 12222");
createConceptMap(url, null, "13333", "Target Code 13333"); // second version is null
// Call translate with no ConceptMap version.
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(url));
inParams.addParameter().setName("system").setValue(new UriType(CS_URL));
inParams.addParameter().setName("targetsystem").setValue(new UriType(CS_URL_2));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = ourClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
// Should return v2 since v2 is the most recently updated version.
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertTrue(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("Matches found!", ((StringType) param.getValue()).getValueAsString());
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParametersByName(respParams, "match").get(0);
assertEquals(3, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "equivalence");
assertEquals("equal", ((CodeType) part.getValue()).getValueAsString());
part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
assertEquals("13333", coding.getCode());
assertEquals("Target Code 13333", coding.getDisplay());
assertFalse(coding.getUserSelected());
assertEquals(CS_URL_2, coding.getSystem());
assertEquals("Version 2", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(url, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateWithConceptMap_WrongUrl_NoVersion() {
String url = "http://url";
createConceptMap(url, "v1", "12222", "Target Code 12222");
createConceptMap(url, "v2", "13333", "Target Code 13333");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType("http://invalid.url.com")); // no exsits url
inParams.addParameter().setName("system").setValue(new UriType(CS_URL));
inParams.addParameter().setName("targetsystem").setValue(new UriType(CS_URL_2));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = ourClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertFalse(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("No matches found!", ((StringType) param.getValue()).getValueAsString());
}
@Test
public void testTranslateWithReverseConceptMapUrlAndVersion() {
String url = "http://url";
createReverseConceptMap(url, "v1", "12222", "Source Code 12222");
createReverseConceptMap(url, "v2", "13333", "Source Code 13333");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(url));
inParams.addParameter().setName("conceptMapVersion").setValue(new StringType("v2"));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
inParams.addParameter().setName("reverse").setValue(new BooleanType(true));
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = ourClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertTrue(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("Matches found!", ((StringType) param.getValue()).getValueAsString());
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParametersByName(respParams, "match").get(0);
assertEquals(2, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
assertEquals("13333", coding.getCode());
assertEquals("Source Code 13333", coding.getDisplay());
assertFalse(coding.getUserSelected());
assertEquals(CS_URL, coding.getSystem());
assertEquals("Version 1", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(url, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateWithReverseConceptMapUrl_NoVersion() {
String url = "http://url";
createReverseConceptMap(url, "v1", "12222", "Source Code 12222");
createReverseConceptMap(url, "v2", "13333", "Source Code 13333");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(url));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
inParams.addParameter().setName("reverse").setValue(new BooleanType(true));
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = ourClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertTrue(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("Matches found!", ((StringType) param.getValue()).getValueAsString());
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParametersByName(respParams, "match").get(0);
assertEquals(2, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
assertEquals("13333", coding.getCode());
assertEquals("Source Code 13333", coding.getDisplay());
assertFalse(coding.getUserSelected());
assertEquals(CS_URL, coding.getSystem());
assertEquals("Version 1", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(url, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateWithReverseConceptMapUrl_NoVersion_null_v1() {
String url = "http://url";
createReverseConceptMap(url, null, "12222", "Source Code 12222");
createReverseConceptMap(url, "v2", "13333", "Source Code 13333");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(url));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
inParams.addParameter().setName("reverse").setValue(new BooleanType(true));
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = ourClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertTrue(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("Matches found!", ((StringType) param.getValue()).getValueAsString());
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParametersByName(respParams, "match").get(0);
assertEquals(2, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
assertEquals("13333", coding.getCode());
assertEquals("Source Code 13333", coding.getDisplay());
assertFalse(coding.getUserSelected());
assertEquals(CS_URL, coding.getSystem());
assertEquals("Version 1", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(url, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateWithReverseConceptMapUrl_NoVersion_null_v2() {
String url = "http://url";
createReverseConceptMap(url, "v1", "12222", "Source Code 12222");
createReverseConceptMap(url, null, "13333", "Source Code 13333");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(url));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
inParams.addParameter().setName("reverse").setValue(new BooleanType(true));
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = ourClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertTrue(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("Matches found!", ((StringType) param.getValue()).getValueAsString());
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParametersByName(respParams, "match").get(0);
assertEquals(2, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
assertEquals("13333", coding.getCode());
assertEquals("Source Code 13333", coding.getDisplay());
assertFalse(coding.getUserSelected());
assertEquals(CS_URL, coding.getSystem());
assertEquals("Version 1", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(url, ((UriType) part.getValue()).getValueAsString());
}
private void createConceptMap(String url, String version, String targetCode, String targetDisplay) {
ConceptMap conceptMap = new ConceptMap();
conceptMap.setUrl(url).setVersion(version).setSource(new UriType(VS_URL)).setTarget(new UriType(VS_URL_2));
ConceptMapGroupComponent group1 = conceptMap.addGroup();
group1.setSource(CS_URL).setSourceVersion("Version 1").setTarget(CS_URL_2).setTargetVersion("Version 2");
SourceElementComponent element1 = group1.addElement();
element1.setCode("11111").setDisplay("Source Code 11111");
TargetElementComponent target1 = element1.addTarget();
target1.setCode(targetCode).setDisplay(targetDisplay).setEquivalence(ConceptMapEquivalence.EQUAL);
IIdType conceptMapId = myConceptMapDao.create(conceptMap, mySrd).getId().toUnqualifiedVersionless();
conceptMap = myConceptMapDao.read(conceptMapId);
ourLog.info("ConceptMap: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
}
private void createReverseConceptMap(String url, String version, String sourceCode, String sourceDisplay) {
//- conceptMap1 v1
ConceptMap conceptMap = new ConceptMap();
conceptMap.setUrl(url).setVersion(version).setSource(new UriType(VS_URL)).setTarget(new UriType(VS_URL_2));
ConceptMapGroupComponent group1 = conceptMap.addGroup();
group1.setSource(CS_URL).setSourceVersion("Version 1").setTarget(CS_URL_2).setTargetVersion("Version 2");
SourceElementComponent element1 = group1.addElement();
element1.setCode(sourceCode).setDisplay(sourceDisplay);
TargetElementComponent target1 = element1.addTarget();
target1.setCode("11111").setDisplay("11111");
IIdType conceptMapId = myConceptMapDao.create(conceptMap, mySrd).getId().toUnqualifiedVersionless();
ConceptMap conceptMap1 = myConceptMapDao.read(conceptMapId);
ourLog.info("ConceptMap : \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap1));
}
}

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hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4CodeSystemValidationTest.java Normal file
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package ca.uhn.fhir.jpa.provider.r4;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.fail;
import java.io.IOException;
import javax.annotation.Nonnull;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
public class ResourceProviderR4CodeSystemValidationTest extends BaseResourceProviderR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderR4CodeSystemValidationTest.class);
private IIdType myCsId;
private static final String CS_ACMS_URL = "http://acme.org";
@BeforeEach
@Transactional
public void before02() throws IOException {
loadAndPersistCodeSystem();
}
private void loadAndPersistCodeSystem() throws IOException {
CodeSystem codeSystem = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
codeSystem.setId("CodeSystem/cs");
persistCodeSystem(codeSystem);
}
private void persistCodeSystem(CodeSystem theCodeSystem) {
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(@Nonnull TransactionStatus theStatus) {
myCsId = myCodeSystemDao.create(theCodeSystem, mySrd).getId().toUnqualifiedVersionless();
}
});
myCodeSystemDao.readEntity(myCsId, null).getId();
}
@Test
public void testValidateCodeFoundByCode() throws Exception {
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CS_ACMS_URL));
inParams.addParameter().setName("code").setValue(new CodeType("8452-5"));
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Systolic blood pressure.inspiration - expiration", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
@Test
public void testValidateCodeNotFoundByCode() throws Exception {
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CS_ACMS_URL));
inParams.addParameter().setName("code").setValue(new CodeType("8452-5-a"));
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals(false, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Unknown code {http://acme.org}8452-5-a", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
@Test
public void testValidateCodeFoundByCodeMatchDisplay() throws Exception {
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CS_ACMS_URL));
inParams.addParameter().setName("code").setValue(new CodeType("8452-5"));
inParams.addParameter().setName("display").setValue(new StringType("Systolic blood pressure.inspiration - expiration"));
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Systolic blood pressure.inspiration - expiration", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
@Test
public void testValidateCodeFoundByCodeNotMatchDisplay() throws Exception {
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CS_ACMS_URL));
inParams.addParameter().setName("code").setValue(new CodeType("8452-5"));
inParams.addParameter().setName("display").setValue(new StringType("Old Systolic blood pressure.inspiration - expiration"));
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals(false, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Unknown code {http://acme.org}8452-5 - Concept Display : Old Systolic blood pressure.inspiration - expiration", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
@Test
public void testValidateCodeFoundByCodeWithoutUrl() throws Exception {
Parameters inParams = new Parameters();
inParams.addParameter().setName("code").setValue(new CodeType("8452-5"));
try {
myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: Either CodeSystem ID or CodeSystem identifier must be provided. Unable to validate.",e.getMessage());
}
}
@Test
public void testValidateCodeFoundByCodeWithId() throws Exception {
Parameters inParams = new Parameters();
inParams.addParameter().setName("code").setValue(new CodeType("8452-5"));
Parameters respParam = myClient.operation().onInstance(myCsId).named("validate-code").withParameters(inParams).execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Systolic blood pressure.inspiration - expiration", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
@Test
public void testValidateCodeWithoutCodeOrCodingOrCodeableConcept() throws Exception {
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CS_ACMS_URL));
inParams.addParameter().setName("display").setValue(new StringType("Systolic blood pressure.inspiration - expiration"));
try {
myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: No code, coding, or codeableConcept provided to validate.",e.getMessage());
}
}
@Test
public void testValidateCodeWithCodeAndCoding() throws Exception {
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CS_ACMS_URL));
inParams.addParameter().setName("code").setValue(new CodeType("8452-5"));
inParams.addParameter().setName("coding").setValue((new Coding().setCode("8452-1")));
try {
myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: $validate-code can only validate (code) OR (coding) OR (codeableConcept)",e.getMessage());
}
}
@Test
public void testValidateCodeFoundByCodingWithUrlNotMatch() throws Exception {
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CS_ACMS_URL));
inParams.addParameter().setName("coding").setValue((new Coding().setCode("8452-5").setSystem("http://url2")));
try {
myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: Coding.system 'http://url2' does not equal with CodeSystem.url 'http://acme.org'. Unable to validate.",e.getMessage());
}
}
@Test
public void testValidateCodeFoundByCoding() throws Exception {
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CS_ACMS_URL));
inParams.addParameter().setName("coding").setValue((new Coding().setCode("8452-5")));
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Systolic blood pressure.inspiration - expiration", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
@Test
public void testValidateCodeFoundByCodingWithSystem() throws Exception {
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CS_ACMS_URL));
inParams.addParameter().setName("coding").setValue((new Coding().setCode("8452-5").setSystem(CS_ACMS_URL)));
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Systolic blood pressure.inspiration - expiration", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
@Test
public void testValidateCodeFoundByCodingUrlNotMatch() throws Exception {
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CS_ACMS_URL));
inParams.addParameter().setName("coding").setValue((new Coding().setCode("8452-5").setSystem("http://url2")));
try {
myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: Coding.system 'http://url2' does not equal with CodeSystem.url 'http://acme.org'. Unable to validate.",e.getMessage());
}
}
@Test
public void testValidateCodeFoundByCodingWithDisplay() throws Exception {
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CS_ACMS_URL));
inParams.addParameter().setName("coding").setValue((new Coding().setCode("8452-5").setDisplay("Systolic blood pressure.inspiration - expiration")));
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Systolic blood pressure.inspiration - expiration", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
@Test
public void testValidateCodeNotFoundByCoding() throws Exception {
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CS_ACMS_URL));
inParams.addParameter().setName("coding").setValue((new Coding().setCode("8452-5-a")));
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals(false, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Unknown code {http://acme.org}8452-5-a", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
@Test
public void testValidateCodeFoundByCodeableConcept() throws Exception {
CodeableConcept cc = new CodeableConcept();
cc.addCoding().setCode("8452-5");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CS_ACMS_URL));
inParams.addParameter().setName("codeableConcept").setValue(cc);
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Systolic blood pressure.inspiration - expiration", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
@Test
public void testValidateCodeFoundByCodeableConceptWithSystem() throws Exception {
CodeableConcept cc = new CodeableConcept();
cc.addCoding().setCode("8452-5").setSystem(CS_ACMS_URL);
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CS_ACMS_URL));
inParams.addParameter().setName("codeableConcept").setValue(cc);
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Systolic blood pressure.inspiration - expiration", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
@Test
public void testValidateCodeFoundByCodeableConceptWithDisplay() throws Exception {
CodeableConcept cc = new CodeableConcept();
cc.addCoding().setCode("8452-5").setSystem(CS_ACMS_URL).setDisplay("Systolic blood pressure.inspiration - expiration");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CS_ACMS_URL));
inParams.addParameter().setName("codeableConcept").setValue(cc);
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Systolic blood pressure.inspiration - expiration", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
@Test
public void testValidateCodeNotFoundByCodeableConcept() throws Exception {
CodeableConcept cc = new CodeableConcept();
cc.addCoding().setCode("8452-5-a");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CS_ACMS_URL));
inParams.addParameter().setName("codeableConcept").setValue(cc);
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals(false, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Unknown code {http://acme.org}8452-5-a", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
@Test
public void testValidateCodeFoundByCodeableConceptUrlNotMatch() throws Exception {
CodeableConcept cc = new CodeableConcept();
cc.addCoding().setCode("8452-5").setSystem("http://url2").setDisplay("Systolic blood pressure.inspiration - expiration");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CS_ACMS_URL));
inParams.addParameter().setName("codeableConcept").setValue(cc);
try {
myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: Coding.system 'http://url2' does not equal with CodeSystem.url 'http://acme.org'. Unable to validate.",e.getMessage());
}
}
@Test
public void testValidateCodeFoundByCodeableConceptWithMultipleMatchedEntries() throws Exception {
CodeableConcept cc = new CodeableConcept();
cc.addCoding().setCode("8452-5").setSystem(CS_ACMS_URL).setDisplay("Systolic blood pressure.inspiration - expiration");
cc.addCoding().setCode("8451-7").setSystem(CS_ACMS_URL).setDisplay("Systolic blood pressure--inspiration");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CS_ACMS_URL));
inParams.addParameter().setName("codeableConcept").setValue(cc);
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Systolic blood pressure.inspiration - expiration", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
@Test
public void testValidateCodeFoundByCodeableConceptWithMultipleMatchedFirstEntry() throws Exception {
CodeableConcept cc = new CodeableConcept();
cc.addCoding().setCode("8452-5").setSystem(CS_ACMS_URL).setDisplay("Systolic blood pressure.inspiration - expiration");
cc.addCoding().setCode("8451-7-a").setSystem(CS_ACMS_URL).setDisplay("Systolic blood pressure--inspiration");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CS_ACMS_URL));
inParams.addParameter().setName("codeableConcept").setValue(cc);
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Systolic blood pressure.inspiration - expiration", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
@Test
public void testValidateCodeFoundByCodeableConceptWithMultipleMatchedSecondEntry() throws Exception {
CodeableConcept cc = new CodeableConcept();
cc.addCoding().setCode("8452-5-a").setSystem(CS_ACMS_URL).setDisplay("Systolic blood pressure.inspiration - expiration");
cc.addCoding().setCode("8451-7").setSystem(CS_ACMS_URL).setDisplay("Systolic blood pressure--inspiration");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CS_ACMS_URL));
inParams.addParameter().setName("codeableConcept").setValue(cc);
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Systolic blood pressure--inspiration", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
@Test
public void testValidateCodeWithUrlAndVersion_v1() {
String url = "http://url";
createCodeSystem(url, "v1", "1", "Code v1 display");
createCodeSystem(url, "v2", "1", "Code v2 display");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(url));
inParams.addParameter().setName("version").setValue(new StringType("v1"));
inParams.addParameter().setName("code").setValue(new CodeType("1"));
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParam));
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Code v1 display", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
@Test
public void testValidateCodeWithUrlAndVersion_v2() {
String url = "http://url";
createCodeSystem(url, "v1", "1", "Code v1 display");
createCodeSystem(url, "v2", "1", "Code v2 display");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(url));
inParams.addParameter().setName("version").setValue(new StringType("v2"));
inParams.addParameter().setName("code").setValue(new CodeType("1"));
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParam));
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Code v2 display", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
@Test
public void testValidateCodeWithUrlAndVersion_noVersion() {
String url = "http://url";
createCodeSystem(url, "v1", "1", "Code v1 display");
createCodeSystem(url, "v2", "1", "Code v2 display");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(url));
inParams.addParameter().setName("code").setValue(new CodeType("1"));
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParam));
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Code v2 display", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
@Test
public void testValidateCodeWithUrlAndVersion_noVersion_null_v1() {
String url = "http://url";
createCodeSystem(url, null, "1", "Code v1 display");
createCodeSystem(url, "v2", "1", "Code v2 display");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(url));
inParams.addParameter().setName("code").setValue(new CodeType("1"));
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParam));
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Code v2 display", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
@Test
public void testValidateCodeWithUrlAndVersion_noVersion_null_v2() {
String url = "http://url";
createCodeSystem(url, "v1", "1", "Code v1 display");
createCodeSystem(url, null, "1", "Code v2 display");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(url));
inParams.addParameter().setName("code").setValue(new CodeType("1"));
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParam));
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Code v2 display", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
private void createCodeSystem(String url, String version, String code, String display) {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(url).setVersion(version);
ConceptDefinitionComponent concept1 = codeSystem.addConcept();
concept1.setCode("1000").setDisplay("Code Dispaly 1000");
ConceptDefinitionComponent concept = codeSystem.addConcept();
concept.setCode(code).setDisplay(display);
ConceptDefinitionComponent concept2 = codeSystem.addConcept();
concept2.setCode("2000").setDisplay("Code Dispaly 2000");
ourLog.info("CodeSystem: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
myCodeSystemDao.create(codeSystem, mySrd);
}
}

188
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ConceptMapTest.java
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@ -1,16 +1,31 @@
package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.rest.api.MethodOutcome;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ConceptMap.ConceptMapGroupComponent;
import org.hl7.fhir.r4.model.ConceptMap.SourceElementComponent;
import org.hl7.fhir.r4.model.ConceptMap.TargetElementComponent;
import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.transaction.annotation.Transactional;
import static org.junit.jupiter.api.Assertions.*;
import ca.uhn.fhir.rest.api.MethodOutcome;
public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(ResourceProviderR4ConceptMapTest.class);
@ -870,6 +885,90 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateWithConcaptMapUrlAndVersion() {
//- conceptMap1 v1
ConceptMap conceptMap1 = new ConceptMap();
conceptMap1.setUrl(CM_URL).setVersion("v1").setSource(new UriType(VS_URL)).setTarget(new UriType(VS_URL_2));
ConceptMapGroupComponent group1 = conceptMap1.addGroup();
group1.setSource(CS_URL).setSourceVersion("Version 1").setTarget(CS_URL_2).setTargetVersion("Version 2");
SourceElementComponent element1 = group1.addElement();
element1.setCode("11111").setDisplay("Source Code 11111");
TargetElementComponent target1 = element1.addTarget();
target1.setCode("12222").setDisplay("Target Code 12222").setEquivalence(ConceptMapEquivalence.EQUAL);
IIdType conceptMapId1 = myConceptMapDao.create(conceptMap1, mySrd).getId().toUnqualifiedVersionless();
conceptMap1 = myConceptMapDao.read(conceptMapId1);
ourLog.info("ConceptMap: 2 \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap1));
//- conceptMap1 v2
ConceptMap conceptMap2 = new ConceptMap();
conceptMap2.setUrl(CM_URL).setVersion("v2").setSource(new UriType(VS_URL)).setTarget(new UriType(VS_URL_2));
ConceptMapGroupComponent group2 = conceptMap2.addGroup();
group2.setSource(CS_URL).setSourceVersion("Version 1").setTarget(CS_URL_2).setTargetVersion("Version 2");
SourceElementComponent element2 = group2.addElement();
element2.setCode("11111").setDisplay("Source Code 11111");
TargetElementComponent target2 = element2.addTarget();
target2.setCode("13333").setDisplay("Target Code 13333").setEquivalence(ConceptMapEquivalence.EQUAL);
IIdType conceptMapId2 = myConceptMapDao.create(conceptMap2, mySrd).getId().toUnqualifiedVersionless();
conceptMap2 = myConceptMapDao.read(conceptMapId2);
ourLog.info("ConceptMap: 2 \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap2));
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CM_URL));
inParams.addParameter().setName("conceptMapVersion").setValue(new StringType("v2"));
inParams.addParameter().setName("system").setValue(new UriType(CS_URL));
inParams.addParameter().setName("targetsystem").setValue(new UriType(CS_URL_2));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = myClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertTrue(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("Matches found!", ((StringType) param.getValue()).getValueAsString());
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParametersByName(respParams, "match").get(0);
assertEquals(3, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "equivalence");
assertEquals("equal", ((CodeType) part.getValue()).getCode());
part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
assertEquals("13333", coding.getCode());
assertEquals("Target Code 13333", coding.getDisplay());
assertFalse(coding.getUserSelected());
assertEquals(CS_URL_2, coding.getSystem());
assertEquals("Version 2", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateWithInstance() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
@ -1621,6 +1720,89 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateWithReverseConcaptMapUrlAndVersion() {
//- conceptMap1 v1
ConceptMap conceptMap1 = new ConceptMap();
conceptMap1.setUrl(CM_URL).setVersion("v1").setSource(new UriType(VS_URL)).setTarget(new UriType(VS_URL_2));
ConceptMapGroupComponent group1 = conceptMap1.addGroup();
group1.setSource(CS_URL).setSourceVersion("Version 1").setTarget(CS_URL_2).setTargetVersion("Version 2");
SourceElementComponent element1 = group1.addElement();
element1.setCode("12222").setDisplay("Source Code 12222");
TargetElementComponent target1 = element1.addTarget();
target1.setCode("11111").setDisplay("11111").setEquivalence(ConceptMapEquivalence.EQUAL);
IIdType conceptMapId1 = myConceptMapDao.create(conceptMap1, mySrd).getId().toUnqualifiedVersionless();
conceptMap1 = myConceptMapDao.read(conceptMapId1);
ourLog.info("ConceptMap: 2 \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap1));
//- conceptMap1 v2
ConceptMap conceptMap2 = new ConceptMap();
conceptMap2.setUrl(CM_URL).setVersion("v2").setSource(new UriType(VS_URL)).setTarget(new UriType(VS_URL_2));
ConceptMapGroupComponent group2 = conceptMap2.addGroup();
group2.setSource(CS_URL).setSourceVersion("Version 1").setTarget(CS_URL_2).setTargetVersion("Version 2");
SourceElementComponent element2 = group2.addElement();
element2.setCode("13333").setDisplay("Source Code 13333");
TargetElementComponent target2 = element2.addTarget();
target2.setCode("11111").setDisplay("Target Code 11111").setEquivalence(ConceptMapEquivalence.EQUAL);
IIdType conceptMapId2 = myConceptMapDao.create(conceptMap2, mySrd).getId().toUnqualifiedVersionless();
conceptMap2 = myConceptMapDao.read(conceptMapId2);
ourLog.info("ConceptMap: 2 \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap2));
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CM_URL));
inParams.addParameter().setName("conceptMapVersion").setValue(new StringType("v2"));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
inParams.addParameter().setName("reverse").setValue(new BooleanType(true));
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = myClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertTrue(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("Matches found!", ((StringType) param.getValue()).getValueAsString());
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParametersByName(respParams, "match").get(0);
assertEquals(3, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "equivalence");
assertEquals("equal", ((CodeType) part.getValue()).getCode());
part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
assertEquals("13333", coding.getCode());
assertEquals("Source Code 13333", coding.getDisplay());
assertFalse(coding.getUserSelected());
assertEquals(CS_URL, coding.getSystem());
assertEquals("Version 1", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateWithReverseAndInstance() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);

58
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r5/ResourceProviderR5CodeSystemTest.java Normal file
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@ -0,0 +1,58 @@
package ca.uhn.fhir.jpa.provider.r5;
import static org.junit.jupiter.api.Assertions.assertEquals;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.UriType;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class ResourceProviderR5CodeSystemTest extends BaseResourceProviderR5Test {
private static final Logger ourLog = LoggerFactory.getLogger(ResourceProviderR5CodeSystemTest.class);
@Test
public void testValidateCodeWithUrlAndVersion_v1() {
String url = "http://url";
createCodeSystem(url, "v1", "1", "Code v1 display");
createCodeSystem(url, "v2", "1", "Code v2 display");
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(url));
inParams.addParameter().setName("version").setValue(new StringType("v1"));
inParams.addParameter().setName("code").setValue(new CodeType("1"));
inParams.addParameter().setName("display").setValue(new StringType("Code v1 display"));
Parameters respParam = myClient.operation().onType(CodeSystem.class).named("validate-code").withParameters(inParams).execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParam));
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
assertEquals("Code v1 display", ((StringType) respParam.getParameter().get(1).getValue()).getValueAsString());
}
private void createCodeSystem(String url, String version, String code, String display) {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(url).setVersion(version);
ConceptDefinitionComponent concept1 = codeSystem.addConcept();
concept1.setCode("1000").setDisplay("Code Dispaly 1000");
ConceptDefinitionComponent concept = codeSystem.addConcept();
concept.setCode(code).setDisplay(display);
ConceptDefinitionComponent concept2 = codeSystem.addConcept();
concept2.setCode("2000").setDisplay("Code Dispaly 2000");
ourLog.info("CodeSystem: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
myCodeSystemDao.create(codeSystem, mySrd);
}
}

191
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r5/ResourceProviderR5ConceptMapTest.java Normal file
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@ -0,0 +1,191 @@
package ca.uhn.fhir.jpa.provider.r5;
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 org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.ConceptMap;
import org.hl7.fhir.r5.model.ConceptMap.ConceptMapGroupComponent;
import org.hl7.fhir.r5.model.ConceptMap.SourceElementComponent;
import org.hl7.fhir.r5.model.ConceptMap.TargetElementComponent;
import org.hl7.fhir.r5.model.Enumerations.ConceptMapRelationship;
import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.UriType;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class ResourceProviderR5ConceptMapTest extends BaseResourceProviderR5Test {
private static final Logger ourLog = LoggerFactory.getLogger(ResourceProviderR5ConceptMapTest.class);
@Test
public void testTranslateWithConcaptMapUrlAndVersion() {
//- conceptMap1 v1
ConceptMap conceptMap1 = new ConceptMap();
conceptMap1.setUrl(CM_URL).setVersion("v1").setSource(new UriType(VS_URL)).setTarget(new UriType(VS_URL_2));
ConceptMapGroupComponent group1 = conceptMap1.addGroup();
group1.setSource(CS_URL).setSourceVersion("Version 1").setTarget(CS_URL_2).setTargetVersion("Version 2");
SourceElementComponent element1 = group1.addElement();
element1.setCode("11111").setDisplay("Source Code 11111");
TargetElementComponent target1 = element1.addTarget();
target1.setCode("12222").setDisplay("Target Code 12222");
IIdType conceptMapId1 = myConceptMapDao.create(conceptMap1, mySrd).getId().toUnqualifiedVersionless();
conceptMap1 = myConceptMapDao.read(conceptMapId1);
ourLog.info("ConceptMap: 2 \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap1));
//- conceptMap1 v2
ConceptMap conceptMap2 = new ConceptMap();
conceptMap2.setUrl(CM_URL).setVersion("v2").setSource(new UriType(VS_URL)).setTarget(new UriType(VS_URL_2));
ConceptMapGroupComponent group2 = conceptMap2.addGroup();
group2.setSource(CS_URL).setSourceVersion("Version 1").setTarget(CS_URL_2).setTargetVersion("Version 2");
SourceElementComponent element2 = group2.addElement();
element2.setCode("11111").setDisplay("Source Code 11111");
TargetElementComponent target2 = element2.addTarget();
target2.setCode("13333").setDisplay("Target Code 13333");
IIdType conceptMapId2 = myConceptMapDao.create(conceptMap2, mySrd).getId().toUnqualifiedVersionless();
conceptMap2 = myConceptMapDao.read(conceptMapId2);
ourLog.info("ConceptMap: 2 \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap2));
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CM_URL));
inParams.addParameter().setName("conceptMapVersion").setValue(new StringType("v2"));
inParams.addParameter().setName("system").setValue(new UriType(CS_URL));
inParams.addParameter().setName("targetsystem").setValue(new UriType(CS_URL_2));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = myClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertTrue(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("Matches found!", ((StringType) param.getValue()).getValueAsString());
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParametersByName(respParams, "match").get(0);
assertEquals(2, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
assertEquals("13333", coding.getCode());
assertEquals("Target Code 13333", coding.getDisplay());
assertFalse(coding.getUserSelected());
assertEquals(CS_URL_2, coding.getSystem());
assertEquals("Version 2", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
}
@Test
public void testTranslateWithReverseConcaptMapUrlAndVersion() {
//- conceptMap1 v1
ConceptMap conceptMap1 = new ConceptMap();
conceptMap1.setUrl(CM_URL).setVersion("v1").setSource(new UriType(VS_URL)).setTarget(new UriType(VS_URL_2));
ConceptMapGroupComponent group1 = conceptMap1.addGroup();
group1.setSource(CS_URL).setSourceVersion("Version 1").setTarget(CS_URL_2).setTargetVersion("Version 2");
SourceElementComponent element1 = group1.addElement();
element1.setCode("12222").setDisplay("Source Code 12222");
TargetElementComponent target1 = element1.addTarget();
target1.setCode("11111").setDisplay("11111").setRelationship(ConceptMapRelationship.EQUIVALENT);
IIdType conceptMapId1 = myConceptMapDao.create(conceptMap1, mySrd).getId().toUnqualifiedVersionless();
conceptMap1 = myConceptMapDao.read(conceptMapId1);
ourLog.info("ConceptMap: 2 \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap1));
//- conceptMap1 v2
ConceptMap conceptMap2 = new ConceptMap();
conceptMap2.setUrl(CM_URL).setVersion("v2").setSource(new UriType(VS_URL)).setTarget(new UriType(VS_URL_2));
ConceptMapGroupComponent group2 = conceptMap2.addGroup();
group2.setSource(CS_URL).setSourceVersion("Version 1").setTarget(CS_URL_2).setTargetVersion("Version 2");
SourceElementComponent element2 = group2.addElement();
element2.setCode("13333").setDisplay("Source Code 13333");
TargetElementComponent target2 = element2.addTarget();
target2.setCode("11111").setDisplay("Target Code 11111").setRelationship(ConceptMapRelationship.EQUIVALENT);
IIdType conceptMapId2 = myConceptMapDao.create(conceptMap2, mySrd).getId().toUnqualifiedVersionless();
conceptMap2 = myConceptMapDao.read(conceptMapId2);
ourLog.info("ConceptMap: 2 \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap2));
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CM_URL));
inParams.addParameter().setName("conceptMapVersion").setValue(new StringType("v2"));
inParams.addParameter().setName("code").setValue(new CodeType("11111"));
inParams.addParameter().setName("reverse").setValue(new BooleanType(true));
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = myClient
.operation()
.onType(ConceptMap.class)
.named("translate")
.withParameters(inParams)
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertTrue(((BooleanType) param.getValue()).booleanValue());
param = getParameterByName(respParams, "message");
assertEquals("Matches found!", ((StringType) param.getValue()).getValueAsString());
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParametersByName(respParams, "match").get(0);
assertEquals(3, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "equivalence");
assertEquals("equivalent", ((CodeType) part.getValue()).getCode());
part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
assertEquals("13333", coding.getCode());
assertEquals("Source Code 13333", coding.getDisplay());
assertFalse(coding.getUserSelected());
assertEquals(CS_URL, coding.getSystem());
assertEquals("Version 1", coding.getVersion());
part = getPartByName(param, "source");
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
}
}

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
View File

@ -165,7 +165,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
assertEquals(1, group.getElement().get(0).getTarget().size());
assertEquals("420710006", group.getElement().get(0).getTarget().get(0).getCode());
assertEquals("Interferon beta (substance)", group.getElement().get(0).getTarget().get(0).getDisplay());
// Document Ontology ValueSet
vs = valueSets.get(LoincDocumentOntologyHandler.DOCUMENT_ONTOLOGY_CODES_VS_ID);
assertEquals(LoincDocumentOntologyHandler.DOCUMENT_ONTOLOGY_CODES_VS_NAME, vs.getName());
@ -218,6 +218,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
// RSNA Playbook - LOINC Part -> RadLex RID Mappings
conceptMap = conceptMaps.get(LoincPartRelatedCodeMappingHandler.LOINC_PART_TO_RID_PART_MAP_ID);
assertEquals(LoincPartRelatedCodeMappingHandler.LOINC_PART_TO_RID_PART_MAP_URI, conceptMap.getUrl());
assertEquals("Beta.1", conceptMap.getVersion());
assertEquals(LoincPartRelatedCodeMappingHandler.LOINC_PART_TO_RID_PART_MAP_NAME, conceptMap.getName());
assertEquals(1, conceptMap.getGroup().size());
group = conceptMap.getGroupFirstRep();
@ -234,6 +235,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
// RSNA Playbook - LOINC Term -> RadLex RPID Mappings
conceptMap = conceptMaps.get(LoincPartRelatedCodeMappingHandler.LOINC_TERM_TO_RPID_PART_MAP_ID);
assertEquals(LoincPartRelatedCodeMappingHandler.LOINC_TERM_TO_RPID_PART_MAP_URI, conceptMap.getUrl());
assertEquals("Beta.1", conceptMap.getVersion());
assertEquals(LoincPartRelatedCodeMappingHandler.LOINC_TERM_TO_RPID_PART_MAP_NAME, conceptMap.getName());
assertEquals(1, conceptMap.getGroup().size());
group = conceptMap.getGroupFirstRep();
@ -300,6 +302,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
ourLog.debug(FhirContext.forCached(FhirVersionEnum.R4).newXmlParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
assertEquals(LoincIeeeMedicalDeviceCodeHandler.LOINC_IEEE_CM_NAME, conceptMap.getName());
assertEquals(LoincIeeeMedicalDeviceCodeHandler.LOINC_IEEE_CM_URI, conceptMap.getUrl());
assertEquals("Beta.1", conceptMap.getVersion());
assertEquals(1, conceptMap.getGroup().size());
assertEquals(ITermLoaderSvc.LOINC_URI, conceptMap.getGroup().get(0).getSource());
assertEquals(ITermLoaderSvc.IEEE_11073_10101_URI, conceptMap.getGroup().get(0).getTarget());

36
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java
View File

@ -27,6 +27,8 @@ import org.hl7.fhir.r4.model.codesystems.HttpVerb;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Pageable;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
@ -59,6 +61,13 @@ public class TerminologySvcImplR4Test extends BaseTermR4Test {
persistConceptMap(conceptMap, HttpVerb.POST);
}
private void createAndPersistConceptMap(String version) {
ConceptMap conceptMap = createConceptMap();
conceptMap.setId("ConceptMap/cm");
conceptMap.setVersion(version);
persistConceptMap(conceptMap, HttpVerb.POST);
}
@SuppressWarnings("EnumSwitchStatementWhichMissesCases")
private void persistConceptMap(ConceptMap theConceptMap, HttpVerb theVerb) {
switch (theVerb) {
@ -273,6 +282,19 @@ public class TerminologySvcImplR4Test extends BaseTermR4Test {
}
@Test
public void testDuplicateConceptMapUrlsAndVersions() {
createAndPersistConceptMap("v1");
try {
createAndPersistConceptMap("v1");
fail();
} catch (UnprocessableEntityException e) {
assertEquals("Can not create multiple ConceptMap resources with ConceptMap.url \"http://example.com/my_concept_map\", ConceptMap.version \"v1\", already have one with resource ID: ConceptMap/" + myConceptMapId.getIdPart(), e.getMessage());
}
}
@Test
public void testDuplicateValueSetUrls() throws Exception {
myDaoConfig.setPreExpandValueSets(true);
@ -299,10 +321,11 @@ public class TerminologySvcImplR4Test extends BaseTermR4Test {
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(@Nonnull TransactionStatus theStatus) {
Optional<TermConceptMap> optionalConceptMap = myTermConceptMapDao.findTermConceptMapByUrl(CM_URL);
assertTrue(optionalConceptMap.isPresent());
Pageable page = PageRequest.of(0, 1);
List<TermConceptMap> optionalConceptMap = myTermConceptMapDao.getTermConceptMapEntitiesByUrlOrderByVersion(page, CM_URL);
assertEquals(1, optionalConceptMap.size());
TermConceptMap conceptMap = optionalConceptMap.get();
TermConceptMap conceptMap = optionalConceptMap.get(0);
ourLog.info("ConceptMap:\n" + conceptMap.toString());
@ -477,10 +500,11 @@ public class TerminologySvcImplR4Test extends BaseTermR4Test {
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(@Nonnull TransactionStatus theStatus) {
Optional<TermConceptMap> optionalConceptMap = myTermConceptMapDao.findTermConceptMapByUrl(CM_URL);
assertTrue(optionalConceptMap.isPresent());
Pageable page = PageRequest.of(0, 1);
List<TermConceptMap> optionalConceptMap = myTermConceptMapDao.getTermConceptMapEntitiesByUrlOrderByVersion(page, CM_URL);
assertEquals(1, optionalConceptMap.size());
TermConceptMap conceptMap = optionalConceptMap.get();
TermConceptMap conceptMap = optionalConceptMap.get(0);
ourLog.info("ConceptMap:\n" + conceptMap.toString());

7
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.migrate.tasks;
*/
import ca.uhn.fhir.jpa.entity.EmpiLink;
import ca.uhn.fhir.jpa.entity.TermConceptMap;
import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
import ca.uhn.fhir.jpa.migrate.taskdef.ArbitrarySqlTask;
@ -143,6 +144,12 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
//EMPI Target Type
empiLink.addColumn("20200727.1","TARGET_TYPE").nullable().type(ColumnTypeEnum.STRING, EmpiLink.TARGET_TYPE_LENGTH);
//ConceptMap add version for search
Builder.BuilderWithTableName trmConceptMap = version.onTable("TRM_CONCEPT_MAP");
trmConceptMap.addColumn("20200910.1", "VER").nullable().type(ColumnTypeEnum.STRING, TermConceptMap.MAX_VER_LENGTH);
trmConceptMap.dropIndex("20200910.2", "IDX_CONCEPT_MAP_URL");
trmConceptMap.addIndex("20200910.3", "IDX_CONCEPT_MAP_URL").unique(true).withColumns("URL", "VER");
//Term CodeSystem Version and Term ValueSet Version
Builder.BuilderWithTableName trmCodeSystemVer = version.onTable("TRM_CODESYSTEM_VER");
trmCodeSystemVer.addIndex("20200923.1", "IDX_CODESYSTEM_AND_VER").unique(true).withColumns("CODESYSTEM_PID", "CS_VERSION_ID");

18
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/CommonCodeSystemsTerminologyService.java
View File

@ -326,6 +326,24 @@ public class CommonCodeSystemsTerminologyService implements IValidationSupport {
return url;
}
public static String getCodeSystemUrl(@Nonnull IBaseResource theCodeSystem) {
String url;
switch (theCodeSystem.getStructureFhirVersionEnum()) {
case R4: {
url = ((org.hl7.fhir.r4.model.CodeSystem) theCodeSystem).getUrl();
break;
}
case R5: {
url = ((org.hl7.fhir.r5.model.CodeSystem) theCodeSystem).getUrl();
break;
}
case DSTU3:
default:
throw new IllegalArgumentException("Can not handle version: " + theCodeSystem.getStructureFhirVersionEnum());
}
return url;
}
public static String getValueSetVersion(@Nonnull IBaseResource theValueSet) {
String version;
switch (theValueSet.getStructureFhirVersionEnum()) {

15
hapi-fhir-validation/src/test/java/org/hl7/fhir/common/hapi/validation/support/CommonCodeSystemsTerminologyServiceTest.java
View File

@ -5,6 +5,8 @@ import ca.uhn.fhir.context.FhirVersionEnum;
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.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ValueSet;
@ -13,6 +15,9 @@ import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.fail;
import javax.annotation.Nonnull;
public class CommonCodeSystemsTerminologyServiceTest {
@ -114,4 +119,14 @@ public class CommonCodeSystemsTerminologyServiceTest {
assertEquals(null, cs);
}
@Test
public void testFetchCodeSystemUrlDstu3() {
try {
CommonCodeSystemsTerminologyService.getCodeSystemUrl(new org.hl7.fhir.dstu3.model.CodeSystem());
fail();
} catch (IllegalArgumentException e) {
assertEquals("Can not handle version: DSTU3", e.getMessage());
}
}
}