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A few fixes resulting from the R5 merge

This commit is contained in:
James Agnew 2019-08-06 17:55:51 -04:00
parent 60eab3ad70
commit b0eb19cf2f
4 changed files with 111 additions and 122 deletions
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20
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/rdf/StreamRDFDedup.java
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@ -1,5 +1,25 @@
package ca.uhn.fhir.util.rdf;
/*-
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.HashSet;
import java.util.LinkedList;

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/rdf/StreamingRDFWriter.java
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@ -1,5 +1,25 @@
package ca.uhn.fhir.util.rdf;
/*-
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.io.OutputStream;
import java.util.Iterator;
import java.util.Map.Entry;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
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@ -313,7 +313,7 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5<ValueSet> imple
if (myDaoConfig.isPreExpandValueSetsExperimental()) {
if (retVal.getDeleted() == null) {
ValueSet valueSet = (ValueSet) theResource;
myHapiTerminologySvc.storeTermValueSetAndChildren(retVal, org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSet));
myHapiTerminologySvc.storeTermValueSet(retVal, org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSet));
} else {
myHapiTerminologySvc.deleteValueSetAndChildren(retVal);
}

185
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR5.java
View File

@ -2,12 +2,10 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.UrlUtil;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.hapi.ctx.IValidationSupport;
@ -53,27 +51,19 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements IValidationSupport, IHapiTerminologySvcR5 {
@Autowired
@Qualifier("myValueSetDaoR5")
private IFhirResourceDao<ValueSet> myValueSetResourceDao;
@Autowired
@Qualifier("myConceptMapDaoR5")
@Qualifier("myConceptMapDaoR4")
private IFhirResourceDao<ConceptMap> myConceptMapResourceDao;
@Autowired
private IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> myCodeSystemResourceDao;
@Qualifier("myCodeSystemDaoR4")
private IFhirResourceDao<CodeSystem> myCodeSystemResourceDao;
@Autowired
@Qualifier("myValueSetDaoR4")
private IFhirResourceDao<ValueSet> myValueSetResourceDao;
@Autowired
private IValidationSupport myValidationSupport;
@Autowired
private IHapiTerminologySvc myTerminologySvc;
@Autowired
private PlatformTransactionManager myTransactionManager;
/**
* Constructor
*/
public HapiTerminologySvcR5() {
super();
}
private void addAllChildren(String theSystemString, ConceptDefinitionComponent theCode, List<VersionIndependentConcept> theListToPopulate) {
if (isNotBlank(theCode.getCode())) {
theListToPopulate.add(new VersionIndependentConcept(theSystemString, theCode.getCode()));
@ -99,112 +89,72 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
@Override
protected IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource) {
CodeSystem resourceToStore;
try {
resourceToStore = org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(theCodeSystemResource);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
validateCodeSystemForStorage(theCodeSystemResource);
if (isBlank(resourceToStore.getIdElement().getIdPart())) {
CodeSystem codeSystemR4 = org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(theCodeSystemResource);
if (isBlank(theCodeSystemResource.getIdElement().getIdPart())) {
String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
return myCodeSystemResourceDao.update(resourceToStore, matchUrl).getId();
return myCodeSystemResourceDao.update(codeSystemR4, matchUrl).getId();
} else {
return myCodeSystemResourceDao.update(resourceToStore).getId();
return myCodeSystemResourceDao.update(codeSystemR4).getId();
}
}
@Override
protected void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
ConceptMap resourceToStore;
try {
resourceToStore = org.hl7.fhir.convertors.conv40_50.ConceptMap.convertConceptMap(theConceptMap);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
if (isBlank(resourceToStore.getIdElement().getIdPart())) {
ConceptMap conceptMapR4 = org.hl7.fhir.convertors.conv40_50.ConceptMap.convertConceptMap(theConceptMap);
if (isBlank(theConceptMap.getIdElement().getIdPart())) {
String matchUrl = "ConceptMap?url=" + UrlUtil.escapeUrlParam(theConceptMap.getUrl());
myConceptMapResourceDao.update(resourceToStore, matchUrl);
myConceptMapResourceDao.update(conceptMapR4, matchUrl);
} else {
myConceptMapResourceDao.update(resourceToStore);
myConceptMapResourceDao.update(conceptMapR4);
}
}
@Override
protected void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
ValueSet valueSetDstu3;
try {
valueSetDstu3 = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(theValueSet);
} catch (FHIRException e) {
throw new InternalErrorException(e);
ValueSet valueSetR4 = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(theValueSet);
if (isBlank(theValueSet.getIdElement().getIdPart())) {
String matchUrl = "ValueSet?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());
myValueSetResourceDao.update(valueSetR4, matchUrl);
} else {
myValueSetResourceDao.update(valueSetR4);
}
}
if (isBlank(valueSetDstu3.getIdElement().getIdPart())) {
String matchUrl = "ValueSet?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());
myValueSetResourceDao.update(valueSetDstu3, matchUrl);
} else {
myValueSetResourceDao.update(valueSetDstu3);
@Override
public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
ValueSet valueSetR5 = myValidationSupport.fetchResource(myContext, ValueSet.class, theValueSet);
if (valueSetR5 == null) {
return Collections.emptyList();
}
return expandValueSetAndReturnVersionIndependentConcepts(org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetR5));
}
@Override
public IBaseResource expandValueSet(IBaseResource theInput) {
org.hl7.fhir.r4.model.ValueSet valueSetToExpand = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet((ValueSet) theInput);
org.hl7.fhir.r4.model.ValueSet valueSetR4 = super.expandValueSet(valueSetToExpand);
return org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetR4);
}
@Override
public void expandValueSet(IBaseResource theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator) {
org.hl7.fhir.r4.model.ValueSet valueSetToExpand = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet((ValueSet) theValueSetToExpand);
super.expandValueSet(valueSetToExpand, theValueSetCodeAccumulator);
}
@Override
public ValueSetExpander.ValueSetExpansionOutcome expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
ValueSet valueSetToExpand = new ValueSet();
valueSetToExpand.getCompose().addInclude(theInclude);
try {
org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
valueSetToExpandR4 = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetToExpand);
org.hl7.fhir.r4.model.ValueSet expandedValueSet = super.expandValueSet(valueSetToExpandR4);
return new ValueSetExpander.ValueSetExpansionOutcome(org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(expandedValueSet));
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
}
@Override
public IBaseResource expandValueSet(IBaseResource theInput) {
ValueSet valueSetToExpand = (ValueSet) theInput;
try {
org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
valueSetToExpandR4 = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetToExpand);
org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSet(valueSetToExpandR4);
return org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(expandedR4);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
}
@Override
public void expandValueSet(IBaseResource theValueSetToExpand, IValueSetCodeAccumulator theValueSetCodeAccumulator) {
ValueSet valueSetToExpand = (ValueSet) theValueSetToExpand;
try {
org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
valueSetToExpandR4 = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetToExpand);
super.expandValueSet(valueSetToExpandR4, theValueSetCodeAccumulator);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
}
@Override
public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
ValueSet vs = myValidationSupport.fetchResource(myContext, ValueSet.class, theValueSet);
if (vs == null) {
return Collections.emptyList();
}
org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
try {
valueSetToExpandR4 = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(vs);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
return expandValueSetAndReturnVersionIndependentConcepts(valueSetToExpandR4);
org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSet(org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetToExpand));
return new ValueSetExpander.ValueSetExpansionOutcome(org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(expandedR4));
}
@Override
@ -223,17 +173,17 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
return null;
}
@Override
public IBaseResource fetchResource(FhirContext theContext, Class theClass, String theUri) {
return null;
}
@CoverageIgnore
@Override
public ValueSet fetchValueSet(FhirContext theContext, String theSystem) {
return null;
}
@Override
public <T extends IBaseResource> T fetchResource(FhirContext theContext, Class<T> theClass, String theUri) {
return null;
}
@CoverageIgnore
@Override
public StructureDefinition fetchStructureDefinition(FhirContext theCtx, String theUrl) {
@ -284,17 +234,19 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
@Override
protected org.hl7.fhir.r4.model.CodeSystem getCodeSystemFromContext(String theSystem) {
CodeSystem codeSystem = myValidationSupport.fetchCodeSystem(myContext, theSystem);
try {
return org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(codeSystem);
} catch (FHIRException e) {
throw new InternalErrorException(e);
CodeSystem codeSystemR5 = myValidationSupport.fetchCodeSystem(myContext, theSystem);
return org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(codeSystemR5);
}
@Override
protected org.hl7.fhir.r4.model.ValueSet getValueSetFromResourceTable(ResourceTable theResourceTable) {
ValueSet valueSetR5 = myValueSetResourceDao.toResource(ValueSet.class, theResourceTable, null, false);
return org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetR5);
}
@Override
public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
return myTerminologySvc.supportsSystem(theSystem);
return supportsSystem(theSystem);
}
@Override
@ -304,25 +256,23 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
@CoverageIgnore
@Override
public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
public IValidationSupport.CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
return txTemplate.execute(t-> {
Optional<TermConcept> codeOpt = myTerminologySvc.findCode(theCodeSystem, theCode);
Optional<TermConcept> codeOpt = findCode(theCodeSystem, theCode);
if (codeOpt.isPresent()) {
ConceptDefinitionComponent def = new ConceptDefinitionComponent();
TermConcept code = codeOpt.get();
ConceptDefinitionComponent def = new ConceptDefinitionComponent();
def.setCode(code.getCode());
def.setDisplay(code.getDisplay());
CodeValidationResult retVal = new CodeValidationResult(def);
IValidationSupport.CodeValidationResult retVal = new IValidationSupport.CodeValidationResult(def);
retVal.setProperties(code.toValidationProperties());
retVal.setCodeSystemName(code.getCodeSystemVersion().getCodeSystem().getName());
return retVal;
}
return new CodeValidationResult(IssueSeverity.ERROR, "Unknown code {" + theCodeSystem + "}" + theCode);
return new IValidationSupport.CodeValidationResult(IssueSeverity.ERROR, "Unknown code {" + theCodeSystem + "}" + theCode);
});
}
@Override
@ -330,5 +280,4 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
return super.lookupCode(theContext, theSystem, theCode);
}
}