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Aphl 300 valueset interceptor (#757)
* ValueSet update interceptor for updating code synonyms --------- Co-authored-by: taha.attari@smilecdr.com <taha.attari@smilecdr.com> Co-authored-by: Adam Stevenson <stevenson_adam@yahoo.com>
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94 changes: 94 additions & 0 deletions
94
plugin/cr/src/main/java/org/opencds/cqf/ruler/cr/ValueSetSynonymUpdateInterceptor.java
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| package org.opencds.cqf.ruler.cr; | ||
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|
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| import java.util.ArrayList; | ||
| import java.util.List; | ||
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| import org.cqframework.fhir.api.FhirDal; | ||
| import org.hl7.fhir.instance.model.api.IBaseResource; | ||
| import org.hl7.fhir.r4.model.CodeableConcept; | ||
| import org.hl7.fhir.r4.model.Library; | ||
| import org.hl7.fhir.r4.model.RelatedArtifact; | ||
| import org.hl7.fhir.r4.model.ResourceType; | ||
| import org.hl7.fhir.r4.model.ValueSet; | ||
| import org.hl7.fhir.r4.model.ValueSet.ConceptReferenceComponent; | ||
| import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent; | ||
| import org.opencds.cqf.ruler.behavior.DaoRegistryUser; | ||
| import org.opencds.cqf.ruler.utility.TypedBundleProvider; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
|
|
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| import ca.uhn.fhir.interceptor.api.Hook; | ||
| import ca.uhn.fhir.interceptor.api.Pointcut; | ||
| import ca.uhn.fhir.jpa.api.dao.DaoRegistry; | ||
| import ca.uhn.fhir.jpa.searchparam.SearchParameterMap; | ||
| import ca.uhn.fhir.rest.api.server.RequestDetails; | ||
| import ca.uhn.fhir.rest.param.TokenParam; | ||
| import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException; | ||
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|
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| public class ValueSetSynonymUpdateInterceptor implements org.opencds.cqf.ruler.api.Interceptor, DaoRegistryUser { | ||
| @Autowired | ||
| private DaoRegistry myDaoRegistry; | ||
|
|
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| private String synonymUrl; | ||
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| ValueSetSynonymUpdateInterceptor(String synonymUrl) { | ||
| this.synonymUrl = synonymUrl; | ||
| } | ||
|
|
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| public DaoRegistry getDaoRegistry() { | ||
| return myDaoRegistry; | ||
| } | ||
|
|
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| /** Handle updates */ | ||
| @Hook(Pointcut.STORAGE_PRESTORAGE_RESOURCE_UPDATED) | ||
| public void update( | ||
| IBaseResource theOldResource, | ||
| IBaseResource theResource, | ||
| RequestDetails theRequestDetails) throws UnprocessableEntityException { | ||
| if (theResource.fhirType().equals(ResourceType.ValueSet.toString())) { | ||
| ValueSet vs = (ValueSet) theResource; | ||
| if (vs.getUrl().equals(this.synonymUrl)) { | ||
| FhirDal fhirDal = new JpaFhirDal(myDaoRegistry,theRequestDetails); | ||
| List<ConceptSetComponent> sets = vs.getCompose().getInclude(); | ||
| List<Library> librariesToUpdate = new ArrayList<Library>(); | ||
| for (ConceptSetComponent set: sets) { | ||
| // for each system in the value set | ||
| String system = set.getSystem(); | ||
| List<ConceptReferenceComponent> concepts = set.getConcept(); | ||
| for (ConceptReferenceComponent concept:concepts) { | ||
| // for each concept.code need to update the extension.valueCodeableConcept.coding.display to concept.designation(where code = synonym).value | ||
| TokenParam token = new TokenParam(system,concept.getCode()); | ||
| SearchParameterMap map = new SearchParameterMap("manifest-contains-code",token); | ||
| TypedBundleProvider<Library> result = search(Library.class, map); | ||
| result.getAllResourcesTyped().stream().forEach(lib -> { | ||
| Library getCachedLibraryOrAdd = librariesToUpdate | ||
| .stream().filter(existing -> existing.getId().equals(lib.getId())).findFirst() | ||
| .orElseGet(() -> { | ||
| librariesToUpdate.add(lib); | ||
| return lib; | ||
| }); | ||
| String newText = concept.getDesignation() | ||
| .stream().filter(designation -> designation.getUse().getCode().equals("synonym")) | ||
| .findFirst().orElseThrow(()-> new UnprocessableEntityException("No synonym found for code: " + system + "|" + concept.getCode())) | ||
| .getValue(); | ||
| updateConditionWithNewSynonym(getCachedLibraryOrAdd,system, concept.getCode(),newText ); | ||
| }); | ||
| } | ||
| } | ||
| for (Library library:librariesToUpdate) { | ||
| fhirDal.update(library); | ||
| } | ||
| } | ||
| } | ||
| } | ||
| private void updateConditionWithNewSynonym(Library library, String system, String code, String newText) { | ||
| List<RelatedArtifact> relatedArtifacts = library.getRelatedArtifact(); | ||
| relatedArtifacts.stream() | ||
| .map(ra -> ra.getExtensionByUrl(KnowledgeArtifactProcessor.valueSetConditionUrl)) | ||
| .filter(ext -> ext != null) | ||
| .map(ext -> (CodeableConcept)ext.getValue()) | ||
| .filter(concept -> concept.getCoding().stream().anyMatch(coding -> coding.getSystem().equals(system) && coding.getCode().equals(code))) | ||
| .forEach(concept -> { | ||
| concept.setText(newText); | ||
| }); | ||
| } | ||
| } |
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69 changes: 69 additions & 0 deletions
69
plugin/cr/src/test/resources/libraries-with-conditions-bundle.json
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| { | ||
| "resourceType": "Bundle", | ||
| "id": "bundle-ersd-specification-example", | ||
| "type": "transaction", | ||
| "entry": [ | ||
| { | ||
| "fullUrl": "http://hl7.org/fhir/us/ecr/Library/SpecificationLibrary", | ||
| "resource": { | ||
| "resourceType": "Library", | ||
| "id": "lib1", | ||
| "relatedArtifact": [ | ||
| { | ||
| "extension": [ | ||
| { | ||
| "url": "http://aphl.org/fhir/vsm/StructureDefinition/vsm-valueset-condition", | ||
| "valueCodeableConcept": { | ||
| "coding": [ | ||
| { | ||
| "system": "http://snomed.info/sct", | ||
| "code": "767146004" | ||
| } | ||
| ], | ||
| "text": "Infection caused by Acanthamoeba (disorder)" | ||
| } | ||
| } | ||
| ], | ||
| "type": "depends-on", | ||
| "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1146.1506|1.0.0" | ||
| } | ||
| ] | ||
| }, | ||
| "request": { | ||
| "method": "PUT", | ||
| "url": "Library/lib1" | ||
| } | ||
| }, | ||
| { | ||
| "fullUrl": "http://hl7.org/fhir/us/ecr/Library/SpecificationLibrary", | ||
| "resource": { | ||
| "resourceType": "Library", | ||
| "id": "lib2", | ||
| "relatedArtifact": [ | ||
| { | ||
| "extension": [ | ||
| { | ||
| "url": "http://aphl.org/fhir/vsm/StructureDefinition/vsm-valueset-condition", | ||
| "valueCodeableConcept": { | ||
| "coding": [ | ||
| { | ||
| "system": "http://snomed.info/sct", | ||
| "code": "49649001" | ||
| } | ||
| ], | ||
| "text": "Infection caused by Acanthamoeba (disorder)" | ||
| } | ||
| } | ||
| ], | ||
| "type": "depends-on", | ||
| "resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1146.1506|1.0.0" | ||
| } | ||
| ] | ||
| }, | ||
| "request": { | ||
| "method": "PUT", | ||
| "url": "Library/lib2" | ||
| } | ||
| } | ||
| ] | ||
| } |
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10
plugin/cr/src/test/resources/manifest-code-search-parameter.json
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| { | ||
| "resourceType": "SearchParameter", | ||
| "id": "manifest-contains-code", | ||
| "status": "active", | ||
| "code": "manifest-contains-code", | ||
| "base": ["Library"], | ||
| "type": "token", | ||
| "description": "Return all Libraries which reference a particular code", | ||
| "expression": "Library.relatedArtifact.extension.where(url.contains('vsm-valueset-condition')).value as CodeableConcept" | ||
| } |
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