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Merge pull request #226 from DBCG/conceptMap
Concept map
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dstu3/src/main/java/org/opencds/cqf/dstu3/providers/ObservationProvider.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,80 @@ | ||
| package org.opencds.cqf.dstu3.providers; | ||
|
|
||
| import ca.uhn.fhir.context.FhirContext; | ||
| import ca.uhn.fhir.rest.annotation.Operation; | ||
| import ca.uhn.fhir.rest.annotation.OperationParam; | ||
| import ca.uhn.fhir.rest.client.api.IGenericClient; | ||
| import ca.uhn.fhir.util.BundleUtil; | ||
| import org.hl7.fhir.dstu3.model.Bundle; | ||
| import org.hl7.fhir.dstu3.model.Coding; | ||
| import org.hl7.fhir.dstu3.model.ConceptMap; | ||
| import org.hl7.fhir.dstu3.model.Observation; | ||
| import org.opencds.cqf.common.config.HapiProperties; | ||
|
|
||
| import java.util.HashMap; | ||
| import java.util.List; | ||
| import java.util.stream.Collectors; | ||
|
|
||
| import static org.opencds.cqf.common.helpers.ClientHelper.getClient; | ||
|
|
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| public class ObservationProvider { | ||
|
|
||
| private FhirContext fhirContext; | ||
|
|
||
| public ObservationProvider(FhirContext fhirContext){ | ||
| this.fhirContext = fhirContext; | ||
| } | ||
|
|
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| @Operation(name = "$transform", idempotent = false, type = Observation.class) | ||
| public Bundle transformObservations( | ||
| @OperationParam(name = "observations") Bundle observationsBundle, | ||
| @OperationParam(name = "conceptMapURL") String conceptMapURL | ||
| ) { | ||
| if(null == observationsBundle) { | ||
| throw new IllegalArgumentException("Unable to perform operation Observation$transform. No Observation bundle passed in."); | ||
| } | ||
| if(null == conceptMapURL) { | ||
| throw new IllegalArgumentException("Unable to perform operation Observation$transform. No concept map url specified."); | ||
| } | ||
| IGenericClient client = getClient(fhirContext, conceptMapURL, HapiProperties.getObservationTransformUsername(), HapiProperties.getObservationTransformPassword() ); | ||
| ConceptMap transformConceptMap = client.read().resource(ConceptMap.class).withUrl (conceptMapURL).execute(); | ||
| if(null == transformConceptMap) { | ||
| throw new IllegalArgumentException("Unable to perform operation Observation$transform. Unable to get concept map."); | ||
| } | ||
| List<Observation> observations = BundleUtil.toListOfResources(fhirContext, observationsBundle).stream() | ||
| .filter(resource -> resource instanceof Observation) | ||
| .map(Observation.class::cast) | ||
| .collect(Collectors.toList()); | ||
| /** | ||
| * TODO - There must be a more efficient way to loop through this, but so far I have not come up with it. | ||
| */ | ||
| transformConceptMap.getGroup().forEach(group -> { | ||
| HashMap<String, ConceptMap.TargetElementComponent> codeMappings = new HashMap<>(); | ||
| String targetSystem = group.getTarget(); | ||
| group.getElement().forEach(codeElement -> { | ||
| codeMappings.put(codeElement.getCode(), codeElement.getTarget().get(0)); | ||
| }); | ||
| observations.forEach(observation -> { | ||
| if(observation.getValue().fhirType().equalsIgnoreCase("codeableconcept")){ | ||
| String obsValueCode = observation.getValueCodeableConcept().getCoding().get(0).getCode(); | ||
| if(obsValueCode != null) { | ||
| if (codeMappings.get(observation.getValueCodeableConcept().getCoding().get(0).getCode()) != null) { | ||
| if (HapiProperties.getObservationTransformReplaceCode()) { | ||
| observation.getValueCodeableConcept().getCoding().get(0).setCode(codeMappings.get(obsValueCode).getCode()); | ||
| observation.getValueCodeableConcept().getCoding().get(0).setDisplay(codeMappings.get(obsValueCode).getDisplay()); | ||
| observation.getValueCodeableConcept().getCoding().get(0).setSystem(targetSystem); | ||
| } else { | ||
| Coding newCoding = new Coding(); | ||
| newCoding.setSystem(targetSystem); | ||
| newCoding.setCode(codeMappings.get(obsValueCode).getCode()); | ||
| newCoding.setDisplay(codeMappings.get(obsValueCode).getDisplay()); | ||
| observation.getValueCodeableConcept().getCoding().add(newCoding); | ||
| } | ||
| } | ||
| } | ||
| } | ||
| }); | ||
| }); | ||
| return observationsBundle; | ||
| } | ||
| } |
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80 changes: 80 additions & 0 deletions
80
r4/src/main/java/org/opencds/cqf/r4/providers/ObservationProvider.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,80 @@ | ||
| package org.opencds.cqf.r4.providers; | ||
|
|
||
| import ca.uhn.fhir.context.FhirContext; | ||
| import ca.uhn.fhir.rest.annotation.Operation; | ||
| import ca.uhn.fhir.rest.annotation.OperationParam; | ||
| import ca.uhn.fhir.rest.client.api.IGenericClient; | ||
| import ca.uhn.fhir.util.BundleUtil; | ||
| import org.hl7.fhir.r4.model.Bundle; | ||
| import org.hl7.fhir.r4.model.Coding; | ||
| import org.hl7.fhir.r4.model.ConceptMap; | ||
| import org.hl7.fhir.r4.model.Observation; | ||
| import org.opencds.cqf.common.config.HapiProperties; | ||
|
|
||
| import java.util.HashMap; | ||
| import java.util.List; | ||
| import java.util.stream.Collectors; | ||
|
|
||
| import static org.opencds.cqf.common.helpers.ClientHelper.getClient; | ||
|
|
||
| public class ObservationProvider { | ||
|
|
||
| private FhirContext fhirContext; | ||
|
|
||
| public ObservationProvider(FhirContext fhirContext){ | ||
| this.fhirContext = fhirContext; | ||
| } | ||
|
|
||
| @Operation(name = "$transform", idempotent = false, type = Observation.class) | ||
| public Bundle transformObservations( | ||
| @OperationParam(name = "observations") Bundle observationsBundle, | ||
| @OperationParam(name = "conceptMapURL") String conceptMapURL | ||
| ) { | ||
| if(null == observationsBundle) { | ||
| throw new IllegalArgumentException("Unable to perform operation Observation$transform. No Observation bundle passed in."); | ||
| } | ||
| if(null == conceptMapURL) { | ||
| throw new IllegalArgumentException("Unable to perform operation Observation$transform. No concept map url specified."); | ||
| } | ||
| IGenericClient client = getClient(fhirContext, conceptMapURL, HapiProperties.getObservationTransformUsername(), HapiProperties.getObservationTransformPassword() ); | ||
| ConceptMap transformConceptMap = client.read().resource(ConceptMap.class).withUrl (conceptMapURL).execute(); | ||
| if(null == transformConceptMap) { | ||
| throw new IllegalArgumentException("Unable to perform operation Observation$transform. Unable to get concept map."); | ||
| } | ||
| List<Observation> observations = BundleUtil.toListOfResources(fhirContext, observationsBundle).stream() | ||
| .filter(resource -> resource instanceof Observation) | ||
| .map(Observation.class::cast) | ||
| .collect(Collectors.toList()); | ||
| /** | ||
| * TODO - There must be a more efficient way to loop through this, but so far I have not come up with it. | ||
| */ | ||
| transformConceptMap.getGroup().forEach(group -> { | ||
| HashMap<String, ConceptMap.TargetElementComponent> codeMappings = new HashMap<>(); | ||
| String targetSystem = group.getTarget(); | ||
| group.getElement().forEach(codeElement -> { | ||
| codeMappings.put(codeElement.getCode(), codeElement.getTarget().get(0)); | ||
| }); | ||
| observations.forEach(observation -> { | ||
| if(observation.getValue().fhirType().equalsIgnoreCase("codeableconcept")){ | ||
| String obsValueCode = observation.getValueCodeableConcept().getCoding().get(0).getCode(); | ||
| if(obsValueCode != null) { | ||
| if (codeMappings.get(observation.getValueCodeableConcept().getCoding().get(0).getCode()) != null) { | ||
| if (HapiProperties.getObservationTransformReplaceCode()) { | ||
| observation.getValueCodeableConcept().getCoding().get(0).setCode(codeMappings.get(obsValueCode).getCode()); | ||
| observation.getValueCodeableConcept().getCoding().get(0).setDisplay(codeMappings.get(obsValueCode).getDisplay()); | ||
| observation.getValueCodeableConcept().getCoding().get(0).setSystem(targetSystem); | ||
| } else { | ||
| Coding newCoding = new Coding(); | ||
| newCoding.setSystem(targetSystem); | ||
| newCoding.setCode(codeMappings.get(obsValueCode).getCode()); | ||
| newCoding.setDisplay(codeMappings.get(obsValueCode).getDisplay()); | ||
| observation.getValueCodeableConcept().getCoding().add(newCoding); | ||
| } | ||
| } | ||
| } | ||
| } | ||
| }); | ||
| }); | ||
| return observationsBundle; | ||
| } | ||
| } |
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