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Merge branch 'vsm_operations' into aphl-300-valueset-interceptor
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25 changes: 25 additions & 0 deletions
25
core/src/main/java/org/opencds/cqf/ruler/provider/HapiFhirRepositoryProvider.java
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| package org.opencds.cqf.ruler.provider; | ||
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| import org.opencds.cqf.ruler.api.OperationProvider; | ||
| import org.opencds.cqf.ruler.behavior.DaoRegistryUser; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
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| import ca.uhn.fhir.cr.repo.HapiFhirRepository; | ||
| import ca.uhn.fhir.jpa.api.dao.DaoRegistry; | ||
| import ca.uhn.fhir.rest.api.server.RequestDetails; | ||
| import ca.uhn.fhir.rest.server.RestfulServer; | ||
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| public class HapiFhirRepositoryProvider implements OperationProvider, DaoRegistryUser { | ||
| @Autowired | ||
| private DaoRegistry myDaoRegistry; | ||
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| @Autowired | ||
| RestfulServer myRestfulServer; | ||
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| public DaoRegistry getDaoRegistry() { | ||
| return myDaoRegistry; | ||
| } | ||
| public HapiFhirRepository getRepository(RequestDetails theRequestDetails) { | ||
| return new HapiFhirRepository(myDaoRegistry, theRequestDetails, myRestfulServer); | ||
| } | ||
| } |
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309 changes: 220 additions & 89 deletions
309
plugin/cr/src/main/java/org/opencds/cqf/ruler/cr/KnowledgeArtifactProcessor.java
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79 changes: 79 additions & 0 deletions
79
plugin/cr/src/main/java/org/opencds/cqf/ruler/cr/TerminologyServerClient.java
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| package org.opencds.cqf.ruler.cr; | ||
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| import ca.uhn.fhir.context.FhirContext; | ||
| import ca.uhn.fhir.rest.client.api.IGenericClient; | ||
| import ca.uhn.fhir.rest.client.interceptor.AdditionalRequestHeadersInterceptor; | ||
| import org.apache.commons.lang3.StringUtils; | ||
| import org.hl7.fhir.r4.model.Parameters; | ||
| import org.hl7.fhir.r4.model.ValueSet; | ||
| import org.jetbrains.annotations.NotNull; | ||
| import org.opencds.cqf.cql.evaluator.fhir.util.Canonicals; | ||
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| import java.nio.charset.StandardCharsets; | ||
| import java.util.Base64; | ||
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| public class TerminologyServerClient { | ||
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| private final FhirContext ctx; | ||
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| private String username; | ||
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| private String getUsername() { | ||
| return username; | ||
| } | ||
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| private void setUsername(String username) { | ||
| this.username = username; | ||
| } | ||
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| private String apiKey; | ||
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| private String getApiKey() { | ||
| return apiKey; | ||
| } | ||
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| private void setApiKey(String apiKey) { | ||
| this.apiKey = apiKey; | ||
| } | ||
| public TerminologyServerClient() { | ||
| ctx = FhirContext.forR4(); | ||
| } | ||
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| public TerminologyServerClient(String username, String apiKey) { | ||
| this(); | ||
| setUsername(username); | ||
| setApiKey(apiKey); | ||
| } | ||
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| public ValueSet expand(ValueSet valueSet, String authoritativeSource, Parameters expansionParameters) { | ||
| IGenericClient fhirClient = ctx.newRestfulGenericClient(getAuthoritativeSourceBase(authoritativeSource)); | ||
| fhirClient.registerInterceptor(getAuthInterceptor(getUsername(), getApiKey())); | ||
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| // Invoke by Value Set ID | ||
| return fhirClient | ||
| .operation() | ||
| .onInstance(valueSet.getId()) | ||
| .named("$expand") | ||
| .withParameters(expansionParameters) | ||
| .returnResourceType(ValueSet.class) | ||
| .execute(); | ||
| } | ||
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| private AdditionalRequestHeadersInterceptor getAuthInterceptor(String username, String apiKey) { | ||
| String authString = StringUtils.join("Basic ", Base64.getEncoder() | ||
| .encodeToString(StringUtils.join(username, ":", apiKey).getBytes(StandardCharsets.UTF_8))); | ||
| AdditionalRequestHeadersInterceptor authInterceptor = new AdditionalRequestHeadersInterceptor(); | ||
| authInterceptor.addHeaderValue("Authorization", authString); | ||
| return authInterceptor; | ||
| } | ||
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| // Strips resource and id from the authoritative source URL, these are not needed as the client constructs the URL. | ||
| // Converts http URLs to https | ||
| private String getAuthoritativeSourceBase(String authoritativeSource) { | ||
| authoritativeSource = authoritativeSource.substring(0, authoritativeSource.indexOf(Canonicals.getResourceType(authoritativeSource))); | ||
| if (authoritativeSource.startsWith("http://")) { | ||
| authoritativeSource = authoritativeSource.replaceFirst("http://", "https://"); | ||
| } | ||
| return authoritativeSource; | ||
| } | ||
| } |
87 changes: 87 additions & 0 deletions
87
plugin/cr/src/main/java/org/opencds/cqf/ruler/cr/r4/helper/ResourceClassMapHelper.java
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| package org.opencds.cqf.ruler.cr.r4.helper; | ||
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| import java.util.HashMap; | ||
| import java.util.Map; | ||
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| import org.hl7.fhir.exceptions.FHIRException; | ||
| import org.hl7.fhir.instance.model.api.IBaseResource; | ||
| import org.hl7.fhir.r4.model.ActivityDefinition; | ||
| import org.hl7.fhir.r4.model.CapabilityStatement; | ||
| import org.hl7.fhir.r4.model.ChargeItemDefinition; | ||
| import org.hl7.fhir.r4.model.CodeSystem; | ||
| import org.hl7.fhir.r4.model.CompartmentDefinition; | ||
| import org.hl7.fhir.r4.model.ConceptMap; | ||
| import org.hl7.fhir.r4.model.EffectEvidenceSynthesis; | ||
| import org.hl7.fhir.r4.model.EventDefinition; | ||
| import org.hl7.fhir.r4.model.Evidence; | ||
| import org.hl7.fhir.r4.model.EvidenceVariable; | ||
| import org.hl7.fhir.r4.model.ExampleScenario; | ||
| import org.hl7.fhir.r4.model.GraphDefinition; | ||
| import org.hl7.fhir.r4.model.ImplementationGuide; | ||
| import org.hl7.fhir.r4.model.Library; | ||
| import org.hl7.fhir.r4.model.Measure; | ||
| import org.hl7.fhir.r4.model.MessageDefinition; | ||
| import org.hl7.fhir.r4.model.NamingSystem; | ||
| import org.hl7.fhir.r4.model.OperationDefinition; | ||
| import org.hl7.fhir.r4.model.PlanDefinition; | ||
| import org.hl7.fhir.r4.model.Questionnaire; | ||
| import org.hl7.fhir.r4.model.ResearchDefinition; | ||
| import org.hl7.fhir.r4.model.ResearchElementDefinition; | ||
| import org.hl7.fhir.r4.model.ResourceType; | ||
| import org.hl7.fhir.r4.model.RiskEvidenceSynthesis; | ||
| import org.hl7.fhir.r4.model.SearchParameter; | ||
| import org.hl7.fhir.r4.model.StructureDefinition; | ||
| import org.hl7.fhir.r4.model.StructureMap; | ||
| import org.hl7.fhir.r4.model.TerminologyCapabilities; | ||
| import org.hl7.fhir.r4.model.TestScript; | ||
| import org.hl7.fhir.r4.model.ValueSet; | ||
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| import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException; | ||
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| public class ResourceClassMapHelper { | ||
| public static final Map<ResourceType, Class<? extends IBaseResource>> resourceTypeToClass = new HashMap<ResourceType, Class<? extends IBaseResource>>() {{ | ||
| put(ResourceType.ActivityDefinition, ActivityDefinition.class); | ||
| put(ResourceType.CapabilityStatement, CapabilityStatement.class); | ||
| put(ResourceType.ChargeItemDefinition, ChargeItemDefinition.class); | ||
| put(ResourceType.CompartmentDefinition, CompartmentDefinition.class); | ||
| put(ResourceType.ConceptMap, ConceptMap.class); | ||
| put(ResourceType.EffectEvidenceSynthesis, EffectEvidenceSynthesis.class); | ||
| put(ResourceType.EventDefinition, EventDefinition.class); | ||
| put(ResourceType.Evidence, Evidence.class); | ||
| put(ResourceType.EvidenceVariable, EvidenceVariable.class); | ||
| put(ResourceType.ExampleScenario, ExampleScenario.class); | ||
| put(ResourceType.GraphDefinition, GraphDefinition.class); | ||
| put(ResourceType.ImplementationGuide, ImplementationGuide.class); | ||
| put(ResourceType.Library, Library.class); | ||
| put(ResourceType.Measure, Measure.class); | ||
| put(ResourceType.MessageDefinition, MessageDefinition.class); | ||
| put(ResourceType.NamingSystem, NamingSystem.class); | ||
| put(ResourceType.OperationDefinition, OperationDefinition.class); | ||
| put(ResourceType.PlanDefinition, PlanDefinition.class); | ||
| put(ResourceType.Questionnaire, Questionnaire.class); | ||
| put(ResourceType.ResearchDefinition, ResearchDefinition.class); | ||
| put(ResourceType.ResearchElementDefinition, ResearchElementDefinition.class); | ||
| put(ResourceType.RiskEvidenceSynthesis, RiskEvidenceSynthesis.class); | ||
| put(ResourceType.SearchParameter, SearchParameter.class); | ||
| put(ResourceType.StructureDefinition, StructureDefinition.class); | ||
| put(ResourceType.StructureMap, StructureMap.class); | ||
| put(ResourceType.TerminologyCapabilities, TerminologyCapabilities.class); | ||
| put(ResourceType.TestScript, TestScript.class); | ||
| put(ResourceType.ValueSet, ValueSet.class); | ||
| put(ResourceType.CodeSystem, CodeSystem.class); | ||
| }}; | ||
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| public static Class<? extends IBaseResource> getClass(String resourceType) throws UnprocessableEntityException { | ||
| ResourceType type = null; | ||
| try { | ||
| type = ResourceType.fromCode(resourceType); | ||
| } catch (FHIRException e) { | ||
| throw new UnprocessableEntityException("Could not find resource type : " + resourceType); | ||
| } | ||
| Class<? extends IBaseResource> retval = resourceTypeToClass.get(type); | ||
| if (retval == null) { | ||
| throw new UnprocessableEntityException(resourceType + " is not a valid KnowledgeArtifact resource type"); | ||
| } | ||
| return retval; | ||
| } | ||
| } |
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