v2 -> v1 plugin

ersd-v2-v1-transform/pom.xml

@@ -0,0 +1,66 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<parent>
+		<groupId>org.opencds.cqf.ruler</groupId>
+		<artifactId>cqf-ruler</artifactId>
+		<version>0.15.0-SNAPSHOT</version>
+		<relativePath>../</relativePath>
+	</parent>
+
+	<groupId>com.transform</groupId>
+	<artifactId>cqf-ruler-ersd-v2-v1-transform-plugin</artifactId>
+	<version>1.0.0</version>
+	<dependencies>
+		<dependency>
+			<groupId>org.opencds.cqf.ruler</groupId>
+			<artifactId>cqf-ruler-core</artifactId>
+			<version>0.15.0-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>org.junit.jupiter</groupId>
+			<artifactId>junit-jupiter-api</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.junit.jupiter</groupId>
+			<artifactId>junit-jupiter-engine</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.opencds.cqf.ruler</groupId>
+			<artifactId>cqf-ruler-test</artifactId>
+			<version>0.15.0-SNAPSHOT</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-web</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-test</artifactId>
+			<scope>test</scope>
+		</dependency>
+	</dependencies>
+	<build>
+		<pluginManagement>
+			<plugins>
+				<plugin>
+					<groupId>org.sonatype.plugins</groupId>
+					<artifactId>nexus-staging-maven-plugin</artifactId>
+					<configuration>
+						<skipNexusStagingDeployMojo>true</skipNexusStagingDeployMojo>
+						<skip>true</skip>
+					</configuration>
+				</plugin>
+			</plugins>
+		</pluginManagement>
+	</build>
+</project>

ersd-v2-v1-transform/src/main/java/com/transform/TransformConfig.java

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+package com.transform;
+
+import org.opencds.cqf.external.annotations.OnR4Condition;
+import org.opencds.cqf.ruler.api.OperationProvider;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Conditional;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+public class TransformConfig {
+  @Bean
+	public TransformProperties transformProperties() {
+		return new TransformProperties();
+	}
+
+	@Bean
+	@Conditional(OnR4Condition.class)
+	public OperationProvider transformProvider() {
+		return new TransformProvider();
+	}
+}

ersd-v2-v1-transform/src/main/java/com/transform/TransformProperties.java

@@ -0,0 +1,27 @@
+package com.transform;
+import org.hl7.fhir.r5.model.IdType;
+import org.opencds.cqf.ruler.behavior.DaoRegistryUser;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.context.properties.ConfigurationProperties;
+
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+
+@ConfigurationProperties(prefix = "transform")
+public class TransformProperties implements DaoRegistryUser {
+  @Autowired
+	private DaoRegistry myDaoRegistry;
+
+  public static final IdType v1PlanDefinitionId = new IdType("PlanDefinition", "plandefinition-ersd-skeleton");
+  public static final String usPHTriggeringVSProfile = "http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-triggering-valueset";
+  public static final String usPHTriggeringVSLibProfile = "http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-triggering-valueset-library";
+  public static final String ersdVSLibProfile = "http://hl7.org/fhir/us/ecr/StructureDefinition/ersd-valueset-library";
+  public static final String ersdVSProfile = "http://hl7.org/fhir/us/ecr/StructureDefinition/ersd-valueset";
+  public static final String ersdPlanDefinitionProfile = "http://hl7.org/fhir/us/ecr/StructureDefinition/ersd-plandefinition";
+  public static final String usPHSpecLibProfile = "http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-specification-library";
+  public static final String usPHUsageContextType = "http://hl7.org/fhir/us/ecr/CodeSystem/us-ph-usage-context-type";
+  public static final String usPHUsageContext = "http://hl7.org/fhir/us/ecr/CodeSystem/us-ph-usage-context";
+
+  public DaoRegistry getDaoRegistry() {
+		return myDaoRegistry;
+	}
+}

ersd-v2-v1-transform/src/main/java/com/transform/TransformProvider.java

@@ -0,0 +1,135 @@
+package com.transform;
+
+import java.util.List;
+import java.util.Optional;
+import java.util.stream.Collectors;
+
+import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.r4.model.CanonicalType;
+import org.hl7.fhir.r4.model.Meta;
+import org.hl7.fhir.r4.model.MetadataResource;
+import org.hl7.fhir.r4.model.PlanDefinition;
+import org.hl7.fhir.r4.model.Reference;
+import org.hl7.fhir.r4.model.ResourceType;
+import org.hl7.fhir.r4.model.UsageContext;
+import org.opencds.cqf.ruler.api.OperationProvider;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.rest.annotation.Operation;
+import ca.uhn.fhir.rest.annotation.OperationParam;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+
+public class TransformProvider implements OperationProvider {
+	@Autowired
+	TransformProperties transformProperties;
+
+	/**
+	 * Implements the $ersd-v2-to-v1-transform operation which transforms an ersd v2 Bundle
+	 * into an ersd v1 compatible bundle
+	 * @return a greeting
+	 */
+	@Description(shortDefinition = "Converts a v2 ERSD bundle into a v1 ERSD bundle", value = "Converts a v2 ERSD bundle into a v1 ERSD bundle")
+	@Operation(idempotent = true, name = "$ersd-v2-to-v1-transform")
+	public Bundle convert_v1(
+		RequestDetails requestDetails,
+		@OperationParam(name = "resource") IBaseResource maybeBundle) throws UnprocessableEntityException {
+		if (maybeBundle == null) {
+			throw new UnprocessableEntityException("Resource is missing");
+		}
+		if (!(maybeBundle instanceof IBaseBundle )) {
+			throw new UnprocessableEntityException("Resource is not a bundle");
+		}
+		Bundle v2 = (Bundle) maybeBundle;
+		removeRootSpecificationLibrary(v2);
+		final PlanDefinition v1PlanDefinition = getV1PlanDefinition(requestDetails);
+		v2.getEntry().stream()
+			.forEach(entry -> {
+				if (entry.getResource() instanceof MetadataResource) {
+					MetadataResource resource = (MetadataResource) entry.getResource();
+					checkAndUpdateV2PlanDefinition(entry, v1PlanDefinition);
+					updateV2TriggeringValueSets(resource, v1PlanDefinition.getUrl());
+					updateV2TriggeringValueSetLibrary(resource);
+					resource.setExperimentalElement(null);
+				}
+			});
+		return v2;
+	}
+	private void removeRootSpecificationLibrary(Bundle v2) {
+		List<BundleEntryComponent> filteredRootLib = v2.getEntry().stream()
+			.filter(entry -> entry.hasResource())
+			.filter(entry -> !(entry.getResource().hasMeta() && entry.getResource().getMeta().hasProfile(TransformProperties.usPHSpecLibProfile))).collect(Collectors.toList());
+		v2.setEntry(filteredRootLib);
+	}
+	private void checkAndUpdateV2PlanDefinition(BundleEntryComponent entry, PlanDefinition v1PlanDefinition) {
+		if (entry.getResource().getResourceType() == ResourceType.PlanDefinition
+			&& entry.getResource().hasMeta()
+			&& entry.getResource().getMeta().getProfile().stream().anyMatch(canonical -> canonical.getValue().contains("/ersd-plandefinition"))) {
+			entry.setResource(v1PlanDefinition);
+		}
+	}
+	private void replaceProfile(Meta meta, String oldProfile, String newProfile) {
+		meta.getProfile().replaceAll(profile -> {
+			if (profile.getValue().equals(oldProfile)) {
+				return new CanonicalType(newProfile);
+			} else {
+				return profile;
+			}
+		});
+	}
+	private void updateV2TriggeringValueSetLibrary(MetadataResource resource) {
+		if (resource.getResourceType() == ResourceType.Library
+			&& resource.hasMeta() 
+			&& resource.getMeta().hasProfile(TransformProperties.usPHTriggeringVSLibProfile)
+		) {
+			replaceProfile(resource.getMeta(), TransformProperties.usPHTriggeringVSLibProfile, TransformProperties.ersdVSLibProfile);
+			List<UsageContext> filteredUseContexts = resource.getUseContext().stream()
+				.filter(useContext -> 
+					 !(useContext.getCode().getCode().equals("reporting")
+					&& useContext.getValueCodeableConcept().hasCoding(TransformProperties.usPHUsageContext, "triggering")) 
+				&& !(useContext.getCode().getCode().equals("specification-type")
+					&& useContext.getValueCodeableConcept().hasCoding(TransformProperties.usPHUsageContext, "value-set-library")))
+				.collect(Collectors.toList());
+			resource.setUseContext(filteredUseContexts);
+		}
+	}
+	private void updateV2TriggeringValueSets(MetadataResource resource, String v1PlanDefinitionUrl) {
+		if (resource.getResourceType() == ResourceType.ValueSet
+		 && resource.hasMeta() 
+		 && resource.getMeta().hasProfile(TransformProperties.usPHTriggeringVSProfile)) {
+			replaceProfile(resource.getMeta(), TransformProperties.usPHTriggeringVSProfile, TransformProperties.ersdVSProfile);
+			resource.getUseContext().stream().forEach(useContext -> {
+				if (useContext.getCode().getCode().equals("program")) {
+					useContext.setValue(new Reference(v1PlanDefinitionUrl));
+				}
+			});
+			List<UsageContext> filteredUseContexts = resource.getUseContext().stream()
+				.filter(useContext -> 
+					 !(useContext.getCode().getCode().equals("reporting")
+					&& useContext.getValueCodeableConcept().hasCoding(TransformProperties.usPHUsageContext, "triggering")) 
+				&& !(useContext.getCode().getCode().equals("priority")
+					&& useContext.getValueCodeableConcept().hasCoding(TransformProperties.usPHUsageContext, "routine")))
+				.collect(Collectors.toList());
+			resource.setUseContext(filteredUseContexts);
+		}
+	}
+	private PlanDefinition getV1PlanDefinition(RequestDetails requestDetails) throws ResourceNotFoundException {
+		Optional<PlanDefinition> maybePlanDefinition = Optional.ofNullable(null);
+		try {
+			PlanDefinition v1PlanDefinition = (PlanDefinition) transformProperties
+				.getDaoRegistry()
+				.getResourceDao(TransformProperties.v1PlanDefinitionId.getResourceType())
+				.read(TransformProperties.v1PlanDefinitionId, requestDetails);	
+			maybePlanDefinition = Optional.of(v1PlanDefinition);
+		} catch (ResourceNotFoundException | ResourceGoneException e) {
+			throw new ResourceNotFoundException("Could not find V1 PlanDefinition");
+		}
+		return maybePlanDefinition.orElseThrow(() -> new ResourceNotFoundException("Could not find V1 PlanDefinition"));
+	}
+}

ersd-v2-v1-transform/src/main/resources/META-INF/spring.factories

@@ -0,0 +1,2 @@
+org.springframework.boot.autoconfigure.EnableAutoConfiguration=\
+com.transform.TransformConfig

ersd-v2-v1-transform/src/test/java/com/transform/TransformProviderIT.java

@@ -0,0 +1,80 @@
+package com.transform;
+
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import java.util.List;
+import java.util.stream.Collectors;
+
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.MetadataResource;
+import org.hl7.fhir.r4.model.Parameters;
+import org.hl7.fhir.r4.model.ResourceType;
+import org.junit.jupiter.api.Test;
+import org.opencds.cqf.ruler.test.RestIntegrationTest;
+import org.springframework.boot.test.context.SpringBootTest;
+
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {
+		TransformConfig.class }, properties = { "hapi.fhir.fhir_version=r4" })
+class TransformProviderIT extends RestIntegrationTest {
+	@Test
+	void testTransformConfig() {
+		loadResource("ersd-v1-plandefinition-skeleton.json");
+		Bundle v2Bundle = (Bundle) loadResource("ersd-bundle-example.json");
+		Parameters v2BundleParams = new Parameters();
+		v2BundleParams.addParameter()
+			.setName("resource")
+			.setResource(v2Bundle);
+		Bundle v1Bundle = getClient()
+				.operation()
+				.onServer()
+				.named("$ersd-v2-to-v1-transform")
+				.withParameters(v2BundleParams)
+				.returnResourceType(Bundle.class)
+				.execute();
+
+		assertNotNull(v1Bundle);
+		List<MetadataResource> entries = v1Bundle.getEntry().stream().map(entry -> (MetadataResource) entry.getResource()).collect(Collectors.toList());
+		List<MetadataResource> ersdValueSets = entries.stream().filter(entry -> entry.getResourceType() == ResourceType.ValueSet 
+			&& entry.hasMeta() 
+			&& entry.getMeta().hasProfile(TransformProperties.ersdVSProfile)).collect(Collectors.toList());
+		List<MetadataResource> ersdValueSetLibrary = entries.stream().filter(entry -> entry.getResourceType() == ResourceType.Library 
+			&& entry.hasMeta() 
+			&& entry.getMeta().hasProfile(TransformProperties.ersdVSLibProfile)).collect(Collectors.toList());
+		List<MetadataResource> containsSpecificationLibrary = entries.stream().filter(entry -> entry.getResourceType() == ResourceType.Library && entry.hasMeta() 
+			&& (entry.getMeta().hasProfile(TransformProperties.usPHSpecLibProfile) || entry.getUrl().equals("http://hl7.org/fhir/us/ecr/Library/SpecificationLibrary"))).collect(Collectors.toList());
+		List<MetadataResource> containsV2PlanDefinition = entries.stream().filter(entry -> entry.getResourceType() == ResourceType.PlanDefinition && entry.hasMeta() 
+			&& entry.getMeta().hasProfile(TransformProperties.ersdPlanDefinitionProfile) && !entry.getName().equals("PlanDefinition_eRSD_Skeleton_Instance")).collect(Collectors.toList());
+		List<MetadataResource> VSTriggeringUseContextsMissingV1PlanDefinitionReference = entries.stream().filter(entry -> entry.getResourceType() == ResourceType.ValueSet && entry.hasMeta() && entry.getMeta().hasProfile(TransformProperties.ersdVSProfile) 
+			&& entry.getUseContext().stream().anyMatch(useContext -> useContext.getCode().getCode().equals("program") && !useContext.getValueReference().getReference().equals("http://hl7.org/fhir/us/ecr/PlanDefinition/plandefinition-ersd-skeleton"))).collect(Collectors.toList());
+		List<MetadataResource> containsV1PlanDefinition = entries.stream().filter(entry -> entry.getResourceType() == ResourceType.PlanDefinition && entry.hasMeta() 
+			&& entry.getMeta().hasProfile(TransformProperties.ersdPlanDefinitionProfile) && entry.getName().equals("PlanDefinition_eRSD_Skeleton_Instance")).collect(Collectors.toList());
+		List<MetadataResource> hasV2TriggeringVSLibUseContexts = entries.stream().filter(entry -> entry.getResourceType() == ResourceType.Library && entry.hasMeta() && entry.getMeta().hasProfile(TransformProperties.ersdVSLibProfile) 
+			&& entry.getUseContext().stream().anyMatch(useContext -> 
+					  (useContext.getCode().getCode().equals("reporting")
+					&& useContext.getValueCodeableConcept().hasCoding(TransformProperties.usPHUsageContext, "triggering"))
+				 || (useContext.getCode().getCode().equals("specification-type")
+					&& useContext.getValueCodeableConcept().hasCoding(TransformProperties.usPHUsageContext, "value-set-library")))
+		).collect(Collectors.toList());
+		List<MetadataResource> hasV2TriggeringVSUseContexts = entries.stream().filter(entry -> entry.getResourceType() == ResourceType.ValueSet && entry.hasMeta() && entry.getMeta().hasProfile(TransformProperties.ersdVSProfile) 
+			&& entry.getUseContext().stream().anyMatch(useContext -> 
+					  (useContext.getCode().getCode().equals("reporting")
+					&& useContext.getValueCodeableConcept().hasCoding(TransformProperties.usPHUsageContext, "triggering"))
+				 || (useContext.getCode().getCode().equals("priority")
+					&& useContext.getValueCodeableConcept().hasCoding(TransformProperties.usPHUsageContext, "routine")))
+		).collect(Collectors.toList());
+		List<MetadataResource> hasUSPHProfiles = entries.stream().filter(entry -> entry.getResourceType() == ResourceType.PlanDefinition && entry.hasMeta() && entry.getMeta().hasProfile() 
+			&& entry.getMeta().getProfile().stream().anyMatch(profile -> profile.getValueAsString().contains("us-ph"))).collect(Collectors.toList());
+		List<MetadataResource> hasExperimental = entries.stream().filter(entry -> entry.hasExperimental()).collect(Collectors.toList());
+		assertTrue(ersdValueSets.size() > 0);
+		assertTrue(ersdValueSetLibrary.size() > 0);
+		assertTrue(containsSpecificationLibrary.size() == 0);
+		assertTrue(containsV2PlanDefinition.size() == 0);
+		assertTrue(containsV1PlanDefinition.size() == 1);
+		assertTrue(VSTriggeringUseContextsMissingV1PlanDefinitionReference.size() == 0);
+		assertTrue(hasV2TriggeringVSLibUseContexts.size() == 0);
+		assertTrue(hasV2TriggeringVSUseContexts.size() == 0);
+		assertTrue(hasUSPHProfiles.size() == 0);
+		assertTrue(hasExperimental.size() == 0);
+	}
+}