Aphl 752 validate operation

core/pom.xml

@@ -52,13 +52,13 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>org.hl7.fhir.r5</artifactId>
-			<version>6.0.15</version>
+			<version>6.0.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>org.hl7.fhir.convertors</artifactId>
-			<version>6.0.15</version>
+			<version>6.0.1</version>
 		</dependency>
 		<dependency>
 			<groupId>org.opencds.cqf.cql</groupId>

external/pom.xml

@@ -15,6 +15,12 @@
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-base</artifactId>
 		</dependency>
+
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>org.hl7.fhir.r5</artifactId>
+			<version>6.0.1</version>
+		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-storage</artifactId>

plugin/cr/pom.xml

@@ -10,18 +10,13 @@
 	<dependencies>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
-			<artifactId>org.hl7.fhir.r5</artifactId>
-			<version>6.0.15</version>
+			<artifactId>org.hl7.fhir.validation</artifactId>
+			<version>6.0.1</version>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>org.hl7.fhir.utilities</artifactId>
-			<version>6.0.15</version>
-		</dependency>
-		<dependency>
-			<groupId>ca.uhn.hapi.fhir</groupId>
-			<artifactId>org.hl7.fhir.convertors</artifactId>
-			<version>6.0.15</version>
+			<version>6.0.1</version>
 		</dependency>
 	</dependencies>
 </project>

plugin/cr/src/main/java/org/opencds/cqf/ruler/cr/KnowledgeArtifactProcessor.java

@@ -151,9 +151,21 @@ public class KnowledgeArtifactProcessor {
 		);
 
 	private BundleEntryComponent createEntry(IBaseResource theResource) {
-		return new Bundle.BundleEntryComponent()
+		BundleEntryComponent entry = new Bundle.BundleEntryComponent()
 				.setResource((Resource) theResource)
 				.setRequest(createRequest(theResource));
+		String fullUrl = entry.getRequest().getUrl();
+		if (theResource instanceof MetadataResource) {
+			MetadataResource resource = (MetadataResource) theResource;
+			if (resource.hasUrl()) {
+				fullUrl = resource.getUrl();
+				if (resource.hasVersion()) {
+					fullUrl += "|" + resource.getVersion();
+				}
+			}
+		}
+		entry.setFullUrl(fullUrl);
+		return entry;
 	}
 
 	private BundleEntryRequestComponent createRequest(IBaseResource theResource) {

plugin/cr/src/main/java/org/opencds/cqf/ruler/cr/RepositoryService.java

@@ -1,9 +1,15 @@
 package org.opencds.cqf.ruler.cr;
 
+import java.io.IOException;
 import java.util.Date;
 import java.util.List;
 
 import org.cqframework.fhir.api.FhirDal;
+import org.hl7.fhir.common.hapi.validation.support.CommonCodeSystemsTerminologyService;
+import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport;
+import org.hl7.fhir.common.hapi.validation.support.NpmPackageValidationSupport;
+import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
+import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
@@ -15,6 +21,7 @@
 import org.hl7.fhir.r4.model.Endpoint;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.MetadataResource;
+import org.hl7.fhir.r4.model.OperationOutcome;
 import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.Resource;
 import org.opencds.cqf.cql.evaluator.fhir.util.Canonicals;
@@ -24,13 +31,18 @@
 import org.opencds.cqf.ruler.provider.DaoRegistryOperationProvider;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
 import ca.uhn.fhir.model.api.annotation.Description;
 import ca.uhn.fhir.rest.annotation.IdParam;
 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.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import ca.uhn.fhir.validation.FhirValidator;
 
 public class RepositoryService extends DaoRegistryOperationProvider {
 
@@ -62,7 +74,7 @@ public class RepositoryService extends DaoRegistryOperationProvider {
 	 * @return An IBaseResource that is the targeted resource, updated with the approval
 	 */
 	@Operation(name = "$crmi.approve", idempotent = true, global = true, type = MetadataResource.class)
-	@Description(shortDefinition = "$approve", value = "Apply an approval to an existing artifact, regardless of status.")
+	@Description(shortDefinition = "$crmi.approve", value = "Apply an approval to an existing artifact, regardless of status.")
 	public Bundle approveOperation(
 			RequestDetails requestDetails,
 			@IdParam IdType theId,
@@ -128,7 +140,7 @@ public Bundle approveOperation(
 	 * @return A transaction bundle result of the newly created resources
 	 */
 	@Operation(name = "$crmi.draft", idempotent = true, global = true, type = MetadataResource.class)
-	@Description(shortDefinition = "$draft", value = "Create a new draft version of the reference artifact")
+	@Description(shortDefinition = "$crmi.draft", value = "Create a new draft version of the reference artifact")
 	public Bundle draftOperation(RequestDetails requestDetails, @IdParam IdType theId, @OperationParam(name = "version") String version)
 		throws FHIRException {
 		FhirDal fhirDal = this.fhirDalFactory.create(requestDetails);
@@ -145,7 +157,7 @@ public Bundle draftOperation(RequestDetails requestDetails, @IdParam IdType theI
 	 * @return A transaction bundle result of the updated resources
 	 */
 	@Operation(name = "$crmi.release", idempotent = true, global = true, type = MetadataResource.class)
-	@Description(shortDefinition = "$release", value = "Release an existing draft artifact")
+	@Description(shortDefinition = "$crmi.release", value = "Release an existing draft artifact")
 	public Bundle releaseOperation(
 		RequestDetails requestDetails,
 		@IdParam IdType theId,
@@ -175,7 +187,7 @@ public Bundle releaseOperation(
 	}
 
 	@Operation(name = "$crmi.package", idempotent = true, global = true, type = MetadataResource.class)
-	@Description(shortDefinition = "$package", value = "Package an artifact and components / dependencies")
+	@Description(shortDefinition = "$crmi.package", value = "Package an artifact and components / dependencies")
 	public Bundle packageOperation(
 		RequestDetails requestDetails,
 		@IdParam IdType theId,
@@ -213,13 +225,55 @@ public Bundle packageOperation(
 
 
 	@Operation(name = "$crmi.revise", idempotent = true, global = true, type = MetadataResource.class)
-	@Description(shortDefinition = "$revise", value = "Update an existing artifact in 'draft' status")
+	@Description(shortDefinition = "$crmi.revise", value = "Update an existing artifact in 'draft' status")
 	public IBaseResource reviseOperation(RequestDetails requestDetails, @OperationParam(name = "resource") IBaseResource resource)
 		throws FHIRException {
 
 		FhirDal fhirDal = fhirDalFactory.create(requestDetails);
 		return (IBaseResource)this.artifactProcessor.revise(fhirDal, (MetadataResource) resource);
 	}
+
+	@Operation(name = "$validate", idempotent = true, global = true, type = MetadataResource.class)
+	@Description(shortDefinition = "$validate", value = "Validate a bundle")
+	public OperationOutcome validateOperation(RequestDetails requestDetails, 
+		@OperationParam(name = "resource") IBaseResource resource,
+		@OperationParam(name = "mode") CodeType mode,
+		@OperationParam(name = "profile") String profile
+	)
+		throws FHIRException {
+		if (mode != null) {
+			throw new NotImplementedOperationException("'mode' Parameter not implemented yet.");
+		}
+		if (profile != null) {
+			throw new NotImplementedOperationException("'profile' Parameter not implemented yet.");
+		}
+		if (resource == null) {
+			throw new UnprocessableEntityException("A FHIR resource must be provided for validation");
+		}
+		FhirContext ctx = this.getFhirContext();
+		if (ctx != null) {
+			FhirValidator validator = ctx.newValidator();
+			validator.setValidateAgainstStandardSchema(false);
+			validator.setValidateAgainstStandardSchematron(false);
+			NpmPackageValidationSupport npm = new NpmPackageValidationSupport(ctx);
+			try {
+				npm.loadPackageFromClasspath("classpath:hl7.fhir.us.ecr-2.1.0.tgz");
+			} catch (IOException e) {
+				throw new InternalErrorException("Could not load package");
+			}
+			ValidationSupportChain chain = new ValidationSupportChain(
+				npm,
+				new DefaultProfileValidationSupport(ctx),
+				new InMemoryTerminologyServerValidationSupport(ctx),
+				new CommonCodeSystemsTerminologyService(ctx)
+			);
+			FhirInstanceValidator myInstanceVal = new FhirInstanceValidator(chain);
+			validator.registerValidatorModule(myInstanceVal);
+			return (OperationOutcome) validator.validateWithResult(resource, null).toOperationOutcome();
+		} else {
+			throw new InternalErrorException("Could not load FHIR Context");
+		}
+	}
 	private BundleEntryComponent createEntry(IBaseResource theResource) {
 		return new Bundle.BundleEntryComponent()
 				.setResource((Resource) theResource)

plugin/cr/src/test/java/org/opencds/cqf/ruler/cr/r4/RepositoryServiceTest.java

@@ -36,6 +36,9 @@
 import org.hl7.fhir.r4.model.Library;
 import org.hl7.fhir.r4.model.Measure;
 import org.hl7.fhir.r4.model.MetadataResource;
+import org.hl7.fhir.r4.model.OperationOutcome;
+import org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity;
+import org.hl7.fhir.r4.model.OperationOutcome.OperationOutcomeIssueComponent;
 import org.hl7.fhir.r4.model.Parameters;
 import org.hl7.fhir.r4.model.PlanDefinition;
 import org.hl7.fhir.r4.model.Reference;
@@ -68,7 +71,7 @@
 	properties = {"hapi.fhir.fhir_version=r4", "hapi.fhir.security.basic_auth.enabled=false"})
 class RepositoryServiceTest extends RestIntegrationTest {
 	private final String specificationLibReference = "Library/SpecificationLibrary";
-	private final String minimalLibReference = "Library/SpecificationLibraryDraftVersion-1-1-1-23";
+	private final String minimalLibReference = "Library/SpecificationLibraryDraftVersion-1-0-0-23";
 	private final List<String> badVersionList = Arrays.asList(
 			"11asd1",
 			"1.1.3.1.1",
@@ -128,7 +131,7 @@ void draftOperation_test() {
 	void draftOperation_version_conflict_test() {
 		loadTransaction("ersd-active-transaction-bundle-example.json");
 		loadResource("minimal-draft-to-test-version-conflict.json");
-		Parameters params = parameters(part("version", "1.1.1.23") );
+		Parameters params = parameters(part("version", "1.0.0.23") );
 		String maybeException = null;
 		try {
 			getClient().operation()
@@ -1153,5 +1156,105 @@ void packageOperation_big_bundle() {
 			.execute();
 		assertTrue(packagedBundle.getEntry().size() == loadedBundle.getEntry().size());
 	}
+
+	@Test
+	void validateOperation() {
+		Bundle ersdExampleSpecBundle = (Bundle) loadResource("ersd-bundle-example.json");
+		Parameters specBundleParams = parameters(
+			part("resource", ersdExampleSpecBundle)
+		);
+		OperationOutcome specBundleOutcome = getClient().operation()
+			.onServer()
+			.named("$validate")
+			.withParameters(specBundleParams)
+			.returnResourceType(OperationOutcome.class)
+			.execute();
+		List<OperationOutcomeIssueComponent> specBundleValidationErrors = specBundleOutcome.getIssue().stream().filter((issue) -> issue.getSeverity() == IssueSeverity.ERROR || issue.getSeverity() == IssueSeverity.FATAL).collect(Collectors.toList());
+		assertTrue(specBundleValidationErrors.size() == 0);
+
+		Bundle ersdExampleSupplementalBundle = (Bundle) loadResource("ersd-supplemental-bundle-example.json");
+		Parameters supplementalBundleParams = parameters(
+			part("resource", ersdExampleSupplementalBundle)
+		);
+		OperationOutcome supplementalBundleOutcome = getClient().operation()
+			.onServer()
+			.named("$validate")
+			.withParameters(supplementalBundleParams)
+			.returnResourceType(OperationOutcome.class)
+			.execute();
+		List<OperationOutcomeIssueComponent> supplementalBundleErrors = supplementalBundleOutcome.getIssue().stream().filter((issue) -> issue.getSeverity() == IssueSeverity.ERROR || issue.getSeverity() == IssueSeverity.FATAL).collect(Collectors.toList());
+		assertTrue(supplementalBundleErrors.size() == 0);
+
+		Library validationErrorLibrary = (Library) loadResource("ersd-active-library-us-ph-validation-failure-example.json");
+		Parameters validationFailedParams = parameters(
+			part("resource", validationErrorLibrary)
+		);
+		OperationOutcome failedValidationOutcome = getClient().operation()
+			.onServer()
+			.named("$validate")
+			.withParameters(validationFailedParams)
+			.returnResourceType(OperationOutcome.class)
+			.execute();
+		List<OperationOutcomeIssueComponent> invalidLibraryErrors = failedValidationOutcome.getIssue().stream().filter((issue) -> issue.getSeverity() == IssueSeverity.ERROR || issue.getSeverity() == IssueSeverity.FATAL).collect(Collectors.toList());
+		assertTrue(invalidLibraryErrors.size() == 5);
+
+		Parameters noResourceParams = parameters();
+		UnprocessableEntityException noResourceException = null;
+		try {	
+			getClient().operation()
+				.onServer()
+				.named("$validate")
+				.withParameters(noResourceParams)
+				.returnResourceType(OperationOutcome.class)
+				.execute();
+		} catch (UnprocessableEntityException e) {
+			noResourceException = e;
+		}
+		assertNotNull(noResourceException);
+		assertTrue(noResourceException.getMessage().contains("resource must be provided"));
+	}
+
+	@Test
+	void validateOperationUnqualifiedRelatedArtifact() {
+		Bundle ersdExampleSpecBundleUnqualifiedPlanDefinition = (Bundle) loadResource("ersd-library-validation-failure-unqualified-plandefinition-bundle.json");
+		Parameters validationFailedUnqualifiedPlanDefinitionParams = parameters(
+			part("resource", ersdExampleSpecBundleUnqualifiedPlanDefinition)
+		);
+		OperationOutcome failedValidationUnqualifiedPlanDefinitionOutcome = getClient().operation()
+			.onServer()
+			.named("$validate")
+			.withParameters(validationFailedUnqualifiedPlanDefinitionParams)
+			.returnResourceType(OperationOutcome.class)
+			.execute();
+		boolean missingPlanDefinitionSliceErrorExists = failedValidationUnqualifiedPlanDefinitionOutcome.getIssue().stream()
+			.anyMatch((issue) -> issue.getDiagnostics().contains("Library.relatedArtifact:slicePlanDefinition: minimum required = 1, but only found 0 (from http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-specification-library|2.1.0)"));
+		assertTrue(missingPlanDefinitionSliceErrorExists);
+	}
+
+	@Test
+	void validatePackageOutput() {
+		loadTransaction("ersd-active-transaction-bundle-example.json");
+		Bundle packagedBundle = getClient().operation()
+			.onInstance(specificationLibReference)
+			.named("$crmi.package")
+			.withParameters(parameters())
+			.returnResourceType(Bundle.class)
+			.execute();
+		Parameters packagedBundleParams = parameters(
+			part("resource", packagedBundle)
+		);
+		OperationOutcome packagedBundleOutcome = getClient().operation()
+			.onServer()
+			.named("$validate")
+			.withParameters(packagedBundleParams)
+			.returnResourceType(OperationOutcome.class)
+			.execute();
+		List<OperationOutcomeIssueComponent> packagedBundleValidationErrors = packagedBundleOutcome.getIssue().stream().filter((issue) -> issue.getSeverity() == IssueSeverity.ERROR || issue.getSeverity() == IssueSeverity.FATAL).collect(Collectors.toList());
+		// currently the packaged bundle is not valid due to:
+		// - bundle.total
+		// - bundle.entry.request
+		// being present on a bundle with type = collection
+		assertTrue(packagedBundleValidationErrors.size() == 2);
+	}
 }