Merge pull request #2141 from jamesagnew/im_20201020_package_installer_enhancements

Enable package installer to load non-Conformance resources

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/2141-enable-non-conformance-resources-in-package-installer.yaml

@@ -0,0 +1,5 @@
+---
+type: add
+issue: 2141
+title: "The Package Installer has been enhanced to allow resources that do not have a url element to be loaded
+   from a package. Resources without url will instead use identifier element."

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/PackageInstallerSvcImpl.java

@@ -20,6 +20,9 @@ package ca.uhn.fhir.jpa.packages;
  * #L%
  */
 
+import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
+import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.support.IValidationSupport;
@@ -46,6 +49,7 @@ import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.hl7.fhir.r4.model.Identifier;
 import org.hl7.fhir.utilities.cache.IPackageCacheManager;
 import org.hl7.fhir.utilities.cache.NpmPackage;
 import org.slf4j.Logger;
@@ -384,9 +388,12 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
 		} else if (resource.getClass().getSimpleName().equals("Subscription")) {
 			String id = extractIdFromSubscription(resource);
 			return SearchParameterMap.newSynchronous().add("_id", new TokenParam(id));
-		} else {
+		} else if (resourceHasUrlElement(resource)) {
 			String url = extractUniqueUrlFromMetadataResource(resource);
 			return SearchParameterMap.newSynchronous().add("url", new UriParam(url));
+		} else {
+			TokenParam identifierToken = extractIdentifierFromOtherResourceTypes(resource);
+			return SearchParameterMap.newSynchronous().add("identifier", identifierToken);
 		}
 	}
 
@@ -412,6 +419,26 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
 		return (String) asPrimitiveType.getValue();
 	}
 
+	private TokenParam extractIdentifierFromOtherResourceTypes(IBaseResource resource) {
+		FhirTerser terser = myFhirContext.newTerser();
+		Identifier identifier = (Identifier) terser.getSingleValueOrNull(resource, "identifier");
+		if (identifier != null) {
+			return new TokenParam(identifier.getSystem(), identifier.getValue());
+		} else {
+			throw new UnsupportedOperationException("Resources in a package must have a url or identifier to be loaded by the package installer.");
+		}
+	}
+
+	private boolean resourceHasUrlElement(IBaseResource resource) {
+		BaseRuntimeElementDefinition<?> def = myFhirContext.getElementDefinition(resource.getClass());
+		if (!(def instanceof BaseRuntimeElementCompositeDefinition)) {
+			throw new IllegalArgumentException("Resource is not a composite type: " + resource.getClass().getName());
+		}
+		BaseRuntimeElementCompositeDefinition<?> currentDef = (BaseRuntimeElementCompositeDefinition<?>) def;
+		BaseRuntimeChildDefinition nextDef = currentDef.getChildByName("url");
+		return nextDef != null;
+	}
+
 	@VisibleForTesting
 	void setFhirContextForUnitTest(FhirContext theCtx) {
 		myFhirContext = theCtx;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/NpmTestR4.java

@@ -11,7 +11,6 @@ import ca.uhn.fhir.jpa.model.entity.NpmPackageEntity;
 import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionEntity;
 import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionResourceEntity;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.ReferenceParam;
@@ -48,6 +47,7 @@ import javax.servlet.http.HttpServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 import java.io.IOException;
+import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -61,6 +61,7 @@ import static org.hamcrest.Matchers.not;
 import static org.junit.jupiter.api.Assertions.assertArrayEquals;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.fail;
 
 public class NpmTestR4 extends BaseJpaR4Test {
 
@@ -236,6 +237,59 @@ public class NpmTestR4 extends BaseJpaR4Test {
 		});
 	}
 
+	@Test
+	public void testInstallR4Package_NonConformanceResources() throws Exception {
+		myDaoConfig.setAllowExternalReferences(true);
+
+		byte[] bytes = loadClasspathBytes("/packages/test-organizations-package.tgz");
+		myFakeNpmServlet.myResponses.put("/test-organizations/1.0.0", bytes);
+
+		List<String> resourceList = new ArrayList<>();
+		resourceList.add("Organization");
+		PackageInstallationSpec spec = new PackageInstallationSpec().setName("test-organizations").setVersion("1.0.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
+		spec.setInstallResourceTypes(resourceList);
+		PackageInstallOutcomeJson outcome = igInstaller.install(spec);
+		assertEquals(3, outcome.getResourcesInstalled().get("Organization"));
+
+		// Be sure no further communication with the server
+		JettyUtil.closeServer(myServer);
+
+		// Search for the installed resources
+		runInTransaction(() -> {
+			SearchParameterMap map = SearchParameterMap.newSynchronous();
+			map.add(Organization.SP_IDENTIFIER, new TokenParam("https://github.com/synthetichealth/synthea", "organization1"));
+			IBundleProvider result = myOrganizationDao.search(map);
+			assertEquals(1, result.sizeOrThrowNpe());
+			map = SearchParameterMap.newSynchronous();
+			map.add(Organization.SP_IDENTIFIER, new TokenParam("https://github.com/synthetichealth/synthea", "organization2"));
+			result = myOrganizationDao.search(map);
+			assertEquals(1, result.sizeOrThrowNpe());
+			map = SearchParameterMap.newSynchronous();
+			map.add(Organization.SP_IDENTIFIER, new TokenParam("https://github.com/synthetichealth/synthea", "organization3"));
+			result = myOrganizationDao.search(map);
+			assertEquals(1, result.sizeOrThrowNpe());
+		});
+
+	}
+
+	@Test
+	public void testInstallR4Package_NoIdentifierNoUrl() throws Exception {
+		myDaoConfig.setAllowExternalReferences(true);
+
+		byte[] bytes = loadClasspathBytes("/packages/test-missing-identifier-package.tgz");
+		myFakeNpmServlet.myResponses.put("/test-organizations/1.0.0", bytes);
+
+		List<String> resourceList = new ArrayList<>();
+		resourceList.add("Organization");
+		PackageInstallationSpec spec = new PackageInstallationSpec().setName("test-organizations").setVersion("1.0.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
+		spec.setInstallResourceTypes(resourceList);
+		try {
+			PackageInstallOutcomeJson outcome = igInstaller.install(spec);
+			fail();
+		} catch (ImplementationGuideInstallationException theE) {
+			assertThat(theE.getMessage(), containsString("Resources in a package must have a url or identifier to be loaded by the package installer."));
+		}
+	}
 
 	@Test
 	public void testInstallR4Package_DraftResourcesNotInstalled() throws Exception {