Update resources on package reinstall (hapifhir#2078)

* Start testing

* Update resources on package install

* Add changelog

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/2078-update-resources-on-package-reinstall.yaml

@@ -0,0 +1,5 @@
+---
+type: add
+issue: 2078
+title: "When using package support to install a package with STORE_AND_INSTALL mode, resources that are already
+   present in the database will now be updated to the contents of the version in the package."

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

@@ -29,11 +29,13 @@
 import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
 import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionEntity;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.param.UriParam;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.util.FhirTerser;
 import ca.uhn.fhir.util.SearchParameterUtil;
 import com.google.common.annotations.VisibleForTesting;
@@ -94,6 +96,8 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
 	private PlatformTransactionManager myTxManager;
 	@Autowired
 	private INpmPackageVersionDao myPackageVersionDao;
+	@Autowired
+	private ISearchParamRegistry mySearchParamRegistry;
 
 	/**
 	 * Constructor
@@ -161,6 +165,9 @@ public PackageInstallOutcomeJson install(PackageInstallationSpec theInstallation
 
 				if (theInstallationSpec.getInstallMode() == PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL) {
 					install(npmPackage, theInstallationSpec, retVal);
+
+					// If any SearchParameters were installed, let's load them right away
+					mySearchParamRegistry.refreshCacheIfNecessary();
 				}
 
 			} catch (IOException e) {
@@ -304,11 +311,20 @@ private void create(IBaseResource theResource, PackageInstallOutcomeJson theOutc
 		IFhirResourceDao dao = myDaoRegistry.getResourceDao(theResource.getClass());
 		SearchParameterMap map = createSearchParameterMapFor(theResource);
 		IBundleProvider searchResult = dao.search(map);
-		if (searchResult.isEmpty()) {
+		if (validForUpload(theResource)) {
+			if (searchResult.isEmpty()) {
 
-			if (validForUpload(theResource)) {
+				ourLog.info("Creating new resource matching {}", map.toNormalizedQueryString(myFhirContext));
 				theOutcome.incrementResourcesInstalled(myFhirContext.getResourceType(theResource));
 				dao.create(theResource);
+
+			} else {
+
+				ourLog.info("Updating existing resource matching {}", map.toNormalizedQueryString(myFhirContext));
+				theOutcome.incrementResourcesInstalled(myFhirContext.getResourceType(theResource));
+				theResource.setId(searchResult.getResources(0,1).get(0).getIdElement().toUnqualifiedVersionless());
+				dao.update(theResource);
+
 			}
 
 		}

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

@@ -11,8 +11,11 @@
 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;
+import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.param.UriParam;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.test.utilities.JettyUtil;
@@ -22,7 +25,13 @@
 import org.eclipse.jetty.servlet.ServletHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.ImplementationGuide;
+import org.hl7.fhir.r4.model.Organization;
+import org.hl7.fhir.r4.model.PractitionerRole;
+import org.hl7.fhir.r4.model.Reference;
+import org.hl7.fhir.r4.model.SearchParameter;
 import org.hl7.fhir.r4.model.StructureDefinition;
 import org.hl7.fhir.utilities.cache.NpmPackage;
 import org.junit.jupiter.api.AfterEach;
@@ -230,7 +239,6 @@ public void testInstallR4Package_Twice() throws Exception {
 	}
 
 
-
 	@Test
 	public void testInstallR4PackageWithNoDescription() throws Exception {
 		myDaoConfig.setAllowExternalReferences(true);
@@ -433,6 +441,53 @@ public void testInstallAlreadyExistingIsIgnored() throws Exception {
 
 	}
 
+	@Test
+	public void testInstallPkgContainingSearchParameter() throws IOException {
+		myDaoConfig.setAllowExternalReferences(true);
+
+		byte[] contents0111 = loadClasspathBytes("/packages/test-exchange-sample.tgz");
+		myFakeNpmServlet.myResponses.put("/test-exchange.fhir.us.com/2.1.1", contents0111);
+
+		contents0111 = loadClasspathBytes("/packages/test-exchange-sample-2.tgz");
+		myFakeNpmServlet.myResponses.put("/test-exchange.fhir.us.com/2.1.2", contents0111);
+
+		// Install older version
+		PackageInstallationSpec spec = new PackageInstallationSpec().setName("test-exchange.fhir.us.com").setVersion("2.1.1").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
+		igInstaller.install(spec);
+
+		IBundleProvider spSearch = mySearchParameterDao.search(SearchParameterMap.newSynchronous("code", new TokenParam("network-id")));
+		assertEquals(1, spSearch.sizeOrThrowNpe());
+		SearchParameter sp = (SearchParameter) spSearch.getResources(0, 1).get(0);
+		assertEquals("network-id", sp.getCode());
+		assertEquals("2.1", sp.getVersion());
+		assertEquals(Enumerations.PublicationStatus.ACTIVE, sp.getStatus());
+
+		Organization org = new Organization();
+		org.setName("Hello");
+		IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
+
+		PractitionerRole pr = new PractitionerRole();
+		pr.addExtension().setUrl("http://test-exchange.com/fhir/us/providerdataexchange/StructureDefinition/networkreference").setValue(new Reference(orgId));
+		myPractitionerRoleDao.create(pr);
+
+		SearchParameterMap map = SearchParameterMap.newSynchronous("network-id", new ReferenceParam(orgId.getValue()));
+		spSearch = myPractitionerRoleDao.search(map);
+		assertEquals(1, spSearch.sizeOrThrowNpe());
+
+		// Install newer version
+		spec = new PackageInstallationSpec().setName("test-exchange.fhir.us.com").setVersion("2.1.2").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
+		igInstaller.install(spec);
+
+		spSearch = mySearchParameterDao.search(SearchParameterMap.newSynchronous("code", new TokenParam("network-id")));
+		assertEquals(1, spSearch.sizeOrThrowNpe());
+		sp = (SearchParameter) spSearch.getResources(0, 1).get(0);
+		assertEquals("network-id", sp.getCode());
+		assertEquals(Enumerations.PublicationStatus.ACTIVE, sp.getStatus());
+		assertEquals("2.2", sp.getVersion());
+
+	}
+
+
 	@Test
 	public void testLoadContents() throws IOException {
 		byte[] contents0111 = loadClasspathBytes("/packages/hl7.fhir.uv.shorthand-0.11.1.tgz");