Merge remote-tracking branch 'remotes/origin/master' into im_20200728_term_multi_version_support

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/atlas/points.json

@@ -243,10 +243,10 @@
 			"description": "With the ACS App, Community Health Agents (CHA) work gets faster and faster, and they can take better care of their community. Best of all, it is 100% free to the Health Agent.",
 			"link": "http://ephealth.com.br/?lang=en",
 			"contactName": "Alan Lescano",
-			"contactEmail": "alan@ephealth.com.br",
+			"contactEmail": "alan.lesc1@gmail.com",
 			"city": "Sao Paulo, Brazil",
-			"lat": -6.6167,
-			"lon": -38.1500,
+			"lat": -23.533773,
+			"lon": -46.625290,
 			"added": "2019-09-29"
 		},
 		{

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-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/changes.yaml

@@ -4,5 +4,11 @@
     title: "The version of a few dependencies have been bumped to the latest versions
     (dependent HAPI modules listed in brackets):
     <ul>
-        <li>Flyway (JPA): 6.4.1-&gt; 6.5.4</li>
+        <li>Jackson (Base): 2.10.0 -&gt; 2.11.2</li>
+        <li>Flyway (JPA): 6.4.1 -&gt; 6.5.4</li>
+        <li>UCUM (JPA): 1.0.2 -&gt; 1.0.3</li>
+        <li>JQuery (Testpage Overlay): 3.3.1 -&gt; 3.5.1</li>
+        <li>Awesome Bootstrap Checkbos (Testpage Overlay): 1.0.1 -&gt; 1.0.2</li>
+        <li>MomentJS (Testpage Overlay): 2.15.1 -&gt; 2.27.0</li>
+        <li>Select2 (Testpage Overlay): 4.0.3 -&gt; 4.0.13</li>
     </ul>"

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

@@ -29,11 +29,13 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 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 class PackageInstallerSvcImpl implements IPackageInstallerSvc {
 
 				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 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
 		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.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;
+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.server.Server;
 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 class NpmTestR4 extends BaseJpaR4Test {
 	}
 
 
-
 	@Test
 	public void testInstallR4PackageWithNoDescription() throws Exception {
 		myDaoConfig.setAllowExternalReferences(true);
@@ -433,6 +441,53 @@ public class NpmTestR4 extends BaseJpaR4Test {
 
 	}
 
+	@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");

hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/ITestDataBuilder.java

@@ -106,6 +106,13 @@ public interface ITestDataBuilder {
 		};
 	}
 
+	/**
+	 * Set Organization.name
+	 */
+	default Consumer<IBaseResource> withName(String theStatus) {
+		return t -> __setPrimitiveChild(getFhirContext(), t, "name", "string", theStatus);
+	}
+
 	default Consumer<IBaseResource> withId(String theId) {
 		return t -> {
 			assertThat(theId, matchesPattern("[a-zA-Z0-9]+"));
@@ -129,6 +136,10 @@ public interface ITestDataBuilder {
 		return createResource("Patient", theModifiers);
 	}
 
+	default IIdType createOrganization(Consumer<IBaseResource>... theModifiers) {
+		return createResource("Organization", theModifiers);
+	}
+
 	default IIdType createResource(String theResourceType, Consumer<IBaseResource>[] theModifiers) {
 		IBaseResource resource = getFhirContext().getResourceDefinition(theResourceType).newInstance();
 		for (Consumer<IBaseResource> next : theModifiers) {
@@ -155,6 +166,30 @@ public interface ITestDataBuilder {
 		};
 	}
 
+	default  Consumer<IBaseResource> withObservationHasMember(@Nullable IIdType theHasMember) {
+		return t -> {
+			if (theHasMember != null) {
+				IBaseReference reference = (IBaseReference) getFhirContext().getElementDefinition("Reference").newInstance();
+				reference.setReference(theHasMember.getValue());
+
+				RuntimeResourceDefinition resourceDef = getFhirContext().getResourceDefinition(t.getClass());
+				resourceDef.getChildByName("hasMember").getMutator().addValue(t, reference);
+			}
+		};
+	}
+
+	default  Consumer<IBaseResource> withOrganization(@Nullable IIdType theHasMember) {
+		return t -> {
+			if (theHasMember != null) {
+				IBaseReference reference = (IBaseReference) getFhirContext().getElementDefinition("Reference").newInstance();
+				reference.setReference(theHasMember.getValue());
+
+				RuntimeResourceDefinition resourceDef = getFhirContext().getResourceDefinition(t.getClass());
+				resourceDef.getChildByName("managingOrganization").getMutator().addValue(t, reference);
+			}
+		};
+	}
+
 	/**
 	 * Users of this API must implement this method
 	 */

hapi-fhir-testpage-overlay/src/main/webapp/WEB-INF/templates/tmpl-head.html

@@ -29,8 +29,8 @@
    <script th:src="@{/resources/moment/min/moment-with-locales.min.js}"></script>
    <link th:href="@{/resources/Eonasdan-bootstrap-datetimepicker/css/bootstrap-datetimepicker.min.css}" rel="stylesheet" />
    <script th:src="@{/resources/Eonasdan-bootstrap-datetimepicker/js/bootstrap-datetimepicker.js}"></script>
-   <link th:href="@{/resources/select2/dist/css/select2.css}" rel="stylesheet"/>
-   <script th:src="@{/resources/select2/dist/js/select2.min.js}"></script>
+   <link th:href="@{/resources/select2/css/select2.css}" rel="stylesheet"/>
+   <script th:src="@{/resources/select2/js/select2.min.js}"></script>
 
 
    <script src="js/RestfulTester.js" type="text/javascript"></script>

hapi-tinder-plugin/pom.xml

@@ -210,7 +210,7 @@
 		<dependency>
 			<groupId>org.apache.ant</groupId>
 			<artifactId>ant</artifactId>
-			<version>1.7.0</version>
+			<version>1.10.8</version>
 		</dependency>
 		
 		<!-- This is just used for  -->

pom.xml

@@ -679,7 +679,7 @@
 	<properties>
 
 		<fhir_core_version>5.1.0</fhir_core_version>
-		<ucum_version>1.0.2</ucum_version>
+		<ucum_version>1.0.3</ucum_version>
 
 		<surefire_jvm_args>-Dfile.encoding=UTF-8 -Xmx2048m</surefire_jvm_args>
 
@@ -726,8 +726,8 @@
 		<hibernate_validator_version>6.1.3.Final</hibernate_validator_version>
 		<httpcore_version>4.4.13</httpcore_version>
 		<httpclient_version>4.5.12</httpclient_version>
-		<jackson_version>2.10.0</jackson_version>
-		<jackson_databind_version>2.10.0</jackson_databind_version>
+		<jackson_version>2.11.2</jackson_version>
+		<jackson_databind_version>2.11.2</jackson_databind_version>
 		<maven_assembly_plugin_version>3.1.0</maven_assembly_plugin_version>
 		<maven_license_plugin_version>1.8</maven_license_plugin_version>
 		<resteasy_version>4.0.0.Beta3</resteasy_version>
@@ -1018,11 +1018,6 @@
 				<artifactId>javax.ws.rs-api</artifactId>
 				<version>2.0.1</version>
 			</dependency>
-			<dependency>
-				<groupId>io.github.devacfr.maven.skins</groupId>
-				<artifactId>reflow-velocity-tools</artifactId>
-				<version>2.0.0-beta2</version>
-			</dependency>
 			<dependency>
 				<groupId>io.swagger</groupId>
 				<artifactId>swagger-annotations</artifactId>
@@ -1572,6 +1567,12 @@
 				<groupId>org.webjars</groupId>
 				<artifactId>bootstrap</artifactId>
 				<version>3.3.7</version>
+				<exclusions>
+					<exclusion>
+						<groupId>org.webjars</groupId>
+						<artifactId>jquery</artifactId>
+					</exclusion>
+				</exclusions>
 			</dependency>
 			<dependency>
 				<groupId>org.webjars</groupId>
@@ -1586,7 +1587,7 @@
 			<dependency>
 				<groupId>org.webjars.bower</groupId>
 				<artifactId>awesome-bootstrap-checkbox</artifactId>
-				<version>1.0.1</version>
+				<version>1.0.2</version>
 			</dependency>
 			<dependency>
 				<groupId>org.webjars</groupId>
@@ -1596,17 +1597,23 @@
 			<dependency>
 				<groupId>org.webjars</groupId>
 				<artifactId>select2</artifactId>
-				<version>4.0.3</version>
+				<version>4.0.13</version>
+				<exclusions>
+					<exclusion>
+						<groupId>org.webjars</groupId>
+						<artifactId>jquery</artifactId>
+					</exclusion>
+				</exclusions>
 			</dependency>
 			<dependency>
 				<groupId>org.webjars.bower</groupId>
 				<artifactId>jquery</artifactId>
-				<version>3.3.1</version>
+				<version>3.5.1</version>
 			</dependency>
 			<dependency>
 				<groupId>org.webjars.bower</groupId>
 				<artifactId>moment</artifactId>
-				<version>2.15.1</version>
+				<version>2.27.0</version>
 			</dependency>
 			<dependency>
 				<groupId>org.xmlunit</groupId>
@@ -1873,49 +1880,6 @@
 						</excludes>
 					</configuration>
 				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-site-plugin</artifactId>
-					<version>3.7.1</version>
-					<configuration>
-						<skip>false</skip>
-						<skipDeploy>true</skipDeploy>
-						<inputEncoding>UTF-8</inputEncoding>
-						<outputEncoding>UTF-8</outputEncoding>
-						<relativizeDecorationLinks>false</relativizeDecorationLinks>
-					</configuration>
-					<dependencies>
-						<dependency>
-							<groupId>org.apache.maven.wagon</groupId>
-							<artifactId>wagon-scm</artifactId>
-						</dependency>
-						<dependency>
-							<groupId>org.apache.maven.scm</groupId>
-							<artifactId>maven-scm-manager-plexus</artifactId>
-						</dependency>
-						<dependency>
-							<groupId>org.apache.maven.scm</groupId>
-							<artifactId>maven-scm-provider-gitexe</artifactId>
-						</dependency>
-						<dependency>
-							<groupId>org.apache.maven.scm</groupId>
-							<artifactId>maven-scm-api</artifactId>
-						</dependency>
-						<!-- <dependency> <groupId>org.apache.maven.doxia</groupId> <artifactId>doxia-core</artifactId> </dependency> -->
-						<dependency>
-							<groupId>org.apache.maven.doxia</groupId>
-							<artifactId>doxia-module-markdown</artifactId>
-						</dependency>
-						<dependency>
-							<groupId>io.github.devacfr.maven.skins</groupId>
-							<artifactId>reflow-velocity-tools</artifactId>
-						</dependency>
-						<dependency>
-							<groupId>org.apache.velocity</groupId>
-							<artifactId>velocity</artifactId>
-						</dependency>
-					</dependencies>
-				</plugin>
 				<!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself. -->
 				<plugin>
 					<groupId>org.eclipse.m2e</groupId>
@@ -2310,59 +2274,6 @@
 					</execution>
 				</executions>
 			</plugin>
-			<plugin>
-				<artifactId>maven-site-plugin</artifactId>
-				<inherited>false</inherited>
-				<executions>
-					<execution>
-						<id>stage-for-scm-publish</id>
-						<phase>post-site</phase>
-						<goals>
-							<goal>stage</goal>
-						</goals>
-						<configuration>
-							<stagingDirectory>${siteMainDirectory}</stagingDirectory>
-						</configuration>
-					</execution>
-				</executions>
-				<dependencies>
-					<dependency>
-						<groupId>org.apache.maven.wagon</groupId>
-						<artifactId>wagon-scm</artifactId>
-						<version>3.0.0</version>
-					</dependency>
-					<dependency>
-						<groupId>org.apache.maven.scm</groupId>
-						<artifactId>maven-scm-manager-plexus</artifactId>
-						<version>1.9.5</version>
-					</dependency>
-					<dependency>
-						<groupId>org.apache.maven.scm</groupId>
-						<artifactId>maven-scm-provider-gitexe</artifactId>
-						<version>1.9.5</version>
-					</dependency>
-					<dependency>
-						<groupId>org.apache.maven.scm</groupId>
-						<artifactId>maven-scm-api</artifactId>
-						<version>1.9.5</version>
-					</dependency>
-					<dependency>
-						<groupId>org.apache.maven.doxia</groupId>
-						<artifactId>doxia-module-markdown</artifactId>
-						<version>1.8</version>
-					</dependency>
-					<dependency>
-						<groupId>io.github.devacfr.maven.skins</groupId>
-						<artifactId>reflow-velocity-tools</artifactId>
-						<version>2.0.0-beta2</version>
-					</dependency>
-					<dependency>
-						<groupId>org.apache.velocity</groupId>
-						<artifactId>velocity</artifactId>
-						<version>1.7</version>
-					</dependency>
-				</dependencies>
-			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-scm-publish-plugin</artifactId>