Merge branch 'rel_5_7'

hapi-fhir-base/src/main/java/ca/uhn/fhir/i18n/Msg.java

@@ -25,7 +25,7 @@ public final class Msg {
 
 	/**
 	 * IMPORTANT: Please update the following comment after you add a new code
-	 * Last code value: 2023
+	 * Last code value: 2024
 	 */
 
 	private Msg() {}

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3347-add-file-support-for-loading-igs.yaml

@@ -0,0 +1,4 @@
+---
+type: add
+issue: 3347
+title: "Added ability to load Implementation Guide packages from filesystem by supporting the file:/ syntax of url."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/changes.yaml

@@ -12,6 +12,7 @@
 <li>Guava (All): 30.1.1-jre -> 31.0.1-jre</li>
 <li>JDOM (XML Patch Support):  2.0.6 -> 2.0.6.1 (Addresses CVE-2021-33813)</li>
 <li>Spring (JPA): 5.3.7 -> 5.3.15</li>
+<li>Spring (JPA): 5.3.7 -> 5.3.15</li>
 <li>Spring-Data (JPA): 2.5.0 -> 2.6.1</li>
 <li>Hibernate ORM (JPA): 5.4.30.Final -> 5.6.2.Final</li>
 <li>Flyway (JPA): 6.5.4 -> 8.4.1</li>
@@ -26,6 +27,8 @@
 <li>Spring Boot (Boot): 2.5.0 -> 2.6.2</li>
 <li>Swagger UI (OpenAPI): 3.46.0 -> 4.1.3</li>
 <li>Resteasy (JAX-RS): 4.0.0.Beta3 -> 5.0.2.Final</li>
+<li>Postgresql (JPA): 42.3.1 -> 42.3.2</li>
+<li>Spring Security Oauth2(Oauth): 2.0.2.RELEASE -> 2.0.17.RELEASE</li>
 </ul>
 "
 

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

@@ -88,7 +88,11 @@ import javax.transaction.Transactional;
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
+import java.net.URI;
+import java.net.URISyntaxException;
 import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -473,7 +477,14 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
 
 	protected byte[] loadPackageUrlContents(String thePackageUrl) {
 		if (thePackageUrl.startsWith("classpath:")) {
-			return ClasspathUtil.loadResourceAsByteArray(thePackageUrl.substring("classpath:".length()));
+			return ClasspathUtil.loadResourceAsByteArray(thePackageUrl.substring("classpath:" .length()));
+		} else if (thePackageUrl.startsWith("file:")) {
+			try {
+				byte[] bytes = Files.readAllBytes(Paths.get(new URI(thePackageUrl)));
+				return bytes;
+			} catch (IOException | URISyntaxException e) {
+				throw new InternalErrorException(Msg.code(2024) + "Error loading \"" + thePackageUrl + "\": " + e.getMessage());
+			}
 		} else {
 			HttpClientConnectionManager connManager = new BasicHttpClientConnectionManager();
 			try (CloseableHttpResponse request = HttpClientBuilder

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/NpmR4Test.java

@@ -59,6 +59,8 @@ import javax.servlet.http.HttpServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -924,20 +926,39 @@ public class NpmR4Test extends BaseJpaR4Test {
 			map.add(StructureDefinition.SP_URL, new UriParam("https://www.medizininformatik-initiative.de/fhir/core/modul-labor/StructureDefinition/LogicalModel/Laborbefund"));
 			IBundleProvider result = myStructureDefinitionDao.search(map);
 			assertEquals(1, result.sizeOrThrowNpe());
-			List<IBaseResource> resources = result.getResources(0,1);
-			assertFalse(((StructureDefinition)resources.get(0)).hasSnapshot());
+			List<IBaseResource> resources = result.getResources(0, 1);
+			assertFalse(((StructureDefinition) resources.get(0)).hasSnapshot());
 
 			// Confirm that DiagnosticLab (a resource StructureDefinition with differential but no snapshot) was created with a generated snapshot.
 			map = SearchParameterMap.newSynchronous();
 			map.add(StructureDefinition.SP_URL, new UriParam("https://www.medizininformatik-initiative.de/fhir/core/modul-labor/StructureDefinition/DiagnosticReportLab"));
 			result = myStructureDefinitionDao.search(map);
 			assertEquals(1, result.sizeOrThrowNpe());
-			resources = result.getResources(0,1);
-			assertTrue(((StructureDefinition)resources.get(0)).hasSnapshot());
+			resources = result.getResources(0, 1);
+			assertTrue(((StructureDefinition) resources.get(0)).hasSnapshot());
 
 		});
 	}
 
+	@Test
+	public void testInstallR4PackageFromFile() {
+
+		Path currentRelativePath = Paths.get("");
+		String s = currentRelativePath.toAbsolutePath().toString();
+		System.out.println("Current absolute path is: " + s);
+
+		String fileUrl = "file:" + s + "/src/test/resources/packages/de.basisprofil.r4-1.2.0.tgz";
+
+		myPackageInstallerSvc.install(new PackageInstallationSpec()
+			.setName("de.basisprofil.r4")
+			.setVersion("1.2.0")
+			.setPackageUrl(fileUrl)
+		);
+		runInTransaction(() -> {
+			assertTrue(myPackageVersionDao.findByPackageIdAndVersion("de.basisprofil.r4", "1.2.0").isPresent());
+		});
+	}
+
 	static class FakeNpmServlet extends HttpServlet {
 
 		private final Map<String, byte[]> myResponses = new HashMap<>();

hapi-fhir-oauth2/pom.xml

@@ -36,7 +36,7 @@
 		<dependency>
 		    <groupId>org.springframework.security.oauth</groupId>
 		    <artifactId>spring-security-oauth2</artifactId>
-		    <version>2.0.2.RELEASE</version>
+		    <version>2.0.17.RELEASE</version>
 		</dependency>
 
 		<!-- Server -->

hapi-tinder-plugin/pom.xml

@@ -188,7 +188,7 @@
 		<dependency>
 			<groupId>org.apache.ant</groupId>
 			<artifactId>ant</artifactId>
-			<version>1.10.10</version>
+			<version>1.10.11</version>
 		</dependency>
 		
 		<!-- This is just used for  -->

pom.xml

@@ -852,7 +852,7 @@
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
         <ebay_cors_filter_version>1.0.1</ebay_cors_filter_version>
 
-        <elastic_apm_version>1.24.0</elastic_apm_version>
+        <elastic_apm_version>1.28.4</elastic_apm_version>
         <!-- CQL Support -->
         <cql-engine.version>1.5.1</cql-engine.version>
         <cql-evaluator.version>1.2.0</cql-evaluator.version>
@@ -1716,7 +1716,7 @@
 			<dependency>
 				<groupId>org.postgresql</groupId>
 				<artifactId>postgresql</artifactId>
-				<version>42.3.1</version>
+				<version>42.3.2</version>
 			</dependency>
 			<dependency>
 				<groupId>org.quartz-scheduler</groupId>

vagrant/chef/cookbooks/apt/Gemfile

@@ -2,7 +2,7 @@ source 'https://rubygems.org'
 
 group :lint do
   gem 'foodcritic', '~> 3.0'
-  gem 'rubocop', '~> 0.23'
+  gem 'rubocop', '~> 0.49.0'
   gem 'rainbow', '< 2.0'
 end
 

vagrant/chef/cookbooks/java/Gemfile

@@ -3,7 +3,7 @@ source 'https://rubygems.org'
 gem 'berkshelf',  '~> 2.0'
 gem 'chefspec',   '~> 3.1'
 gem 'foodcritic', '~> 3.0'
-gem 'rubocop',    '~> 0.12'
+gem 'rubocop',    '~> 0.49.0'
 
 group :integration do
   gem 'test-kitchen',    '~> 1.2.1'