Merge remote-tracking branch 'origin/feature/karaf4.2' into develop

cytoscape · Dec 7, 2017 · fa04a4e · fa04a4e
2 parents 2b1e6c0 + 9054b6c
commit fa04a4e
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Showing 6 changed files with 50 additions and 106 deletions.
diff --git a/pom.xml b/pom.xml
@@ -11,7 +11,8 @@
 		<bundle.namespace>org.cytoscape.rest</bundle.namespace>
 		<maven-compiler-plugin.version>3.5.1</maven-compiler-plugin.version>
 		<maven-bundle-plugin.version>3.2.0</maven-bundle-plugin.version>
-		<osgi.api.version>4.2.0</osgi.api.version>
+		<osgi.api.version>6.0.0</osgi.api.version>
+		<osgi.compendium.version>5.0.0</osgi.compendium.version>
 		<junit.version>4.12</junit.version>
 		<jersey.version>2.23</jersey.version>
 
@@ -207,21 +208,12 @@
 						</goals>
 						<configuration>
 							<artifactItems>
-								<artifactItem>
-									<groupId>org.apache.felix</groupId>
-									<artifactId>org.apache.felix.metatype</artifactId>
-									<version>1.0.10</version>
-								</artifactItem>
 								<artifactItem>
 									<groupId>org.apache.felix</groupId>
 									<artifactId>org.apache.felix.scr</artifactId>
-									<version>1.8.2</version>
-								</artifactItem>
-								<artifactItem>
-									<groupId>org.apache.karaf.scr</groupId>
-									<artifactId>org.apache.karaf.scr.command</artifactId>
-									<version>3.0.3</version>
+									<version>2.0.12</version>
 								</artifactItem>
+
 							</artifactItems>
 							<outputDirectory>src/main/resources/karaf-scr</outputDirectory>
 							<stripVersion>false</stripVersion>
@@ -238,12 +230,7 @@
 								<artifactItem>
 									<groupId>org.apache.karaf.http</groupId>
 									<artifactId>org.apache.karaf.http.core</artifactId>
-									<version>3.0.3</version>
-								</artifactItem>
-								<artifactItem>
-									<groupId>org.apache.karaf.http</groupId>
-									<artifactId>org.apache.karaf.http.command</artifactId>
-									<version>3.0.3</version>
+									<version>4.2.0-SNAPSHOT</version>
 								</artifactItem>
 							</artifactItems>
 							<outputDirectory>src/main/resources/karaf-http</outputDirectory>
@@ -261,17 +248,17 @@
 								<artifactItem>
 									<groupId>org.glassfish.hk2</groupId>
 									<artifactId>hk2-api</artifactId>
-									<version>2.4.0-b34</version>
+									<version>2.4.0</version>
 								</artifactItem>
 								<artifactItem>
 									<groupId>org.glassfish.hk2</groupId>
 									<artifactId>hk2-locator</artifactId>
-									<version>2.4.0-b34</version>
+									<version>2.4.0</version>
 								</artifactItem>
 								<artifactItem>
 									<groupId>org.glassfish.hk2</groupId>
 									<artifactId>hk2-utils</artifactId>
-									<version>2.4.0-b34</version>
+									<version>2.4.0</version>
 								</artifactItem>
 								<artifactItem>
 									<groupId>org.glassfish.hk2</groupId>
@@ -281,12 +268,12 @@
 								<artifactItem>
 									<groupId>org.glassfish.hk2.external</groupId>
 									<artifactId>javax.inject</artifactId>
-									<version>2.4.0-b34</version>
+									<version>2.4.0</version>
 								</artifactItem>
 								<artifactItem>
 									<groupId>org.glassfish.hk2.external</groupId>
 									<artifactId>aopalliance-repackaged</artifactId>
-									<version>2.4.0-b34</version>
+									<version>2.4.0</version>
 								</artifactItem>
 							</artifactItems>
 							<outputDirectory>src/main/resources/hk2</outputDirectory>
@@ -415,7 +402,7 @@
 								<artifactItem>
 									<groupId>com.eclipsesource.jaxrs</groupId>
 									<artifactId>provider-gson</artifactId>
-									<version>2.2</version>
+									<version>2.3</version>
 								</artifactItem>
 							</artifactItems>
 							<outputDirectory>src/main/resources/osgi-jax-rs-connector</outputDirectory>
@@ -674,7 +661,7 @@
 		<dependency>
 			<groupId>org.osgi</groupId>
 			<artifactId>org.osgi.compendium</artifactId>
-			<version>${osgi.api.version}</version>
+			<version>${osgi.compendium.version}</version>
 			<scope>provided</scope>
 		</dependency>
 

diff --git a/src/main/java/org/cytoscape/rest/internal/task/OSGiJAXRSManager.java b/src/main/java/org/cytoscape/rest/internal/task/OSGiJAXRSManager.java
@@ -23,60 +23,16 @@ public class OSGiJAXRSManager
 
 	private String port;
 
-	private static final String PAX_JETTY_PATH = "pax-jetty/";
-
-	//Bundles should stay in this order.
-	private static final String[] PAX_JETTY_BUNDLES = {
-			PAX_JETTY_PATH + "org.apache.servicemix.specs.activation-api-1.1-2.2.0.jar",
-			PAX_JETTY_PATH + "geronimo-servlet_3.0_spec-1.0.jar",
-			PAX_JETTY_PATH + "mail-1.4.4.jar",
-			PAX_JETTY_PATH + "geronimo-jta_1.1_spec-1.1.1.jar",
-			PAX_JETTY_PATH + "geronimo-annotation_1.1_spec-1.0.1.jar",
-			PAX_JETTY_PATH + "geronimo-jaspic_1.0_spec-1.1.jar",
-			PAX_JETTY_PATH + "asm-all-5.0.2.jar",
-			PAX_JETTY_PATH + "jetty-all-server-8.1.15.v20140411.jar"
-	};
-
-	private static final String PAX_HTTP_PATH = "pax-http/";
-
-	private static final String[] PAX_HTTP_BUNDLES = {
-			PAX_HTTP_PATH + "ops4j-base-lang-1.4.0.jar",
-			PAX_HTTP_PATH + "pax-swissbox-core-1.7.0.jar",
-			// Already included in pax-jetty
-			// PAX_HTTP_PATH + "asm-all-5.0.2.jar",
-			PAX_HTTP_PATH + "xbean-bundleutils-3.18.jar",
-			PAX_HTTP_PATH + "xbean-reflect-3.18.jar",
-			PAX_HTTP_PATH + "xbean-finder-3.18.jar",
-			PAX_HTTP_PATH + "pax-web-api-3.1.4.jar",
-			PAX_HTTP_PATH + "pax-web-spi-3.1.4.jar",
-			PAX_HTTP_PATH + "pax-web-runtime-3.1.4.jar",
-			PAX_HTTP_PATH + "pax-web-jetty-3.1.4.jar"
-	};
-
-	private static final String KARAF_SCR_PATH = "karaf-scr/";
-
-	private static final String[] KARAF_SCR_BUNDLES = {
-			KARAF_SCR_PATH + "org.apache.felix.metatype-1.0.10.jar",
-			KARAF_SCR_PATH + "org.apache.felix.scr-1.8.2.jar",
-			KARAF_SCR_PATH + "org.apache.karaf.scr.command-3.0.3.jar"
-	};
-
-	private static final String KARAF_HTTP_PATH = "karaf-http/";
-
-	private static final String[] KARAF_HTTP_BUNDLES = {
-			KARAF_HTTP_PATH + "org.apache.karaf.http.core-3.0.3.jar",
-			KARAF_HTTP_PATH + "org.apache.karaf.http.command-3.0.3.jar"
-	};
-
+
 	private static final String HK2_PATH = "hk2/";
 
 	private static final String[] HK2_BUNDLES = {
-			HK2_PATH + "hk2-api-2.4.0-b34.jar",
-			HK2_PATH + "hk2-locator-2.4.0-b34.jar",
-			HK2_PATH + "hk2-utils-2.4.0-b34.jar",
+			HK2_PATH + "hk2-api-2.4.0.jar",
+			HK2_PATH + "hk2-locator-2.4.0.jar",
+			HK2_PATH + "hk2-utils-2.4.0.jar",
 			HK2_PATH + "osgi-resource-locator-1.0.1.jar",
-			HK2_PATH + "javax.inject-2.4.0-b34.jar",
-			HK2_PATH + "aopalliance-repackaged-2.4.0-b34.jar",
+			HK2_PATH + "javax.inject-2.4.0.jar",
+			HK2_PATH + "aopalliance-repackaged-2.4.0.jar",
 
 	};
 
@@ -98,7 +54,7 @@ public class OSGiJAXRSManager
 	private static final String JERSEY_MISC_PATH = "jersey-misc/";
 
 	private static final String[] JERSEY_MISC_BUNDLES = {
-			JERSEY_MISC_PATH + "javax.annotation-api-1.2.jar",
+			//JERSEY_MISC_PATH + "javax.annotation-api-1.2.jar",
 			JERSEY_MISC_PATH + "validation-api-1.1.0.Final.jar",
 			JERSEY_MISC_PATH + "javassist-3.18.1-GA.jar",
 			JERSEY_MISC_PATH + "mimepull-1.9.6.jar",
@@ -109,10 +65,10 @@ public class OSGiJAXRSManager
 	private static final String[] OSGI_JAX_RS_CONNECTOR_BUNDLES = {
 			//OSGI_JAX_RS_CONNECTOR_BUNDLES_PATH + "javax.servlet-api-3.1.0.jar",
 			//OSGI_JAX_RS_CONNECTOR_BUNDLES_PATH + "jersey-min-2.22.1.jar",
-			OSGI_JAX_RS_CONNECTOR_BUNDLES_PATH + "consumer-5.3.jar",
+			//OSGI_JAX_RS_CONNECTOR_BUNDLES_PATH + "consumer-5.3.jar",
 			OSGI_JAX_RS_CONNECTOR_BUNDLES_PATH + "publisher-5.3.jar",
 			//OSGI_JAX_RS_CONNECTOR_BUNDLES_PATH + "gson-2.3.jar",
-			OSGI_JAX_RS_CONNECTOR_BUNDLES_PATH + "provider-gson-2.2.jar",
+			OSGI_JAX_RS_CONNECTOR_BUNDLES_PATH + "provider-gson-2.3.jar",
 	};
 
 	public void installOSGiJAXRSBundles(BundleContext bundleContext, String port) throws Exception 
@@ -123,10 +79,10 @@ public void installOSGiJAXRSBundles(BundleContext bundleContext, String port) th
 		this.port = port;
 		setPortConfig(context);
 
-		installBundlesFromResources(bundleContext, PAX_JETTY_BUNDLES);
-		installBundlesFromResources(bundleContext, PAX_HTTP_BUNDLES);
-		installBundlesFromResources(bundleContext, KARAF_SCR_BUNDLES);
-		installBundlesFromResources(bundleContext, KARAF_HTTP_BUNDLES);
+		//installBundlesFromResources(bundleContext, PAX_JETTY_BUNDLES);
+		//installBundlesFromResources(bundleContext, PAX_HTTP_BUNDLES);
+		//installBundlesFromResources(bundleContext, KARAF_SCR_BUNDLES);
+		//installBundlesFromResources(bundleContext, KARAF_HTTP_BUNDLES);
 
 		setRootResourceConfig(context);
 

diff --git a/src/main/java/org/cytoscape/rest/internal/task/ResourceManager.java b/src/main/java/org/cytoscape/rest/internal/task/ResourceManager.java
@@ -1,6 +1,7 @@
 package org.cytoscape.rest.internal.task;
 
 import java.util.ArrayList;
+import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
 import java.util.Properties;
@@ -68,7 +69,7 @@ public void registerResourceServices() throws Exception
 
 		for (Class<?> clazz : coreResourceClasses){
 			Object instance = injector.getInstance(clazz);
-			serviceRegistrations.add(bundleContext.registerService(clazz.getName(), instance, new Properties()));
+			serviceRegistrations.add(bundleContext.registerService(clazz.getName(), instance, new Hashtable<String, Object>()));
 		}
 
 		for (Map.Entry<Class<?>, Module> entry : shimResources.entrySet()){
@@ -80,7 +81,7 @@ public void registerResourceServices() throws Exception
 					Injector appInjector = Guice.createInjector(entry.getValue());
 					appInjector.injectMembers(instance);
 				}
-				serviceRegistrations.add(bundleContext.registerService(entry.getKey().getName(), instance, new Properties()));
+				serviceRegistrations.add(bundleContext.registerService(entry.getKey().getName(), instance, new Hashtable<String, Object>()));
 			}
 			else
 			{
@@ -97,7 +98,7 @@ public void registerResourceServices() throws Exception
 		swaggerResourceTracker = new SwaggerResourceTracker(bundleContext,bundleContext.createFilter(ANY_SERVICE_FILTER), swagger);
 		swaggerResourceTracker.open();
 
-		serviceRegistrations.add(bundleContext.registerService(CyRESTSwagger.class.getName(), swagger, new Properties()));
+		serviceRegistrations.add(bundleContext.registerService(CyRESTSwagger.class.getName(), swagger, new Hashtable<String, Object>()));
 
 		loadTime = System.currentTimeMillis() - loadTime;
 

diff --git a/src/test/java/org/cytoscape/rest/CyActivatorTest.java b/src/test/java/org/cytoscape/rest/CyActivatorTest.java
@@ -114,7 +114,7 @@ public URL answer(InvocationOnMock invocation) throws MalformedURLException {
 		when(configAdmin.getConfiguration("org.ops4j.pax.logging")).thenReturn(configuration);
 		when(configAdmin.getConfiguration("org.ops4j.pax.web", null)).thenReturn(configuration);
 		when(configAdmin.getConfiguration("com.eclipsesource.jaxrs.connector", null)).thenReturn(configuration);
-		Dictionary<String,String> dictionary = new Hashtable<String, String>();
+		Dictionary<String,Object> dictionary = new Hashtable<String, Object>();
 		dictionary.put("log4j.appender.file.File", "dummyLogLocation");
 		when(configuration.getProperties()).thenReturn(dictionary);
 

diff --git a/src/test/java/org/cytoscape/rest/OSGiJAXRSConnectorIntegrationTest.java b/src/test/java/org/cytoscape/rest/OSGiJAXRSConnectorIntegrationTest.java
@@ -65,27 +65,24 @@ public class OSGiJAXRSConnectorIntegrationTest
 	private static final String KARAF_SCR_PATH = "karaf-scr/";
 
 	private static final String[] KARAF_SCR_BUNDLES = {
-			KARAF_SCR_PATH + "org.apache.felix.metatype-1.0.10.jar",
-			KARAF_SCR_PATH + "org.apache.felix.scr-1.8.2.jar",
-			KARAF_SCR_PATH + "org.apache.karaf.scr.command-3.0.3.jar"
+			KARAF_SCR_PATH + "org.apache.felix.scr-2.0.12.jar"
 	};
 
 	private static final String KARAF_HTTP_PATH = "karaf-http/";
 
 	private static final String[] KARAF_HTTP_BUNDLES = {
-			KARAF_HTTP_PATH + "org.apache.karaf.http.core-3.0.3.jar",
-			KARAF_HTTP_PATH + "org.apache.karaf.http.command-3.0.3.jar"
+			KARAF_HTTP_PATH + "org.apache.karaf.http.core-4.2.0-SNAPSHOT.jar"
 	};
 
 	private static final String HK2_PATH = "hk2/";
 
 	private static final String[] HK2_BUNDLES = {
-			HK2_PATH + "hk2-api-2.4.0-b34.jar",
-			HK2_PATH + "hk2-locator-2.4.0-b34.jar",
-			HK2_PATH + "hk2-utils-2.4.0-b34.jar",
+			HK2_PATH + "hk2-api-2.4.0.jar",
+			HK2_PATH + "hk2-locator-2.4.0.jar",
+			HK2_PATH + "hk2-utils-2.4.0.jar",
 			HK2_PATH + "osgi-resource-locator-1.0.1.jar",
-			HK2_PATH + "javax.inject-2.4.0-b34.jar",
-			HK2_PATH + "aopalliance-repackaged-2.4.0-b34.jar",
+			HK2_PATH + "javax.inject-2.4.0.jar",
+			HK2_PATH + "aopalliance-repackaged-2.4.0.jar",
 
 	};
 
@@ -107,7 +104,7 @@ public class OSGiJAXRSConnectorIntegrationTest
 	private static final String JERSEY_MISC_PATH = "jersey-misc/";
 
 	private static final String[] JERSEY_MISC_BUNDLES = {
-			JERSEY_MISC_PATH + "javax.annotation-api-1.2.jar",
+			//JERSEY_MISC_PATH + "javax.annotation-api-1.2.jar",
 			JERSEY_MISC_PATH + "validation-api-1.1.0.Final.jar",
 			JERSEY_MISC_PATH + "javassist-3.18.1-GA.jar",
 			JERSEY_MISC_PATH + "mimepull-1.9.6.jar",
@@ -116,16 +113,18 @@ public class OSGiJAXRSConnectorIntegrationTest
 	private static final String OSGI_JAX_RS_CONNECTOR_BUNDLES_PATH = "osgi-jax-rs-connector/";
 
 	private static final String[] OSGI_JAX_RS_CONNECTOR_BUNDLES = {
-			OSGI_JAX_RS_CONNECTOR_BUNDLES_PATH + "consumer-5.3.jar",
+			//OSGI_JAX_RS_CONNECTOR_BUNDLES_PATH + "javax.servlet-api-3.1.0.jar",
+
+			//OSGI_JAX_RS_CONNECTOR_BUNDLES_PATH + "consumer-5.3.jar",
 			OSGI_JAX_RS_CONNECTOR_BUNDLES_PATH + "publisher-5.3.jar",
-			OSGI_JAX_RS_CONNECTOR_BUNDLES_PATH + "provider-gson-2.2.jar",
+			OSGI_JAX_RS_CONNECTOR_BUNDLES_PATH + "provider-gson-2.3.jar",
 	};
 
 	private static final String[][] allBundles = {
-			PAX_JETTY_BUNDLES,
-			PAX_HTTP_BUNDLES,
-			KARAF_SCR_BUNDLES,
-			KARAF_HTTP_BUNDLES,
+			//PAX_JETTY_BUNDLES,
+			//PAX_HTTP_BUNDLES,
+			//KARAF_SCR_BUNDLES,
+			//KARAF_HTTP_BUNDLES,
 			JERSEY_MISC_BUNDLES,
 			HK2_BUNDLES,
 			GLASSFISH_JERSEY_BUNDLES,
@@ -198,7 +197,7 @@ public void testResourcesExist()
 		for (String[] resourceGroup : allBundles) {
 			for (String resource : resourceGroup) {
 				File f = new File("./src/main/resources/" + resource);
-				assertTrue(f.exists());
+				assertTrue("File does not exist: " + f.getAbsolutePath(), f.exists());
 			}
 		}
 	}

diff --git a/src/test/java/org/cytoscape/rest/ResourceManagerTest.java b/src/test/java/org/cytoscape/rest/ResourceManagerTest.java
@@ -10,6 +10,7 @@
 
 import java.net.URI;
 import java.util.HashMap;
+import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
 import java.util.Properties;
@@ -175,7 +176,7 @@ public void testRegisterResourceServices() throws Exception
 		assertEquals(TestClass.class, instances.get(0).getClass());
 		TestClass testClassInstance = (TestClass) instances.get(0);
 		assertEquals("1234", testClassInstance.cyRestPort);
-		verify(context).registerService(TestClass.class.getName(), new TestClass(), new Properties());
+		verify(context).registerService(TestClass.class.getName(), new TestClass(), new Hashtable<String, Object>());
 	}
 
 	@Test
@@ -186,7 +187,7 @@ public void testRegisterShimResourceServices() throws Exception
 		assertEquals(TestShimClass.class, instances.get(1).getClass());
 		TestShimClass testShimClassInstance = (TestShimClass) instances.get(1);
 		assertEquals(new Float(0.13f), testShimClassInstance.injected);
-		verify(context).registerService(TestShimClass.class.getName(), new TestShimClass(), new Properties());
+		verify(context).registerService(TestShimClass.class.getName(), new TestShimClass(), new Hashtable<String, Object>());
 	}
 
 	@Test