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Posted to commits@taverna.apache.org by st...@apache.org on 2016/05/16 10:12:20 UTC

[1/4] incubator-taverna-language git commit: Re-enabled wfdesc by default in databundle

Repository: incubator-taverna-language
Updated Branches:
  refs/heads/master c1e4da5db -> 32a439e9c


Re-enabled wfdesc by default in databundle


Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/02b36962
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/02b36962
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/02b36962

Branch: refs/heads/master
Commit: 02b3696277942f3e68941ce3472f1ca1326b627e
Parents: c1e4da5
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Mon May 16 10:33:53 2016 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Mon May 16 10:33:53 2016 +0100

----------------------------------------------------------------------
 taverna-databundle/pom.xml | 15 ---------------
 1 file changed, 15 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/02b36962/taverna-databundle/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-databundle/pom.xml b/taverna-databundle/pom.xml
index eefb74a..cb9bb61 100644
--- a/taverna-databundle/pom.xml
+++ b/taverna-databundle/pom.xml
@@ -33,18 +33,6 @@
             <version>${jena.version}</version>
         </dependency>
 
-    <dependency>
-      <groupId>org.apache.servicemix.bundles</groupId>
-      <artifactId>org.apache.servicemix.bundles.xerces</artifactId>
-      <version>${servicemix.xerces.version}</version>
-    </dependency>
-        <!-- JENA-1178 workaround: Upgrade jsonlld-java -->
-    <dependency>
-      <groupId>com.github.jsonld-java</groupId>
-      <artifactId>jsonld-java</artifactId>
-      <version>${jsonldjava.version}</version>
-     </dependency>
-
         <dependency>
           <groupId>${project.groupId}</groupId>
           <artifactId>taverna-scufl2-wfbundle</artifactId>
@@ -56,14 +44,11 @@
           <version>${project.version}</version>
           <scope>test</scope>
         </dependency>
-        <!-- Temporarily disabled
         <dependency>
           <groupId>${project.groupId}</groupId>
           <artifactId>taverna-scufl2-wfdesc</artifactId>
           <version>${project.version}</version>
-          <optional>true</optional>
         </dependency>
-         -->
         <dependency>
           <groupId>${project.groupId}</groupId>
           <artifactId>taverna-robundle</artifactId>


[3/4] incubator-taverna-language git commit: newer Jackson

Posted by st...@apache.org.
newer Jackson


Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/d40623b1
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/d40623b1
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/d40623b1

Branch: refs/heads/master
Commit: d40623b190aedeefd8c1dd0142aa4ac9a7e8f3fb
Parents: f937678
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Mon May 16 11:02:53 2016 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Mon May 16 11:02:53 2016 +0100

----------------------------------------------------------------------
 taverna-scufl2-wfdesc/pom.xml                   | 29 +++++---------------
 .../taverna/scufl2/wfdesc/WfdescAgent.java      |  9 +++---
 2 files changed, 11 insertions(+), 27 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/d40623b1/taverna-scufl2-wfdesc/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/pom.xml b/taverna-scufl2-wfdesc/pom.xml
index 4cc8023..c60646c 100755
--- a/taverna-scufl2-wfdesc/pom.xml
+++ b/taverna-scufl2-wfdesc/pom.xml
@@ -85,20 +85,15 @@
 							<pluginExecutions>
 								<pluginExecution>
 									<pluginExecutionFilter>
-										<groupId>
-											org.apache.jena
-										</groupId>
-										<artifactId>
-											jena-maven-tools
-										</artifactId>
-										<versionRange>
-											[3.0.1,)
-										</versionRange>
+										<groupId>org.apache.jena</groupId>
+										<artifactId>jena-maven-tools</artifactId>
+										<versionRange>[${jena.version},)</versionRange>
 										<goals>
 											<goal>translate</goal>
 										</goals>
 									</pluginExecutionFilter>
 									<action>
+										<!-- Make target/generated-source/jena -->
 										<execute />
 									</action>
 								</pluginExecution>
@@ -140,17 +135,7 @@
 			<artifactId>jena-osgi</artifactId>
 			<version>${jena.version}</version>
 		</dependency>
-    <dependency>
-      <groupId>org.apache.servicemix.bundles</groupId>
-      <artifactId>org.apache.servicemix.bundles.xerces</artifactId>
-      <version>${servicemix.xerces.version}</version>
-    </dependency>
-        <!-- JENA-1178 workaround: Upgrade jsonlld-java -->
-    <dependency>
-      <groupId>com.github.jsonld-java</groupId>
-      <artifactId>jsonld-java</artifactId>
-      <version>${jsonldjava.version}</version>
-     </dependency>
+
 
 		<dependency>
 			<groupId>junit</groupId>
@@ -167,8 +152,8 @@
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>org.codehaus.jackson</groupId>
-			<artifactId>jackson-mapper-asl</artifactId>
+			<groupId>com.fasterxml.jackson.core</groupId>
+			<artifactId>jackson-databind</artifactId>
 			<version>${jackson.version}</version>
 			<type>jar</type>
 		</dependency>

http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/d40623b1/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/WfdescAgent.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/WfdescAgent.java b/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/WfdescAgent.java
index a75d9ba..0a0209e 100644
--- a/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/WfdescAgent.java
+++ b/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/WfdescAgent.java
@@ -25,11 +25,10 @@ package org.apache.taverna.scufl2.wfdesc;
 import java.io.IOException;
 import java.net.URI;
 
-import org.codehaus.jackson.JsonNode;
-import org.codehaus.jackson.JsonParseException;
-import org.codehaus.jackson.map.JsonMappingException;
-import org.codehaus.jackson.map.ObjectMapper;
-
+import com.fasterxml.jackson.core.JsonParseException;
+import com.fasterxml.jackson.databind.JsonMappingException;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import com.sun.jersey.api.client.Client;
 import com.sun.jersey.api.client.WebResource;
 


[2/4] incubator-taverna-language git commit: ConvertToWfdesc removed in favour of tavlang tool

Posted by st...@apache.org.
ConvertToWfdesc removed in favour of tavlang tool


Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/f9376783
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/f9376783
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/f9376783

Branch: refs/heads/master
Commit: f93767837c2ce3720ee06fb462f6f090968dbf79
Parents: 02b3696
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Mon May 16 11:01:28 2016 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Mon May 16 11:01:28 2016 +0100

----------------------------------------------------------------------
 .../taverna/scufl2/wfdesc/ConvertToWfdesc.java  |  76 --------
 .../scufl2/wfdesc/TestConvertToWfdesc.java      | 188 -------------------
 2 files changed, 264 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/f9376783/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ConvertToWfdesc.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ConvertToWfdesc.java b/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ConvertToWfdesc.java
deleted file mode 100644
index fa9f28c..0000000
--- a/taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/ConvertToWfdesc.java
+++ /dev/null
@@ -1,76 +0,0 @@
-package org.apache.taverna.scufl2.wfdesc;
-
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
-*/
-
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Arrays;
-
-import javax.xml.bind.JAXBException;
-
-import org.apache.log4j.BasicConfigurator;
-import org.apache.log4j.Logger;
-import org.apache.log4j.Level;
-import org.apache.taverna.scufl2.api.container.WorkflowBundle;
-import org.apache.taverna.scufl2.api.io.ReaderException;
-import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
-import org.apache.taverna.scufl2.api.io.WriterException;
-
-
-public class ConvertToWfdesc {
-	
-	static {
-		BasicConfigurator.configure();
-        Logger.getRootLogger().setLevel(Level.WARN);
-	}
-	
-	public static void main(String[] args) throws JAXBException, IOException,
-			ReaderException, WriterException {
-		WorkflowBundleIO io = new WorkflowBundleIO();
-		if (Arrays.asList(args).contains("-h") || Arrays.asList(args).contains("--help")) {
-			System.out.println("scufl2-to-wfdesc [workflow] ...");
-			System.out.println("");
-			System.out.println("Converts each of the workflow files to wfdesc.");
-			System.out.println("See http://purl.org/wf4ever/model");
-			System.out.println("The wfdesc will be stored in a matching filename with ");
-			System.out.println("the .wfdesc.ttl extension.");
-			System.out.println("If no arguments are given, read from STDIN and write to STDOUT.");
-			return;
-		}
-		if (args.length==0) {
-			WorkflowBundle wfBundle = io.readBundle(System.in, null);
-			io.writeBundle(wfBundle, System.out,
-					"text/vnd.wf4ever.wfdesc+turtle");
-		}
-		for (String filepath : args) {
-			File original = new File(filepath);
-			String filename = original.getName();
-			filename = filename.replaceFirst("\\..*", "") + ".wfdesc.ttl";
-			File wfdesc = new File(original.getParentFile(), filename);
-			WorkflowBundle wfBundle = io.readBundle(original, null);
-			io.writeBundle(wfBundle, wfdesc,
-					"text/vnd.wf4ever.wfdesc+turtle");
-			System.out.println("Converted " + original.getPath() + " to " + wfdesc.getPath());
-		}
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/f9376783/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestConvertToWfdesc.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestConvertToWfdesc.java b/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestConvertToWfdesc.java
deleted file mode 100644
index 7528457..0000000
--- a/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestConvertToWfdesc.java
+++ /dev/null
@@ -1,188 +0,0 @@
-package org.apache.taverna.scufl2.wfdesc;
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
-*/
-
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.PrintStream;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.commons.io.IOUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class TestConvertToWfdesc {
-	private static final boolean DEBUG = false;
-	private static final String HELLOANYONE_T2FLOW = "helloanyone.t2flow";
-	private static final String HELLOWORLD_T2FLOW = "helloworld.t2flow";
-	private File helloworldT2flow;
-	private File helloanyoneT2flow;
-	private File helloworldWfdesc;
-	private File helloanyoneWfdesc;
-	private InputStream origIn;
-	private PrintStream origOut;
-	private PrintStream origErr;
-	
-	@Before
-	public void copyT2flow() throws IOException {
-		File tempdir = File.createTempFile("scufl2-wfdesc", "test");
-		tempdir.delete();
-		assertTrue(tempdir.mkdir());
-		if (DEBUG) {
-			System.out.println("Copying to " + tempdir);
-		}
-		
-		helloworldT2flow = new File(tempdir, HELLOWORLD_T2FLOW);
-		FileUtils.copyInputStreamToFile(getClass().getResourceAsStream("/" + HELLOWORLD_T2FLOW), helloworldT2flow);
-		
-		helloanyoneT2flow = new File(tempdir, HELLOANYONE_T2FLOW);
-		FileUtils.copyInputStreamToFile(getClass().getResourceAsStream("/" + HELLOANYONE_T2FLOW), helloanyoneT2flow);
-		
-		helloworldWfdesc = new File(tempdir, "helloworld.wfdesc.ttl");
-		
-		helloanyoneWfdesc = new File(tempdir, "helloanyone.wfdesc.ttl");
-	}
-	
-	@After
-	public void deleteTemp() throws IOException {
-		if (DEBUG) {
-			return;
-		}
-		for (File f : new File[] { helloworldT2flow, helloanyoneT2flow,
-				helloworldWfdesc, helloanyoneWfdesc,
-				helloworldT2flow.getParentFile() }) {
-			f.delete();
-		}		
-	}
-	
-	@Before
-	public void origStd() {
-		origIn = System.in;
-		origOut = System.out;
-		origErr = System.err;
-	}
-	
-	@After
-	public void restoreStd() {
-		System.setIn(origIn);
-		System.setOut(origOut);
-		System.setErr(origErr);	
-	}
-	
-	@Test
-	public void help() throws Exception {
-		help("-h");
-		help("--help");
-	}
-	
-	private void help(String argName) throws Exception {
-		ByteArrayOutputStream out = new ByteArrayOutputStream();
-		PrintStream outBuf = new PrintStream(out);
-		
-		ByteArrayOutputStream err = new ByteArrayOutputStream();
-		PrintStream errBuf = new PrintStream(err);
-		
-		try {
-			System.setOut(outBuf);
-			System.setErr(errBuf);	
-			ConvertToWfdesc.main(new String[]{argName});
-		} finally {
-			restoreStd();
-		}
-		out.flush();
-		out.close();
-		err.flush();
-		err.close();
-		
-		assertEquals(0, err.size());		
-		String help = out.toString("utf-8");
-//		System.out.println(help);
-		assertTrue(help.contains("scufl2-to-wfdesc"));
-		assertTrue(help.contains("\nIf no arguments are given"));
-	}
-	
-	@Test
-	public void stdin() throws Exception {
-		byte[] input = IOUtils.toByteArray(getClass().getResourceAsStream("/" + HELLOWORLD_T2FLOW));
-		assertTrue(input.length > 0);
-		InputStream in = new ByteArrayInputStream(input);
-		ByteArrayOutputStream out = new ByteArrayOutputStream();
-		PrintStream outBuf = new PrintStream(out);
-		try {
-			System.setIn(in);
-			System.setOut(outBuf);		
-			ConvertToWfdesc.main(new String[]{});
-		} finally {
-			restoreStd();
-		}
-		out.flush();
-		out.close();
-		String turtle = out.toString("utf-8");
-		//System.out.println(turtle);
-		assertTrue(turtle.contains("Hello_World"));
-		assertTrue(turtle.contains("processor/hello/out/value"));
-	}
-	
-	@Test
-	public void convert() throws Exception {		
-		assertFalse(helloworldWfdesc.exists());
-		assertFalse(helloanyoneWfdesc.exists());
-		ConvertToWfdesc.main(new String[]{helloworldT2flow.getAbsolutePath(), helloanyoneT2flow.getAbsolutePath() });
-		assertTrue(helloworldWfdesc.exists());
-		assertTrue(helloanyoneWfdesc.exists());
-
-		// FIXME: Update test to use Jena
-
-//		Repository myRepository = new SailRepository(new MemoryStore());
-//		myRepository.initialize();
-//		RepositoryConnection con = myRepository.getConnection();
-//		con.add(helloworldWfdesc, helloworldWfdesc.toURI().toASCIIString(), RDFFormat.TURTLE);
-////		assertTrue(con.prepareTupleQuery(QueryLanguage.SPARQL,
-//		assertTrue(con.prepareBooleanQuery(QueryLanguage.SPARQL, 
-//				"PREFIX wfdesc: <http://purl.org/wf4ever/wfdesc#>  " +
-//				"ASK { " +
-//				"?wf a wfdesc:Workflow, wfdesc:Process ;" +
-//				"  wfdesc:hasOutput ?greeting; " +
-//				"  wfdesc:hasDataLink ?link; " +
-//				"  wfdesc:hasSubProcess ?hello . " +
-//				"?hello a wfdesc:Process ;" +
-//				"  wfdesc:hasOutput ?value . " +
-//				"?greeting a wfdesc:Output . " +
-//				"?value a wfdesc:Output . " +
-//				"?link a wfdesc:DataLink ; " +
-//				"  wfdesc:hasSource ?value ; " +
-//				"  wfdesc:hasSink ?greeting . " +				
-//			    "}").evaluate());
-		
-	}
-	
-	
-	
-}


[4/4] incubator-taverna-language git commit: TAVERNA-970 Move Jena and its dependencies to top-level pom

Posted by st...@apache.org.
TAVERNA-970 Move Jena and its dependencies to top-level pom


Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/32a439e9
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/32a439e9
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/32a439e9

Branch: refs/heads/master
Commit: 32a439e9cc71c247fa2d2b1e34480a3ce79bd1a5
Parents: d40623b
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Mon May 16 11:11:56 2016 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Mon May 16 11:11:56 2016 +0100

----------------------------------------------------------------------
 pom.xml                           | 28 ++++++++++++++++++++++++++++
 taverna-robundle/pom.xml          | 26 --------------------------
 taverna-scufl2-annotation/pom.xml | 14 ++------------
 3 files changed, 30 insertions(+), 38 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/32a439e9/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index af7942d..d597b19 100644
--- a/pom.xml
+++ b/pom.xml
@@ -246,6 +246,34 @@
 			</dependency>
 		</dependencies>
 	</dependencyManagement>
+<dependencies>
+  <!-- Common dependencies on jena-osgi, which requires some
+additional dependencies to be a happy OSGi bundle -->
+
+	<dependency>
+		<groupId>org.apache.jena</groupId>
+		<artifactId>jena-osgi</artifactId>
+		<version>${jena.version}</version>
+	</dependency>
+    <dependency>
+      <groupId>org.apache.servicemix.bundles</groupId>
+      <artifactId>org.apache.servicemix.bundles.xerces</artifactId>
+      <version>${servicemix.xerces.version}</version>
+    </dependency>
+        <!-- JENA-1178 workaround: Upgrade jsonlld-java -->
+    <dependency>
+      <groupId>com.github.jsonld-java</groupId>
+      <artifactId>jsonld-java</artifactId>
+      <version>${jsonldjava.version}</version>
+     </dependency>
+    <!-- Needed by Jena -->
+    <dependency>
+      <groupId>com.github.andrewoma.dexx</groupId>
+      <artifactId>collection</artifactId>
+      <version>${dexx.collection.version}</version>
+    </dependency>
+
+</dependencies>
 
 	<modules>
     <module>taverna-baclava-language</module>

http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/32a439e9/taverna-robundle/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-robundle/pom.xml b/taverna-robundle/pom.xml
index be1f5f2..a6fe7d7 100644
--- a/taverna-robundle/pom.xml
+++ b/taverna-robundle/pom.xml
@@ -61,19 +61,6 @@
 			<version>${jena.version}</version>
 		</dependency>
 
-    <!-- Needed by jena-osgi -->
-    <dependency>
-      <groupId>org.apache.servicemix.bundles</groupId>
-      <artifactId>org.apache.servicemix.bundles.xerces</artifactId>
-      <version>${servicemix.xerces.version}</version>
-    </dependency>
-	<!-- JENA-1178 workaround: Upgrade jsonlld-java -->
-    <dependency>
-      <groupId>com.github.jsonld-java</groupId>
-      <artifactId>jsonld-java</artifactId>
-      <version>${jsonldjava.version}</version>
-     </dependency>
-
 
 
 <!--
@@ -100,19 +87,6 @@
 
 	<build>
 		<plugins>
-			<plugin>
-				<groupId>org.apache.felix</groupId>
-				<artifactId>maven-bundle-plugin</artifactId>
-				<extensions>true</extensions>
-        <!--
-				<configuration>
-					<instructions>
-						<Embed-Dependency>*;groupId=com.github.jsonld-java</Embed-Dependency>
-						<Embed-Transitive>true</Embed-Transitive>
-					</instructions>
-				</configuration>
-        -->
-			</plugin>
       <plugin>
           <groupId>org.jvnet.jaxb2.maven2</groupId>
           <artifactId>maven-jaxb2-plugin</artifactId>

http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/32a439e9/taverna-scufl2-annotation/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-annotation/pom.xml b/taverna-scufl2-annotation/pom.xml
index 7c1ee19..ca6ee7a 100644
--- a/taverna-scufl2-annotation/pom.xml
+++ b/taverna-scufl2-annotation/pom.xml
@@ -47,19 +47,9 @@
 		<dependency>
 			<groupId>org.apache.jena</groupId>
 			<artifactId>jena-osgi</artifactId>
-      <version>${jena.version}</version>
+			<version>${jena.version}</version>
 		</dependency>
-    <dependency>
-      <groupId>org.apache.servicemix.bundles</groupId>
-      <artifactId>org.apache.servicemix.bundles.xerces</artifactId>
-      <version>${servicemix.xerces.version}</version>
-    </dependency>
-        <!-- JENA-1178 workaround: Upgrade jsonlld-java -->
-    <dependency>
-      <groupId>com.github.jsonld-java</groupId>
-      <artifactId>jsonld-java</artifactId>
-      <version>${jsonldjava.version}</version>
-     </dependency>
+
 
 	</dependencies>
 </project>