[1/2] incubator-taverna-osgi git commit: TAVERNA-899 package org.apache.taverna.mavenplugin

[st...@apache.org]

Repository: incubator-taverna-osgi
Updated Branches:
  refs/heads/master 33defe425 -> c660ed5cd


http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/BundleArtifact.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/BundleArtifact.java b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/BundleArtifact.java
new file mode 100644
index 0000000..6d106ab
--- /dev/null
+++ b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/BundleArtifact.java
@@ -0,0 +1,62 @@
+/**
+ * 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.
+ */
+package org.apache.taverna.mavenplugin;
+
+import org.apache.maven.artifact.Artifact;
+
+/**
+ *
+ *
+ * @author David Withers
+ */
+public class BundleArtifact {
+
+	private Artifact artifact;
+	private String symbolicName;
+	private String version;
+
+	public BundleArtifact(Artifact artifact, String symbolicName, String version) {
+		this.artifact = artifact;
+		this.symbolicName = symbolicName;
+		this.version = version;
+	}
+
+	public Artifact getArtifact() {
+		return artifact;
+	}
+
+	public void setArtifact(Artifact artifact) {
+		this.artifact = artifact;
+	}
+
+	public String getSymbolicName() {
+		return symbolicName;
+	}
+
+	public void setSymbolicName(String symbolicName) {
+		this.symbolicName = symbolicName;
+	}
+
+	public String getVersion() {
+		return version;
+	}
+
+	public void setVersion(String version) {
+		this.version = version;
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/MavenOsgiUtils.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/MavenOsgiUtils.java b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/MavenOsgiUtils.java
new file mode 100644
index 0000000..f6cdb64
--- /dev/null
+++ b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/MavenOsgiUtils.java
@@ -0,0 +1,411 @@
+/**
+ * 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.
+ */
+package org.apache.taverna.mavenplugin;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.jar.Attributes;
+import java.util.jar.JarFile;
+import java.util.jar.Manifest;
+
+import org.apache.maven.RepositoryUtils;
+import org.apache.maven.artifact.Artifact;
+import org.apache.maven.plugin.MojoExecutionException;
+import org.apache.maven.plugin.logging.Log;
+import org.apache.maven.project.DefaultDependencyResolutionRequest;
+import org.apache.maven.project.DependencyResolutionException;
+import org.apache.maven.project.DependencyResolutionResult;
+import org.apache.maven.project.MavenProject;
+import org.apache.maven.project.ProjectDependenciesResolver;
+import org.apache.taverna.profile.xml.jaxb.BundleInfo;
+import org.eclipse.aether.RepositorySystemSession;
+import org.eclipse.aether.graph.DependencyNode;
+import org.eclipse.aether.util.filter.ScopeDependencyFilter;
+
+import aQute.bnd.header.Attrs;
+import aQute.bnd.header.OSGiHeader;
+import aQute.bnd.header.Parameters;
+import aQute.bnd.osgi.Constants;
+import aQute.bnd.version.Version;
+import aQute.bnd.version.VersionRange;
+
+/**
+ * @author David Withers
+ */
+public class MavenOsgiUtils {
+
+	private final MavenProject project;
+	private final RepositorySystemSession repositorySystemSession;
+	private final ProjectDependenciesResolver projectDependenciesResolver;
+	private final Log log;
+
+	private Set<String> javaPackages;
+	private Set<String> systemPackages;
+
+	public MavenOsgiUtils(MavenProject project, RepositorySystemSession repositorySystemSession,
+			ProjectDependenciesResolver projectDependenciesResolver, Log log) {
+		this(project, repositorySystemSession, projectDependenciesResolver, new HashSet<String>(),
+				log);
+	}
+
+	public MavenOsgiUtils(MavenProject project, RepositorySystemSession repositorySystemSession,
+			ProjectDependenciesResolver projectDependenciesResolver, Set<String> systemPackages,
+			Log log) {
+		this.project = project;
+		this.repositorySystemSession = repositorySystemSession;
+		this.projectDependenciesResolver = projectDependenciesResolver;
+		this.systemPackages = systemPackages;
+		this.log = log;
+		javaPackages = Utils.getJavaPackages(log);
+	}
+
+	public Set<BundleArtifact> getBundleDependencies(String... scopes)
+			throws MojoExecutionException {
+		ScopeDependencyFilter scopeFilter = new ScopeDependencyFilter(Arrays.asList(scopes), null);
+
+		DefaultDependencyResolutionRequest dependencyResolutionRequest = new DefaultDependencyResolutionRequest(
+				project, repositorySystemSession);
+		dependencyResolutionRequest.setResolutionFilter(scopeFilter);
+
+		DependencyResolutionResult dependencyResolutionResult;
+		try {
+			dependencyResolutionResult = projectDependenciesResolver
+					.resolve(dependencyResolutionRequest);
+		} catch (DependencyResolutionException ex) {
+			throw new MojoExecutionException(ex.getMessage(), ex);
+		}
+
+		DependencyNode dependencyGraph = dependencyResolutionResult.getDependencyGraph();
+		if (dependencyGraph != null) {
+			checkBundleDependencies(dependencyGraph.getChildren());
+			return getBundleArtifacts(dependencyGraph.getChildren());
+		} else {
+			return new HashSet<BundleArtifact>();
+		}
+	}
+
+	public Set<BundleArtifact> getBundleArtifacts(List<DependencyNode> nodes) {
+		Set<BundleArtifact> bundleArtifacts = new HashSet<BundleArtifact>();
+		for (DependencyNode node : nodes) {
+			Artifact artifact = RepositoryUtils.toArtifact(node.getDependency().getArtifact());
+			String symbolicName = getManifestAttribute(artifact, Constants.BUNDLE_SYMBOLICNAME);
+			if (symbolicName != null) {
+				String version = getManifestAttribute(artifact, Constants.BUNDLE_VERSION);
+				bundleArtifacts.add(new BundleArtifact(artifact, symbolicName, version));
+				bundleArtifacts.addAll(getBundleArtifacts(node.getChildren()));
+			} else {
+				log.warn("Not an OSGi bundle : " + artifact.getId());
+			}
+		}
+		return bundleArtifacts;
+	}
+
+	public Set<Artifact> getAllArtifacts(List<DependencyNode> nodes) {
+		Set<Artifact> artifacts = new HashSet<Artifact>();
+		for (DependencyNode node : nodes) {
+			Artifact artifact = RepositoryUtils.toArtifact(node.getDependency().getArtifact());
+			if (isBundle(artifact)) {
+				artifacts.add(artifact);
+				artifacts.addAll(getAllArtifacts(node.getChildren()));
+			}
+		}
+		return artifacts;
+	}
+
+	public Set<Artifact> getArtifacts(List<DependencyNode> nodes) {
+		Set<Artifact> artifacts = new HashSet<Artifact>();
+		for (DependencyNode node : nodes) {
+			Artifact artifact = RepositoryUtils.toArtifact(node.getDependency().getArtifact());
+			if (isBundle(artifact)) {
+				artifacts.add(artifact);
+			}
+		}
+		return artifacts;
+	}
+
+	public List<BundleInfo> getBundles(Set<BundleArtifact> bundleDependencies)
+			throws MojoExecutionException {
+		List<BundleInfo> bundles = new ArrayList<BundleInfo>();
+		for (BundleArtifact bundleArtifact : bundleDependencies) {
+			Artifact artifact = bundleArtifact.getArtifact();
+			BundleInfo bundle = new BundleInfo();
+			bundle.setSymbolicName(bundleArtifact.getSymbolicName());
+			bundle.setVersion(bundleArtifact.getVersion());
+			bundle.setFileName(new File(artifact.getGroupId(), artifact.getFile().getName())
+					.getPath());
+			bundles.add(bundle);
+		}
+		Collections.sort(bundles, new BundleComparator());
+		return bundles;
+	}
+
+	public Map<String, Set<PackageVersion>> getPackageDependencies(List<DependencyNode> nodes) {
+		Map<String, Set<PackageVersion>> exportVersions = calculatePackageVersions(
+				getAllArtifacts(nodes), true, false);
+		return getPackageDependencies(getArtifacts(nodes), exportVersions);
+	}
+
+	public Map<String, Set<PackageVersion>> getPackageDependencies(Set<Artifact> requiredArtifacts,
+			Map<String, Set<PackageVersion>> exportVersions) {
+		Map<String, Set<PackageVersion>> importVersions = calculatePackageVersions(
+				requiredArtifacts, false, true);
+		Set<Artifact> newRequiredArtifacts = new HashSet<Artifact>();
+		for (Entry<String, Set<PackageVersion>> entry : importVersions.entrySet()) {
+			if (!javaPackages.contains(entry.getKey())) {
+				String packageName = entry.getKey();
+				Set<PackageVersion> importsVersions = entry.getValue();
+				Set<PackageVersion> exportsVersions = exportVersions.get(packageName);
+				if (exportVersions.containsKey(entry.getKey())) {
+					for (Artifact artifact : getRequiredArtifacts(importsVersions, exportsVersions)) {
+						if (!requiredArtifacts.contains(artifact)) {
+							newRequiredArtifacts.add(artifact);
+						}
+					}
+				}
+			}
+		}
+		if (!newRequiredArtifacts.isEmpty()) {
+			newRequiredArtifacts.addAll(requiredArtifacts);
+			return getPackageDependencies(newRequiredArtifacts, exportVersions);
+		}
+		return importVersions;
+	}
+
+	/**
+	 * Returns the minimum set of artifacts required to satisfy the range of importVersions.
+	 *
+	 * @param importsVersions
+	 *            the version ranges required for the package
+	 * @param exportVersions
+	 *            the available versions for the package
+	 * @return the minimum set of artifacts required to satisfy the range of importVersions
+	 */
+	private Set<Artifact> getRequiredArtifacts(Set<PackageVersion> importsVersions,
+			Set<PackageVersion> exportVersions) {
+		Set<Artifact> requiredArtifacts = new HashSet<Artifact>();
+		List<Set<PackageVersion>> exportsSubsets = Utils.getSubsets(exportVersions);
+		for (Set<PackageVersion> exportsSubset : exportsSubsets) {
+			if (satisfiesImports(importsVersions, exportsSubset)) {
+				for (PackageVersion exportVersion : exportsSubset) {
+					requiredArtifacts.add(exportVersion.getArtifact());
+				}
+				break;
+			}
+		}
+		return requiredArtifacts;
+	}
+
+	private boolean satisfiesImports(Set<PackageVersion> imports, Set<PackageVersion> exports) {
+		for (PackageVersion importVersion : imports) {
+			if (!satisfiesImport(importVersion, exports)) {
+				return false;
+			}
+		}
+		return true;
+	}
+
+	private boolean satisfiesImport(PackageVersion importVersion, Set<PackageVersion> exports) {
+		for (PackageVersion exportVersion : exports) {
+			if (importVersion.getVersionRange().includes(exportVersion.getVersionRange().getLow())) {
+				return true;
+			}
+		}
+		return false;
+	}
+
+	public void checkBundleDependencies(List<DependencyNode> nodes) {
+		Map<Artifact, Set<Package>> unresolvedArtifacts = new HashMap<Artifact, Set<Package>>();
+		Set<Artifact> artifacts = getAllArtifacts(nodes);
+		Map<String, Set<PackageVersion>> exports = calculatePackageVersions(artifacts, true, false);
+		for (Artifact artifact : artifacts) {
+			if (isBundle(artifact)) {
+				Parameters imports = getManifestAttributeParameters(artifact,
+						Constants.IMPORT_PACKAGE);
+				if (imports != null) {
+					for (String packageName : imports.keySet()) {
+						boolean exportMissing = true;
+						VersionRange importRange = null;
+						Attrs attrs = imports.get(packageName);
+						if (isOptional(attrs)) {
+							exportMissing = false;
+						} else if (javaPackages.contains(packageName)
+								|| systemPackages.contains(packageName)
+								|| packageName.startsWith("org.osgi.")) {
+							exportMissing = false;
+						} else if (attrs == null || attrs.get(Constants.VERSION_ATTRIBUTE) == null) {
+							if (exports.containsKey(packageName)) {
+								exportMissing = false;
+							}
+						} else {
+							importRange = getVersionRange(attrs);
+							if (exports.containsKey(packageName)) {
+								for (PackageVersion exportVersion : exports.get(packageName)) {
+									if (importRange.includes(exportVersion.getVersionRange()
+											.getLow())) {
+										exportMissing = false;
+										break;
+									}
+								}
+							}
+						}
+						if (exportMissing) {
+							if (!unresolvedArtifacts.containsKey(artifact)) {
+								unresolvedArtifacts.put(artifact, new HashSet<Package>());
+							}
+							unresolvedArtifacts.get(artifact).add(
+									new Package(packageName, importRange));
+						}
+					}
+				}
+			}
+		}
+		for (Entry<Artifact, Set<Package>> unresolvedArtifact : unresolvedArtifacts.entrySet()) {
+			log.warn("Bundle : " + unresolvedArtifact.getKey().getId()
+					+ " has unresolved package dependencies:");
+			for (Package unresolvedPackage : unresolvedArtifact.getValue()) {
+				log.warn("    " + unresolvedPackage);
+			}
+		}
+	}
+
+	public Map<String, Set<PackageVersion>> calculatePackageVersions(Set<Artifact> artifacts,
+			boolean export, boolean unique) {
+		Map<String, Set<PackageVersion>> packageVersions = new HashMap<String, Set<PackageVersion>>();
+		for (Artifact artifact : artifacts) {
+			if (isBundle(artifact)) {
+				Parameters packages = getManifestAttributeParameters(artifact,
+						export ? Constants.EXPORT_PACKAGE : Constants.IMPORT_PACKAGE);
+				if (packages != null) {
+					for (String packageName : packages.keySet()) {
+						if (!packageVersions.containsKey(packageName)) {
+							packageVersions.put(packageName, new HashSet<PackageVersion>());
+						}
+						Set<PackageVersion> versions = packageVersions.get(packageName);
+						VersionRange versionRange = getVersionRange(packages.get(packageName));
+						boolean optional = isOptional(packages.get(packageName));
+						if (unique) {
+							// check if this version range is unique
+							boolean uniqueVersion = true;
+							for (PackageVersion version : versions) {
+								if (equals(versionRange, version.getVersionRange())) {
+									uniqueVersion = false;
+									break;
+								}
+							}
+							if (uniqueVersion) {
+								versions.add(new PackageVersion(versionRange, artifact, optional));
+							}
+						} else {
+							versions.add(new PackageVersion(versionRange, artifact, optional));
+						}
+					}
+				}
+			}
+		}
+		return packageVersions;
+	}
+
+	public Version getVersion(Attrs attrs) {
+		if (attrs == null) {
+			return Version.LOWEST;
+		}
+		return Version.parseVersion(attrs.get(Constants.VERSION_ATTRIBUTE));
+	}
+
+	public VersionRange getVersionRange(Attrs attrs) {
+		if (attrs == null) {
+			return new VersionRange("0");
+		}
+		String version = attrs.get(Constants.VERSION_ATTRIBUTE);
+		if (version == null) {
+			return new VersionRange("0");
+		}
+		return new VersionRange(version);
+	}
+
+	public boolean isBundle(Artifact artifact) {
+		return getManifestAttribute(artifact, Constants.BUNDLE_SYMBOLICNAME) != null;
+	}
+
+	public boolean isOptional(Attrs attrs) {
+		return attrs != null && "optional".equals(attrs.get(Constants.RESOLUTION_DIRECTIVE));
+	}
+
+	public boolean equals(VersionRange v1, VersionRange v2) {
+		return v1 == v2 || v1.toString().equals(v2.toString());
+	}
+
+	public Parameters getManifestAttributeParameters(Artifact artifact, String attributeName) {
+		String attributeValue = getManifestAttribute(artifact, attributeName);
+		if (attributeValue != null) {
+			return OSGiHeader.parseHeader(attributeValue);
+		}
+		return null;
+	}
+
+	public String getManifestAttribute(Artifact artifact, String attributeName) {
+		Manifest manifest = getManifest(artifact);
+		if (manifest != null) {
+			Attributes mainAttributes = manifest.getMainAttributes();
+			return mainAttributes.getValue(attributeName);
+		}
+		return null;
+	}
+
+	public Manifest getManifest(Artifact artifact) {
+		if (artifact != null) {
+			File file = artifact.getFile();
+			if (file != null) {
+				try {
+					JarFile jarFile = new JarFile(artifact.getFile());
+					return jarFile.getManifest();
+				} catch (IOException e) {
+					return null;
+				}
+			}
+		}
+		return null;
+	}
+
+	private final class BundleComparator implements Comparator<BundleInfo> {
+
+		@Override
+		public int compare(BundleInfo bundle1, BundleInfo bundle2) {
+			return bundle1.getSymbolicName().compareTo(bundle2.getSymbolicName());
+		}
+
+	}
+
+	// public static void main(String[] args) throws Exception {
+	// MavenOsgiUtils mavenOsgiUtils = new MavenOsgiUtils();
+	// Parameters exports = mavenOsgiUtils.getImports(new
+	// File("/Users/david/Documents/workspace-trunk/taverna-plugin-impl/target/taverna-plugin-impl-0.1.0-SNAPSHOT.jar"));
+	// for (String key : exports.keySet()) {
+	// System.out.println(key + " " + mavenOsgiUtils.getVersionRange(exports.get(key)));
+	// }
+	// }
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/Package.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/Package.java b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/Package.java
new file mode 100644
index 0000000..ad92979
--- /dev/null
+++ b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/Package.java
@@ -0,0 +1,42 @@
+/**
+ * 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.
+ */
+package org.apache.taverna.mavenplugin;
+
+import aQute.bnd.version.VersionRange;
+
+/**
+ * @author David Withers
+ */
+public class Package {
+
+	private String name;
+	private VersionRange versionRange;
+
+	public Package(String name, VersionRange versionRange) {
+		this.name = name;
+		this.versionRange = versionRange;
+	}
+
+	@Override
+	public String toString() {
+		if (versionRange == null) {
+			return name;
+		} else {
+			return name + ";version=\"" + versionRange + "\"";
+		}
+	}
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/PackageVersion.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/PackageVersion.java b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/PackageVersion.java
new file mode 100644
index 0000000..f4bfdf2
--- /dev/null
+++ b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/PackageVersion.java
@@ -0,0 +1,73 @@
+/**
+ * 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.
+ */
+package org.apache.taverna.mavenplugin;
+
+import org.apache.maven.artifact.Artifact;
+
+import aQute.bnd.version.VersionRange;
+
+/**
+ *
+ *
+ * @author David Withers
+ */
+public class PackageVersion {
+
+	private VersionRange versionRange;
+	private Artifact artifact;
+	private boolean optional;
+
+	public PackageVersion(VersionRange versionRange, Artifact artifact) {
+		this(versionRange, artifact, false);
+	}
+
+	public PackageVersion(VersionRange versionRange, Artifact artifact, boolean optional) {
+		this.versionRange = versionRange;
+		this.artifact = artifact;
+		this.optional = optional;
+	}
+
+	@Override
+	public String toString() {
+		return versionRange + (optional ? "" : "") + "(from " + artifact.getId() + ")";
+	}
+
+	public VersionRange getVersionRange() {
+		return versionRange;
+	}
+
+	public void setVersionRange(VersionRange versionRange) {
+		this.versionRange = versionRange;
+	}
+
+	public Artifact getArtifact() {
+		return artifact;
+	}
+
+	public void setArtifact(Artifact artifact) {
+		this.artifact = artifact;
+	}
+
+	public boolean isOptional() {
+		return optional;
+	}
+
+	public void setOptional(boolean optional) {
+		this.optional = optional;
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaPluginDeployFileMojo.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaPluginDeployFileMojo.java b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaPluginDeployFileMojo.java
new file mode 100644
index 0000000..ea373a2
--- /dev/null
+++ b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaPluginDeployFileMojo.java
@@ -0,0 +1,230 @@
+/**
+ * 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.
+ */
+package org.apache.taverna.mavenplugin;
+
+import static org.apache.taverna.mavenplugin.TavernaPluginGenerateMojo.META_INF_TAVERNA;
+import static org.apache.taverna.mavenplugin.TavernaPluginGenerateMojo.PLUGIN_FILE;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.jar.JarFile;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipException;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Marshaller;
+import javax.xml.bind.Unmarshaller;
+
+import org.apache.maven.plugin.MojoExecutionException;
+import org.apache.maven.plugins.annotations.Mojo;
+import org.apache.maven.plugins.annotations.Parameter;
+import org.apache.maven.wagon.ConnectionException;
+import org.apache.maven.wagon.ResourceDoesNotExistException;
+import org.apache.maven.wagon.UnsupportedProtocolException;
+import org.apache.maven.wagon.Wagon;
+import org.apache.maven.wagon.authentication.AuthenticationException;
+import org.apache.maven.wagon.observers.Debug;
+import org.apache.maven.wagon.repository.Repository;
+import org.apache.taverna.plugin.xml.jaxb.PluginInfo;
+import org.apache.taverna.plugin.xml.jaxb.PluginVersions;
+import org.apache.taverna.plugin.xml.jaxb.Plugins;
+import org.apache.taverna.versions.xml.jaxb.Version;
+
+/**
+ * Deploys the Taverna plugin using <code>scp</code> or <code>file</code> protocol to the site URL
+ * specified.
+ *
+ * @author David Withers
+ */
+@Mojo(name = "plugin-deploy-file", requiresProject=false, requiresDirectInvocation = true)
+public class TavernaPluginDeployFileMojo extends AbstractWagonMojo {
+
+	private static final String PLUGIN_FILE_ENTRY = META_INF_TAVERNA + "/" + PLUGIN_FILE;
+
+	private static final String PLUGINS_FILE = "plugins.xml";
+
+	@Parameter(defaultValue = "http://updates.taverna.org.uk/workbench/3.0/dev/", required = true)
+	protected String site;
+
+	@Parameter(property = "file", required = true)
+	protected File file;
+
+	@Parameter(property = "url", required = true)
+	protected String url;
+
+	@Parameter(property = "serverId", required = true)
+	protected String serverId;
+
+	public void execute() throws MojoExecutionException {
+		if (!file.exists()) {
+			throw new MojoExecutionException("The Taverna Plugin file " + file
+					+ " does not exist");
+		}
+
+		JarFile pluginJarFile;
+		try {
+			pluginJarFile = new JarFile(file);
+		} catch (ZipException e) {
+			throw new MojoExecutionException(file + " is not a valid Taverna Plugin file", e);
+		} catch (IOException e) {
+			throw new MojoExecutionException("Error opening Taverna Plugin file: " + file, e);
+		}
+
+		ZipEntry pluginFileEntry = pluginJarFile.getJarEntry(PLUGIN_FILE_ENTRY);
+		if (pluginFileEntry == null) {
+			throw new MojoExecutionException(file
+					+ " is not a valid Taverna Plugin file, missing " + PLUGIN_FILE_ENTRY);
+		}
+
+		JAXBContext jaxbContext;
+		try {
+			jaxbContext = JAXBContext.newInstance(PluginInfo.class, Plugins.class);
+		} catch (JAXBException e) {
+			throw new MojoExecutionException("Error setting up JAXB context ", e);
+		}
+
+		PluginInfo plugin;
+		try {
+			InputStream inputStream = pluginJarFile.getInputStream(pluginFileEntry);
+			Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
+			plugin = (PluginInfo) unmarshaller.unmarshal(inputStream);
+			inputStream.close();
+		} catch (IOException e) {
+			throw new MojoExecutionException("Error reading " + file, e);
+		} catch (JAXBException e) {
+			throw new MojoExecutionException("Error reading " + file, e);
+		}
+
+		getLog().debug("The Taverna plugin will be deployed to '" + url + "'");
+
+		Repository repository = new Repository(serverId, url);
+
+		// create the wagon
+		Wagon wagon;
+		try {
+			wagon = wagonManager.getWagon(repository.getProtocol());
+		} catch (UnsupportedProtocolException e) {
+			throw new MojoExecutionException("Unsupported protocol: '" + repository.getProtocol()
+					+ "'", e);
+		}
+
+		Debug debug = new Debug();
+		if (getLog().isDebugEnabled()) {
+			wagon.addSessionListener(debug);
+			wagon.addTransferListener(debug);
+		}
+
+		// connect to the plugin site
+		try {
+			wagon.connect(repository, wagonManager.getAuthenticationInfo(serverId),
+					wagonManager.getProxy(repository.getProtocol()));
+		} catch (ConnectionException e) {
+			throw new MojoExecutionException("Error connecting to plugin site at " + url, e);
+		} catch (AuthenticationException e) {
+			throw new MojoExecutionException("Authentication error connecting to plugin site at "
+					+ url, e);
+		}
+
+		try {
+			File pluginsFile = File.createTempFile("taverna", null);
+
+			// fetch the plugins file
+			Plugins plugins;
+			try {
+				Utils.downloadFile(PLUGINS_FILE, pluginsFile, wagon, getLog());
+				try {
+					Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
+					plugins = (Plugins) unmarshaller.unmarshal(pluginsFile);
+				} catch (JAXBException e) {
+					throw new MojoExecutionException("Error reading " + pluginsFile, e);
+				}
+			} catch (ResourceDoesNotExistException e) {
+				getLog().info("Creating new plugins file");
+				plugins = new Plugins();
+			}
+
+			String deployedPluginFile = plugin.getId() + "-" + plugin.getVersion() + ".jar";
+
+			if (addPlugin(plugins, plugin, deployedPluginFile)) {
+				// write the new plugin site file
+				try {
+					Marshaller marshaller = jaxbContext.createMarshaller();
+					marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
+					marshaller.setProperty(Marshaller.JAXB_SCHEMA_LOCATION,
+							TavernaPluginGenerateMojo.SCHEMA_LOCATION);
+					marshaller.marshal(plugins, pluginsFile);
+				} catch (JAXBException e) {
+					throw new MojoExecutionException("Error writing " + PLUGINS_FILE, e);
+				}
+
+				// upload the plugin to the update site
+				Utils.uploadFile(file, deployedPluginFile, wagon, getLog());
+				// upload the plugin site file
+				Utils.uploadFile(pluginsFile, PLUGINS_FILE, wagon, getLog());
+			}
+		} catch (IOException e) {
+			throw new MojoExecutionException("Error writing " + PLUGINS_FILE, e);
+		} finally {
+			disconnectWagon(wagon, debug);
+		}
+	}
+
+	private boolean addPlugin(Plugins plugins, PluginInfo pluginInfo, String pluginURL) {
+		PluginVersions plugin = getPlugin(plugins, pluginInfo);
+		Version latestVersion = plugin.getLatestVersion();
+		if (latestVersion != null && latestVersion.getVersion().equals(pluginInfo.getVersion())) {
+			getLog().error(
+					String.format("%1$s version %2$s has already been deployed",
+							pluginInfo.getName(), pluginInfo.getVersion()));
+			return false;
+		}
+		Version newPluginVersion = new Version();
+		newPluginVersion.setVersion(pluginInfo.getVersion());
+		newPluginVersion.setFile(pluginURL);
+
+		getLog().info(
+				String.format("Adding %1$s version %2$s", pluginInfo.getName(),
+						pluginInfo.getVersion()));
+		if (plugin.getLatestVersion() != null) {
+			plugin.getPreviousVersion().add(plugin.getLatestVersion());
+		}
+		plugin.setLatestVersion(newPluginVersion);
+		return true;
+	}
+
+	private PluginVersions getPlugin(Plugins plugins, PluginInfo pluginInfo) {
+		PluginVersions pluginVersions = null;
+		for (PluginVersions existingPlugin : plugins.getPlugin()) {
+			if (existingPlugin.getId().equals(pluginInfo.getId())) {
+				pluginVersions = existingPlugin;
+				break;
+			}
+		}
+		if (pluginVersions == null) {
+			pluginVersions = new PluginVersions();
+			pluginVersions.setId(pluginInfo.getId());
+			plugins.getPlugin().add(pluginVersions);
+		}
+		pluginVersions.setName(pluginInfo.getName());
+		pluginVersions.setDescription(pluginInfo.getDescription());
+		pluginVersions.setOrganization(pluginInfo.getOrganization());
+		return pluginVersions;
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaPluginDeployMojo.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaPluginDeployMojo.java b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaPluginDeployMojo.java
new file mode 100644
index 0000000..6591d61
--- /dev/null
+++ b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaPluginDeployMojo.java
@@ -0,0 +1,215 @@
+/**
+ * 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.
+ */
+package org.apache.taverna.mavenplugin;
+
+import java.io.File;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Marshaller;
+import javax.xml.bind.Unmarshaller;
+
+import org.apache.maven.plugin.MojoExecutionException;
+import org.apache.maven.plugins.annotations.LifecyclePhase;
+import org.apache.maven.plugins.annotations.Mojo;
+import org.apache.maven.wagon.ConnectionException;
+import org.apache.maven.wagon.ResourceDoesNotExistException;
+import org.apache.maven.wagon.UnsupportedProtocolException;
+import org.apache.maven.wagon.Wagon;
+import org.apache.maven.wagon.authentication.AuthenticationException;
+import org.apache.maven.wagon.observers.Debug;
+import org.apache.maven.wagon.repository.Repository;
+import org.apache.taverna.plugin.xml.jaxb.PluginInfo;
+import org.apache.taverna.plugin.xml.jaxb.PluginVersions;
+import org.apache.taverna.plugin.xml.jaxb.Plugins;
+import org.apache.taverna.versions.xml.jaxb.Version;
+
+/**
+ * Deploys the Taverna plugin using <code>scp</code> or <code>file</code> protocol to the site URL
+ * specified in the <code>&lt;distributionManagement&gt;</code> section of the POM.
+ *
+ * @author David Withers
+ */
+@Mojo(name = "plugin-deploy", defaultPhase = LifecyclePhase.DEPLOY)
+public class TavernaPluginDeployMojo extends AbstractDeployMojo {
+
+	private static final String PLUGINS_FILE = "plugins.xml";
+
+	private File tempDirectory;
+
+	public void execute() throws MojoExecutionException {
+		tempDirectory = new File(buildDirectory, TavernaProfileGenerateMojo.TAVERNA_TMP);
+		tempDirectory.mkdirs();
+		if (artifact == null) {
+			throw new MojoExecutionException(
+					"The Taverna Plugin does not exist, please run taverna:plugin-generate first");
+		}
+
+		File artifactFile = artifact.getFile();
+		if (artifactFile == null) {
+			throw new MojoExecutionException(
+					"The Taverna Plugin does not exist, please run taverna:plugin-generate first");
+		}
+
+		File pluginDirectory = new File(outputDirectory, TavernaPluginGenerateMojo.META_INF_TAVERNA);
+		File pluginFile = new File(pluginDirectory, TavernaPluginGenerateMojo.PLUGIN_FILE);
+		if (!pluginFile.exists()) {
+			throw new MojoExecutionException(
+					"The Taverna Plugin does not exist, please run taverna:plugin-generate first");
+		}
+
+		JAXBContext jaxbContext;
+		try {
+			jaxbContext = JAXBContext.newInstance(PluginInfo.class, Plugins.class);
+		} catch (JAXBException e) {
+			throw new MojoExecutionException("Error setting up JAXB context ", e);
+		}
+
+		PluginInfo plugin;
+		try {
+			Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
+			plugin = (PluginInfo) unmarshaller.unmarshal(pluginFile);
+		} catch (JAXBException e) {
+			throw new MojoExecutionException("Error reading " + pluginFile, e);
+		}
+
+		if (deploymentRepository == null) {
+			throw new MojoExecutionException(
+					"Missing repository information in the distribution management element in the project.");
+		}
+
+		String url = deploymentRepository.getUrl();
+		String id = deploymentRepository.getId();
+
+		if (url == null) {
+			throw new MojoExecutionException(
+					"The URL to the Taverna plugin site is missing in the project descriptor.");
+		}
+		getLog().debug("The Taverna plugin will be deployed to '" + url + "'");
+
+		Repository repository = new Repository(id, url);
+
+		// create the wagon
+		Wagon wagon;
+		try {
+			wagon = wagonManager.getWagon(repository.getProtocol());
+		} catch (UnsupportedProtocolException e) {
+			throw new MojoExecutionException("Unsupported protocol: '" + repository.getProtocol()
+					+ "'", e);
+		}
+
+		Debug debug = new Debug();
+		if (getLog().isDebugEnabled()) {
+			wagon.addSessionListener(debug);
+			wagon.addTransferListener(debug);
+		}
+
+		// connect to the plugin site
+		try {
+			wagon.connect(repository, wagonManager.getAuthenticationInfo(id),
+					wagonManager.getProxy(repository.getProtocol()));
+		} catch (ConnectionException e) {
+			throw new MojoExecutionException("Error connecting to plugin site at " + url, e);
+		} catch (AuthenticationException e) {
+			throw new MojoExecutionException("Authentication error connecting to plugin site at "
+					+ url, e);
+		}
+
+		try {
+			String deployedPluginFile = project.getGroupId() + "." + project.getArtifactId() + "-"
+					+ plugin.getVersion() + ".jar";
+
+			// fetch the plugins file
+			Plugins plugins;
+			File pluginsFile = new File(tempDirectory, PLUGINS_FILE);
+			try {
+				Utils.downloadFile(PLUGINS_FILE, pluginsFile, wagon, getLog());
+				try {
+					Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
+					plugins = (Plugins) unmarshaller.unmarshal(pluginsFile);
+				} catch (JAXBException e) {
+					throw new MojoExecutionException("Error reading " + pluginsFile, e);
+				}
+			} catch (ResourceDoesNotExistException e) {
+				getLog().info("Creating new plugins file");
+				plugins = new Plugins();
+			}
+
+			if (addPlugin(plugins, plugin, deployedPluginFile)) {
+				// write the new plugin site file
+				try {
+					Marshaller marshaller = jaxbContext.createMarshaller();
+					marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
+					marshaller.setProperty(Marshaller.JAXB_SCHEMA_LOCATION,
+							TavernaPluginGenerateMojo.SCHEMA_LOCATION);
+					marshaller.marshal(plugins, pluginsFile);
+				} catch (JAXBException e) {
+					throw new MojoExecutionException("Error writing " + PLUGINS_FILE, e);
+				}
+
+				// upload the plugin to the update site
+				Utils.uploadFile(artifactFile, deployedPluginFile, wagon, getLog());
+				// upload the plugin site file
+				Utils.uploadFile(pluginsFile, PLUGINS_FILE, wagon, getLog());
+			}
+		} finally {
+			disconnectWagon(wagon, debug);
+		}
+	}
+
+	private boolean addPlugin(Plugins plugins, PluginInfo pluginInfo, String pluginURL) {
+		PluginVersions plugin = getPlugin(plugins, pluginInfo);
+		Version latestVersion = plugin.getLatestVersion();
+		if (latestVersion != null && latestVersion.getVersion().equals(pluginInfo.getVersion())) {
+			getLog().error(
+					String.format("%1$s version %2$s has already been deployed", pluginInfo.getName(),
+							pluginInfo.getVersion()));
+			return false;
+		}
+		Version newPluginVersion = new Version();
+		newPluginVersion.setVersion(pluginInfo.getVersion());
+		newPluginVersion.setFile(pluginURL);
+
+		getLog().info(
+				String.format("Adding %1$s version %2$s", pluginInfo.getName(), pluginInfo.getVersion()));
+		if (plugin.getLatestVersion() != null) {
+			plugin.getPreviousVersion().add(plugin.getLatestVersion());
+		}
+		plugin.setLatestVersion(newPluginVersion);
+		return true;
+	}
+
+	private PluginVersions getPlugin(Plugins plugins, PluginInfo pluginInfo) {
+		PluginVersions pluginVersions = null;
+		for (PluginVersions existingPlugin : plugins.getPlugin()) {
+			if (existingPlugin.getId().equals(pluginInfo.getId())) {
+				pluginVersions = existingPlugin;
+				break;
+			}
+		}
+		if (pluginVersions == null) {
+			pluginVersions = new PluginVersions();
+			pluginVersions.setId(pluginInfo.getId());
+			plugins.getPlugin().add(pluginVersions);
+		}
+		pluginVersions.setName(pluginInfo.getName());
+		pluginVersions.setDescription(pluginInfo.getDescription());
+		pluginVersions.setOrganization(pluginInfo.getOrganization());
+		return pluginVersions;
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaPluginGenerateMojo.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaPluginGenerateMojo.java b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaPluginGenerateMojo.java
new file mode 100644
index 0000000..a53ecff
--- /dev/null
+++ b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaPluginGenerateMojo.java
@@ -0,0 +1,137 @@
+/**
+ * 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.
+ */
+package org.apache.taverna.mavenplugin;
+
+import java.io.File;
+import java.util.List;
+import java.util.Set;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Marshaller;
+
+import org.apache.maven.artifact.Artifact;
+import org.apache.maven.model.Organization;
+import org.apache.maven.plugin.AbstractMojo;
+import org.apache.maven.plugin.MojoExecutionException;
+import org.apache.maven.plugin.MojoFailureException;
+import org.apache.maven.plugins.annotations.Component;
+import org.apache.maven.plugins.annotations.LifecyclePhase;
+import org.apache.maven.plugins.annotations.Mojo;
+import org.apache.maven.plugins.annotations.Parameter;
+import org.apache.maven.plugins.annotations.ResolutionScope;
+import org.apache.maven.project.MavenProject;
+import org.apache.maven.project.ProjectDependenciesResolver;
+import org.apache.maven.shared.osgi.DefaultMaven2OsgiConverter;
+import org.apache.maven.shared.osgi.Maven2OsgiConverter;
+import org.apache.taverna.plugin.xml.jaxb.PluginInfo;
+import org.apache.taverna.profile.xml.jaxb.BundleInfo;
+import org.eclipse.aether.RepositorySystemSession;
+
+/**
+ * Generates a Taverna plugin definition file.
+ *
+ * @author David Withers
+ */
+@Mojo(name = "plugin-generate", defaultPhase = LifecyclePhase.GENERATE_RESOURCES, requiresDependencyResolution = ResolutionScope.RUNTIME)
+public class TavernaPluginGenerateMojo extends AbstractMojo {
+
+	public static final String PLUGIN_FILE = "plugin.xml";
+
+	public static final String META_INF_TAVERNA = "META-INF/taverna";
+
+	public static final String SCHEMA_LOCATION = "http://ns.taverna.org.uk/2013/application/plugin http://localhost/2013/application/plugin/ApplicationPlugin.xsd";
+
+	@Component
+	private MavenProject project;
+
+	@Component
+	private ProjectDependenciesResolver projectDependenciesResolver;
+
+    @Parameter(defaultValue = "${repositorySystemSession}", readonly = true)
+	private RepositorySystemSession repositorySystemSession;
+
+	@Parameter(defaultValue = "${project.build.outputDirectory}", required = true)
+	protected File outputDirectory;
+
+	@Parameter(defaultValue = "${project.description}", required = true)
+	protected String description;
+
+	@Parameter(defaultValue = "${project.organization}", required = true)
+	protected Organization organization;
+
+	private MavenOsgiUtils osgiUtils;
+
+	private Maven2OsgiConverter maven2OsgiConverter = new DefaultMaven2OsgiConverter();
+
+	public void execute() throws MojoExecutionException, MojoFailureException {
+		try {
+			osgiUtils = new MavenOsgiUtils(project, repositorySystemSession,
+					projectDependenciesResolver, getLog());
+			createPluginDefinition();
+		} catch (JAXBException e) {
+			throw new MojoExecutionException("Error generating Taverna plugin", e);
+		}
+	}
+
+	/**
+	 * Generates the Taverna plugin definition file.
+	 *
+	 * @return the <code>File</code> that the Taverna plugin definition has been written to
+	 * @throws JAXBException
+	 * @throws MojoExecutionException
+	 */
+	private File createPluginDefinition() throws JAXBException, MojoExecutionException {
+		String groupId = project.getGroupId();
+		String artifactId = project.getArtifactId();
+		String version = maven2OsgiConverter.getVersion(project.getVersion());
+		if (version.endsWith("SNAPSHOT")) {
+			version = version.substring(0, version.indexOf("SNAPSHOT")) + Utils.timestamp();
+		}
+
+		File pluginDirectory = new File(outputDirectory, META_INF_TAVERNA);
+		pluginDirectory.mkdirs();
+		File pluginFile = new File(pluginDirectory, PLUGIN_FILE);
+
+		PluginInfo pluginInfo = new PluginInfo();
+		pluginInfo.setId(groupId + "." + artifactId);
+		pluginInfo.setName(project.getName());
+		pluginInfo.setVersion(version);
+		pluginInfo.setDescription(description);
+		pluginInfo.setOrganization(organization.getName());
+
+		Set<BundleArtifact> bundleDependencies = osgiUtils.getBundleDependencies(
+				Artifact.SCOPE_COMPILE, Artifact.SCOPE_RUNTIME);
+
+		List<BundleInfo> runtimeBundles = osgiUtils.getBundles(bundleDependencies);
+		if (!runtimeBundles.isEmpty()) {
+			List<BundleInfo> bundles = pluginInfo.getBundle();
+			for (BundleInfo bundle : runtimeBundles) {
+				bundles.add(bundle);
+			}
+		}
+
+		JAXBContext jaxbContext = JAXBContext.newInstance(PluginInfo.class);
+		Marshaller marshaller = jaxbContext.createMarshaller();
+		marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
+		marshaller.setProperty(Marshaller.JAXB_SCHEMA_LOCATION, SCHEMA_LOCATION);
+		marshaller.marshal(pluginInfo, pluginFile);
+
+		return pluginFile;
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaPluginPrepareBundlesMojo.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaPluginPrepareBundlesMojo.java b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaPluginPrepareBundlesMojo.java
new file mode 100644
index 0000000..9e48115
--- /dev/null
+++ b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaPluginPrepareBundlesMojo.java
@@ -0,0 +1,80 @@
+/**
+ * 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.
+ */
+package org.apache.taverna.mavenplugin;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Set;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.maven.artifact.Artifact;
+import org.apache.maven.plugin.AbstractMojo;
+import org.apache.maven.plugin.MojoExecutionException;
+import org.apache.maven.plugin.MojoFailureException;
+import org.apache.maven.plugins.annotations.Component;
+import org.apache.maven.plugins.annotations.LifecyclePhase;
+import org.apache.maven.plugins.annotations.Mojo;
+import org.apache.maven.plugins.annotations.Parameter;
+import org.apache.maven.plugins.annotations.ResolutionScope;
+import org.apache.maven.project.MavenProject;
+import org.apache.maven.project.ProjectDependenciesResolver;
+import org.eclipse.aether.RepositorySystemSession;
+
+/**
+ * Prepares the plugin OSGi bundles.
+ *
+ * @author David Withers
+ */
+@Mojo(name = "plugin-prepare-bundles", defaultPhase = LifecyclePhase.PREPARE_PACKAGE, requiresDependencyResolution = ResolutionScope.RUNTIME)
+public class TavernaPluginPrepareBundlesMojo extends AbstractMojo {
+
+	@Component
+	private MavenProject project;
+
+	@Component
+	private ProjectDependenciesResolver projectDependenciesResolver;
+
+	@Parameter(defaultValue = "${repositorySystemSession}", readonly = true)
+	private RepositorySystemSession repositorySystemSession;
+
+	/**
+	 * The directory where the plugin OSGi bundles file will be put.
+	 */
+	@Parameter(defaultValue = "${project.build.outputDirectory}", required = true)
+	protected File outputDirectory;
+
+	private MavenOsgiUtils osgiUtils;
+
+	public void execute() throws MojoExecutionException, MojoFailureException {
+		osgiUtils = new MavenOsgiUtils(project, repositorySystemSession,
+				projectDependenciesResolver, getLog());
+		outputDirectory.mkdirs();
+
+		Set<BundleArtifact> bundleDependencies = osgiUtils.getBundleDependencies(
+				Artifact.SCOPE_COMPILE, Artifact.SCOPE_RUNTIME);
+		try {
+			for (BundleArtifact bundleArtifact : bundleDependencies) {
+				Artifact artifact = bundleArtifact.getArtifact();
+				FileUtils.copyFileToDirectory(bundleArtifact.getArtifact().getFile(), new File(
+						outputDirectory, artifact.getGroupId()));
+			}
+		} catch (IOException e) {
+			throw new MojoExecutionException("Error copying dependecies to archive directory", e);
+		}
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaProfileDeployMojo.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaProfileDeployMojo.java b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaProfileDeployMojo.java
new file mode 100644
index 0000000..fc0891d
--- /dev/null
+++ b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaProfileDeployMojo.java
@@ -0,0 +1,270 @@
+/**
+ * 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.
+ */
+package org.apache.taverna.mavenplugin;
+
+import java.io.File;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Marshaller;
+import javax.xml.bind.Unmarshaller;
+
+import org.apache.maven.plugin.MojoExecutionException;
+import org.apache.maven.plugins.annotations.LifecyclePhase;
+import org.apache.maven.plugins.annotations.Mojo;
+import org.apache.maven.wagon.ConnectionException;
+import org.apache.maven.wagon.ResourceDoesNotExistException;
+import org.apache.maven.wagon.UnsupportedProtocolException;
+import org.apache.maven.wagon.Wagon;
+import org.apache.maven.wagon.authentication.AuthenticationException;
+import org.apache.maven.wagon.observers.Debug;
+import org.apache.maven.wagon.repository.Repository;
+import org.apache.taverna.profile.xml.jaxb.ApplicationProfile;
+import org.apache.taverna.profile.xml.jaxb.BundleInfo;
+import org.apache.taverna.profile.xml.jaxb.UpdateSite;
+import org.apache.taverna.versions.xml.jaxb.Version;
+import org.apache.taverna.versions.xml.jaxb.Versions;
+
+/**
+ * Deploys the application profile using <code>scp</code> or <code>file</code> protocol to the site
+ * URL specified in the <code>&lt;distributionManagement&gt;</code> section of the POM.
+ *
+ * @author David Withers
+ */
+@Mojo(name = "profile-deploy", defaultPhase = LifecyclePhase.DEPLOY)
+public class TavernaProfileDeployMojo extends AbstractDeployMojo {
+
+	private static final String UPDATES_FILE = "updates.xml";
+
+	private File tempDirectory;
+
+	public void execute() throws MojoExecutionException {
+		tempDirectory = new File(buildDirectory, TavernaProfileGenerateMojo.TAVERNA_TMP);
+		tempDirectory.mkdirs();
+		if (artifact == null) {
+			throw new MojoExecutionException(
+					"The application profile does not exist, please run taverna:profile-generate first");
+		}
+
+		File artifactFile = artifact.getFile();
+		if (artifactFile == null) {
+			throw new MojoExecutionException(
+					"The application profile does not exist, please run taverna:profile-generate first");
+		}
+
+		JAXBContext jaxbContext;
+		try {
+			jaxbContext = JAXBContext.newInstance(ApplicationProfile.class, UpdateSite.class);
+		} catch (JAXBException e) {
+			throw new MojoExecutionException("Error setting up JAXB context ", e);
+		}
+
+		ApplicationProfile applicationProfile;
+		try {
+			Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
+			applicationProfile = (ApplicationProfile) unmarshaller.unmarshal(artifactFile);
+		} catch (JAXBException e) {
+			throw new MojoExecutionException("Error reading " + artifactFile, e);
+		}
+
+		if (deploymentRepository == null) {
+			throw new MojoExecutionException(
+					"Missing repository information in the distribution management element in the project.");
+		}
+
+		String url = deploymentRepository.getUrl();
+		String id = deploymentRepository.getId();
+
+		if (url == null) {
+			throw new MojoExecutionException(
+					"The URL to the update site is missing in the project descriptor.");
+		}
+		getLog().debug("The Taverna application will be deployed to '" + url + "'");
+
+		Repository repository = new Repository(id, url);
+
+		// create the wagon
+		Wagon wagon;
+		try {
+			wagon = wagonManager.getWagon(repository.getProtocol());
+		} catch (UnsupportedProtocolException e) {
+			throw new MojoExecutionException("Unsupported protocol: '" + repository.getProtocol()
+					+ "'", e);
+		}
+
+		Debug debug = new Debug();
+		if (getLog().isDebugEnabled()) {
+			wagon.addSessionListener(debug);
+			wagon.addTransferListener(debug);
+		}
+
+		// connect to the update site
+		try {
+			wagon.connect(repository, wagonManager.getAuthenticationInfo(id),
+					wagonManager.getProxy(repository.getProtocol()));
+		} catch (ConnectionException e) {
+			throw new MojoExecutionException("Error connecting to " + url, e);
+		} catch (AuthenticationException e) {
+			throw new MojoExecutionException("Authentication error connecting to " + url, e);
+		}
+
+		try {
+			// upload the application profile to the update site
+			String deployedProfileFile = "ApplicationProfile" + "-" + applicationProfile.getVersion()
+					+ ".xml";
+			Utils.uploadFile(artifactFile, deployedProfileFile, wagon, getLog());
+
+			// fetch the applications file
+			UpdateSite updateSite;
+			File updatesFile = new File(tempDirectory, UPDATES_FILE);
+			try {
+				Utils.downloadFile(UPDATES_FILE, updatesFile, wagon, getLog());
+				try {
+					Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
+					updateSite = (UpdateSite) unmarshaller
+							.unmarshal(updatesFile);
+				} catch (JAXBException e) {
+					throw new MojoExecutionException("Error reading " + updatesFile, e);
+				}
+			} catch(ResourceDoesNotExistException e) {
+				getLog().info("Creating new application versions file");
+				updateSite = new UpdateSite();
+				Versions versions = new Versions();
+				versions.setId(applicationProfile.getId());
+				versions.setName(applicationProfile.getName());
+				updateSite.setVersions(versions);
+			}
+
+			Version latestVersion = updateSite.getVersions().getLatestVersion();
+			if (latestVersion != null) {
+				File latestProfileFile = new File(tempDirectory, "ApplicationProfile-" + latestVersion.getVersion()
+						+ ".xml");
+				try {
+					Utils.downloadFile(latestVersion.getFile(), latestProfileFile, wagon, getLog());
+				} catch (ResourceDoesNotExistException e) {
+					throw new MojoExecutionException(latestVersion.getFile() + " does not exist", e);
+				}
+				ApplicationProfile latestProfile;
+				try {
+					Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
+					latestProfile = (ApplicationProfile) unmarshaller.unmarshal(latestProfileFile);
+				} catch (JAXBException e) {
+					throw new MojoExecutionException("Error reading " + latestProfileFile, e);
+				}
+				Set<BundleInfo> requiredBundles = getRequiredBundles(latestProfile, applicationProfile);
+				if (requiredBundles.isEmpty()) {
+					getLog().warn("No new bundles to upload");
+				} else {
+					// upload new bundles to the update site
+					uploadBundles(requiredBundles, wagon);
+				}
+			}
+
+			if (addApplicationVersion(updateSite.getVersions(), applicationProfile,
+					deployedProfileFile)) {
+				// write the new application versions list
+				try {
+					Marshaller marshaller = jaxbContext.createMarshaller();
+					marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
+					marshaller.setProperty(Marshaller.JAXB_SCHEMA_LOCATION, TavernaProfileGenerateMojo.SCHEMA_LOCATION);
+					marshaller.marshal(updateSite, updatesFile);
+				} catch (JAXBException e) {
+					throw new MojoExecutionException("Error writing " + UPDATES_FILE, e);
+				}
+
+				// upload the new application versions list to the update site
+				Utils.uploadFile(updatesFile, UPDATES_FILE, wagon, getLog());
+			}
+		}
+		finally {
+			disconnectWagon(wagon, debug);
+		}
+	}
+
+	/**
+	 * Adds an new application version to the application versions if the version doesn't already
+	 * exist.
+	 *
+	 * @param applicationVersions
+	 *            the ApplicationVersions document
+	 * @param applicationProfile
+	 *            the applicationProfile
+	 * @param profileURL
+	 * @return true if a new version was added to the ApplicationVersions document; false if the
+	 *         version already exits
+	 */
+	private boolean addApplicationVersion(Versions applicationVersions,
+			ApplicationProfile applicationProfile, String profileURL) {
+		Version latestVersion = applicationVersions.getLatestVersion();
+		if (latestVersion != null
+				&& latestVersion.getVersion().equals(applicationProfile.getVersion())) {
+			getLog().error(
+					String.format("%1$s version %2$s has already been deployed",
+							applicationProfile.getName(), applicationProfile.getVersion()));
+			return false;
+		}
+
+		Version newApplicationVersion = new Version();
+		newApplicationVersion.setVersion(applicationProfile.getVersion());
+		newApplicationVersion.setFile(profileURL);
+
+		getLog().info(
+				String.format("Adding %1$s version %2$s", applicationProfile.getName(),
+						applicationProfile.getVersion()));
+		if (applicationVersions.getLatestVersion() != null) {
+			applicationVersions.getPreviousVersion().add(applicationVersions.getLatestVersion());
+		}
+		applicationVersions.setLatestVersion(newApplicationVersion);
+		return true;
+	}
+
+	/**
+	 * @param requiredBundles
+	 * @throws MojoExecutionException
+	 */
+	private void uploadBundles(Set<BundleInfo> requiredBundles, Wagon wagon) throws MojoExecutionException {
+		File libDirectory = new File(tempDirectory, "lib");
+		for (BundleInfo bundle : requiredBundles) {
+			Utils.uploadFile(new File(libDirectory, bundle.getFileName()), "lib/" + bundle.getFileName(), wagon, getLog());
+		}
+	}
+
+	private Set<BundleInfo> getRequiredBundles(ApplicationProfile currentProfile,
+			ApplicationProfile newProfile) {
+		Set<BundleInfo> requiredBundles = new HashSet<BundleInfo>();
+		Map<String, BundleInfo> currentBundles = new HashMap<String, BundleInfo>();
+		for (BundleInfo bundle : currentProfile.getBundle()) {
+			currentBundles.put(bundle.getSymbolicName(), bundle);
+		}
+		for (BundleInfo bundle : newProfile.getBundle()) {
+			if (currentBundles.containsKey(bundle.getSymbolicName())) {
+				BundleInfo currentBundle = currentBundles.get(bundle.getSymbolicName());
+				if (!bundle.getVersion().equals(currentBundle.getVersion())) {
+					requiredBundles.add(bundle);
+				}
+			} else {
+				requiredBundles.add(bundle);
+			}
+		}
+		return requiredBundles;
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaProfileGenerateMojo.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaProfileGenerateMojo.java b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaProfileGenerateMojo.java
new file mode 100644
index 0000000..39c1110
--- /dev/null
+++ b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/TavernaProfileGenerateMojo.java
@@ -0,0 +1,216 @@
+/**
+ * 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.
+ */
+package org.apache.taverna.mavenplugin;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Marshaller;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.maven.artifact.Artifact;
+import org.apache.maven.plugin.AbstractMojo;
+import org.apache.maven.plugin.MojoExecutionException;
+import org.apache.maven.plugin.MojoFailureException;
+import org.apache.maven.plugins.annotations.Component;
+import org.apache.maven.plugins.annotations.LifecyclePhase;
+import org.apache.maven.plugins.annotations.Mojo;
+import org.apache.maven.plugins.annotations.Parameter;
+import org.apache.maven.plugins.annotations.ResolutionScope;
+import org.apache.maven.project.MavenProject;
+import org.apache.maven.project.ProjectDependenciesResolver;
+import org.apache.maven.shared.osgi.DefaultMaven2OsgiConverter;
+import org.apache.maven.shared.osgi.Maven2OsgiConverter;
+import org.apache.taverna.profile.xml.jaxb.ApplicationProfile;
+import org.apache.taverna.profile.xml.jaxb.BundleInfo;
+import org.apache.taverna.profile.xml.jaxb.FrameworkConfiguration;
+import org.apache.taverna.profile.xml.jaxb.Updates;
+import org.eclipse.aether.RepositorySystemSession;
+
+/**
+ * Generates an application profile file.
+ *
+ * @author David Withers
+ */
+@Mojo(name = "profile-generate", defaultPhase = LifecyclePhase.GENERATE_RESOURCES, requiresDependencyResolution = ResolutionScope.RUNTIME)
+public class TavernaProfileGenerateMojo extends AbstractMojo {
+
+	public static final String SYSTEM_PACKAGES = "org.osgi.framework.system.packages.extra";
+
+	public static final String SCHEMA_LOCATION = "http://ns.taverna.org.uk/2013/application/profile http://localhost/2013/application/profile/ApplicationProfile.xsd";
+
+	public static final String TAVERNA_TMP = "taverna-tmp";
+
+	public static final String APPLICATION_PROFILE_FILE = "ApplicationProfile.xml";
+
+	@Component
+	private MavenProject project;
+
+	@Component
+	private ProjectDependenciesResolver projectDependenciesResolver;
+
+	@Parameter(defaultValue = "${repositorySystemSession}", readonly = true)
+	private RepositorySystemSession repositorySystemSession;
+
+	/**
+	 * The directory where the generated <code>ApplicationProfile.xml</code> file will be put.
+	 */
+	@Parameter(defaultValue = "${project.build.directory}", required = true)
+	protected File outputDirectory;
+
+	@Parameter(defaultValue = "SNAPSHOT")
+	private String buildNumber;
+
+	@Parameter
+	private List<FrameworkConfiguration> frameworkConfigurations;
+
+	@Parameter(required = true)
+	private String updateSite;
+
+	@Parameter(defaultValue = "updates.xml")
+	private String updatesFile;
+
+	@Parameter(defaultValue = "lib")
+	private String libDirectory;
+
+	@Parameter(required = true)
+	private String pluginSite;
+
+	@Parameter(defaultValue = "plugins.xml")
+	private String pluginsFile;
+
+	private Maven2OsgiConverter maven2OsgiConverter = new DefaultMaven2OsgiConverter();
+
+	private MavenOsgiUtils osgiUtils;
+
+	private File tempDirectory;
+
+	public void execute() throws MojoExecutionException, MojoFailureException {
+		try {
+			osgiUtils = new MavenOsgiUtils(project, repositorySystemSession,
+					projectDependenciesResolver, getSystemPackages(), getLog());
+			tempDirectory = new File(outputDirectory, TAVERNA_TMP);
+
+			File profileFile = createApplicationProfile();
+			project.getArtifact().setFile(profileFile);
+
+			copyDependencies();
+
+		} catch (JAXBException e) {
+			throw new MojoExecutionException("Error generating application profile", e);
+		}
+	}
+
+	private void copyDependencies() throws MojoExecutionException {
+		File libDirectory = new File(tempDirectory, "lib");
+		libDirectory.mkdirs();
+
+		try {
+			for (Artifact artifact : project.getArtifacts()) {
+				FileUtils.copyFileToDirectory(artifact.getFile(),
+						new File(libDirectory, artifact.getGroupId()));
+			}
+		} catch (IOException e) {
+			throw new MojoExecutionException("Error copying dependecies to lib directory", e);
+		}
+
+	}
+
+	/**
+	 * Generates the application profile file.
+	 *
+	 * @return the <code>File</code> that the application profile has been written to
+	 * @throws JAXBException
+	 *             if the application profile cannot be created
+	 * @throws MojoExecutionException
+	 */
+	private File createApplicationProfile() throws JAXBException, MojoExecutionException {
+		String groupId = project.getGroupId();
+		String artifactId = project.getArtifactId();
+		String version = maven2OsgiConverter.getVersion(project.getVersion());
+		if (version.endsWith("SNAPSHOT")) {
+			version = version.substring(0, version.indexOf("SNAPSHOT")) + buildNumber;
+		}
+
+		tempDirectory.mkdirs();
+		File applicationProfileFile = new File(tempDirectory, APPLICATION_PROFILE_FILE);
+
+		ApplicationProfile applicationProfile = new ApplicationProfile();
+		applicationProfile.setId(groupId + "." + artifactId);
+		applicationProfile.setName(project.getName());
+		applicationProfile.setVersion(version);
+
+		Updates updates = new Updates();
+		updates.setUpdateSite(updateSite);
+		updates.setUpdatesFile(updatesFile);
+		updates.setLibDirectory(libDirectory);
+		updates.setPluginSite(pluginSite);
+		updates.setPluginsFile(pluginsFile);
+		applicationProfile.setUpdates(updates);
+
+		List<FrameworkConfiguration> frameworkConfiguration = applicationProfile
+				.getFrameworkConfiguration();
+		for (FrameworkConfiguration configuration : frameworkConfigurations) {
+			frameworkConfiguration.add(configuration);
+		}
+
+		Set<BundleArtifact> bundleDependencies = osgiUtils.getBundleDependencies(
+				Artifact.SCOPE_COMPILE, Artifact.SCOPE_RUNTIME);
+		List<BundleInfo> runtimeBundles = osgiUtils.getBundles(bundleDependencies);
+		if (!runtimeBundles.isEmpty()) {
+			List<BundleInfo> bundles = applicationProfile.getBundle();
+			for (BundleInfo bundle : runtimeBundles) {
+				bundles.add(bundle);
+			}
+		}
+
+		JAXBContext jaxbContext = JAXBContext.newInstance(ApplicationProfile.class);
+		Marshaller marshaller = jaxbContext.createMarshaller();
+		marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
+		marshaller.setProperty(Marshaller.JAXB_SCHEMA_LOCATION, SCHEMA_LOCATION);
+		marshaller.marshal(applicationProfile, applicationProfileFile);
+
+		return applicationProfileFile;
+	}
+
+	private Set<String> getSystemPackages() {
+		Set<String> systemPackages = new HashSet<String>();
+		if (frameworkConfigurations != null) {
+			for (FrameworkConfiguration configuration : frameworkConfigurations) {
+				if (SYSTEM_PACKAGES.equals(configuration.getName())) {
+					String packagesString = configuration.getValue();
+					if (packagesString != null) {
+						String[] packages = packagesString.split(",");
+						for (String packageString : packages) {
+							String[] packageProperties = packageString.split(";");
+							if (packageProperties.length > 0) {
+								systemPackages.add(packageProperties[0]);
+							}
+						}
+					}
+				}
+			}
+		}
+		return systemPackages;
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/Utils.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/Utils.java b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/Utils.java
new file mode 100644
index 0000000..28e1019
--- /dev/null
+++ b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/Utils.java
@@ -0,0 +1,167 @@
+/**
+ * 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.
+ */
+package org.apache.taverna.mavenplugin;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.URLEncoder;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.commons.codec.digest.DigestUtils;
+import org.apache.commons.io.FileUtils;
+import org.apache.maven.plugin.MojoExecutionException;
+import org.apache.maven.plugin.logging.Log;
+import org.apache.maven.wagon.ResourceDoesNotExistException;
+import org.apache.maven.wagon.TransferFailedException;
+import org.apache.maven.wagon.Wagon;
+import org.apache.maven.wagon.authorization.AuthorizationException;
+
+/**
+ * @author David Withers
+ */
+public class Utils {
+
+	public static String uploadFile(File file, String resourceName, Wagon wagon, Log log)
+			throws MojoExecutionException {
+		String resourceUrl = getResourceUrl(wagon, resourceName);
+		File digestFile = new File(file.getPath() + ".md5");
+		try {
+			String digestString = DigestUtils.md5Hex(new FileInputStream(file));
+			FileUtils.writeStringToFile(digestFile, digestString);
+		} catch (IOException e) {
+			throw new MojoExecutionException(
+					String.format("Error generating digest for %1$s", file), e);
+		}
+		try {
+			log.info(String.format("Uploading %1$s to %2$s", file, resourceUrl));
+			wagon.put(file, resourceName);
+			wagon.put(digestFile, resourceName + ".md5");
+		} catch (TransferFailedException e) {
+			throw new MojoExecutionException(String.format("Error transferring %1$s to %2$s", file,
+					resourceUrl), e);
+		} catch (ResourceDoesNotExistException e) {
+			throw new MojoExecutionException(String.format("%1$s does not exist", resourceUrl), e);
+		} catch (AuthorizationException e) {
+			throw new MojoExecutionException(String.format(
+					"Authentication error transferring %1$s to %2$s", file, resourceUrl), e);
+		}
+		return resourceUrl;
+	}
+
+	public static void downloadFile(String resourceName, File file, Wagon wagon, Log log)
+			throws MojoExecutionException, ResourceDoesNotExistException {
+		String resourceUrl = getResourceUrl(wagon, resourceName);
+		File digestFile = new File(file.getPath() + ".md5");
+		try {
+			log.info(String.format("Downloading %1$s to %2$s", resourceUrl, file));
+			wagon.get(resourceName, file);
+			wagon.get(resourceName + ".md5", digestFile);
+		} catch (TransferFailedException e) {
+			throw new MojoExecutionException(String.format("Error transferring %1$s to %2$s",
+					resourceUrl, file), e);
+		} catch (AuthorizationException e) {
+			throw new MojoExecutionException(String.format(
+					"Authentication error transferring %1$s to %2$s", resourceUrl, file), e);
+		}
+		try {
+			String digestString1 = DigestUtils.md5Hex(new FileInputStream(file));
+			String digestString2 = FileUtils.readFileToString(digestFile);
+			if (!digestString1.equals(digestString2)) {
+				throw new MojoExecutionException(String.format(
+						"Error downloading file: digsests not equal. (%1$s != %2$s)",
+						digestString1, digestString2));
+			}
+		} catch (IOException e) {
+			throw new MojoExecutionException(String.format("Error checking digest for %1$s", file),
+					e);
+		}
+	}
+
+	public static String getResourceUrl(Wagon wagon, String resourceName) {
+		StringBuilder urlBuilder = new StringBuilder(wagon.getRepository().getUrl());
+		for (String part : resourceName.split("/")) {
+			urlBuilder.append('/');
+			urlBuilder.append(URLEncoder.encode(part));
+		}
+		return urlBuilder.toString();
+	}
+
+	public static String timestamp() {
+		SimpleDateFormat dateFormat = new SimpleDateFormat("yyyyMMdd'T'HHmm");
+		return dateFormat.format(new Date());
+	}
+
+	public static Set<String> getJavaPackages(Log log) {
+		Set<String> javaPackages = new HashSet<String>();
+		InputStream resource = Utils.class.getClassLoader().getResourceAsStream("java7-packages");
+		if (resource != null) {
+			BufferedReader reader = new BufferedReader(new InputStreamReader(resource));
+			try {
+				String line = reader.readLine();
+				while (line != null) {
+					if (!line.isEmpty() && ! line.startsWith("#")) {
+						javaPackages.add(line.trim());
+					}
+					line = reader.readLine();
+				}
+			} catch (IOException e) {
+				log.warn(
+						"Problem while reading to readinf java package list from resource file java7-packages",
+						e);
+			}
+		} else {
+			log.warn("Unable to read java package list from resource file java7-packages");
+		}
+		return javaPackages;
+	}
+
+	public static <T> List<Set<T>> getSubsets(Set<T> set) {
+		List<Set<T>> subsets = new ArrayList<Set<T>>();
+        List<T> list = new ArrayList<T>(set);
+		int numOfSubsets = 1 << set.size();
+		for (int i = 0; i < numOfSubsets; i++){
+			Set<T> subset = new HashSet<T>();
+		    for (int j = 0; j < numOfSubsets; j++){
+		        if (((i>>j) & 1) == 1) {
+		            subset.add(list.get(j));
+		        }
+		    }
+		    if (!subset.isEmpty()) {
+		    	subsets.add(subset);
+		    }
+		}
+		Collections.sort(subsets, new Comparator<Set<T>>() {
+			@Override
+			public int compare(Set<T> o1, Set<T> o2) {
+				return o1.size() - o2.size();
+			}
+		});
+		return subsets;
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/test/java/net/sf/taverna/t2/maven/plugins/TavernaPluginGenerateMojoTest.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/test/java/net/sf/taverna/t2/maven/plugins/TavernaPluginGenerateMojoTest.java b/taverna-maven-plugin/src/test/java/net/sf/taverna/t2/maven/plugins/TavernaPluginGenerateMojoTest.java
deleted file mode 100644
index 04e5042..0000000
--- a/taverna-maven-plugin/src/test/java/net/sf/taverna/t2/maven/plugins/TavernaPluginGenerateMojoTest.java
+++ /dev/null
@@ -1,76 +0,0 @@
-/**
- * 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.
- */
-package net.sf.taverna.t2.maven.plugins;
-
-import org.apache.maven.plugin.testing.AbstractMojoTestCase;
-import org.junit.Ignore;
-import org.junit.Test;
-
-/**
- * Unit tests for TavernaPluginGenerateMojo.
- *
- * @author David Withers
- */
-public class TavernaPluginGenerateMojoTest extends AbstractMojoTestCase {
-
-	private TavernaPluginGenerateMojo tavernaPluginGenerateMojo;
-
-	/**
-	 * @throws java.lang.Exception
-	 */
-	@Ignore
-	public void setUp() throws Exception {
-//		super.setUp();
-//
-//		File pluginXml = new File( getBasedir(), "src/test/resources/unit/plugin-config.xml" );
-//        tavernaPluginGenerateMojo = (TavernaPluginGenerateMojo) lookupMojo( "plugin-generate", pluginXml );
-//
-//		MavenProject mavenProject = (MavenProject) getVariableValueFromObject(tavernaPluginGenerateMojo, "project");
-//
-//		Artifact artifact = new DefaultArtifact("net.sf.taverna.t2", "example-plugin", VersionRange
-//				.createFromVersion("0.1.0"), "compile", "jar", "", null);
-//        artifact.setRepository(new DefaultArtifactRepository("id1",
-//				"http://www.mygrid.org.uk/maven/repository", new DefaultRepositoryLayout()));
-//		mavenProject.setArtifact(artifact);
-//
-//
-//		Artifact dependency = new DefaultArtifact("com.example.test", "test-artifact", VersionRange
-//				.createFromVersion("1.3.5"), "compile", "jar", "", null);
-//		dependency.setGroupId("com.example.test");
-//		dependency.setArtifactId("test-artifact");
-//		dependency.setVersion("1.3.5");
-//		dependency.setRepository(new DefaultArtifactRepository("id2",
-//				"http://www.example.com/maven/repository", new DefaultRepositoryLayout()));
-//		mavenProject.setDependencyArtifacts(Collections.singleton(dependency));
-//
-//		MavenSession session = new MavenSession(getContainer(), (RepositorySystemSession) null, (MavenExecutionRequest) null, (MavenExecutionResult) null);
-//		setVariableValueToObject(tavernaPluginGenerateMojo, "session", session);
-	}
-
-	/**
-	 * Test method for
-	 * {@link net.sf.taverna.t2.maven.plugins.TavernaPluginGenerateMojo#execute()}
-	 *
-	 * @throws Exception
-	 */
-	@Test
-	@Ignore
-	public void testExecute() throws Exception {
-//		tavernaPluginGenerateMojo.execute();
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/test/java/net/sf/taverna/t2/maven/plugins/TestUtils.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/test/java/net/sf/taverna/t2/maven/plugins/TestUtils.java b/taverna-maven-plugin/src/test/java/net/sf/taverna/t2/maven/plugins/TestUtils.java
deleted file mode 100644
index 0f3c1db..0000000
--- a/taverna-maven-plugin/src/test/java/net/sf/taverna/t2/maven/plugins/TestUtils.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/**
- * 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.
- */
-package net.sf.taverna.t2.maven.plugins;
-
-import static org.junit.Assert.*;
-
-import java.util.Set;
-
-import org.apache.maven.plugin.logging.Log;
-import org.apache.maven.plugin.testing.SilentLog;
-import org.junit.Test;
-
-public class TestUtils {
-
-	@Test
-	public void getJavaPackages() throws Exception {
-		Log log = new SilentLog();
-		Set<String> packages = Utils.getJavaPackages(log);
-		assertTrue(packages.contains("java.util"));
-		assertTrue(packages.contains("org.xml.sax.helpers"));
-		for (String pkg: packages) { 
-			assertFalse(pkg.isEmpty());
-			assertFalse(pkg.contains(" "));
-			assertFalse(pkg.contains("#"));
-			assertTrue(pkg.contains("."));
-		}
-	}
-	
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/test/java/org/apache/taverna/mavenplugin/TavernaPluginGenerateMojoTest.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/test/java/org/apache/taverna/mavenplugin/TavernaPluginGenerateMojoTest.java b/taverna-maven-plugin/src/test/java/org/apache/taverna/mavenplugin/TavernaPluginGenerateMojoTest.java
new file mode 100644
index 0000000..5501061
--- /dev/null
+++ b/taverna-maven-plugin/src/test/java/org/apache/taverna/mavenplugin/TavernaPluginGenerateMojoTest.java
@@ -0,0 +1,77 @@
+/**
+ * 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.
+ */
+package org.apache.taverna.mavenplugin;
+
+import org.apache.maven.plugin.testing.AbstractMojoTestCase;
+import org.apache.taverna.mavenplugin.TavernaPluginGenerateMojo;
+import org.junit.Ignore;
+import org.junit.Test;
+
+/**
+ * Unit tests for TavernaPluginGenerateMojo.
+ *
+ * @author David Withers
+ */
+public class TavernaPluginGenerateMojoTest extends AbstractMojoTestCase {
+
+	private TavernaPluginGenerateMojo tavernaPluginGenerateMojo;
+
+	/**
+	 * @throws java.lang.Exception
+	 */
+	@Ignore
+	public void setUp() throws Exception {
+//		super.setUp();
+//
+//		File pluginXml = new File( getBasedir(), "src/test/resources/unit/plugin-config.xml" );
+//        tavernaPluginGenerateMojo = (TavernaPluginGenerateMojo) lookupMojo( "plugin-generate", pluginXml );
+//
+//		MavenProject mavenProject = (MavenProject) getVariableValueFromObject(tavernaPluginGenerateMojo, "project");
+//
+//		Artifact artifact = new DefaultArtifact("net.sf.taverna.t2", "example-plugin", VersionRange
+//				.createFromVersion("0.1.0"), "compile", "jar", "", null);
+//        artifact.setRepository(new DefaultArtifactRepository("id1",
+//				"http://www.mygrid.org.uk/maven/repository", new DefaultRepositoryLayout()));
+//		mavenProject.setArtifact(artifact);
+//
+//
+//		Artifact dependency = new DefaultArtifact("com.example.test", "test-artifact", VersionRange
+//				.createFromVersion("1.3.5"), "compile", "jar", "", null);
+//		dependency.setGroupId("com.example.test");
+//		dependency.setArtifactId("test-artifact");
+//		dependency.setVersion("1.3.5");
+//		dependency.setRepository(new DefaultArtifactRepository("id2",
+//				"http://www.example.com/maven/repository", new DefaultRepositoryLayout()));
+//		mavenProject.setDependencyArtifacts(Collections.singleton(dependency));
+//
+//		MavenSession session = new MavenSession(getContainer(), (RepositorySystemSession) null, (MavenExecutionRequest) null, (MavenExecutionResult) null);
+//		setVariableValueToObject(tavernaPluginGenerateMojo, "session", session);
+	}
+
+	/**
+	 * Test method for
+	 * {@link org.apache.taverna.mavenplugin.TavernaPluginGenerateMojo#execute()}
+	 *
+	 * @throws Exception
+	 */
+	@Test
+	@Ignore
+	public void testExecute() throws Exception {
+//		tavernaPluginGenerateMojo.execute();
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/test/java/org/apache/taverna/mavenplugin/TestUtils.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/test/java/org/apache/taverna/mavenplugin/TestUtils.java b/taverna-maven-plugin/src/test/java/org/apache/taverna/mavenplugin/TestUtils.java
new file mode 100644
index 0000000..e4bdf65
--- /dev/null
+++ b/taverna-maven-plugin/src/test/java/org/apache/taverna/mavenplugin/TestUtils.java
@@ -0,0 +1,44 @@
+/**
+ * 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.
+ */
+package org.apache.taverna.mavenplugin;
+
+import static org.junit.Assert.*;
+
+import java.util.Set;
+
+import org.apache.maven.plugin.logging.Log;
+import org.apache.maven.plugin.testing.SilentLog;
+import org.apache.taverna.mavenplugin.Utils;
+import org.junit.Test;
+
+public class TestUtils {
+
+	@Test
+	public void getJavaPackages() throws Exception {
+		Log log = new SilentLog();
+		Set<String> packages = Utils.getJavaPackages(log);
+		assertTrue(packages.contains("java.util"));
+		assertTrue(packages.contains("org.xml.sax.helpers"));
+		for (String pkg: packages) { 
+			assertFalse(pkg.isEmpty());
+			assertFalse(pkg.contains(" "));
+			assertFalse(pkg.contains("#"));
+			assertTrue(pkg.contains("."));
+		}
+	}
+	
+}

[2/2] incubator-taverna-osgi git commit: TAVERNA-899 package org.apache.taverna.mavenplugin

[st...@apache.org]

TAVERNA-899 package org.apache.taverna.mavenplugin


Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/commit/c660ed5c
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/tree/c660ed5c
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/diff/c660ed5c

Branch: refs/heads/master
Commit: c660ed5cd8370cfb403e7872b2912fef2d7b8139
Parents: 33defe4
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Wed Feb 17 10:36:40 2016 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Wed Feb 17 10:36:40 2016 +0000

----------------------------------------------------------------------
 .../t2/maven/plugins/AbstractDeployMojo.java    |  52 ---
 .../t2/maven/plugins/AbstractWagonMojo.java     |  56 ---
 .../t2/maven/plugins/BundleArtifact.java        |  62 ---
 .../t2/maven/plugins/MavenOsgiUtils.java        | 411 -------------------
 .../sf/taverna/t2/maven/plugins/Package.java    |  42 --
 .../t2/maven/plugins/PackageVersion.java        |  73 ----
 .../plugins/TavernaPluginDeployFileMojo.java    | 230 -----------
 .../maven/plugins/TavernaPluginDeployMojo.java  | 215 ----------
 .../plugins/TavernaPluginGenerateMojo.java      | 137 -------
 .../TavernaPluginPrepareBundlesMojo.java        |  80 ----
 .../maven/plugins/TavernaProfileDeployMojo.java | 270 ------------
 .../plugins/TavernaProfileGenerateMojo.java     | 216 ----------
 .../net/sf/taverna/t2/maven/plugins/Utils.java  | 167 --------
 .../taverna/mavenplugin/AbstractDeployMojo.java |  52 +++
 .../taverna/mavenplugin/AbstractWagonMojo.java  |  56 +++
 .../taverna/mavenplugin/BundleArtifact.java     |  62 +++
 .../taverna/mavenplugin/MavenOsgiUtils.java     | 411 +++++++++++++++++++
 .../org/apache/taverna/mavenplugin/Package.java |  42 ++
 .../taverna/mavenplugin/PackageVersion.java     |  73 ++++
 .../TavernaPluginDeployFileMojo.java            | 230 +++++++++++
 .../mavenplugin/TavernaPluginDeployMojo.java    | 215 ++++++++++
 .../mavenplugin/TavernaPluginGenerateMojo.java  | 137 +++++++
 .../TavernaPluginPrepareBundlesMojo.java        |  80 ++++
 .../mavenplugin/TavernaProfileDeployMojo.java   | 270 ++++++++++++
 .../mavenplugin/TavernaProfileGenerateMojo.java | 216 ++++++++++
 .../org/apache/taverna/mavenplugin/Utils.java   | 167 ++++++++
 .../plugins/TavernaPluginGenerateMojoTest.java  |  76 ----
 .../sf/taverna/t2/maven/plugins/TestUtils.java  |  43 --
 .../TavernaPluginGenerateMojoTest.java          |  77 ++++
 .../apache/taverna/mavenplugin/TestUtils.java   |  44 ++
 30 files changed, 2132 insertions(+), 2130 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/AbstractDeployMojo.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/AbstractDeployMojo.java b/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/AbstractDeployMojo.java
deleted file mode 100644
index 7d24e82..0000000
--- a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/AbstractDeployMojo.java
+++ /dev/null
@@ -1,52 +0,0 @@
-/**
- * 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.
- */
-package net.sf.taverna.t2.maven.plugins;
-
-import java.io.File;
-
-import org.apache.maven.artifact.Artifact;
-import org.apache.maven.artifact.repository.ArtifactRepository;
-import org.apache.maven.plugins.annotations.Component;
-import org.apache.maven.plugins.annotations.Parameter;
-import org.apache.maven.project.MavenProject;
-
-/**
- * Abstract Mojo for deploying artifacts.
- *
- * @author David Withers
- */
-public abstract class AbstractDeployMojo extends AbstractWagonMojo {
-
-	@Component
-	protected MavenProject project;
-
-	/**
-	 * Directory containing the generated Taverna plugin.
-	 */
-	@Parameter(defaultValue = "${project.build.directory}", required = true)
-	protected File buildDirectory;
-
-	@Parameter(defaultValue = "${project.build.outputDirectory}", required = true)
-	protected File outputDirectory;
-
-	@Parameter(defaultValue = "${project.artifact}", required = true, readonly = true)
-	protected Artifact artifact;
-
-	@Parameter(defaultValue = "${project.distributionManagementArtifactRepository}", required = true, readonly = true)
-	protected ArtifactRepository deploymentRepository;
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/AbstractWagonMojo.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/AbstractWagonMojo.java b/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/AbstractWagonMojo.java
deleted file mode 100644
index 954d6f2..0000000
--- a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/AbstractWagonMojo.java
+++ /dev/null
@@ -1,56 +0,0 @@
-/**
- * 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.
- */
-package net.sf.taverna.t2.maven.plugins;
-
-import org.apache.maven.artifact.manager.WagonManager;
-import org.apache.maven.plugin.AbstractMojo;
-import org.apache.maven.plugins.annotations.Component;
-import org.apache.maven.wagon.ConnectionException;
-import org.apache.maven.wagon.Wagon;
-import org.apache.maven.wagon.observers.Debug;
-
-/**
- * Abstract Mojo for using the wagon.
- *
- * @author David Withers
- */
-public abstract class AbstractWagonMojo extends AbstractMojo {
-
-	@Component
-	protected WagonManager wagonManager;
-
-	/**
-	 * Disconnect the wagon.
-	 *
-	 * @param wagon
-	 *            the wagon to disconnect
-	 * @param debug
-	 */
-	protected void disconnectWagon(Wagon wagon, Debug debug) {
-		if (getLog().isDebugEnabled()) {
-			wagon.removeTransferListener(debug);
-			wagon.removeSessionListener(debug);
-		}
-		try {
-			wagon.disconnect();
-		} catch (ConnectionException e) {
-			getLog().error("Error disconnecting wagon - ignored", e);
-		}
-	}
-
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/BundleArtifact.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/BundleArtifact.java b/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/BundleArtifact.java
deleted file mode 100644
index 9d04aec..0000000
--- a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/BundleArtifact.java
+++ /dev/null
@@ -1,62 +0,0 @@
-/**
- * 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.
- */
-package net.sf.taverna.t2.maven.plugins;
-
-import org.apache.maven.artifact.Artifact;
-
-/**
- *
- *
- * @author David Withers
- */
-public class BundleArtifact {
-
-	private Artifact artifact;
-	private String symbolicName;
-	private String version;
-
-	public BundleArtifact(Artifact artifact, String symbolicName, String version) {
-		this.artifact = artifact;
-		this.symbolicName = symbolicName;
-		this.version = version;
-	}
-
-	public Artifact getArtifact() {
-		return artifact;
-	}
-
-	public void setArtifact(Artifact artifact) {
-		this.artifact = artifact;
-	}
-
-	public String getSymbolicName() {
-		return symbolicName;
-	}
-
-	public void setSymbolicName(String symbolicName) {
-		this.symbolicName = symbolicName;
-	}
-
-	public String getVersion() {
-		return version;
-	}
-
-	public void setVersion(String version) {
-		this.version = version;
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/MavenOsgiUtils.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/MavenOsgiUtils.java b/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/MavenOsgiUtils.java
deleted file mode 100644
index 0baedb4..0000000
--- a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/MavenOsgiUtils.java
+++ /dev/null
@@ -1,411 +0,0 @@
-/**
- * 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.
- */
-package net.sf.taverna.t2.maven.plugins;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.jar.Attributes;
-import java.util.jar.JarFile;
-import java.util.jar.Manifest;
-
-import org.apache.maven.RepositoryUtils;
-import org.apache.maven.artifact.Artifact;
-import org.apache.maven.plugin.MojoExecutionException;
-import org.apache.maven.plugin.logging.Log;
-import org.apache.maven.project.DefaultDependencyResolutionRequest;
-import org.apache.maven.project.DependencyResolutionException;
-import org.apache.maven.project.DependencyResolutionResult;
-import org.apache.maven.project.MavenProject;
-import org.apache.maven.project.ProjectDependenciesResolver;
-import org.apache.taverna.profile.xml.jaxb.BundleInfo;
-import org.eclipse.aether.RepositorySystemSession;
-import org.eclipse.aether.graph.DependencyNode;
-import org.eclipse.aether.util.filter.ScopeDependencyFilter;
-
-import aQute.bnd.header.Attrs;
-import aQute.bnd.header.OSGiHeader;
-import aQute.bnd.header.Parameters;
-import aQute.bnd.osgi.Constants;
-import aQute.bnd.version.Version;
-import aQute.bnd.version.VersionRange;
-
-/**
- * @author David Withers
- */
-public class MavenOsgiUtils {
-
-	private final MavenProject project;
-	private final RepositorySystemSession repositorySystemSession;
-	private final ProjectDependenciesResolver projectDependenciesResolver;
-	private final Log log;
-
-	private Set<String> javaPackages;
-	private Set<String> systemPackages;
-
-	public MavenOsgiUtils(MavenProject project, RepositorySystemSession repositorySystemSession,
-			ProjectDependenciesResolver projectDependenciesResolver, Log log) {
-		this(project, repositorySystemSession, projectDependenciesResolver, new HashSet<String>(),
-				log);
-	}
-
-	public MavenOsgiUtils(MavenProject project, RepositorySystemSession repositorySystemSession,
-			ProjectDependenciesResolver projectDependenciesResolver, Set<String> systemPackages,
-			Log log) {
-		this.project = project;
-		this.repositorySystemSession = repositorySystemSession;
-		this.projectDependenciesResolver = projectDependenciesResolver;
-		this.systemPackages = systemPackages;
-		this.log = log;
-		javaPackages = Utils.getJavaPackages(log);
-	}
-
-	public Set<BundleArtifact> getBundleDependencies(String... scopes)
-			throws MojoExecutionException {
-		ScopeDependencyFilter scopeFilter = new ScopeDependencyFilter(Arrays.asList(scopes), null);
-
-		DefaultDependencyResolutionRequest dependencyResolutionRequest = new DefaultDependencyResolutionRequest(
-				project, repositorySystemSession);
-		dependencyResolutionRequest.setResolutionFilter(scopeFilter);
-
-		DependencyResolutionResult dependencyResolutionResult;
-		try {
-			dependencyResolutionResult = projectDependenciesResolver
-					.resolve(dependencyResolutionRequest);
-		} catch (DependencyResolutionException ex) {
-			throw new MojoExecutionException(ex.getMessage(), ex);
-		}
-
-		DependencyNode dependencyGraph = dependencyResolutionResult.getDependencyGraph();
-		if (dependencyGraph != null) {
-			checkBundleDependencies(dependencyGraph.getChildren());
-			return getBundleArtifacts(dependencyGraph.getChildren());
-		} else {
-			return new HashSet<BundleArtifact>();
-		}
-	}
-
-	public Set<BundleArtifact> getBundleArtifacts(List<DependencyNode> nodes) {
-		Set<BundleArtifact> bundleArtifacts = new HashSet<BundleArtifact>();
-		for (DependencyNode node : nodes) {
-			Artifact artifact = RepositoryUtils.toArtifact(node.getDependency().getArtifact());
-			String symbolicName = getManifestAttribute(artifact, Constants.BUNDLE_SYMBOLICNAME);
-			if (symbolicName != null) {
-				String version = getManifestAttribute(artifact, Constants.BUNDLE_VERSION);
-				bundleArtifacts.add(new BundleArtifact(artifact, symbolicName, version));
-				bundleArtifacts.addAll(getBundleArtifacts(node.getChildren()));
-			} else {
-				log.warn("Not an OSGi bundle : " + artifact.getId());
-			}
-		}
-		return bundleArtifacts;
-	}
-
-	public Set<Artifact> getAllArtifacts(List<DependencyNode> nodes) {
-		Set<Artifact> artifacts = new HashSet<Artifact>();
-		for (DependencyNode node : nodes) {
-			Artifact artifact = RepositoryUtils.toArtifact(node.getDependency().getArtifact());
-			if (isBundle(artifact)) {
-				artifacts.add(artifact);
-				artifacts.addAll(getAllArtifacts(node.getChildren()));
-			}
-		}
-		return artifacts;
-	}
-
-	public Set<Artifact> getArtifacts(List<DependencyNode> nodes) {
-		Set<Artifact> artifacts = new HashSet<Artifact>();
-		for (DependencyNode node : nodes) {
-			Artifact artifact = RepositoryUtils.toArtifact(node.getDependency().getArtifact());
-			if (isBundle(artifact)) {
-				artifacts.add(artifact);
-			}
-		}
-		return artifacts;
-	}
-
-	public List<BundleInfo> getBundles(Set<BundleArtifact> bundleDependencies)
-			throws MojoExecutionException {
-		List<BundleInfo> bundles = new ArrayList<BundleInfo>();
-		for (BundleArtifact bundleArtifact : bundleDependencies) {
-			Artifact artifact = bundleArtifact.getArtifact();
-			BundleInfo bundle = new BundleInfo();
-			bundle.setSymbolicName(bundleArtifact.getSymbolicName());
-			bundle.setVersion(bundleArtifact.getVersion());
-			bundle.setFileName(new File(artifact.getGroupId(), artifact.getFile().getName())
-					.getPath());
-			bundles.add(bundle);
-		}
-		Collections.sort(bundles, new BundleComparator());
-		return bundles;
-	}
-
-	public Map<String, Set<PackageVersion>> getPackageDependencies(List<DependencyNode> nodes) {
-		Map<String, Set<PackageVersion>> exportVersions = calculatePackageVersions(
-				getAllArtifacts(nodes), true, false);
-		return getPackageDependencies(getArtifacts(nodes), exportVersions);
-	}
-
-	public Map<String, Set<PackageVersion>> getPackageDependencies(Set<Artifact> requiredArtifacts,
-			Map<String, Set<PackageVersion>> exportVersions) {
-		Map<String, Set<PackageVersion>> importVersions = calculatePackageVersions(
-				requiredArtifacts, false, true);
-		Set<Artifact> newRequiredArtifacts = new HashSet<Artifact>();
-		for (Entry<String, Set<PackageVersion>> entry : importVersions.entrySet()) {
-			if (!javaPackages.contains(entry.getKey())) {
-				String packageName = entry.getKey();
-				Set<PackageVersion> importsVersions = entry.getValue();
-				Set<PackageVersion> exportsVersions = exportVersions.get(packageName);
-				if (exportVersions.containsKey(entry.getKey())) {
-					for (Artifact artifact : getRequiredArtifacts(importsVersions, exportsVersions)) {
-						if (!requiredArtifacts.contains(artifact)) {
-							newRequiredArtifacts.add(artifact);
-						}
-					}
-				}
-			}
-		}
-		if (!newRequiredArtifacts.isEmpty()) {
-			newRequiredArtifacts.addAll(requiredArtifacts);
-			return getPackageDependencies(newRequiredArtifacts, exportVersions);
-		}
-		return importVersions;
-	}
-
-	/**
-	 * Returns the minimum set of artifacts required to satisfy the range of importVersions.
-	 *
-	 * @param importsVersions
-	 *            the version ranges required for the package
-	 * @param exportVersions
-	 *            the available versions for the package
-	 * @return the minimum set of artifacts required to satisfy the range of importVersions
-	 */
-	private Set<Artifact> getRequiredArtifacts(Set<PackageVersion> importsVersions,
-			Set<PackageVersion> exportVersions) {
-		Set<Artifact> requiredArtifacts = new HashSet<Artifact>();
-		List<Set<PackageVersion>> exportsSubsets = Utils.getSubsets(exportVersions);
-		for (Set<PackageVersion> exportsSubset : exportsSubsets) {
-			if (satisfiesImports(importsVersions, exportsSubset)) {
-				for (PackageVersion exportVersion : exportsSubset) {
-					requiredArtifacts.add(exportVersion.getArtifact());
-				}
-				break;
-			}
-		}
-		return requiredArtifacts;
-	}
-
-	private boolean satisfiesImports(Set<PackageVersion> imports, Set<PackageVersion> exports) {
-		for (PackageVersion importVersion : imports) {
-			if (!satisfiesImport(importVersion, exports)) {
-				return false;
-			}
-		}
-		return true;
-	}
-
-	private boolean satisfiesImport(PackageVersion importVersion, Set<PackageVersion> exports) {
-		for (PackageVersion exportVersion : exports) {
-			if (importVersion.getVersionRange().includes(exportVersion.getVersionRange().getLow())) {
-				return true;
-			}
-		}
-		return false;
-	}
-
-	public void checkBundleDependencies(List<DependencyNode> nodes) {
-		Map<Artifact, Set<Package>> unresolvedArtifacts = new HashMap<Artifact, Set<Package>>();
-		Set<Artifact> artifacts = getAllArtifacts(nodes);
-		Map<String, Set<PackageVersion>> exports = calculatePackageVersions(artifacts, true, false);
-		for (Artifact artifact : artifacts) {
-			if (isBundle(artifact)) {
-				Parameters imports = getManifestAttributeParameters(artifact,
-						Constants.IMPORT_PACKAGE);
-				if (imports != null) {
-					for (String packageName : imports.keySet()) {
-						boolean exportMissing = true;
-						VersionRange importRange = null;
-						Attrs attrs = imports.get(packageName);
-						if (isOptional(attrs)) {
-							exportMissing = false;
-						} else if (javaPackages.contains(packageName)
-								|| systemPackages.contains(packageName)
-								|| packageName.startsWith("org.osgi.")) {
-							exportMissing = false;
-						} else if (attrs == null || attrs.get(Constants.VERSION_ATTRIBUTE) == null) {
-							if (exports.containsKey(packageName)) {
-								exportMissing = false;
-							}
-						} else {
-							importRange = getVersionRange(attrs);
-							if (exports.containsKey(packageName)) {
-								for (PackageVersion exportVersion : exports.get(packageName)) {
-									if (importRange.includes(exportVersion.getVersionRange()
-											.getLow())) {
-										exportMissing = false;
-										break;
-									}
-								}
-							}
-						}
-						if (exportMissing) {
-							if (!unresolvedArtifacts.containsKey(artifact)) {
-								unresolvedArtifacts.put(artifact, new HashSet<Package>());
-							}
-							unresolvedArtifacts.get(artifact).add(
-									new Package(packageName, importRange));
-						}
-					}
-				}
-			}
-		}
-		for (Entry<Artifact, Set<Package>> unresolvedArtifact : unresolvedArtifacts.entrySet()) {
-			log.warn("Bundle : " + unresolvedArtifact.getKey().getId()
-					+ " has unresolved package dependencies:");
-			for (Package unresolvedPackage : unresolvedArtifact.getValue()) {
-				log.warn("    " + unresolvedPackage);
-			}
-		}
-	}
-
-	public Map<String, Set<PackageVersion>> calculatePackageVersions(Set<Artifact> artifacts,
-			boolean export, boolean unique) {
-		Map<String, Set<PackageVersion>> packageVersions = new HashMap<String, Set<PackageVersion>>();
-		for (Artifact artifact : artifacts) {
-			if (isBundle(artifact)) {
-				Parameters packages = getManifestAttributeParameters(artifact,
-						export ? Constants.EXPORT_PACKAGE : Constants.IMPORT_PACKAGE);
-				if (packages != null) {
-					for (String packageName : packages.keySet()) {
-						if (!packageVersions.containsKey(packageName)) {
-							packageVersions.put(packageName, new HashSet<PackageVersion>());
-						}
-						Set<PackageVersion> versions = packageVersions.get(packageName);
-						VersionRange versionRange = getVersionRange(packages.get(packageName));
-						boolean optional = isOptional(packages.get(packageName));
-						if (unique) {
-							// check if this version range is unique
-							boolean uniqueVersion = true;
-							for (PackageVersion version : versions) {
-								if (equals(versionRange, version.getVersionRange())) {
-									uniqueVersion = false;
-									break;
-								}
-							}
-							if (uniqueVersion) {
-								versions.add(new PackageVersion(versionRange, artifact, optional));
-							}
-						} else {
-							versions.add(new PackageVersion(versionRange, artifact, optional));
-						}
-					}
-				}
-			}
-		}
-		return packageVersions;
-	}
-
-	public Version getVersion(Attrs attrs) {
-		if (attrs == null) {
-			return Version.LOWEST;
-		}
-		return Version.parseVersion(attrs.get(Constants.VERSION_ATTRIBUTE));
-	}
-
-	public VersionRange getVersionRange(Attrs attrs) {
-		if (attrs == null) {
-			return new VersionRange("0");
-		}
-		String version = attrs.get(Constants.VERSION_ATTRIBUTE);
-		if (version == null) {
-			return new VersionRange("0");
-		}
-		return new VersionRange(version);
-	}
-
-	public boolean isBundle(Artifact artifact) {
-		return getManifestAttribute(artifact, Constants.BUNDLE_SYMBOLICNAME) != null;
-	}
-
-	public boolean isOptional(Attrs attrs) {
-		return attrs != null && "optional".equals(attrs.get(Constants.RESOLUTION_DIRECTIVE));
-	}
-
-	public boolean equals(VersionRange v1, VersionRange v2) {
-		return v1 == v2 || v1.toString().equals(v2.toString());
-	}
-
-	public Parameters getManifestAttributeParameters(Artifact artifact, String attributeName) {
-		String attributeValue = getManifestAttribute(artifact, attributeName);
-		if (attributeValue != null) {
-			return OSGiHeader.parseHeader(attributeValue);
-		}
-		return null;
-	}
-
-	public String getManifestAttribute(Artifact artifact, String attributeName) {
-		Manifest manifest = getManifest(artifact);
-		if (manifest != null) {
-			Attributes mainAttributes = manifest.getMainAttributes();
-			return mainAttributes.getValue(attributeName);
-		}
-		return null;
-	}
-
-	public Manifest getManifest(Artifact artifact) {
-		if (artifact != null) {
-			File file = artifact.getFile();
-			if (file != null) {
-				try {
-					JarFile jarFile = new JarFile(artifact.getFile());
-					return jarFile.getManifest();
-				} catch (IOException e) {
-					return null;
-				}
-			}
-		}
-		return null;
-	}
-
-	private final class BundleComparator implements Comparator<BundleInfo> {
-
-		@Override
-		public int compare(BundleInfo bundle1, BundleInfo bundle2) {
-			return bundle1.getSymbolicName().compareTo(bundle2.getSymbolicName());
-		}
-
-	}
-
-	// public static void main(String[] args) throws Exception {
-	// MavenOsgiUtils mavenOsgiUtils = new MavenOsgiUtils();
-	// Parameters exports = mavenOsgiUtils.getImports(new
-	// File("/Users/david/Documents/workspace-trunk/taverna-plugin-impl/target/taverna-plugin-impl-0.1.0-SNAPSHOT.jar"));
-	// for (String key : exports.keySet()) {
-	// System.out.println(key + " " + mavenOsgiUtils.getVersionRange(exports.get(key)));
-	// }
-	// }
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/Package.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/Package.java b/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/Package.java
deleted file mode 100644
index 5b06032..0000000
--- a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/Package.java
+++ /dev/null
@@ -1,42 +0,0 @@
-/**
- * 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.
- */
-package net.sf.taverna.t2.maven.plugins;
-
-import aQute.bnd.version.VersionRange;
-
-/**
- * @author David Withers
- */
-public class Package {
-
-	private String name;
-	private VersionRange versionRange;
-
-	public Package(String name, VersionRange versionRange) {
-		this.name = name;
-		this.versionRange = versionRange;
-	}
-
-	@Override
-	public String toString() {
-		if (versionRange == null) {
-			return name;
-		} else {
-			return name + ";version=\"" + versionRange + "\"";
-		}
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/PackageVersion.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/PackageVersion.java b/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/PackageVersion.java
deleted file mode 100644
index bac7c41..0000000
--- a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/PackageVersion.java
+++ /dev/null
@@ -1,73 +0,0 @@
-/**
- * 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.
- */
-package net.sf.taverna.t2.maven.plugins;
-
-import org.apache.maven.artifact.Artifact;
-
-import aQute.bnd.version.VersionRange;
-
-/**
- *
- *
- * @author David Withers
- */
-public class PackageVersion {
-
-	private VersionRange versionRange;
-	private Artifact artifact;
-	private boolean optional;
-
-	public PackageVersion(VersionRange versionRange, Artifact artifact) {
-		this(versionRange, artifact, false);
-	}
-
-	public PackageVersion(VersionRange versionRange, Artifact artifact, boolean optional) {
-		this.versionRange = versionRange;
-		this.artifact = artifact;
-		this.optional = optional;
-	}
-
-	@Override
-	public String toString() {
-		return versionRange + (optional ? "" : "") + "(from " + artifact.getId() + ")";
-	}
-
-	public VersionRange getVersionRange() {
-		return versionRange;
-	}
-
-	public void setVersionRange(VersionRange versionRange) {
-		this.versionRange = versionRange;
-	}
-
-	public Artifact getArtifact() {
-		return artifact;
-	}
-
-	public void setArtifact(Artifact artifact) {
-		this.artifact = artifact;
-	}
-
-	public boolean isOptional() {
-		return optional;
-	}
-
-	public void setOptional(boolean optional) {
-		this.optional = optional;
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaPluginDeployFileMojo.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaPluginDeployFileMojo.java b/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaPluginDeployFileMojo.java
deleted file mode 100644
index 8e97a32..0000000
--- a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaPluginDeployFileMojo.java
+++ /dev/null
@@ -1,230 +0,0 @@
-/**
- * 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.
- */
-package net.sf.taverna.t2.maven.plugins;
-
-import static net.sf.taverna.t2.maven.plugins.TavernaPluginGenerateMojo.META_INF_TAVERNA;
-import static net.sf.taverna.t2.maven.plugins.TavernaPluginGenerateMojo.PLUGIN_FILE;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.jar.JarFile;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipException;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Marshaller;
-import javax.xml.bind.Unmarshaller;
-
-import org.apache.maven.plugin.MojoExecutionException;
-import org.apache.maven.plugins.annotations.Mojo;
-import org.apache.maven.plugins.annotations.Parameter;
-import org.apache.maven.wagon.ConnectionException;
-import org.apache.maven.wagon.ResourceDoesNotExistException;
-import org.apache.maven.wagon.UnsupportedProtocolException;
-import org.apache.maven.wagon.Wagon;
-import org.apache.maven.wagon.authentication.AuthenticationException;
-import org.apache.maven.wagon.observers.Debug;
-import org.apache.maven.wagon.repository.Repository;
-import org.apache.taverna.plugin.xml.jaxb.PluginInfo;
-import org.apache.taverna.plugin.xml.jaxb.PluginVersions;
-import org.apache.taverna.plugin.xml.jaxb.Plugins;
-import org.apache.taverna.versions.xml.jaxb.Version;
-
-/**
- * Deploys the Taverna plugin using <code>scp</code> or <code>file</code> protocol to the site URL
- * specified.
- *
- * @author David Withers
- */
-@Mojo(name = "plugin-deploy-file", requiresProject=false, requiresDirectInvocation = true)
-public class TavernaPluginDeployFileMojo extends AbstractWagonMojo {
-
-	private static final String PLUGIN_FILE_ENTRY = META_INF_TAVERNA + "/" + PLUGIN_FILE;
-
-	private static final String PLUGINS_FILE = "plugins.xml";
-
-	@Parameter(defaultValue = "http://updates.taverna.org.uk/workbench/3.0/dev/", required = true)
-	protected String site;
-
-	@Parameter(property = "file", required = true)
-	protected File file;
-
-	@Parameter(property = "url", required = true)
-	protected String url;
-
-	@Parameter(property = "serverId", required = true)
-	protected String serverId;
-
-	public void execute() throws MojoExecutionException {
-		if (!file.exists()) {
-			throw new MojoExecutionException("The Taverna Plugin file " + file
-					+ " does not exist");
-		}
-
-		JarFile pluginJarFile;
-		try {
-			pluginJarFile = new JarFile(file);
-		} catch (ZipException e) {
-			throw new MojoExecutionException(file + " is not a valid Taverna Plugin file", e);
-		} catch (IOException e) {
-			throw new MojoExecutionException("Error opening Taverna Plugin file: " + file, e);
-		}
-
-		ZipEntry pluginFileEntry = pluginJarFile.getJarEntry(PLUGIN_FILE_ENTRY);
-		if (pluginFileEntry == null) {
-			throw new MojoExecutionException(file
-					+ " is not a valid Taverna Plugin file, missing " + PLUGIN_FILE_ENTRY);
-		}
-
-		JAXBContext jaxbContext;
-		try {
-			jaxbContext = JAXBContext.newInstance(PluginInfo.class, Plugins.class);
-		} catch (JAXBException e) {
-			throw new MojoExecutionException("Error setting up JAXB context ", e);
-		}
-
-		PluginInfo plugin;
-		try {
-			InputStream inputStream = pluginJarFile.getInputStream(pluginFileEntry);
-			Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
-			plugin = (PluginInfo) unmarshaller.unmarshal(inputStream);
-			inputStream.close();
-		} catch (IOException e) {
-			throw new MojoExecutionException("Error reading " + file, e);
-		} catch (JAXBException e) {
-			throw new MojoExecutionException("Error reading " + file, e);
-		}
-
-		getLog().debug("The Taverna plugin will be deployed to '" + url + "'");
-
-		Repository repository = new Repository(serverId, url);
-
-		// create the wagon
-		Wagon wagon;
-		try {
-			wagon = wagonManager.getWagon(repository.getProtocol());
-		} catch (UnsupportedProtocolException e) {
-			throw new MojoExecutionException("Unsupported protocol: '" + repository.getProtocol()
-					+ "'", e);
-		}
-
-		Debug debug = new Debug();
-		if (getLog().isDebugEnabled()) {
-			wagon.addSessionListener(debug);
-			wagon.addTransferListener(debug);
-		}
-
-		// connect to the plugin site
-		try {
-			wagon.connect(repository, wagonManager.getAuthenticationInfo(serverId),
-					wagonManager.getProxy(repository.getProtocol()));
-		} catch (ConnectionException e) {
-			throw new MojoExecutionException("Error connecting to plugin site at " + url, e);
-		} catch (AuthenticationException e) {
-			throw new MojoExecutionException("Authentication error connecting to plugin site at "
-					+ url, e);
-		}
-
-		try {
-			File pluginsFile = File.createTempFile("taverna", null);
-
-			// fetch the plugins file
-			Plugins plugins;
-			try {
-				Utils.downloadFile(PLUGINS_FILE, pluginsFile, wagon, getLog());
-				try {
-					Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
-					plugins = (Plugins) unmarshaller.unmarshal(pluginsFile);
-				} catch (JAXBException e) {
-					throw new MojoExecutionException("Error reading " + pluginsFile, e);
-				}
-			} catch (ResourceDoesNotExistException e) {
-				getLog().info("Creating new plugins file");
-				plugins = new Plugins();
-			}
-
-			String deployedPluginFile = plugin.getId() + "-" + plugin.getVersion() + ".jar";
-
-			if (addPlugin(plugins, plugin, deployedPluginFile)) {
-				// write the new plugin site file
-				try {
-					Marshaller marshaller = jaxbContext.createMarshaller();
-					marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
-					marshaller.setProperty(Marshaller.JAXB_SCHEMA_LOCATION,
-							TavernaPluginGenerateMojo.SCHEMA_LOCATION);
-					marshaller.marshal(plugins, pluginsFile);
-				} catch (JAXBException e) {
-					throw new MojoExecutionException("Error writing " + PLUGINS_FILE, e);
-				}
-
-				// upload the plugin to the update site
-				Utils.uploadFile(file, deployedPluginFile, wagon, getLog());
-				// upload the plugin site file
-				Utils.uploadFile(pluginsFile, PLUGINS_FILE, wagon, getLog());
-			}
-		} catch (IOException e) {
-			throw new MojoExecutionException("Error writing " + PLUGINS_FILE, e);
-		} finally {
-			disconnectWagon(wagon, debug);
-		}
-	}
-
-	private boolean addPlugin(Plugins plugins, PluginInfo pluginInfo, String pluginURL) {
-		PluginVersions plugin = getPlugin(plugins, pluginInfo);
-		Version latestVersion = plugin.getLatestVersion();
-		if (latestVersion != null && latestVersion.getVersion().equals(pluginInfo.getVersion())) {
-			getLog().error(
-					String.format("%1$s version %2$s has already been deployed",
-							pluginInfo.getName(), pluginInfo.getVersion()));
-			return false;
-		}
-		Version newPluginVersion = new Version();
-		newPluginVersion.setVersion(pluginInfo.getVersion());
-		newPluginVersion.setFile(pluginURL);
-
-		getLog().info(
-				String.format("Adding %1$s version %2$s", pluginInfo.getName(),
-						pluginInfo.getVersion()));
-		if (plugin.getLatestVersion() != null) {
-			plugin.getPreviousVersion().add(plugin.getLatestVersion());
-		}
-		plugin.setLatestVersion(newPluginVersion);
-		return true;
-	}
-
-	private PluginVersions getPlugin(Plugins plugins, PluginInfo pluginInfo) {
-		PluginVersions pluginVersions = null;
-		for (PluginVersions existingPlugin : plugins.getPlugin()) {
-			if (existingPlugin.getId().equals(pluginInfo.getId())) {
-				pluginVersions = existingPlugin;
-				break;
-			}
-		}
-		if (pluginVersions == null) {
-			pluginVersions = new PluginVersions();
-			pluginVersions.setId(pluginInfo.getId());
-			plugins.getPlugin().add(pluginVersions);
-		}
-		pluginVersions.setName(pluginInfo.getName());
-		pluginVersions.setDescription(pluginInfo.getDescription());
-		pluginVersions.setOrganization(pluginInfo.getOrganization());
-		return pluginVersions;
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaPluginDeployMojo.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaPluginDeployMojo.java b/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaPluginDeployMojo.java
deleted file mode 100644
index 0141d71..0000000
--- a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaPluginDeployMojo.java
+++ /dev/null
@@ -1,215 +0,0 @@
-/**
- * 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.
- */
-package net.sf.taverna.t2.maven.plugins;
-
-import java.io.File;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Marshaller;
-import javax.xml.bind.Unmarshaller;
-
-import org.apache.maven.plugin.MojoExecutionException;
-import org.apache.maven.plugins.annotations.LifecyclePhase;
-import org.apache.maven.plugins.annotations.Mojo;
-import org.apache.maven.wagon.ConnectionException;
-import org.apache.maven.wagon.ResourceDoesNotExistException;
-import org.apache.maven.wagon.UnsupportedProtocolException;
-import org.apache.maven.wagon.Wagon;
-import org.apache.maven.wagon.authentication.AuthenticationException;
-import org.apache.maven.wagon.observers.Debug;
-import org.apache.maven.wagon.repository.Repository;
-import org.apache.taverna.plugin.xml.jaxb.PluginInfo;
-import org.apache.taverna.plugin.xml.jaxb.PluginVersions;
-import org.apache.taverna.plugin.xml.jaxb.Plugins;
-import org.apache.taverna.versions.xml.jaxb.Version;
-
-/**
- * Deploys the Taverna plugin using <code>scp</code> or <code>file</code> protocol to the site URL
- * specified in the <code>&lt;distributionManagement&gt;</code> section of the POM.
- *
- * @author David Withers
- */
-@Mojo(name = "plugin-deploy", defaultPhase = LifecyclePhase.DEPLOY)
-public class TavernaPluginDeployMojo extends AbstractDeployMojo {
-
-	private static final String PLUGINS_FILE = "plugins.xml";
-
-	private File tempDirectory;
-
-	public void execute() throws MojoExecutionException {
-		tempDirectory = new File(buildDirectory, TavernaProfileGenerateMojo.TAVERNA_TMP);
-		tempDirectory.mkdirs();
-		if (artifact == null) {
-			throw new MojoExecutionException(
-					"The Taverna Plugin does not exist, please run taverna:plugin-generate first");
-		}
-
-		File artifactFile = artifact.getFile();
-		if (artifactFile == null) {
-			throw new MojoExecutionException(
-					"The Taverna Plugin does not exist, please run taverna:plugin-generate first");
-		}
-
-		File pluginDirectory = new File(outputDirectory, TavernaPluginGenerateMojo.META_INF_TAVERNA);
-		File pluginFile = new File(pluginDirectory, TavernaPluginGenerateMojo.PLUGIN_FILE);
-		if (!pluginFile.exists()) {
-			throw new MojoExecutionException(
-					"The Taverna Plugin does not exist, please run taverna:plugin-generate first");
-		}
-
-		JAXBContext jaxbContext;
-		try {
-			jaxbContext = JAXBContext.newInstance(PluginInfo.class, Plugins.class);
-		} catch (JAXBException e) {
-			throw new MojoExecutionException("Error setting up JAXB context ", e);
-		}
-
-		PluginInfo plugin;
-		try {
-			Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
-			plugin = (PluginInfo) unmarshaller.unmarshal(pluginFile);
-		} catch (JAXBException e) {
-			throw new MojoExecutionException("Error reading " + pluginFile, e);
-		}
-
-		if (deploymentRepository == null) {
-			throw new MojoExecutionException(
-					"Missing repository information in the distribution management element in the project.");
-		}
-
-		String url = deploymentRepository.getUrl();
-		String id = deploymentRepository.getId();
-
-		if (url == null) {
-			throw new MojoExecutionException(
-					"The URL to the Taverna plugin site is missing in the project descriptor.");
-		}
-		getLog().debug("The Taverna plugin will be deployed to '" + url + "'");
-
-		Repository repository = new Repository(id, url);
-
-		// create the wagon
-		Wagon wagon;
-		try {
-			wagon = wagonManager.getWagon(repository.getProtocol());
-		} catch (UnsupportedProtocolException e) {
-			throw new MojoExecutionException("Unsupported protocol: '" + repository.getProtocol()
-					+ "'", e);
-		}
-
-		Debug debug = new Debug();
-		if (getLog().isDebugEnabled()) {
-			wagon.addSessionListener(debug);
-			wagon.addTransferListener(debug);
-		}
-
-		// connect to the plugin site
-		try {
-			wagon.connect(repository, wagonManager.getAuthenticationInfo(id),
-					wagonManager.getProxy(repository.getProtocol()));
-		} catch (ConnectionException e) {
-			throw new MojoExecutionException("Error connecting to plugin site at " + url, e);
-		} catch (AuthenticationException e) {
-			throw new MojoExecutionException("Authentication error connecting to plugin site at "
-					+ url, e);
-		}
-
-		try {
-			String deployedPluginFile = project.getGroupId() + "." + project.getArtifactId() + "-"
-					+ plugin.getVersion() + ".jar";
-
-			// fetch the plugins file
-			Plugins plugins;
-			File pluginsFile = new File(tempDirectory, PLUGINS_FILE);
-			try {
-				Utils.downloadFile(PLUGINS_FILE, pluginsFile, wagon, getLog());
-				try {
-					Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
-					plugins = (Plugins) unmarshaller.unmarshal(pluginsFile);
-				} catch (JAXBException e) {
-					throw new MojoExecutionException("Error reading " + pluginsFile, e);
-				}
-			} catch (ResourceDoesNotExistException e) {
-				getLog().info("Creating new plugins file");
-				plugins = new Plugins();
-			}
-
-			if (addPlugin(plugins, plugin, deployedPluginFile)) {
-				// write the new plugin site file
-				try {
-					Marshaller marshaller = jaxbContext.createMarshaller();
-					marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
-					marshaller.setProperty(Marshaller.JAXB_SCHEMA_LOCATION,
-							TavernaPluginGenerateMojo.SCHEMA_LOCATION);
-					marshaller.marshal(plugins, pluginsFile);
-				} catch (JAXBException e) {
-					throw new MojoExecutionException("Error writing " + PLUGINS_FILE, e);
-				}
-
-				// upload the plugin to the update site
-				Utils.uploadFile(artifactFile, deployedPluginFile, wagon, getLog());
-				// upload the plugin site file
-				Utils.uploadFile(pluginsFile, PLUGINS_FILE, wagon, getLog());
-			}
-		} finally {
-			disconnectWagon(wagon, debug);
-		}
-	}
-
-	private boolean addPlugin(Plugins plugins, PluginInfo pluginInfo, String pluginURL) {
-		PluginVersions plugin = getPlugin(plugins, pluginInfo);
-		Version latestVersion = plugin.getLatestVersion();
-		if (latestVersion != null && latestVersion.getVersion().equals(pluginInfo.getVersion())) {
-			getLog().error(
-					String.format("%1$s version %2$s has already been deployed", pluginInfo.getName(),
-							pluginInfo.getVersion()));
-			return false;
-		}
-		Version newPluginVersion = new Version();
-		newPluginVersion.setVersion(pluginInfo.getVersion());
-		newPluginVersion.setFile(pluginURL);
-
-		getLog().info(
-				String.format("Adding %1$s version %2$s", pluginInfo.getName(), pluginInfo.getVersion()));
-		if (plugin.getLatestVersion() != null) {
-			plugin.getPreviousVersion().add(plugin.getLatestVersion());
-		}
-		plugin.setLatestVersion(newPluginVersion);
-		return true;
-	}
-
-	private PluginVersions getPlugin(Plugins plugins, PluginInfo pluginInfo) {
-		PluginVersions pluginVersions = null;
-		for (PluginVersions existingPlugin : plugins.getPlugin()) {
-			if (existingPlugin.getId().equals(pluginInfo.getId())) {
-				pluginVersions = existingPlugin;
-				break;
-			}
-		}
-		if (pluginVersions == null) {
-			pluginVersions = new PluginVersions();
-			pluginVersions.setId(pluginInfo.getId());
-			plugins.getPlugin().add(pluginVersions);
-		}
-		pluginVersions.setName(pluginInfo.getName());
-		pluginVersions.setDescription(pluginInfo.getDescription());
-		pluginVersions.setOrganization(pluginInfo.getOrganization());
-		return pluginVersions;
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaPluginGenerateMojo.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaPluginGenerateMojo.java b/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaPluginGenerateMojo.java
deleted file mode 100644
index d2162fe..0000000
--- a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaPluginGenerateMojo.java
+++ /dev/null
@@ -1,137 +0,0 @@
-/**
- * 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.
- */
-package net.sf.taverna.t2.maven.plugins;
-
-import java.io.File;
-import java.util.List;
-import java.util.Set;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Marshaller;
-
-import org.apache.maven.artifact.Artifact;
-import org.apache.maven.model.Organization;
-import org.apache.maven.plugin.AbstractMojo;
-import org.apache.maven.plugin.MojoExecutionException;
-import org.apache.maven.plugin.MojoFailureException;
-import org.apache.maven.plugins.annotations.Component;
-import org.apache.maven.plugins.annotations.LifecyclePhase;
-import org.apache.maven.plugins.annotations.Mojo;
-import org.apache.maven.plugins.annotations.Parameter;
-import org.apache.maven.plugins.annotations.ResolutionScope;
-import org.apache.maven.project.MavenProject;
-import org.apache.maven.project.ProjectDependenciesResolver;
-import org.apache.maven.shared.osgi.DefaultMaven2OsgiConverter;
-import org.apache.maven.shared.osgi.Maven2OsgiConverter;
-import org.apache.taverna.plugin.xml.jaxb.PluginInfo;
-import org.apache.taverna.profile.xml.jaxb.BundleInfo;
-import org.eclipse.aether.RepositorySystemSession;
-
-/**
- * Generates a Taverna plugin definition file.
- *
- * @author David Withers
- */
-@Mojo(name = "plugin-generate", defaultPhase = LifecyclePhase.GENERATE_RESOURCES, requiresDependencyResolution = ResolutionScope.RUNTIME)
-public class TavernaPluginGenerateMojo extends AbstractMojo {
-
-	public static final String PLUGIN_FILE = "plugin.xml";
-
-	public static final String META_INF_TAVERNA = "META-INF/taverna";
-
-	public static final String SCHEMA_LOCATION = "http://ns.taverna.org.uk/2013/application/plugin http://localhost/2013/application/plugin/ApplicationPlugin.xsd";
-
-	@Component
-	private MavenProject project;
-
-	@Component
-	private ProjectDependenciesResolver projectDependenciesResolver;
-
-    @Parameter(defaultValue = "${repositorySystemSession}", readonly = true)
-	private RepositorySystemSession repositorySystemSession;
-
-	@Parameter(defaultValue = "${project.build.outputDirectory}", required = true)
-	protected File outputDirectory;
-
-	@Parameter(defaultValue = "${project.description}", required = true)
-	protected String description;
-
-	@Parameter(defaultValue = "${project.organization}", required = true)
-	protected Organization organization;
-
-	private MavenOsgiUtils osgiUtils;
-
-	private Maven2OsgiConverter maven2OsgiConverter = new DefaultMaven2OsgiConverter();
-
-	public void execute() throws MojoExecutionException, MojoFailureException {
-		try {
-			osgiUtils = new MavenOsgiUtils(project, repositorySystemSession,
-					projectDependenciesResolver, getLog());
-			createPluginDefinition();
-		} catch (JAXBException e) {
-			throw new MojoExecutionException("Error generating Taverna plugin", e);
-		}
-	}
-
-	/**
-	 * Generates the Taverna plugin definition file.
-	 *
-	 * @return the <code>File</code> that the Taverna plugin definition has been written to
-	 * @throws JAXBException
-	 * @throws MojoExecutionException
-	 */
-	private File createPluginDefinition() throws JAXBException, MojoExecutionException {
-		String groupId = project.getGroupId();
-		String artifactId = project.getArtifactId();
-		String version = maven2OsgiConverter.getVersion(project.getVersion());
-		if (version.endsWith("SNAPSHOT")) {
-			version = version.substring(0, version.indexOf("SNAPSHOT")) + Utils.timestamp();
-		}
-
-		File pluginDirectory = new File(outputDirectory, META_INF_TAVERNA);
-		pluginDirectory.mkdirs();
-		File pluginFile = new File(pluginDirectory, PLUGIN_FILE);
-
-		PluginInfo pluginInfo = new PluginInfo();
-		pluginInfo.setId(groupId + "." + artifactId);
-		pluginInfo.setName(project.getName());
-		pluginInfo.setVersion(version);
-		pluginInfo.setDescription(description);
-		pluginInfo.setOrganization(organization.getName());
-
-		Set<BundleArtifact> bundleDependencies = osgiUtils.getBundleDependencies(
-				Artifact.SCOPE_COMPILE, Artifact.SCOPE_RUNTIME);
-
-		List<BundleInfo> runtimeBundles = osgiUtils.getBundles(bundleDependencies);
-		if (!runtimeBundles.isEmpty()) {
-			List<BundleInfo> bundles = pluginInfo.getBundle();
-			for (BundleInfo bundle : runtimeBundles) {
-				bundles.add(bundle);
-			}
-		}
-
-		JAXBContext jaxbContext = JAXBContext.newInstance(PluginInfo.class);
-		Marshaller marshaller = jaxbContext.createMarshaller();
-		marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
-		marshaller.setProperty(Marshaller.JAXB_SCHEMA_LOCATION, SCHEMA_LOCATION);
-		marshaller.marshal(pluginInfo, pluginFile);
-
-		return pluginFile;
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaPluginPrepareBundlesMojo.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaPluginPrepareBundlesMojo.java b/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaPluginPrepareBundlesMojo.java
deleted file mode 100644
index 66f08ad..0000000
--- a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaPluginPrepareBundlesMojo.java
+++ /dev/null
@@ -1,80 +0,0 @@
-/**
- * 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.
- */
-package net.sf.taverna.t2.maven.plugins;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Set;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.maven.artifact.Artifact;
-import org.apache.maven.plugin.AbstractMojo;
-import org.apache.maven.plugin.MojoExecutionException;
-import org.apache.maven.plugin.MojoFailureException;
-import org.apache.maven.plugins.annotations.Component;
-import org.apache.maven.plugins.annotations.LifecyclePhase;
-import org.apache.maven.plugins.annotations.Mojo;
-import org.apache.maven.plugins.annotations.Parameter;
-import org.apache.maven.plugins.annotations.ResolutionScope;
-import org.apache.maven.project.MavenProject;
-import org.apache.maven.project.ProjectDependenciesResolver;
-import org.eclipse.aether.RepositorySystemSession;
-
-/**
- * Prepares the plugin OSGi bundles.
- *
- * @author David Withers
- */
-@Mojo(name = "plugin-prepare-bundles", defaultPhase = LifecyclePhase.PREPARE_PACKAGE, requiresDependencyResolution = ResolutionScope.RUNTIME)
-public class TavernaPluginPrepareBundlesMojo extends AbstractMojo {
-
-	@Component
-	private MavenProject project;
-
-	@Component
-	private ProjectDependenciesResolver projectDependenciesResolver;
-
-	@Parameter(defaultValue = "${repositorySystemSession}", readonly = true)
-	private RepositorySystemSession repositorySystemSession;
-
-	/**
-	 * The directory where the plugin OSGi bundles file will be put.
-	 */
-	@Parameter(defaultValue = "${project.build.outputDirectory}", required = true)
-	protected File outputDirectory;
-
-	private MavenOsgiUtils osgiUtils;
-
-	public void execute() throws MojoExecutionException, MojoFailureException {
-		osgiUtils = new MavenOsgiUtils(project, repositorySystemSession,
-				projectDependenciesResolver, getLog());
-		outputDirectory.mkdirs();
-
-		Set<BundleArtifact> bundleDependencies = osgiUtils.getBundleDependencies(
-				Artifact.SCOPE_COMPILE, Artifact.SCOPE_RUNTIME);
-		try {
-			for (BundleArtifact bundleArtifact : bundleDependencies) {
-				Artifact artifact = bundleArtifact.getArtifact();
-				FileUtils.copyFileToDirectory(bundleArtifact.getArtifact().getFile(), new File(
-						outputDirectory, artifact.getGroupId()));
-			}
-		} catch (IOException e) {
-			throw new MojoExecutionException("Error copying dependecies to archive directory", e);
-		}
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaProfileDeployMojo.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaProfileDeployMojo.java b/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaProfileDeployMojo.java
deleted file mode 100644
index d2f9d75..0000000
--- a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaProfileDeployMojo.java
+++ /dev/null
@@ -1,270 +0,0 @@
-/**
- * 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.
- */
-package net.sf.taverna.t2.maven.plugins;
-
-import java.io.File;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Marshaller;
-import javax.xml.bind.Unmarshaller;
-
-import org.apache.maven.plugin.MojoExecutionException;
-import org.apache.maven.plugins.annotations.LifecyclePhase;
-import org.apache.maven.plugins.annotations.Mojo;
-import org.apache.maven.wagon.ConnectionException;
-import org.apache.maven.wagon.ResourceDoesNotExistException;
-import org.apache.maven.wagon.UnsupportedProtocolException;
-import org.apache.maven.wagon.Wagon;
-import org.apache.maven.wagon.authentication.AuthenticationException;
-import org.apache.maven.wagon.observers.Debug;
-import org.apache.maven.wagon.repository.Repository;
-import org.apache.taverna.profile.xml.jaxb.ApplicationProfile;
-import org.apache.taverna.profile.xml.jaxb.BundleInfo;
-import org.apache.taverna.profile.xml.jaxb.UpdateSite;
-import org.apache.taverna.versions.xml.jaxb.Version;
-import org.apache.taverna.versions.xml.jaxb.Versions;
-
-/**
- * Deploys the application profile using <code>scp</code> or <code>file</code> protocol to the site
- * URL specified in the <code>&lt;distributionManagement&gt;</code> section of the POM.
- *
- * @author David Withers
- */
-@Mojo(name = "profile-deploy", defaultPhase = LifecyclePhase.DEPLOY)
-public class TavernaProfileDeployMojo extends AbstractDeployMojo {
-
-	private static final String UPDATES_FILE = "updates.xml";
-
-	private File tempDirectory;
-
-	public void execute() throws MojoExecutionException {
-		tempDirectory = new File(buildDirectory, TavernaProfileGenerateMojo.TAVERNA_TMP);
-		tempDirectory.mkdirs();
-		if (artifact == null) {
-			throw new MojoExecutionException(
-					"The application profile does not exist, please run taverna:profile-generate first");
-		}
-
-		File artifactFile = artifact.getFile();
-		if (artifactFile == null) {
-			throw new MojoExecutionException(
-					"The application profile does not exist, please run taverna:profile-generate first");
-		}
-
-		JAXBContext jaxbContext;
-		try {
-			jaxbContext = JAXBContext.newInstance(ApplicationProfile.class, UpdateSite.class);
-		} catch (JAXBException e) {
-			throw new MojoExecutionException("Error setting up JAXB context ", e);
-		}
-
-		ApplicationProfile applicationProfile;
-		try {
-			Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
-			applicationProfile = (ApplicationProfile) unmarshaller.unmarshal(artifactFile);
-		} catch (JAXBException e) {
-			throw new MojoExecutionException("Error reading " + artifactFile, e);
-		}
-
-		if (deploymentRepository == null) {
-			throw new MojoExecutionException(
-					"Missing repository information in the distribution management element in the project.");
-		}
-
-		String url = deploymentRepository.getUrl();
-		String id = deploymentRepository.getId();
-
-		if (url == null) {
-			throw new MojoExecutionException(
-					"The URL to the update site is missing in the project descriptor.");
-		}
-		getLog().debug("The Taverna application will be deployed to '" + url + "'");
-
-		Repository repository = new Repository(id, url);
-
-		// create the wagon
-		Wagon wagon;
-		try {
-			wagon = wagonManager.getWagon(repository.getProtocol());
-		} catch (UnsupportedProtocolException e) {
-			throw new MojoExecutionException("Unsupported protocol: '" + repository.getProtocol()
-					+ "'", e);
-		}
-
-		Debug debug = new Debug();
-		if (getLog().isDebugEnabled()) {
-			wagon.addSessionListener(debug);
-			wagon.addTransferListener(debug);
-		}
-
-		// connect to the update site
-		try {
-			wagon.connect(repository, wagonManager.getAuthenticationInfo(id),
-					wagonManager.getProxy(repository.getProtocol()));
-		} catch (ConnectionException e) {
-			throw new MojoExecutionException("Error connecting to " + url, e);
-		} catch (AuthenticationException e) {
-			throw new MojoExecutionException("Authentication error connecting to " + url, e);
-		}
-
-		try {
-			// upload the application profile to the update site
-			String deployedProfileFile = "ApplicationProfile" + "-" + applicationProfile.getVersion()
-					+ ".xml";
-			Utils.uploadFile(artifactFile, deployedProfileFile, wagon, getLog());
-
-			// fetch the applications file
-			UpdateSite updateSite;
-			File updatesFile = new File(tempDirectory, UPDATES_FILE);
-			try {
-				Utils.downloadFile(UPDATES_FILE, updatesFile, wagon, getLog());
-				try {
-					Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
-					updateSite = (UpdateSite) unmarshaller
-							.unmarshal(updatesFile);
-				} catch (JAXBException e) {
-					throw new MojoExecutionException("Error reading " + updatesFile, e);
-				}
-			} catch(ResourceDoesNotExistException e) {
-				getLog().info("Creating new application versions file");
-				updateSite = new UpdateSite();
-				Versions versions = new Versions();
-				versions.setId(applicationProfile.getId());
-				versions.setName(applicationProfile.getName());
-				updateSite.setVersions(versions);
-			}
-
-			Version latestVersion = updateSite.getVersions().getLatestVersion();
-			if (latestVersion != null) {
-				File latestProfileFile = new File(tempDirectory, "ApplicationProfile-" + latestVersion.getVersion()
-						+ ".xml");
-				try {
-					Utils.downloadFile(latestVersion.getFile(), latestProfileFile, wagon, getLog());
-				} catch (ResourceDoesNotExistException e) {
-					throw new MojoExecutionException(latestVersion.getFile() + " does not exist", e);
-				}
-				ApplicationProfile latestProfile;
-				try {
-					Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
-					latestProfile = (ApplicationProfile) unmarshaller.unmarshal(latestProfileFile);
-				} catch (JAXBException e) {
-					throw new MojoExecutionException("Error reading " + latestProfileFile, e);
-				}
-				Set<BundleInfo> requiredBundles = getRequiredBundles(latestProfile, applicationProfile);
-				if (requiredBundles.isEmpty()) {
-					getLog().warn("No new bundles to upload");
-				} else {
-					// upload new bundles to the update site
-					uploadBundles(requiredBundles, wagon);
-				}
-			}
-
-			if (addApplicationVersion(updateSite.getVersions(), applicationProfile,
-					deployedProfileFile)) {
-				// write the new application versions list
-				try {
-					Marshaller marshaller = jaxbContext.createMarshaller();
-					marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
-					marshaller.setProperty(Marshaller.JAXB_SCHEMA_LOCATION, TavernaProfileGenerateMojo.SCHEMA_LOCATION);
-					marshaller.marshal(updateSite, updatesFile);
-				} catch (JAXBException e) {
-					throw new MojoExecutionException("Error writing " + UPDATES_FILE, e);
-				}
-
-				// upload the new application versions list to the update site
-				Utils.uploadFile(updatesFile, UPDATES_FILE, wagon, getLog());
-			}
-		}
-		finally {
-			disconnectWagon(wagon, debug);
-		}
-	}
-
-	/**
-	 * Adds an new application version to the application versions if the version doesn't already
-	 * exist.
-	 *
-	 * @param applicationVersions
-	 *            the ApplicationVersions document
-	 * @param applicationProfile
-	 *            the applicationProfile
-	 * @param profileURL
-	 * @return true if a new version was added to the ApplicationVersions document; false if the
-	 *         version already exits
-	 */
-	private boolean addApplicationVersion(Versions applicationVersions,
-			ApplicationProfile applicationProfile, String profileURL) {
-		Version latestVersion = applicationVersions.getLatestVersion();
-		if (latestVersion != null
-				&& latestVersion.getVersion().equals(applicationProfile.getVersion())) {
-			getLog().error(
-					String.format("%1$s version %2$s has already been deployed",
-							applicationProfile.getName(), applicationProfile.getVersion()));
-			return false;
-		}
-
-		Version newApplicationVersion = new Version();
-		newApplicationVersion.setVersion(applicationProfile.getVersion());
-		newApplicationVersion.setFile(profileURL);
-
-		getLog().info(
-				String.format("Adding %1$s version %2$s", applicationProfile.getName(),
-						applicationProfile.getVersion()));
-		if (applicationVersions.getLatestVersion() != null) {
-			applicationVersions.getPreviousVersion().add(applicationVersions.getLatestVersion());
-		}
-		applicationVersions.setLatestVersion(newApplicationVersion);
-		return true;
-	}
-
-	/**
-	 * @param requiredBundles
-	 * @throws MojoExecutionException
-	 */
-	private void uploadBundles(Set<BundleInfo> requiredBundles, Wagon wagon) throws MojoExecutionException {
-		File libDirectory = new File(tempDirectory, "lib");
-		for (BundleInfo bundle : requiredBundles) {
-			Utils.uploadFile(new File(libDirectory, bundle.getFileName()), "lib/" + bundle.getFileName(), wagon, getLog());
-		}
-	}
-
-	private Set<BundleInfo> getRequiredBundles(ApplicationProfile currentProfile,
-			ApplicationProfile newProfile) {
-		Set<BundleInfo> requiredBundles = new HashSet<BundleInfo>();
-		Map<String, BundleInfo> currentBundles = new HashMap<String, BundleInfo>();
-		for (BundleInfo bundle : currentProfile.getBundle()) {
-			currentBundles.put(bundle.getSymbolicName(), bundle);
-		}
-		for (BundleInfo bundle : newProfile.getBundle()) {
-			if (currentBundles.containsKey(bundle.getSymbolicName())) {
-				BundleInfo currentBundle = currentBundles.get(bundle.getSymbolicName());
-				if (!bundle.getVersion().equals(currentBundle.getVersion())) {
-					requiredBundles.add(bundle);
-				}
-			} else {
-				requiredBundles.add(bundle);
-			}
-		}
-		return requiredBundles;
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaProfileGenerateMojo.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaProfileGenerateMojo.java b/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaProfileGenerateMojo.java
deleted file mode 100644
index 879885e..0000000
--- a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/TavernaProfileGenerateMojo.java
+++ /dev/null
@@ -1,216 +0,0 @@
-/**
- * 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.
- */
-package net.sf.taverna.t2.maven.plugins;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Marshaller;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.maven.artifact.Artifact;
-import org.apache.maven.plugin.AbstractMojo;
-import org.apache.maven.plugin.MojoExecutionException;
-import org.apache.maven.plugin.MojoFailureException;
-import org.apache.maven.plugins.annotations.Component;
-import org.apache.maven.plugins.annotations.LifecyclePhase;
-import org.apache.maven.plugins.annotations.Mojo;
-import org.apache.maven.plugins.annotations.Parameter;
-import org.apache.maven.plugins.annotations.ResolutionScope;
-import org.apache.maven.project.MavenProject;
-import org.apache.maven.project.ProjectDependenciesResolver;
-import org.apache.maven.shared.osgi.DefaultMaven2OsgiConverter;
-import org.apache.maven.shared.osgi.Maven2OsgiConverter;
-import org.apache.taverna.profile.xml.jaxb.ApplicationProfile;
-import org.apache.taverna.profile.xml.jaxb.BundleInfo;
-import org.apache.taverna.profile.xml.jaxb.FrameworkConfiguration;
-import org.apache.taverna.profile.xml.jaxb.Updates;
-import org.eclipse.aether.RepositorySystemSession;
-
-/**
- * Generates an application profile file.
- *
- * @author David Withers
- */
-@Mojo(name = "profile-generate", defaultPhase = LifecyclePhase.GENERATE_RESOURCES, requiresDependencyResolution = ResolutionScope.RUNTIME)
-public class TavernaProfileGenerateMojo extends AbstractMojo {
-
-	public static final String SYSTEM_PACKAGES = "org.osgi.framework.system.packages.extra";
-
-	public static final String SCHEMA_LOCATION = "http://ns.taverna.org.uk/2013/application/profile http://localhost/2013/application/profile/ApplicationProfile.xsd";
-
-	public static final String TAVERNA_TMP = "taverna-tmp";
-
-	public static final String APPLICATION_PROFILE_FILE = "ApplicationProfile.xml";
-
-	@Component
-	private MavenProject project;
-
-	@Component
-	private ProjectDependenciesResolver projectDependenciesResolver;
-
-	@Parameter(defaultValue = "${repositorySystemSession}", readonly = true)
-	private RepositorySystemSession repositorySystemSession;
-
-	/**
-	 * The directory where the generated <code>ApplicationProfile.xml</code> file will be put.
-	 */
-	@Parameter(defaultValue = "${project.build.directory}", required = true)
-	protected File outputDirectory;
-
-	@Parameter(defaultValue = "SNAPSHOT")
-	private String buildNumber;
-
-	@Parameter
-	private List<FrameworkConfiguration> frameworkConfigurations;
-
-	@Parameter(required = true)
-	private String updateSite;
-
-	@Parameter(defaultValue = "updates.xml")
-	private String updatesFile;
-
-	@Parameter(defaultValue = "lib")
-	private String libDirectory;
-
-	@Parameter(required = true)
-	private String pluginSite;
-
-	@Parameter(defaultValue = "plugins.xml")
-	private String pluginsFile;
-
-	private Maven2OsgiConverter maven2OsgiConverter = new DefaultMaven2OsgiConverter();
-
-	private MavenOsgiUtils osgiUtils;
-
-	private File tempDirectory;
-
-	public void execute() throws MojoExecutionException, MojoFailureException {
-		try {
-			osgiUtils = new MavenOsgiUtils(project, repositorySystemSession,
-					projectDependenciesResolver, getSystemPackages(), getLog());
-			tempDirectory = new File(outputDirectory, TAVERNA_TMP);
-
-			File profileFile = createApplicationProfile();
-			project.getArtifact().setFile(profileFile);
-
-			copyDependencies();
-
-		} catch (JAXBException e) {
-			throw new MojoExecutionException("Error generating application profile", e);
-		}
-	}
-
-	private void copyDependencies() throws MojoExecutionException {
-		File libDirectory = new File(tempDirectory, "lib");
-		libDirectory.mkdirs();
-
-		try {
-			for (Artifact artifact : project.getArtifacts()) {
-				FileUtils.copyFileToDirectory(artifact.getFile(),
-						new File(libDirectory, artifact.getGroupId()));
-			}
-		} catch (IOException e) {
-			throw new MojoExecutionException("Error copying dependecies to lib directory", e);
-		}
-
-	}
-
-	/**
-	 * Generates the application profile file.
-	 *
-	 * @return the <code>File</code> that the application profile has been written to
-	 * @throws JAXBException
-	 *             if the application profile cannot be created
-	 * @throws MojoExecutionException
-	 */
-	private File createApplicationProfile() throws JAXBException, MojoExecutionException {
-		String groupId = project.getGroupId();
-		String artifactId = project.getArtifactId();
-		String version = maven2OsgiConverter.getVersion(project.getVersion());
-		if (version.endsWith("SNAPSHOT")) {
-			version = version.substring(0, version.indexOf("SNAPSHOT")) + buildNumber;
-		}
-
-		tempDirectory.mkdirs();
-		File applicationProfileFile = new File(tempDirectory, APPLICATION_PROFILE_FILE);
-
-		ApplicationProfile applicationProfile = new ApplicationProfile();
-		applicationProfile.setId(groupId + "." + artifactId);
-		applicationProfile.setName(project.getName());
-		applicationProfile.setVersion(version);
-
-		Updates updates = new Updates();
-		updates.setUpdateSite(updateSite);
-		updates.setUpdatesFile(updatesFile);
-		updates.setLibDirectory(libDirectory);
-		updates.setPluginSite(pluginSite);
-		updates.setPluginsFile(pluginsFile);
-		applicationProfile.setUpdates(updates);
-
-		List<FrameworkConfiguration> frameworkConfiguration = applicationProfile
-				.getFrameworkConfiguration();
-		for (FrameworkConfiguration configuration : frameworkConfigurations) {
-			frameworkConfiguration.add(configuration);
-		}
-
-		Set<BundleArtifact> bundleDependencies = osgiUtils.getBundleDependencies(
-				Artifact.SCOPE_COMPILE, Artifact.SCOPE_RUNTIME);
-		List<BundleInfo> runtimeBundles = osgiUtils.getBundles(bundleDependencies);
-		if (!runtimeBundles.isEmpty()) {
-			List<BundleInfo> bundles = applicationProfile.getBundle();
-			for (BundleInfo bundle : runtimeBundles) {
-				bundles.add(bundle);
-			}
-		}
-
-		JAXBContext jaxbContext = JAXBContext.newInstance(ApplicationProfile.class);
-		Marshaller marshaller = jaxbContext.createMarshaller();
-		marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
-		marshaller.setProperty(Marshaller.JAXB_SCHEMA_LOCATION, SCHEMA_LOCATION);
-		marshaller.marshal(applicationProfile, applicationProfileFile);
-
-		return applicationProfileFile;
-	}
-
-	private Set<String> getSystemPackages() {
-		Set<String> systemPackages = new HashSet<String>();
-		if (frameworkConfigurations != null) {
-			for (FrameworkConfiguration configuration : frameworkConfigurations) {
-				if (SYSTEM_PACKAGES.equals(configuration.getName())) {
-					String packagesString = configuration.getValue();
-					if (packagesString != null) {
-						String[] packages = packagesString.split(",");
-						for (String packageString : packages) {
-							String[] packageProperties = packageString.split(";");
-							if (packageProperties.length > 0) {
-								systemPackages.add(packageProperties[0]);
-							}
-						}
-					}
-				}
-			}
-		}
-		return systemPackages;
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/Utils.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/Utils.java b/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/Utils.java
deleted file mode 100644
index a1c8395..0000000
--- a/taverna-maven-plugin/src/main/java/net/sf/taverna/t2/maven/plugins/Utils.java
+++ /dev/null
@@ -1,167 +0,0 @@
-/**
- * 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.
- */
-package net.sf.taverna.t2.maven.plugins;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.URLEncoder;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.Date;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.commons.codec.digest.DigestUtils;
-import org.apache.commons.io.FileUtils;
-import org.apache.maven.plugin.MojoExecutionException;
-import org.apache.maven.plugin.logging.Log;
-import org.apache.maven.wagon.ResourceDoesNotExistException;
-import org.apache.maven.wagon.TransferFailedException;
-import org.apache.maven.wagon.Wagon;
-import org.apache.maven.wagon.authorization.AuthorizationException;
-
-/**
- * @author David Withers
- */
-public class Utils {
-
-	public static String uploadFile(File file, String resourceName, Wagon wagon, Log log)
-			throws MojoExecutionException {
-		String resourceUrl = getResourceUrl(wagon, resourceName);
-		File digestFile = new File(file.getPath() + ".md5");
-		try {
-			String digestString = DigestUtils.md5Hex(new FileInputStream(file));
-			FileUtils.writeStringToFile(digestFile, digestString);
-		} catch (IOException e) {
-			throw new MojoExecutionException(
-					String.format("Error generating digest for %1$s", file), e);
-		}
-		try {
-			log.info(String.format("Uploading %1$s to %2$s", file, resourceUrl));
-			wagon.put(file, resourceName);
-			wagon.put(digestFile, resourceName + ".md5");
-		} catch (TransferFailedException e) {
-			throw new MojoExecutionException(String.format("Error transferring %1$s to %2$s", file,
-					resourceUrl), e);
-		} catch (ResourceDoesNotExistException e) {
-			throw new MojoExecutionException(String.format("%1$s does not exist", resourceUrl), e);
-		} catch (AuthorizationException e) {
-			throw new MojoExecutionException(String.format(
-					"Authentication error transferring %1$s to %2$s", file, resourceUrl), e);
-		}
-		return resourceUrl;
-	}
-
-	public static void downloadFile(String resourceName, File file, Wagon wagon, Log log)
-			throws MojoExecutionException, ResourceDoesNotExistException {
-		String resourceUrl = getResourceUrl(wagon, resourceName);
-		File digestFile = new File(file.getPath() + ".md5");
-		try {
-			log.info(String.format("Downloading %1$s to %2$s", resourceUrl, file));
-			wagon.get(resourceName, file);
-			wagon.get(resourceName + ".md5", digestFile);
-		} catch (TransferFailedException e) {
-			throw new MojoExecutionException(String.format("Error transferring %1$s to %2$s",
-					resourceUrl, file), e);
-		} catch (AuthorizationException e) {
-			throw new MojoExecutionException(String.format(
-					"Authentication error transferring %1$s to %2$s", resourceUrl, file), e);
-		}
-		try {
-			String digestString1 = DigestUtils.md5Hex(new FileInputStream(file));
-			String digestString2 = FileUtils.readFileToString(digestFile);
-			if (!digestString1.equals(digestString2)) {
-				throw new MojoExecutionException(String.format(
-						"Error downloading file: digsests not equal. (%1$s != %2$s)",
-						digestString1, digestString2));
-			}
-		} catch (IOException e) {
-			throw new MojoExecutionException(String.format("Error checking digest for %1$s", file),
-					e);
-		}
-	}
-
-	public static String getResourceUrl(Wagon wagon, String resourceName) {
-		StringBuilder urlBuilder = new StringBuilder(wagon.getRepository().getUrl());
-		for (String part : resourceName.split("/")) {
-			urlBuilder.append('/');
-			urlBuilder.append(URLEncoder.encode(part));
-		}
-		return urlBuilder.toString();
-	}
-
-	public static String timestamp() {
-		SimpleDateFormat dateFormat = new SimpleDateFormat("yyyyMMdd'T'HHmm");
-		return dateFormat.format(new Date());
-	}
-
-	public static Set<String> getJavaPackages(Log log) {
-		Set<String> javaPackages = new HashSet<String>();
-		InputStream resource = Utils.class.getClassLoader().getResourceAsStream("java7-packages");
-		if (resource != null) {
-			BufferedReader reader = new BufferedReader(new InputStreamReader(resource));
-			try {
-				String line = reader.readLine();
-				while (line != null) {
-					if (!line.isEmpty() && ! line.startsWith("#")) {
-						javaPackages.add(line.trim());
-					}
-					line = reader.readLine();
-				}
-			} catch (IOException e) {
-				log.warn(
-						"Problem while reading to readinf java package list from resource file java7-packages",
-						e);
-			}
-		} else {
-			log.warn("Unable to read java package list from resource file java7-packages");
-		}
-		return javaPackages;
-	}
-
-	public static <T> List<Set<T>> getSubsets(Set<T> set) {
-		List<Set<T>> subsets = new ArrayList<Set<T>>();
-        List<T> list = new ArrayList<T>(set);
-		int numOfSubsets = 1 << set.size();
-		for (int i = 0; i < numOfSubsets; i++){
-			Set<T> subset = new HashSet<T>();
-		    for (int j = 0; j < numOfSubsets; j++){
-		        if (((i>>j) & 1) == 1) {
-		            subset.add(list.get(j));
-		        }
-		    }
-		    if (!subset.isEmpty()) {
-		    	subsets.add(subset);
-		    }
-		}
-		Collections.sort(subsets, new Comparator<Set<T>>() {
-			@Override
-			public int compare(Set<T> o1, Set<T> o2) {
-				return o1.size() - o2.size();
-			}
-		});
-		return subsets;
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/AbstractDeployMojo.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/AbstractDeployMojo.java b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/AbstractDeployMojo.java
new file mode 100644
index 0000000..c9feec1
--- /dev/null
+++ b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/AbstractDeployMojo.java
@@ -0,0 +1,52 @@
+/**
+ * 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.
+ */
+package org.apache.taverna.mavenplugin;
+
+import java.io.File;
+
+import org.apache.maven.artifact.Artifact;
+import org.apache.maven.artifact.repository.ArtifactRepository;
+import org.apache.maven.plugins.annotations.Component;
+import org.apache.maven.plugins.annotations.Parameter;
+import org.apache.maven.project.MavenProject;
+
+/**
+ * Abstract Mojo for deploying artifacts.
+ *
+ * @author David Withers
+ */
+public abstract class AbstractDeployMojo extends AbstractWagonMojo {
+
+	@Component
+	protected MavenProject project;
+
+	/**
+	 * Directory containing the generated Taverna plugin.
+	 */
+	@Parameter(defaultValue = "${project.build.directory}", required = true)
+	protected File buildDirectory;
+
+	@Parameter(defaultValue = "${project.build.outputDirectory}", required = true)
+	protected File outputDirectory;
+
+	@Parameter(defaultValue = "${project.artifact}", required = true, readonly = true)
+	protected Artifact artifact;
+
+	@Parameter(defaultValue = "${project.distributionManagementArtifactRepository}", required = true, readonly = true)
+	protected ArtifactRepository deploymentRepository;
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-osgi/blob/c660ed5c/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/AbstractWagonMojo.java
----------------------------------------------------------------------
diff --git a/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/AbstractWagonMojo.java b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/AbstractWagonMojo.java
new file mode 100644
index 0000000..7844a2a
--- /dev/null
+++ b/taverna-maven-plugin/src/main/java/org/apache/taverna/mavenplugin/AbstractWagonMojo.java
@@ -0,0 +1,56 @@
+/**
+ * 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.
+ */
+package org.apache.taverna.mavenplugin;
+
+import org.apache.maven.artifact.manager.WagonManager;
+import org.apache.maven.plugin.AbstractMojo;
+import org.apache.maven.plugins.annotations.Component;
+import org.apache.maven.wagon.ConnectionException;
+import org.apache.maven.wagon.Wagon;
+import org.apache.maven.wagon.observers.Debug;
+
+/**
+ * Abstract Mojo for using the wagon.
+ *
+ * @author David Withers
+ */
+public abstract class AbstractWagonMojo extends AbstractMojo {
+
+	@Component
+	protected WagonManager wagonManager;
+
+	/**
+	 * Disconnect the wagon.
+	 *
+	 * @param wagon
+	 *            the wagon to disconnect
+	 * @param debug
+	 */
+	protected void disconnectWagon(Wagon wagon, Debug debug) {
+		if (getLog().isDebugEnabled()) {
+			wagon.removeTransferListener(debug);
+			wagon.removeSessionListener(debug);
+		}
+		try {
+			wagon.disconnect();
+		} catch (ConnectionException e) {
+			getLog().error("Error disconnecting wagon - ignored", e);
+		}
+	}
+
+
+}