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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:39:54 UTC

[03/51] [partial] incubator-taverna-language git commit: temporarily empty repository

http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-scufl2-ucfpackage/LICENSE-odfdom.txt
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diff --git a/taverna-scufl2-ucfpackage/LICENSE-odfdom.txt b/taverna-scufl2-ucfpackage/LICENSE-odfdom.txt
deleted file mode 100644
index 29f81d8..0000000
--- a/taverna-scufl2-ucfpackage/LICENSE-odfdom.txt
+++ /dev/null
@@ -1,201 +0,0 @@
-                                 Apache License
-                           Version 2.0, January 2004
-                        http://www.apache.org/licenses/
-
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http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-scufl2-ucfpackage/pom.xml
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diff --git a/taverna-scufl2-ucfpackage/pom.xml b/taverna-scufl2-ucfpackage/pom.xml
deleted file mode 100644
index 5411dc0..0000000
--- a/taverna-scufl2-ucfpackage/pom.xml
+++ /dev/null
@@ -1,105 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-   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.
--->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-	<modelVersion>4.0.0</modelVersion>
-	<parent>
-		<groupId>org.apache.taverna.language</groupId>
-		<artifactId>taverna-language</artifactId>
-		<version>0.16.1-incubating-SNAPSHOT</version>
-	</parent>
-	<artifactId>taverna-scufl2-ucfpackage</artifactId>
-	<packaging>bundle</packaging>
-	<name>Apache Taverna Scufl 2 UCF Package</name>
-	<description>Adobe UCF compatible Package API, making a structured ZIP file with manifest</description>
-	<dependencies>
-		<dependency>
-			<groupId>commons-io</groupId>
-			<artifactId>commons-io</artifactId>
-      <version>${commons.io.version}</version>
-			<scope>test</scope>
-		</dependency>
-		<dependency>
-      <groupId>org.jdom</groupId>
-      <artifactId>com.springsource.org.jdom</artifactId>
-      <version>${jdom.version}</version>
-			<scope>test</scope>
-		</dependency>
-		<dependency>
-			<groupId>org.jaxen</groupId>
-			<artifactId>com.springsource.org.jaxen</artifactId>
-      <version>${jaxen.version}</version>
-			<scope>test</scope>
-		</dependency>
-	</dependencies>
-	<licenses>
-		<license>
-			<name>Apache 2</name>
-			<url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
-			<comments>The package uk.org.taverna.scul2.ucfpackage.impl.odfdom
-				contains a patched subset of ODFDOM 0.8.6 -
-				http://odftoolkit.org/projects/odfdom/pages/Home
-				Copyright 2008, 2010 Oracle and/or its affiliates.
-				All rights reserved. Copyright 2009 IBM. All rights reserved.</comments>
-		</license>
-	</licenses>
-
-	<build>
-		<plugins>
-      <!--
-			<plugin>
-				<groupId>org.codehaus.mojo</groupId>
-				<artifactId>jaxb2-maven-plugin</artifactId>
-				<executions>
-					<execution>
-						<id>jaxb</id>
-						<phase>generate-sources</phase>
-						<goals>
-							<goal>xjc</goal>
-						</goals>
-					</execution>
-				</executions>
-			</plugin>
-      -->
-            <plugin>
-                <groupId>org.jvnet.jaxb2.maven2</groupId>
-                <artifactId>maven-jaxb2-plugin</artifactId>
-                <executions>
-                    <execution>
-                        <goals>
-                            <goal>generate</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
-
-	            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-compiler-plugin</artifactId>
-                <configuration>
-                    <source>1.7</source>
-                    <target>1.7</target>
-                </configuration>
-            </plugin>
-                <plugin>
-        <groupId>org.apache.rat</groupId>
-        <artifactId>apache-rat-plugin</artifactId>
-      </plugin>
-                  </plugins>
-            </build>
-	<!-- -->
-</project>

http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-scufl2-ucfpackage/src/main/java/org/apache/taverna/scufl2/ucfpackage/UCFPackage.java
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diff --git a/taverna-scufl2-ucfpackage/src/main/java/org/apache/taverna/scufl2/ucfpackage/UCFPackage.java b/taverna-scufl2-ucfpackage/src/main/java/org/apache/taverna/scufl2/ucfpackage/UCFPackage.java
deleted file mode 100644
index b806ffe..0000000
--- a/taverna-scufl2-ucfpackage/src/main/java/org/apache/taverna/scufl2/ucfpackage/UCFPackage.java
+++ /dev/null
@@ -1,664 +0,0 @@
-package org.apache.taverna.scufl2.ucfpackage;
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
-*/
-
-
-import static java.io.File.createTempFile;
-import static java.util.logging.Level.INFO;
-
-import java.io.BufferedInputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.io.PipedInputStream;
-import java.io.PipedOutputStream;
-import java.net.URI;
-import java.nio.charset.Charset;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.logging.Logger;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Marshaller;
-import javax.xml.bind.Unmarshaller;
-
-import org.apache.taverna.scufl2.ucfpackage.impl.odfdom.pkg.OdfPackage;
-import org.apache.taverna.scufl2.ucfpackage.impl.odfdom.pkg.manifest.OdfFileEntry;
-import org.oasis_open.names.tc.opendocument.xmlns.container.Container;
-import org.oasis_open.names.tc.opendocument.xmlns.container.Container.RootFiles;
-import org.oasis_open.names.tc.opendocument.xmlns.container.ObjectFactory;
-import org.oasis_open.names.tc.opendocument.xmlns.container.RootFile;
-import org.w3c.dom.Document;
-
-
-public class UCFPackage implements Cloneable {
-	private static Logger logger = Logger.getLogger(UCFPackage.class.getName());
-	private static final String CONTAINER_XML = "META-INF/container.xml";
-	private static final Charset UTF_8 = Charset.forName("utf-8");
-	public static final String MIME_BINARY = "application/octet-stream";
-	public static final String MIME_TEXT_PLAIN = "text/plain";
-	public static final String MIME_TEXT_XML = "text/xml";
-	public static final String MIME_RDF = "application/rdf+xml";
-	public static final String MIME_EPUB = "application/epub+zip";
-	public static final String MIME_WORKFLOW_BUNDLE = "application/vnd.taverna.workflow-bundle";
-	public static final String MIME_DATA_BUNDLE = "application/vnd.taverna.data-bundle";
-	public static final String MIME_WORKFLOW_RUN_BUNDLE = "application/vnd.taverna.workflow-run-bundle";
-	public static final String MIME_SERVICE_BUNDLE = "application/vnd.taverna.service-bundle";
-
-	private static Charset ASCII = Charset.forName("ascii");
-	private OdfPackage odfPackage;
-	private static JAXBContext jaxbContext;
-	private JAXBElement<Container> containerXml;
-	private boolean createdContainerXml = false;
-	private static ObjectFactory containerFactory = new ObjectFactory();
-
-	public UCFPackage() throws IOException {
-		try {
-			odfPackage = OdfPackage.create();
-			parseContainerXML();
-		} catch (IOException e) {
-			throw e;
-		} catch (Exception e) {
-			throw new IOException("Could not create empty UCF Package", e);
-		}
-		// odfPackage.setMediaType(MIME_EPUB);
-	}
-
-	public UCFPackage(File containerFile) throws IOException {
-		open(containerFile);
-	}
-
-	protected void open(File containerFile) throws IOException {
-		try (BufferedInputStream stream = new BufferedInputStream(
-				new FileInputStream(containerFile))) {
-			open(stream);
-		}
-	}
-
-	public UCFPackage(InputStream inputStream) throws IOException {
-		open(inputStream);
-	}
-
-	protected void open(InputStream inputStream) throws IOException {
-		try {
-			odfPackage = OdfPackage.loadPackage(inputStream);
-			parseContainerXML();
-		} catch (IOException e) {
-			throw e;
-		} catch (Exception e) {
-			throw new IOException(
-					"Could not load UCF Package from input stream", e);
-		}
-	}
-
-	@SuppressWarnings("unchecked")
-	protected void parseContainerXML() throws IOException {
-		createdContainerXml = false;
-		InputStream containerStream = getResourceAsInputStream(CONTAINER_XML);
-		if (containerStream == null) {
-			// Make an empty containerXml
-			Container container = containerFactory.createContainer();
-			containerXml = containerFactory.createContainer(container);
-			createdContainerXml = true;
-			return;
-		}
-		try {
-			Unmarshaller unMarshaller = createUnMarshaller();
-			containerXml = (JAXBElement<Container>) unMarshaller
-					.unmarshal(containerStream);
-		} catch (JAXBException e) {
-			throw new IOException("Could not parse " + CONTAINER_XML, e);
-		}
-	}
-
-	public String getPackageMediaType() {
-		return odfPackage.getMediaType();
-	}
-
-	public void setPackageMediaType(String mediaType) {
-		if (mediaType == null || !mediaType.contains("/"))
-			throw new IllegalArgumentException("Invalid media type "
-					+ mediaType);
-		if (!ASCII.newEncoder().canEncode(mediaType))
-			throw new IllegalArgumentException("Media type must be ASCII: "
-					+ mediaType);
-		odfPackage.setMediaType(mediaType);
-	}
-
-	public void save(File packageFile) throws IOException {
-		File tempFile = createTempFile("." + packageFile.getName(), ".tmp",
-				packageFile.getCanonicalFile().getParentFile());
-		prepareAndSave(tempFile);
-		boolean renamed = tempFile.renameTo(packageFile);
-		if (!renamed && packageFile.exists() && tempFile.exists()) {
-			// Could happen on Windows
-			if (!packageFile.delete())
-				// Could have been permission problem
-				throw new IOException("Could not delete existing "
-						+ packageFile);
-			renamed = tempFile.renameTo(packageFile);
-		}
-		if (!renamed)
-			throw new IOException("Could not rename temp file " + tempFile
-					+ " to " + packageFile);
-	}
-
-	protected void prepareAndSave(File tempFile) throws IOException {
-		if (getPackageMediaType() == null)
-			throw new IllegalStateException("Package media type must be set");
-
-		// Write using temp file, and do rename in the end
-
-		try {
-			prepareContainerXML();
-			odfPackage.save(tempFile);
-		} catch (IOException e) {
-			throw e;
-		} catch (Exception e) {
-			throw new IOException("Could not save bundle to " + tempFile, e);
-		} finally {
-			odfPackage.close();
-		}
-
-		try {
-			open(tempFile);
-		} catch (Exception e) {
-			throw new IOException("Could not reload package from " + tempFile,
-					e);
-		}
-	}
-
-	protected void prepareContainerXML() throws IOException {
-		if (containerXml == null || createdContainerXml
-				&& containerXml.getValue().getRootFilesOrAny() == null)
-			return;
-
-		/* Check if we should prune <rootFiles> */
-		Iterator<Object> iterator = containerXml.getValue().getRootFilesOrAny()
-				.iterator();
-		boolean foundAlready = false;
-		while (iterator.hasNext()) {
-			Object anyOrRoot = iterator.next();
-			if (!(anyOrRoot instanceof JAXBElement))
-				continue;
-			@SuppressWarnings("rawtypes")
-			JAXBElement elem = (JAXBElement) anyOrRoot;
-			if (!elem.getDeclaredType().equals(RootFiles.class))
-				continue;
-			RootFiles rootFiles = (RootFiles) elem.getValue();
-			if (foundAlready
-					|| (rootFiles.getOtherAttributes().isEmpty() && rootFiles
-							.getAnyOrRootFile().isEmpty())) {
-				// Delete it!
-				System.err.println("Deleting unneccessary <rootFiles>");
-				iterator.remove();
-			}
-			foundAlready = true;
-		}
-
-		Marshaller marshaller;
-		try {
-			marshaller = createMarshaller();
-			// XMLStreamWriter xmlStreamWriter = XMLOutputFactory
-			// .newInstance().createXMLStreamWriter(outStream);
-			// xmlStreamWriter.setDefaultNamespace(containerElem.getName()
-			// .getNamespaceURI());
-			//
-			// xmlStreamWriter.setPrefix("dsig",
-			// "http://www.w3.org/2000/09/xmldsig#");
-			// xmlStreamWriter.setPrefix("xmlenc",
-			// "http://www.w3.org/2001/04/xmlenc#");
-			try (OutputStream outStream = odfPackage
-					.insertOutputStream(CONTAINER_XML)) {
-				// FIXME: Set namespace prefixes and default namespace
-				marshaller.setProperty("jaxb.formatted.output", true);
-				// TODO: Ensure using default namespace
-				marshaller.marshal(containerXml, outStream);
-			}
-		} catch (IOException e) {
-			throw e;
-		} catch (Exception e) {
-			throw new IOException("Could not parse " + CONTAINER_XML, e);
-		}
-	}
-
-	protected static synchronized Marshaller createMarshaller()
-			throws JAXBException {
-		return getJaxbContext().createMarshaller();
-	}
-
-	protected static synchronized Unmarshaller createUnMarshaller()
-			throws JAXBException {
-		return getJaxbContext().createUnmarshaller();
-	}
-
-	protected static synchronized JAXBContext getJaxbContext()
-			throws JAXBException {
-		if (jaxbContext == null)
-			jaxbContext = JAXBContext
-					.newInstance(
-							org.oasis_open.names.tc.opendocument.xmlns.container.ObjectFactory.class,
-							org.w3._2000._09.xmldsig_.ObjectFactory.class,
-							org.w3._2001._04.xmlenc_.ObjectFactory.class);
-		return jaxbContext;
-	}
-
-	public void addResource(String stringValue, String path, String mediaType)
-			throws IOException {
-		try {
-			odfPackage.insert(stringValue.getBytes(UTF_8), path, mediaType);
-		} catch (IOException e) {
-			throw e;
-		} catch (Exception e) {
-			throw new IOException("Could not add " + path, e);
-		}
-		parseContainerXML();
-	}
-
-	public void addResource(byte[] bytesValue, String path, String mediaType)
-			throws IOException {
-		try {
-			odfPackage.insert(bytesValue, path, mediaType);
-		} catch (IOException e) {
-			throw e;
-		} catch (Exception e) {
-			throw new IOException("Could not add " + path, e);
-		}
-		if (path.equals(CONTAINER_XML))
-			parseContainerXML();
-	}
-
-	public void addResource(Document document, String path, String mediaType)
-			throws IOException {
-		try {
-			odfPackage.insert(document, path, mediaType);
-		} catch (IOException e) {
-			throw e;
-		} catch (Exception e) {
-			throw new IOException("Could not add " + path, e);
-		}
-		if (path.equals(CONTAINER_XML))
-			parseContainerXML();
-	}
-
-	public void addResource(InputStream inputStream, String path,
-			String mediaType) throws IOException {
-		try {
-			odfPackage.insert(inputStream, path, mediaType);
-		} catch (IOException e) {
-			throw e;
-		} catch (Exception e) {
-			throw new IOException("Could not add " + path, e);
-		}
-		if (path.equals(CONTAINER_XML))
-			parseContainerXML();
-	}
-
-	public void addResource(URI uri, String path, String mediaType)
-			throws IOException {
-		try {
-			odfPackage.insert(uri, path, mediaType);
-		} catch (IOException e) {
-			throw e;
-		} catch (Exception e) {
-			throw new IOException("Could not add " + path, e);
-		}
-
-		if (path.equals(CONTAINER_XML))
-			parseContainerXML();
-	}
-
-	public String getResourceAsString(String path) throws IOException {
-		try {
-			return new String(odfPackage.getBytes(path), UTF_8);
-		} catch (IOException e) {
-			throw e;
-		} catch (Exception e) {
-			throw new IOException("Could not get " + path, e);
-		}
-	}
-
-	public byte[] getResourceAsBytes(String path) throws IOException {
-		try {
-			return odfPackage.getBytes(path);
-		} catch (IOException e) {
-			throw e;
-		} catch (Exception e) {
-			throw new IOException("Could not get " + path, e);
-		}
-	}
-
-	public InputStream getResourceAsInputStream(String path) throws IOException {
-		try {
-			return odfPackage.getInputStream(path);
-		} catch (IOException e) {
-			throw e;
-		} catch (Exception e) {
-			throw new IOException("Could not get " + path, e);
-		}
-	}
-
-	public Map<String, ResourceEntry> listResources() {
-		return listResources("", false);
-	}
-
-	public Map<String, ResourceEntry> listResources(String folderPath) {
-		return listResources(folderPath, false);
-	}
-
-	protected Map<String, ResourceEntry> listResources(String folderPath,
-			boolean recursive) {
-		if (!folderPath.isEmpty() && !folderPath.endsWith("/"))
-			folderPath = folderPath + "/";
-		HashMap<String, ResourceEntry> content = new HashMap<>();
-
-		for (Entry<String, OdfFileEntry> entry : odfPackage
-				.getManifestEntries().entrySet()) {
-			String entryPath = entry.getKey();
-			if (!entryPath.startsWith(folderPath))
-				continue;
-			String subPath = entryPath.substring(folderPath.length(),
-					entryPath.length());
-			if (subPath.isEmpty())
-				// The folder itself
-				continue;
-			int firstSlash = subPath.indexOf("/");
-			if (!recursive && firstSlash > -1
-					&& firstSlash < subPath.length() - 1)
-				/*
-				 * Children of a folder (note that we'll include the folder
-				 * itself which ends in /)
-				 */
-				continue;
-			content.put(subPath, new ResourceEntry(entry.getValue()));
-		}
-		return content;
-	}
-
-	public void removeResource(String path) {
-		if (!odfPackage.contains(path))
-			return;
-		if (path.endsWith("/"))
-			for (ResourceEntry childEntry : listResources(path).values())
-				removeResource(childEntry.getPath());
-		odfPackage.remove(path);
-	}
-
-	public class ResourceEntry {
-		private final String path;
-		private final long size;
-		private String mediaType;
-		private String version;
-
-		protected ResourceEntry(OdfFileEntry odfEntry) {
-			path = odfEntry.getPath();
-			size = odfEntry.getSize();
-			mediaType = odfEntry.getMediaType();
-			version = odfEntry.getVersion();
-		}
-
-		public String getPath() {
-			return path;
-		}
-
-		public long getSize() {
-			return size;
-		}
-
-		public String getMediaType() {
-			return mediaType;
-		}
-
-		public boolean isFolder() {
-			return path.endsWith("/");
-		}
-
-		public UCFPackage getUcfPackage() {
-			return UCFPackage.this;
-		}
-
-		@Override
-		public boolean equals(Object obj) {
-			if (!(obj instanceof ResourceEntry))
-				return false;
-			ResourceEntry other = (ResourceEntry) obj;
-
-			if (!getUcfPackage().equals(other.getUcfPackage()))
-				return false;
-			return getPath().equals(other.getPath());
-		}
-
-		@Override
-		public int hashCode() {
-			final int prime = 31;
-			int result = 1;
-			result = prime * result + getUcfPackage().hashCode();
-			result = prime * result + ((path == null) ? 0 : path.hashCode());
-			return result;
-		}
-
-		public String getVersion() {
-			return version;
-		}
-	}
-
-	public Map<String, ResourceEntry> listAllResources() {
-		return listResources("", true);
-	}
-
-	public void setRootFile(String path) {
-		setRootFile(path, null);
-	}
-
-	@SuppressWarnings("rawtypes")
-	public void setRootFile(String path, String version) {
-		ResourceEntry rootFile = getResourceEntry(path);
-		if (rootFile == null)
-			throw new IllegalArgumentException("Unknown resource: " + path);
-		odfPackage.getManifestEntries().get(path).setVersion(version);
-
-		Container container = containerXml.getValue();
-
-		RootFiles rootFiles = getRootFiles(container);
-		String mediaType = rootFile.getMediaType();
-		boolean foundExisting = false;
-		// Check any existing files for matching path/mime type
-		Iterator<Object> anyOrRootIt = rootFiles.getAnyOrRootFile().iterator();
-		while (anyOrRootIt.hasNext()) {
-			Object anyOrRoot = anyOrRootIt.next();
-			if (anyOrRoot instanceof JAXBElement)
-				anyOrRoot = ((JAXBElement) anyOrRoot).getValue();
-			if (!(anyOrRoot instanceof RootFile))
-				continue;
-			RootFile rootFileElem = (RootFile) anyOrRoot;
-			if (!rootFileElem.getFullPath().equals(path)
-					&& !rootFileElem.getMediaType().equals(mediaType))
-				// Different path and media type - ignore
-				continue;
-			if (foundExisting) {
-				// Duplicate path/media type, we'll remove it
-				anyOrRootIt.remove();
-				continue;
-			}
-			rootFileElem.setFullPath(rootFile.getPath());
-			if (mediaType != null)
-				rootFileElem.setMediaType(mediaType);
-
-			foundExisting = true;
-		}
-		if (!foundExisting) {
-			RootFile rootFileElem = containerFactory.createRootFile();
-			rootFileElem.setFullPath(rootFile.getPath());
-			rootFileElem.setMediaType(mediaType);
-			rootFiles.getAnyOrRootFile().add(
-					containerFactory
-							.createContainerRootFilesRootFile(rootFileElem));
-			// rootFiles.getAnyOrRootFile().add(rootFileElem);
-		}
-	}
-
-	protected RootFiles getRootFiles(Container container) {
-		for (Object o : container.getRootFilesOrAny()) {
-			if (o instanceof JAXBElement) {
-				@SuppressWarnings("rawtypes")
-				JAXBElement jaxbElement = (JAXBElement) o;
-				o = jaxbElement.getValue();
-			}
-			if (o instanceof RootFiles)
-				return (RootFiles) o;
-		}
-		// Not found - add it
-		RootFiles rootFiles = containerFactory.createContainerRootFiles();
-		container.getRootFilesOrAny().add(
-				containerFactory.createContainerRootFiles(rootFiles));
-		return rootFiles;
-	}
-
-	@SuppressWarnings("rawtypes")
-	public List<ResourceEntry> getRootFiles() {
-		ArrayList<UCFPackage.ResourceEntry> rootFiles = new ArrayList<>();
-		if (containerXml == null)
-			return rootFiles;
-
-		RootFiles rootFilesElem = getRootFiles(containerXml.getValue());
-		for (Object anyOrRoot : rootFilesElem.getAnyOrRootFile()) {
-			if (anyOrRoot instanceof JAXBElement)
-				anyOrRoot = ((JAXBElement) anyOrRoot).getValue();
-			if (!(anyOrRoot instanceof RootFile))
-				continue;
-			RootFile rf = (RootFile) anyOrRoot;
-			ResourceEntry entry = getResourceEntry(rf.getFullPath());
-			if (rf.getMediaType() != null
-					&& rf.getMediaType() != entry.mediaType)
-				// Override the mime type in the returned entry
-				entry.mediaType = rf.getMediaType();
-			rootFiles.add(entry);
-		}
-		return rootFiles;
-	}
-
-	public ResourceEntry getResourceEntry(String path) {
-		OdfFileEntry odfFileEntry = odfPackage.getManifestEntries().get(path);
-		if (odfFileEntry == null)
-			return null;
-		return new ResourceEntry(odfFileEntry);
-	}
-
-	@SuppressWarnings("rawtypes")
-	public void unsetRootFile(String path) {
-		Container container = containerXml.getValue();
-		RootFiles rootFiles = getRootFiles(container);
-		Iterator<Object> anyOrRootIt = rootFiles.getAnyOrRootFile().iterator();
-		while (anyOrRootIt.hasNext()) {
-			Object anyOrRoot = anyOrRootIt.next();
-			if (anyOrRoot instanceof JAXBElement)
-				anyOrRoot = ((JAXBElement) anyOrRoot).getValue();
-			if (!(anyOrRoot instanceof RootFile))
-				continue;
-			RootFile rootFileElem = (RootFile) anyOrRoot;
-			if (rootFileElem.getFullPath().equals(path))
-				anyOrRootIt.remove();
-		}
-	}
-
-	protected JAXBElement<Container> getContainerXML() {
-		return containerXml;
-	}
-
-	public void save(OutputStream output) throws IOException {
-		File tempFile = createTempFile("ucfpackage", ".tmp");
-		prepareAndSave(tempFile);
-
-		// Copy file to the output
-
-		// Note - Should use IOUtils, but we're trying to avoid external dependencies
-		try (InputStream inStream = new FileInputStream(tempFile)) {
-			byte[] buffer = new byte[8192];
-			int n = 0;
-			do {
-				output.write(buffer, 0, n);
-				n = inStream.read(buffer);
-			} while (n > -1);
-		} finally {
-			tempFile.delete();
-		}
-	}
-
-	public OutputStream addResourceUsingOutputStream(String path,
-			String mediaType) throws IOException {
-		if (path.equals(CONTAINER_XML))
-			// as we need to parse it after insertion, this must fail
-			throw new IllegalArgumentException("Can't add " + CONTAINER_XML
-					+ " using OutputStream");
-		try {
-			return odfPackage.insertOutputStream(path, mediaType);
-		} catch (IOException e) {
-			throw e;
-		} catch (Exception e) {
-			throw new IOException("Could not add " + path, e);
-		}
-	}
-
-	@Override
-	public UCFPackage clone() {
-		final PipedOutputStream outputStream = new PipedOutputStream();
-		try {
-			try (PipedInputStream inputStream = copyToOutputStream(outputStream)) {
-				return new UCFPackage(inputStream);
-			}
-		} catch (IOException e) {
-			throw new RuntimeException("Could not clone UCFPackage", e);
-		}
-	}
-
-	private PipedInputStream copyToOutputStream(
-			final PipedOutputStream outputStream) throws IOException {
-		PipedInputStream inputStream = new PipedInputStream(outputStream);
-		new Thread("Cloning " + this) {
-			@Override
-			public void run() {
-				try {
-					try {
-						save(outputStream);
-					} finally {
-						outputStream.close();
-					}
-				} catch (IOException e) {
-					logger.log(INFO,
-							"Could not save/close UCF package while cloning", e);
-				}
-			}
-		}.start();
-		return inputStream;
-	}
-
-	public String getRootFileVersion(String rootFile) {
-		return getResourceEntry(rootFile).getVersion();
-	}
-}