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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:40:35 UTC
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http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/README.md
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-RO bundle API
-=============
-
-
-[](https://travis-ci.org/wf4ever/robundle)
-[](http://dx.doi.org/10.5072/zenodo.12703)
-
-
-
-
-
-API for building researchobject.org RO bundles.
-
-Complies with [RO bundle specification](https://w3id.org/bundle) version [1.0](https://w3id.org/bundle/2014-11-05/).
-
-This API is built on the Java 7 NIO Files and uses the
-[Java 7 ZIP file provider](http://docs.oracle.com/javase/7/docs/technotes/guides/io/fsp/zipfilesystemprovider.html) to generate the RO Bundle.
-
-The class
-[org.apache.taverna.robundle.Bundles](src/main/java/org/purl/wf4ever/robundle/Bundles.java) complements the
-Java 7 [java.nio.Files](http://docs.oracle.com/javase/7/docs/api/java/nio/file/Files.html) API
-with more specific helper methods to work with RO Bundles.
-
-This API is the basis for the [Taverna Data Bundles API](https://github.com/myGrid/databundles).
-
-
-Slides
-------
-
-[](http://www.slideshare.net/soilandreyes/diving-into-research-objects)
-
-[Slides 2014-04-24](https://onedrive.live.com/view.aspx?cid=37935FEEE4DF1087&resid=37935FEEE4DF1087%21679&app=PowerPoint&authkey=%21AI6c4YT_419J3zY&wdo=1)
-
-
-Usage
------
-
-If you use [Maven 3](http://maven.apache.org/), then add to your `pom.xml`:
-
-```xml
-<dependencies>
- <dependency>
- <groupId>org.apache.taverna.robundle</groupId>
- <artifactId>robundle</artifactId>
- <version>0.5.0</version>
- </dependency>
-</dependencies>
-<repositories>
- <repository>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository</url>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- </repository>
-</repositories>
-```
-
-To find the latest `<version>` (in case the above has not been updated), see the
-list of [robundle releases](https://github.com/wf4ever/robundle/releases). To download a precompiled
-binary JAR, see the [myGrid's Maven repository](http://www.mygrid.org.uk/maven/repository/org/purl/wf4ever/robundle/robundle/).
-
-Building
---------
-If you are building from source (this repository), then:
-
-```mvn clean install```
-
-should normally work, given a recent version of [Maven 3](http://maven.apache.org/download.cgi) and
-[Java 7 SDK](http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html).
-
-[myGrid's Jenkins installation](http://build.mygrid.org.uk/ci/) has automated builds of
-[robundle](http://build.mygrid.org.uk/ci/job/robundle/), which are deployed
-to [myGrid's snapshot Maven repository](http://www.mygrid.org.uk/maven/snapshot-repository/org/purl/wf4ever/robundle/robundle/).
-
-To use a snapshot build, add this repository to `pom.xml`:
-
-```xml
-<repository>
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
-</repository>
-```
-
-Then change your `<dependency>` to match the `-SNAPSHOT` version in this project's [pom.xml](pom.xml).
-
-
-Supported bundle formats
-------------------------
-
-* [RO bundle specification](https://w3id.org/bundle).
-* [Adobe UFC](https://wikidocs.adobe.com/wiki/display/PDFNAV/UCF+overview)
-* [ePub OCF](http://www.idpf.org/epub3/latest/ocf)
-* [Open Document package (ODF)](http://docs.oasis-open.org/office/v1.2/os/OpenDocument-v1.2-os-part3.html#__RefHeading__752807_826425813)
-* [COMBINE Archive (OMEX)](http://co.mbine.org/documents/archive)
-* [ZIP](http://www.pkware.com/documents/casestudies/APPNOTE.TXT)
-
-The `Bundles` API will load a bundle in any of the formats above, converging
-them to a [Research Object Bundle](https://w3id.org/bundle),
-while still maintaining the manifests of the other formats,
-if they exist within the bundle.
-
-Thus, if you open say a [COMBINE Archive](http://co.mbine.org/documents/archive) and add a couple of resources,
-indicating their mediatype using `bundle.getManifest().getAggregation(path).setMediaType("a/b")`, then
-when closing this bundle, the API will generate both an RO Bundle manifest and a COMBINE manifest
-that reflect this.
-
-
-
-
-Example of use
---------------
-
-Example in full is at [org.apache.taverna.robundle.TestExample](src/test/java/org/purl/wf4ever/robundle/TestExample.java)
-
-```java
- // Create a new (temporary) RO bundle
- Bundle bundle = Bundles.createBundle();
-
- // Get the inputs
- Path inputs = bundle.getRoot().resolve("inputs");
- Files.createDirectory(inputs);
-
- // Get an input port:
- Path in1 = inputs.resolve("in1");
-
- // Setting a string value for the input port:
- Bundles.setStringValue(in1, "Hello");
-
- // And retrieving it
- if (Bundles.isValue(in1)) {
- System.out.println(Bundles.getStringValue(in1));
- }
-
- // Or just use the regular Files methods:
- for (String line : Files.readAllLines(in1, Charset.forName("UTF-8"))) {
- System.out.println(line);
- }
-
- // Binaries and large files are done through the Files API
- try (OutputStream out = Files.newOutputStream(in1,
- StandardOpenOption.APPEND)) {
- out.write(32);
- }
- // Or Java 7 style
- Path localFile = Files.createTempFile("", ".txt");
- Files.copy(in1, localFile, StandardCopyOption.REPLACE_EXISTING);
- System.out.println("Written to: " + localFile);
-
- Files.copy(localFile, bundle.getRoot().resolve("out1"));
-
- // Representing references
- URI ref = URI.create("http://example.com/external.txt");
- Path out3 = bundle.getRoot().resolve("out3");
- System.out.println(Bundles.setReference(out3, ref));
- if (Bundles.isReference(out3)) {
- URI resolved = Bundles.getReference(out3);
- System.out.println(resolved);
- }
-
- // Saving a bundle:
- Path zip = Files.createTempFile("bundle", ".zip");
- Bundles.closeAndSaveBundle(bundle, zip);
- // NOTE: From now "bundle" and its Path's are CLOSED
- // and can no longer be accessed
-
- System.out.println("Saved to " + zip);
-
- // Loading a bundle back from disk
- try (Bundle bundle2 = Bundles.openBundle(zip)) {
- assertEquals(zip, bundle2.getSource());
- }
- ```
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/pom.xml
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diff --git a/taverna-robundle/pom.xml b/taverna-robundle/pom.xml
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-<?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>
- <packaging>bundle</packaging>
- <parent>
- <groupId>org.apache.taverna.language</groupId>
- <artifactId>taverna-language</artifactId>
- <version>0.16.1-incubating-SNAPSHOT</version>
- </parent>
- <artifactId>taverna-robundle</artifactId>
- <name>Apache Taverna RO Bundle API</name>
- <description>API for dealing with RO Bundles</description>
- <dependencies>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>commons-io</groupId>
- <artifactId>commons-io</artifactId>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-core</artifactId>
- </dependency>
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-annotations</artifactId>
- <version>${jackson.version}</version>
- </dependency>
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-databind</artifactId>
- </dependency>
- <dependency>
- <groupId>com.github.jsonld-java</groupId>
- <artifactId>jsonld-java</artifactId>
- <version>${jsonld.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>commons-configuration</groupId>
- <artifactId>commons-configuration</artifactId>
- <version>1.9</version>
- </dependency>
- <dependency>
- <groupId>org.apache.jena</groupId>
- <artifactId>jena-arq</artifactId>
- <version>${jena.version}</version>
- <exclusions>
- <exclusion>
- <artifactId>httpclient</artifactId>
- <groupId>org.apache.httpcomponents</groupId>
- </exclusion>
- </exclusions>
- </dependency>
-<!--
- <dependency>
- <groupId>com.sun.xml.bind</groupId>
- <artifactId>jaxb-impl</artifactId>
- <version>2.2.7</version>
- </dependency>
--->
- <dependency>
- <groupId>com.sun.xml.bind</groupId>
- <artifactId>jaxb-osgi</artifactId>
- <version>${jaxb.version}</version>
- </dependency>
-<!-- for UUIDv5 SHA named
- <dependency>
- <groupId>com.fasterxml.uuid</groupId>
- <artifactId>java-uuid-generator</artifactId>
- <version>3.1.3</version>
- <type>bundle</type>
- </dependency>
--->
- </dependencies>
-
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.felix</groupId>
- <artifactId>maven-bundle-plugin</artifactId>
- <extensions>true</extensions>
- <configuration>
- <instructions>
- <Embed-Dependency>*;groupId=com.github.jsonld-java</Embed-Dependency>
- <Embed-Transitive>true</Embed-Transitive>
- </instructions>
- </configuration>
- </plugin>
- <plugin>
- <groupId>org.codehaus.mojo</groupId>
- <artifactId>jaxb2-maven-plugin</artifactId>
- <executions>
- <execution>
- <id>jaxb-xsd</id>
- <phase>generate-sources</phase>
- <goals>
- <goal>xjc</goal>
- </goals>
- <configuration>
- <!-- <packageName>oasis.names.tc.opendocument.xmlns.manifest</packageName>-->
- </configuration>
- </execution>
- </executions>
- </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-robundle/src/main/java/org/apache/taverna/robundle/Bundle.java
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diff --git a/taverna-robundle/src/main/java/org/apache/taverna/robundle/Bundle.java b/taverna-robundle/src/main/java/org/apache/taverna/robundle/Bundle.java
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-package org.apache.taverna.robundle;
-
-/*
- * 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.nio.file.Files.deleteIfExists;
-import static java.nio.file.Files.exists;
-import static java.nio.file.Files.newInputStream;
-import static org.apache.taverna.robundle.Bundles.getManifestPath;
-
-import java.io.Closeable;
-import java.io.IOException;
-import java.io.InputStream;
-import java.nio.file.FileSystem;
-import java.nio.file.Path;
-
-import org.apache.taverna.robundle.fs.BundleFileSystem;
-import org.apache.taverna.robundle.manifest.Manifest;
-import org.apache.taverna.robundle.manifest.RDFToManifest;
-import org.apache.taverna.robundle.manifest.combine.CombineManifest;
-import org.apache.taverna.robundle.manifest.odf.ODFManifest;
-
-public class Bundle implements Closeable {
- private boolean deleteOnClose;
- private Manifest manifest;
- private final Path root;
-
- public Bundle(Path root, boolean deleteOnClose) {
- this.root = root;
- this.setDeleteOnClose(deleteOnClose);
- }
-
- @Override
- public void close() throws IOException {
- close(isDeleteOnClose());
- }
-
- protected void close(boolean deleteOnClose) throws IOException {
- if (!getFileSystem().isOpen())
- return;
-
- if (!deleteOnClose) {
- // update manifest
- getManifest().populateFromBundle();
- getManifest().writeAsJsonLD();
- if (ODFManifest.containsManifest(this))
- getManifest().writeAsODFManifest();
- if (CombineManifest.containsManifest(this))
- getManifest().writeAsCombineManifest();
- } else {
- /*
- * FIXME: Enable this if closing temporary bundles is slow doing
- * closing (as those files are being compressed):
- * RecursiveDeleteVisitor.deleteRecursively(getRoot());
- */
- }
- getFileSystem().close();
- if (deleteOnClose)
- deleteIfExists(getSource());
- }
-
- public FileSystem getFileSystem() {
- return getRoot().getFileSystem();
- }
-
- public Manifest getManifest() throws IOException {
- if (manifest == null)
- synchronized (this) {
- if (manifest == null)
- manifest = readOrPopulateManifest();
- }
- return manifest;
- }
-
- public Path getPath(String path) {
- return getRoot().resolve(path);
- }
-
- public Path getRoot() {
- return root;
- }
-
- public Path getSource() {
- BundleFileSystem fs = (BundleFileSystem) getFileSystem();
- return fs.getSource();
- }
-
- public boolean isDeleteOnClose() {
- return deleteOnClose;
- }
-
- protected Manifest readOrPopulateManifest() throws IOException {
- Manifest newManifest = new Manifest(this);
- Path manifestPath = getManifestPath(this);
- if (exists(manifestPath)) {
- try (InputStream manifestStream = newInputStream(manifestPath)) {
- new RDFToManifest().readTo(manifestStream, newManifest,
- manifestPath.toUri());
- }
- // TODO: Also support reading manifest.rdf?
- } else if (ODFManifest.containsManifest(this)) {
- new ODFManifest(newManifest).readManifestXML();
- } else if (CombineManifest.containsManifest(this)) {
- new CombineManifest(newManifest).readCombineArchive();
- } else {
- // Fallback (might be a fresh or 3rd party bundle), populate from
- // zip content
- newManifest.populateFromBundle();
- }
- return newManifest;
- }
-
- public void setDeleteOnClose(boolean deleteOnClose) {
- this.deleteOnClose = deleteOnClose;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/main/java/org/apache/taverna/robundle/Bundles.java
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diff --git a/taverna-robundle/src/main/java/org/apache/taverna/robundle/Bundles.java b/taverna-robundle/src/main/java/org/apache/taverna/robundle/Bundles.java
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--- a/taverna-robundle/src/main/java/org/apache/taverna/robundle/Bundles.java
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-package org.apache.taverna.robundle;
-
-/*
- * 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.nio.file.Files.copy;
-import static java.nio.file.Files.createDirectories;
-import static java.nio.file.Files.createTempFile;
-import static java.nio.file.Files.deleteIfExists;
-import static java.nio.file.Files.exists;
-import static java.nio.file.Files.isDirectory;
-import static java.nio.file.Files.isRegularFile;
-import static java.nio.file.Files.move;
-import static java.nio.file.Files.newBufferedReader;
-import static java.nio.file.Files.newBufferedWriter;
-import static java.nio.file.Files.newDirectoryStream;
-import static java.nio.file.Files.readAllBytes;
-import static java.nio.file.Files.write;
-import static java.nio.file.StandardCopyOption.ATOMIC_MOVE;
-import static java.nio.file.StandardCopyOption.REPLACE_EXISTING;
-import static java.nio.file.StandardOpenOption.CREATE;
-import static java.nio.file.StandardOpenOption.TRUNCATE_EXISTING;
-import static org.apache.taverna.robundle.fs.BundleFileSystemProvider.APPLICATION_VND_WF4EVER_ROBUNDLE_ZIP;
-import static org.apache.taverna.robundle.fs.BundleFileSystemProvider.MIMETYPE_FILE;
-import static org.apache.taverna.robundle.fs.BundleFileSystemProvider.newFileSystemFromExisting;
-import static org.apache.taverna.robundle.fs.BundleFileSystemProvider.newFileSystemFromNew;
-import static org.apache.taverna.robundle.fs.BundleFileSystemProvider.newFileSystemFromTemporary;
-import static org.apache.taverna.robundle.utils.PathHelper.relativizeFromBase;
-import static org.apache.taverna.robundle.utils.TemporaryFiles.temporaryBundle;
-
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.net.URL;
-import java.nio.charset.Charset;
-import java.nio.file.AtomicMoveNotSupportedException;
-import java.nio.file.CopyOption;
-import java.nio.file.DirectoryNotEmptyException;
-import java.nio.file.DirectoryStream;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.text.MessageFormat;
-
-import org.apache.commons.configuration.ConfigurationException;
-import org.apache.commons.configuration.HierarchicalINIConfiguration;
-import org.apache.taverna.robundle.fs.BundleFileSystem;
-import org.apache.taverna.robundle.utils.RecursiveCopyFileVisitor;
-import org.apache.taverna.robundle.utils.RecursiveDeleteVisitor;
-
-/**
- * Utility functions for dealing with RO bundles.
- * <p>
- * The style of using this class is similar to that of {@link Files}. In fact, a
- * RO bundle is implemented as a set of {@link Path}s.
- *
- * @author Stian Soiland-Reyes
- */
-public class Bundles {
- private static final String ANNOTATIONS = "annotations";
- private static final Charset ASCII = Charset.forName("ASCII");
- private static final String DOT_RO = ".ro";
-
- protected static final String DOT_URL = ".url";
-
- private static final String INI_INTERNET_SHORTCUT = "InternetShortcut";
- private static final String INI_URL = "URL";
- private static final Charset LATIN1 = Charset.forName("Latin1");
- private static final String MANIFEST_JSON = "manifest.json";
- private static final Charset UTF8 = Charset.forName("UTF-8");
-
- public static void closeAndSaveBundle(Bundle bundle, Path destination)
- throws IOException {
- Path zipPath = closeBundle(bundle);
- if (bundle.isDeleteOnClose()) {
- safeMove(zipPath, destination);
- } else {
- safeCopy(zipPath, destination);
- }
- }
-
- public static Path closeBundle(Bundle bundle) throws IOException {
- Path path = bundle.getSource();
- bundle.close(false);
- return path;
- }
-
- public static void copyRecursively(final Path source,
- final Path destination, final CopyOption... copyOptions)
- throws IOException {
- RecursiveCopyFileVisitor.copyRecursively(source, destination,
- copyOptions);
- }
-
- public static Bundle createBundle() throws IOException {
- BundleFileSystem fs = newFileSystemFromTemporary();
- return new Bundle(fs.getRootDirectory(), true);
- }
-
- public static Bundle createBundle(Path path) throws IOException {
- BundleFileSystem fs = newFileSystemFromNew(path);
- return new Bundle(fs.getRootDirectory(), false);
- }
-
- public static void deleteRecursively(Path p) throws IOException {
- RecursiveDeleteVisitor.deleteRecursively(p);
- }
-
- protected static String filenameWithoutExtension(Path entry) {
- String fileName = entry.getFileName().toString();
- int lastDot = fileName.lastIndexOf(".");
- if (lastDot < 0)
- // return fileName;
- return fileName.replace("/", "");
- return fileName.substring(0, lastDot);
- }
-
- public static Path getAnnotations(Bundle bundle) throws IOException {
- Path dir = bundle.getFileSystem().getPath(DOT_RO, ANNOTATIONS);
- createDirectories(dir);
- return dir;
- }
-
- public static Path getManifestPath(Bundle bundle) {
- return bundle.getRoot().resolve(DOT_RO).resolve(MANIFEST_JSON);
- }
-
- public static String getMimeType(Bundle bundle) throws IOException {
- Path mimetypePath = bundle.getRoot().resolve(MIMETYPE_FILE);
- String mimetype = getStringValue(mimetypePath);
- if (mimetype == null || mimetype.isEmpty())
- return APPLICATION_VND_WF4EVER_ROBUNDLE_ZIP;
- return mimetype.trim();
- }
-
- public static URI getReference(Path path) throws IOException {
- if (path == null || isMissing(path))
- return null;
- if (!isReference(path))
- throw new IllegalArgumentException("Not a reference: " + path);
- // Note: Latin1 is chosen here because it would not bail out on
- // "strange" characters. We actually parse the URL as ASCII
- path = withExtension(path, DOT_URL);
- try (BufferedReader r = newBufferedReader(path, LATIN1)) {
- HierarchicalINIConfiguration ini = new HierarchicalINIConfiguration();
- ini.load(r);
-
- String urlStr = ini.getSection(INI_INTERNET_SHORTCUT).getString(
- INI_URL);
-
- // String urlStr = ini.get(INI_INTERNET_SHORTCUT, INI_URL);
- if (urlStr == null)
- throw new IOException("Invalid/unsupported URL format: " + path);
- return URI.create(urlStr);
- } catch (ConfigurationException e) {
- throw new IOException("Can't parse reference: " + path, e);
- }
- }
-
- public static String getStringValue(Path path) throws IOException {
- if (path == null || isMissing(path))
- return null;
- if (!isValue(path))
- throw new IllegalArgumentException("Not a value: " + path);
- return new String(readAllBytes(path), UTF8);
- }
-
- public static boolean isMissing(Path item) {
- return !exists(item) && !isReference(item);
- }
-
- public static boolean isReference(Path path) {
- return isRegularFile(withExtension(path, DOT_URL));
- }
-
- public static boolean isValue(Path path) {
- return !isReference(path) && isRegularFile(path);
- }
-
- public static Bundle openBundle(InputStream in) throws IOException {
- Path path = temporaryBundle();
- copy(in, path);
- Bundle bundle = openBundle(path);
- bundle.setDeleteOnClose(true);
- return bundle;
- }
-
- public static Bundle openBundle(Path zip) throws IOException {
- BundleFileSystem fs = newFileSystemFromExisting(zip);
- return new Bundle(fs.getRootDirectory(), false);
- }
-
- public static Bundle openBundle(URL url) throws IOException {
- try {
- if ("file".equals(url.getProtocol()))
- return openBundle(Paths.get(url.toURI()));
- else
- try (InputStream in = url.openStream()) {
- return openBundle(in);
- }
- } catch (URISyntaxException e) {
- throw new IllegalArgumentException("Invalid URL " + url, e);
- }
- }
-
- public static Bundle openBundleReadOnly(Path zip) throws IOException {
- Path tmpBundle = temporaryBundle();
- // BundleFileSystemProvider requires write-access, so we'll have to copy
- // it
- copy(zip, tmpBundle);
- BundleFileSystem fs = newFileSystemFromExisting(tmpBundle);
- // And this temporary file will be deleted afterwards
- return new Bundle(fs.getRootDirectory(), true);
- }
-
- public static void safeCopy(Path source, Path destination)
- throws IOException {
- safeMoveOrCopy(source, destination, false);
- }
-
- public static void safeMove(Path source, Path destination)
- throws IOException {
- safeMoveOrCopy(source, destination, true);
- }
-
- protected static void safeMoveOrCopy(Path source, Path destination,
- boolean move) throws IOException {
- // First just try to do an atomic move with overwrite
- try {
- if (move
- && source.getFileSystem().provider()
- .equals(destination.getFileSystem().provider())) {
- move(source, destination, ATOMIC_MOVE, REPLACE_EXISTING);
- return;
- }
- } catch (AtomicMoveNotSupportedException ex) {
- // Do the fallback by temporary files below
- }
-
- destination = destination.toAbsolutePath();
-
- String tmpName = destination.getFileName().toString();
- Path tmpDestination = createTempFile(destination.getParent(), tmpName,
- ".tmp");
- Path backup = null;
- try {
- if (move) {
- /*
- * This might do a copy if filestores differ .. hence to avoid
- * an incomplete (and partially overwritten) destination, we do
- * it first to a temporary file
- */
- move(source, tmpDestination, REPLACE_EXISTING);
- } else {
- copy(source, tmpDestination, REPLACE_EXISTING);
- }
-
- if (exists(destination)) {
- if (isDirectory(destination))
- // ensure it is empty
- try (DirectoryStream<Path> ds = newDirectoryStream(destination)) {
- if (ds.iterator().hasNext())
- throw new DirectoryNotEmptyException(
- destination.toString());
- }
- // Keep the files for roll-back in case it goes bad
- backup = createTempFile(destination.getParent(), tmpName,
- ".orig");
- move(destination, backup, REPLACE_EXISTING);
- }
- // OK ; let's swap over
- try {
- // prefer ATOMIC_MOVE
- move(tmpDestination, destination, REPLACE_EXISTING, ATOMIC_MOVE);
- } catch (AtomicMoveNotSupportedException ex) {
- /*
- * possibly a network file system as src/dest should be in same
- * folder
- */
- move(tmpDestination, destination, REPLACE_EXISTING);
- } finally {
- if (!exists(destination) && backup != null)
- // Restore the backup
- move(backup, destination);
- }
- // It went well, tidy up
- if (backup != null)
- deleteIfExists(backup);
- } finally {
- deleteIfExists(tmpDestination);
- }
- }
-
- public static void setMimeType(Bundle bundle, String mimetype)
- throws IOException {
- if (!ASCII.newEncoder().canEncode(mimetype))
- throw new IllegalArgumentException("mimetype must be ASCII, not "
- + mimetype);
- if (mimetype.contains("\n") || mimetype.contains("\r"))
- throw new IllegalArgumentException(
- "mimetype can't contain newlines");
- if (!mimetype.contains("/"))
- throw new IllegalArgumentException("Invalid mimetype: " + mimetype);
-
- Path root = bundle.getRoot();
- Path mimetypePath = root.resolve(MIMETYPE_FILE);
- if (!isRegularFile(mimetypePath)) {
- /*
- * It would require low-level zip-modification to properly add
- * 'mimetype' now
- */
- throw new IOException("Special file '" + MIMETYPE_FILE
- + "' missing from bundle, can't set mimetype");
- }
- setStringValue(mimetypePath, mimetype);
- }
-
- public static Path setReference(Path path, URI ref) throws IOException {
- path = withExtension(path, DOT_URL);
-
- // We'll save a IE-like .url "Internet shortcut" in INI format.
-
- // HierarchicalINIConfiguration ini = new
- // HierarchicalINIConfiguration();
- // ini.getSection(INI_INTERNET_SHORTCUT).addProperty(INI_URL,
- // ref.toASCIIString());
-
- // Ini ini = new Wini();
- // ini.getConfig().setLineSeparator("\r\n");
- // ini.put(INI_INTERNET_SHORTCUT, INI_URL, ref.toASCIIString());
-
- /*
- * Neither of the above create a .url that is compatible with Safari on
- * Mac OS (which expects "URL=" rather than "URL = ", so instead we make
- * it manually with MessageFormat.format:
- */
-
- // Includes a terminating double line-feed -- which Safari might also
- // need
- String iniTmpl = "[{0}]\r\n{1}={2}\r\n\r\n";
- String ini = MessageFormat.format(iniTmpl, INI_INTERNET_SHORTCUT,
- INI_URL, ref.toASCIIString());
-
- // NOTE: We use Latin1 here, but because of
- try (BufferedWriter w = newBufferedWriter(path, ASCII,
- TRUNCATE_EXISTING, CREATE)) {
- // ini.save(w);
- // ini.store(w);
- w.write(ini);
- // } catch (ConfigurationException e) {
- // throw new IOException("Can't write shortcut to " + path, e);
- }
- return path;
- }
-
- public static void setStringValue(Path path, String string)
- throws IOException {
- write(path, string.getBytes(UTF8), TRUNCATE_EXISTING, CREATE);
- }
-
- public static Path uriToBundlePath(Bundle bundle, URI uri) {
- URI rootUri = bundle.getRoot().toUri();
- uri = relativizeFromBase(uri, rootUri);
- if (uri.isAbsolute() || uri.getFragment() != null)
- return null;
- return bundle.getFileSystem().provider().getPath(rootUri.resolve(uri));
- }
-
- protected static Path withExtension(Path path, String extension) {
- if (!extension.isEmpty() && !extension.startsWith("."))
- throw new IllegalArgumentException(
- "Extension must be empty or start with .");
- String p = path.getFileName().toString();
- if (!extension.isEmpty()
- && p.toLowerCase().endsWith(extension.toLowerCase()))
- return path;
- // Everything after the last . - or just the end
- String newP = p.replaceFirst("(\\.[^.]*)?$", extension);
- return path.resolveSibling(newP);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/main/java/org/apache/taverna/robundle/fs/BundleFileStore.java
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/main/java/org/apache/taverna/robundle/fs/BundleFileStore.java b/taverna-robundle/src/main/java/org/apache/taverna/robundle/fs/BundleFileStore.java
deleted file mode 100644
index 208f979..0000000
--- a/taverna-robundle/src/main/java/org/apache/taverna/robundle/fs/BundleFileStore.java
+++ /dev/null
@@ -1,98 +0,0 @@
-package org.apache.taverna.robundle.fs;
-
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- */
-
-
-import java.io.IOException;
-import java.nio.file.FileStore;
-import java.nio.file.attribute.FileAttributeView;
-import java.nio.file.attribute.FileStoreAttributeView;
-
-public class BundleFileStore extends FileStore {
-
- // private final BundleFileSystem fs;
- private final FileStore origFileStore;
-
- protected BundleFileStore(BundleFileSystem fs, FileStore origFileStore) {
- if (fs == null || origFileStore == null) {
- throw new NullPointerException();
- }
- // this.fs = fs;
- this.origFileStore = origFileStore;
- }
-
- @Override
- public Object getAttribute(String attribute) throws IOException {
- return origFileStore.getAttribute(attribute);
- }
-
- @Override
- public <V extends FileStoreAttributeView> V getFileStoreAttributeView(
- Class<V> type) {
- return origFileStore.getFileStoreAttributeView(type);
- }
-
- @Override
- public long getTotalSpace() throws IOException {
- return origFileStore.getTotalSpace();
- }
-
- @Override
- public long getUnallocatedSpace() throws IOException {
- return origFileStore.getUnallocatedSpace();
- }
-
- @Override
- public long getUsableSpace() throws IOException {
- return origFileStore.getUsableSpace();
- }
-
- @Override
- public boolean isReadOnly() {
- return origFileStore.isReadOnly();
- }
-
- @Override
- public String name() {
- return origFileStore.name();
- }
-
- @Override
- public boolean supportsFileAttributeView(
- Class<? extends FileAttributeView> type) {
- return origFileStore.supportsFileAttributeView(type);
- }
-
- @Override
- public boolean supportsFileAttributeView(String name) {
- return origFileStore.supportsFileAttributeView(name);
- }
-
- @Override
- public String toString() {
- return origFileStore.toString();
- }
-
- @Override
- public String type() {
- return "bundle";
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/main/java/org/apache/taverna/robundle/fs/BundleFileSystem.java
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/main/java/org/apache/taverna/robundle/fs/BundleFileSystem.java b/taverna-robundle/src/main/java/org/apache/taverna/robundle/fs/BundleFileSystem.java
deleted file mode 100644
index 363b8cf..0000000
--- a/taverna-robundle/src/main/java/org/apache/taverna/robundle/fs/BundleFileSystem.java
+++ /dev/null
@@ -1,223 +0,0 @@
-package org.apache.taverna.robundle.fs;
-
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- */
-
-
-import java.io.IOException;
-import java.net.URI;
-import java.nio.file.ClosedFileSystemException;
-import java.nio.file.FileStore;
-import java.nio.file.FileSystem;
-import java.nio.file.Path;
-import java.nio.file.PathMatcher;
-import java.nio.file.Paths;
-import java.nio.file.WatchService;
-import java.nio.file.attribute.UserPrincipalLookupService;
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.Set;
-
-public class BundleFileSystem extends FileSystem {
-
- protected final URI baseURI;
- private FileSystem origFS;
- private final String separator;
- private final Path source;
-
- protected BundleFileSystem(FileSystem origFS, URI baseURI) {
- if (origFS == null || baseURI == null) {
- throw new NullPointerException();
- }
- this.origFS = origFS;
- this.baseURI = baseURI;
- this.separator = origFS.getSeparator();
- this.source = findSource();
-
- }
-
- @Override
- public void close() throws IOException {
- if (origFS == null) {
- return;
- }
- origFS.close();
- // De-reference the original ZIP file system so it can be
- // garbage collected
- origFS = null;
- }
-
- protected Path findSource() {
- Path zipRoot = getRootDirectory().getZipPath();
- URI uri = zipRoot.toUri();
- String schemeSpecific;
- if (provider().getJarDoubleEscaping()) {
- schemeSpecific = uri.getSchemeSpecificPart();
- } else {
- // http://dev.mygrid.org.uk/issues/browse/T3-954
- schemeSpecific = uri.getRawSchemeSpecificPart();
- }
- if (!schemeSpecific.endsWith("!/")) { // sanity check
- throw new IllegalStateException("Can't parse JAR URI: " + uri);
- }
- URI zip = URI.create(schemeSpecific.substring(0,
- schemeSpecific.length() - 2));
- return Paths.get(zip); // Look up our path
- }
-
- public URI getBaseURI() {
- return baseURI;
- }
-
- protected BundleFileStore getFileStore() {
- // We assume there's only one file store, as is true for ZipProvider
- return new BundleFileStore(this, getOrigFS().getFileStores().iterator()
- .next());
- }
-
- @Override
- public Iterable<FileStore> getFileStores() {
- return Collections.<FileStore> singleton(getFileStore());
- }
-
- /**
- * Thread-safe ClosedFileSystemException test
- *
- * @return
- */
- protected FileSystem getOrigFS() {
- FileSystem orig = origFS;
- if (orig == null || !orig.isOpen()) {
- throw new ClosedFileSystemException();
- }
- return orig;
- }
-
- @Override
- public Path getPath(String first, String... more) {
- Path zipPath = getOrigFS().getPath(first, more);
- return wrap(zipPath);
- }
-
- @Override
- public PathMatcher getPathMatcher(String syntaxAndPattern) {
- final PathMatcher zipMatcher = getOrigFS().getPathMatcher(
- syntaxAndPattern);
- return new PathMatcher() {
- @Override
- public boolean matches(Path path) {
- return zipMatcher.matches(unwrap(path));
- }
- };
- }
-
- @Override
- public Iterable<Path> getRootDirectories() {
- return Collections.<Path> singleton(getRootDirectory());
- }
-
- public BundlePath getRootDirectory() {
- return wrap(getOrigFS().getRootDirectories().iterator().next());
- }
-
- @Override
- public String getSeparator() {
- return separator;
- }
-
- public Path getSource() {
- return source;
- }
-
- @Override
- public UserPrincipalLookupService getUserPrincipalLookupService() {
- throw new UnsupportedOperationException();
- }
-
- @Override
- public boolean isOpen() {
- if (origFS == null) {
- return false;
- }
- return origFS.isOpen();
- }
-
- @Override
- public boolean isReadOnly() {
- return getOrigFS().isReadOnly();
- }
-
- @Override
- public WatchService newWatchService() throws IOException {
- throw new UnsupportedOperationException();
- }
-
- @Override
- public BundleFileSystemProvider provider() {
- return BundleFileSystemProvider.getInstance();
- }
-
- @Override
- public Set<String> supportedFileAttributeViews() {
- if (origFS == null) {
- throw new ClosedFileSystemException();
- }
- return origFS.supportedFileAttributeViews();
- }
-
- protected Path unwrap(Path bundlePath) {
- if (!(bundlePath instanceof BundlePath)) {
- // assume it's already unwrapped for some reason (for instance being
- // null)
- return bundlePath;
- }
- return ((BundlePath) bundlePath).getZipPath();
- }
-
- protected BundlePath wrap(Path zipPath) {
- if (zipPath == null) {
- return null;
- }
- if (zipPath instanceof BundlePath) {
- throw new IllegalArgumentException("Did not expect BundlePath: "
- + zipPath);
- }
- return new BundlePath(this, zipPath);
- }
-
- protected Iterator<Path> wrapIterator(final Iterator<Path> iterator) {
- return new Iterator<Path>() {
- @Override
- public boolean hasNext() {
- return iterator.hasNext();
- }
-
- @Override
- public Path next() {
- return wrap(iterator.next());
- }
-
- @Override
- public void remove() {
- iterator.remove();
- }
- };
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/main/java/org/apache/taverna/robundle/fs/BundleFileSystemProvider.java
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/main/java/org/apache/taverna/robundle/fs/BundleFileSystemProvider.java b/taverna-robundle/src/main/java/org/apache/taverna/robundle/fs/BundleFileSystemProvider.java
deleted file mode 100644
index 807c9fd..0000000
--- a/taverna-robundle/src/main/java/org/apache/taverna/robundle/fs/BundleFileSystemProvider.java
+++ /dev/null
@@ -1,695 +0,0 @@
-package org.apache.taverna.robundle.fs;
-
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- */
-
-
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.lang.ref.WeakReference;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.nio.ByteBuffer;
-import java.nio.MappedByteBuffer;
-import java.nio.channels.FileChannel;
-import java.nio.channels.FileLock;
-import java.nio.channels.ReadableByteChannel;
-import java.nio.channels.SeekableByteChannel;
-import java.nio.channels.WritableByteChannel;
-import java.nio.charset.Charset;
-import java.nio.file.AccessMode;
-import java.nio.file.CopyOption;
-import java.nio.file.DirectoryStream;
-import java.nio.file.DirectoryStream.Filter;
-import java.nio.file.FileAlreadyExistsException;
-import java.nio.file.FileStore;
-import java.nio.file.FileSystem;
-import java.nio.file.FileSystemAlreadyExistsException;
-import java.nio.file.FileSystemNotFoundException;
-import java.nio.file.FileSystems;
-import java.nio.file.Files;
-import java.nio.file.LinkOption;
-import java.nio.file.NoSuchFileException;
-import java.nio.file.OpenOption;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.nio.file.StandardOpenOption;
-import java.nio.file.attribute.BasicFileAttributes;
-import java.nio.file.attribute.FileAttribute;
-import java.nio.file.attribute.FileAttributeView;
-import java.nio.file.spi.FileSystemProvider;
-import java.util.EnumSet;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.Map;
-import java.util.Set;
-import java.util.UUID;
-import java.util.zip.CRC32;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipOutputStream;
-
-import org.apache.taverna.robundle.utils.TemporaryFiles;
-
-public class BundleFileSystemProvider extends FileSystemProvider {
- public class BundleFileChannel extends FileChannel {
-
- @SuppressWarnings("unused")
- private FileAttribute<?>[] attrs;
- private FileChannel fc;
- @SuppressWarnings("unused")
- private Set<? extends OpenOption> options;
- @SuppressWarnings("unused")
- private Path path;
-
- public BundleFileChannel(FileChannel fc, Path path,
- Set<? extends OpenOption> options, FileAttribute<?>[] attrs) {
- this.fc = fc;
- this.path = path;
- this.options = options;
- this.attrs = attrs;
- }
-
- @Override
- public void force(boolean metaData) throws IOException {
- fc.force(metaData);
- }
-
- @Override
- protected void implCloseChannel() throws IOException {
- fc.close();
- // TODO: Update manifest
- }
-
- @Override
- public FileLock lock(long position, long size, boolean shared)
- throws IOException {
- return fc.lock(position, size, shared);
- }
-
- @Override
- public MappedByteBuffer map(MapMode mode, long position, long size)
- throws IOException {
- return fc.map(mode, position, size);
- }
-
- @Override
- public long position() throws IOException {
- return fc.position();
- }
-
- @Override
- public FileChannel position(long newPosition) throws IOException {
- return fc.position(newPosition);
- }
-
- @Override
- public int read(ByteBuffer dst) throws IOException {
- return fc.read(dst);
- }
-
- @Override
- public int read(ByteBuffer dst, long position) throws IOException {
- return fc.read(dst, position);
- }
-
- @Override
- public long read(ByteBuffer[] dsts, int offset, int length)
- throws IOException {
- return fc.read(dsts, offset, length);
- }
-
- @Override
- public long size() throws IOException {
- return fc.size();
- }
-
- @Override
- public long transferFrom(ReadableByteChannel src, long position,
- long count) throws IOException {
- return fc.transferFrom(src, position, count);
- }
-
- @Override
- public long transferTo(long position, long count,
- WritableByteChannel target) throws IOException {
- return fc.transferTo(position, count, target);
- }
-
- @Override
- public FileChannel truncate(long size) throws IOException {
- return fc.truncate(size);
- }
-
- @Override
- public FileLock tryLock(long position, long size, boolean shared)
- throws IOException {
- return fc.tryLock(position, size, shared);
- }
-
- @Override
- public int write(ByteBuffer src) throws IOException {
- return fc.write(src);
- }
-
- @Override
- public int write(ByteBuffer src, long position) throws IOException {
- return fc.write(src, position);
- }
-
- @Override
- public long write(ByteBuffer[] srcs, int offset, int length)
- throws IOException {
- return fc.write(srcs, offset, length);
- }
-
- }
-
- private static class Singleton {
- // Fallback for OSGi environments
- private static final BundleFileSystemProvider INSTANCE = new BundleFileSystemProvider();
- }
-
- private static final String APP = "app";
-
- public static final String APPLICATION_VND_WF4EVER_ROBUNDLE_ZIP = "application/vnd.wf4ever.robundle+zip";
- public static final String MIMETYPE_FILE = "mimetype";
-
- /**
- * The list of open file systems. This is static so that it is shared across
- * eventual multiple instances of this provider (such as when running in an
- * OSGi environment). Access to this map should be synchronized to avoid
- * opening a file system that is not in the map.
- */
- protected static Map<URI, WeakReference<BundleFileSystem>> openFilesystems = new HashMap<>();
-
- private static final Charset UTF8 = Charset.forName("UTF-8");
-
- protected static void addMimeTypeToZip(ZipOutputStream out, String mimetype)
- throws IOException {
- if (mimetype == null) {
- mimetype = APPLICATION_VND_WF4EVER_ROBUNDLE_ZIP;
- }
- // FIXME: Make the mediatype a parameter
- byte[] bytes = mimetype.getBytes(UTF8);
-
- // We'll have to do the mimetype file quite low-level
- // in order to ensure it is STORED and not COMPRESSED
-
- ZipEntry entry = new ZipEntry(MIMETYPE_FILE);
- entry.setMethod(ZipEntry.STORED);
- entry.setSize(bytes.length);
- CRC32 crc = new CRC32();
- crc.update(bytes);
- entry.setCrc(crc.getValue());
-
- out.putNextEntry(entry);
- out.write(bytes);
- out.closeEntry();
- }
-
- protected static void createBundleAsZip(Path bundle, String mimetype)
- throws FileNotFoundException, IOException {
- // Create ZIP file as
- // http://docs.oracle.com/javase/7/docs/technotes/guides/io/fsp/zipfilesystemprovider.html
- try (ZipOutputStream out = new ZipOutputStream(Files.newOutputStream(
- bundle, StandardOpenOption.CREATE,
- StandardOpenOption.TRUNCATE_EXISTING))) {
- addMimeTypeToZip(out, mimetype);
- }
- }
-
- public static BundleFileSystemProvider getInstance() {
- for (FileSystemProvider provider : FileSystemProvider
- .installedProviders()) {
- if (provider instanceof BundleFileSystemProvider) {
- return (BundleFileSystemProvider) provider;
- }
- }
- // Not installed!
- // Fallback for OSGi environments
- return Singleton.INSTANCE;
- }
-
- public static BundleFileSystem newFileSystemFromExisting(Path bundle)
- throws FileNotFoundException, IOException {
- URI w;
- try {
- w = new URI(APP, bundle.toUri().toASCIIString(), null);
- } catch (URISyntaxException e) {
- throw new IllegalArgumentException("Can't create app: URI for "
- + bundle);
- }
-
- Map<String, Object> options = new HashMap<>();
-
- // useTempFile not needed as we override
- // newByteChannel to use newFileChannel() - which don't
- // consume memory
- // options.put("useTempFile", true);
-
- FileSystem fs = FileSystems.newFileSystem(w, options,
- BundleFileSystemProvider.class.getClassLoader());
- return (BundleFileSystem) fs;
-
- // To avoid multiple instances of this provider in an OSGi environment,
- // the above official API calls could be replaced with:
-
- // return getInstance().newFileSystem(w, Collections.<String, Object>
- // emptyMap());
-
- // which would fall back to Singleton.INSTANCE if there is no provider.
- }
-
- public static BundleFileSystem newFileSystemFromNew(Path bundle)
- throws FileNotFoundException, IOException {
- return newFileSystemFromNew(bundle,
- APPLICATION_VND_WF4EVER_ROBUNDLE_ZIP);
- }
-
- public static BundleFileSystem newFileSystemFromNew(Path bundle,
- String mimetype) throws FileNotFoundException, IOException {
- createBundleAsZip(bundle, mimetype);
- return newFileSystemFromExisting(bundle);
- }
-
- public static BundleFileSystem newFileSystemFromTemporary()
- throws IOException {
- Path bundle = TemporaryFiles.temporaryBundle();
- BundleFileSystem fs = BundleFileSystemProvider.newFileSystemFromNew(
- bundle, null);
- return fs;
- }
-
- private Boolean jarDoubleEscaping;
-
- /**
- * Public constructor provided for FileSystemProvider.installedProviders().
- * Use #getInstance() instead.
- *
- * @deprecated
- */
- @Deprecated
- public BundleFileSystemProvider() {
- }
-
- private boolean asBoolean(Object object, boolean defaultValue) {
- if (object instanceof Boolean) {
- return (Boolean) object;
- }
- if (object instanceof String) {
- return Boolean.valueOf((String) object);
- }
- return defaultValue;
- }
-
- protected URI baseURIFor(URI uri) {
- if (!(uri.getScheme().equals(APP))) {
- throw new IllegalArgumentException("Unsupported scheme in: " + uri);
- }
- if (!uri.isOpaque()) {
- return uri.resolve("/");
- }
- Path localPath = localPathFor(uri);
- Path realPath;
- try {
- realPath = localPath.toRealPath();
- } catch (IOException ex) {
- realPath = localPath.toAbsolutePath();
- }
- // Generate a UUID from the MD5 of the URI of the real path (!)
- UUID uuid = UUID.nameUUIDFromBytes(realPath.toUri().toASCIIString()
- .getBytes(UTF8));
- try {
- return new URI(APP, uuid.toString(), "/", null);
- } catch (URISyntaxException e) {
- throw new IllegalStateException("Can't create app:// URI for: "
- + uuid);
- }
- }
-
- @Override
- public void checkAccess(Path path, AccessMode... modes) throws IOException {
- BundleFileSystem fs = (BundleFileSystem) path.getFileSystem();
- origProvider(path).checkAccess(fs.unwrap(path), modes);
- }
-
- @Override
- public void copy(Path source, Path target, CopyOption... options)
- throws IOException {
- BundleFileSystem fs = (BundleFileSystem) source.getFileSystem();
- origProvider(source)
- .copy(fs.unwrap(source), fs.unwrap(target), options);
- }
-
- @Override
- public void createDirectory(Path dir, FileAttribute<?>... attrs)
- throws IOException {
- // Workaround http://stackoverflow.com/questions/16588321/
- if (Files.exists(dir)) {
- throw new FileAlreadyExistsException(dir.toString());
- }
- BundleFileSystem fs = (BundleFileSystem) dir.getFileSystem();
- origProvider(dir).createDirectory(fs.unwrap(dir), attrs);
- }
-
- @Override
- public void delete(Path path) throws IOException {
- BundleFileSystem fs = (BundleFileSystem) path.getFileSystem();
- origProvider(path).delete(fs.unwrap(path));
- }
-
- @Override
- public boolean equals(Object obj) {
- return getClass() == obj.getClass();
- }
-
- @Override
- public <V extends FileAttributeView> V getFileAttributeView(Path path,
- Class<V> type, LinkOption... options) {
- BundleFileSystem fs = (BundleFileSystem) path.getFileSystem();
- if (path.toAbsolutePath().equals(fs.getRootDirectory())) {
- // Bug in ZipFS, it will fall over as there is no entry for /
- //
- // Instead we'll just give a view of the source (e.g. the zipfile
- // itself).
- // Modifying its times is a bit futile since they are likely to be
- // overriden when closing, but this avoids a NullPointerException
- // in Files.setTimes().
- return Files.getFileAttributeView(fs.getSource(), type, options);
- }
- return origProvider(path).getFileAttributeView(fs.unwrap(path), type,
- options);
- }
-
- @Override
- public FileStore getFileStore(Path path) throws IOException {
- BundlePath bpath = (BundlePath) path;
- return bpath.getFileSystem().getFileStore();
- }
-
- @Override
- public BundleFileSystem getFileSystem(URI uri) {
- synchronized (openFilesystems) {
- URI baseURI = baseURIFor(uri);
- WeakReference<BundleFileSystem> ref = openFilesystems.get(baseURI);
- if (ref == null) {
- throw new FileSystemNotFoundException(uri.toString());
- }
- BundleFileSystem fs = ref.get();
- if (fs == null) {
- openFilesystems.remove(baseURI);
- throw new FileSystemNotFoundException(uri.toString());
- }
- return fs;
- }
- }
-
- protected boolean getJarDoubleEscaping() {
- if (jarDoubleEscaping != null) {
- return jarDoubleEscaping;
- }
- // https://bugs.openjdk.java.net/browse/JDK-8001178 introduced an
- // inconsistent
- // URI syntax. Before 7u40, jar: URIs to ZipFileSystemProvided had to
- // have
- // double-escaped the URI for the ZIP file, after 7u40 it is only
- // escaped once.
- // E.g.
- // to open before 7u40 you needed
- // jar:file:///file%2520with%2520spaces.zip, now you need
- // jar:file:///file%20with%20spaces.zip
- //
- // The new format is now consistent with URL.openStream() and
- // URLClassLoader's traditional jar: syntax, but somehow
- // zippath.toUri() still returns the double-escaped one, which
- // should only affects BundleFileSystem.findSource(). To help
- // findSource()
- // if this new bug is later fixed, we here detect which escaping style
- // is used.
-
- String name = "jar test";
- try {
- Path tmp = Files.createTempFile(name, ".zip");
- if (!tmp.toUri().toASCIIString().contains("jar%20test")) {
- // Hmm.. spaces not allowed in tmp? As we don't know, we'll
- // assume Java 7 behaviour
- jarDoubleEscaping = false;
- return jarDoubleEscaping;
- }
- createBundleAsZip(tmp, null);
- try (FileSystem fs = FileSystems.newFileSystem(tmp, null)) {
- URI root = fs.getRootDirectories().iterator().next().toUri();
- if (root.toASCIIString().contains("jar%2520test")) {
- jarDoubleEscaping = true;
- } else {
- jarDoubleEscaping = false;
- }
- }
- Files.delete(tmp);
- } catch (IOException e) {
- // Unknown error.. we'll assume Java 7 behaviour
- jarDoubleEscaping = true;
- }
- return jarDoubleEscaping;
-
- }
-
- @Override
- public Path getPath(URI uri) {
- BundleFileSystem fs = getFileSystem(uri);
- Path r = fs.getRootDirectory();
- if (uri.isOpaque()) {
- return r;
- } else {
- return r.resolve(uri.getPath());
- }
- }
-
- @Override
- public String getScheme() {
- return APP;
- }
-
- @Override
- public int hashCode() {
- return getClass().hashCode();
- }
-
- @Override
- public boolean isHidden(Path path) throws IOException {
- BundleFileSystem fs = (BundleFileSystem) path.getFileSystem();
- return origProvider(path).isHidden(fs.unwrap(path));
- }
-
- @Override
- public boolean isSameFile(Path path, Path path2) throws IOException {
- BundleFileSystem fs = (BundleFileSystem) path.getFileSystem();
- return origProvider(path).isSameFile(fs.unwrap(path), fs.unwrap(path2));
- }
-
- private Path localPathFor(URI uri) {
- URI localUri = URI.create(uri.getSchemeSpecificPart());
- return Paths.get(localUri);
- }
-
- @Override
- public void move(Path source, Path target, CopyOption... options)
- throws IOException {
- BundleFileSystem fs = (BundleFileSystem) source.getFileSystem();
- origProvider(source)
- .copy(fs.unwrap(source), fs.unwrap(target), options);
- }
-
- @Override
- public SeekableByteChannel newByteChannel(Path path,
- Set<? extends OpenOption> options, FileAttribute<?>... attrs)
- throws IOException {
- final BundleFileSystem fs = (BundleFileSystem) path.getFileSystem();
- Path zipPath = fs.unwrap(path);
- if (options.contains(StandardOpenOption.WRITE)
- || options.contains(StandardOpenOption.APPEND)) {
-
- if (Files.isDirectory(zipPath)) {
- // Workaround for ZIPFS allowing dir and folder to somewhat
- // co-exist
- throw new FileAlreadyExistsException("Directory <"
- + zipPath.toString() + "> exists");
- }
- Path parent = zipPath.getParent();
-
- if (parent != null && !Files.isDirectory(parent)) {
- throw new NoSuchFileException(zipPath.toString(),
- parent.toString(), "Parent of file is not a directory");
- }
- if (options.contains(StandardOpenOption.CREATE_NEW)) {
- } else if (options.contains(StandardOpenOption.CREATE)
- && !Files.exists(zipPath)) {
- // Workaround for bug in ZIPFS in Java 7 -
- // it only creates new files on
- // StandardOpenOption.CREATE_NEW
- //
- // We'll fake it and just create file first using the legacy
- // newByteChannel()
- // - we can't inject CREATE_NEW option as it
- // could be that there are two concurrent calls to CREATE
- // the very same file,
- // with CREATE_NEW the second thread would then fail.
-
- EnumSet<StandardOpenOption> opts = EnumSet
- .of(StandardOpenOption.WRITE,
- StandardOpenOption.CREATE_NEW);
- origProvider(path).newFileChannel(zipPath, opts, attrs).close();
-
- }
- }
-
- // Implement by newFileChannel to avoid memory leaks and
- // allow manifest to be updated
- return newFileChannel(path, options, attrs);
- }
-
- @Override
- public DirectoryStream<Path> newDirectoryStream(Path dir,
- final Filter<? super Path> filter) throws IOException {
- final BundleFileSystem fs = (BundleFileSystem) dir.getFileSystem();
- final DirectoryStream<Path> stream = origProvider(dir)
- .newDirectoryStream(fs.unwrap(dir), new Filter<Path>() {
- @Override
- public boolean accept(Path entry) throws IOException {
- return filter.accept(fs.wrap(entry));
- }
- });
- return new DirectoryStream<Path>() {
- @Override
- public void close() throws IOException {
- stream.close();
- }
-
- @Override
- public Iterator<Path> iterator() {
- return fs.wrapIterator(stream.iterator());
- }
- };
- }
-
- @Override
- public FileChannel newFileChannel(Path path,
- Set<? extends OpenOption> options, FileAttribute<?>... attrs)
- throws IOException {
- final BundleFileSystem fs = (BundleFileSystem) path.getFileSystem();
- FileChannel fc = origProvider(path).newFileChannel(fs.unwrap(path),
- options, attrs);
- return new BundleFileChannel(fc, path, options, attrs);
- }
-
- @Override
- public FileSystem newFileSystem(Path path, Map<String, ?> env)
- throws IOException {
- URI uri;
- try {
- uri = new URI(APP, path.toUri().toASCIIString(), null);
- } catch (URISyntaxException e) {
- throw new IllegalArgumentException("Can't create app: URI for "
- + path);
- }
- return newFileSystem(uri, env);
- }
-
- @Override
- public BundleFileSystem newFileSystem(URI uri, Map<String, ?> env)
- throws IOException {
-
- Path localPath = localPathFor(uri);
- URI baseURI = baseURIFor(uri);
-
- if (asBoolean(env.get("create"), false)) {
- createBundleAsZip(localPath, (String) env.get("mimetype"));
- }
-
- BundleFileSystem fs;
- synchronized (openFilesystems) {
- WeakReference<BundleFileSystem> existingRef = openFilesystems
- .get(baseURI);
- if (existingRef != null) {
- BundleFileSystem existing = existingRef.get();
- if (existing != null && existing.isOpen()) {
- throw new FileSystemAlreadyExistsException(
- baseURI.toASCIIString());
- }
- }
- FileSystem origFs = FileSystems.newFileSystem(localPath, null);
- fs = new BundleFileSystem(origFs, baseURI);
- openFilesystems.put(baseURI,
- new WeakReference<BundleFileSystem>(fs));
- }
- return fs;
- }
-
- @Override
- public InputStream newInputStream(Path path, OpenOption... options)
- throws IOException {
- // Avoid copying out to a file, like newByteChannel / newFileChannel
- BundleFileSystem fs = (BundleFileSystem) path.getFileSystem();
- return origProvider(path).newInputStream(fs.unwrap(path), options);
- }
-
- @Override
- public OutputStream newOutputStream(Path path, OpenOption... options)
- throws IOException {
- BundleFileSystem fileSystem = (BundleFileSystem) path.getFileSystem();
- if (fileSystem.getRootDirectory().resolve(path)
- .equals(fileSystem.getRootDirectory().resolve(MIMETYPE_FILE))) {
- // Special case to avoid compression
- return origProvider(path).newOutputStream(fileSystem.unwrap(path),
- options);
- }
- return super.newOutputStream(path, options);
- }
-
- private FileSystemProvider origProvider(Path path) {
- return ((BundlePath) path).getFileSystem().getOrigFS().provider();
- }
-
- @Override
- public <A extends BasicFileAttributes> A readAttributes(Path path,
- Class<A> type, LinkOption... options) throws IOException {
- BundleFileSystem fs = (BundleFileSystem) path.getFileSystem();
- return origProvider(path)
- .readAttributes(fs.unwrap(path), type, options);
- }
-
- @Override
- public Map<String, Object> readAttributes(Path path, String attributes,
- LinkOption... options) throws IOException {
- BundleFileSystem fs = (BundleFileSystem) path.getFileSystem();
- return origProvider(path).readAttributes(fs.unwrap(path), attributes,
- options);
- }
-
- @Override
- public void setAttribute(Path path, String attribute, Object value,
- LinkOption... options) throws IOException {
- BundleFileSystem fs = (BundleFileSystem) path.getFileSystem();
- origProvider(path).setAttribute(fs.unwrap(path), attribute, value,
- options);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/main/java/org/apache/taverna/robundle/fs/BundleFileTypeDetector.java
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/main/java/org/apache/taverna/robundle/fs/BundleFileTypeDetector.java b/taverna-robundle/src/main/java/org/apache/taverna/robundle/fs/BundleFileTypeDetector.java
deleted file mode 100644
index 03f8272..0000000
--- a/taverna-robundle/src/main/java/org/apache/taverna/robundle/fs/BundleFileTypeDetector.java
+++ /dev/null
@@ -1,90 +0,0 @@
-package org.apache.taverna.robundle.fs;
-
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- */
-
-
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.nio.ByteBuffer;
-import java.nio.channels.SeekableByteChannel;
-import java.nio.charset.Charset;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.StandardOpenOption;
-import java.nio.file.spi.FileTypeDetector;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipError;
-import java.util.zip.ZipException;
-import java.util.zip.ZipInputStream;
-
-public class BundleFileTypeDetector extends FileTypeDetector {
-
- private static final String APPLICATION_ZIP = "application/zip";
- private static final Charset ASCII = Charset.forName("ASCII");
- private static final Charset LATIN1 = Charset.forName("ISO-8859-1");
- private static final String MIMETYPE = "mimetype";
-
- @Override
- public String probeContentType(Path path) throws IOException {
-
- ByteBuffer buf = ByteBuffer.allocate(256);
- try (SeekableByteChannel byteChannel = Files.newByteChannel(path,
- StandardOpenOption.READ)) {
- int read = byteChannel.read(buf);
- if (read < 38) {
- return null;
- }
- ;
- }
- buf.flip();
-
- // Look for PK
-
- byte[] firstBytes = buf.array();
- String pk = new String(firstBytes, 0, 2, LATIN1);
- if (!(pk.equals("PK") && firstBytes[2] == 3 && firstBytes[3] == 4)) {
- // Did not match magic numbers of ZIP as specified in ePub OCF
- // http://www.idpf.org/epub/30/spec/epub30-ocf.html#app-media-type
- return null;
- }
-
- String mimetype = new String(firstBytes, 30, 8, LATIN1);
- if (!mimetype.equals(MIMETYPE)) {
- return APPLICATION_ZIP;
- }
- // Read the 'mimetype' file.
- try (ZipInputStream is = new ZipInputStream(new ByteArrayInputStream(
- firstBytes))) {
- ZipEntry entry = is.getNextEntry();
- if (!MIMETYPE.equals(entry.getName())) {
- return APPLICATION_ZIP;
- }
- byte[] mediaTypeBuffer = new byte[256];
- int size = is.read(mediaTypeBuffer);
- if (size < 1) {
- return APPLICATION_ZIP;
- }
- return new String(mediaTypeBuffer, 0, size, ASCII);
- } catch (ZipException | ZipError e) {
- return null;
- }
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/main/java/org/apache/taverna/robundle/fs/BundlePath.java
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/main/java/org/apache/taverna/robundle/fs/BundlePath.java b/taverna-robundle/src/main/java/org/apache/taverna/robundle/fs/BundlePath.java
deleted file mode 100644
index 93da6c0..0000000
--- a/taverna-robundle/src/main/java/org/apache/taverna/robundle/fs/BundlePath.java
+++ /dev/null
@@ -1,221 +0,0 @@
-package org.apache.taverna.robundle.fs;
-
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- */
-
-
-import java.io.File;
-import java.io.IOException;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.nio.file.LinkOption;
-import java.nio.file.Path;
-import java.nio.file.WatchEvent.Kind;
-import java.nio.file.WatchEvent.Modifier;
-import java.nio.file.WatchKey;
-import java.nio.file.WatchService;
-import java.util.Iterator;
-
-public class BundlePath implements Path {
-
- private final BundleFileSystem fs;
-
- private final Path zipPath;
-
- protected BundlePath(BundleFileSystem fs, Path zipPath) {
- if (fs == null || zipPath == null) {
- throw new NullPointerException();
- }
- this.fs = fs;
- this.zipPath = zipPath;
- }
-
- @Override
- public int compareTo(Path other) {
- return zipPath.compareTo(fs.unwrap(other));
- }
-
- @Override
- public boolean endsWith(Path other) {
- return zipPath.endsWith(fs.unwrap(other));
- }
-
- @Override
- public boolean endsWith(String other) {
- return zipPath.endsWith(other);
- }
-
- @Override
- public boolean equals(Object other) {
- if (!(other instanceof BundlePath)) {
- return false;
- }
- BundlePath bundlePath = (BundlePath) other;
- return zipPath.equals(fs.unwrap(bundlePath));
- }
-
- @Override
- public BundlePath getFileName() {
- return fs.wrap(zipPath.getFileName());
- }
-
- @Override
- public BundleFileSystem getFileSystem() {
- return fs;
- }
-
- @Override
- public BundlePath getName(int index) {
- return fs.wrap(zipPath.getName(index));
- }
-
- @Override
- public int getNameCount() {
- return zipPath.getNameCount();
- }
-
- @Override
- public BundlePath getParent() {
- return fs.wrap(zipPath.getParent());
- }
-
- @Override
- public BundlePath getRoot() {
- return fs.wrap(zipPath.getRoot());
- }
-
- protected Path getZipPath() {
- return zipPath;
- }
-
- @Override
- public int hashCode() {
- return zipPath.hashCode();
- }
-
- @Override
- public boolean isAbsolute() {
- return zipPath.isAbsolute();
- }
-
- @Override
- public Iterator<Path> iterator() {
- return fs.wrapIterator(zipPath.iterator());
- }
-
- @Override
- public BundlePath normalize() {
- return fs.wrap(zipPath.normalize());
- }
-
- @Override
- public WatchKey register(WatchService watcher, Kind<?>... events)
- throws IOException {
- throw new UnsupportedOperationException();
- }
-
- @Override
- public WatchKey register(WatchService watcher, Kind<?>[] events,
- Modifier... modifiers) throws IOException {
- throw new UnsupportedOperationException();
- }
-
- @Override
- public BundlePath relativize(Path other) {
- return fs.wrap(zipPath.relativize(fs.unwrap(other)));
- }
-
- @Override
- public BundlePath resolve(Path other) {
- return fs.wrap(zipPath.resolve(fs.unwrap(other)));
- }
-
- @Override
- public BundlePath resolve(String other) {
- return fs.wrap(zipPath.resolve(other));
- }
-
- @Override
- public BundlePath resolveSibling(Path other) {
- return fs.wrap(zipPath.resolveSibling(fs.unwrap(other)));
- }
-
- @Override
- public BundlePath resolveSibling(String other) {
- return fs.wrap(zipPath.resolveSibling(other));
- }
-
- @Override
- public boolean startsWith(Path other) {
- return zipPath.startsWith(fs.unwrap(other));
- }
-
- @Override
- public boolean startsWith(String other) {
- return zipPath.startsWith(other);
- }
-
- @Override
- public BundlePath subpath(int beginIndex, int endIndex) {
- return fs.wrap(zipPath.subpath(beginIndex, endIndex));
- }
-
- @Override
- public BundlePath toAbsolutePath() {
- return fs.wrap(zipPath.toAbsolutePath());
- }
-
- @Override
- public File toFile() {
- throw new UnsupportedOperationException();
- }
-
- @Override
- public BundlePath toRealPath(LinkOption... options) throws IOException {
- return fs.wrap(zipPath.toRealPath(options));
- }
-
- /**
- * Note: This method is used by JSON serialization and should return a valid
- * relative path from .ro/ or /
- */
- @Override
- public String toString() {
- if (zipPath.isAbsolute() && zipPath.startsWith("/.ro/")) {
- Path base = fs.getRootDirectory().zipPath.resolve(".ro");
- return base.relativize(zipPath).toString();
- } else {
- return zipPath.toString();
- }
- }
-
- @Override
- public URI toUri() {
- Path abs = zipPath.toAbsolutePath();
- URI pathRel;
- try {
- pathRel = new URI(null, null, abs.toString(), null);
- } catch (URISyntaxException e) {
- throw new IllegalStateException("Can't create URL for " + zipPath,
- e);
- }
- return fs.getBaseURI().resolve(pathRel);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/Agent.java
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/Agent.java b/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/Agent.java
deleted file mode 100644
index 17a7c42..0000000
--- a/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/Agent.java
+++ /dev/null
@@ -1,63 +0,0 @@
-package org.apache.taverna.robundle.manifest;
-
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- */
-
-
-import java.net.URI;
-
-import com.fasterxml.jackson.annotation.JsonPropertyOrder;
-
-@JsonPropertyOrder(value = { "uri", "orcid", "name" })
-public class Agent {
- private String name;
- private URI orcid;
- private URI uri;
-
- public Agent() {
- }
-
- public Agent(String name) {
- setName(name);
- }
-
- public String getName() {
- return name;
- }
-
- public URI getOrcid() {
- return orcid;
- }
-
- public URI getUri() {
- return uri;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public void setOrcid(URI orcid) {
- this.orcid = orcid;
- }
-
- public void setUri(URI uri) {
- this.uri = uri;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/Manifest.java
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/Manifest.java b/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/Manifest.java
deleted file mode 100644
index e8a6394..0000000
--- a/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/Manifest.java
+++ /dev/null
@@ -1,450 +0,0 @@
-package org.apache.taverna.robundle.manifest;
-
-/*
- * 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 com.fasterxml.jackson.databind.SerializationFeature.FAIL_ON_EMPTY_BEANS;
-import static com.fasterxml.jackson.databind.SerializationFeature.INDENT_OUTPUT;
-import static com.fasterxml.jackson.databind.SerializationFeature.WRITE_EMPTY_JSON_ARRAYS;
-import static com.fasterxml.jackson.databind.SerializationFeature.WRITE_NULL_MAP_VALUES;
-import static java.nio.file.FileVisitResult.CONTINUE;
-import static java.nio.file.FileVisitResult.SKIP_SUBTREE;
-import static java.nio.file.Files.createDirectories;
-import static java.nio.file.Files.getLastModifiedTime;
-import static java.nio.file.Files.isDirectory;
-import static java.nio.file.Files.newBufferedWriter;
-import static java.nio.file.Files.walkFileTree;
-import static java.nio.file.StandardOpenOption.CREATE;
-import static java.nio.file.StandardOpenOption.TRUNCATE_EXISTING;
-import static java.nio.file.StandardOpenOption.WRITE;
-import static java.nio.file.attribute.FileTime.fromMillis;
-import static org.apache.taverna.robundle.Bundles.uriToBundlePath;
-
-import java.io.IOException;
-import java.io.Writer;
-import java.net.URI;
-import java.nio.charset.Charset;
-import java.nio.file.FileVisitResult;
-import java.nio.file.Path;
-import java.nio.file.SimpleFileVisitor;
-import java.nio.file.attribute.BasicFileAttributes;
-import java.nio.file.attribute.FileTime;
-import java.util.ArrayList;
-import java.util.GregorianCalendar;
-import java.util.HashSet;
-import java.util.LinkedHashMap;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Locale;
-import java.util.Map;
-import java.util.Set;
-import java.util.logging.Logger;
-
-import org.apache.taverna.robundle.Bundle;
-import org.apache.taverna.robundle.manifest.combine.CombineManifest;
-import org.apache.taverna.robundle.manifest.odf.ODFManifest;
-
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonInclude.Include;
-import com.fasterxml.jackson.annotation.JsonProperty;
-import com.fasterxml.jackson.annotation.JsonPropertyOrder;
-import com.fasterxml.jackson.annotation.JsonValue;
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-@JsonPropertyOrder(value = { "@context", "id", "manifest", "createdOn",
- "createdBy", "createdOn", "authoredOn", "authoredBy", "history",
- "aggregates", "annotations", "@graph" })
-public class Manifest {
- public abstract class FileTimeMixin {
- @Override
- @JsonValue
- public abstract String toString();
- }
-
- public abstract class PathMixin {
- @Override
- @JsonValue
- public abstract String toString();
- }
-
- private static Logger logger = Logger.getLogger(Manifest.class
- .getCanonicalName());
-
- private static final String MANIFEST_JSON = "manifest.json";
-
- private static final String META_INF = "/META-INF";
-
- private static final String MIMETYPE = "/mimetype";
- private static final String RO = "/.ro";
- private static URI ROOT = URI.create("/");
-
- public static FileTime now() {
- return fromMillis(new GregorianCalendar().getTimeInMillis());
- }
-
- protected static Path withSlash(Path dir) {
- if (dir == null)
- return null;
- if (isDirectory(dir)) {
- Path fname = dir.getFileName();
- if (fname == null)
- return dir;
- String fnameStr = fname.toString();
- if (fnameStr.endsWith("/"))
- return dir;
- return dir.resolveSibling(fnameStr + "/");
- }
- return dir;
- }
-
- private Map<URI, PathMetadata> aggregates = new LinkedHashMap<>();
- private List<PathAnnotation> annotations = new ArrayList<>();
- private List<Agent> authoredBy = new ArrayList<>();
- private FileTime authoredOn;
- private Bundle bundle;
- private Agent createdBy = null;
- private FileTime createdOn = now();
- private List<String> graph;
- private List<Path> history = new ArrayList<>();
- private URI id = URI.create("/");
- private List<Path> manifest = new ArrayList<>();
-
- public Manifest(Bundle bundle) {
- this.bundle = bundle;
- }
-
- public List<PathMetadata> getAggregates() {
- return new ArrayList<>(aggregates.values());
- }
-
- public PathMetadata getAggregation(Path file) {
- URI fileUri = file.toUri();
- return getAggregation(fileUri);
- }
-
- public PathMetadata getAggregation(URI uri) {
- uri = relativeToBundleRoot(uri);
- PathMetadata metadata = aggregates.get(uri);
- if (metadata == null) {
- metadata = new PathMetadata();
- if (!uri.isAbsolute() && uri.getFragment() == null) {
- Path path = uriToBundlePath(bundle, uri);
- metadata.setFile(path);
- metadata.setMediatype(guessMediaType(path));
- } else {
- metadata.setUri(uri);
- }
- aggregates.put(uri, metadata);
- }
- return metadata;
- }
-
- public List<PathAnnotation> getAnnotations() {
- return annotations;
- }
-
- public List<Agent> getAuthoredBy() {
- return authoredBy;
- }
-
- public FileTime getAuthoredOn() {
- return authoredOn;
- }
-
- @JsonIgnore
- public URI getBaseURI() {
- return getBundle().getRoot().toUri();
- }
-
- @JsonIgnore
- public Bundle getBundle() {
- return bundle;
- }
-
- @JsonProperty(value = "@context")
- public List<Object> getContext() {
- ArrayList<Object> context = new ArrayList<>();
- // HashMap<Object, Object> map = new HashMap<>();
- // map.put("@base", getBaseURI());
- // context.add(map);
- context.add(URI.create("https://w3id.org/bundle/context"));
- return context;
- }
-
- public Agent getCreatedBy() {
- return createdBy;
- }
-
- public FileTime getCreatedOn() {
- return createdOn;
- }
-
- public List<String> getGraph() {
- return graph;
- }
-
- public List<Path> getHistory() {
- return history;
- }
-
- public URI getId() {
- return id;
- }
-
- public List<Path> getManifest() {
- return manifest;
- }
-
- /**
- * Guess media type based on extension
- *
- * @see http://wf4ever.github.io/ro/bundle/#media-types
- *
- * @param file
- * A Path to a file
- * @return media-type, e.g. <code>application/xml</code> or
- * <code>text/plain; charset="utf-8"</code>
- */
- public String guessMediaType(Path file) {
- if (file.getFileName() == null)
- return null;
- String filename = file.getFileName().toString()
- .toLowerCase(Locale.ENGLISH);
- if (filename.endsWith(".txt"))
- return "text/plain; charset=\"utf-8\"";
- if (filename.endsWith(".ttl"))
- return "text/turtle; charset=\"utf-8\"";
- if (filename.endsWith(".rdf") || filename.endsWith(".owl"))
- return "application/rdf+xml";
- if (filename.endsWith(".json"))
- return "application/json";
- if (filename.endsWith(".jsonld"))
- return "application/ld+json";
- if (filename.endsWith(".xml"))
- return "application/xml";
-
- // A few extra, common ones
-
- if (filename.endsWith(".png"))
- return "image/png";
- if (filename.endsWith(".svg"))
- return "image/svg+xml";
- if (filename.endsWith(".jpg") || filename.endsWith(".jpeg"))
- return "image/jpeg";
- if (filename.endsWith(".pdf"))
- return "application/pdf";
- return "application/octet-stream";
- }
-
- public void populateFromBundle() throws IOException {
- final Set<Path> potentiallyEmptyFolders = new LinkedHashSet<>();
-
- final Set<URI> existingAggregationsToPrune = new HashSet<>(
- aggregates.keySet());
-
- walkFileTree(bundle.getRoot(), new SimpleFileVisitor<Path>() {
- @SuppressWarnings("deprecation")
- @Override
- public FileVisitResult postVisitDirectory(Path dir, IOException exc)
- throws IOException {
- super.postVisitDirectory(dir, exc);
- if (potentiallyEmptyFolders.remove(dir)) {
- URI uri = relativeToBundleRoot(dir.toUri());
- existingAggregationsToPrune.remove(uri);
- PathMetadata metadata = aggregates.get(uri);
- if (metadata == null) {
- metadata = new PathMetadata();
- aggregates.put(uri, metadata);
- }
- metadata.setFile(withSlash(dir));
- metadata.setFolder(withSlash(dir.getParent()));
- metadata.setProxy();
- metadata.setCreatedOn(getLastModifiedTime(dir));
- potentiallyEmptyFolders.remove(withSlash(dir.getParent()));
- return CONTINUE;
- }
- return CONTINUE;
- }
-
- @Override
- public FileVisitResult preVisitDirectory(Path dir,
- BasicFileAttributes attrs) throws IOException {
- if (dir.startsWith(RO) || dir.startsWith(META_INF))
- return SKIP_SUBTREE;
- potentiallyEmptyFolders.add(withSlash(dir));
- potentiallyEmptyFolders.remove(withSlash(dir.getParent()));
- return CONTINUE;
- }
-
- @SuppressWarnings("deprecation")
- @Override
- public FileVisitResult visitFile(Path file,
- BasicFileAttributes attrs) throws IOException {
- potentiallyEmptyFolders.remove(withSlash(file.getParent()));
- if (file.startsWith(MIMETYPE))
- return CONTINUE;
- if (manifest.contains(file))
- // Don't aggregate the manifests
- return CONTINUE;
-
- // super.visitFile(file, attrs);
- URI uri = relativeToBundleRoot(file.toUri());
- existingAggregationsToPrune.remove(uri);
- PathMetadata metadata = aggregates.get(uri);
- if (metadata == null) {
- metadata = new PathMetadata();
- aggregates.put(uri, metadata);
- }
- metadata.setFile(file);
- if (metadata.getMediatype() == null)
- // Don't override if already set
- metadata.setMediatype(guessMediaType(file));
- metadata.setFolder(withSlash(file.getParent()));
- metadata.setProxy();
- metadata.setCreatedOn(getLastModifiedTime(file));
- potentiallyEmptyFolders.remove(file.getParent());
- return CONTINUE;
- }
- });
- for (URI preExisting : existingAggregationsToPrune) {
- PathMetadata meta = aggregates.get(preExisting);
- if (meta.getFile() != null)
- /*
- * Don't remove 'virtual' resources, only aggregations that went
- * to files
- */
- aggregates.remove(preExisting);
- }
- }
-
- public URI relativeToBundleRoot(URI uri) {
- uri = ROOT.resolve(bundle.getRoot().toUri().relativize(uri));
- return uri;
- }
-
- @SuppressWarnings("deprecation")
- public void setAggregates(List<PathMetadata> aggregates) {
- this.aggregates.clear();
-
- for (PathMetadata meta : aggregates) {
- URI uri = null;
- if (meta.getFile() != null) {
- uri = relativeToBundleRoot(meta.getFile().toUri());
- } else if (meta.getUri() != null) {
- uri = relativeToBundleRoot(meta.getUri());
- } else {
- uri = relativeToBundleRoot(meta.getProxy());
- }
- if (uri == null) {
- logger.warning("Unknown URI for aggregation " + meta);
- continue;
- }
- this.aggregates.put(uri, meta);
- }
- }
-
- public void setAnnotations(List<PathAnnotation> annotations) {
- this.annotations = annotations;
- }
-
- public void setAuthoredBy(List<Agent> authoredBy) {
- if (authoredBy == null)
- throw new NullPointerException("authoredBy can't be null");
- this.authoredBy = authoredBy;
- }
-
- public void setAuthoredOn(FileTime authoredOn) {
- this.authoredOn = authoredOn;
- }
-
- public void setBundle(Bundle bundle) {
- this.bundle = bundle;
- }
-
- public void setCreatedBy(Agent createdBy) {
- this.createdBy = createdBy;
- }
-
- public void setCreatedOn(FileTime createdOn) {
- this.createdOn = createdOn;
- }
-
- public void setGraph(List<String> graph) {
- this.graph = graph;
- }
-
- public void setHistory(List<Path> history) {
- if (history == null)
- throw new NullPointerException("history can't be null");
- this.history = history;
- }
-
- public void setId(URI id) {
- this.id = id;
- }
-
- public void setManifest(List<Path> manifest) {
- this.manifest = manifest;
- }
-
- public void writeAsCombineManifest() throws IOException {
- new CombineManifest(this).createManifestXML();
- }
-
- /**
- * Write as an RO Bundle JSON-LD manifest
- *
- * @return The path of the written manifest (e.g. ".ro/manifest.json")
- * @throws IOException
- */
- public Path writeAsJsonLD() throws IOException {
- Path jsonld = bundle.getFileSystem().getPath(RO, MANIFEST_JSON);
- createDirectories(jsonld.getParent());
- // Files.createFile(jsonld);
- if (!getManifest().contains(jsonld))
- getManifest().add(0, jsonld);
- ObjectMapper om = new ObjectMapper();
- om.addMixInAnnotations(Path.class, PathMixin.class);
- om.addMixInAnnotations(FileTime.class, FileTimeMixin.class);
- om.enable(INDENT_OUTPUT);
- om.disable(WRITE_EMPTY_JSON_ARRAYS);
- om.disable(FAIL_ON_EMPTY_BEANS);
- om.disable(WRITE_NULL_MAP_VALUES);
-
- om.setSerializationInclusion(Include.NON_NULL);
- try (Writer w = newBufferedWriter(jsonld, Charset.forName("UTF-8"),
- WRITE, TRUNCATE_EXISTING, CREATE)) {
- om.writeValue(w, this);
- }
- return jsonld;
- }
-
- /**
- * Write as a ODF manifest.xml
- *
- * @see http
- * ://docs.oasis-open.org/office/v1.2/os/OpenDocument-v1.2-os-part3.
- * html#__RefHeading__752807_826425813
- * @return The path of the written manifest (e.g. "META-INF/manifest.xml")
- * @throws IOException
- */
- public Path writeAsODFManifest() throws IOException {
- return new ODFManifest(this).createManifestXML();
- }
-}