read/write resources using ROBundle instead of ODFdom Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/041a9f39 Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/041a9f39 Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/041a9f39
Branch: refs/heads/ucfpackage-robundle Commit: 041a9f39c17df2b8bfd2f06a484555a0e8feac79 Parents: bb7f4d9 Author: Stian Soiland-Reyes <[email protected]> Authored: Wed Dec 11 16:21:43 2013 +0000 Committer: Stian Soiland-Reyes <[email protected]> Committed: Thu Jul 2 15:03:50 2015 +0100 ---------------------------------------------------------------------- .../taverna/scufl2/ucfpackage/UCFPackage.java | 332 ++++++++----------- 1 file changed, 143 insertions(+), 189 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/041a9f39/taverna-scufl2-ucfpackage/src/main/java/org/apache/taverna/scufl2/ucfpackage/UCFPackage.java ---------------------------------------------------------------------- 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 index b806ffe..fcfc55f 100644 --- 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 @@ -24,9 +24,7 @@ package org.apache.taverna.scufl2.ucfpackage; 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; @@ -34,12 +32,16 @@ import java.io.PipedInputStream; import java.io.PipedOutputStream; import java.net.URI; import java.nio.charset.Charset; +import java.nio.file.DirectoryStream; +import java.nio.file.Files; +import java.nio.file.Path; 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.Map.Entry; +import java.util.logging.Level; import java.util.logging.Logger; import javax.xml.bind.JAXBContext; @@ -54,9 +56,13 @@ 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.purl.wf4ever.robundle.Bundle; +import org.purl.wf4ever.robundle.Bundles; +import org.purl.wf4ever.robundle.manifest.Manifest; +import org.purl.wf4ever.robundle.manifest.PathMetadata; +import org.purl.wf4ever.robundle.utils.RecursiveDeleteVisitor; 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"; @@ -67,19 +73,18 @@ public class UCFPackage implements Cloneable { 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 Bundle bundle; private static ObjectFactory containerFactory = new ObjectFactory(); public UCFPackage() throws IOException { try { + bundle = Bundles.createBundle(); odfPackage = OdfPackage.create(); parseContainerXML(); } catch (IOException e) { @@ -95,10 +100,15 @@ public class UCFPackage implements Cloneable { } protected void open(File containerFile) throws IOException { - try (BufferedInputStream stream = new BufferedInputStream( - new FileInputStream(containerFile))) { - open(stream); - } + bundle = Bundles.openBundleReadOnly(containerFile.toPath()); +// +// BufferedInputStream stream = new BufferedInputStream( +// new FileInputStream(containerFile)); +// try { +// open(stream); +// } finally { +// stream.close(); +// } } public UCFPackage(InputStream inputStream) throws IOException { @@ -107,7 +117,7 @@ public class UCFPackage implements Cloneable { protected void open(InputStream inputStream) throws IOException { try { - odfPackage = OdfPackage.loadPackage(inputStream); +// odfPackage = OdfPackage.loadPackage(inputStream); parseContainerXML(); } catch (IOException e) { throw e; @@ -138,60 +148,31 @@ public class UCFPackage implements Cloneable { } public String getPackageMediaType() { - return odfPackage.getMediaType(); + try { + return Bundles.getMimeType(bundle); + } catch (IOException e) { + return MIME_WORKFLOW_BUNDLE; + } } 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); - } + try { + Bundles.setMimeType(bundle, mediaType); + } catch (IOException e) { + throw new RuntimeException("Can't set media type", e); + } +} 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"); + prepareContainerXML(); - // 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); - } + Path source = bundle.getSource(); + boolean deleteOnClose = bundle.isDeleteOnClose(); + bundle.setDeleteOnClose(false); + Bundles.closeAndSaveBundle(bundle, packageFile.toPath()); + // Re-open the original source (usually a tmpfile) + bundle = Bundles.openBundle(source); + bundle.setDeleteOnClose(deleteOnClose); } protected void prepareContainerXML() throws IOException { @@ -271,27 +252,18 @@ public class UCFPackage implements Cloneable { 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(); + Path bundlePath = bundle.getRoot().resolve(path); + Bundles.setStringValue(bundlePath, stringValue); + Manifest manifest = bundle.getManifest(); + manifest.getAggregation(bundlePath).setMediatype(mediaType); } 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(); + Path bundlePath = bundle.getRoot().resolve(path); + Files.write(bundlePath, bytesValue); + Manifest manifest = bundle.getManifest(); + manifest.getAggregation(bundlePath).setMediatype(mediaType); } public void addResource(Document document, String path, String mediaType) @@ -309,59 +281,33 @@ public class UCFPackage implements Cloneable { 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(); + Path bundlePath = bundle.getRoot().resolve(path); + Files.copy(inputStream, bundlePath); + Manifest manifest = bundle.getManifest(); + manifest.getAggregation(bundlePath).setMediatype(mediaType); } 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(); + Path bundlePath = bundle.getRoot().resolve(path); + Bundles.setReference(bundlePath, uri); + Manifest manifest = bundle.getManifest(); + manifest.getAggregation(bundlePath).setMediatype(mediaType); } 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); - } + Path bundlePath = bundle.getRoot().resolve(path); + return Bundles.getStringValue(bundlePath); } 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); - } + Path bundlePath = bundle.getRoot().resolve(path); + return Files.readAllBytes(bundlePath); } 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); - } + Path bundlePath = bundle.getRoot().resolve(path); + return Files.newInputStream(bundlePath); } public Map<String, ResourceEntry> listResources() { @@ -374,69 +320,57 @@ public class UCFPackage implements Cloneable { 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())); - } + Path bundlePath = bundle.getRoot().resolve(folderPath); + + HashMap<String, ResourceEntry> content = new HashMap<String, ResourceEntry>(); + try (DirectoryStream<Path> ds = Files.newDirectoryStream(bundlePath)) { + for (Path path : ds) { + content.put(path.toString(), new ResourceEntry(path)); + } + } catch (IOException e) { + throw new RuntimeException("Can't list resources of " +folderPath, e); + } 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); + Path bundlePath = bundle.getRoot().resolve(path); + try { + RecursiveDeleteVisitor.deleteRecursively(bundlePath); + } catch (IOException e) { + throw new RuntimeException("Could not delete " + path + " or its children", e); + } } 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(); - } + private Path path; - public String getPath() { - return path; + public ResourceEntry(Path path) { + this.path = path; + } + + public String getPath() { + return path.toString(); } public long getSize() { - return size; + try { + return Files.size(path); + } catch (IOException e) { + throw new RuntimeException("Can't determine size of " + path, e); + } } public String getMediaType() { - return mediaType; + try { + return bundle.getManifest().getAggregation(path).getMediatype(); + } catch (IOException e) { + throw new RuntimeException("Can't get media type for " + path, e); + } } public boolean isFolder() { - return path.endsWith("/"); + return Files.isDirectory(path); } public UCFPackage getUcfPackage() { @@ -444,6 +378,11 @@ public class UCFPackage implements Cloneable { } @Override + public String toString() { + return getPath(); + }; + + @Override public boolean equals(Object obj) { if (!(obj instanceof ResourceEntry)) return false; @@ -451,7 +390,8 @@ public class UCFPackage implements Cloneable { if (!getUcfPackage().equals(other.getUcfPackage())) return false; - return getPath().equals(other.getPath()); + } + return path.equals(other.path); } @Override @@ -463,9 +403,23 @@ public class UCFPackage implements Cloneable { return result; } - public String getVersion() { - return version; - } + public String getVersion() { + URI conformsTo; + try { + conformsTo = bundle.getManifest().getAggregation(path).getConformsTo(); + } catch (IOException e) { + throw new RuntimeException("Can't look up version for " + path, e); + } + if (conformsTo != null) { + URI scufl2Release = URI.create("http://ns.taverna.org.uk/2010/scufl2/";); + URI version = scufl2Release.relativize(conformsTo); + if (!version.isAbsolute()) { + return version.toString(); + } + } + return null; + + } } public Map<String, ResourceEntry> listAllResources() { @@ -555,19 +509,24 @@ public class UCFPackage implements Cloneable { RootFile rf = (RootFile) anyOrRoot; ResourceEntry entry = getResourceEntry(rf.getFullPath()); if (rf.getMediaType() != null - && rf.getMediaType() != entry.mediaType) + && rf.getMediaType() != entry.getMediaType()) { // Override the mime type in the returned entry - entry.mediaType = rf.getMediaType(); + PathMetadata aggr; + try { + aggr = bundle.getManifest().getAggregation(entry.path); + } catch (IOException e) { + throw new RuntimeException("Can't get aggregation for " + entry, e); + } + aggr.setMediatype(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); + Path bundlePath = bundle.getRoot().resolve(path); + return new ResourceEntry(bundlePath); } @SuppressWarnings("rawtypes") @@ -592,22 +551,17 @@ public class UCFPackage implements Cloneable { } 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(); - } + prepareContainerXML(); + Path source = bundle.getSource(); + boolean deleteOnClose = bundle.isDeleteOnClose(); + bundle.setDeleteOnClose(false); + Bundles.closeBundle(bundle); + + Files.copy(source, output); + + // Re-open the original source (usually a tmpfile) + bundle = Bundles.openBundle(source); + bundle.setDeleteOnClose(deleteOnClose); } public OutputStream addResourceUsingOutputStream(String path,
