cloning and stream handling 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/d3c571e5 Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/d3c571e5 Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/d3c571e5
Branch: refs/heads/ucfpackage-robundle Commit: d3c571e5f1a7d8c5cafed65fb126c04248db7b04 Parents: 041a9f3 Author: Stian Soiland-Reyes <[email protected]> Authored: Wed Dec 11 16:40:05 2013 +0000 Committer: Stian Soiland-Reyes <[email protected]> Committed: Thu Jul 2 15:05:41 2015 +0100 ---------------------------------------------------------------------- .../taverna/scufl2/ucfpackage/UCFPackage.java | 112 +++++++++++++------ 1 file changed, 76 insertions(+), 36 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/d3c571e5/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 fcfc55f..a1e32d3 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 @@ -61,10 +61,12 @@ 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.purl.wf4ever.robundle.utils.TemporaryFiles; import org.w3c.dom.Document; public class UCFPackage implements Cloneable { private static Logger logger = Logger.getLogger(UCFPackage.class.getName()); + private static final URI VERSION_BASE = URI.create("http://ns.taverna.org.uk/2010/scufl2/";); private static final String CONTAINER_XML = "META-INF/container.xml"; private static final Charset UTF_8 = Charset.forName("utf-8"); public static final String MIME_BINARY = "application/octet-stream"; @@ -75,7 +77,7 @@ public class UCFPackage implements Cloneable { public static final String MIME_WORKFLOW_BUNDLE = "application/vnd.taverna.workflow-bundle"; private static Charset ASCII = Charset.forName("ascii"); - private OdfPackage odfPackage; +// private OdfPackage odfPackage; private static JAXBContext jaxbContext; private JAXBElement<Container> containerXml; private boolean createdContainerXml = false; @@ -85,7 +87,7 @@ public class UCFPackage implements Cloneable { public UCFPackage() throws IOException { try { bundle = Bundles.createBundle(); - odfPackage = OdfPackage.create(); + //odfPackage = OdfPackage.create(); parseContainerXML(); } catch (IOException e) { throw e; @@ -101,23 +103,24 @@ public class UCFPackage implements Cloneable { protected void open(File containerFile) throws IOException { bundle = Bundles.openBundleReadOnly(containerFile.toPath()); -// -// BufferedInputStream stream = new BufferedInputStream( -// new FileInputStream(containerFile)); -// try { -// open(stream); -// } finally { -// stream.close(); -// } + parseContainerXML(); } public UCFPackage(InputStream inputStream) throws IOException { open(inputStream); } - protected void open(InputStream inputStream) throws IOException { + protected UCFPackage(Bundle bundle) { + this.bundle = bundle; + } + + protected void open(InputStream inputStream) throws IOException { try { -// odfPackage = OdfPackage.loadPackage(inputStream); + Path bundlePath = TemporaryFiles.temporaryBundle(); + Files.copy(inputStream, bundlePath); + bundle = Bundles.openBundle(bundlePath); + bundle.setDeleteOnClose(true); + parseContainerXML(); } catch (IOException e) { throw e; @@ -215,13 +218,16 @@ public class UCFPackage implements Cloneable { // "http://www.w3.org/2000/09/xmldsig#";); // xmlStreamWriter.setPrefix("xmlenc", // "http://www.w3.org/2001/04/xmlenc#";); - try (OutputStream outStream = odfPackage - .insertOutputStream(CONTAINER_XML)) { - // FIXME: Set namespace prefixes and default namespace - marshaller.setProperty("jaxb.formatted.output", true); - // TODO: Ensure using default namespace - marshaller.marshal(containerXml, outStream); - } + outStream = Files.newOutputStream(bundle.getRoot().resolve(CONTAINER_XML)); + //outStream = odfPackage.insertOutputStream(CONTAINER_XML); + + // FIXME: Set namespace prefixes and default namespace + + marshaller.setProperty("jaxb.formatted.output", true); + + // TODO: Ensure using default namespace + marshaller.marshal(containerXml, outStream); + } catch (IOException e) { throw e; } catch (Exception e) { @@ -343,6 +349,7 @@ public class UCFPackage implements Cloneable { } public class ResourceEntry { + private Path path; public ResourceEntry(Path path) { @@ -411,8 +418,7 @@ public class UCFPackage implements Cloneable { 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); + URI version = VERSION_BASE.relativize(conformsTo); if (!version.isAbsolute()) { return version.toString(); } @@ -435,7 +441,19 @@ public class UCFPackage implements Cloneable { ResourceEntry rootFile = getResourceEntry(path); if (rootFile == null) throw new IllegalArgumentException("Unknown resource: " + path); - odfPackage.getManifestEntries().get(path).setVersion(version); + } + + URI conformsTo = null; + if (version != null) { + conformsTo = VERSION_BASE.resolve(version); + PathMetadata aggregation; + try { + aggregation = bundle.getManifest().getAggregation(rootFile.path); + } catch (IOException e) { + throw new RuntimeException("Can't get root file aggregation for " + path, e); + } + aggregation.setConformsTo(conformsTo); + } Container container = containerXml.getValue(); @@ -570,25 +588,47 @@ public class UCFPackage implements Cloneable { // as we need to parse it after insertion, this must fail throw new IllegalArgumentException("Can't add " + CONTAINER_XML + " using OutputStream"); - try { - return odfPackage.insertOutputStream(path, mediaType); - } catch (IOException e) { - throw e; - } catch (Exception e) { - throw new IOException("Could not add " + path, e); + // as we need to parse it after insertion } + Path bundlePath = bundle.getRoot().resolve(path); + return Files.newOutputStream(bundlePath); } @Override public UCFPackage clone() { - final PipedOutputStream outputStream = new PipedOutputStream(); - try { - try (PipedInputStream inputStream = copyToOutputStream(outputStream)) { - return new UCFPackage(inputStream); - } - } catch (IOException e) { - throw new RuntimeException("Could not clone UCFPackage", e); - } + + try { + prepareContainerXML(); + } catch (IOException e) { + throw new RuntimeException("Could not prepare " + CONTAINER_XML, e); + } + + Path source = bundle.getSource(); + boolean deleteOnClose = bundle.isDeleteOnClose(); + bundle.setDeleteOnClose(false); + try { + Bundles.closeBundle(bundle); + } catch (IOException e) { + throw new RuntimeException("Could not save bundle to " + source, e); + } + + Bundle clonedBundle; + try { + clonedBundle = Bundles.openBundleReadOnly(source); + } catch (IOException e) { + throw new RuntimeException("Could not copy bundle from " + source, e); + } + + // Re-open the original source (usually a tmpfile) + try { + bundle = Bundles.openBundle(source); + } catch (IOException e) { + throw new RuntimeException("Could not re-open from " + source, e); + } + bundle.setDeleteOnClose(deleteOnClose); + + return new UCFPackage(clonedBundle); + } private PipedInputStream copyToOutputStream(
