http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/ProfileParser.java ---------------------------------------------------------------------- diff --git a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/ProfileParser.java b/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/ProfileParser.java deleted file mode 100644 index 1c22929..0000000 --- a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/ProfileParser.java +++ /dev/null @@ -1,356 +0,0 @@ -package org.apache.taverna.scufl2.rdfxml; -/* - * - * 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.io.InputStream; -import java.net.URI; -import java.util.Iterator; -import java.util.logging.Level; -import java.util.logging.Logger; - -import javax.xml.bind.JAXBElement; -import javax.xml.bind.JAXBException; - -import org.apache.taverna.scufl2.api.activity.Activity; -import org.apache.taverna.scufl2.api.common.Configurable; -import org.apache.taverna.scufl2.api.container.WorkflowBundle; -import org.apache.taverna.scufl2.api.core.Processor; -import org.apache.taverna.scufl2.api.io.ReaderException; -import org.apache.taverna.scufl2.api.port.InputActivityPort; -import org.apache.taverna.scufl2.api.port.InputProcessorPort; -import org.apache.taverna.scufl2.api.port.OutputActivityPort; -import org.apache.taverna.scufl2.api.port.OutputProcessorPort; -import org.apache.taverna.scufl2.api.profiles.ProcessorBinding; -import org.apache.taverna.scufl2.api.profiles.ProcessorInputPortBinding; -import org.apache.taverna.scufl2.api.profiles.ProcessorOutputPortBinding; -import org.w3c.dom.Element; -import org.w3c.dom.Node; -import org.w3c.dom.NodeList; - -import org.apache.taverna.scufl2.rdfxml.jaxb.Configuration; -import org.apache.taverna.scufl2.rdfxml.jaxb.ProcessorBinding.InputPortBinding; -import org.apache.taverna.scufl2.rdfxml.jaxb.ProcessorBinding.OutputPortBinding; -import org.apache.taverna.scufl2.rdfxml.jaxb.Profile; -import org.apache.taverna.scufl2.rdfxml.jaxb.ProfileDocument; - -public class ProfileParser extends AbstractParser { - private static Logger logger = Logger.getLogger(ProfileParser.class - .getCanonicalName()); - - public ProfileParser() { - super(); - } - - public ProfileParser(ThreadLocal<ParserState> parserState) { - super(parserState); - } - - @SuppressWarnings("unused") - private Element getChildElement(Element element) { - for (Node node : nodeIterable(element.getChildNodes())) - if (node instanceof Element) - return (Element) node; - return null; - } - - private Iterable<Node> nodeIterable(final NodeList childNodes) { - return new Iterable<Node>() { - @Override - public Iterator<Node> iterator() { - return new Iterator<Node>() { - int position = 0; - - @Override - public boolean hasNext() { - return childNodes.getLength() > position; - } - - @Override - public Node next() { - return childNodes.item(position++); - } - - @Override - public void remove() { - Node node = childNodes.item(position); - node.getParentNode().removeChild(node); - } - }; - } - }; - } - - protected void parseActivity( - org.apache.taverna.scufl2.rdfxml.jaxb.Activity original) { - Activity activity = new Activity(); - - getParserState().push(activity); - try { - mapBean(original.getAbout(), activity); - if (original.getName() != null) - activity.setName(original.getName()); - activity.setParent(getParserState().getCurrent( - org.apache.taverna.scufl2.api.profiles.Profile.class)); - if (original.getType() != null) - activity.setType(resolve(original.getType().getResource())); - for (org.apache.taverna.scufl2.rdfxml.jaxb.Activity.InputActivityPort inputActivityPort : original - .getInputActivityPort()) - parseInputActivityPort(inputActivityPort.getInputActivityPort()); - for (org.apache.taverna.scufl2.rdfxml.jaxb.Activity.OutputActivityPort outputActivityPort : original - .getOutputActivityPort()) - parseOutputActivityPort(outputActivityPort - .getOutputActivityPort()); - } finally { - getParserState().pop(); - } - } - - private static final URI INTERNAL_DISPATCH_PREFIX = URI.create("http://ns.taverna.org.uk/2010/scufl2/taverna/dispatchlayer/";); - - protected void parseConfiguration(Configuration original) - throws ReaderException { - org.apache.taverna.scufl2.api.configurations.Configuration config = new org.apache.taverna.scufl2.api.configurations.Configuration(); - - boolean ignoreConfig = false; - - if (original.getType() != null) { - URI type = resolve(original.getType().getResource()); - if (! INTERNAL_DISPATCH_PREFIX.relativize(type).isAbsolute()) { - logger.fine("Ignoring unsupported Dispatch stack configuration (SCUFL2-130)"); - logger.finest(original.getAbout()); - ignoreConfig = true; - } - config.setType(type); - } - - if (original.getName() != null) - config.setName(original.getName()); - - if (!ignoreConfig) { - mapBean(original.getAbout(), config); - - if (original.getConfigure() != null) { - Configurable configurable = resolveBeanUri(original - .getConfigure().getResource(), Configurable.class); - config.setConfigures(configurable); - } - config.setParent(getParserState().getCurrent( - org.apache.taverna.scufl2.api.profiles.Profile.class)); - } - - getParserState().push(config); - - if (original.getSeeAlso() != null) { - String about = original.getSeeAlso().getResource(); - if (about != null) { - URI resource = resolve(about); - URI bundleBase = parserState .get().getLocation(); - URI path = uriTools.relativePath(bundleBase, resource); - if (ignoreConfig) { - logger.finest("Deleting " + path + " (SCUFL2-130)"); - parserState.get().getUcfPackage().removeResource(path.getRawPath()); - } else { - try { - // TODO: Should the path in the UCF Package be %-escaped or not? - // See TestRDFXMLWriter.awkwardFilenames - config.setJson(parserState.get().getUcfPackage().getResourceAsString(path.getRawPath())); - } catch (IllegalArgumentException e) { - logger.log(Level.WARNING, "Could not parse JSON configuration " + path, e); - } catch (IOException e) { - logger.log(Level.WARNING, "Could not load JSON configuration " + path, e); - } - } - } - } - - for (Object o : original.getAny()) { - // Legacy SCUFL2 <= 0.11.0 PropertyResource configuration - // Just ignoring it for now :( - // - // TODO: Parse and represent as JSON-LD? - logger.warning("Ignoring unsupported PropertyResource (from wfbundle 0.2.0 or older) for " + config + " " + o); - } - - getParserState().pop(); - } - - protected void parseInputActivityPort( - org.apache.taverna.scufl2.rdfxml.jaxb.InputActivityPort original) { - InputActivityPort port = new InputActivityPort(); - mapBean(original.getAbout(), port); - port.setParent(getParserState().getCurrent(Activity.class)); - - port.setName(original.getName()); - if (original.getPortDepth() != null) - port.setDepth(original.getPortDepth().getValue()); - } - - protected void parseInputPortBinding( - org.apache.taverna.scufl2.rdfxml.jaxb.InputPortBinding original) - throws ReaderException { - ProcessorInputPortBinding binding = new ProcessorInputPortBinding(); - mapBean(original.getAbout(), binding); - - binding.setBoundActivityPort(resolveBeanUri(original - .getBindInputActivityPort().getResource(), - InputActivityPort.class)); - binding.setBoundProcessorPort(resolveBeanUri(original - .getBindInputProcessorPort().getResource(), - InputProcessorPort.class)); - binding.setParent(getParserState().getCurrent(ProcessorBinding.class)); - } - - protected void parseOutputActivityPort( - org.apache.taverna.scufl2.rdfxml.jaxb.OutputActivityPort original) { - OutputActivityPort port = new OutputActivityPort(); - mapBean(original.getAbout(), port); - port.setParent(getParserState().getCurrent(Activity.class)); - - port.setName(original.getName()); - if (original.getPortDepth() != null) - port.setDepth(original.getPortDepth().getValue()); - if (original.getGranularPortDepth() != null) - port.setGranularDepth(original.getGranularPortDepth().getValue()); - } - - protected void parseOutputPortBinding( - org.apache.taverna.scufl2.rdfxml.jaxb.OutputPortBinding original) - throws ReaderException { - ProcessorOutputPortBinding binding = new ProcessorOutputPortBinding(); - mapBean(original.getAbout(), binding); - - binding.setBoundActivityPort(resolveBeanUri(original - .getBindOutputActivityPort().getResource(), - OutputActivityPort.class)); - binding.setBoundProcessorPort(resolveBeanUri(original - .getBindOutputProcessorPort().getResource(), - OutputProcessorPort.class)); - binding.setParent(getParserState().getCurrent(ProcessorBinding.class)); - } - - protected void parseProcessorBinding( - org.apache.taverna.scufl2.rdfxml.jaxb.ProcessorBinding original) - throws ReaderException { - org.apache.taverna.scufl2.api.profiles.ProcessorBinding binding = new org.apache.taverna.scufl2.api.profiles.ProcessorBinding(); - binding.setParent(getParserState().getCurrent( - org.apache.taverna.scufl2.api.profiles.Profile.class)); - mapBean(original.getAbout(), binding); - getParserState().push(binding); - - if (original.getName() != null) - binding.setName(original.getName()); - if (original.getActivityPosition() != null) - binding.setActivityPosition(original.getActivityPosition() - .getValue()); - - URI processorUri = resolve(original.getBindProcessor().getResource()); - URI activityUri = resolve(original.getBindActivity().getResource()); - - binding.setBoundProcessor((Processor) resolveBeanUri(processorUri)); - binding.setBoundActivity((Activity) resolveBeanUri(activityUri)); - - for (InputPortBinding inputPortBinding : original.getInputPortBinding()) - parseInputPortBinding(inputPortBinding.getInputPortBinding()); - for (OutputPortBinding outputPortBinding : original - .getOutputPortBinding()) - parseOutputPortBinding(outputPortBinding.getOutputPortBinding()); - - getParserState().pop(); - } - - protected void parseProfile(Profile original, URI profileUri) { - org.apache.taverna.scufl2.api.profiles.Profile p = new org.apache.taverna.scufl2.api.profiles.Profile(); - p.setParent(getParserState().getCurrent(WorkflowBundle.class)); - - getParserState().push(p); - - if (original.getAbout() != null) { - URI about = getParserState().getCurrentBase().resolve( - original.getAbout()); - mapBean(about, p); - } else - mapBean(profileUri, p); - - if (original.getName() != null) - p.setName(original.getName()); - // Note - we'll pop() in profileSecond() instead - } - - protected void parseProfileSecond(Profile profileElem) { - // TODO: Parse activates config etc. - getParserState().pop(); - } - - protected void readProfile(URI profileUri, URI source) - throws ReaderException, IOException { - if (source.isAbsolute()) - throw new ReaderException("Can't read external profile source " - + source); - InputStream bundleStream = getParserState().getUcfPackage() - .getResourceAsInputStream(source.getRawPath()); - if (bundleStream == null) - throw new ReaderException("Can't find profile " + source.getPath()); - readProfile(profileUri, source, bundleStream); - } - - @SuppressWarnings("unchecked") - protected void readProfile(URI profileUri, URI source, - InputStream bundleStream) throws ReaderException, IOException { - JAXBElement<ProfileDocument> elem; - try { - elem = (JAXBElement<ProfileDocument>) unmarshaller - .unmarshal(bundleStream); - } catch (JAXBException e) { - throw new ReaderException("Can't parse profile document " + source, - e); - } - - URI base = getParserState().getLocation().resolve(source); - if (elem.getValue().getBase() != null) - base = base.resolve(elem.getValue().getBase()); - - getParserState().setCurrentBase(base); - - org.apache.taverna.scufl2.rdfxml.jaxb.Profile profileElem = null; - for (Object any : elem.getValue().getAny()) - if (any instanceof org.apache.taverna.scufl2.rdfxml.jaxb.Profile) { - if (profileElem != null) - throw new ReaderException("More than one <Profile> found"); - profileElem = (org.apache.taverna.scufl2.rdfxml.jaxb.Profile) any; - parseProfile(profileElem, profileUri); - } else if (any instanceof org.apache.taverna.scufl2.rdfxml.jaxb.Activity) { - if (profileElem == null) - throw new ReaderException("No <Profile> found"); - parseActivity((org.apache.taverna.scufl2.rdfxml.jaxb.Activity) any); - } else if (any instanceof org.apache.taverna.scufl2.rdfxml.jaxb.ProcessorBinding) { - if (profileElem == null) - throw new ReaderException("No <Profile> found"); - parseProcessorBinding((org.apache.taverna.scufl2.rdfxml.jaxb.ProcessorBinding) any); - } else if (any instanceof org.apache.taverna.scufl2.rdfxml.jaxb.Configuration) { - if (profileElem == null) - throw new ReaderException("No <Profile> found"); - parseConfiguration((org.apache.taverna.scufl2.rdfxml.jaxb.Configuration) any); - } - parseProfileSecond(profileElem); - } -}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLReader.java ---------------------------------------------------------------------- diff --git a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLReader.java b/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLReader.java deleted file mode 100644 index dd81ba0..0000000 --- a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLReader.java +++ /dev/null @@ -1,80 +0,0 @@ -package org.apache.taverna.scufl2.rdfxml; -/* - * - * 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.io.InputStream; -import java.net.URI; -import java.nio.charset.Charset; -import java.util.Collections; -import java.util.Set; - -import org.apache.taverna.scufl2.api.container.WorkflowBundle; -import org.apache.taverna.scufl2.api.io.ReaderException; -import org.apache.taverna.scufl2.api.io.WorkflowBundleReader; -import org.apache.taverna.scufl2.ucfpackage.UCFPackage; - - -public class RDFXMLReader implements WorkflowBundleReader { - public static final String APPLICATION_VND_TAVERNA_SCUFL2_WORKFLOW_BUNDLE = "application/vnd.taverna.scufl2.workflow-bundle"; - public static final String APPLICATION_RDF_XML = "application/rdf+xml"; - - @Override - public Set<String> getMediaTypes() { - return Collections.singleton(APPLICATION_VND_TAVERNA_SCUFL2_WORKFLOW_BUNDLE); - } - - @Override - public WorkflowBundle readBundle(File bundleFile, String mediaType) - throws ReaderException, IOException { - UCFPackage ucfPackage = new UCFPackage(bundleFile); - WorkflowBundleParser deserializer = new WorkflowBundleParser(); - return deserializer.readWorkflowBundle(ucfPackage, bundleFile.toURI()); - } - - @Override - public WorkflowBundle readBundle(InputStream inputStream, String mediaType) - throws ReaderException, IOException { - UCFPackage ucfPackage = new UCFPackage(inputStream); - WorkflowBundleParser deserializer = new WorkflowBundleParser(); - return deserializer.readWorkflowBundle(ucfPackage, URI.create("")); - } - - @Override - public String guessMediaTypeForSignature(byte[] firstBytes) { - if (firstBytes.length < 100) - return null; - Charset latin1 = Charset.forName("ISO-8859-1"); - String pk = new String(firstBytes, 0, 2, latin1); - if (!pk.equals("PK")) - return null; - String mimetype = new String(firstBytes, 30, 8, latin1); - if (!mimetype.equals("mimetype")) - return null; - String bundle = new String(firstBytes, 38, - APPLICATION_VND_TAVERNA_SCUFL2_WORKFLOW_BUNDLE.length(), latin1); - if (!bundle.equals(APPLICATION_VND_TAVERNA_SCUFL2_WORKFLOW_BUNDLE)) - return null; - return APPLICATION_VND_TAVERNA_SCUFL2_WORKFLOW_BUNDLE; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLSerializer.java ---------------------------------------------------------------------- diff --git a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLSerializer.java b/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLSerializer.java deleted file mode 100644 index 3ab7501..0000000 --- a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLSerializer.java +++ /dev/null @@ -1,860 +0,0 @@ -package org.apache.taverna.scufl2.rdfxml; -/* - * - * 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.lang.Boolean.TRUE; -import static java.util.logging.Level.FINE; -import static java.util.logging.Level.WARNING; -import static javax.xml.XMLConstants.W3C_XML_SCHEMA_NS_URI; -import static javax.xml.bind.Marshaller.JAXB_FORMATTED_OUTPUT; - -import java.io.IOException; -import java.io.OutputStream; -import java.net.URI; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Stack; -import java.util.logging.Logger; - -import javax.xml.bind.JAXBContext; -import javax.xml.bind.JAXBElement; -import javax.xml.bind.JAXBException; -import javax.xml.bind.Marshaller; -import javax.xml.validation.Schema; -import javax.xml.validation.SchemaFactory; - -import org.apache.taverna.scufl2.api.activity.Activity; -import org.apache.taverna.scufl2.api.annotation.Annotation; -import org.apache.taverna.scufl2.api.common.Typed; -import org.apache.taverna.scufl2.api.common.URITools; -import org.apache.taverna.scufl2.api.common.Visitor; -import org.apache.taverna.scufl2.api.common.WorkflowBean; -import org.apache.taverna.scufl2.api.configurations.Configuration; -import org.apache.taverna.scufl2.api.container.WorkflowBundle; -import org.apache.taverna.scufl2.api.core.BlockingControlLink; -import org.apache.taverna.scufl2.api.core.DataLink; -import org.apache.taverna.scufl2.api.core.Processor; -import org.apache.taverna.scufl2.api.core.Workflow; -import org.apache.taverna.scufl2.api.io.WriterException; -import org.apache.taverna.scufl2.api.iterationstrategy.CrossProduct; -import org.apache.taverna.scufl2.api.iterationstrategy.DotProduct; -import org.apache.taverna.scufl2.api.iterationstrategy.IterationStrategyStack; -import org.apache.taverna.scufl2.api.iterationstrategy.IterationStrategyTopNode; -import org.apache.taverna.scufl2.api.iterationstrategy.PortNode; -import org.apache.taverna.scufl2.api.port.InputActivityPort; -import org.apache.taverna.scufl2.api.port.InputProcessorPort; -import org.apache.taverna.scufl2.api.port.InputWorkflowPort; -import org.apache.taverna.scufl2.api.port.OutputActivityPort; -import org.apache.taverna.scufl2.api.port.OutputProcessorPort; -import org.apache.taverna.scufl2.api.port.OutputWorkflowPort; -import org.apache.taverna.scufl2.api.profiles.ProcessorBinding; -import org.apache.taverna.scufl2.api.profiles.ProcessorInputPortBinding; -import org.apache.taverna.scufl2.api.profiles.ProcessorOutputPortBinding; -import org.apache.taverna.scufl2.api.profiles.Profile; -import org.apache.taverna.scufl2.rdfxml.impl.NamespacePrefixMapperJAXB_RI; -import org.apache.taverna.scufl2.ucfpackage.UCFPackage; -import org.w3._1999._02._22_rdf_syntax_ns_.RDF; -import org.w3._1999._02._22_rdf_syntax_ns_.Resource; -import org.w3._1999._02._22_rdf_syntax_ns_.Type; -import org.w3._2000._01.rdf_schema_.SeeAlso; -import org.xml.sax.SAXException; - -import org.apache.taverna.scufl2.rdfxml.jaxb.Blocking; -import org.apache.taverna.scufl2.rdfxml.jaxb.Control; -import org.apache.taverna.scufl2.rdfxml.jaxb.DataLink.MergePosition; -import org.apache.taverna.scufl2.rdfxml.jaxb.DataLinkEntry; -import org.apache.taverna.scufl2.rdfxml.jaxb.GranularPortDepth; -import org.apache.taverna.scufl2.rdfxml.jaxb.IterationStrategyStack.IterationStrategies; -import org.apache.taverna.scufl2.rdfxml.jaxb.ObjectFactory; -import org.apache.taverna.scufl2.rdfxml.jaxb.PortDepth; -import org.apache.taverna.scufl2.rdfxml.jaxb.PortNode.DesiredDepth; -import org.apache.taverna.scufl2.rdfxml.jaxb.ProcessorBinding.ActivityPosition; -import org.apache.taverna.scufl2.rdfxml.jaxb.ProcessorBinding.InputPortBinding; -import org.apache.taverna.scufl2.rdfxml.jaxb.ProcessorBinding.OutputPortBinding; -import org.apache.taverna.scufl2.rdfxml.jaxb.ProductOf; -import org.apache.taverna.scufl2.rdfxml.jaxb.ProfileDocument; -import org.apache.taverna.scufl2.rdfxml.jaxb.SeeAlsoType; -import org.apache.taverna.scufl2.rdfxml.jaxb.WorkflowBundleDocument; -import org.apache.taverna.scufl2.rdfxml.jaxb.WorkflowDocument; - -public class RDFXMLSerializer { - private static final String DOT_RDF = ".rdf"; - protected static final URI OA = URI.create("http://www.w3.org/ns/oa#";); - protected static final URI PAV = URI.create("http://purl.org/pav/";); - private static boolean warnedOnce = false; - - public class ProfileSerialisationVisitor implements Visitor { - private org.apache.taverna.scufl2.rdfxml.jaxb.Activity activity; - private final ProfileDocument doc; - private org.apache.taverna.scufl2.rdfxml.jaxb.Profile profileElem; - private Profile profile; - private org.apache.taverna.scufl2.rdfxml.jaxb.ProcessorBinding processorBindingElem; - - public ProfileSerialisationVisitor(ProfileDocument doc) { - this.doc = doc; - } - - private void activity(Activity node) { - activity = objectFactory.createActivity(); - activity.setAbout(uri(node)); - activity.setType(type(node)); - activity.setName(node.getName()); - doc.getAny().add(activity); - } - - private void configuration(Configuration node) { - org.apache.taverna.scufl2.rdfxml.jaxb.Configuration configuration = objectFactory - .createConfiguration(); - configuration.setConfigure(resource(uri(node.getConfigures()))); - configuration.setName(node.getName()); - configuration.setType(type(node)); - - URI configUri = uriTools.relativeUriForBean(node, profile); - String jsonPath = configUri.toString().replaceFirst("/$", ".json"); - - URI profilePath = uriTools.relativeUriForBean(profile, profile.getParent()); - - String bundlePath = profilePath + jsonPath; - - UCFPackage bundle = profile.getParent().getResources(); - try { - bundle.addResource(node.getJsonAsString(), bundlePath, "application/json"); - } catch (IOException e) { - logger.log(WARNING, "Can't save JSON to " + bundlePath, e); - } - configuration.setAbout(configUri.toString()); - - SeeAlso seeAlso = rdfsObjectFactory.createSeeAlso(); - seeAlso.setResource(jsonPath); - configuration.setSeeAlso(seeAlso); - - // TODO: No way in API to mark non-activated configurations - profileElem.getActivateConfiguration().add(resource(uri(node))); - doc.getAny().add(configuration); - } - - private GranularPortDepth granularPortDepth(Integer integer) { - if (integer == null) - return null; - GranularPortDepth p = objectFactory.createGranularPortDepth(); - p.setValue(integer); - p.setDatatype(p.getDatatype()); - return p; - } - - private void inputActivityPort(InputActivityPort node) { - org.apache.taverna.scufl2.rdfxml.jaxb.InputActivityPort inputActivityPort = objectFactory - .createInputActivityPort(); - inputActivityPort.setAbout(uri(node)); - inputActivityPort.setName(node.getName()); - inputActivityPort.setPortDepth(portDepth(node.getDepth())); - - org.apache.taverna.scufl2.rdfxml.jaxb.Activity.InputActivityPort wrapper = objectFactory - .createActivityInputActivityPort(); - wrapper.setInputActivityPort(inputActivityPort); - activity.getInputActivityPort().add(wrapper); - } - - private void outputActivityPort(OutputActivityPort node) { - org.apache.taverna.scufl2.rdfxml.jaxb.OutputActivityPort outputActivityPort = objectFactory - .createOutputActivityPort(); - outputActivityPort.setAbout(uri(node)); - outputActivityPort.setName(node.getName()); - outputActivityPort.setPortDepth(portDepth(node.getDepth())); - outputActivityPort.setGranularPortDepth(granularPortDepth(node - .getGranularDepth())); - - org.apache.taverna.scufl2.rdfxml.jaxb.Activity.OutputActivityPort wrapper = objectFactory - .createActivityOutputActivityPort(); - wrapper.setOutputActivityPort(outputActivityPort); - activity.getOutputActivityPort().add(wrapper); - } - - private PortDepth portDepth(Integer integer) { - if (integer == null) - return null; - PortDepth p = objectFactory.createPortDepth(); - p.setValue(integer); - p.setDatatype(p.getDatatype()); - return p; - } - - private void processorBinding(ProcessorBinding node) { - processorBindingElem = objectFactory.createProcessorBinding(); - processorBindingElem.setAbout(uri(node)); - processorBindingElem.setName(node.getName()); - processorBindingElem.setBindActivity(resource(uri(node - .getBoundActivity()))); - processorBindingElem.setBindProcessor(resource(uri(node - .getBoundProcessor()))); - if (node.getActivityPosition() != null) { - ActivityPosition value = new ActivityPosition(); - value.setDatatype(value.getDatatype()); - value.setValue(node.getActivityPosition()); - processorBindingElem.setActivityPosition(value); - } - - profileElem.getProcessorBinding().add(resource(uri(node))); - doc.getAny().add(processorBindingElem); - } - - private void processorInputPortBinding(ProcessorInputPortBinding node) { - org.apache.taverna.scufl2.rdfxml.jaxb.InputPortBinding inputBinding = objectFactory - .createInputPortBinding(); - inputBinding.setAbout(uri(node)); - inputBinding.setBindInputActivityPort(resource(uri(node - .getBoundActivityPort()))); - inputBinding.setBindInputProcessorPort(resource(uri(node - .getBoundProcessorPort()))); - InputPortBinding b = objectFactory - .createProcessorBindingInputPortBinding(); - b.setInputPortBinding(inputBinding); - processorBindingElem.getInputPortBinding().add(b); - } - - private void processorOutputPortBinding(ProcessorOutputPortBinding node) { - org.apache.taverna.scufl2.rdfxml.jaxb.OutputPortBinding outputBinding = objectFactory - .createOutputPortBinding(); - outputBinding.setAbout(uri(node)); - outputBinding.setBindOutputActivityPort(resource(uri(node - .getBoundActivityPort()))); - outputBinding.setBindOutputProcessorPort(resource(uri(node - .getBoundProcessorPort()))); - OutputPortBinding b = objectFactory - .createProcessorBindingOutputPortBinding(); - b.setOutputPortBinding(outputBinding); - processorBindingElem.getOutputPortBinding().add(b); - } - - private void profile(Profile node) { - profile = node; - profileElem = objectFactory.createProfile(); - profileElem.setAbout(uri(node)); - profileElem.setName(node.getName()); - doc.getAny().add(profileElem); - } - - private String uri(WorkflowBean node) { - return uriTools.relativeUriForBean(node, profile).toASCIIString(); - } - - @Override - public boolean visit(WorkflowBean node) { - if (node instanceof Profile) - profile((Profile) node); - else if (node instanceof Activity) - activity((Activity) node); - else if (node instanceof InputActivityPort) - inputActivityPort((InputActivityPort) node); - else if (node instanceof OutputActivityPort) - outputActivityPort((OutputActivityPort) node); - else if (node instanceof ProcessorBinding) - processorBinding((ProcessorBinding) node); - else if (node instanceof ProcessorInputPortBinding) - processorInputPortBinding((ProcessorInputPortBinding) node); - else if (node instanceof ProcessorOutputPortBinding) - processorOutputPortBinding((ProcessorOutputPortBinding) node); - else if (node instanceof Configuration) - configuration((Configuration) node); - else - throw new IllegalStateException("Unexpected node " + node); - return true; - } - - @Override - public boolean visitEnter(WorkflowBean node) { - return visit(node); - } - - @Override - public boolean visitLeave(WorkflowBean node) { - return true; - } - } - - public class WorkflowSerialisationVisitor implements Visitor { - private final org.apache.taverna.scufl2.rdfxml.jaxb.Workflow workflow; - private org.apache.taverna.scufl2.rdfxml.jaxb.Processor proc; - private Workflow wf; - @SuppressWarnings("unused") - private org.apache.taverna.scufl2.rdfxml.jaxb.DispatchStack dispatchStack; - private org.apache.taverna.scufl2.rdfxml.jaxb.IterationStrategyStack iterationStrategyStack; - private IterationStrategies iterationStrategies; - private Stack<List<Object>> productStack; - - public WorkflowSerialisationVisitor( - org.apache.taverna.scufl2.rdfxml.jaxb.Workflow workflow) { - this.workflow = workflow; - } - - private GranularPortDepth makeGranularPortDepth(Integer granularDepth) { - if (granularDepth == null) - return null; - GranularPortDepth portDepth = objectFactory - .createGranularPortDepth(); - portDepth.setValue(granularDepth); - portDepth.setDatatype(portDepth.getDatatype()); - return portDepth; - } - - private PortDepth makePortDepth(Integer depth) { - if (depth == null) - return null; - PortDepth portDepth = objectFactory.createPortDepth(); - portDepth.setValue(depth); - portDepth.setDatatype(portDepth.getDatatype()); - return portDepth; - } - - private Resource makeResource(URI uri) { - Resource resource = rdfObjectFactory.createResource(); - resource.setResource(uri.toASCIIString()); - return resource; - } - - @Override - public boolean visit(WorkflowBean node) { - if (node instanceof Workflow) { - wf = (Workflow) node; - workflow.setAbout(""); - workflow.setName(wf.getName()); - - if (wf.getIdentifier() != null) { - Resource wfId = rdfObjectFactory.createResource(); - wfId.setResource(wf.getIdentifier().toASCIIString()); - workflow.setWorkflowIdentifier(wfId); - } - } - - URI uri = uriTools.relativeUriForBean(node, wf); - - if (node instanceof InputWorkflowPort) { - InputWorkflowPort ip = (InputWorkflowPort) node; - org.apache.taverna.scufl2.rdfxml.jaxb.Workflow.InputWorkflowPort inP = objectFactory - .createWorkflowInputWorkflowPort(); - org.apache.taverna.scufl2.rdfxml.jaxb.InputWorkflowPort inPort = objectFactory - .createInputWorkflowPort(); - inP.setInputWorkflowPort(inPort); - inPort.setName(ip.getName()); - - URI portURI = uriTools.relativeUriForBean(ip, ip.getParent()); - inPort.setAbout(portURI.toASCIIString()); - - PortDepth portDepth = makePortDepth(ip.getDepth()); - inPort.setPortDepth(portDepth); - workflow.getInputWorkflowPort().add(inP); - } - if (node instanceof OutputWorkflowPort) { - OutputWorkflowPort op = (OutputWorkflowPort) node; - org.apache.taverna.scufl2.rdfxml.jaxb.Workflow.OutputWorkflowPort inP = objectFactory - .createWorkflowOutputWorkflowPort(); - org.apache.taverna.scufl2.rdfxml.jaxb.OutputWorkflowPort outPort = objectFactory - .createOutputWorkflowPort(); - inP.setOutputWorkflowPort(outPort); - outPort.setName(op.getName()); - - URI portURI = uriTools.relativeUriForBean(op, op.getParent()); - outPort.setAbout(portURI.toASCIIString()); - workflow.getOutputWorkflowPort().add(inP); - } - if (node instanceof Processor) { - Processor processor = (Processor) node; - org.apache.taverna.scufl2.rdfxml.jaxb.Workflow.Processor wfProc = objectFactory - .createWorkflowProcessor(); - proc = objectFactory.createProcessor(); - wfProc.setProcessor(proc); - proc.setName(processor.getName()); - URI procUri = uriTools.relativeUriForBean(processor, wf); - proc.setAbout(procUri.toASCIIString()); - wfProc.setProcessor(proc); - workflow.getProcessor().add(wfProc); - } - if (node instanceof InputProcessorPort) { - InputProcessorPort inPort = (InputProcessorPort) node; - org.apache.taverna.scufl2.rdfxml.jaxb.InputProcessorPort port = objectFactory - .createInputProcessorPort(); - port.setAbout(uri.toASCIIString()); - port.setName(inPort.getName()); - port.setPortDepth(makePortDepth(inPort.getDepth())); - org.apache.taverna.scufl2.rdfxml.jaxb.Processor.InputProcessorPort inputProcessorPort = objectFactory - .createProcessorInputProcessorPort(); - inputProcessorPort.setInputProcessorPort(port); - proc.getInputProcessorPort().add(inputProcessorPort); - } - if (node instanceof OutputProcessorPort) { - org.apache.taverna.scufl2.rdfxml.jaxb.OutputProcessorPort port; - OutputProcessorPort outPort = (OutputProcessorPort) node; - port = objectFactory.createOutputProcessorPort(); - port.setAbout(uri.toASCIIString()); - port.setName(outPort.getName()); - port.setPortDepth(makePortDepth(outPort.getDepth())); - port.setGranularPortDepth(makeGranularPortDepth(outPort - .getGranularDepth())); - - org.apache.taverna.scufl2.rdfxml.jaxb.Processor.OutputProcessorPort outputProcessorPort = objectFactory - .createProcessorOutputProcessorPort(); - outputProcessorPort.setOutputProcessorPort(port); - proc.getOutputProcessorPort().add(outputProcessorPort); - } - if (node instanceof IterationStrategyStack) { - iterationStrategyStack = objectFactory - .createIterationStrategyStack(); - iterationStrategyStack.setAbout(uri.toASCIIString()); - org.apache.taverna.scufl2.rdfxml.jaxb.Processor.IterationStrategyStack processorIterationStrategyStack = objectFactory - .createProcessorIterationStrategyStack(); - processorIterationStrategyStack - .setIterationStrategyStack(iterationStrategyStack); - proc.setIterationStrategyStack(processorIterationStrategyStack); - productStack = new Stack<List<Object>>(); - } - if (node instanceof IterationStrategyTopNode - && productStack.isEmpty()) { - iterationStrategies = objectFactory - .createIterationStrategyStackIterationStrategies(); - iterationStrategyStack - .setIterationStrategies(iterationStrategies); - iterationStrategies.setParseType(iterationStrategies - .getParseType()); - List<Object> dotProductOrCrossProduct = iterationStrategies - .getDotProductOrCrossProduct(); - productStack.add(dotProductOrCrossProduct); - } - if (node instanceof CrossProduct) { - org.apache.taverna.scufl2.rdfxml.jaxb.CrossProduct crossProduct = objectFactory - .createCrossProduct(); - crossProduct.setAbout(uri.toASCIIString()); - productStack.peek().add(crossProduct); - ProductOf productOf = objectFactory.createProductOf(); - productOf.setParseType(productOf.getParseType()); - crossProduct.setProductOf(productOf); - productStack.add(crossProduct.getProductOf().getCrossProductOrDotProductOrPortNode()); - } - if (node instanceof DotProduct) { - org.apache.taverna.scufl2.rdfxml.jaxb.DotProduct dotProduct = objectFactory - .createDotProduct(); - dotProduct.setAbout(uri.toASCIIString()); - productStack.peek().add(dotProduct); - ProductOf productOf = objectFactory.createProductOf(); - productOf.setParseType(productOf.getParseType()); - dotProduct.setProductOf(productOf); - productStack.add(dotProduct.getProductOf() - .getCrossProductOrDotProductOrPortNode()); - } - if (node instanceof PortNode) { - PortNode portNode = (PortNode) node; - InputProcessorPort inPort = portNode.getInputProcessorPort(); - URI portUri = uriTools.relativeUriForBean(inPort, wf); - org.apache.taverna.scufl2.rdfxml.jaxb.PortNode port = objectFactory.createPortNode(); - port.setAbout(uri.toASCIIString()); - if (portNode.getDesiredDepth() != null) { - DesiredDepth value = objectFactory.createPortNodeDesiredDepth(); - value.setDatatype(value.getDatatype()); - value.setValue(portNode.getDesiredDepth()); - port.setDesiredDepth(value); - } - port.setIterateOverInputPort(makeResource(portUri)); - productStack.peek().add(port); - } - if (node instanceof DataLink) { - DataLink dataLink = (DataLink) node; - org.apache.taverna.scufl2.rdfxml.jaxb.DataLink link = objectFactory - .createDataLink(); - link.setAbout(uri.toASCIIString()); - URI fromUri = uriTools.relativeUriForBean( - dataLink.getReceivesFrom(), wf); - URI toUri = uriTools.relativeUriForBean(dataLink.getSendsTo(), - wf); - link.setReceiveFrom(makeResource(fromUri)); - link.setSendTo(makeResource(toUri)); - - if (dataLink.getMergePosition() != null) { - MergePosition value = objectFactory.createDataLinkMergePosition(); - value.setValue(dataLink - .getMergePosition()); - value.setDatatype(value.getDatatype()); - link.setMergePosition(value); - } - - DataLinkEntry linkEntry = objectFactory.createDataLinkEntry(); - linkEntry.setDataLink(link); - workflow.getDatalink().add(linkEntry); - } - if (node instanceof BlockingControlLink) { - BlockingControlLink controlLink = (BlockingControlLink) node; - URI blockUri = uriTools.relativeUriForBean( - controlLink.getBlock(), wf); - URI untilUri = uriTools.relativeUriForBean( - controlLink.getUntilFinished(), wf); - - Blocking blocking = objectFactory.createBlocking(); - blocking.setAbout(uri.toASCIIString()); - blocking.setBlock(makeResource(blockUri)); - blocking.setUntilFinished(makeResource(untilUri)); - - Control control = objectFactory.createControl(); - control.setBlocking(blocking); - workflow.getControl().add(control); - } - - // TODO: Datalinks - - return true; - } - - @Override - public boolean visitEnter(WorkflowBean node) { - return visit(node); - } - - @Override - public boolean visitLeave(WorkflowBean node) { - if (node instanceof IterationStrategyTopNode) - // Actually for any Cross/Dot product - productStack.pop(); - return true; - } - } - - protected synchronized static JAXBContext getJAxbContextStatic() - throws JAXBException { - if (jaxbContextStatic == null) { - Class<?>[] packages = { ObjectFactory.class, - org.w3._1999._02._22_rdf_syntax_ns_.ObjectFactory.class, - org.w3._2000._01.rdf_schema_.ObjectFactory.class }; - jaxbContextStatic = JAXBContext.newInstance(packages); - } - return jaxbContextStatic; - } - - public void annotation(final Annotation ann) { - URI wfBundleURI = uriTools.uriForBean(wfBundle); - URI annUri = uriTools.uriForBean(ann); - URI bodyURI = ann.getBody(); - if (bodyURI == null || bodyURI.isAbsolute()) - // Workaround with separate file for the annotation alone - bodyURI = annUri.resolve(uriTools.validFilename(ann.getName()) + DOT_RDF); - URI pathUri = uriTools.relativePath(wfBundleURI, bodyURI); - if (ann.getBody() == null || ann.getBody().equals(wfBundleURI.resolve(pathUri))) - // Set the relative path - ann.setBody(pathUri); - - // TODO: Add annotation to RO manifest - -// // Miniature OA description for now -// // See http://openannotation.org/spec/core/20130205/ -// final PropertyResource annProv = new PropertyResource(); -// annProv.setResourceURI(annUri); -// annProv.setTypeURI(OA.resolve("#Annotation")); -// -// if (ann.getAnnotatedAt() != null) { -// annProv.addProperty(OA.resolve("#annotedAt"), -// new PropertyLiteral(ann.getAnnotatedAt())); -// } -// if (ann.getSerializedAt() != null) { -// annProv.addProperty(OA.resolve("#serializedAt"), -// new PropertyLiteral(ann.getSerializedAt())); -// } -// -// if (ann.getAnnotatedBy() != null) { -// annProv.addPropertyReference(OA.resolve("#annotatedBy"), -// ann.getAnnotatedBy()); -// } -// if (ann.getSerializedBy() != null) { -// annProv.addPropertyReference(OA.resolve("#serializedBy"), -// ann.getSerializedBy()); -// } -// -// if (ann.getBody() != null) { -// annProv.addPropertyReference(OA.resolve("#hasBody"), ann.getBody()); -// } else if (! ann.getBodyStatements().isEmpty()){ -// // FIXME: Hack - Our body is also the annotation! -// annProv.addPropertyReference(OA.resolve("#hasBody"), pathUri); -// } -// -// // CHECK: should this be a relative reference instead? -// annProv.addPropertyReference(OA.resolve("#hasTarget"), -// uriTools.uriForBean(ann.getTarget())); -// // Serialize the metadata -// -// -// try { -// /* -// * TODO: Serialize manually with nicer indentation/namespaces etc., -// * as done for our other RDF/XML documents -// */ -// wfBundle.getResources() -// .addResource(visitor.getDoc(), pathUri.toASCIIString(), APPLICATION_RDF_XML); -// } catch (IOException e) { -// logger.log(Level.WARNING, "Can't write annotation to " + pathUri, e); -// } - - } - - private ObjectFactory objectFactory = new ObjectFactory(); - - private org.w3._2000._01.rdf_schema_.ObjectFactory rdfsObjectFactory = new org.w3._2000._01.rdf_schema_.ObjectFactory(); - private org.w3._1999._02._22_rdf_syntax_ns_.ObjectFactory rdfObjectFactory = new org.w3._1999._02._22_rdf_syntax_ns_.ObjectFactory(); - private URITools uriTools = new URITools(); - private boolean usingSchema = false; - - private WorkflowBundle wfBundle; - - private JAXBContext jaxbContext; - - private Map<WorkflowBean, URI> seeAlsoUris = new HashMap<>(); - private static JAXBContext jaxbContextStatic; - private static Logger logger = Logger.getLogger(RDFXMLSerializer.class - .getCanonicalName()); - public RDFXMLSerializer() { - } - - public RDFXMLSerializer(WorkflowBundle wfBundle) { - setWfBundle(wfBundle); - } - - public JAXBContext getJaxbContext() throws JAXBException { - if (jaxbContext == null) - return getJAxbContextStatic(); - return jaxbContext; - } - - public Marshaller getMarshaller() { - String schemaPath = "xsd/scufl2.xsd"; - Marshaller marshaller; - try { - marshaller = getJaxbContext().createMarshaller(); - - if (isUsingSchema()) { - SchemaFactory schemaFactory = SchemaFactory - .newInstance(W3C_XML_SCHEMA_NS_URI); - Schema schema = schemaFactory.newSchema(getClass().getResource( - schemaPath)); - // FIXME: re-enable schema - marshaller.setSchema(schema); - } - marshaller.setProperty(JAXB_FORMATTED_OUTPUT, TRUE); - marshaller - .setProperty( - "jaxb.schemaLocation", - "http://ns.taverna.org.uk/2010/scufl2# http://ns.taverna.org.uk/2010/scufl2/scufl2.xsd " - + "http://www.w3.org/1999/02/22-rdf-syntax-ns# http://ns.taverna.org.uk/2010/scufl2/rdf.xsd";); - } catch (JAXBException e) { - throw new IllegalStateException(e); - } catch (SAXException e) { - throw new IllegalStateException("Could not load schema " - + schemaPath, e); - } - setPrefixMapper(marshaller); - return marshaller; - } - - public WorkflowBundle getWfBundle() { - return wfBundle; - } - - public boolean isUsingSchema() { - return usingSchema; - } - - protected ProfileDocument makeProfile(Profile pf, URI path) { - ProfileDocument doc = objectFactory.createProfileDocument(); - - objectFactory.createProfile(); - pf.accept(new ProfileSerialisationVisitor(doc) { - }); - return doc; - } - - protected org.apache.taverna.scufl2.rdfxml.jaxb.Workflow makeWorkflow( - Workflow wf, URI documentPath) { - org.apache.taverna.scufl2.rdfxml.jaxb.Workflow workflow = objectFactory - .createWorkflow(); - wf.accept(new WorkflowSerialisationVisitor(workflow) { - }); - return workflow; - } - - protected org.apache.taverna.scufl2.rdfxml.jaxb.WorkflowBundle makeWorkflowBundleElem() { - org.apache.taverna.scufl2.rdfxml.jaxb.WorkflowBundle bundle = objectFactory - .createWorkflowBundle(); - // FIXME: Support other URIs - bundle.setAbout(""); - bundle.setName(wfBundle.getName()); - - if (wfBundle.getGlobalBaseURI() != null) { - Resource globalBaseURI = rdfObjectFactory.createResource(); - globalBaseURI.setResource(wfBundle.getGlobalBaseURI().toASCIIString()); - bundle.setGlobalBaseURI(globalBaseURI); - } - - for (Workflow wf : wfBundle.getWorkflows()) { - org.apache.taverna.scufl2.rdfxml.jaxb.WorkflowBundle.Workflow wfElem = objectFactory - .createWorkflowBundleWorkflow(); - SeeAlsoType seeAlsoElem = objectFactory.createSeeAlsoType(); - seeAlsoElem.setAbout(uriTools.relativeUriForBean(wf, wfBundle) - .toASCIIString()); - - if (seeAlsoUris.containsKey(wf)) { - SeeAlso seeAlso = rdfsObjectFactory.createSeeAlso(); - seeAlso.setResource(seeAlsoUris.get(wf).toASCIIString()); - seeAlsoElem.setSeeAlso(seeAlso); - } else - logger.warning("Can't find bundle URI for workflow document " - + wf.getName()); - - wfElem.setWorkflow(seeAlsoElem); - bundle.getWorkflow().add(wfElem); - - if (wfBundle.getMainWorkflow() == wf) { - Resource mainWorkflow = rdfObjectFactory.createResource(); - mainWorkflow.setResource(seeAlsoElem.getAbout()); - bundle.setMainWorkflow(mainWorkflow); - } - } - - for (Profile pf : wfBundle.getProfiles()) { - org.apache.taverna.scufl2.rdfxml.jaxb.WorkflowBundle.Profile wfElem = objectFactory - .createWorkflowBundleProfile(); - SeeAlsoType seeAlsoElem = objectFactory.createSeeAlsoType(); - seeAlsoElem.setAbout(uriTools.relativeUriForBean(pf, wfBundle) - .toASCIIString()); - - if (seeAlsoUris.containsKey(pf)) { - SeeAlso seeAlso = rdfsObjectFactory.createSeeAlso(); - seeAlso.setResource(seeAlsoUris.get(pf).toASCIIString()); - seeAlsoElem.setSeeAlso(seeAlso); - } else - logger.warning("Can't find bundle URI for profile document " - + pf.getName()); - - wfElem.setProfile(seeAlsoElem); - bundle.getProfile().add(wfElem); - - if (wfBundle.getMainProfile() == pf) { - Resource mainProfile = rdfObjectFactory.createResource(); - mainProfile.setResource(seeAlsoElem.getAbout()); - bundle.setMainProfile(mainProfile); - } - } - - for (Annotation ann : wfBundle.getAnnotations()) - annotation(ann); - - return bundle; - } - - public void profileDoc(OutputStream outputStream, Profile pf, URI path) - throws JAXBException, WriterException { - ProfileDocument doc = makeProfile(pf, path); - - URI wfUri = uriTools.relativeUriForBean(pf, wfBundle); - doc.setBase(uriTools.relativePath(path, wfUri).toASCIIString()); - - JAXBElement<RDF> element = rdfObjectFactory.createRDF(doc); - getMarshaller().marshal(element, outputStream); - seeAlsoUris.put(pf, path); - } - - private Resource resource(String uri) { - Resource r = rdfObjectFactory.createResource(); - r.setResource(uri); - return r; - } - - public void setJaxbContext(JAXBContext jaxbContext) { - this.jaxbContext = jaxbContext; - } - - protected void setPrefixMapper(Marshaller marshaller) { - boolean setPrefixMapper = false; - - try { - /* - * This only works with JAXB RI, in which case we can set the - * namespace prefix mapper - */ - Class.forName("com.sun.xml.bind.marshaller.NamespacePrefixMapper"); - marshaller.setProperty("com.sun.xml.bind.namespacePrefixMapper", - new NamespacePrefixMapperJAXB_RI()); - /* - * Note: A similar mapper for the built-in java - * (com.sun.xml.bind.internal.namespacePrefixMapper) is no longer - * included here, as it will not (easily) compile with Maven. - */ - setPrefixMapper = true; - } catch (Exception e) { - logger.log(FINE, "Can't find NamespacePrefixMapper", e); - } - - if (!setPrefixMapper && ! warnedOnce) { - logger.info("Could not set prefix mapper (missing or incompatible JAXB) " - + "- will use prefixes ns0, ns1, .."); - warnedOnce = true; - } - } - - public void setUsingSchema(boolean usingSchema) { - this.usingSchema = usingSchema; - } - - public void setWfBundle(WorkflowBundle wfBundle) { - this.wfBundle = wfBundle; - } - - private Type type(Typed typed) { - if (typed.getType() == null) - return null; - Type t = rdfObjectFactory.createType(); - t.setResource(typed.getType().toASCIIString()); - return t; - } - - public void workflowBundleDoc(OutputStream outputStream, URI path) - throws JAXBException, WriterException { - org.apache.taverna.scufl2.rdfxml.jaxb.WorkflowBundle bundle = makeWorkflowBundleElem(); - WorkflowBundleDocument doc = objectFactory - .createWorkflowBundleDocument(); - doc.getAny().add(bundle); - - doc.setBase(path.relativize(URI.create("./")).toASCIIString()); - JAXBElement<RDF> element = rdfObjectFactory.createRDF(doc); - - getMarshaller().marshal(element, outputStream); - seeAlsoUris.put(wfBundle, path); - } - - public void workflowDoc(OutputStream outputStream, Workflow wf, URI path) - throws JAXBException, WriterException { - org.apache.taverna.scufl2.rdfxml.jaxb.Workflow wfElem = makeWorkflow(wf, - path); - WorkflowDocument doc = objectFactory.createWorkflowDocument(); - doc.getAny().add(wfElem); - - URI wfUri = uriTools.relativeUriForBean(wf, wfBundle); - doc.setBase(uriTools.relativePath(path, wfUri).toASCIIString()); - - JAXBElement<RDF> element = rdfObjectFactory.createRDF(doc); - getMarshaller().marshal(element, outputStream); - seeAlsoUris.put(wf, path); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLWriter.java ---------------------------------------------------------------------- diff --git a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLWriter.java b/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLWriter.java deleted file mode 100644 index 3670898..0000000 --- a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLWriter.java +++ /dev/null @@ -1,164 +0,0 @@ -package org.apache.taverna.scufl2.rdfxml; -/* - * - * 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 org.apache.taverna.scufl2.rdfxml.RDFXMLReader.APPLICATION_RDF_XML; -import static org.apache.taverna.scufl2.rdfxml.RDFXMLReader.APPLICATION_VND_TAVERNA_SCUFL2_WORKFLOW_BUNDLE; - -import java.io.File; -import java.io.IOException; -import java.io.OutputStream; -import java.net.URI; -import java.util.Collections; -import java.util.Set; - -import javax.xml.bind.JAXBException; - -import org.apache.taverna.scufl2.api.annotation.Revision; -import org.apache.taverna.scufl2.api.annotation.Revisioned; -import org.apache.taverna.scufl2.api.common.URITools; -import org.apache.taverna.scufl2.api.container.WorkflowBundle; -import org.apache.taverna.scufl2.api.core.Workflow; -import org.apache.taverna.scufl2.api.io.WorkflowBundleWriter; -import org.apache.taverna.scufl2.api.io.WriterException; -import org.apache.taverna.scufl2.api.profiles.Profile; -import org.apache.taverna.scufl2.ucfpackage.UCFPackage; - - -public class RDFXMLWriter implements WorkflowBundleWriter { - private static final String WF = "wf-"; - private static final String REVISIONS = "-revisions"; - protected static final String RDF = ".rdf"; - protected static final String WORKFLOW = "workflow/"; - protected static final String HISTORY = "history/"; - protected static final String PROFILE = "profile/"; - protected static final String WORKFLOW_BUNDLE_RDF = "workflowBundle.rdf"; - - private static URITools uriTools = new URITools(); - - public static final URITools getUriTools() { - return uriTools; - } - - public static final void setUriTools(URITools uriTools) { - RDFXMLWriter.uriTools = uriTools; - } - - /** - * Version of Workflow Bundle format - */ - public final String WORKFLOW_BUNDLE_VERSION = "0.4.0"; - - @Override - public Set<String> getMediaTypes() { - return Collections - .singleton(APPLICATION_VND_TAVERNA_SCUFL2_WORKFLOW_BUNDLE); - } - - @Override - public void writeBundle(WorkflowBundle wfBundle, File destination, - String mediaType) throws WriterException, IOException { - UCFPackage ucfPackage = makeUCFPackage(wfBundle); - ucfPackage.save(destination); - } - - protected UCFPackage makeUCFPackage(WorkflowBundle wfBundle) - throws IOException, WriterException { - //UCFPackage ucfPackage = new UCFPackage(); - UCFPackage ucfPackage = wfBundle.getResources(); - if (ucfPackage.getPackageMediaType() == null) - ucfPackage - .setPackageMediaType(APPLICATION_VND_TAVERNA_SCUFL2_WORKFLOW_BUNDLE); - - RDFXMLSerializer serializer = new RDFXMLSerializer(wfBundle); - - for (Workflow wf : wfBundle.getWorkflows()) { - String path = WORKFLOW + uriTools.validFilename(wf.getName()) + RDF; - - try (OutputStream outputStream = ucfPackage - .addResourceUsingOutputStream(path, APPLICATION_RDF_XML)) { - serializer.workflowDoc(outputStream, wf, URI.create(path)); - } catch (JAXBException e) { - throw new WriterException("Can't generate " + path, e); - } - - path = HISTORY + WF + - uriTools.validFilename(wf.getName()) + REVISIONS + RDF; - addRevisions(wf, path, wfBundle); - } - - for (Profile pf : wfBundle.getProfiles()) { - String path = PROFILE + uriTools.validFilename(pf.getName()) + RDF; - try (OutputStream outputStream = ucfPackage - .addResourceUsingOutputStream(path, APPLICATION_RDF_XML)) { - serializer.profileDoc(outputStream, pf, URI.create(path)); - } catch (JAXBException e) { - throw new WriterException("Can't generate " + path, e); - } - path = HISTORY + "pf-" + - uriTools.validFilename(pf.getName()) + REVISIONS + RDF; - addRevisions(pf, path, wfBundle); - } - - try (OutputStream outputStream = ucfPackage - .addResourceUsingOutputStream(WORKFLOW_BUNDLE_RDF, - APPLICATION_RDF_XML)) { - serializer.workflowBundleDoc(outputStream, - URI.create(WORKFLOW_BUNDLE_RDF)); - } catch (JAXBException e) { - throw new WriterException("Can't generate " + WORKFLOW_BUNDLE_RDF, - e); - } - - if (ucfPackage.getPackageMediaType().equals( - APPLICATION_VND_TAVERNA_SCUFL2_WORKFLOW_BUNDLE)) - ucfPackage - .setRootFile(WORKFLOW_BUNDLE_RDF, WORKFLOW_BUNDLE_VERSION); - - String path = HISTORY + "wfbundle" + REVISIONS + RDF; - addRevisions(wfBundle, path, wfBundle); - - return ucfPackage; - } - - - protected void addRevisions(Revisioned revisioned, String path, WorkflowBundle wfBundle) throws WriterException { - @SuppressWarnings("unused") - URI uriBase = uriTools.uriForBean(wfBundle).resolve(path); - Revision currentRevision = revisioned.getCurrentRevision(); - if (currentRevision == null) - return; -// try { -// wfBundle.getResources() -// .addResource(visitor.getDoc(), path, APPLICATION_RDF_XML); -// } catch (IOException e) { -// throw new WriterException("Can't write revisions to " + path, e); -// } - } - - @Override - public void writeBundle(WorkflowBundle wfBundle, OutputStream output, - String mediaType) throws WriterException, IOException { - UCFPackage ucfPackage = makeUCFPackage(wfBundle); - ucfPackage.save(output); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/RevisionParser.java ---------------------------------------------------------------------- diff --git a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/RevisionParser.java b/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/RevisionParser.java deleted file mode 100644 index 366069b..0000000 --- a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/RevisionParser.java +++ /dev/null @@ -1,173 +0,0 @@ -package org.apache.taverna.scufl2.rdfxml; -/* - * - * 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.InputStream; -import java.net.URI; -import java.util.LinkedHashMap; -import java.util.LinkedHashSet; -import java.util.Map; -import java.util.Set; - -import javax.xml.bind.JAXBContext; -import javax.xml.bind.JAXBElement; -import javax.xml.bind.JAXBException; -import javax.xml.bind.Unmarshaller; -import javax.xml.datatype.XMLGregorianCalendar; - -import org.apache.taverna.scufl2.api.annotation.Revision; -import org.apache.taverna.scufl2.api.io.ReaderException; -import org.purl.wf4ever.roevo.jaxb.Change; -import org.purl.wf4ever.roevo.jaxb.ChangeSpecification; -import org.purl.wf4ever.roevo.jaxb.ChangeSpecification.HasChange; -import org.purl.wf4ever.roevo.jaxb.RoEvoDocument; -import org.purl.wf4ever.roevo.jaxb.VersionableResource; -import org.w3._1999._02._22_rdf_syntax_ns_.Resource; - - -public class RevisionParser { - private JAXBContext jaxbContext; - - protected JAXBContext getJaxbContext() throws JAXBException { - if (jaxbContext == null) { - Class<?>[] packages = { - org.purl.wf4ever.roevo.jaxb.ObjectFactory.class, - org.w3.prov.jaxb.ObjectFactory.class, - org.w3._1999._02._22_rdf_syntax_ns_.ObjectFactory.class, - org.w3._2000._01.rdf_schema_.ObjectFactory.class }; - jaxbContext = JAXBContext.newInstance(packages); - } - return jaxbContext; - } - - @SuppressWarnings({ "unchecked" }) - public Map<URI, Revision> readRevisionChain( - InputStream revisionDocumentStream, URI base) - throws ReaderException { - JAXBElement<RoEvoDocument> roEvoDoc; - try { - Unmarshaller unmarshaller = getJaxbContext().createUnmarshaller(); - roEvoDoc = (JAXBElement<RoEvoDocument>) unmarshaller - .unmarshal(revisionDocumentStream); - } catch (JAXBException e) { - throw new ReaderException(e); - } - - RoEvoDocument document = roEvoDoc.getValue(); - if (document.getBase() != null) - base = base.resolve(document.getBase()); - Map<URI, Revision> revisions = new LinkedHashMap<>(); - // NOTE: Silly hack to iterate/cast in one go.. will it work? - for (VersionableResource verResource : document.getAny().toArray( - new VersionableResource[0])) - parse(base, verResource, revisions); - return revisions; - } - - private Revision parse(URI base, VersionableResource verResource, - Map<URI, Revision> revisions) throws ReaderException { - URI uri = base.resolve(verResource.getAbout()); - Revision revision = addOrExisting(uri, revisions); - - if (verResource.getGeneratedAtTime() != null) { - XMLGregorianCalendar xmlCal = verResource.getGeneratedAtTime() - .getValue(); - revision.setGeneratedAtTime(xmlCal.toGregorianCalendar()); - } - - Resource wasRevisionOf = verResource.getWasRevisionOf(); - if (wasRevisionOf != null) { - // TODO Put these in a map - Revision r = addOrExisting( - base.resolve(wasRevisionOf.getResource()), revisions); - revision.setPreviousRevision(r); - } - - if (verResource.getWasChangedBy() != null) { - ChangeSpecification changeSpec = verResource.getWasChangedBy() - .getChangeSpecification(); - if (changeSpec.getFromVersion() != null) { - Revision r = addOrExisting( - base.resolve(changeSpec.getFromVersion().getResource()), - revisions); - if (revision.getPreviousRevision() != null - && revision.getPreviousRevision() != r) - throw new ReaderException( - "Inconsistent previous revision: " - + revision.getPreviousRevision() - .getIdentifier() + " or " - + r.getIdentifier()); - revision.setPreviousRevision(r); - } - - if (changeSpec.getType() != null) - revision.setChangeSpecificationType(base.resolve(changeSpec - .getType().getResource())); - - for (HasChange hasChange : changeSpec.getHasChange()) { - if (hasChange.getAddition() != null) { - Set<URI> additions = parse(hasChange.getAddition(), base); - // Note: Use addAll in case a buggy XML has multiple - // <hasChange><Addition> - revision.getAdditionOf().addAll(additions); - } - if (hasChange.getModification() != null) { - Set<URI> modifications = parse(hasChange.getModification(), - base); - revision.getModificationsOf().addAll(modifications); - } - if (hasChange.getRemoval() != null) { - Set<URI> removals = parse(hasChange.getRemoval(), base); - revision.getRemovalOf().addAll(removals); - } - } - } - - for (Resource assoc : verResource.getWasAttributedTo()) - revision.getWasAttributedTo() - .add(base.resolve(assoc.getResource())); - - for (Resource assoc : verResource.getHadOriginalSource()) { - Revision r = addOrExisting(base.resolve(assoc.getResource()), - revisions); - revision.getHadOriginalSources().add(r); - } - - return revision; - } - - private Revision addOrExisting(URI uri, Map<URI, Revision> revisions) { - Revision rev = revisions.get(uri); - if (rev != null) - return rev; - rev = new Revision(uri, null); - revisions.put(uri, rev); - return rev; - } - - private Set<URI> parse(Change addition, URI base) { - Set<URI> uris = new LinkedHashSet<>(); - for (Resource r : addition.getRelatedResource()) - uris.add(base.resolve(r.getResource())); - return uris; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/WorkflowBundleParser.java ---------------------------------------------------------------------- diff --git a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/WorkflowBundleParser.java b/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/WorkflowBundleParser.java deleted file mode 100644 index 4e56a1f..0000000 --- a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/WorkflowBundleParser.java +++ /dev/null @@ -1,190 +0,0 @@ -package org.apache.taverna.scufl2.rdfxml; -/* - * - * 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 org.apache.taverna.scufl2.rdfxml.RDFXMLReader.APPLICATION_RDF_XML; -import static org.apache.taverna.scufl2.rdfxml.RDFXMLReader.APPLICATION_VND_TAVERNA_SCUFL2_WORKFLOW_BUNDLE; -import static org.apache.taverna.scufl2.rdfxml.RDFXMLWriter.WORKFLOW_BUNDLE_RDF; - -import java.io.IOException; -import java.io.InputStream; -import java.net.URI; - -import javax.xml.bind.JAXBElement; -import javax.xml.bind.JAXBException; - -import org.apache.taverna.scufl2.api.container.WorkflowBundle; -import org.apache.taverna.scufl2.api.core.Workflow; -import org.apache.taverna.scufl2.api.io.ReaderException; -import org.apache.taverna.scufl2.ucfpackage.UCFPackage; -import org.apache.taverna.scufl2.ucfpackage.UCFPackage.ResourceEntry; - -import org.apache.taverna.scufl2.rdfxml.jaxb.WorkflowBundleDocument; - -public class WorkflowBundleParser extends AbstractParser { - - private WorkflowParser workflowParser; - private ProfileParser profileParser; - - public WorkflowBundleParser() { - super(); - workflowParser = new WorkflowParser(parserState); - profileParser = new ProfileParser(parserState); - } - - protected String findWorkflowBundlePath() { - if (APPLICATION_VND_TAVERNA_SCUFL2_WORKFLOW_BUNDLE - .equals(getParserState().getUcfPackage().getPackageMediaType())) - for (ResourceEntry potentialRoot : getParserState().getUcfPackage() - .getRootFiles()) - if (APPLICATION_RDF_XML.equals(potentialRoot.getMediaType())) - return potentialRoot.getPath(); - return WORKFLOW_BUNDLE_RDF; - } - - protected WorkflowBundle parseWorkflowBundle( - org.apache.taverna.scufl2.rdfxml.jaxb.WorkflowBundle wb, URI base) - throws ReaderException, IOException { - WorkflowBundle workflowBundle = new WorkflowBundle(); - getParserState().push(workflowBundle); - try { - workflowBundle.setResources(getParserState().getUcfPackage()); - if (wb.getName() != null) - workflowBundle.setName(wb.getName()); - if (wb.getGlobalBaseURI() != null - && wb.getGlobalBaseURI().getResource() != null) - workflowBundle.setGlobalBaseURI(base.resolve(wb - .getGlobalBaseURI().getResource())); - mapBean(base.resolve(wb.getAbout()), workflowBundle); - for (org.apache.taverna.scufl2.rdfxml.jaxb.WorkflowBundle.Workflow wfEntry : wb - .getWorkflow()) { - URI wfUri = base.resolve(wfEntry.getWorkflow().getAbout()); - String resource = wfEntry.getWorkflow().getSeeAlso() - .getResource(); - URI source = uriTools.relativePath(getParserState() - .getLocation(), base.resolve(resource)); - workflowParser.readWorkflow(wfUri, source); - } - for (org.apache.taverna.scufl2.rdfxml.jaxb.WorkflowBundle.Profile pfEntry : wb - .getProfile()) { - URI wfUri = base.resolve(pfEntry.getProfile().getAbout()); - String resource = pfEntry.getProfile().getSeeAlso() - .getResource(); - URI source = uriTools.relativePath(getParserState() - .getLocation(), base.resolve(resource)); - profileParser.readProfile(wfUri, source); - } - - if (wb.getMainWorkflow() != null - && wb.getMainWorkflow().getResource() != null) { - URI mainWfUri = base - .resolve(wb.getMainWorkflow().getResource()); - Workflow mainWorkflow = (Workflow) resolveBeanUri(mainWfUri); - if (mainWorkflow == null) - throw new ReaderException("Unknown main workflow " - + mainWfUri + ", got" - + getParserState().getUriToBean().keySet()); - workflowBundle.setMainWorkflow(mainWorkflow); - } - if (wb.getMainProfile() != null - && wb.getMainProfile().getResource() != null) { - URI profileUri = base - .resolve(wb.getMainProfile().getResource()); - org.apache.taverna.scufl2.api.profiles.Profile mainWorkflow = (org.apache.taverna.scufl2.api.profiles.Profile) resolveBeanUri(profileUri); - workflowBundle.setMainProfile(mainWorkflow); - } - } finally { - getParserState().pop(); - } - return workflowBundle; - } - - @SuppressWarnings("unchecked") - public WorkflowBundle readWorkflowBundle(UCFPackage ucfPackage, - URI suggestedLocation) throws IOException, ReaderException { - try { - getParserState().setUcfPackage(ucfPackage); - getParserState().setLocation(suggestedLocation); - if (getParserState().getLocation() == null) { - getParserState().setLocation(URI.create("")); - } else if (!getParserState().getLocation().getRawPath() - .endsWith("/")) { - if (getParserState().getLocation().getQuery() != null - || getParserState().getLocation().getFragment() != null) - /* - * Ouch.. Perhaps some silly website with ?bundleId=15 ? - * We'll better conserve that somehow. Let's do the jar: - * trick and hope it works. Have to escape evil chars. - */ - getParserState().setLocation( - URI.create("jar:" - + getParserState().getLocation() - .toASCIIString() - .replace("?", "%63") - .replace("#", "#35") + "!/")); - else - /* - * Simple, pretend we're one level down inside the ZIP file - * as a directory - */ - getParserState().setLocation( - getParserState().getLocation().resolve( - getParserState().getLocation().getRawPath() - + "/")); - } - String workflowBundlePath = findWorkflowBundlePath(); - - InputStream bundleStream = getParserState().getUcfPackage() - .getResourceAsInputStream(workflowBundlePath); - - JAXBElement<WorkflowBundleDocument> elem; - try { - elem = (JAXBElement<WorkflowBundleDocument>) unmarshaller - .unmarshal(bundleStream); - } catch (JAXBException e) { - throw new ReaderException( - "Can't parse workflow bundle document " - + workflowBundlePath, e); - } - WorkflowBundleDocument workflowBundleDocument = elem.getValue(); - - URI base = getParserState().getLocation().resolve( - workflowBundlePath); - if (workflowBundleDocument.getBase() != null) - base = getParserState().getLocation().resolve( - workflowBundleDocument.getBase()); - - if (workflowBundleDocument.getAny().size() != 1) - throw new ReaderException( - "Invalid WorkflowBundleDocument, expected only one <WorkflowBundle>"); - - org.apache.taverna.scufl2.rdfxml.jaxb.WorkflowBundle wb = (org.apache.taverna.scufl2.rdfxml.jaxb.WorkflowBundle) workflowBundleDocument - .getAny().get(0); - WorkflowBundle workflowBundle = parseWorkflowBundle(wb, base); - - scufl2Tools.setParents(workflowBundle); - return workflowBundle; - } finally { - clearParserState(); - } - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/WorkflowParser.java ---------------------------------------------------------------------- diff --git a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/WorkflowParser.java b/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/WorkflowParser.java deleted file mode 100644 index 6d84ef7..0000000 --- a/taverna-scufl2-rdfxml/src/main/java/org/apache/taverna/scufl2/rdfxml/WorkflowParser.java +++ /dev/null @@ -1,381 +0,0 @@ -package org.apache.taverna.scufl2.rdfxml; -/* - * - * 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.io.InputStream; -import java.net.URI; -import java.util.List; -import java.util.logging.Logger; - -import javax.xml.bind.JAXBElement; -import javax.xml.bind.JAXBException; - -import org.apache.taverna.scufl2.api.common.WorkflowBean; -import org.apache.taverna.scufl2.api.container.WorkflowBundle; -import org.apache.taverna.scufl2.api.core.BlockingControlLink; -import org.apache.taverna.scufl2.api.core.Processor; -import org.apache.taverna.scufl2.api.core.Workflow; -import org.apache.taverna.scufl2.api.io.ReaderException; -import org.apache.taverna.scufl2.api.iterationstrategy.IterationStrategyParent; -import org.apache.taverna.scufl2.api.port.ReceiverPort; -import org.apache.taverna.scufl2.api.port.SenderPort; - -import org.apache.taverna.scufl2.rdfxml.jaxb.Blocking; -import org.apache.taverna.scufl2.rdfxml.jaxb.CrossProduct; -import org.apache.taverna.scufl2.rdfxml.jaxb.DataLink; -import org.apache.taverna.scufl2.rdfxml.jaxb.DispatchStack; -import org.apache.taverna.scufl2.rdfxml.jaxb.DotProduct; -import org.apache.taverna.scufl2.rdfxml.jaxb.IterationStrategyStack; -import org.apache.taverna.scufl2.rdfxml.jaxb.PortNode; -import org.apache.taverna.scufl2.rdfxml.jaxb.Processor.InputProcessorPort; -import org.apache.taverna.scufl2.rdfxml.jaxb.Processor.OutputProcessorPort; -import org.apache.taverna.scufl2.rdfxml.jaxb.ProductOf; -import org.apache.taverna.scufl2.rdfxml.jaxb.WorkflowDocument; - -import com.fasterxml.jackson.databind.node.JsonNodeFactory; - -public class WorkflowParser extends AbstractParser { - private static Logger logger = Logger.getLogger(WorkflowParser.class - .getCanonicalName()); - @SuppressWarnings("unused") - private static final JsonNodeFactory JSON_NODE_FACTORY = JsonNodeFactory.instance; - - public WorkflowParser() { - } - - public WorkflowParser(ThreadLocal<ParserState> parserState) { - super(parserState); - } - - protected void parseControlLink(Blocking original) { - URI blockUri = getParserState().getCurrentBase().resolve( - original.getBlock().getResource()); - URI untilFinishedUri = getParserState().getCurrentBase().resolve( - original.getUntilFinished().getResource()); - WorkflowBean block = resolveBeanUri(blockUri); - WorkflowBean untilFinished = resolveBeanUri(untilFinishedUri); - - BlockingControlLink blocking = new BlockingControlLink(); - blocking.setBlock((org.apache.taverna.scufl2.api.core.Processor) block); - blocking.setUntilFinished((org.apache.taverna.scufl2.api.core.Processor) untilFinished); - - blocking.setParent(getParserState().getCurrent(Workflow.class)); - mapBean(getParserState().getCurrentBase().resolve(original.getAbout()), - blocking); - } - - protected void parseCrossDotOrPortNodeList(List<Object> nodeList) - throws ReaderException { - for (Object node : nodeList) - if (node instanceof DotProduct) - parseDotProduct((DotProduct) node); - else if (node instanceof CrossProduct) - parseCrossProduct((CrossProduct) node); - else if (node instanceof PortNode) - parsePortNode((PortNode) node); - else - throw new ReaderException("Unexpected node " + node); - } - - protected void parseCrossProduct(CrossProduct original) - throws ReaderException { - org.apache.taverna.scufl2.api.iterationstrategy.CrossProduct cross = new org.apache.taverna.scufl2.api.iterationstrategy.CrossProduct(); - mapBean(getParserState().getCurrentBase().resolve(original.getAbout()), - cross); - cross.setParent(getParserState().getCurrent( - IterationStrategyParent.class)); - getParserState().push(cross); - try { - parseProductOf(original.getProductOf()); - } finally { - getParserState().pop(); - } - } - - protected void parseDataLink(DataLink original) { - URI fromUri = getParserState().getCurrentBase().resolve( - original.getReceiveFrom().getResource()); - URI toUri = getParserState().getCurrentBase().resolve( - original.getSendTo().getResource()); - WorkflowBean from = resolveBeanUri(fromUri); - WorkflowBean to = resolveBeanUri(toUri); - - org.apache.taverna.scufl2.api.core.DataLink link = new org.apache.taverna.scufl2.api.core.DataLink(); - link.setReceivesFrom((SenderPort) from); - link.setSendsTo((ReceiverPort) to); - if (original.getMergePosition() != null) - link.setMergePosition(original.getMergePosition().getValue()); - link.setParent(getParserState().getCurrent(Workflow.class)); - mapBean(getParserState().getCurrentBase().resolve(original.getAbout()), - link); - } - - protected void parseDispatchStack(DispatchStack original) { - logger.fine("Ignoring Dispatch stack: not supported (SCUFL2-130)"); - return; - -// // FIXME: Legacy code - support parsing old dispatch stack configurations -// Processor processor = getParserState().getCurrent( -// org.apache.taverna.scufl2.api.core.Processor.class); -// ObjectNode config = JSON_NODE_FACTORY.objectNode(); -// getParserState().getDispatchConfigs().put(processor, config); -// if (original.getDispatchStackLayers() != null) { -// for (DispatchStackLayer dispatchStackLayer : original -// .getDispatchStackLayers().getDispatchStackLayer()) { -// parseDispatchStackLayer(dispatchStackLayer); -// } -// } - } - -// protected void parseDispatchStackLayer(DispatchStackLayer original) { -// Processor processor = getParserState().getCurrent(Processor.class); -// URI type = getParserState().getCurrentBase().resolve( -// original.getType().getResource()); -// URI config = getParserState().getCurrentBase().resolve(original.getAbout()); -// // TODO: SCUFL2-130 -// // Add Legacy code for wfbundle 0.3.0 to -// // support parsing old dispatch stack configurations -// // -// // The difficult bit is that the layers themselves has moved to -// // to be a Configuration on a Processor - but we are here within -// // parsing of the Workflow. In 0.3.0 each layer is then configured -// // separately. So we need to pass over somehow the current stack -// // to the ParserState so that it can be picked up in ProfileParser -// // and added to each of the profiles -- or at least where the -// // stack layers have been configured. -// // -// // Here's an idea on how it can work. Here we should push each layer to a -// // List<Pair<URI,URI>> that we can keep in the ParserState. -// // Then, within ProfileParser, we can pick them up and -// // recreate what the Processor config would look like for -// // the default configs - and then delete those dangling configs -// } - - protected void parseDotProduct(DotProduct original) throws ReaderException { - org.apache.taverna.scufl2.api.iterationstrategy.DotProduct dot = new org.apache.taverna.scufl2.api.iterationstrategy.DotProduct(); - mapBean(getParserState().getCurrentBase().resolve(original.getAbout()), - dot); - dot.setParent(getParserState() - .getCurrent(IterationStrategyParent.class)); - - getParserState().push(dot); - try { - parseProductOf(original.getProductOf()); - } finally { - getParserState().pop(); - } - } - - protected void parseInputWorkflowPort( - org.apache.taverna.scufl2.rdfxml.jaxb.InputWorkflowPort original) { - org.apache.taverna.scufl2.api.port.InputWorkflowPort port = new org.apache.taverna.scufl2.api.port.InputWorkflowPort(); - port.setName(original.getName()); - if (original.getPortDepth() != null) - port.setDepth(original.getPortDepth().getValue()); - port.setParent(getParserState().getCurrent(Workflow.class)); - mapBean(getParserState().getCurrentBase().resolve(original.getAbout()), - port); - } - - protected void parseIterationStrategyStack(IterationStrategyStack original) - throws ReaderException { - org.apache.taverna.scufl2.api.iterationstrategy.IterationStrategyStack iterationStrategyStack = new org.apache.taverna.scufl2.api.iterationstrategy.IterationStrategyStack(); - iterationStrategyStack.setParent(getParserState().getCurrent( - Processor.class)); - - mapBean(getParserState().getCurrentBase().resolve(original.getAbout()), - iterationStrategyStack); - if (original.getIterationStrategies() != null) { - getParserState().push(iterationStrategyStack); - try { - parseCrossDotOrPortNodeList(original.getIterationStrategies() - .getDotProductOrCrossProduct()); - } finally { - getParserState().pop(); - } - } - } - - protected void parseOutputWorkflowPort( - org.apache.taverna.scufl2.rdfxml.jaxb.OutputWorkflowPort original) { - org.apache.taverna.scufl2.api.port.OutputWorkflowPort port = new org.apache.taverna.scufl2.api.port.OutputWorkflowPort(); - port.setName(original.getName()); - port.setParent(getParserState().getCurrent(Workflow.class)); - mapBean(getParserState().getCurrentBase().resolve(original.getAbout()), - port); - } - - protected void parsePortNode(PortNode original) { - org.apache.taverna.scufl2.api.iterationstrategy.PortNode node = new org.apache.taverna.scufl2.api.iterationstrategy.PortNode(); - node.setParent(getParserState().getCurrent( - IterationStrategyParent.class)); - if (original.getDesiredDepth() != null) - node.setDesiredDepth(original.getDesiredDepth().getValue()); - mapBean(getParserState().getCurrentBase().resolve(original.getAbout()), - node); - URI inputPortUri = getParserState().getCurrentBase().resolve( - original.getIterateOverInputPort().getResource()); - org.apache.taverna.scufl2.api.port.InputProcessorPort inputPort = (org.apache.taverna.scufl2.api.port.InputProcessorPort) resolveBeanUri(inputPortUri); - node.setInputProcessorPort(inputPort); - } - - protected void parseProcessor( - org.apache.taverna.scufl2.rdfxml.jaxb.Processor processor) - throws ReaderException { - org.apache.taverna.scufl2.api.core.Processor p = new org.apache.taverna.scufl2.api.core.Processor(); - getParserState().push(p); - try { - p.setParent(getParserState().getCurrent(Workflow.class)); - mapBean(getParserState().getCurrentBase().resolve( - processor.getAbout()), p); - if (processor.getName() != null) - p.setName(processor.getName()); - for (InputProcessorPort inputProcessorPort : processor - .getInputProcessorPort()) - processorInputProcessorPort(inputProcessorPort - .getInputProcessorPort()); - for (OutputProcessorPort outputProcessorPort : processor - .getOutputProcessorPort()) - processorOutputProcessorPort(outputProcessorPort - .getOutputProcessorPort()); - if (processor.getDispatchStack() != null) - // Legacy wfbundle - parseDispatchStack(processor.getDispatchStack() - .getDispatchStack()); - if (processor.getIterationStrategyStack() != null) - parseIterationStrategyStack(processor - .getIterationStrategyStack() - .getIterationStrategyStack()); - } finally { - getParserState().pop(); - } - } - - protected void parseProductOf(ProductOf productOf) throws ReaderException { - if (productOf == null) - return; - parseCrossDotOrPortNodeList(productOf - .getCrossProductOrDotProductOrPortNode()); - } - - protected void parseWorkflow( - org.apache.taverna.scufl2.rdfxml.jaxb.Workflow workflow, URI wfUri) - throws ReaderException { - Workflow wf = new Workflow(); - wf.setParent(getParserState().getCurrent(WorkflowBundle.class)); - - if (workflow.getAbout() != null) - mapBean(getParserState().getCurrentBase().resolve( - workflow.getAbout()), wf); - // TODO: Compare resolved URI with desired wfUri - else - mapBean(wfUri, wf); - - getParserState().push(wf); - try { - if (workflow.getName() != null) - wf.setName(workflow.getName()); - if (workflow.getWorkflowIdentifier() != null - && workflow.getWorkflowIdentifier().getResource() != null) - wf.setIdentifier(getParserState().getCurrentBase().resolve( - workflow.getWorkflowIdentifier().getResource())); - - for (org.apache.taverna.scufl2.rdfxml.jaxb.Workflow.InputWorkflowPort inputWorkflowPort : workflow - .getInputWorkflowPort()) - parseInputWorkflowPort(inputWorkflowPort.getInputWorkflowPort()); - for (org.apache.taverna.scufl2.rdfxml.jaxb.Workflow.OutputWorkflowPort outputWorkflowPort : workflow - .getOutputWorkflowPort()) - parseOutputWorkflowPort(outputWorkflowPort - .getOutputWorkflowPort()); - for (org.apache.taverna.scufl2.rdfxml.jaxb.Workflow.Processor processor : workflow - .getProcessor()) - parseProcessor(processor.getProcessor()); - for (org.apache.taverna.scufl2.rdfxml.jaxb.DataLinkEntry dataLinkEntry : workflow - .getDatalink()) - parseDataLink(dataLinkEntry.getDataLink()); - for (org.apache.taverna.scufl2.rdfxml.jaxb.Control c : workflow - .getControl()) - parseControlLink(c.getBlocking()); - } finally { - getParserState().pop(); - } - } - - protected void processorInputProcessorPort( - org.apache.taverna.scufl2.rdfxml.jaxb.InputProcessorPort original) { - org.apache.taverna.scufl2.api.port.InputProcessorPort port = new org.apache.taverna.scufl2.api.port.InputProcessorPort(); - port.setName(original.getName()); - if (original.getPortDepth() != null) - port.setDepth(original.getPortDepth().getValue()); - port.setParent(getParserState().getCurrent(Processor.class)); - mapBean(getParserState().getCurrentBase().resolve(original.getAbout()), - port); - } - - protected void processorOutputProcessorPort( - org.apache.taverna.scufl2.rdfxml.jaxb.OutputProcessorPort original) { - org.apache.taverna.scufl2.api.port.OutputProcessorPort port = new org.apache.taverna.scufl2.api.port.OutputProcessorPort(); - port.setName(original.getName()); - if (original.getPortDepth() != null) - port.setDepth(original.getPortDepth().getValue()); - if (original.getGranularPortDepth() != null) - port.setGranularDepth(original.getGranularPortDepth().getValue()); - port.setParent(getParserState().getCurrent( - org.apache.taverna.scufl2.api.core.Processor.class)); - mapBean(getParserState().getCurrentBase().resolve(original.getAbout()), - port); - } - - @SuppressWarnings("unchecked") - protected void readWorkflow(URI wfUri, URI source) throws ReaderException, - IOException { - if (source.isAbsolute()) - throw new ReaderException("Can't read external workflow source " - + source); - - InputStream bundleStream = getParserState().getUcfPackage() - .getResourceAsInputStream(source.getRawPath()); - - JAXBElement<WorkflowDocument> elem; - try { - elem = (JAXBElement<WorkflowDocument>) unmarshaller - .unmarshal(bundleStream); - } catch (JAXBException e) { - throw new ReaderException( - "Can't parse workflow document " + source, e); - } - - URI base = getParserState().getLocation().resolve(source); - if (elem.getValue().getBase() != null) - base = base.resolve(elem.getValue().getBase()); - - if (elem.getValue().getAny().size() != 1) - throw new ReaderException("Expects only a <Workflow> element in " - + source); - org.apache.taverna.scufl2.rdfxml.jaxb.Workflow workflow = (org.apache.taverna.scufl2.rdfxml.jaxb.Workflow) elem - .getValue().getAny().get(0); - - getParserState().setCurrentBase(base); - parseWorkflow(workflow, wfUri); - } -}
