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.apache.taverna.scufl2.xml.rdf.RDF;
import org.apache.taverna.scufl2.xml.rdf.Resource;
import org.apache.taverna.scufl2.xml.rdf.Type;
import org.apache.taverna.scufl2.xml.rdfs.SeeAlso;
import org.xml.sax.SAXException;
import org.apache.taverna.scufl2.xml.Blocking;
import org.apache.taverna.scufl2.xml.Control;
import org.apache.taverna.scufl2.xml.DataLink.MergePosition;
import org.apache.taverna.scufl2.xml.DataLinkEntry;
import org.apache.taverna.scufl2.xml.GranularPortDepth;
import org.apache.taverna.scufl2.xml.IterationStrategyStack.IterationStrategies;
import org.apache.taverna.scufl2.xml.ObjectFactory;
import org.apache.taverna.scufl2.xml.PortDepth;
import org.apache.taverna.scufl2.xml.PortNode.DesiredDepth;
import org.apache.taverna.scufl2.xml.ProcessorBinding.ActivityPosition;
import org.apache.taverna.scufl2.xml.ProcessorBinding.InputPortBinding;
import org.apache.taverna.scufl2.xml.ProcessorBinding.OutputPortBinding;
import org.apache.taverna.scufl2.xml.ProductOf;
import org.apache.taverna.scufl2.xml.ProfileDocument;
import org.apache.taverna.scufl2.xml.SeeAlsoType;
import org.apache.taverna.scufl2.xml.WorkflowBundleDocument;
import org.apache.taverna.scufl2.xml.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.xml.Activity activity;
private final ProfileDocument doc;
private org.apache.taverna.scufl2.xml.Profile profileElem;
private Profile profile;
private org.apache.taverna.scufl2.xml.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.xml.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.xml.InputActivityPort inputActivityPort = objectFactory
.createInputActivityPort();
inputActivityPort.setAbout(uri(node));
inputActivityPort.setName(node.getName());
inputActivityPort.setPortDepth(portDepth(node.getDepth()));
org.apache.taverna.scufl2.xml.Activity.InputActivityPort wrapper = objectFactory
.createActivityInputActivityPort();
wrapper.setInputActivityPort(inputActivityPort);
activity.getInputActivityPort().add(wrapper);
}
private void outputActivityPort(OutputActivityPort node) {
org.apache.taverna.scufl2.xml.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.xml.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.xml.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.xml.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.xml.Workflow workflow;
private org.apache.taverna.scufl2.xml.Processor proc;
private Workflow wf;
@SuppressWarnings("unused")
private org.apache.taverna.scufl2.xml.DispatchStack dispatchStack;
private org.apache.taverna.scufl2.xml.IterationStrategyStack iterationStrategyStack;
private IterationStrategies iterationStrategies;
private Stack<List<Object>> productStack;
public WorkflowSerialisationVisitor(
org.apache.taverna.scufl2.xml.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.xml.Workflow.InputWorkflowPort inP = objectFactory
.createWorkflowInputWorkflowPort();
org.apache.taverna.scufl2.xml.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.xml.Workflow.OutputWorkflowPort inP = objectFactory
.createWorkflowOutputWorkflowPort();
org.apache.taverna.scufl2.xml.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.xml.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.xml.InputProcessorPort port = objectFactory
.createInputProcessorPort();
port.setAbout(uri.toASCIIString());
port.setName(inPort.getName());
port.setPortDepth(makePortDepth(inPort.getDepth()));
org.apache.taverna.scufl2.xml.Processor.InputProcessorPort inputProcessorPort = objectFactory
.createProcessorInputProcessorPort();
inputProcessorPort.setInputProcessorPort(port);
proc.getInputProcessorPort().add(inputProcessorPort);
}
if (node instanceof OutputProcessorPort) {
org.apache.taverna.scufl2.xml.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.xml.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.xml.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.xml.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.xml.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.xml.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.xml.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.apache.taverna.scufl2.xml.rdf.ObjectFactory.class,
org.apache.taverna.scufl2.xml.rdfs.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.apache.taverna.scufl2.xml.rdfs.ObjectFactory rdfsObjectFactory = new org.apache.taverna.scufl2.xml.rdfs.ObjectFactory();
private org.apache.taverna.scufl2.xml.rdf.ObjectFactory rdfObjectFactory = new org.apache.taverna.scufl2.xml.rdf.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.xml.Workflow makeWorkflow(
Workflow wf, URI documentPath) {
org.apache.taverna.scufl2.xml.Workflow workflow = objectFactory
.createWorkflow();
wf.accept(new WorkflowSerialisationVisitor(workflow) {
});
return workflow;
}
protected org.apache.taverna.scufl2.xml.WorkflowBundle makeWorkflowBundleElem() {
org.apache.taverna.scufl2.xml.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.xml.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.xml.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.xml.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.xml.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);
}
}