Menu
▾
▴
[Treebase-guts] SF.net SVN: treebase:[939] trunk/treebase-core/src/main/java/org/cipres/ treebase/service/nexus/NexusServiceRDFa.java
|
From: <rv...@us...> - 2011-08-25 10:30:26
|
Revision: 939
http://treebase.svn.sourceforge.net/treebase/?rev=939&view=rev
Author: rvos
Date: 2011-08-25 10:30:19 +0000 (Thu, 25 Aug 2011)
Log Message:
-----------
Because the nexml2cdao.xsl sheet has subsumed the functionality of the RDFa2RDFXML.xsl sheet this class has been considerably simplified: we now no longer need to do two transformations and reconcile the two resulting RDF graphs - we only need to do the one and return its results.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java 2011-08-25 09:20:59 UTC (rev 938)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java 2011-08-25 10:30:19 UTC (rev 939)
@@ -1,38 +1,17 @@
package org.cipres.treebase.service.nexus;
import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLEncoder;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
import java.util.Properties;
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.apache.log4j.Logger;
-import org.cipres.treebase.Constants;
-import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.domain.nexus.NexusDataSet;
import org.cipres.treebase.domain.nexus.nexml.NexmlDocumentConverter;
import org.cipres.treebase.domain.study.Study;
import org.dom4j.DocumentException;
-import org.dom4j.Node;
-import org.dom4j.QName;
import org.dom4j.io.DocumentResult;
import org.dom4j.io.DocumentSource;
import org.dom4j.io.SAXReader;
-import org.jdom.Namespace;
-import org.nexml.model.Document;
-import org.nexml.model.DocumentFactory;
import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerConfigurationException;
import javax.xml.transform.TransformerException;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.stream.StreamSource;
@@ -43,14 +22,23 @@
*
*/
public class NexusServiceRDFa extends NexusServiceNexml {
- private static final Logger LOGGER = Logger.getLogger(NexusServiceRDFa.class);
/**
*
*/
public String serialize(NexusDataSet nexusDataSet,Properties properties) {
NexmlDocumentConverter ndc = getNexmlDocumentConverter(null, properties);
- return transform(ndc.fromTreeBaseToXml(nexusDataSet).getXmlString());
+ String result = null;
+ try {
+ result = transform(ndc.fromTreeBaseToXml(nexusDataSet).getXmlString());
+ } catch (DocumentException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (TransformerException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return result;
}
/**
@@ -58,7 +46,17 @@
*/
public String serialize(NexusDataSet nexusDataSet,Properties properties,Study study) {
NexmlDocumentConverter ndc = getNexmlDocumentConverter(study, properties);
- return transform(ndc.fromTreeBaseToXml(nexusDataSet).getXmlString());
+ String result = null;
+ try {
+ result = transform(ndc.fromTreeBaseToXml(nexusDataSet).getXmlString());
+ } catch (DocumentException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (TransformerException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return result;
}
/**
@@ -66,7 +64,17 @@
*/
public String serialize(NexusDataSet nexusDataSet) {
NexmlDocumentConverter ndc = getNexmlDocumentConverter(null, null);
- return transform(ndc.fromTreeBaseToXml(nexusDataSet).getXmlString());
+ String result = null;
+ try {
+ result = transform(ndc.fromTreeBaseToXml(nexusDataSet).getXmlString());
+ } catch (DocumentException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (TransformerException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return result;
}
/**
@@ -74,7 +82,17 @@
*/
public String serialize(Study study,Properties properties) {
NexmlDocumentConverter ndc = getNexmlDocumentConverter(study, properties);
- return transform(ndc.fromTreeBaseToXml(study).getXmlString());
+ String result = null;
+ try {
+ result = transform(ndc.fromTreeBaseToXml(study).getXmlString());
+ } catch (DocumentException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (TransformerException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return result;
}
/**
@@ -82,105 +100,37 @@
*/
public String serialize(Study study) {
NexmlDocumentConverter ndc = getNexmlDocumentConverter(study, null);
- return transform(ndc.fromTreeBaseToXml(study).getXmlString());
- }
-
- /**
- * Changes local URIs into global ones, based on owl:sameAs annotations
- * @param cdaoDoc
- */
- private void normalizeCdaoDoc (org.dom4j.Document cdaoDoc) {
- Map<String,String> resourceForId = new HashMap<String,String>();
- QName rdfAboutQName = QName.get("about", "rdf", Constants.RDFURI.toString());
- QName rdfResourceQName = QName.get("resource", "rdf", Constants.RDFURI.toString());
- QName rdfIDQName = QName.get("ID", "rdf", Constants.RDFURI.toString());
-
- LOGGER.info("inside normalizeCdaoDoc");
- List<org.dom4j.Element> sameAsObjects = cdaoDoc.selectNodes("//owl:sameAs[@rdf:resource]");
- for ( org.dom4j.Element sameAsElt : sameAsObjects ) {
- org.dom4j.Element subjectElt = sameAsElt.getParent();
- String id = subjectElt.attributeValue(rdfAboutQName).substring(1); // remove #
- String resource = sameAsElt.attributeValue(rdfResourceQName);
- resourceForId.put(id, resource);
- subjectElt.detach();
- }
-
- // replace ID attributes
- List<org.dom4j.Element> identifiableObjects = cdaoDoc.selectNodes("//rdf:Description[@rdf:ID]");
- for ( org.dom4j.Element identifiableObject : identifiableObjects ) {
- String rdfID = identifiableObject.attributeValue(rdfIDQName);
- if ( resourceForId.containsKey(rdfID) ) {
- org.dom4j.Attribute idAttr = identifiableObject.attribute(rdfIDQName);
- identifiableObject.remove(idAttr);
- identifiableObject.addAttribute(rdfAboutQName, resourceForId.get(rdfID));
- }
- }
-
- // replace about and resource references
- for ( String rdfID : resourceForId.keySet() ) {
- List<org.dom4j.Element> referencingObjects = cdaoDoc.selectNodes("//rdf:Description[@rdf:about='#"+rdfID+"']");
- referencingObjects.addAll(cdaoDoc.selectNodes("//*[@rdf:resource='#"+rdfID+"']"));
- for ( org.dom4j.Element referencingObject : referencingObjects ) {
- org.dom4j.Attribute attr = referencingObject.attribute(rdfAboutQName);
- if ( null == attr ) {
- attr = referencingObject.attribute(rdfResourceQName);
- }
- if ( null != attr ) {
- attr.setValue(resourceForId.get(rdfID));
- }
- }
+ String result = null;
+ try {
+ result = transform(ndc.fromTreeBaseToXml(study).getXmlString());
+ } catch (DocumentException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (TransformerException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
}
-
+ return result;
}
+
/**
*
* @param input
* @return
+ * @throws DocumentException
+ * @throws TransformerException
*/
- @SuppressWarnings("unchecked")
- private String transform(String input) {
+ private String transform(String input) throws DocumentException, TransformerException {
SAXReader reader = new SAXReader();
- ByteArrayInputStream bs = new ByteArrayInputStream(input.getBytes());
- org.dom4j.Document nexmlDocument = null;
- try {
- nexmlDocument = reader.read( bs );
- } catch (DocumentException e) {
- System.out.println(input);
- e.printStackTrace();
- }
-
- TransformerFactory factory = TransformerFactory.newInstance();
- Transformer rdfaTransformer = null;
- Transformer cdaoTransformer = null;
- try {
- rdfaTransformer = factory.newTransformer( new StreamSource( "http://www.nexml.org/nexml/xslt/RDFa2RDFXML.xsl" ) );
- cdaoTransformer = factory.newTransformer( new StreamSource( "http://www.nexml.org/nexml/xslt/nexml2cdao.xsl" ) );
- } catch (TransformerConfigurationException e1) {
- e1.printStackTrace();
- }
- DocumentSource nexmlSource = new DocumentSource( nexmlDocument );
- DocumentResult rdfaResult = new DocumentResult();
+ org.dom4j.Document nexmlDocument = reader.read( new ByteArrayInputStream(input.getBytes()) );
+
DocumentResult cdaoResult = new DocumentResult();
- try {
- rdfaTransformer.transform( nexmlSource, rdfaResult );
- cdaoTransformer.transform( nexmlSource, cdaoResult );
- } catch (TransformerException e) {
- e.printStackTrace();
- }
+
+ Transformer cdaoTransformer = TransformerFactory.newInstance().newTransformer( new StreamSource( "http://www.nexml.org/nexml/xslt/nexml2cdao.xsl" ) );
+ cdaoTransformer.transform( new DocumentSource( nexmlDocument ), cdaoResult );
- org.dom4j.Document rdfaDoc = rdfaResult.getDocument();
org.dom4j.Document cdaoDoc = cdaoResult.getDocument();
- QName qName = QName.get("base", "xml", "http://www.w3.org/XML/1998/namespace");
- String sourceBase = nexmlDocument.getRootElement().attributeValue(qName);
- cdaoDoc.getRootElement().setAttributeValue(qName, sourceBase);
- Iterator<org.dom4j.Element> elementIterator = rdfaDoc.getRootElement().elementIterator();
- while ( elementIterator.hasNext() ) {
- org.dom4j.Element elt = elementIterator.next();
- elt.detach();
- cdaoDoc.getRootElement().add(elt);
- }
- normalizeCdaoDoc(cdaoDoc);
return cdaoDoc.asXML();
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
