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From: <rv...@us...> - 2009-06-25 02:50:16
|
Revision: 112
http://treebase.svn.sourceforge.net/treebase/?rev=112&view=rev
Author: rvos
Date: 2009-06-25 02:50:10 +0000 (Thu, 25 Jun 2009)
Log Message:
-----------
Adding NexusServiceRDFa serialization service
Added Paths:
-----------
trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java
Added: 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 (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java 2009-06-25 02:50:10 UTC (rev 112)
@@ -0,0 +1,83 @@
+/**
+ *
+ */
+package org.cipres.treebase.service.nexus;
+
+import java.io.ByteArrayInputStream;
+
+import javax.xml.parsers.ParserConfigurationException;
+
+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.io.DocumentResult;
+import org.dom4j.io.DocumentSource;
+import org.dom4j.io.SAXReader;
+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;
+
+
+/**
+ * @author rvosa
+ *
+ */
+public class NexusServiceRDFa extends NexusServiceNexml {
+ public String serialize(NexusDataSet nexusDataSet) {
+ Document document = null;
+ try {
+ document = DocumentFactory.createDocument();
+ } catch (ParserConfigurationException e) {
+ e.printStackTrace();
+ }
+ NexmlDocumentConverter ndc = new NexmlDocumentConverter(null,getTaxonLabelHome(),document);
+ String NeXML = ndc.fromTreeBaseToXml(nexusDataSet).getXmlString();
+ return transform(NeXML);
+ }
+
+ public String serialize(Study study) {
+ Document document = null;
+ try {
+ document = DocumentFactory.createDocument();
+ } catch (ParserConfigurationException e) {
+ e.printStackTrace();
+ }
+ NexmlDocumentConverter ndc = new NexmlDocumentConverter(study,getTaxonLabelHome(),document);
+ String NeXML = ndc.fromTreeBaseToXml(study).getXmlString();
+ return transform(NeXML);
+ }
+
+ private String transform(String input) {
+ SAXReader reader = new SAXReader();
+ ByteArrayInputStream bs = new ByteArrayInputStream(input.getBytes());
+ org.dom4j.Document jDomDocument = null;
+ try {
+ jDomDocument = reader.read( bs );
+ } catch (DocumentException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ TransformerFactory factory = TransformerFactory.newInstance();
+ Transformer transformer = null;
+ try {
+ transformer = factory.newTransformer( new StreamSource( "http://www.nexml.org/nexml/xslt/RDFa2RDFXML.xsl" ) );
+ } catch (TransformerConfigurationException e1) {
+ e1.printStackTrace();
+ }
+ DocumentSource source = new DocumentSource( jDomDocument );
+ DocumentResult result = new DocumentResult();
+ try {
+ transformer.transform( source, result );
+ } catch (TransformerException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ org.dom4j.Document transformedDoc = result.getDocument();
+ return transformedDoc.asXML();
+ }
+}
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|
|
From: <rv...@us...> - 2009-06-28 10:13:13
|
Revision: 138
http://treebase.svn.sourceforge.net/treebase/?rev=138&view=rev
Author: rvos
Date: 2009-06-28 10:12:13 +0000 (Sun, 28 Jun 2009)
Log Message:
-----------
xml:base attribute now correctly copied from input nexml document to output rdf document.
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 2009-06-28 10:11:30 UTC (rev 137)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java 2009-06-28 10:12:13 UTC (rev 138)
@@ -12,11 +12,14 @@
import org.cipres.treebase.domain.nexus.nexml.NexmlDocumentConverter;
import org.cipres.treebase.domain.study.Study;
import org.dom4j.DocumentException;
+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;
@@ -95,6 +98,9 @@
e.printStackTrace();
}
org.dom4j.Document transformedDoc = result.getDocument();
+ QName qName = QName.get("base", "xml", "http://www.w3.org/XML/1998/namespace");
+ String sourceBase = jDomDocument.getRootElement().attributeValue(qName);
+ transformedDoc.getRootElement().setAttributeValue(qName, sourceBase);
return transformedDoc.asXML();
}
}
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|
|
From: <rv...@us...> - 2010-02-11 06:37:25
|
Revision: 489
http://treebase.svn.sourceforge.net/treebase/?rev=489&view=rev
Author: rvos
Date: 2010-02-11 06:37:11 +0000 (Thu, 11 Feb 2010)
Log Message:
-----------
Completed nexml2cdao conversion.
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 2010-02-10 02:04:54 UTC (rev 488)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java 2010-02-11 06:37:11 UTC (rev 489)
@@ -1,6 +1,12 @@
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.Iterator;
import java.util.Properties;
import javax.xml.parsers.ParserConfigurationException;
@@ -72,32 +78,41 @@
private String transform(String input) {
SAXReader reader = new SAXReader();
ByteArrayInputStream bs = new ByteArrayInputStream(input.getBytes());
- org.dom4j.Document jDomDocument = null;
+ org.dom4j.Document nexmlDocument = null;
try {
- jDomDocument = reader.read( bs );
+ nexmlDocument = reader.read( bs );
} catch (DocumentException e) {
- // TODO Auto-generated catch block
e.printStackTrace();
}
+
TransformerFactory factory = TransformerFactory.newInstance();
- Transformer transformer = null;
+ Transformer rdfaTransformer = null;
+ Transformer cdaoTransformer = null;
try {
- transformer = factory.newTransformer( new StreamSource( "http://www.nexml.org/nexml/xslt/RDFa2RDFXML.xsl" ) );
+ 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 source = new DocumentSource( jDomDocument );
- DocumentResult result = new DocumentResult();
+ DocumentSource nexmlSource = new DocumentSource( nexmlDocument );
+ DocumentResult rdfaResult = new DocumentResult();
+ DocumentResult cdaoResult = new DocumentResult();
try {
- transformer.transform( source, result );
- } catch (TransformerException e) {
- // TODO Auto-generated catch block
+ rdfaTransformer.transform( nexmlSource, rdfaResult );
+ cdaoTransformer.transform( nexmlSource, cdaoResult );
+ } catch (TransformerException e) {
e.printStackTrace();
}
- org.dom4j.Document transformedDoc = result.getDocument();
+
+ 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 = jDomDocument.getRootElement().attributeValue(qName);
- transformedDoc.getRootElement().setAttributeValue(qName, sourceBase);
- return transformedDoc.asXML();
+ String sourceBase = nexmlDocument.getRootElement().attributeValue(qName);
+ cdaoDoc.getRootElement().setAttributeValue(qName, sourceBase);
+ Iterator<org.dom4j.Element> elementIterator = rdfaDoc.getRootElement().elementIterator();
+ while ( elementIterator.hasNext() ) {
+ cdaoDoc.getRootElement().add(elementIterator.next());
+ }
+ return cdaoDoc.asXML();
}
}
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|
|
From: <rv...@us...> - 2010-02-11 06:52:03
|
Revision: 490
http://treebase.svn.sourceforge.net/treebase/?rev=490&view=rev
Author: rvos
Date: 2010-02-11 06:51:56 +0000 (Thu, 11 Feb 2010)
Log Message:
-----------
Fixed org.dom4j.IllegalAddException
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 2010-02-11 06:37:11 UTC (rev 489)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java 2010-02-11 06:51:56 UTC (rev 490)
@@ -109,9 +109,11 @@
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();
+ Iterator<org.dom4j.Element> elementIterator = rdfaDoc.getRootElement().elementIterator();
while ( elementIterator.hasNext() ) {
- cdaoDoc.getRootElement().add(elementIterator.next());
+ org.dom4j.Element elt = elementIterator.next();
+ elt.detach();
+ cdaoDoc.getRootElement().add(elt);
}
return cdaoDoc.asXML();
}
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|
|
From: <rv...@us...> - 2010-03-12 23:34:19
|
Revision: 565
http://treebase.svn.sourceforge.net/treebase/?rev=565&view=rev
Author: rvos
Date: 2010-03-12 23:34:13 +0000 (Fri, 12 Mar 2010)
Log Message:
-----------
Flattened rdf triples. TODO: replace id attributes with purl URIs.
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 2010-03-12 23:32:59 UTC (rev 564)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java 2010-03-12 23:34:13 UTC (rev 565)
@@ -11,6 +11,8 @@
import javax.xml.parsers.ParserConfigurationException;
+import org.apache.log4j.Logger;
+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;
@@ -35,46 +37,86 @@
*
*/
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());
}
+
+ /**
+ *
+ */
public String serialize(NexusDataSet nexusDataSet) {
- /*
- Document document = null;
- try {
- document = DocumentFactory.createDocument();
- } catch (ParserConfigurationException e) {
- e.printStackTrace();
- }
- NexmlDocumentConverter ndc = new NexmlDocumentConverter(null,getTaxonLabelHome(),document);
- String NeXML = ndc.fromTreeBaseToXml(nexusDataSet).getXmlString();
- return transform(NeXML);
- */
NexmlDocumentConverter ndc = getNexmlDocumentConverter(null, null);
return transform(ndc.fromTreeBaseToXml(nexusDataSet).getXmlString());
}
+ /**
+ *
+ */
public String serialize(Study study,Properties properties) {
NexmlDocumentConverter ndc = getNexmlDocumentConverter(study, properties);
return transform(ndc.fromTreeBaseToXml(study).getXmlString());
}
+
+ /**
+ *
+ */
public String serialize(Study study) {
- /*
- Document document = null;
- try {
- document = DocumentFactory.createDocument();
- } catch (ParserConfigurationException e) {
- e.printStackTrace();
- }
- NexmlDocumentConverter ndc = new NexmlDocumentConverter(study,getTaxonLabelHome(),document);
- String NeXML = ndc.fromTreeBaseToXml(study).getXmlString();
- return transform(NeXML);
- */
NexmlDocumentConverter ndc = getNexmlDocumentConverter(study, null);
return transform(ndc.fromTreeBaseToXml(study).getXmlString());
}
+ /**
+ *
+ * @param cdaoDoc
+ */
+ private void normalizeCdaoDoc (org.dom4j.Document cdaoDoc) {
+
+ LOGGER.info("inside normalizeCdaoDoc");
+ Iterator<org.dom4j.Element> parentIterator = cdaoDoc.getRootElement().elementIterator();
+ while ( parentIterator.hasNext() ) {
+ org.dom4j.Element parent = parentIterator.next();
+ QName rdfIDQName = QName.get("ID", "rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
+ String rdfID = parent.attributeValue(rdfIDQName);
+ if ( ! TreebaseUtil.isEmpty(rdfID) ) {
+
+ LOGGER.info("going to flatten ID "+rdfID);
+ Iterator<org.dom4j.Element> childIterator = cdaoDoc.getRootElement().elementIterator();
+ while ( childIterator.hasNext() ) {
+ org.dom4j.Element child = childIterator.next();
+ QName rdfAboutQName = QName.get("about", "rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
+ String rdfAbout = child.attributeValue(rdfAboutQName);
+
+ if ( ! TreebaseUtil.isEmpty(rdfAbout) && rdfAbout.equals("#"+rdfID) ) {
+
+ LOGGER.info("found referencing element");
+ Iterator<org.dom4j.Element> grandChildIterator = child.elementIterator();
+ while ( grandChildIterator.hasNext() ) {
+ org.dom4j.Element grandChild = grandChildIterator.next();
+ grandChild.detach();
+ parent.add(grandChild);
+ }
+
+ childIterator.remove();
+ }
+
+ }
+ }
+ }
+
+ }
+
+ /**
+ *
+ * @param input
+ * @return
+ */
+ @SuppressWarnings("unchecked")
private String transform(String input) {
SAXReader reader = new SAXReader();
ByteArrayInputStream bs = new ByteArrayInputStream(input.getBytes());
@@ -82,6 +124,7 @@
try {
nexmlDocument = reader.read( bs );
} catch (DocumentException e) {
+ System.out.println(input);
e.printStackTrace();
}
@@ -115,6 +158,7 @@
elt.detach();
cdaoDoc.getRootElement().add(elt);
}
+ normalizeCdaoDoc(cdaoDoc);
return cdaoDoc.asXML();
}
}
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|
|
From: <rv...@us...> - 2010-06-03 17:14:52
|
Revision: 710
http://treebase.svn.sourceforge.net/treebase/?rev=710&view=rev
Author: rvos
Date: 2010-06-03 17:14:46 +0000 (Thu, 03 Jun 2010)
Log Message:
-----------
Now changes local URIs into global ones, based on the owl:sameAs value
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 2010-06-03 17:13:16 UTC (rev 709)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java 2010-06-03 17:14:46 UTC (rev 710)
@@ -6,17 +6,23 @@
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;
@@ -72,42 +78,50 @@
}
/**
- *
+ * 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");
- Iterator<org.dom4j.Element> parentIterator = cdaoDoc.getRootElement().elementIterator();
- while ( parentIterator.hasNext() ) {
- org.dom4j.Element parent = parentIterator.next();
- QName rdfIDQName = QName.get("ID", "rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
- String rdfID = parent.attributeValue(rdfIDQName);
- if ( ! TreebaseUtil.isEmpty(rdfID) ) {
-
- LOGGER.info("going to flatten ID "+rdfID);
- Iterator<org.dom4j.Element> childIterator = cdaoDoc.getRootElement().elementIterator();
- while ( childIterator.hasNext() ) {
- org.dom4j.Element child = childIterator.next();
- QName rdfAboutQName = QName.get("about", "rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
- String rdfAbout = child.attributeValue(rdfAboutQName);
-
- if ( ! TreebaseUtil.isEmpty(rdfAbout) && rdfAbout.equals("#"+rdfID) ) {
-
- LOGGER.info("found referencing element");
- Iterator<org.dom4j.Element> grandChildIterator = child.elementIterator();
- while ( grandChildIterator.hasNext() ) {
- org.dom4j.Element grandChild = grandChildIterator.next();
- grandChild.detach();
- parent.add(grandChild);
- }
-
- childIterator.remove();
- }
-
- }
+ 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));
+ }
+ }
+ }
}
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|
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();
}
}
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