Thread: [Treebase-guts] SF.net SVN: treebase:[122] trunk/treebase-core/src/main/java/org/cipres/ treebase

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Revision: 122
          http://treebase.svn.sourceforge.net/treebase/?rev=122&view=rev
Author:   rvos
Date:     2009-06-25 13:38:28 +0000 (Thu, 25 Jun 2009)

Log Message:
-----------
Changed base URI handling

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusService.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNCL.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusService.java
===================================================================

--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusService.java	2009-06-25 13:32:10 UTC (rev 121)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusService.java	2009-06-25 13:38:28 UTC (rev 122)
@@ -23,6 +23,7 @@
 
 import java.io.File;
 import java.util.Collection;
+import java.util.Properties;
 
 import org.cipres.treebase.domain.study.Study;
 import org.cipres.treebase.event.ProgressionListener;
@@ -66,6 +67,7 @@
 	 * @return a serialization of the supplied NexusDataSet
 	 */
 	String serialize(NexusDataSet pNexusDataSet);
+	String serialize(NexusDataSet pNexusDataSet, Properties pProperties);
 	
 	/**
 	 * Write the NexusDataSet to a string that represents the object.
@@ -76,5 +78,7 @@
 	 * @return a serialization of the supplied Study
 	 */	
 	String serialize(Study pStudy);
+	String serialize(Study pStudy, Properties pProperties);
+	
 
 }

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java	2009-06-25 13:32:10 UTC (rev 121)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java	2009-06-25 13:38:28 UTC (rev 122)
@@ -26,6 +26,11 @@
 		super(study, taxonLabelHome, document);
 	}
 	
+	public NexmlDocumentConverter(Study study, TaxonLabelHome taxonLabelHome,
+			Document document,String baseURI) {
+		super(study, taxonLabelHome, document,baseURI);
+	}	
+	
 	/**
 	 * 
 	 * @param pDocument

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java	2009-06-25 13:32:10 UTC (rev 121)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java	2009-06-25 13:38:28 UTC (rev 122)
@@ -23,8 +23,10 @@
 public class NexmlObjectConverter extends AbstractNexusConverter {
 	protected static URI mDCURI;
 	protected static URI mPrismURI;
+	protected URI mBaseURI;
 	private static String mDCURIString = "http://purl.org/dc/elements/1.1/";
 	private static String mPrismURIString = "http://prismstandard.org/namespaces/1.2/basic/";
+	private static String mBaseURIString = "http://purl.org/PHYLO/TREEBASE/PHYLOWS/";
 	private static String mDCIdentifier = "dc:identifier";	
 	public static String TreeBASE2Prefix = "TreeBASE2";
 	private Document mDocument;
@@ -34,18 +36,30 @@
 	 * @param study
 	 * @param taxonLabelHome
 	 */
-	public NexmlObjectConverter(Study study, TaxonLabelHome taxonLabelHome, Document document) {
+	public NexmlObjectConverter(Study study, TaxonLabelHome taxonLabelHome, Document document, String baseURI) {
 		try {
 			mDCURI = new URI(mDCURIString);
 			mPrismURI = new URI(mPrismURIString);
+			if ( null != baseURI ) {
+				mBaseURI = new URI(baseURI);
+			}
+			else {
+				mBaseURI = new URI(mBaseURIString);
+			}
 		} catch (URISyntaxException e) {
 			e.printStackTrace();
-		}			
+		}
+		document.setBaseURI(mBaseURI);
 		setTaxonLabelHome(taxonLabelHome);
 		setStudy(study);
 		setDocument(document);
-	}	
+	}
 	
+	public NexmlObjectConverter(Study study, TaxonLabelHome taxonLabelHome, Document document) {
+		this(study,taxonLabelHome,document,null);
+	}
+
+	
 	/**
 	 * 
 	 * @param tbPersistable
@@ -64,11 +78,12 @@
 	protected void attachTreeBaseID(Annotatable annotatable,TBPersistable tbPersistable,Class<?> persistableClass) {
 		if ( null != tbPersistable.getId() ) {
 			attachAnnotation(mDCIdentifier,makeNamespacedID(tbPersistable,persistableClass),mDCURI,annotatable);			
-			String uriString = "http://localhost:8080/treebase-web/PhyloWS/" + makeNamespacedID(tbPersistable,persistableClass);
+			String uriString = mBaseURI.toString() + makeNamespacedID(tbPersistable,persistableClass);
 			try {
 				annotatable.addAnnotationValue("dc:relation",mDCURI, new URI(uriString));
-			} catch ( Exception e ) {
-				
+			} catch (URISyntaxException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
 			}
 		}
 	}
@@ -165,5 +180,13 @@
 			character = iterator.next();
 		}
 		return result.toString();
+	}
+
+	public URI getBaseURI() {
+		return mBaseURI;
+	}
+
+	public void setBaseURI(URI baseURI) {
+		mBaseURI = baseURI;
 	}	
 }

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java	2009-06-25 13:32:10 UTC (rev 121)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java	2009-06-25 13:38:28 UTC (rev 122)
@@ -22,6 +22,7 @@
 
 import java.io.File;
 import java.util.Collection;
+import java.util.Properties;
 
 import org.apache.log4j.Logger;
 
@@ -222,4 +223,14 @@
 		return null;
 	}
 
+	public String serialize(NexusDataSet nexusDataSet, Properties properties) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	public String serialize(Study study, Properties properties) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
 }

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNCL.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNCL.java	2009-06-25 13:32:10 UTC (rev 121)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNCL.java	2009-06-25 13:38:28 UTC (rev 122)
@@ -22,6 +22,7 @@
 
 import java.io.File;
 import java.util.Collection;
+import java.util.Properties;
 
 import org.apache.log4j.Logger;
 
@@ -174,4 +175,14 @@
 		return null;
 	}
 
+	public String serialize(NexusDataSet nexusDataSet, Properties properties) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	public String serialize(Study study, Properties properties) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
 }

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java	2009-06-25 13:32:10 UTC (rev 121)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java	2009-06-25 13:38:28 UTC (rev 122)
@@ -1,7 +1,10 @@
 package org.cipres.treebase.service.nexus;
 
 import java.io.File;
+import java.net.URI;
+import java.net.URISyntaxException;
 import java.util.Collection;
+import java.util.Properties;
 
 import javax.xml.parsers.ParserConfigurationException;
 
@@ -63,6 +66,7 @@
 	}
 
 	public String serialize(NexusDataSet nexusDataSet) {
+		/*
 		Document document = null;
 		try {
 			document = DocumentFactory.createDocument();
@@ -71,9 +75,12 @@
 		}
 		NexmlDocumentConverter ndc = new NexmlDocumentConverter(null,getTaxonLabelHome(),document);
 		return ndc.fromTreeBaseToXml(nexusDataSet).getXmlString();
+		*/
+		return serialize(nexusDataSet,null);
 	}
 
 	public String serialize(Study study) {
+		/*
 		Document document = null;
 		try {
 			document = DocumentFactory.createDocument();
@@ -82,6 +89,8 @@
 		}
 		NexmlDocumentConverter ndc = new NexmlDocumentConverter(study,getTaxonLabelHome(),document);
 		return ndc.fromTreeBaseToXml(study).getXmlString();
+		*/
+		return serialize(study,null);
 	}
 
 	public TaxonLabelHome getTaxonLabelHome() {
@@ -91,5 +100,59 @@
 	public void setTaxonLabelHome(TaxonLabelHome taxonLabelHome) {
 		mTaxonLabelHome = taxonLabelHome;
 	}
+	
+	protected NexmlDocumentConverter getNexmlDocumentConverter(Study study,Properties properties) {
+		String baseURI = null;
+		if ( null != properties ) {
+			baseURI = properties.getProperty("nexml.uri.base");
+		}
+		Document document = null;
+		try {
+			document = DocumentFactory.createDocument();
+			document.setBaseURI(new URI(baseURI));//NPE
+		} catch (URISyntaxException e) {
+			e.printStackTrace();
+		} catch (ParserConfigurationException e) {
+			e.printStackTrace();
+		}
+		NexmlDocumentConverter ndc = new NexmlDocumentConverter(study,getTaxonLabelHome(),document,baseURI);
+		return ndc;
+	}
 
+	public String serialize(NexusDataSet nexusDataSet, Properties properties) {
+		/*
+		String baseURI = null;
+		if ( null != properties ) {
+			baseURI = properties.getProperty("nexml.uri.base");
+		}
+		Document document = null;
+		try {
+			document = DocumentFactory.createDocument();
+		} catch (ParserConfigurationException e) {
+			e.printStackTrace();
+		}		
+		NexmlDocumentConverter ndc = new NexmlDocumentConverter(null,getTaxonLabelHome(),document,baseURI);
+		*/
+		NexmlDocumentConverter ndc = this.getNexmlDocumentConverter(null, properties);
+		return ndc.fromTreeBaseToXml(nexusDataSet).getXmlString();
+	}
+
+	public String serialize(Study study, Properties properties) {
+		/*
+		String baseURI = null;
+		if ( null != properties ) {
+			baseURI = properties.getProperty("nexml.uri.base");
+		}		
+		Document document = null;
+		try {
+			document = DocumentFactory.createDocument();
+		} catch (ParserConfigurationException e) {
+			e.printStackTrace();
+		}
+		NexmlDocumentConverter ndc = new NexmlDocumentConverter(study,getTaxonLabelHome(),document,baseURI);
+		*/
+		NexmlDocumentConverter ndc = this.getNexmlDocumentConverter(study, properties);
+		return ndc.fromTreeBaseToXml(study).getXmlString();
+	}
+
 }

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	2009-06-25 13:32:10 UTC (rev 121)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java	2009-06-25 13:38:28 UTC (rev 122)
@@ -4,6 +4,7 @@
 package org.cipres.treebase.service.nexus;
 
 import java.io.ByteArrayInputStream;
+import java.util.Properties;
 
 import javax.xml.parsers.ParserConfigurationException;
 
@@ -28,7 +29,12 @@
  *
  */
 public class NexusServiceRDFa extends NexusServiceNexml {
+	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();
@@ -38,9 +44,17 @@
 		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();
@@ -50,6 +64,9 @@
 		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());		
 	}
 	
 	private String transform(String input) {


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Thread: [Treebase-guts] SF.net SVN: treebase:[122] trunk/treebase-core/src/main/java/org/cipres/ treebase

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