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[Treebase-guts] SF.net SVN: treebase:[122] trunk/treebase-core/src/main/java/org/cipres/ treebase
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From: <rv...@us...> - 2009-06-25 14:09:05
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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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