Revision: 14941
http://gate.svn.sourceforge.net/gate/?rev=14941&view=rev
Author: markagreenwood
Date: 2012-01-09 10:54:30 +0000 (Mon, 09 Jan 2012)
Log Message:
-----------
we now pass in a loaded ontology instance rather than a URL to give us more
flexibility on how the ontology is loaded
Modified Paths:
--------------
gate/trunk/plugins/Ontology_BDM_Computation/creole.xml
gate/trunk/plugins/Ontology_BDM_Computation/src/gate/bdmComp/BDMCompMain.java
gate/trunk/plugins/Ontology_BDM_Computation/src/gate/bdmComp/TestBDMCompPlugin.java
Modified: gate/trunk/plugins/Ontology_BDM_Computation/creole.xml
===================================================================
--- gate/trunk/plugins/Ontology_BDM_Computation/creole.xml 2012-01-09
10:43:38 UTC (rev 14940)
+++ gate/trunk/plugins/Ontology_BDM_Computation/creole.xml 2012-01-09
10:54:30 UTC (rev 14941)
@@ -11,9 +11,9 @@
<CLASS>gate.bdmComp.BDMCompMain</CLASS>
<JAR>BDMCompMain.jar</JAR>
- <PARAMETER NAME="ontologyURL"
- COMMENT="The URL storing the ontology used for BDM computing"
RUNTIME="true"
- OPTIONAL="false">java.net.URL</PARAMETER>
+ <PARAMETER NAME="ontology"
+ COMMENT="The ontology used for BDM computing" RUNTIME="true"
+ OPTIONAL="false">gate.creole.ontology.Ontology</PARAMETER>
<PARAMETER NAME="outputBDMFile"
COMMENT="The URL storing the BDM scores" RUNTIME="true"
Modified:
gate/trunk/plugins/Ontology_BDM_Computation/src/gate/bdmComp/BDMCompMain.java
===================================================================
---
gate/trunk/plugins/Ontology_BDM_Computation/src/gate/bdmComp/BDMCompMain.java
2012-01-09 10:43:38 UTC (rev 14940)
+++
gate/trunk/plugins/Ontology_BDM_Computation/src/gate/bdmComp/BDMCompMain.java
2012-01-09 10:54:30 UTC (rev 14941)
@@ -14,6 +14,14 @@
package gate.bdmComp;
+import gate.Factory;
+import gate.ProcessingResource;
+import gate.creole.AbstractLanguageAnalyser;
+import gate.creole.ExecutionException;
+import gate.creole.ResourceInstantiationException;
+import gate.creole.ontology.OClass;
+import gate.creole.ontology.Ontology;
+
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileNotFoundException;
@@ -21,23 +29,12 @@
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.UnsupportedEncodingException;
-import java.net.MalformedURLException;
import java.net.URISyntaxException;
import java.net.URL;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Set;
-import gate.Factory;
-import gate.FeatureMap;
-import gate.Gate;
-import gate.ProcessingResource;
-import gate.creole.AbstractLanguageAnalyser;
-import gate.creole.ExecutionException;
-import gate.creole.ResourceInstantiationException;
-import gate.creole.ontology.OClass;
-import gate.creole.ontology.Ontology;
-
/**
* TODO: the output file is always growing for each run of the PR
* it's like if the local variables are not reset for each run so it
@@ -45,10 +42,8 @@
*/
public class BDMCompMain extends AbstractLanguageAnalyser implements
ProcessingResource {
- /** File name or URL storing the ontology. */
- URL ontologyURL = null;
/** The ontology used. */
- Ontology ontologyUsed = null;
+ Ontology ontology = null;
/** The file storing the BDM score. */
URL outputBDMFile = null;
/** store the BDM information for each pair of concepts. */
@@ -87,38 +82,26 @@
/** load the ontology. */
//if(ontologyUsed == null || ontologyUsed.toString().trim() == "") {
- if(ontologyURL == null || ontologyURL.toString().trim() == "") {
+ if(ontology == null) {
throw new ExecutionException("No ontology: neither using a loaded
ontology nor giving the ontology URL!");
- } else {
+ }
+ /*else {
// step 3: set the parameters
- FeatureMap fm = Factory.newFeatureMap();
- fm.put("rdfXmlURL", ontologyURL);
- String baseURI=ontologyURL.toURI().toString();
- baseURI = baseURI.substring(0,baseURI.lastIndexOf('/')+1);
- fm.put("baseURI", baseURI);
-
- // step 4: finally create an instance of ontology
- try {
- ontologyUsed =
(Ontology)Factory.createResource("gate.creole.ontology.impl.sesame.OWLIMOntology",
fm);
- }
- catch(ResourceInstantiationException e) {
- e.printStackTrace();
- }
- }
+ }*/
//}
//write the header of the bdm score file
if(isExistingResultFile) {
bdmResultsWriter.append("##The following are the BDM scores for
");
- bdmResultsWriter.append("each pair of concepts in the ontology
named "+ontologyUsed.getName()+".\n");
+ bdmResultsWriter.append("each pair of concepts in the ontology
named "+ontology.getName()+".\n");
}
// retrieving a list of top classes
- Set<OClass> topClasses = ontologyUsed.getOClasses(true);
+ Set<OClass> topClasses = ontology.getOClasses(true);
if(topClasses.size()>1) {
System.out.println("The ontology has "+topClasses.size() +" top
classes!!");
}
// retrieving a list of all classes
- Set<OClass> allConcepts = ontologyUsed.getOClasses(false);
+ Set<OClass> allConcepts = ontology.getOClasses(false);
//assign a number id to each class
HashMap<Integer,OClass> id2concept= new HashMap<Integer,OClass>();
@@ -130,7 +113,7 @@
++num;
}
- System.out.println("ontology "+ontologyUsed.getName()+",
allConcepts="+allConcepts.size());
+ System.out.println("ontology "+ontology.getName()+",
allConcepts="+allConcepts.size());
//for each concept, get the chain from it to the top class
HashMap<OClass,String> concept2chain = new HashMap<OClass,String>();
@@ -354,7 +337,7 @@
}
}
// unload the ontology
- if (ontologyUsed != null) Factory.deleteResource(ontologyUsed);
+ if (ontology != null) Factory.deleteResource(ontology);
}
@@ -377,19 +360,19 @@
// System.out.println("****** curCon="+curCon.getName()+"*"+",
num="+superCons.size());
//}
for(OClass oneCon:superCons) {
- oneCon = (OClass)
ontologyUsed.getOResourceByName(oneCon.getName());
+ oneCon = (OClass) ontology.getOResourceByName(oneCon.getName());
chainNow += obtainAChain(oneCon, chainSofar);
}
}
return chainNow;
}
- public void setOntologyURL(URL ontoU) {
- this.ontologyURL = ontoU;
+ public void setOntology(Ontology ontology) {
+ this.ontology = ontology;
}
- public URL getOntologyURL() {
- return this.ontologyURL;
+ public Ontology getOntology() {
+ return this.ontology;
}
public void setOutputBDMFile(URL ontoU) {
this.outputBDMFile = ontoU;
Modified:
gate/trunk/plugins/Ontology_BDM_Computation/src/gate/bdmComp/TestBDMCompPlugin.java
===================================================================
---
gate/trunk/plugins/Ontology_BDM_Computation/src/gate/bdmComp/TestBDMCompPlugin.java
2012-01-09 10:43:38 UTC (rev 14940)
+++
gate/trunk/plugins/Ontology_BDM_Computation/src/gate/bdmComp/TestBDMCompPlugin.java
2012-01-09 10:54:30 UTC (rev 14941)
@@ -5,6 +5,7 @@
import gate.FeatureMap;
import gate.Gate;
import gate.GateConstants;
+import gate.creole.ontology.Ontology;
import gate.util.GateException;
import java.io.File;
@@ -98,7 +99,18 @@
File testOnto = new File(corpusDirName, "protont.owl");
File bdmFile = new File(corpusDirName, "protont-bdm.txt");
- bdmM.setOntologyURL(testOnto.toURI().toURL()); //("ann1;ann2;ann3");
+ FeatureMap fm = Factory.newFeatureMap();
+ fm.put("rdfXmlURL", testOnto.toURI().toURL());
+
+ String baseURI=testOnto.getParentFile().toURI().toString();
+ baseURI = baseURI.substring(0,baseURI.lastIndexOf('/')+1);
+ fm.put("baseURI", baseURI);
+
+ fm.put("loadImports", Boolean.FALSE);
+
+ Ontology ontology =
(Ontology)Factory.createResource("gate.creole.ontology.impl.sesame.OWLIMOntology",
fm);
+
+ bdmM.setOntology(ontology); //("ann1;ann2;ann3");
bdmM.setOutputBDMFile(bdmFile.toURI().toURL());
//bdmM.setAnnTypesAndFeats("Os;sent->Op");
//bdmM.setVerbosity("0");
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