Revision: 14917
http://gate.svn.sourceforge.net/gate/?rev=14917&view=rev
Author: markagreenwood
Date: 2012-01-06 17:45:07 +0000 (Fri, 06 Jan 2012)
Log Message:
-----------
move the APF XML exporter into it's plugin folder and out of the main tree
Modified Paths:
--------------
gate/trunk/plugins/Obsolete/apf-exporter/creole.xml
Added Paths:
-----------
gate/trunk/plugins/Obsolete/apf-exporter/src/gate/creole/APFormatExporter.java
Removed Paths:
-------------
gate/trunk/src/gate/creole/APFormatExporter.java
Modified: gate/trunk/plugins/Obsolete/apf-exporter/creole.xml
===================================================================
--- gate/trunk/plugins/Obsolete/apf-exporter/creole.xml 2012-01-06 17:43:00 UTC
(rev 14916)
+++ gate/trunk/plugins/Obsolete/apf-exporter/creole.xml 2012-01-06 17:45:07 UTC
(rev 14917)
@@ -1,6 +1,7 @@
<?xml version="1.0"?>
<!-- $Id$ -->
<CREOLE-DIRECTORY>
+ <JAR>apf-exporter.jar</JAR>
<CREOLE>
<!-- creole.xml for the APF exporter -->
<RESOURCE>
Copied:
gate/trunk/plugins/Obsolete/apf-exporter/src/gate/creole/APFormatExporter.java
(from rev 14895, gate/trunk/src/gate/creole/APFormatExporter.java)
===================================================================
---
gate/trunk/plugins/Obsolete/apf-exporter/src/gate/creole/APFormatExporter.java
(rev 0)
+++
gate/trunk/plugins/Obsolete/apf-exporter/src/gate/creole/APFormatExporter.java
2012-01-06 17:45:07 UTC (rev 14917)
@@ -0,0 +1,464 @@
+/*
+ * APFormatExporter.java
+ *
+ * Copyright (c) 1995-2010, The University of Sheffield. See the file
+ * COPYRIGHT.txt in the software or at http://gate.ac.uk/gate/COPYRIGHT.txt
+ *
+ * This file is part of GATE (see http://gate.ac.uk/), and is free
+ * software, licenced under the GNU Library General Public License,
+ * Version 2, June 1991 (in the distribution as file licence.html,
+ * and also available at http://gate.ac.uk/gate/licence.html).
+ *
+ * Cristian URSU, 26/Oct/2001
+ *
+ * $Id$
+ */
+
+package gate.creole;
+
+import java.io.*;
+import java.net.URL;
+import java.util.*;
+
+import gate.*;
+import gate.util.*;
+
+/** This class implements a APF xml exporter. It works on documents or corpora
+ * to export them in the APF format.
+ */
+public class APFormatExporter extends AbstractLanguageAnalyser
+ implements ANNIEConstants{
+ public static final String
+ APF_EXP_DOCUMENT_PARAMETER_NAME = "document";
+
+ public static final String
+ APF_EXP_SOURCE_PARAMETER_NAME = "source";
+
+ public static final String
+ APF_EXP_DTD_PARAMETER_NAME = "dtdFileName";
+
+ public static final String
+ APF_EXP_PATH_PARAMETER_NAME = "exportFilePath";
+
+ public static final String
+ APF_EXP_TYPES_PARAMETER_NAME = "exportedTypes";
+
+ public static final String
+ APF_EXP_WRITE_SOURCE_PARAMETER_NAME = "isSourceWritten";
+
+ /** Debug flag */
+ private static final boolean DEBUG = false;
+ /** Constructor does nothing. This PR is bean like initialized*/
+ public APFormatExporter() {}
+
+ /** Run the resource and does the entire export process*/
+ public void execute() throws ExecutionException{
+ // Check if the thing can be run
+ if(document == null)
+ throw new ExecutionException("No document found to export in APF
format!");
+ if (exportedTypes == null)
+ throw new ExecutionException("No export types found.");
+ xmlDoc = new StringBuffer(10*(document.getContent().size().intValue()));
+ initDocId();
+ if (docId == null)
+ throw new ExecutionException("Couldn't detect the document's ID");
+ if (DEBUG)
+ Out.prln("Document id = "+ docId);
+
+ String exportFilePathStr = null;
+ if (exportFilePath == null)
+ exportFilePathStr = new String(document.getSourceUrl().getFile() +
+ ".apf.xml");
+ else
+ exportFilePathStr = exportFilePath.getPath()+ "/"
+ + gate.util.Files.getLastPathComponent(
+ document.getSourceUrl().getFile()) + ".apf.xml";
+
+ if (DEBUG)
+ Out.prln("Export file path = "+ exportFilePathStr);
+//*
+ // Prepare to write into the xmlFile
+ OutputStreamWriter writer = null;
+ try{
+ writer = new OutputStreamWriter(
+ new FileOutputStream(new File(exportFilePathStr)));
+
+ // Write (test the toXml() method)
+ // This Action is added only when a gate.Document is created.
+ // So, is Bor sure that the resource is a gate.Document
+ serializeDocumentToAPF();
+ writer.write(xmlDoc.toString());
+ writer.flush();
+ writer.close();
+ }catch (Exception e){
+ throw new ExecutionException(e);
+ }// End try
+//*/
+ } // execute()
+
+
+ /** Initialise this resource, and returns it. */
+ public Resource init() throws ResourceInstantiationException {
+ return this;
+ } // init()
+
+ /** Java bean style mutator for exportedTypes */
+ public void setExportedTypes(List anExportedTypesList){
+ exportedTypes = anExportedTypesList;
+ }// setExportedTypes();
+
+ /** Java bean style accesor for exportedTypes */
+ public List getExportedTypes(){
+ return exportedTypes;
+ }// getExportedTypes()
+
+ /** Java bean style mutator for dtdFileName */
+ public void setDtdFileName(String aDtdFileName){
+ dtdFileName = aDtdFileName;
+ }// setDtdFileName();
+
+ /** Java bean style accesor for DtdFileName */
+ public String getDtdFileName(){
+ return dtdFileName;
+ }// getDtdFileName()
+
+ /** Java bean style mutator for exportFilePath */
+ public void setExportFilePath(URL anExportFilePath){
+ exportFilePath = anExportFilePath;
+ }// setExportFilePath();
+
+ /** Java bean style accesor for exportFilePath */
+ public URL getExportFilePath(){
+ return exportFilePath;
+ }// getDtdFileName()
+
+ /** Java bean style mutator for source */
+ public void setSource(String aSource){
+ source = aSource;
+ }// setSource();
+
+ /** Java bean style accesor for source */
+ public String getSource(){
+ return source;
+ }// getSource()
+
+ /** Java bean style accesor for isSourceWritten */
+ public Boolean getIsSourceWritten() {
+ return new Boolean(isSourceWritten);
+ }
+
+ /** Java bean style mutator for isSourceWritten */
+ public void setIsSourceWritten(Boolean aIsSourceWritten){
+ isSourceWritten = aIsSourceWritten.booleanValue();
+ }// setIsSourceWritten();
+
+
+
+ /** Initialises the docId with documents' file name without the complete
path*/
+ private void initDocId(){
+ String fileName = "";
+ fileName = gate.util.Files.getLastPathComponent(
+ document.getSourceUrl().getFile());
+ // File name contains now the last token
+ if (DEBUG)
+ Out.prln("From initDocId, fileName ="+ fileName);
+ StringTokenizer fileNameTokenizer = new StringTokenizer(fileName,".");
+ StringBuffer tmpDocId = new StringBuffer("");
+ while(fileNameTokenizer.hasMoreTokens()){
+ String token = (String)fileNameTokenizer.nextToken();
+ // We don't want to append the last token
+ if (fileNameTokenizer.hasMoreTokens())
+ tmpDocId.append(token + ".");
+ }// End while
+ // if tokenization had place
+ if (tmpDocId.length() > 0){
+ // Remove the last dot
+ tmpDocId.replace(tmpDocId.length()-1,tmpDocId.length(),"");
+ docId = tmpDocId.toString();
+ }// End if
+ }// initDocId()
+
+ /** Returns the xml document conforming to APF dtd.*/
+ protected void serializeDocumentToAPF(){
+ xmlDoc.append("<?xml version=\"1.0\" ?>\n");
+ xmlDoc.append("<!DOCTYPE source_file SYSTEM ");
+ if (dtdFileName == null)
+ xmlDoc.append("\"ace-rdc.v2.0.1.dtd\"");
+ else
+ xmlDoc.append("\""+dtdFileName+"\"");
+ xmlDoc.append(">\n");
+ xmlDoc.append("<source_file TYPE=\"text\"");
+ if (isSourceWritten) {
+ AnnotationSet docTypeAnns = document.getAnnotations(
+ GateConstants.ORIGINAL_MARKUPS_ANNOT_SET_NAME).get("DOCTYPE");
+ if (docTypeAnns == null || docTypeAnns.isEmpty())
+ xmlDoc.append(" SOURCE=\""+ source+ "\" ");
+ else {
+ Annotation docTypeAnn = (Annotation) docTypeAnns.iterator().next();
+ if (docTypeAnn.getFeatures().get("SOURCE") == null)
+ xmlDoc.append(" SOURCE=\""+ source+ "\" ");
+ else
+ xmlDoc.append(" SOURCE=\""+ docTypeAnn.getFeatures().get("SOURCE")+
"\" ");
+ }//if no doc type annotations
+ }
+ xmlDoc.append("VERSION=\"2.0\" URI=\"");
+ xmlDoc.append(docId);
+ xmlDoc.append("-lf\">\n");
+ xmlDoc.append(" <document DOCID=\"");
+ xmlDoc.append(docId + "\">\n");
+ serializeEntities();
+ xmlDoc.append(" </document>\n");
+ xmlDoc.append("</source_file>");
+ }// serializeDocumentToAPF()
+
+ /** Transforms all the entities from exportedTypes found in the GATE document
+ * into their xml representation
+ */
+ protected void serializeEntities(){
+ // If no types founded then simply return
+ if (exportedTypes == null || exportedTypes.isEmpty()) return;
+
+ Map entitiesMap = null;
+ if ( document.getFeatures() == null ||
+ document.getFeatures().get(DOCUMENT_COREF_FEATURE_NAME)== null)
+ entitiesMap = new HashMap();
+ else
+ entitiesMap = (Map)document.getFeatures().
+ get(DOCUMENT_COREF_FEATURE_NAME);
+ Map namedAnnotSetMap = null;
+ if (document.getNamedAnnotationSets() == null)
+ namedAnnotSetMap = new HashMap();
+ else
+ namedAnnotSetMap = new HashMap(document.getNamedAnnotationSets());
+ // Add the default annoattion set
+ namedAnnotSetMap.put(null,document.getAnnotations());
+ // The entities map is a map from annotation sets names to list of lists
+ // Each list element is composed from annotations refering the same entity
+ // All the entities that are in the exportedTypes need to be serialized.
+ Iterator exportedTypesIter = exportedTypes.iterator();
+ while(exportedTypesIter.hasNext()){
+ String entityType = (String)exportedTypesIter.next();
+ // Serialize all entities of type
+ // The keys in the entitesMap are annotation sets names. The null key
+ // designates the default annotation.
+ Set annotationSetNames = namedAnnotSetMap.keySet();
+ Iterator annotationSetNamesIter = annotationSetNames.iterator();
+ while (annotationSetNamesIter.hasNext()){
+ Object annotSetName = annotationSetNamesIter.next();
+ // This list contains entities found in the annotSetName
+ List entitiesList = (List) entitiesMap.get(annotSetName);
+ if (entitiesList == null) entitiesList = new ArrayList();
+ // This annotation set will contain all annotations of "entityType"
+ AnnotationSet annotSet = null;
+ Set serializationAnnotSet = null;
+ annotSet = (AnnotationSet)namedAnnotSetMap.get(annotSetName);
+ if (annotSet == null || annotSet.get(entityType) == null) continue;
+ serializationAnnotSet = new HashSet(annotSet.get(entityType));
+ // All annotations from annotSet will be serialized as entities unless
+ // some of them are present in the entities map
+ // Now we are searching for the entityType in the entitiesMap and
+ // serialize it from there. After that, remove all annotations
+ // entityType present in entitiesMap from annotSet and serialize the
+ // remaining entities.
+ //Iterate through the entitiesList in searching for entityType
+ Iterator entitiesListIter = entitiesList.iterator();
+ while (entitiesListIter.hasNext()){
+ List entity = (List)entitiesListIter.next();
+ // We want now to accesate an annotation from the entity list to get
+ // its type and compare it with entityType
+ String theEntityType = new String("");
+ if (entity != null && !entity.isEmpty()){
+ Integer annotId = (Integer)entity.get(0);
+ Annotation a = (Annotation)annotSet.get(annotId);
+ if (a != null) theEntityType = a.getType();
+ }// End if
+ // The the types are equal then serialize the entities
+ if (theEntityType.equals(entityType)){
+ List ent = new ArrayList();
+ Iterator entityIter = entity.iterator();
+ while(entityIter.hasNext()){
+ Integer id = (Integer)entityIter.next();
+ ent.add(annotSet.get(id));
+ }// End while
+ serializeAnEntity(ent);
+ // Remove all annotation from entity that apear in annotSet
+ serializationAnnotSet.removeAll(ent);
+ }// End if
+ }// End while(entitiesListIter.hasNext())
+ // Serialize the remaining entities in annotSet
+ Iterator serializationAnnotSetIter = serializationAnnotSet.iterator();
+ while(serializationAnnotSetIter.hasNext()){
+ Annotation annotEntity = (Annotation)
serializationAnnotSetIter.next();
+ List ent = new ArrayList();
+ ent.add(annotEntity);
+ serializeAnEntity(ent);
+ }// End while(annotSetIter.hasNext())
+ }// End while(entitiesKeysIter.hasNext())
+ }// End while(exportedTypesIter.hasNext())
+ }// serializeEntities()
+
+ /** Writes an entity in the xmlDoc conforming to APF standards.
+ * @param anEntity represents a list with annotations that refer the same
+ * entity. Those annotations were detected and constructed by the
+ * orthomatcher.
+ */
+ private void serializeAnEntity(List anEntity){
+ if (anEntity == null || anEntity.isEmpty()) return;
+ // Write the entities tags
+ xmlDoc.append(" <entity ID=\"" + docId + "-" + getNextEntityId() +
"\">\n");
+ // We know for sure that the list is not empty (see above)
+ Annotation a = (Annotation) anEntity.get(0);
+ xmlDoc.append(" <entity_type GENERIC=\"FALSE\">" +
a.getType().toUpperCase() +
+ "</entity_type>\n");
+ // Write the entities mentions
+ Iterator anEntityIter = anEntity.iterator();
+ while(anEntityIter.hasNext()){
+ Annotation ann = (Annotation)anEntityIter.next();
+ serializeAnEntityMention(ann);
+ }// End while(anEntityIter.hasNext())
+ // Write the entities attributes
+ xmlDoc.append(" <entity_attributes>\n");
+ anEntityIter = anEntity.iterator();
+ while(anEntityIter.hasNext()){
+ Annotation ann = (Annotation)anEntityIter.next();
+ serializeAnEntityAttributes(ann);
+ }// End while(anEntityIter.hasNext())
+ xmlDoc.append(" </entity_attributes>\n");
+ xmlDoc.append(" </entity>\n");
+ }// End serializeAnEntity();
+
+ /** This method serializes an entity mention from an Annotation*/
+ private void serializeAnEntityMention(Annotation ann){
+ if (ann == null) return;
+ String entityMentionType = "NAME";
+ String entityMentionRole = null;
+ String entityMentionReference = null;
+ String entityMentionGeneric = null;
+
+ FeatureMap fm = ann.getFeatures();
+ if (fm != null){
+ if( null != fm.get("ENTITY_MENTION_TYPE"))
+ entityMentionType = (String) fm.get("ENTITY_MENTION_TYPE");
+
+ entityMentionRole = (String) fm.get("ROLE");
+ entityMentionReference = (String) fm.get("REFERENCE");
+ entityMentionGeneric = (String) fm.get("GENERIC");
+ }// End if
+ String str1 = (entityMentionRole == null)? "" :
+ ("ROLE=\"" + entityMentionRole + "\"");
+ String str2 = (entityMentionReference == null)? "" :
+ ("REFERENCE=\"" + entityMentionReference + "\"");
+ String str3 = (entityMentionGeneric == null)? "" :
+ ("GENERIC=\"" + entityMentionGeneric + "\"");
+
+/* modified by Di - the new scorer needs a unique ID for each mention as well
*/
+
+ xmlDoc.append(" <entity_mention TYPE=\"" + entityMentionType+"\"" +
+ str1 + " " + str2 + " " + str3 + "ID=\"" + "M" + getNextMentionId()
+"\">\n"
+ );
+
+ // extent
+ xmlDoc.append(" <extent>\n");
+ xmlDoc.append(" <charseq>\n");
+ try{
+ xmlDoc.append(" <!-- string = \"" +
+ document.getContent().getContent(ann.getStartNode().getOffset(),
+ ann.getEndNode().getOffset())+"\"
-->\n");
+ }catch (InvalidOffsetException ioe){
+ Err.prln("APFormatExporter:Warning: Couldn't access text between"+
+ " offsets:" + ann.getStartNode().getOffset() + " and "+
+ ann.getEndNode().getOffset());
+ }// End try
+ xmlDoc.append(" <start>"+ann.getStartNode().getOffset()+
+ "</start><end>"+(ann.getEndNode().getOffset().longValue() -
1)+"</end>\n");
+ xmlDoc.append(" </charseq>\n");
+ xmlDoc.append(" </extent>\n");
+ // head
+ xmlDoc.append(" <head>\n");
+ xmlDoc.append(" <charseq>\n");
+ try{
+ xmlDoc.append(" <!-- string = \"" +
+ document.getContent().getContent(ann.getStartNode().getOffset(),
+ ann.getEndNode().getOffset())+"\"
-->\n");
+ }catch (InvalidOffsetException ioe){
+ Err.prln("APFormatExporter:Warning: Couldn't access text between"+
+ " offsets:" + ann.getStartNode().getOffset() + " and "+
+ ann.getEndNode().getOffset());
+ }// End try
+ xmlDoc.append(" <start>"+ann.getStartNode().getOffset()+
+ "</start><end>"+(ann.getEndNode().getOffset().longValue() -
1)+"</end>\n");
+ xmlDoc.append(" </charseq>\n");
+ xmlDoc.append(" </head>\n");
+ xmlDoc.append(" </entity_mention>\n");
+ }//serializeAnEntityMention();
+
+ /** This method serializes an entity attribute from an Annotation*/
+ private void serializeAnEntityAttributes(Annotation ann){
+ if (ann == null) return;
+ boolean isAttribute = false;
+ if ("NAME".equals(ann.getFeatures().get("ENTITY_MENTION_TYPE"))
+ ||
+ null == ann.getFeatures().get("ENTITY_MENTION_TYPE"))
+ isAttribute = true;
+ if (! isAttribute)
+ return;
+
+ // name
+ xmlDoc.append(" <name>\n");
+ xmlDoc.append(" <charseq>\n");
+ try{
+ xmlDoc.append(" <!-- string = \"" +
+ document.getContent().getContent(ann.getStartNode().getOffset(),
+ ann.getEndNode().getOffset())+"\"
-->\n");
+ }catch (InvalidOffsetException ioe){
+ Err.prln("APFormatExporter:Warning: Couldn't access text between"+
+ " offsets:" + ann.getStartNode().getOffset() + " and "+
+ ann.getEndNode().getOffset());
+ }// End try
+ xmlDoc.append(" <start>"+ann.getStartNode().getOffset()+
+ "</start><end>"+(ann.getEndNode().getOffset().longValue() -
1)+"</end>\n");
+ xmlDoc.append(" </charseq>\n");
+ xmlDoc.append(" </name>\n");
+ }//serializeAnEntityMention();
+
+ /** Returns the next safe ID for an entity*/
+ private int getNextEntityId(){
+ return entityId ++;
+ }// getNextEntityId()
+
+ /** added by Di - returns the next safe ID for an entity mention */
+ private int getNextMentionId(){
+ return mentionId ++;
+ }
+
+
+ /** This list of strings represents the entities type that will be exported*/
+ private List exportedTypes = null;
+ /** This is the name of the dtd file. If it's not present no dtd would be
+ * written in the APF file.
+ */
+ private String dtdFileName = null;
+ /** This field represent the document id and it is used in generating the
+ * entities IDs. It is the file name of the document, without the extension
+ */
+ private String docId = null;
+
+ /** This field represent an unique entity ID generator*/
+ private int entityId = 1;
+
+ /** added by Di - this field represents a unique entity ID generator */
+ private int mentionId = 1;
+
+ /** This is the xmlDoc that will be created*/
+ private StringBuffer xmlDoc = null;
+
+ private URL exportFilePath = null;
+
+ /** The source attribute for source*/
+ private String source = null;
+
+ /** The source attribute for source*/
+ private boolean isSourceWritten = true;
+
+
+}// APFormatExporter
Deleted: gate/trunk/src/gate/creole/APFormatExporter.java
===================================================================
--- gate/trunk/src/gate/creole/APFormatExporter.java 2012-01-06 17:43:00 UTC
(rev 14916)
+++ gate/trunk/src/gate/creole/APFormatExporter.java 2012-01-06 17:45:07 UTC
(rev 14917)
@@ -1,464 +0,0 @@
-/*
- * APFormatExporter.java
- *
- * Copyright (c) 1995-2010, The University of Sheffield. See the file
- * COPYRIGHT.txt in the software or at http://gate.ac.uk/gate/COPYRIGHT.txt
- *
- * This file is part of GATE (see http://gate.ac.uk/), and is free
- * software, licenced under the GNU Library General Public License,
- * Version 2, June 1991 (in the distribution as file licence.html,
- * and also available at http://gate.ac.uk/gate/licence.html).
- *
- * Cristian URSU, 26/Oct/2001
- *
- * $Id$
- */
-
-package gate.creole;
-
-import java.io.*;
-import java.net.URL;
-import java.util.*;
-
-import gate.*;
-import gate.util.*;
-
-/** This class implements a APF xml exporter. It works on documents or corpora
- * to export them in the APF format.
- */
-public class APFormatExporter extends AbstractLanguageAnalyser
- implements ANNIEConstants{
- public static final String
- APF_EXP_DOCUMENT_PARAMETER_NAME = "document";
-
- public static final String
- APF_EXP_SOURCE_PARAMETER_NAME = "source";
-
- public static final String
- APF_EXP_DTD_PARAMETER_NAME = "dtdFileName";
-
- public static final String
- APF_EXP_PATH_PARAMETER_NAME = "exportFilePath";
-
- public static final String
- APF_EXP_TYPES_PARAMETER_NAME = "exportedTypes";
-
- public static final String
- APF_EXP_WRITE_SOURCE_PARAMETER_NAME = "isSourceWritten";
-
- /** Debug flag */
- private static final boolean DEBUG = false;
- /** Constructor does nothing. This PR is bean like initialized*/
- public APFormatExporter() {}
-
- /** Run the resource and does the entire export process*/
- public void execute() throws ExecutionException{
- // Check if the thing can be run
- if(document == null)
- throw new ExecutionException("No document found to export in APF
format!");
- if (exportedTypes == null)
- throw new ExecutionException("No export types found.");
- xmlDoc = new StringBuffer(10*(document.getContent().size().intValue()));
- initDocId();
- if (docId == null)
- throw new ExecutionException("Couldn't detect the document's ID");
- if (DEBUG)
- Out.prln("Document id = "+ docId);
-
- String exportFilePathStr = null;
- if (exportFilePath == null)
- exportFilePathStr = new String(document.getSourceUrl().getFile() +
- ".apf.xml");
- else
- exportFilePathStr = exportFilePath.getPath()+ "/"
- + gate.util.Files.getLastPathComponent(
- document.getSourceUrl().getFile()) + ".apf.xml";
-
- if (DEBUG)
- Out.prln("Export file path = "+ exportFilePathStr);
-//*
- // Prepare to write into the xmlFile
- OutputStreamWriter writer = null;
- try{
- writer = new OutputStreamWriter(
- new FileOutputStream(new File(exportFilePathStr)));
-
- // Write (test the toXml() method)
- // This Action is added only when a gate.Document is created.
- // So, is Bor sure that the resource is a gate.Document
- serializeDocumentToAPF();
- writer.write(xmlDoc.toString());
- writer.flush();
- writer.close();
- }catch (Exception e){
- throw new ExecutionException(e);
- }// End try
-//*/
- } // execute()
-
-
- /** Initialise this resource, and returns it. */
- public Resource init() throws ResourceInstantiationException {
- return this;
- } // init()
-
- /** Java bean style mutator for exportedTypes */
- public void setExportedTypes(List anExportedTypesList){
- exportedTypes = anExportedTypesList;
- }// setExportedTypes();
-
- /** Java bean style accesor for exportedTypes */
- public List getExportedTypes(){
- return exportedTypes;
- }// getExportedTypes()
-
- /** Java bean style mutator for dtdFileName */
- public void setDtdFileName(String aDtdFileName){
- dtdFileName = aDtdFileName;
- }// setDtdFileName();
-
- /** Java bean style accesor for DtdFileName */
- public String getDtdFileName(){
- return dtdFileName;
- }// getDtdFileName()
-
- /** Java bean style mutator for exportFilePath */
- public void setExportFilePath(URL anExportFilePath){
- exportFilePath = anExportFilePath;
- }// setExportFilePath();
-
- /** Java bean style accesor for exportFilePath */
- public URL getExportFilePath(){
- return exportFilePath;
- }// getDtdFileName()
-
- /** Java bean style mutator for source */
- public void setSource(String aSource){
- source = aSource;
- }// setSource();
-
- /** Java bean style accesor for source */
- public String getSource(){
- return source;
- }// getSource()
-
- /** Java bean style accesor for isSourceWritten */
- public Boolean getIsSourceWritten() {
- return new Boolean(isSourceWritten);
- }
-
- /** Java bean style mutator for isSourceWritten */
- public void setIsSourceWritten(Boolean aIsSourceWritten){
- isSourceWritten = aIsSourceWritten.booleanValue();
- }// setIsSourceWritten();
-
-
-
- /** Initialises the docId with documents' file name without the complete
path*/
- private void initDocId(){
- String fileName = "";
- fileName = gate.util.Files.getLastPathComponent(
- document.getSourceUrl().getFile());
- // File name contains now the last token
- if (DEBUG)
- Out.prln("From initDocId, fileName ="+ fileName);
- StringTokenizer fileNameTokenizer = new StringTokenizer(fileName,".");
- StringBuffer tmpDocId = new StringBuffer("");
- while(fileNameTokenizer.hasMoreTokens()){
- String token = (String)fileNameTokenizer.nextToken();
- // We don't want to append the last token
- if (fileNameTokenizer.hasMoreTokens())
- tmpDocId.append(token + ".");
- }// End while
- // if tokenization had place
- if (tmpDocId.length() > 0){
- // Remove the last dot
- tmpDocId.replace(tmpDocId.length()-1,tmpDocId.length(),"");
- docId = tmpDocId.toString();
- }// End if
- }// initDocId()
-
- /** Returns the xml document conforming to APF dtd.*/
- protected void serializeDocumentToAPF(){
- xmlDoc.append("<?xml version=\"1.0\" ?>\n");
- xmlDoc.append("<!DOCTYPE source_file SYSTEM ");
- if (dtdFileName == null)
- xmlDoc.append("\"ace-rdc.v2.0.1.dtd\"");
- else
- xmlDoc.append("\""+dtdFileName+"\"");
- xmlDoc.append(">\n");
- xmlDoc.append("<source_file TYPE=\"text\"");
- if (isSourceWritten) {
- AnnotationSet docTypeAnns = document.getAnnotations(
- GateConstants.ORIGINAL_MARKUPS_ANNOT_SET_NAME).get("DOCTYPE");
- if (docTypeAnns == null || docTypeAnns.isEmpty())
- xmlDoc.append(" SOURCE=\""+ source+ "\" ");
- else {
- Annotation docTypeAnn = (Annotation) docTypeAnns.iterator().next();
- if (docTypeAnn.getFeatures().get("SOURCE") == null)
- xmlDoc.append(" SOURCE=\""+ source+ "\" ");
- else
- xmlDoc.append(" SOURCE=\""+ docTypeAnn.getFeatures().get("SOURCE")+
"\" ");
- }//if no doc type annotations
- }
- xmlDoc.append("VERSION=\"2.0\" URI=\"");
- xmlDoc.append(docId);
- xmlDoc.append("-lf\">\n");
- xmlDoc.append(" <document DOCID=\"");
- xmlDoc.append(docId + "\">\n");
- serializeEntities();
- xmlDoc.append(" </document>\n");
- xmlDoc.append("</source_file>");
- }// serializeDocumentToAPF()
-
- /** Transforms all the entities from exportedTypes found in the GATE document
- * into their xml representation
- */
- protected void serializeEntities(){
- // If no types founded then simply return
- if (exportedTypes == null || exportedTypes.isEmpty()) return;
-
- Map entitiesMap = null;
- if ( document.getFeatures() == null ||
- document.getFeatures().get(DOCUMENT_COREF_FEATURE_NAME)== null)
- entitiesMap = new HashMap();
- else
- entitiesMap = (Map)document.getFeatures().
- get(DOCUMENT_COREF_FEATURE_NAME);
- Map namedAnnotSetMap = null;
- if (document.getNamedAnnotationSets() == null)
- namedAnnotSetMap = new HashMap();
- else
- namedAnnotSetMap = new HashMap(document.getNamedAnnotationSets());
- // Add the default annoattion set
- namedAnnotSetMap.put(null,document.getAnnotations());
- // The entities map is a map from annotation sets names to list of lists
- // Each list element is composed from annotations refering the same entity
- // All the entities that are in the exportedTypes need to be serialized.
- Iterator exportedTypesIter = exportedTypes.iterator();
- while(exportedTypesIter.hasNext()){
- String entityType = (String)exportedTypesIter.next();
- // Serialize all entities of type
- // The keys in the entitesMap are annotation sets names. The null key
- // designates the default annotation.
- Set annotationSetNames = namedAnnotSetMap.keySet();
- Iterator annotationSetNamesIter = annotationSetNames.iterator();
- while (annotationSetNamesIter.hasNext()){
- Object annotSetName = annotationSetNamesIter.next();
- // This list contains entities found in the annotSetName
- List entitiesList = (List) entitiesMap.get(annotSetName);
- if (entitiesList == null) entitiesList = new ArrayList();
- // This annotation set will contain all annotations of "entityType"
- AnnotationSet annotSet = null;
- Set serializationAnnotSet = null;
- annotSet = (AnnotationSet)namedAnnotSetMap.get(annotSetName);
- if (annotSet == null || annotSet.get(entityType) == null) continue;
- serializationAnnotSet = new HashSet(annotSet.get(entityType));
- // All annotations from annotSet will be serialized as entities unless
- // some of them are present in the entities map
- // Now we are searching for the entityType in the entitiesMap and
- // serialize it from there. After that, remove all annotations
- // entityType present in entitiesMap from annotSet and serialize the
- // remaining entities.
- //Iterate through the entitiesList in searching for entityType
- Iterator entitiesListIter = entitiesList.iterator();
- while (entitiesListIter.hasNext()){
- List entity = (List)entitiesListIter.next();
- // We want now to accesate an annotation from the entity list to get
- // its type and compare it with entityType
- String theEntityType = new String("");
- if (entity != null && !entity.isEmpty()){
- Integer annotId = (Integer)entity.get(0);
- Annotation a = (Annotation)annotSet.get(annotId);
- if (a != null) theEntityType = a.getType();
- }// End if
- // The the types are equal then serialize the entities
- if (theEntityType.equals(entityType)){
- List ent = new ArrayList();
- Iterator entityIter = entity.iterator();
- while(entityIter.hasNext()){
- Integer id = (Integer)entityIter.next();
- ent.add(annotSet.get(id));
- }// End while
- serializeAnEntity(ent);
- // Remove all annotation from entity that apear in annotSet
- serializationAnnotSet.removeAll(ent);
- }// End if
- }// End while(entitiesListIter.hasNext())
- // Serialize the remaining entities in annotSet
- Iterator serializationAnnotSetIter = serializationAnnotSet.iterator();
- while(serializationAnnotSetIter.hasNext()){
- Annotation annotEntity = (Annotation)
serializationAnnotSetIter.next();
- List ent = new ArrayList();
- ent.add(annotEntity);
- serializeAnEntity(ent);
- }// End while(annotSetIter.hasNext())
- }// End while(entitiesKeysIter.hasNext())
- }// End while(exportedTypesIter.hasNext())
- }// serializeEntities()
-
- /** Writes an entity in the xmlDoc conforming to APF standards.
- * @param anEntity represents a list with annotations that refer the same
- * entity. Those annotations were detected and constructed by the
- * orthomatcher.
- */
- private void serializeAnEntity(List anEntity){
- if (anEntity == null || anEntity.isEmpty()) return;
- // Write the entities tags
- xmlDoc.append(" <entity ID=\"" + docId + "-" + getNextEntityId() +
"\">\n");
- // We know for sure that the list is not empty (see above)
- Annotation a = (Annotation) anEntity.get(0);
- xmlDoc.append(" <entity_type GENERIC=\"FALSE\">" +
a.getType().toUpperCase() +
- "</entity_type>\n");
- // Write the entities mentions
- Iterator anEntityIter = anEntity.iterator();
- while(anEntityIter.hasNext()){
- Annotation ann = (Annotation)anEntityIter.next();
- serializeAnEntityMention(ann);
- }// End while(anEntityIter.hasNext())
- // Write the entities attributes
- xmlDoc.append(" <entity_attributes>\n");
- anEntityIter = anEntity.iterator();
- while(anEntityIter.hasNext()){
- Annotation ann = (Annotation)anEntityIter.next();
- serializeAnEntityAttributes(ann);
- }// End while(anEntityIter.hasNext())
- xmlDoc.append(" </entity_attributes>\n");
- xmlDoc.append(" </entity>\n");
- }// End serializeAnEntity();
-
- /** This method serializes an entity mention from an Annotation*/
- private void serializeAnEntityMention(Annotation ann){
- if (ann == null) return;
- String entityMentionType = "NAME";
- String entityMentionRole = null;
- String entityMentionReference = null;
- String entityMentionGeneric = null;
-
- FeatureMap fm = ann.getFeatures();
- if (fm != null){
- if( null != fm.get("ENTITY_MENTION_TYPE"))
- entityMentionType = (String) fm.get("ENTITY_MENTION_TYPE");
-
- entityMentionRole = (String) fm.get("ROLE");
- entityMentionReference = (String) fm.get("REFERENCE");
- entityMentionGeneric = (String) fm.get("GENERIC");
- }// End if
- String str1 = (entityMentionRole == null)? "" :
- ("ROLE=\"" + entityMentionRole + "\"");
- String str2 = (entityMentionReference == null)? "" :
- ("REFERENCE=\"" + entityMentionReference + "\"");
- String str3 = (entityMentionGeneric == null)? "" :
- ("GENERIC=\"" + entityMentionGeneric + "\"");
-
-/* modified by Di - the new scorer needs a unique ID for each mention as well
*/
-
- xmlDoc.append(" <entity_mention TYPE=\"" + entityMentionType+"\"" +
- str1 + " " + str2 + " " + str3 + "ID=\"" + "M" + getNextMentionId()
+"\">\n"
- );
-
- // extent
- xmlDoc.append(" <extent>\n");
- xmlDoc.append(" <charseq>\n");
- try{
- xmlDoc.append(" <!-- string = \"" +
- document.getContent().getContent(ann.getStartNode().getOffset(),
- ann.getEndNode().getOffset())+"\"
-->\n");
- }catch (InvalidOffsetException ioe){
- Err.prln("APFormatExporter:Warning: Couldn't access text between"+
- " offsets:" + ann.getStartNode().getOffset() + " and "+
- ann.getEndNode().getOffset());
- }// End try
- xmlDoc.append(" <start>"+ann.getStartNode().getOffset()+
- "</start><end>"+(ann.getEndNode().getOffset().longValue() -
1)+"</end>\n");
- xmlDoc.append(" </charseq>\n");
- xmlDoc.append(" </extent>\n");
- // head
- xmlDoc.append(" <head>\n");
- xmlDoc.append(" <charseq>\n");
- try{
- xmlDoc.append(" <!-- string = \"" +
- document.getContent().getContent(ann.getStartNode().getOffset(),
- ann.getEndNode().getOffset())+"\"
-->\n");
- }catch (InvalidOffsetException ioe){
- Err.prln("APFormatExporter:Warning: Couldn't access text between"+
- " offsets:" + ann.getStartNode().getOffset() + " and "+
- ann.getEndNode().getOffset());
- }// End try
- xmlDoc.append(" <start>"+ann.getStartNode().getOffset()+
- "</start><end>"+(ann.getEndNode().getOffset().longValue() -
1)+"</end>\n");
- xmlDoc.append(" </charseq>\n");
- xmlDoc.append(" </head>\n");
- xmlDoc.append(" </entity_mention>\n");
- }//serializeAnEntityMention();
-
- /** This method serializes an entity attribute from an Annotation*/
- private void serializeAnEntityAttributes(Annotation ann){
- if (ann == null) return;
- boolean isAttribute = false;
- if ("NAME".equals(ann.getFeatures().get("ENTITY_MENTION_TYPE"))
- ||
- null == ann.getFeatures().get("ENTITY_MENTION_TYPE"))
- isAttribute = true;
- if (! isAttribute)
- return;
-
- // name
- xmlDoc.append(" <name>\n");
- xmlDoc.append(" <charseq>\n");
- try{
- xmlDoc.append(" <!-- string = \"" +
- document.getContent().getContent(ann.getStartNode().getOffset(),
- ann.getEndNode().getOffset())+"\"
-->\n");
- }catch (InvalidOffsetException ioe){
- Err.prln("APFormatExporter:Warning: Couldn't access text between"+
- " offsets:" + ann.getStartNode().getOffset() + " and "+
- ann.getEndNode().getOffset());
- }// End try
- xmlDoc.append(" <start>"+ann.getStartNode().getOffset()+
- "</start><end>"+(ann.getEndNode().getOffset().longValue() -
1)+"</end>\n");
- xmlDoc.append(" </charseq>\n");
- xmlDoc.append(" </name>\n");
- }//serializeAnEntityMention();
-
- /** Returns the next safe ID for an entity*/
- private int getNextEntityId(){
- return entityId ++;
- }// getNextEntityId()
-
- /** added by Di - returns the next safe ID for an entity mention */
- private int getNextMentionId(){
- return mentionId ++;
- }
-
-
- /** This list of strings represents the entities type that will be exported*/
- private List exportedTypes = null;
- /** This is the name of the dtd file. If it's not present no dtd would be
- * written in the APF file.
- */
- private String dtdFileName = null;
- /** This field represent the document id and it is used in generating the
- * entities IDs. It is the file name of the document, without the extension
- */
- private String docId = null;
-
- /** This field represent an unique entity ID generator*/
- private int entityId = 1;
-
- /** added by Di - this field represents a unique entity ID generator */
- private int mentionId = 1;
-
- /** This is the xmlDoc that will be created*/
- private StringBuffer xmlDoc = null;
-
- private URL exportFilePath = null;
-
- /** The source attribute for source*/
- private String source = null;
-
- /** The source attribute for source*/
- private boolean isSourceWritten = true;
-
-
-}// APFormatExporter
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