Revision: 15967
http://gate.svn.sourceforge.net/gate/?rev=15967&view=rev
Author: valyt
Date: 2012-07-23 10:54:49 +0000 (Mon, 23 Jul 2012)
Log Message:
-----------
New PR in Tools: Configurable Exporter.
Modified Paths:
--------------
gate/trunk/.classpath
Added Paths:
-----------
gate/trunk/plugins/Tools/src/gate/configurableexporter/
gate/trunk/plugins/Tools/src/gate/configurableexporter/ConfigurableExporter.java
Modified: gate/trunk/.classpath
===================================================================
--- gate/trunk/.classpath 2012-07-23 01:18:50 UTC (rev 15966)
+++ gate/trunk/.classpath 2012-07-23 10:54:49 UTC (rev 15967)
@@ -1,6 +1,7 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="src" path="src"/>
+ <classpathentry kind="src" output="plugins/Tools/classes"
path="plugins/Tools/src"/>
<classpathentry kind="src" output="plugins/Coref_Tools/classes"
path="plugins/Coref_Tools/src"/>
<classpathentry kind="src" output="plugins/JAPE_Plus/classes"
path="plugins/JAPE_Plus/src"/>
<classpathentry kind="src" output="plugins/Groovy/build"
path="plugins/Groovy/src"/>
@@ -101,7 +102,6 @@
<classpathentry exported="true" kind="lib" path="lib/commons-lang.jar"/>
<classpathentry exported="true" kind="lib" path="lib/bcprov-jdk15.jar"/>
<classpathentry exported="true" kind="lib"
path="lib/poi-scratchpad.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/wstx-lgpl.jar"/>
<classpathentry exported="true" kind="lib" path="lib/dom4j.jar"/>
<classpathentry exported="true" kind="lib" path="lib/lucene-core.jar"/>
<classpathentry exported="true" kind="lib" path="lib/fontbox.jar"/>
@@ -110,5 +110,7 @@
<classpathentry exported="true" kind="lib" path="lib/poi.jar"/>
<classpathentry exported="true" kind="lib" path="lib/spring-beans.jar"/>
<classpathentry exported="true" kind="lib"
path="lib/metadata-extractor.jar"/>
+ <classpathentry exported="true" kind="lib"
path="lib/woodstox-core-lgpl.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/stax2-api.jar"/>
<classpathentry kind="output" path="classes"/>
</classpath>
Added:
gate/trunk/plugins/Tools/src/gate/configurableexporter/ConfigurableExporter.java
===================================================================
---
gate/trunk/plugins/Tools/src/gate/configurableexporter/ConfigurableExporter.java
(rev 0)
+++
gate/trunk/plugins/Tools/src/gate/configurableexporter/ConfigurableExporter.java
2012-07-23 10:54:49 UTC (rev 15967)
@@ -0,0 +1,333 @@
+/*
+ * ConfigurableExporter.java
+ *
+ * Copyright (c) 1995-2012, 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).
+ *
+ * $id$
+ */
+
+package gate.configurableexporter;
+
+import gate.Annotation;
+import gate.AnnotationSet;
+import gate.Document;
+import gate.ProcessingResource;
+import gate.Resource;
+import gate.Utils;
+import gate.creole.AbstractLanguageAnalyser;
+import gate.creole.ExecutionException;
+import gate.creole.ResourceInstantiationException;
+import gate.creole.metadata.CreoleParameter;
+import gate.creole.metadata.CreoleResource;
+import gate.creole.metadata.Optional;
+import gate.creole.metadata.RunTime;
+import gate.util.OffsetComparator;
+
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+import java.io.PrintStream;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.List;
+
+
+
+
+/**
+ * Configurable Exporter takes a configuration file specifying the
+ * format of the output file. The configuration file consists of a
+ * single line specifying output format with annotation names
+ * surrounded by three angle brackets. E.g.<br>
+ *
+ * <pre>
+ * {index}, {class}, "{content}"
+ * </pre>
+ *
+ * might result in an output file something like
+ * <pre>
+ * 10000004, A, "Some text .."
+ * 10000005, A, "Some more text .."
+ * 10000006, B, "Further text .."
+ * 10000007, B, "Additional text .."
+ * 10000008, B, "Yet more text .."
+ * </pre>
+ * Annotation features can also be specified using dot notation,
+ * for example;
+ * <pre>
+ * {index}, {instance.class}, "{content}"
+ * </pre>
+ * The PR is useful for outputting data for use in machine learning,
+ * and so each line is considered an "instance". Instance is specified
+ * at run time, and by default is a document, but might be an
+ * annotation type. Instances are output one per line and the config
+ * file specifies how to output each instance. Annotations included
+ * in the output file are the first incidence of the specified type in
+ * the instance. If there is ever a need for it I might fix it so you
+ * can output more than one incidence of the same annotation type.
+ *
+ */
+@CreoleResource(name = "Configurable Exporter",
+ comment = "Allows annotations to be exported according to a specified
format.")
+public class ConfigurableExporter extends AbstractLanguageAnalyser implements
+ ProcessingResource,
+ Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = -7237223509897088067L;
+
+ /**
+ * The ConfigurableExporter configuration file.
+ *
+ */
+ private java.net.URL configFileURL;
+
+ /**
+ * The file to export the data to.
+ *
+ */
+ private java.net.URL outputURL;
+
+ /**
+ * The annotation set from which to draw the annotations.
+ *
+ */
+ private String inputASName;
+
+ /**
+ * The annotation type to be treated as instance.
+ *
+ */
+ private String instanceName;
+
+ private int numberOfAnnotationSlots = -1;
+ private int numberOfBridgeTextSlots = -1;
+ private static int maxslotsno = 50;
+ private String[][] annsToInsert = new String[maxslotsno][2];
+ private String[] bridges = new String[maxslotsno];
+
+ private PrintStream outputStream = System.out;
+
+ @CreoleParameter(comment = "The configuration file specifying output
format.",
+ defaultValue="resources/configurableexporter/example.conf",
+ suffixes=".conf")
+ public void setConfigFileURL(java.net.URL configFileURL) {
+ this.configFileURL = configFileURL;
+ }
+
+ public java.net.URL getConfigFileURL() {
+ return configFileURL;
+ }
+
+
+ @RunTime
+ @Optional
+ @CreoleParameter(comment = "The file to which data will be output. Leave " +
+ "blank for output to messages tab or standard out.")
+ public void setOutputURL(java.net.URL output) {
+ this.outputURL = output;
+ outputStream = System.out;
+ if(outputURL!=null){
+ try {
+ outputStream = new PrintStream(this.outputURL.getFile());
+ } catch (Exception e){
+ e.printStackTrace();
+ }
+ }
+ }
+
+ public java.net.URL getOutputURL() {
+ return this.outputURL;
+ }
+
+
+ @RunTime
+ @Optional
+ @CreoleParameter(comment = "The name for annotation set used as input to " +
+ "the exporter.")
+ public void setInputASName(String iasn) {
+ this.inputASName = iasn;
+ }
+
+ public String getInputASName() {
+ return this.inputASName;
+ }
+
+
+ @RunTime
+ @Optional
+ @CreoleParameter(comment = "The annotation type to be treated as instance. "
+
+ "Leave blank to use document as instance.")
+ public void setInstanceName(String inst) {
+ this.instanceName = inst;
+ }
+
+ public String getInstanceName() {
+ return this.instanceName;
+ }
+
+ @Override
+ public Resource init() throws ResourceInstantiationException {
+ this.numberOfAnnotationSlots = -1;
+ this.numberOfBridgeTextSlots = -1;
+ this.annsToInsert = new String[maxslotsno][2];
+ this.bridges = new String[maxslotsno];
+
+ if(configFileURL == null) throw new IllegalArgumentException(
+ "No value provided for the configFileURL parameter");
+
+ String strLine = null;
+ try {
+ BufferedReader in =
+ new BufferedReader(new
InputStreamReader(configFileURL.openStream()));
+ if((strLine = in.readLine()) != null) {
+ int upto = 0;
+ int thisSlot = 0;
+ while(upto < strLine.length() && thisSlot < maxslotsno) {
+ int startAnnoName = strLine.indexOf("{", upto);
+ int endAnnoName = strLine.indexOf("}", upto);
+ if(startAnnoName == -1 && endAnnoName == -1) {
+ bridges[thisSlot] = strLine.substring(upto, strLine.length());
+ this.numberOfBridgeTextSlots = thisSlot + 1;
+ upto = strLine.length();
+ } else if((startAnnoName == -1 && endAnnoName != -1)
+ || (startAnnoName != -1 && endAnnoName == -1)) {
+ throw new ResourceInstantiationException(
+ "Failed to parse configuration file for Configurable " +
+ "Exporter.");
+ } else {
+ bridges[thisSlot] = strLine.substring(upto, startAnnoName);
+ String thisAnnToInsert =
+ strLine.substring(startAnnoName + 1, endAnnoName);
+ String[] annotationTypeAndFeature = thisAnnToInsert.split("\\.",
2);
+ this.annsToInsert[thisSlot][0] = annotationTypeAndFeature[0];
+ if(annotationTypeAndFeature.length == 2) {
+ this.annsToInsert[thisSlot][1] = annotationTypeAndFeature[1];
+ } else {
+ this.annsToInsert[thisSlot][1] = null;
+ }
+ upto = endAnnoName + 1;
+ this.numberOfAnnotationSlots = thisSlot + 1;
+ this.numberOfBridgeTextSlots = thisSlot + 1;
+ }
+ thisSlot++;
+ }
+ }
+ } catch(Exception e) {
+ System.out.println("Failed to access configuration file.");
+ e.printStackTrace();
+ }
+ return this;
+ }
+
+ @Override
+ public void execute() throws ExecutionException {
+ Document doc = getDocument();
+
+ // Get the output annotation set
+ AnnotationSet inputAS = null;
+ if(inputASName == null || inputASName.equals("")) {
+ inputAS = doc.getAnnotations();
+ } else {
+ inputAS = doc.getAnnotations(inputASName);
+ }
+
+ List<Annotation> instances = null;
+ if(instanceName == null || instanceName.equals("")) {
+ // There is no instance name so we will create one instance (line) per
+ // document.
+ // Here, we find the first annotation of the right type for each slot in
+ // the config file.
+ for(int i = 0; i < this.numberOfAnnotationSlots; i++) {
+ this.outputStream.print(this.bridges[i]);
+ // Check the annotation type isn't null
+ if(annsToInsert[i][0] != null) {
+ List<Annotation> typedAnnotations = Utils.inDocumentOrder(
+ inputAS.get(this.annsToInsert[i][0]));
+ Annotation annotationToPrint = typedAnnotations.get(0);
+ if(this.annsToInsert[i][1] != null) {
+ this.outputStream.print(annotationToPrint.getFeatures().get(
+ this.annsToInsert[i][1]));
+ } else {
+ // We have no feature to print so we will just print the text
+ long startNode = annotationToPrint.getStartNode().getOffset();
+ long endNode = annotationToPrint.getEndNode().getOffset();
+ String annotationText = "";
+ try {
+ annotationText =
+ doc.getContent().getContent(startNode, endNode).toString();
+ } catch(Exception e) {
+ e.printStackTrace();
+ }
+ this.outputStream.print(annotationText);
+ }
+ }
+ }
+ if(this.numberOfBridgeTextSlots > this.numberOfAnnotationSlots) {
+ this.outputStream.print(this.bridges[this.numberOfBridgeTextSlots -
1]);
+ }
+ this.outputStream.println();
+ } else {
+ // We have an instance type so we will create one output line per
+ // instance.
+ instances = Utils.inDocumentOrder(inputAS.get(this.instanceName));
+
+ Iterator<Annotation> instanceAnnotationsIterator = instances.iterator();
+ while(instanceAnnotationsIterator.hasNext()) {
+ Annotation thisInstanceAnnotation = instanceAnnotationsIterator.next();
+ long startSearch = thisInstanceAnnotation.getStartNode().getOffset();
+ long endSearch = thisInstanceAnnotation.getEndNode().getOffset();
+
+ // Here, we find the first annotation of the right type within the span
+ // of the
+ // instance annotation for each slot in the config file.
+ for(int i = 0; i < this.numberOfAnnotationSlots; i++) {
+ this.outputStream.print(this.bridges[i]);
+ List<Annotation> typedAnnotations = Utils.inDocumentOrder(
+ inputAS.get(this.annsToInsert[i][0], startSearch, endSearch));
+ if(typedAnnotations.size() > 0) {
+ Annotation annotationToPrint = typedAnnotations.get(0);
+ if(this.annsToInsert[i][1] != null) {
+ this.outputStream.print(annotationToPrint.getFeatures().get(
+ this.annsToInsert[i][1]));
+ } else {
+ // We have no feature to print so we will just print the text
+ long startNode = annotationToPrint.getStartNode().getOffset();
+ long endNode = annotationToPrint.getEndNode().getOffset();
+ String annotationText = "";
+ try {
+ annotationText =
+ doc.getContent().getContent(startNode, endNode).toString();
+ } catch(Exception e) {
+ e.printStackTrace();
+ }
+ this.outputStream.print(annotationText);
+ }
+ }
+ }
+ if(this.numberOfBridgeTextSlots > this.numberOfAnnotationSlots) {
+ this.outputStream
+ .print(this.bridges[this.numberOfBridgeTextSlots - 1]);
+ }
+ this.outputStream.println();
+ }
+ }
+
+ }
+
+
+ @Override
+ public synchronized void interrupt() {
+ super.interrupt();
+ }
+
+}
Property changes on:
gate/trunk/plugins/Tools/src/gate/configurableexporter/ConfigurableExporter.java
___________________________________________________________________
Added: svn:mime-type
+ text/plain
Added: svn:keywords
+ Id
Added: svn:eol-style
+ native
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