Revision: 19047
http://sourceforge.net/p/gate/code/19047
Author: ian_roberts
Date: 2015-12-23 14:08:05 +0000 (Wed, 23 Dec 2015)
Log Message:
-----------
Pulled out the common parts of pubmed and cochrane formats into something
parameterizable, so we can use it as a basis for other formats that use the
same database-style "KEY: value" type of syntax.
Modified Paths:
--------------
gate/trunk/plugins/Format_PubMed/build.xml
gate/trunk/plugins/Format_PubMed/src/gate/corpora/CochraneTextDocumentFormat.java
gate/trunk/plugins/Format_PubMed/src/gate/corpora/PubmedTextDocumentFormat.java
Modified: gate/trunk/plugins/Format_PubMed/build.xml
===================================================================
--- gate/trunk/plugins/Format_PubMed/build.xml 2015-12-23 02:22:20 UTC (rev
19046)
+++ gate/trunk/plugins/Format_PubMed/build.xml 2015-12-23 14:08:05 UTC (rev
19047)
@@ -37,8 +37,8 @@
<target name="compile" depends="init"
description="compile the source " >
<!-- Compile the java code from ${src} into ${build} -->
- <javac srcdir="${src}" destdir="${build}" source="1.6" target="1.6"
- classpathref="compile.classpath">
+ <javac srcdir="${src}" destdir="${build}" source="1.7" target="1.7"
+ classpathref="compile.classpath" debug="true"
debuglevel="lines,source">
<compilerarg value="-Xmaxwarns" />
<compilerarg value="${gate.compile.maxwarnings}" />
<compilerarg value="-Xlint:all" />
@@ -55,7 +55,7 @@
classpathref="compile.classpath"
encoding="UTF-8"
windowtitle="${plugin.name} JavaDoc"
- source="1.6">
+ source="1.7">
<sourcepath>
<pathelement location="${src}" />
</sourcepath>
Modified:
gate/trunk/plugins/Format_PubMed/src/gate/corpora/CochraneTextDocumentFormat.java
===================================================================
---
gate/trunk/plugins/Format_PubMed/src/gate/corpora/CochraneTextDocumentFormat.java
2015-12-23 02:22:20 UTC (rev 19046)
+++
gate/trunk/plugins/Format_PubMed/src/gate/corpora/CochraneTextDocumentFormat.java
2015-12-23 14:08:05 UTC (rev 19047)
@@ -15,29 +15,15 @@
*/
package gate.corpora;
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.Serializable;
-import java.io.StringReader;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.apache.log4j.Logger;
-
-import gate.AnnotationSet;
-import gate.Document;
-import gate.Factory;
-import gate.GateConstants;
import gate.Resource;
import gate.creole.ResourceInstantiationException;
import gate.creole.metadata.AutoInstance;
+import gate.creole.metadata.CreoleParameter;
import gate.creole.metadata.CreoleResource;
import gate.util.DocumentFormatException;
-import gate.util.InvalidOffsetException;
-import gate.util.Strings;
+import java.util.List;
+
/**
* A document format analyser for Cochrane text documents. Use mime type value
* "text/x-cochrane", or file extension ".cochrane.txt" to access this document
@@ -49,7 +35,7 @@
"the correct file extension.",
autoinstances = {@AutoInstance(hidden=true)},
isPrivate = true)
-public class CochraneTextDocumentFormat extends TextualDocumentFormat {
+public class CochraneTextDocumentFormat extends PubmedTextDocumentFormat {
private static final long serialVersionUID = 8362288605943414676L;
@@ -61,19 +47,7 @@
private static final String COCHRANE_ID = "ID";
- protected static final Logger logger = Logger.getLogger(
- CochraneTextDocumentFormat.class);
-
/* (non-Javadoc)
- * @see gate.DocumentFormat#supportsRepositioning()
- */
- @Override
- public Boolean supportsRepositioning() {
- return false;
- }
-
-
- /* (non-Javadoc)
* @see gate.corpora.TextualDocumentFormat#init()
*/
@Override
@@ -104,127 +78,23 @@
mimeString2mimeTypeMap.remove(mime.getType() + "/" + mime.getSubtype());
suffixes2mimeTypeMap.remove("cochrane.txt");
}
+
+ @CreoleParameter(defaultValue = "(?<CODE>[A-Z]+): (?<VALUE>.*)")
+ public void setFieldPattern(String fieldPattern) {
+ super.setFieldPattern(fieldPattern);
+ }
- /* (non-Javadoc)
- * @see gate.corpora.TextualDocumentFormat#unpackMarkup(gate.Document)
- */
- @Override
- public void unpackMarkup(Document doc) throws DocumentFormatException {
- try {
- BufferedReader content = new BufferedReader(new StringReader(
- doc.getContent().toString()));
- Map<String, Serializable> fields = new HashMap<String, Serializable>();
- String line = content.readLine();
- String key = null;
- StringBuilder value = new StringBuilder();
- Pattern linePatt = Pattern.compile("([A-Z]+): (.*)");
- while(line!= null) {
- Matcher matcher = linePatt.matcher(line);
- if(matcher.matches()) {
- // new field
- if(key != null) {
- // save old value
- PubmedUtils.addFieldValue(key, value.toString(), fields);
- }
- key = matcher.group(1).trim();
- value.delete(0, value.length());
- value.append(matcher.group(2));
- } else {
- // a non-assignment line -> append to previous value
- if(value.length() == 0) {
- logger.warn("Ignoring invalid input line:\"" +
- line + "\"");
- } else {
- value.append(Strings.getNl()).append(line.trim());
- }
- }
- line = content.readLine();
- }
- if(key != null) {
- // save old value
- PubmedUtils.addFieldValue(key, value.toString(), fields);
- }
- StringBuilder docText = new StringBuilder();
- // add document title
- int titleStart = docText.length();
- int titleEnd = titleStart;
- Serializable aField = fields.remove(COCHRANE_TITLE);
- if(aField != null) {
- docText.append(PubmedUtils.getFieldValueString(aField));
- titleEnd = docText.length();
- docText.append(Strings.getNl()).append(Strings.getNl());
- } else {
- String docName = doc.getName();
- logger.warn("Could not find document title in document " +
- (docName != null ? docName : ""));
- }
- // add ID
- int idStart = docText.length();
- int idEnd = idStart;
- aField = fields.get(COCHRANE_ID);
- if(aField != null) {
- docText.append(PubmedUtils.getFieldValueString(aField));
- idEnd = docText.length();
- docText.append(Strings.getNl()).append(Strings.getNl());
- } else {
- String docName = doc.getName();
- logger.warn("Could not find document ID in document " +
- (docName != null ? docName : ""));
- }
- // add authors
- int authorStart = docText.length();
- int authorEnd = authorStart;
- aField = fields.get(COCHRANE_AUTHORS);
- if(aField != null) {
- docText.append(PubmedUtils.getFieldValueString(aField));
- authorEnd = docText.length();
- docText.append(Strings.getNl()).append(Strings.getNl());
- } else {
- String docName = doc.getName();
- logger.warn("Could not find document authors in document " +
- (docName != null ? docName : ""));
- }
- // and the document abstract
- aField = fields.remove(COCHRANE_ABSTRACT);
- int absStart = docText.length();
- if(aField != null) {
- docText.append(PubmedUtils.getFieldValueString(aField));
- } else {
- String docName = doc.getName();
- logger.warn("Could not find document abstract in document " +
- (docName != null ? docName : ""));
- }
- int absEnd = docText.length();
- doc.setContent(new DocumentContentImpl(docText.toString()));
-
- AnnotationSet origMkups = doc.getAnnotations(
- GateConstants.ORIGINAL_MARKUPS_ANNOT_SET_NAME);
- if(titleEnd > titleStart){
- origMkups.add((long)titleStart, (long)titleEnd, "title",
- Factory.newFeatureMap());
- }
- if(idEnd > idStart){
- origMkups.add((long)idStart, (long)idEnd, "id",
- Factory.newFeatureMap());
- }
- if(authorEnd > authorStart) {
- origMkups.add((long)authorStart, (long)authorEnd, "authors",
- Factory.newFeatureMap());
- }
- if(absEnd > absStart) {
- origMkups.add((long)absStart, (long)absEnd, "abstract",
- Factory.newFeatureMap());
- }
- // everything else becomes document features
- doc.getFeatures().putAll(fields);
- } catch(IOException e) {
- throw new DocumentFormatException("Error while unpacking markup",e);
- } catch(InvalidOffsetException e) {
- throw new DocumentFormatException("Error while unpacking markup",e);
- }
-
- // now let the text unpacker also do its job
- super.unpackMarkup(doc);
- }
-
+
+ @CreoleParameter(defaultValue = COCHRANE_TITLE + "=title;" + COCHRANE_ID +
+ "=id;" + COCHRANE_AUTHORS + "=authors;" + COCHRANE_ABSTRACT +
+ "=abstract")
+ public void setFieldsForText(List<String> fieldsForText) {
+ super.setFieldsForText(fieldsForText);
+ }
+
+ @CreoleParameter(defaultValue = COCHRANE_TITLE + ";" + COCHRANE_ABSTRACT)
+ public void setExcludeFromFeatures(List<String> excludeFromFeatures) {
+ super.setExcludeFromFeatures(excludeFromFeatures);
+ }
+
}
Modified:
gate/trunk/plugins/Format_PubMed/src/gate/corpora/PubmedTextDocumentFormat.java
===================================================================
---
gate/trunk/plugins/Format_PubMed/src/gate/corpora/PubmedTextDocumentFormat.java
2015-12-23 02:22:20 UTC (rev 19046)
+++
gate/trunk/plugins/Format_PubMed/src/gate/corpora/PubmedTextDocumentFormat.java
2015-12-23 14:08:05 UTC (rev 19047)
@@ -22,7 +22,9 @@
import gate.Resource;
import gate.creole.ResourceInstantiationException;
import gate.creole.metadata.AutoInstance;
+import gate.creole.metadata.CreoleParameter;
import gate.creole.metadata.CreoleResource;
+import gate.creole.metadata.Optional;
import gate.util.DocumentFormatException;
import gate.util.InvalidOffsetException;
import gate.util.Strings;
@@ -32,6 +34,7 @@
import java.io.Serializable;
import java.io.StringReader;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
@@ -64,6 +67,14 @@
protected static final Logger logger = Logger.getLogger(
PubmedTextDocumentFormat.class);
+ protected String fieldPattern;
+
+ protected String ignorePattern;
+
+ protected List<String> fieldsForText;
+
+ protected List<String> excludeFromFeatures;
+
/* (non-Javadoc)
* @see gate.DocumentFormat#supportsRepositioning()
*/
@@ -72,6 +83,57 @@
return false;
}
+ @CreoleParameter(comment = "Regular expression that matches the (whole of
the) "
+ + "first line of a new field. The expression should include two named "
+ + "capturing groups, <CODE> for the field code and <VALUE> for the "
+ + "field value.", defaultValue = "(?<CODE>....)- (?<VALUE>.*)")
+ public void setFieldPattern(String fieldPattern) {
+ this.fieldPattern = fieldPattern;
+ }
+
+ public String getFieldPattern() {
+ return fieldPattern;
+ }
+
+ @Optional
+ @CreoleParameter(comment = "Regular expression that matches (the whole of) "
+ + "any lines that should be silently ignored. If unspecified, all "
+ + "lines are considered.")
+ public void setIgnorePattern(String ignorePattern) {
+ this.ignorePattern = ignorePattern;
+ }
+
+ public String getIgnorePattern() {
+ return ignorePattern;
+ }
+
+ @CreoleParameter(comment = "Fields which should be mapped into the document "
+ + "text. Each entry in this list should be a string of the form "
+ + "fieldcode=annotationtype, the corresponding fields will be "
+ + "concatenated together, separated by blank lines, to form the content "
+ + "of the unpacked document, and each will be covered by an annotation
of "
+ + "the appropriate type in the Original markups set.",
+ defaultValue = PUBMED_TITLE + "=title;" + PUBMED_ID + "=id;" +
+ PUBMED_AUTHORS + "=authors;" + PUBMED_ABSTRACT + "=abstract")
+ public void setFieldsForText(List<String> fieldsForText) {
+ this.fieldsForText = fieldsForText;
+ }
+
+ public List<String> getFieldsForText() {
+ return fieldsForText;
+ }
+
+ @CreoleParameter(comment = "Fields which should not be mapped to document "
+ + "features. All fields found in the text which are not mentioned here "
+ + "will be stored as features on the document.",
+ defaultValue = PUBMED_TITLE + ";" + PUBMED_ABSTRACT)
+ public void setExcludeFromFeatures(List<String> excludeFromFeatures) {
+ this.excludeFromFeatures = excludeFromFeatures;
+ }
+
+ public List<String> getExcludeFromFeatures() {
+ return excludeFromFeatures;
+ }
/* (non-Javadoc)
* @see gate.corpora.TextualDocumentFormat#init()
@@ -118,25 +180,32 @@
String line = content.readLine();
String key = null;
StringBuilder value = new StringBuilder();
- Pattern linePatt = Pattern.compile("(....)- (.*)");
+ Pattern ignorePatt = null;
+ if(ignorePattern != null) {
+ ignorePatt = Pattern.compile(ignorePattern);
+ }
+ Pattern linePatt = Pattern.compile(fieldPattern);
while(line!= null) {
- Matcher matcher = linePatt.matcher(line);
- if(matcher.matches()) {
- // new field
- if(key != null) {
- // save old value
- PubmedUtils.addFieldValue(key, value.toString(), fields);
- }
- key = matcher.group(1).trim();
- value.delete(0, value.length());
- value.append(matcher.group(2));
- } else {
- // a non-assignment line -> append to previous value
- if(value.length() == 0) {
- logger.warn("Ignoring invalid input line:\"" +
- line + "\"");
+ // skip ignorable lines
+ if(ignorePatt == null || !ignorePatt.matcher(line).matches()) {
+ Matcher matcher = linePatt.matcher(line);
+ if(matcher.matches()) {
+ // new field
+ if(key != null) {
+ // save old value
+ PubmedUtils.addFieldValue(key, value.toString(), fields);
+ }
+ key = matcher.group("CODE").trim();
+ value.delete(0, value.length());
+ value.append(matcher.group("VALUE"));
} else {
- value.append(Strings.getNl()).append(line.trim());
+ // a non-assignment line -> append to previous value
+ if(value.length() == 0) {
+ logger.warn("Ignoring invalid input line:\"" +
+ line + "\"");
+ } else {
+ value.append(Strings.getNl()).append(line.trim());
+ }
}
}
line = content.readLine();
@@ -146,77 +215,41 @@
PubmedUtils.addFieldValue(key, value.toString(), fields);
}
StringBuilder docText = new StringBuilder();
- // add document title
- int titleStart = docText.length();
- int titleEnd = titleStart;
- Serializable aField = fields.remove(PUBMED_TITLE);
- if(aField != null) {
- docText.append(PubmedUtils.getFieldValueString(aField));
- titleEnd = docText.length();
- docText.append(Strings.getNl()).append(Strings.getNl());
- } else {
- String docName = doc.getName();
- logger.warn("Could not find document title in document " +
- (docName != null ? docName : ""));
+ // build document text
+ int[] starts = new int[fieldsForText.size()];
+ int[] ends = new int[fieldsForText.size()];
+ for(int i = 0; i < fieldsForText.size(); i++) {
+ String[] field = fieldsForText.get(i).split("=", 2);
+ starts[i] = docText.length();
+ ends[i] = starts[i];
+ Serializable aField = fields.get(field[0]);
+ if(aField != null) {
+ docText.append(PubmedUtils.getFieldValueString(aField));
+ ends[i] = docText.length();
+ docText.append(Strings.getNl()).append(Strings.getNl());
+ } else {
+ String docName = doc.getName();
+ logger.warn("Could not find " + field[1] + " in document " +
+ (docName != null ? docName : ""));
+ }
}
- // add ID
- int idStart = docText.length();
- int idEnd = idStart;
- aField = fields.get(PUBMED_ID);
- if(aField != null) {
- docText.append(PubmedUtils.getFieldValueString(aField));
- idEnd = docText.length();
- docText.append(Strings.getNl()).append(Strings.getNl());
- } else {
- String docName = doc.getName();
- logger.warn("Could not find document ID in document " +
- (docName != null ? docName : ""));
- }
- // add authors
- int authorStart = docText.length();
- int authorEnd = authorStart;
- aField = fields.get(PUBMED_AUTHORS);
- if(aField != null) {
- docText.append(PubmedUtils.getFieldValueString(aField));
- authorEnd = docText.length();
- docText.append(Strings.getNl()).append(Strings.getNl());
- } else {
- String docName = doc.getName();
- logger.warn("Could not find document authors in document " +
- (docName != null ? docName : ""));
- }
- // and the document abstract
- aField = fields.remove(PUBMED_ABSTRACT);
- int absStart = docText.length();
- if(aField != null) {
- docText.append(PubmedUtils.getFieldValueString(aField));
- } else {
- String docName = doc.getName();
- logger.warn("Could not find document abstract in document " +
- (docName != null ? docName : ""));
- }
- int absEnd = docText.length();
+
doc.setContent(new DocumentContentImpl(docText.toString()));
AnnotationSet origMkups = doc.getAnnotations(
GateConstants.ORIGINAL_MARKUPS_ANNOT_SET_NAME);
- if(titleEnd > titleStart){
- origMkups.add((long)titleStart, (long)titleEnd, "title",
- Factory.newFeatureMap());
+ for(int i = 0; i < fieldsForText.size(); i++) {
+ String[] field = fieldsForText.get(i).split("=", 2);
+ if(ends[i] > starts[i]) {
+ origMkups.add((long)starts[i], (long)ends[i], field[1],
+ Factory.newFeatureMap());
+ }
}
- if(idEnd > idStart){
- origMkups.add((long)idStart, (long)idEnd, "id",
- Factory.newFeatureMap());
+
+ // everything else becomes document features
+ for(String keyToExclude : excludeFromFeatures) {
+ fields.remove(keyToExclude);
}
- if(authorEnd > authorStart) {
- origMkups.add((long)authorStart, (long)authorEnd, "authors",
- Factory.newFeatureMap());
- }
- if(absEnd > absStart) {
- origMkups.add((long)absStart, (long)absEnd, "abstract",
- Factory.newFeatureMap());
- }
- // everything else becomes document features
doc.getFeatures().putAll(fields);
} catch(IOException e) {
throw new DocumentFormatException("Error while unpacking markup",e);
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