Revision: 19249
http://sourceforge.net/p/gate/code/19249
Author: markagreenwood
Date: 2016-04-20 10:03:32 +0000 (Wed, 20 Apr 2016)
Log Message:
-----------
some debugging output and changes from trunk merged in
Modified Paths:
--------------
gate/branches/sawdust2/build/build.properties
gate/branches/sawdust2/build/build.txt
gate/branches/sawdust2/build/deploy/plugins/gate-8.1.xml
gate/branches/sawdust2/plugins/Crowd_Sourcing/src/gate/crowdsource/classification/EntityClassificationJobBuilder.java
gate/branches/sawdust2/plugins/Crowd_Sourcing/src/gate/crowdsource/rest/CrowdFlowerClient.java
gate/branches/sawdust2/plugins/Format_CSV/gcp/csv4gcp.jar
gate/branches/sawdust2/plugins/Format_CSV/gcp/src/gate/cloud/io/csv/CSVStreamingOutputHandler.java
gate/branches/sawdust2/src/main/gate/Plugin.java
gate/branches/sawdust2/src/main/gate/creole/CreoleAnnotationHandler.java
gate/branches/sawdust2/src/main/gate/gui/SerialControllerEditor.java
Property Changed:
----------------
gate/branches/sawdust2/
gate/branches/sawdust2/build/
gate/branches/sawdust2/build/deploy/
gate/branches/sawdust2/plugins/
gate/branches/sawdust2/src/
Index: gate/branches/sawdust2
===================================================================
--- gate/branches/sawdust2 2016-04-20 09:46:44 UTC (rev 19248)
+++ gate/branches/sawdust2 2016-04-20 10:03:32 UTC (rev 19249)
Property changes on: gate/branches/sawdust2
___________________________________________________________________
Modified: svn:mergeinfo
## -4,4 +4,4 ##
/gate/branches/release-8.1:18736-18747
/gate/branches/sawdust:17055-17079
/gate/tags/release-7.0:15399-15407
-/gate/trunk:19181
+/gate/trunk:19180-19248
\ No newline at end of property
Index: gate/branches/sawdust2/build
===================================================================
--- gate/branches/sawdust2/build 2016-04-20 09:46:44 UTC (rev 19248)
+++ gate/branches/sawdust2/build 2016-04-20 10:03:32 UTC (rev 19249)
Property changes on: gate/branches/sawdust2/build
___________________________________________________________________
Modified: svn:mergeinfo
## -4,4 +4,4 ##
/gate/branches/release-8.1/build:18736-18747
/gate/branches/sawdust/build:17055-17079
/gate/tags/release-7.0/build:15399-15407
-/gate/trunk/build:3-7
+/gate/trunk/build:3-7,19180-19248
\ No newline at end of property
Modified: gate/branches/sawdust2/build/build.properties
===================================================================
--- gate/branches/sawdust2/build/build.properties 2016-04-20 09:46:44 UTC
(rev 19248)
+++ gate/branches/sawdust2/build/build.properties 2016-04-20 10:03:32 UTC
(rev 19249)
@@ -1,4 +1,4 @@
#Build Number for ANT. Do not edit!
-#Sat Apr 02 02:08:02 BST 2016
+#Wed Apr 20 02:08:12 BST 2016
cvs.version=$Id\: build.properties 7542 2006-07-17 14\:26\:51Z ian_roberts $
-build.number=5431
+build.number=5449
Modified: gate/branches/sawdust2/build/build.txt
===================================================================
--- gate/branches/sawdust2/build/build.txt 2016-04-20 09:46:44 UTC (rev
19248)
+++ gate/branches/sawdust2/build/build.txt 2016-04-20 10:03:32 UTC (rev
19249)
@@ -1 +1 @@
-5430
\ No newline at end of file
+5448
\ No newline at end of file
Index: gate/branches/sawdust2/build/deploy
===================================================================
--- gate/branches/sawdust2/build/deploy 2016-04-20 09:46:44 UTC (rev 19248)
+++ gate/branches/sawdust2/build/deploy 2016-04-20 10:03:32 UTC (rev 19249)
Property changes on: gate/branches/sawdust2/build/deploy
___________________________________________________________________
Modified: svn:mergeinfo
## -6,3 +6,4 ##
/gate/branches/release-8.1/build/deploy:18736-18747
/gate/branches/sawdust/build/deploy:17055-17079
/gate/tags/release-7.0/build/deploy:15399-15407
+/gate/trunk/build/deploy:19180-19248
\ No newline at end of property
Modified: gate/branches/sawdust2/build/deploy/plugins/gate-8.1.xml
===================================================================
--- gate/branches/sawdust2/build/deploy/plugins/gate-8.1.xml 2016-04-20
09:46:44 UTC (rev 19248)
+++ gate/branches/sawdust2/build/deploy/plugins/gate-8.1.xml 2016-04-20
10:03:32 UTC (rev 19249)
@@ -20,8 +20,8 @@
downloadURL="https://github.com/johann-petrak/gateplugin-VirtualCorpus/releases/download/V0.16/VirtualCorpus-0.16.zip";
/>
<CreolePlugin
-
url="https://raw.githubusercontent.com/GateNLP/gateplugin-LearningFramework/V2_0/";
-
downloadURL="https://github.com/GateNLP/gateplugin-LearningFramework/releases/download/V2_0/gateplugin-LearningFramework-2.0.zip";
+
url="https://raw.githubusercontent.com/GateNLP/gateplugin-LearningFramework/V2_1/";
+
downloadURL="https://github.com/GateNLP/gateplugin-LearningFramework/releases/download/V2_1/gateplugin-LearningFramework-2.1.zip";
/>
<CreolePlugin
url="https://raw.githubusercontent.com/GenevieveGorrell/gateplugin-LearningFramework/version_1_0/";
Index: gate/branches/sawdust2/plugins
===================================================================
--- gate/branches/sawdust2/plugins 2016-04-20 09:46:44 UTC (rev 19248)
+++ gate/branches/sawdust2/plugins 2016-04-20 10:03:32 UTC (rev 19249)
Property changes on: gate/branches/sawdust2/plugins
___________________________________________________________________
Modified: svn:mergeinfo
## -3,4 +3,4 ##
/gate/branches/release-8.1/plugins:18736-18747
/gate/branches/sawdust/plugins:17055-17079
/gate/tags/release-7.0/plugins:15399-15407
-/gate/trunk/plugins:3-390,19181
+/gate/trunk/plugins:3-390,19180-19248
\ No newline at end of property
Modified:
gate/branches/sawdust2/plugins/Crowd_Sourcing/src/gate/crowdsource/classification/EntityClassificationJobBuilder.java
===================================================================
---
gate/branches/sawdust2/plugins/Crowd_Sourcing/src/gate/crowdsource/classification/EntityClassificationJobBuilder.java
2016-04-20 09:46:44 UTC (rev 19248)
+++
gate/branches/sawdust2/plugins/Crowd_Sourcing/src/gate/crowdsource/classification/EntityClassificationJobBuilder.java
2016-04-20 10:03:32 UTC (rev 19249)
@@ -180,21 +180,27 @@
AnnotationSet thisEntityContext =
Utils.getCoveringAnnotations(contextAnnotations, entity);
- if(thisEntityContext.isEmpty()) {
- log.warn(entityAnnotationType + " with ID " + entity.getId()
- + " at offsets (" + Utils.start(entity) + ":"
- + Utils.end(entity) + ") in document "
- + getDocument().getName() + " has no surrounding "
- + contextAnnotationType + " - ignored");
+
+ if (contextASName != null) {
+ if(thisEntityContext.isEmpty()) {
+ log.warn(entityAnnotationType + " with ID " + entity.getId()
+ + " at offsets (" + Utils.start(entity) + ":"
+ + Utils.end(entity) + ") in document "
+ + getDocument().getName() + " has no surrounding "
+ + contextAnnotationType + " - ignored");
+ } else {
+ // get the "closest" context, i.e. the shortest annotation in
+ // the covering set.
+ // usually we'd expect this set to contain just one annotation
+ Annotation context =
+ Collections.min(thisEntityContext,
+ ANNOTATION_LENGTH_COMPARATOR);
+ crowdFlowerClient.createClassificationUnit(jobId, getDocument(),
+ entityASName, context, entity);
+ }
} else {
- // get the "closest" context, i.e. the shortest annotation in
- // the covering set.
- // usually we'd expect this set to contain just one annotation
- Annotation context =
- Collections.min(thisEntityContext,
- ANNOTATION_LENGTH_COMPARATOR);
crowdFlowerClient.createClassificationUnit(jobId, getDocument(),
- entityASName, context, entity);
+ entityASName, entity, entity);
}
}
fireProcessFinished();
Modified:
gate/branches/sawdust2/plugins/Crowd_Sourcing/src/gate/crowdsource/rest/CrowdFlowerClient.java
===================================================================
---
gate/branches/sawdust2/plugins/Crowd_Sourcing/src/gate/crowdsource/rest/CrowdFlowerClient.java
2016-04-20 09:46:44 UTC (rev 19248)
+++
gate/branches/sawdust2/plugins/Crowd_Sourcing/src/gate/crowdsource/rest/CrowdFlowerClient.java
2016-04-20 10:03:32 UTC (rev 19249)
@@ -15,10 +15,7 @@
import static gate.crowdsource.CrowdFlowerConstants.*;
-import gate.Annotation;
-import gate.AnnotationSet;
-import gate.Document;
-import gate.Utils;
+import gate.*;
import gate.util.GateRuntimeException;
import java.io.ByteArrayOutputStream;
@@ -149,6 +146,60 @@
/**
* <p>
+ * Generates the text required to display the context for a
classification,
+ * either based on the document content, or on features present in the
annotation.
+ *
+ * If any of leftContext, rightContext, or entity are set as features on
the annotation,
+ * the text will be generated using those.
+ *
+ * If none of these are present, the contents of the context and target
feature will be
+ * combined to give the document text used.
+ * </p>
+ * @param doc The document containing text that will be used if needed
+ * @param context The context annotation in which the entity will be couched
+ * @param target The target entity to display.
+ * @return
+ */
+ private String createClassificationUnitText(Document doc, Annotation context,
+ Annotation target) {
+ FeatureMap targetFeatures = target.getFeatures();
+
+ try {
+ // Fill in each part of the text individually, starting with the entity
itself.
+ String entity; // No initialiser needed as we're guaranteed to overwrite
it.
+
+ if (targetFeatures.containsKey("entity")) {
+ entity = (String) targetFeatures.get("entity");
+ } else {
+ entity = Utils.stringFor(doc, target);
+ }
+
+ // Look for the left context.
+ String leftContext = "";
+
+ if (targetFeatures.containsKey("leftContext")) {
+ leftContext = (String) targetFeatures.get("leftContext");
+ } else if (context != null) {
+ leftContext = Utils.stringFor(doc, Utils.start(context),
Utils.start(target));
+ }
+
+ // Look for the right context.
+ String rightContext = "";
+
+ if (targetFeatures.containsKey("rightContext")) {
+ rightContext = (String) targetFeatures.get("rightContext");
+ } else if (context != null) {
+ rightContext = Utils.stringFor(doc, Utils.end(target),
Utils.end(context));
+ }
+
+ return leftContext + "<span class=\"gate-entity\">" + entity + "</span>"
+ rightContext;
+ } catch (ClassCastException e) {
+ throw new ClassCastException("Features entity, leftContext and
rightContext must be String, if provided.");
+ }
+
+ }
+ /**
+ * <p>
* Create a single unit in a classification job for the given
* annotation. If the unit is created successfully, its ID will be
* stored as a {@link Long} valued feature named <code>cf_unit</code>
@@ -176,6 +227,13 @@
* created - typically things like "none" (none of the available
* options is correct) or "nae" (the target is not an entity).
* </p>
+ *
+ * <p>
+ * If the target annotation has a feature named "leftContext", "rightContext"
+ * or "entity", these will be used to generate the entity text for display.
+ * Otherwise, the text will be taken from the document, as covered by the
+ * context and target annotations.
+ * </p>
*
* @param jobId the CrowdFlower job ID
* @param doc the document containing the annotation
@@ -191,17 +249,23 @@
*/
public long createClassificationUnit(long jobId, Document doc, String asName,
Annotation context, Annotation target) {
- String text = Utils.stringFor(doc, context);
- String entity = Utils.stringFor(doc, target);
+
+ String entity; // No initialiser needed as we're guaranteed to overwrite
it.
+
+ if (target.getFeatures().containsKey("entity")) {
+ entity = (String) target.getFeatures().get("entity");
+ if (entity == null) {
+ throw new NullPointerException("Given entity feature was null");
+ }
+ } else {
+ entity = Utils.stringFor(doc, target);
+ }
+
+ String text = createClassificationUnitText(doc, context, target);
+
String documentId = String.valueOf(doc.getLRPersistenceId());
int formDataSize = 10; // text + entity + docId + asName + annId
- // insert highlight span into text
- int entityStart = (int)(Utils.start(target) - Utils.start(context));
- int entityEnd = entityStart + entity.length();
- text =
- text.substring(0, entityStart) + "<span class=\"gate-entity\">"
- + entity + "</span>" + text.substring(entityEnd);
Object options = target.getFeatures().get("options");
if(options != null) {
@@ -387,7 +451,7 @@
+ " <cml:checkbox name=\"noentities\" label=\"");
StringEscapeUtils.escapeXml(cml, noEntitiesCaption);
cml.append("\" value=\"1\"\n"
- + " only-if=\"!answer:required\" validates=\"required\"/>\n"
+ + " only-if=\"!answer\" validates=\"required\"/>\n"
+ "</div>\n");
if(commentCaption != null) {
cml.append("<cml:text name=\"comment\" label=\"");
Modified: gate/branches/sawdust2/plugins/Format_CSV/gcp/csv4gcp.jar
===================================================================
(Binary files differ)
Modified:
gate/branches/sawdust2/plugins/Format_CSV/gcp/src/gate/cloud/io/csv/CSVStreamingOutputHandler.java
===================================================================
---
gate/branches/sawdust2/plugins/Format_CSV/gcp/src/gate/cloud/io/csv/CSVStreamingOutputHandler.java
2016-04-20 09:46:44 UTC (rev 19248)
+++
gate/branches/sawdust2/plugins/Format_CSV/gcp/src/gate/cloud/io/csv/CSVStreamingOutputHandler.java
2016-04-20 10:03:32 UTC (rev 19249)
@@ -45,6 +45,8 @@
public static final String PARAM_ANNOTATION_SET_NAME = "annotationSetName";
public static final String PARAM_ANNOTATION_TYPE = "annotationType";
+
+ public static final String PARAM_CONTAINED_ONLY = "containedOnly";
private static final Logger logger = Logger
.getLogger(CSVStreamingOutputHandler.class);
@@ -58,6 +60,8 @@
protected String annotationSetName, annotationType;
protected String[] columns;
+
+ protected boolean containedOnly;
@Override
protected void configImpl(Map<String, String> configData) throws IOException,
@@ -99,6 +103,12 @@
// at the document level as if the param was missing
if(annotationType != null && annotationType.trim().equals(""))
annotationType = null;
+
+ // should we only look at annotations contained within the annotationType
or
+ // do we allow overlapping ones as well?
+ containedOnly =
+ configData.containsKey(PARAM_CONTAINED_ONLY) ? Boolean
+ .parseBoolean(configData.get(PARAM_CONTAINED_ONLY)) : true;
}
@Override
@@ -191,8 +201,16 @@
if(within != null) {
// if we have been provided with an annotation to limit the search then
- // get just those contained within it
- annots = Utils.getContainedAnnotations(annots, within);
+ // get just those either....
+
+ if (containedOnly) {
+ // contained within the annotation
+ annots = Utils.getContainedAnnotations(annots, within);
+ }
+ else {
+ // or partially overlapping with it
+ annots = Utils.getOverlappingAnnotations(annots, within);
+ }
}
// if there are no annotations then we can quit
Index: gate/branches/sawdust2/src
===================================================================
--- gate/branches/sawdust2/src 2016-04-20 09:46:44 UTC (rev 19248)
+++ gate/branches/sawdust2/src 2016-04-20 10:03:32 UTC (rev 19249)
Property changes on: gate/branches/sawdust2/src
___________________________________________________________________
Modified: svn:mergeinfo
## -4,4 +4,4 ##
/gate/branches/release-8.1/src:18736-18747
/gate/branches/sawdust/src:17055-17079
/gate/tags/release-7.0/src:15399-15407
-/gate/trunk/src:3-7
+/gate/trunk/src:3-7,19180-19248
\ No newline at end of property
Modified: gate/branches/sawdust2/src/main/gate/Plugin.java
===================================================================
--- gate/branches/sawdust2/src/main/gate/Plugin.java 2016-04-20 09:46:44 UTC
(rev 19248)
+++ gate/branches/sawdust2/src/main/gate/Plugin.java 2016-04-20 10:03:32 UTC
(rev 19249)
@@ -139,7 +139,7 @@
org.jdom.Document creoleDoc = getCreoleXML();
XMLOutputter xmlOut = new XMLOutputter(Format.getPrettyFormat());
- log.debug(xmlOut.outputString(creoleDoc));
+ System.out.println(xmlOut.outputString(creoleDoc));
final Map<String, ResourceInfo> resInfos = new LinkedHashMap<String,
ResourceInfo>();
List<Element> jobsList = new ArrayList<Element>();
Modified:
gate/branches/sawdust2/src/main/gate/creole/CreoleAnnotationHandler.java
===================================================================
--- gate/branches/sawdust2/src/main/gate/creole/CreoleAnnotationHandler.java
2016-04-20 09:46:44 UTC (rev 19248)
+++ gate/branches/sawdust2/src/main/gate/creole/CreoleAnnotationHandler.java
2016-04-20 10:03:32 UTC (rev 19249)
@@ -196,6 +196,7 @@
throws MalformedURLException {
if("JAR".equals(jdomElt.getName())) {
URL url = new URL(plugin.getBaseURL(), jdomElt.getTextTrim());
+ System.out.println("adding: "+url);
try {
java.io.InputStream s = url.openStream();
s.close();
Modified: gate/branches/sawdust2/src/main/gate/gui/SerialControllerEditor.java
===================================================================
--- gate/branches/sawdust2/src/main/gate/gui/SerialControllerEditor.java
2016-04-20 09:46:44 UTC (rev 19248)
+++ gate/branches/sawdust2/src/main/gate/gui/SerialControllerEditor.java
2016-04-20 10:03:32 UTC (rev 19249)
@@ -542,8 +542,20 @@
for(int row : rows) {
if(row > 0) {
//move it up
+ List<RunningStrategy> strategies = null;
+ if(conditionalMode) {
+ strategies = new
ArrayList<RunningStrategy>(((ConditionalController)controller)
+ .getRunningStrategies());
+ RunningStrategy straegy = strategies.remove(row);
+ strategies.add(row-1, straegy);
+ }
+
ProcessingResource value = controller.remove(row);
controller.add(row - 1, value);
+
+ if(conditionalMode) {
+
((ConditionalController)controller).setRunningStrategies(strategies);;
+ }
}
}
// memberPRsTableModel.fireTableDataChanged();
@@ -577,9 +589,22 @@
for(int i = rows.length - 1; i >= 0; i--){
int row = rows[i];
if(row < controller.getPRs().size() -1){
+
+ List<RunningStrategy> strategies = null;
+ if(conditionalMode) {
+ strategies = new
ArrayList<RunningStrategy>(((ConditionalController)controller)
+ .getRunningStrategies());
+ RunningStrategy straegy = strategies.remove(row);
+ strategies.add(row+1, straegy);
+ }
+
//move it down
ProcessingResource value = controller.remove(row);
controller.add(row + 1, value);
+
+ if(conditionalMode) {
+
((ConditionalController)controller).setRunningStrategies(strategies);;
+ }
}
}
// memberPRsTableModel.fireTableDataChanged();
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