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Posted to commits@ctakes.apache.org by se...@apache.org on 2017/04/17 02:38:56 UTC
svn commit: r1791649 - in /ctakes/trunk:
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/
ctakes-asserti...
Author: seanfinan
Date: Mon Apr 17 02:38:55 2017
New Revision: 1791649
URL: http://svn.apache.org/viewvc?rev=1791649&view=rev
Log:
ctakes - 424 : new pipebitinfo
Modified:
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/JudgeAttributeInstances.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/GoldEntityAndAttributeReader.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java
ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java
ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MarkableHeadTreeCreator.java
ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MarkableSalienceAnnotator.java
ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterRankingCoreferenceAnnotator.java
ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java
ctakes/trunk/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgAnnotator.java
ctakes/trunk/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgBaseTokenAnnotator.java
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/IdentifiedAnnotationExpander.java
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/LocationOfRelationExtractorAnnotator.java
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ManagesTreatsRelationExtractorAnnotator.java
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ManifestationOfRelationExtractorAnnotator.java
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationStatsCalculator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKDocTimeRelAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConsecutiveSentencesEventEventRelationAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConsecutiveSentencesEventTimeRelationAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/CrossSentenceTemporalRelationAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeI2B2RelationAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeSelfRelationAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventToClearTKEventAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/I2B2TemporalXMLReader.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/MetaTimeAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/F1BaselineEventTimeRelationAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimePosBasedAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimePositionBasedAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenAndBIOBasedAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenAndPosBasedAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenBasedAnnotator.java
ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/MetaMapToCTakesAnnotator.java
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java Mon Apr 17 02:38:55 2017
@@ -1,23 +1,24 @@
-/**
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- */
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
package org.apache.ctakes.assertion.attributes;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.log4j.Logger;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -37,6 +38,11 @@ import org.apache.ctakes.typesystem.type
*
*/
+@PipeBitInfo(
+ name = "Generic Status Annotator",
+ description = "Annotates the Generic status for Identified Annotations.",
+ dependencies = { PipeBitInfo.TypeProduct.SENTENCE, PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION }
+)
public class GenericAttributeAnalysisEngine extends JCasAnnotator_ImplBase {
public Logger logger = Logger.getLogger(getClass().getName());
@@ -54,7 +60,7 @@ public class GenericAttributeAnalysisEng
mention.setGeneric( GenericAttributeClassifier.getGeneric(jCas, mention) );
// System.err.println("Word:"+mention.getCoveredText()+", overwrote generic "+oldgeneric+" with "+mention.getGeneric());
}
-
+
}
}
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/JudgeAttributeInstances.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/JudgeAttributeInstances.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/JudgeAttributeInstances.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/JudgeAttributeInstances.java Mon Apr 17 02:38:55 2017
@@ -49,6 +49,7 @@ import java.util.HashMap;
import java.util.HashSet;
import org.apache.ctakes.assertion.eval.AssertionEvaluation.Options;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.relation.Relation;
@@ -79,6 +80,12 @@ import org.xml.sax.SAXException;
* @author Philip Ogren
*/
+@PipeBitInfo(
+ name = "Judged Attribute XMI Writer",
+ description = "Writes XMI File based upon judged attributes.",
+ role = PipeBitInfo.Role.WRITER,
+ dependencies = { PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION }
+)
public class JudgeAttributeInstances extends JCasConsumer_ImplBase {
/**
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/GoldEntityAndAttributeReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/GoldEntityAndAttributeReader.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/GoldEntityAndAttributeReader.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/GoldEntityAndAttributeReader.java Mon Apr 17 02:38:55 2017
@@ -26,6 +26,7 @@ import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.CAS;
@@ -50,6 +51,12 @@ import org.apache.ctakes.core.util.Mappe
* @author stephen wu
*
*/
+@PipeBitInfo(
+ name = "Knowtator XML Reader (Generic)",
+ description = "Read named entity annotations from knowtator xml files into the CAS.",
+ role = PipeBitInfo.Role.SPECIAL,
+ products = { PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION, PipeBitInfo.TypeProduct.GENERIC_RELATION }
+)
public class GoldEntityAndAttributeReader extends JCasAnnotator_ImplBase {
// paramater that should contain the path to knowtator xml files
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java Mon Apr 17 02:38:55 2017
@@ -26,6 +26,7 @@ import java.util.Iterator;
import java.util.List;
import org.apache.ctakes.assertion.util.AssertionConst;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
@@ -53,6 +54,10 @@ import org.apache.uima.fit.factory.Colle
import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
import org.apache.uima.fit.util.JCasUtil;
+import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.*;
+import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.COREFERENCE_RELATION;
+import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.MARKABLE;
+
/**
*
* Read in gold annotations from XMI and create a view within the current CAS, and copy the
@@ -61,6 +66,14 @@ import org.apache.uima.fit.util.JCasUtil
* gold standard, using XMI that had already been created by the Apache cTAKES 3.0 gold standard reader.
*
*/
+@PipeBitInfo(
+ name = "Gold View Merger",
+ description = "Read in gold annotations from XMI and create a view within the current CAS, and copy the" +
+ " gold annotations into the new view within the current CAS.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { DOCUMENT_ID },
+ products = { IDENTIFIED_ANNOTATION }
+)
public class MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas extends JCasAnnotator_ImplBase {
static final Logger LOGGER = Logger.getLogger(MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.class.getName());
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java Mon Apr 17 02:38:55 2017
@@ -26,6 +26,7 @@ import org.apache.ctakes.assertion.attri
import org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection;
import org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection;
import org.apache.ctakes.assertion.medfacts.cleartk.extractors.ContextWordWindowExtractor;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
@@ -35,6 +36,11 @@ import org.apache.uima.resource.Resource
import org.cleartk.ml.Instance;
import org.cleartk.ml.jar.GenericJarClassifierFactory;
+@PipeBitInfo(
+ name = "Generic Status ClearTK Annotator",
+ description = "Annotates the Generic status for Identified Annotations.",
+ dependencies = { PipeBitInfo.TypeProduct.SENTENCE, PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION }
+)
public class GenericCleartkAnalysisEngine extends
AssertionCleartkAnalysisEngine {
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java Mon Apr 17 02:38:55 2017
@@ -26,6 +26,7 @@ import org.apache.ctakes.assertion.attri
import org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection;
import org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection;
import org.apache.ctakes.assertion.medfacts.cleartk.extractors.ContextWordWindowExtractor;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.uima.UimaContext;
@@ -36,6 +37,11 @@ import org.apache.uima.resource.Resource
import org.cleartk.ml.Instance;
import org.cleartk.ml.jar.GenericJarClassifierFactory;
+@PipeBitInfo(
+ name = "History of ClearTK Annotator",
+ description = "Annotate History of property.",
+ dependencies = { PipeBitInfo.TypeProduct.SENTENCE, PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION }
+)
public class HistoryCleartkAnalysisEngine extends
AssertionCleartkAnalysisEngine {
Modified: ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java (original)
+++ ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java Mon Apr 17 02:38:55 2017
@@ -18,6 +18,7 @@
*/
package org.apache.ctakes.clinicalpipeline.ae;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.WordTokenUtil;
import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
@@ -47,6 +48,11 @@ import java.util.Set;
*
* @author Mayo Clinic
*/
+@PipeBitInfo(
+ name = "Extraction Prepper",
+ description = "Assigns IDs and Canonical text to Identified Annotations.",
+ dependencies = { PipeBitInfo.TypeProduct.SECTION, PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION }
+)
public class ExtractionPrepAnnotator extends JCasAnnotator_ImplBase {
private String iv_annotVerPropKey;
private int iv_annotVer;
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java Mon Apr 17 02:38:55 2017
@@ -4,6 +4,7 @@ package org.apache.ctakes.core.cc.pretty
import org.apache.ctakes.core.cc.pretty.SemanticGroup;
import org.apache.ctakes.core.cc.pretty.textspan.DefaultTextSpan;
import org.apache.ctakes.core.cc.pretty.textspan.TextSpan;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.resource.FileLocator;
import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
import org.apache.ctakes.core.util.OntologyConceptUtil;
@@ -30,12 +31,21 @@ import java.util.stream.Collectors;
import static org.apache.ctakes.core.config.ConfigParameterConstants.DESC_OUTPUTDIR;
import static org.apache.ctakes.core.config.ConfigParameterConstants.PARAM_OUTPUTDIR;
+import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.*;
+import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.TEMPORAL_RELATION;
/**
* @author SPF , chip-nlp
* @version %I%
* @since 9/8/2016
*/
+@PipeBitInfo(
+ name = "HTML Writer",
+ description = "Writes html files with document text and simple markups (Semantic Group, CUI, Negation).",
+ role = PipeBitInfo.Role.WRITER,
+ dependencies = { DOCUMENT_ID, SENTENCE, BASE_TOKEN },
+ usables = { DOCUMENT_ID_PREFIX, IDENTIFIED_ANNOTATION, EVENT, TIMEX, TEMPORAL_RELATION }
+)
final public class HtmlTextWriter extends CasConsumer_ImplBase {
static private final Logger LOGGER = Logger.getLogger( "HtmlTextWriter" );
Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MarkableHeadTreeCreator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MarkableHeadTreeCreator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MarkableHeadTreeCreator.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MarkableHeadTreeCreator.java Mon Apr 17 02:38:55 2017
@@ -3,6 +3,7 @@ package org.apache.ctakes.coreference.ae
import java.util.Comparator;
import java.util.Map;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
import org.apache.ctakes.dependency.parser.util.DependencyUtility;
import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
@@ -17,6 +18,12 @@ import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceInitializationException;
import org.cleartk.util.ViewUriUtil;
+@PipeBitInfo(
+ name = "Markable Head Tree Creator",
+ description = "Annotates Markables.",
+ dependencies = { PipeBitInfo.TypeProduct.DOCUMENT_ID,
+ PipeBitInfo.TypeProduct.MARKABLE, PipeBitInfo.TypeProduct.DEPENDENCY_NODE }
+)
public class MarkableHeadTreeCreator extends JCasAnnotator_ImplBase {
private static final String MAP_KEY = "MarkableHeadMap";
Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MarkableSalienceAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MarkableSalienceAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MarkableSalienceAnnotator.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MarkableSalienceAnnotator.java Mon Apr 17 02:38:55 2017
@@ -5,6 +5,7 @@ import java.util.ArrayList;
import java.util.List;
import java.util.Map;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.coreference.ae.features.salience.ClinicalFeatureExtractor;
import org.apache.ctakes.coreference.ae.features.salience.GrammaticalRoleFeatureExtractor;
import org.apache.ctakes.coreference.ae.features.salience.MorphosyntacticFeatureExtractor;
@@ -26,6 +27,14 @@ import org.cleartk.ml.jar.DefaultDataWri
import org.cleartk.ml.jar.DirectoryDataWriterFactory;
import org.cleartk.ml.jar.GenericJarClassifierFactory;
+@PipeBitInfo(
+ name = "Markable Salience Annotator",
+ description = "Annotates Markable Salience.",
+ role = PipeBitInfo.Role.ANNOTATOR,
+ dependencies = { PipeBitInfo.TypeProduct.PARAGRAPH, PipeBitInfo.TypeProduct.SENTENCE,
+ PipeBitInfo.TypeProduct.MARKABLE, PipeBitInfo.TypeProduct.DEPENDENCY_NODE },
+ usables = { PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION }
+)
public class MarkableSalienceAnnotator extends CleartkAnnotator<Boolean> {
List<FeatureExtractor1<Markable>> extractors = new ArrayList<>();
Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterRankingCoreferenceAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterRankingCoreferenceAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterRankingCoreferenceAnnotator.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterRankingCoreferenceAnnotator.java Mon Apr 17 02:38:55 2017
@@ -12,6 +12,7 @@ import java.util.Map;
import java.util.Random;
import java.util.Set;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.ListFactory;
import org.apache.ctakes.coreference.ae.features.cluster.MentionClusterAgreementFeaturesExtractor;
import org.apache.ctakes.coreference.ae.features.cluster.MentionClusterAttributeFeaturesExtractor;
@@ -62,6 +63,16 @@ import org.cleartk.ml.jar.GenericJarClas
import org.cleartk.ml.svmlight.rank.QidInstance;
import org.cleartk.util.ViewUriUtil;
+import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.*;
+import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.COREFERENCE_RELATION;
+import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.MARKABLE;
+
+@PipeBitInfo(
+ name = "Coreference using Cluster Rank",
+ description = "Coreference annotator using mention-synchronous paradigm.",
+ dependencies = { BASE_TOKEN, SENTENCE, SECTION, PARAGRAPH, IDENTIFIED_ANNOTATION, MARKABLE },
+ products = { COREFERENCE_RELATION }
+)
public class MentionClusterRankingCoreferenceAnnotator extends CleartkAnnotator<Double> {
public static final String NO_RELATION_CATEGORY = "-NONE-";
public static final String CLUSTER_RELATION_CATEGORY = "CoreferenceClusterMember";
Modified: ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java (original)
+++ ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java Mon Apr 17 02:38:55 2017
@@ -5,12 +5,14 @@ import io.github.lukehutch.fastclasspath
import io.github.lukehutch.fastclasspathscanner.ScanInterruptedException;
import io.github.lukehutch.fastclasspathscanner.matchprocessor.SubclassMatchProcessor;
import io.github.lukehutch.fastclasspathscanner.scanner.ScanResult;
+import org.apache.ctakes.core.util.DotLogger;
import org.apache.log4j.Logger;
import org.apache.uima.analysis_component.Annotator_ImplBase;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.collection.CasConsumer_ImplBase;
import org.apache.uima.collection.CollectionReader_ImplBase;
+import java.io.IOException;
import java.lang.reflect.Modifier;
import java.util.ArrayList;
import java.util.Collection;
@@ -74,12 +76,12 @@ public enum PipeBitFinder {
// Don't want super-primitive cleartk or uima classes
final FastClasspathScanner scanner = new FastClasspathScanner();
LOGGER.info( "Starting Scan for Pipeline Bits" );
- try {
+ try ( DotLogger dotter = new DotLogger() ){
scanner.matchSubclassesOf( CollectionReader_ImplBase.class, readerAdder )
.matchSubclassesOf( Annotator_ImplBase.class, annotatorAdder )
.matchSubclassesOf( CasConsumer_ImplBase.class, writerAdder );
final ScanResult result = scanner.scan();
- } catch ( ScanInterruptedException siE ) {
+ } catch ( ScanInterruptedException | IOException siE ) {
LOGGER.error( siE.getMessage() );
}
// Get rid of the abstract classes
Modified: ctakes/trunk/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgAnnotator.java (original)
+++ ctakes/trunk/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgAnnotator.java Mon Apr 17 02:38:55 2017
@@ -41,6 +41,7 @@ import java.util.StringTokenizer;
import java.util.Vector;
import org.apache.commons.io.FileUtils;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.ListFactory;
import org.apache.ctakes.lvg.resource.LvgCmdApiResource;
import org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl;
@@ -73,6 +74,11 @@ import org.apache.uima.fit.factory.Exter
* the cache, this may be bad if it is misspelled in the case where the
* misspelling is a word in the lexicon.
*/
+@PipeBitInfo(
+ name = "LVG Annotator",
+ description = "Adds cononical form of words.",
+ dependencies = { PipeBitInfo.TypeProduct.SECTION, PipeBitInfo.TypeProduct.BASE_TOKEN }
+)
public class LvgAnnotator extends JCasAnnotator_ImplBase {
public static final String[] defaultExclusionWords = {"And", "and", "By", "by", "For", "for", "In", "in", "Of", "of", "On", "on", "The", "the", "To", "to", "With", "with"};
public static final String[] defaultTreebankMap = {"adj|JJ", "adv|RB", "aux|AUX", "compl|CS", "conj|CC", "det|DET", "modal|MD", "noun|NN", "prep|IN", "pron|PRP", "verb|VB"};
Modified: ctakes/trunk/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgBaseTokenAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgBaseTokenAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgBaseTokenAnnotator.java (original)
+++ ctakes/trunk/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgBaseTokenAnnotator.java Mon Apr 17 02:38:55 2017
@@ -18,6 +18,7 @@
*/
package org.apache.ctakes.lvg.ae;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.util.ListFactory;
import org.apache.ctakes.lvg.resource.LvgCmdApiResource;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
@@ -65,6 +66,11 @@ import org.apache.uima.resource.Resource
* the cache, this may be bad if it is misspelled in the case where the
* misspelling is a word in the lexicon.
*/
+@PipeBitInfo(
+ name = "LVG Basetoken Annotator",
+ description = "Adds cononical form of Base Tokens.",
+ dependencies = { PipeBitInfo.TypeProduct.SECTION, PipeBitInfo.TypeProduct.BASE_TOKEN }
+)
public class LvgBaseTokenAnnotator extends JCasAnnotator_ImplBase {
/**
* Value is "PostLemmas". This parameter determines whether the feature
Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/IdentifiedAnnotationExpander.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/IdentifiedAnnotationExpander.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/IdentifiedAnnotationExpander.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/IdentifiedAnnotationExpander.java Mon Apr 17 02:38:55 2017
@@ -24,6 +24,7 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode;
import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
@@ -38,6 +39,12 @@ import com.google.common.base.Functions;
import com.google.common.collect.Lists;
import com.google.common.collect.Ordering;
+@PipeBitInfo(
+ name = "Identified Annotation Expander",
+ description = "Enlarges the text span of an identified annotation based upon part of speech.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION }
+)
public class IdentifiedAnnotationExpander extends JCasAnnotator_ImplBase {
@Override
Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/LocationOfRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/LocationOfRelationExtractorAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/LocationOfRelationExtractorAnnotator.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/LocationOfRelationExtractorAnnotator.java Mon Apr 17 02:38:55 2017
@@ -23,6 +23,7 @@ import java.util.Collection;
import java.util.List;
import java.util.Map;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation;
import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
import org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation;
@@ -40,6 +41,13 @@ import org.apache.uima.fit.util.JCasUtil
* Identifies Location_Of relations between {@link EventMention}s and
* {@link AnatomicalSiteMention}s.
*/
+@PipeBitInfo(
+ name = "Location of Annotator",
+ description = "Annotates Location Of relations.",
+ role = PipeBitInfo.Role.ANNOTATOR,
+ dependencies = { PipeBitInfo.TypeProduct.SENTENCE, PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION },
+ products = { PipeBitInfo.TypeProduct.LOCATION_RELATION }
+)
public class LocationOfRelationExtractorAnnotator extends RelationExtractorAnnotator {
@Override
Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ManagesTreatsRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ManagesTreatsRelationExtractorAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ManagesTreatsRelationExtractorAnnotator.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ManagesTreatsRelationExtractorAnnotator.java Mon Apr 17 02:38:55 2017
@@ -21,6 +21,7 @@ package org.apache.ctakes.relationextrac
import java.util.ArrayList;
import java.util.List;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
import org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation;
import org.apache.ctakes.typesystem.type.relation.RelationArgument;
@@ -41,6 +42,13 @@ import org.apache.uima.jcas.tcas.Annotat
* arg1: drug, procedure
* arg2: disease/disorder, sign/symptom, anatomical site
*/
+@PipeBitInfo(
+ name = "Manages / Treats Annotator",
+ description = "Annotates Manages / Treats relations.",
+ role = PipeBitInfo.Role.ANNOTATOR,
+ dependencies = { PipeBitInfo.TypeProduct.SENTENCE, PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION },
+ products = { PipeBitInfo.TypeProduct.GENERIC_RELATION }
+)
public class ManagesTreatsRelationExtractorAnnotator extends RelationExtractorAnnotator {
@Override
Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ManifestationOfRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ManifestationOfRelationExtractorAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ManifestationOfRelationExtractorAnnotator.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ManifestationOfRelationExtractorAnnotator.java Mon Apr 17 02:38:55 2017
@@ -21,6 +21,7 @@ package org.apache.ctakes.relationextrac
import java.util.ArrayList;
import java.util.List;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
import org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation;
import org.apache.ctakes.typesystem.type.relation.RelationArgument;
@@ -45,6 +46,13 @@ import org.apache.uima.jcas.tcas.Annotat
* arg1: disease/disorder, sign/symptom
* arg2: disease/disorder
*/
+@PipeBitInfo(
+ name = "Manifestation of Annotator",
+ description = "Annotates Manifestation Of relations.",
+ role = PipeBitInfo.Role.ANNOTATOR,
+ dependencies = { PipeBitInfo.TypeProduct.SENTENCE, PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION },
+ products = { PipeBitInfo.TypeProduct.GENERIC_RELATION }
+)
public class ManifestationOfRelationExtractorAnnotator extends RelationExtractorAnnotator {
@Override
Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationStatsCalculator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationStatsCalculator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationStatsCalculator.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationStatsCalculator.java Mon Apr 17 02:38:55 2017
@@ -21,6 +21,7 @@ package org.apache.ctakes.relationextrac
import java.util.Collection;
import java.util.List;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator;
import org.apache.ctakes.relationextractor.ae.LocationOfRelationExtractorAnnotator;
import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.IdentifiedAnnotationPair;
@@ -51,6 +52,14 @@ import com.google.common.collect.Multise
* @author dmitriy dligach
*
*/
+@PipeBitInfo(
+ name = "Gold Stats Calculator",
+ description = "Count various stats such as token and relation counts based on the gold standard data.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.SENTENCE, PipeBitInfo.TypeProduct.BASE_TOKEN,
+ PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION, PipeBitInfo.TypeProduct.GENERIC_RELATION,
+ PipeBitInfo.TypeProduct.LOCATION_RELATION, PipeBitInfo.TypeProduct.DEGREE_RELATION }
+)
public class GoldAnnotationStatsCalculator extends JCasAnnotator_ImplBase {
public static final String goldViewName = "GoldView";
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKDocTimeRelAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKDocTimeRelAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKDocTimeRelAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKDocTimeRelAnnotator.java Mon Apr 17 02:38:55 2017
@@ -41,7 +41,7 @@ import java.util.Map;
*
*/
@PipeBitInfo(
- name = "DocTimeRel Annotator (ClearTK)",
+ name = "DocTimeRel ClearTK Annotator",
description = "Annotates event relativity to document creation time.",
dependencies = { PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION, PipeBitInfo.TypeProduct.EVENT }
)
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConsecutiveSentencesEventEventRelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConsecutiveSentencesEventEventRelationAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConsecutiveSentencesEventEventRelationAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConsecutiveSentencesEventEventRelationAnnotator.java Mon Apr 17 02:38:55 2017
@@ -35,7 +35,7 @@ import java.util.*;
//import org.apache.ctakes.typesystem.type.textspan.Paragraph;
@PipeBitInfo(
- name = "Consecutive Sentence E-E TLinker",
+ name = "E-E Consecutive Sentence TLinker",
description = "Creates Event - Event TLinks between consecutive sentences.",
dependencies = { PipeBitInfo.TypeProduct.SECTION, PipeBitInfo.TypeProduct.SENTENCE,
PipeBitInfo.TypeProduct.EVENT },
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConsecutiveSentencesEventTimeRelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConsecutiveSentencesEventTimeRelationAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConsecutiveSentencesEventTimeRelationAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConsecutiveSentencesEventTimeRelationAnnotator.java Mon Apr 17 02:38:55 2017
@@ -35,7 +35,7 @@ import java.util.*;
//import org.apache.ctakes.typesystem.type.textspan.Paragraph;
@PipeBitInfo(
- name = "Consecutive Sentence E-T TLinker",
+ name = "E-T Consecutive Sentence TLinker",
description = "Creates Event - Time TLinks between consecutive sentences.",
dependencies = { PipeBitInfo.TypeProduct.SECTION, PipeBitInfo.TypeProduct.SENTENCE,
PipeBitInfo.TypeProduct.EVENT, PipeBitInfo.TypeProduct.TIMEX },
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/CrossSentenceTemporalRelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/CrossSentenceTemporalRelationAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/CrossSentenceTemporalRelationAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/CrossSentenceTemporalRelationAnnotator.java Mon Apr 17 02:38:55 2017
@@ -20,7 +20,7 @@ import org.apache.uima.fit.util.JCasUtil
import org.apache.uima.jcas.JCas;
@PipeBitInfo(
- name = "Cross- Sentence E-E TLinker",
+ name = "E-E Cross- Sentence TLinker",
description = "Creates Event - Event TLinks across sentences.",
dependencies = { PipeBitInfo.TypeProduct.EVENT, PipeBitInfo.TypeProduct.TIMEX },
products = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeI2B2RelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeI2B2RelationAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeI2B2RelationAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeI2B2RelationAnnotator.java Mon Apr 17 02:38:55 2017
@@ -24,6 +24,7 @@ import java.util.Collection;
import java.util.List;
import java.util.Map;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
import org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor;
import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
@@ -73,6 +74,13 @@ import org.apache.uima.fit.util.JCasUtil
import com.google.common.collect.Lists;
+@PipeBitInfo(
+ name = "E-T I2B2 TLinker",
+ description = "Creates Event - Time TLinks with I2B2 model.",
+ dependencies = { PipeBitInfo.TypeProduct.SECTION, PipeBitInfo.TypeProduct.SENTENCE,
+ PipeBitInfo.TypeProduct.EVENT, PipeBitInfo.TypeProduct.TIMEX },
+ products = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+)
public class EventTimeI2B2RelationAnnotator extends RelationExtractorAnnotator {
public static AnalysisEngineDescription createDataWriterDescription(
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java Mon Apr 17 02:38:55 2017
@@ -23,6 +23,7 @@ import java.util.Arrays;
import java.util.List;
import java.util.Map;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
import org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor;
import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
@@ -73,6 +74,13 @@ import org.apache.uima.fit.util.JCasUtil
import com.google.common.collect.Lists;
+@PipeBitInfo(
+ name = "E-T TLinker",
+ description = "Creates Event - Time TLinks.",
+ dependencies = { PipeBitInfo.TypeProduct.SECTION, PipeBitInfo.TypeProduct.SENTENCE,
+ PipeBitInfo.TypeProduct.EVENT, PipeBitInfo.TypeProduct.TIMEX },
+ products = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+)
public class EventTimeRelationAnnotator extends RelationExtractorAnnotator {
public static AnalysisEngineDescription createDataWriterDescription(
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeSelfRelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeSelfRelationAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeSelfRelationAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeSelfRelationAnnotator.java Mon Apr 17 02:38:55 2017
@@ -24,6 +24,7 @@ import java.util.Collection;
import java.util.List;
import java.util.Map;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
import org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor;
import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
@@ -83,6 +84,13 @@ import org.apache.uima.fit.util.JCasUtil
import com.google.common.collect.Lists;
+@PipeBitInfo(
+ name = "E-T Self TLinker",
+ description = "Creates Event - Time TLinks.",
+ dependencies = { PipeBitInfo.TypeProduct.SECTION, PipeBitInfo.TypeProduct.SENTENCE,
+ PipeBitInfo.TypeProduct.EVENT, PipeBitInfo.TypeProduct.TIMEX },
+ products = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+)
public class EventTimeSelfRelationAnnotator extends TemporalRelationExtractorAnnotator {
public static AnalysisEngineDescription createDataWriterDescription(
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventToClearTKEventAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventToClearTKEventAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventToClearTKEventAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventToClearTKEventAnnotator.java Mon Apr 17 02:38:55 2017
@@ -18,6 +18,7 @@
*/
package org.apache.ctakes.temporal.ae;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -34,6 +35,11 @@ import org.apache.uima.fit.util.JCasUtil
* @author Chen Lin
*
*/
+@PipeBitInfo(
+ name = "ClearTK Event Creator",
+ description = "Creates ClearTK Events from cTAKES Events.",
+ dependencies = { PipeBitInfo.TypeProduct.EVENT }
+)
public class EventToClearTKEventAnnotator extends JCasAnnotator_ImplBase {
public EventToClearTKEventAnnotator() {
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/I2B2TemporalXMLReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/I2B2TemporalXMLReader.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/I2B2TemporalXMLReader.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/I2B2TemporalXMLReader.java Mon Apr 17 02:38:55 2017
@@ -25,6 +25,7 @@ import java.util.HashMap;
import java.util.Map;
import java.util.Set;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.refsem.Event;
import org.apache.ctakes.typesystem.type.refsem.EventProperties;
@@ -48,6 +49,15 @@ import org.jdom2.input.SAXBuilder;
import com.google.common.collect.Sets;
+import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.*;
+import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.TEMPORAL_RELATION;
+
+@PipeBitInfo(
+ name = "I2B2 XML Reader (THYME)",
+ description = "Reads annotations from THYME schema I2B2 XML files in a directory.",
+ role = PipeBitInfo.Role.SPECIAL,
+ products = { PipeBitInfo.TypeProduct.EVENT, PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+)
public class I2B2TemporalXMLReader extends JCasAnnotator_ImplBase {
public static final String PARAM_INPUT_DIR = "PARAM_INPUT_DIR";
@ConfigurationParameter(
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/MetaTimeAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/MetaTimeAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/MetaTimeAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/MetaTimeAnnotator.java Mon Apr 17 02:38:55 2017
@@ -22,6 +22,7 @@ import java.io.File;
import java.util.ArrayList;
import java.util.List;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.temporal.eval.THYMEData;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.textsem.TimeMention;
@@ -49,6 +50,12 @@ import org.apache.uima.fit.factory.Aggre
import org.apache.uima.fit.factory.AnalysisEngineFactory;
import org.apache.uima.fit.util.JCasUtil;
+@PipeBitInfo(
+ name = "Meta Time Annotator",
+ description = "...",
+ dependencies = { PipeBitInfo.TypeProduct.SECTION, PipeBitInfo.TypeProduct.SENTENCE,
+ PipeBitInfo.TypeProduct.BASE_TOKEN, PipeBitInfo.TypeProduct.TIMEX }
+)
public class MetaTimeAnnotator extends TemporalSequenceAnnotator_ImplBase {
private BioChunking<BaseToken, TimeMention> timeChunking;
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java Mon Apr 17 02:38:55 2017
@@ -24,6 +24,7 @@ import java.net.URI;
import java.util.ArrayList;
import java.util.List;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.temporal.ae.feature.ParseSpanFeatureExtractor;
import org.apache.ctakes.temporal.ae.feature.TimeWordTypeExtractor;
import org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection;
@@ -60,6 +61,13 @@ import org.cleartk.ml.jar.DefaultDataWri
import org.cleartk.ml.jar.DirectoryDataWriterFactory;
import org.cleartk.ml.jar.GenericJarClassifierFactory;
+@PipeBitInfo(
+ name = "Time Annotator",
+ description = "...",
+ dependencies = { PipeBitInfo.TypeProduct.SECTION, PipeBitInfo.TypeProduct.SENTENCE,
+ PipeBitInfo.TypeProduct.BASE_TOKEN },
+ products = { PipeBitInfo.TypeProduct.TIMEX }
+)
public class TimeAnnotator extends TemporalEntityAnnotator_ImplBase {
public static final String PARAM_FEATURE_SELECTION_THRESHOLD = "WhetherToDoFeatureSelection";
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/F1BaselineEventTimeRelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/F1BaselineEventTimeRelationAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/F1BaselineEventTimeRelationAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/F1BaselineEventTimeRelationAnnotator.java Mon Apr 17 02:38:55 2017
@@ -26,6 +26,7 @@ import java.util.HashSet;
import java.util.List;
import java.util.Set;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
@@ -46,6 +47,11 @@ import com.google.common.base.Functions;
import com.google.common.collect.Lists;
import com.google.common.collect.Ordering;
+@PipeBitInfo(
+ name = "E-T Baseline Scorer",
+ description = "Prints Event - Time Scores ...",
+ dependencies = { PipeBitInfo.TypeProduct.SENTENCE, PipeBitInfo.TypeProduct.EVENT, PipeBitInfo.TypeProduct.TIMEX }
+)
public class F1BaselineEventTimeRelationAnnotator extends
RelationExtractorAnnotator {
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimePosBasedAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimePosBasedAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimePosBasedAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimePosBasedAnnotator.java Mon Apr 17 02:38:55 2017
@@ -6,6 +6,7 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.temporal.ae.TemporalRelationExtractorAnnotator.IdentifiedAnnotationPair;
import org.apache.ctakes.temporal.nn.data.ArgContextProvider;
import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
@@ -26,6 +27,13 @@ import org.cleartk.util.ViewUriUtil;
import com.google.common.collect.Lists;
+@PipeBitInfo(
+ name = "E-T POS TLinker",
+ description = "Creates Event - Time TLinks with Parts of Speech.",
+ dependencies = { PipeBitInfo.TypeProduct.SECTION, PipeBitInfo.TypeProduct.SENTENCE,
+ PipeBitInfo.TypeProduct.EVENT, PipeBitInfo.TypeProduct.TIMEX },
+ products = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+)
public class EventTimePosBasedAnnotator extends CleartkAnnotator<String> {
public static final String NO_RELATION_CATEGORY = "none";
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimePositionBasedAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimePositionBasedAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimePositionBasedAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimePositionBasedAnnotator.java Mon Apr 17 02:38:55 2017
@@ -6,6 +6,7 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.temporal.ae.TemporalRelationExtractorAnnotator.IdentifiedAnnotationPair;
import org.apache.ctakes.temporal.nn.data.ArgContextProvider;
import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
@@ -26,6 +27,13 @@ import org.cleartk.util.ViewUriUtil;
import com.google.common.collect.Lists;
+@PipeBitInfo(
+ name = "E-T Position TLinker",
+ description = "Creates Event - Event TLinks with position.",
+ dependencies = { PipeBitInfo.TypeProduct.SECTION, PipeBitInfo.TypeProduct.SENTENCE,
+ PipeBitInfo.TypeProduct.EVENT, PipeBitInfo.TypeProduct.TIMEX },
+ products = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+)
public class EventTimePositionBasedAnnotator extends CleartkAnnotator<String> {
public static final String NO_RELATION_CATEGORY = "none";
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenAndBIOBasedAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenAndBIOBasedAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenAndBIOBasedAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenAndBIOBasedAnnotator.java Mon Apr 17 02:38:55 2017
@@ -7,6 +7,7 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.temporal.ae.TemporalRelationExtractorAnnotator.IdentifiedAnnotationPair;
import org.apache.ctakes.temporal.nn.data.ArgContextProvider;
import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
@@ -28,6 +29,13 @@ import org.cleartk.util.ViewUriUtil;
import com.google.common.collect.Lists;
+@PipeBitInfo(
+ name = "E-T BIO TLinker",
+ description = "Creates Event - Time TLinks from Begin, Inner, Outer.",
+ dependencies = { PipeBitInfo.TypeProduct.SECTION, PipeBitInfo.TypeProduct.SENTENCE,
+ PipeBitInfo.TypeProduct.EVENT, PipeBitInfo.TypeProduct.TIMEX },
+ products = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+)
public class EventTimeTokenAndBIOBasedAnnotator extends CleartkAnnotator<String> {
public static final String NO_RELATION_CATEGORY = "none";
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenAndPosBasedAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenAndPosBasedAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenAndPosBasedAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenAndPosBasedAnnotator.java Mon Apr 17 02:38:55 2017
@@ -7,6 +7,7 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.temporal.ae.TemporalRelationExtractorAnnotator.IdentifiedAnnotationPair;
import org.apache.ctakes.temporal.nn.data.ArgContextProvider;
import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
@@ -28,6 +29,13 @@ import org.cleartk.util.ViewUriUtil;
import com.google.common.collect.Lists;
+@PipeBitInfo(
+ name = "E-T POS and Token TLinker",
+ description = "Creates Event - Time TLinks from Part of Speech and Token Type.",
+ dependencies = { PipeBitInfo.TypeProduct.SECTION, PipeBitInfo.TypeProduct.SENTENCE,
+ PipeBitInfo.TypeProduct.EVENT, PipeBitInfo.TypeProduct.TIMEX },
+ products = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+)
public class EventTimeTokenAndPosBasedAnnotator extends CleartkAnnotator<String> {
public static final String NO_RELATION_CATEGORY = "none";
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenBasedAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenBasedAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenBasedAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenBasedAnnotator.java Mon Apr 17 02:38:55 2017
@@ -14,6 +14,7 @@ import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.resource.FileLocator;
import org.apache.ctakes.temporal.ae.TemporalRelationExtractorAnnotator.IdentifiedAnnotationPair;
import org.apache.ctakes.temporal.nn.data.ArgContextProvider;
@@ -36,6 +37,13 @@ import org.cleartk.util.ViewUriUtil;
import com.google.common.collect.Lists;
+@PipeBitInfo(
+ name = "E-T Token TLinker",
+ description = "Creates Event - Time TLinks from Token type.",
+ dependencies = { PipeBitInfo.TypeProduct.SECTION, PipeBitInfo.TypeProduct.SENTENCE,
+ PipeBitInfo.TypeProduct.EVENT, PipeBitInfo.TypeProduct.TIMEX },
+ products = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+)
public class EventTimeTokenBasedAnnotator extends CleartkAnnotator<String> {
public static final String NO_RELATION_CATEGORY = "none";
Modified: ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/MetaMapToCTakesAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/MetaMapToCTakesAnnotator.java?rev=1791649&r1=1791648&r2=1791649&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/MetaMapToCTakesAnnotator.java (original)
+++ ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/MetaMapToCTakesAnnotator.java Mon Apr 17 02:38:55 2017
@@ -28,6 +28,7 @@ import java.util.Set;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
@@ -58,6 +59,13 @@ import org.apache.uima.resource.Resource
* @author vijay
*
*/
+@PipeBitInfo(
+ name = "Metamap Annotation xlater",
+ description = "Create MedicationEventMention/EntityMention annotations for each set of" +
+ " CandidateConcept annotations that span the same text.",
+ role = PipeBitInfo.Role.SPECIAL,
+ products = { PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION }
+)
public class MetaMapToCTakesAnnotator extends JCasAnnotator_ImplBase {
private static final Log log = LogFactory
.getLog(MetaMapToCTakesAnnotator.class);