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Posted to commits@ctakes.apache.org by ja...@apache.org on 2013/08/02 18:48:16 UTC
svn commit: r1509770 [1/4] - in /ctakes/branches/ctakes-3.1.0: ./
ctakes-assertion-res/ ctakes-assertion-zoner-res/ ctakes-assertion-zoner/
ctakes-assertion/
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/
ctak...
Author: james-masanz
Date: Fri Aug 2 16:48:14 2013
New Revision: 1509770
URL: http://svn.apache.org/r1509770
Log:
Merged latest trunk changes to ctakes-3.1.0 branch to pick up re-trained chunker model and chunker descriptor
Added:
ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AnnotationStatisticsCompact.java
- copied unchanged from r1509769, ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AnnotationStatisticsCompact.java
ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SRLFeatureExtractor.java
- copied unchanged from r1509769, ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SRLFeatureExtractor.java
ctakes/branches/ctakes-3.1.0/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/models/chunker-model.zip
- copied unchanged from r1509769, ctakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/models/chunker-model.zip
ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/BinaryAlphaFeatureSelection.java
- copied unchanged from r1509769, ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/BinaryAlphaFeatureSelection.java
ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/OddsRatioFeatureSelection.java
- copied unchanged from r1509769, ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/OddsRatioFeatureSelection.java
Modified:
ctakes/branches/ctakes-3.1.0/ (props changed)
ctakes/branches/ctakes-3.1.0/ctakes-assertion-res/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-assertion-zoner-res/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-assertion-zoner/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-assertion/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/Chi2FeatureSelection.java
ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java
ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java
ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java
ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java
ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java
ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java
ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java
ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateChi2GridSearch.java
ctakes/branches/ctakes-3.1.0/ctakes-chunker/ (props changed)
ctakes/branches/ctakes-3.1.0/ctakes-chunker-res/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-chunker/desc/Chunker.xml
ctakes/branches/ctakes-3.1.0/ctakes-chunker/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-clinical-pipeline/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-constituency-parser-res/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-constituency-parser/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-context-tokenizer/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-core-res/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-core/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-coreference-res/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-coreference/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-dependency-parser-res/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-dependency-parser/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-dictionary-lookup-res/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-dictionary-lookup/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-distribution/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-drug-ner-res/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-drug-ner/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-lvg-res/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-lvg/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-ne-contexts-res/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-ne-contexts/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-pad-term-spotter-res/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-pad-term-spotter/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-pos-tagger-res/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-pos-tagger/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-preprocessor/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-regression-test/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java
ctakes/branches/ctakes-3.1.0/ctakes-relation-extractor-res/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-relation-extractor/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-side-effect-res/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-side-effect/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-smoking-status-res/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-smoking-status/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-template-filler/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-temporal-res/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-temporal/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java
ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java
ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/Chi2FeatureSelection.java
ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java
ctakes/branches/ctakes-3.1.0/ctakes-type-system/pom.xml
ctakes/branches/ctakes-3.1.0/ctakes-utils/pom.xml
ctakes/branches/ctakes-3.1.0/pom.xml
Propchange: ctakes/branches/ctakes-3.1.0/
------------------------------------------------------------------------------
svn:mergeinfo = /ctakes/trunk:1506998-1509769
Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion-res/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion-res/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion-res/pom.xml Fri Aug 2 16:48:14 2013
@@ -24,7 +24,7 @@
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
- <version>3.1.0-SNAPSHOT</version>
+ <version>3.1.0</version>
</parent>
<artifactId>ctakes-assertion-res</artifactId>
<name>Apache cTAKES Resources assertion</name>
Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion-zoner-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion-zoner-res/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion-zoner-res/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion-zoner-res/pom.xml Fri Aug 2 16:48:14 2013
@@ -24,7 +24,7 @@
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
- <version>3.1.0-SNAPSHOT</version>
+ <version>3.1.0</version>
</parent>
<artifactId>ctakes-assertion-zoner-res</artifactId>
<name>Apache cTAKES Resources assertion-zoner</name>
Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion-zoner/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion-zoner/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion-zoner/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion-zoner/pom.xml Fri Aug 2 16:48:14 2013
@@ -1,65 +1,65 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
- 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.
-
--->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <artifactId>ctakes-assertion-zoner</artifactId>
- <name>Apache cTAKES Assertion's zoner</name>
- <parent>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes</artifactId>
- <version>3.1.0-SNAPSHOT</version>
- </parent>
- <dependencies>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-assertion-zoner-res</artifactId>
- </dependency>
- <dependency>
- <groupId>net.sf.mastif</groupId>
- <artifactId>mastif-zoner</artifactId>
- <version>1.4</version>
- </dependency>
- <dependency>
- <groupId>org.apache.uima</groupId>
- <artifactId>uimaj-core</artifactId>
- </dependency>
- <dependency>
- <groupId>org.uimafit</groupId>
- <artifactId>uimafit</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-core</artifactId>
- </dependency>
- </dependencies>
- <build>
- <plugins>
- <plugin>
- <groupId>org.cleartk</groupId>
- <artifactId>jcasgen-maven-plugin</artifactId>
- <configuration>
- <typeSystem>src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml</typeSystem>
- </configuration>
- </plugin>
- </plugins>
- </build>
-</project>
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ 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.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <artifactId>ctakes-assertion-zoner</artifactId>
+ <name>Apache cTAKES Assertion's zoner</name>
+ <parent>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes</artifactId>
+ <version>3.1.0</version>
+ </parent>
+ <dependencies>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-assertion-zoner-res</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.mastif</groupId>
+ <artifactId>mastif-zoner</artifactId>
+ <version>1.4</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.uima</groupId>
+ <artifactId>uimaj-core</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.uimafit</groupId>
+ <artifactId>uimafit</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-core</artifactId>
+ </dependency>
+ </dependencies>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.cleartk</groupId>
+ <artifactId>jcasgen-maven-plugin</artifactId>
+ <configuration>
+ <typeSystem>src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml</typeSystem>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+</project>
Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/pom.xml Fri Aug 2 16:48:14 2013
@@ -1,239 +1,239 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
- 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.
-
--->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <artifactId>ctakes-assertion</artifactId>
- <name>Apache cTAKES Assertion</name>
- <parent>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes</artifactId>
- <version>3.1.0-SNAPSHOT</version>
- </parent>
- <dependencies>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-assertion-res</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-assertion-zoner</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-type-system</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-dictionary-lookup</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-core</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-constituency-parser</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-utils</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-pos-tagger</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-dependency-parser</artifactId>
- </dependency>
- <dependency>
- <groupId>org.cleartk</groupId>
- <artifactId>cleartk-ml</artifactId>
- </dependency>
- <dependency>
- <groupId>org.cleartk</groupId>
- <artifactId>cleartk-ml-libsvm</artifactId>
- </dependency>
- <dependency>
- <groupId>org.cleartk</groupId>
- <artifactId>cleartk-ml-opennlp-maxent</artifactId>
- </dependency>
- <dependency>
- <groupId>org.cleartk</groupId>
- <artifactId>cleartk-util</artifactId>
- </dependency>
- <dependency>
- <groupId>org.cleartk</groupId>
- <artifactId>cleartk-eval</artifactId>
- </dependency>
- <dependency>
- <groupId>args4j</groupId>
- <artifactId>args4j</artifactId>
- </dependency>
- <dependency>
- <groupId>commons-io</groupId>
- <artifactId>commons-io</artifactId>
- </dependency>
- <dependency>
- <groupId>commons-lang</groupId>
- <artifactId>commons-lang</artifactId>
- </dependency>
- <dependency>
- <groupId>commons-logging</groupId>
- <artifactId>commons-logging</artifactId>
- </dependency>
- <dependency>
- <groupId>com.google.guava</groupId>
- <artifactId>guava</artifactId>
- </dependency>
- <dependency>
- <groupId>commons-cli</groupId>
- <artifactId>commons-cli</artifactId>
- </dependency>
- <dependency>
- <groupId>com.carrotsearch</groupId>
- <artifactId>hppc</artifactId>
- </dependency>
-
-
- <dependency>
- <groupId>jdom</groupId>
- <artifactId>jdom</artifactId>
- </dependency>
-
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- </dependency>
-
- <dependency>
- <groupId>log4j</groupId>
- <artifactId>log4j</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.opennlp</groupId>
- <artifactId>opennlp-maxent</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.opennlp</groupId>
- <artifactId>opennlp-tools</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.lucene</groupId>
- <artifactId>lucene-core</artifactId>
- </dependency>
- <dependency>
- <groupId>tw.edu.ntu.csie</groupId>
- <artifactId>libsvm</artifactId>
- </dependency>
-
- <dependency>
- <groupId>org.springframework</groupId>
- <artifactId>spring-core</artifactId>
- </dependency>
-
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- </dependency>
- <dependency>
- <groupId>org.uimafit</groupId>
- <artifactId>uimafit</artifactId>
- </dependency>
-
- <dependency>
- <groupId>org.codehaus.jackson</groupId>
- <artifactId>jackson-core-asl</artifactId>
- <version>1.5.0</version>
- </dependency>
- <dependency>
- <groupId>org.codehaus.jackson</groupId>
- <artifactId>jackson-mapper-asl</artifactId>
- <version>1.5.0</version>
- </dependency>
-
- <dependency>
- <groupId>org.scala-lang</groupId>
- <artifactId>scala-library</artifactId>
- <version>2.9.0</version>
- </dependency>
- <dependency>
- <groupId>org.scala-tools.sbinary</groupId>
- <artifactId>sbinary_2.9.0</artifactId>
- <version>0.4.0</version>
- </dependency>
-
- <!-- Dependencies that still need to be uploaded to Maven Central; when
- done, the dependency versions should be moved into the parent pom -->
- <dependency>
- <groupId>org.mitre.medfacts</groupId>
- <artifactId>medfacts-i2b2</artifactId>
- <version>1.2</version>
- <scope>system</scope>
- <systemPath>${project.basedir}/lib/med-facts-i2b2-1.2-SNAPSHOT.jar</systemPath>
- </dependency>
- <dependency>
- <groupId>org.mitre.medfacts</groupId>
- <artifactId>medfacts-zoner</artifactId>
- <version>1.1</version>
- <scope>system</scope>
- <systemPath>${project.basedir}/lib/med-facts-zoner-1.1.jar</systemPath>
- </dependency>
- <dependency>
- <groupId>org.mitre.jcarafe.core</groupId>
- <artifactId>jcarafe.core</artifactId>
- <version>2.9.1</version>
- <scope>system</scope>
- <systemPath>${project.basedir}/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar</systemPath>
- </dependency>
- <dependency>
- <groupId>org.mitre.jcarafe.ext</groupId>
- <artifactId>jcarafe.ext</artifactId>
- <version>2.9.1</version>
- <scope>system</scope>
- <systemPath>${project.basedir}/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar</systemPath>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-lvg</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-context-tokenizer</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-chunker</artifactId>
- </dependency>
- </dependencies>
- <build>
- <plugins>
- <plugin>
- <groupId>org.cleartk</groupId>
- <artifactId>jcasgen-maven-plugin</artifactId>
- <configuration>
- <typeSystem>src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml</typeSystem>
- </configuration>
- </plugin>
- </plugins>
- </build>
-</project>
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ 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.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <artifactId>ctakes-assertion</artifactId>
+ <name>Apache cTAKES Assertion</name>
+ <parent>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes</artifactId>
+ <version>3.1.0</version>
+ </parent>
+ <dependencies>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-assertion-res</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-assertion-zoner</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-type-system</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-dictionary-lookup</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-core</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-constituency-parser</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-utils</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-pos-tagger</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-dependency-parser</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.cleartk</groupId>
+ <artifactId>cleartk-ml</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.cleartk</groupId>
+ <artifactId>cleartk-ml-libsvm</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.cleartk</groupId>
+ <artifactId>cleartk-ml-opennlp-maxent</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.cleartk</groupId>
+ <artifactId>cleartk-util</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.cleartk</groupId>
+ <artifactId>cleartk-eval</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>args4j</groupId>
+ <artifactId>args4j</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>commons-lang</groupId>
+ <artifactId>commons-lang</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>commons-logging</groupId>
+ <artifactId>commons-logging</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>com.google.guava</groupId>
+ <artifactId>guava</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>commons-cli</groupId>
+ <artifactId>commons-cli</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>com.carrotsearch</groupId>
+ <artifactId>hppc</artifactId>
+ </dependency>
+
+
+ <dependency>
+ <groupId>jdom</groupId>
+ <artifactId>jdom</artifactId>
+ </dependency>
+
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ </dependency>
+
+ <dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.opennlp</groupId>
+ <artifactId>opennlp-maxent</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.opennlp</groupId>
+ <artifactId>opennlp-tools</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.lucene</groupId>
+ <artifactId>lucene-core</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>tw.edu.ntu.csie</groupId>
+ <artifactId>libsvm</artifactId>
+ </dependency>
+
+ <dependency>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-core</artifactId>
+ </dependency>
+
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.uimafit</groupId>
+ <artifactId>uimafit</artifactId>
+ </dependency>
+
+ <dependency>
+ <groupId>org.codehaus.jackson</groupId>
+ <artifactId>jackson-core-asl</artifactId>
+ <version>1.5.0</version>
+ </dependency>
+ <dependency>
+ <groupId>org.codehaus.jackson</groupId>
+ <artifactId>jackson-mapper-asl</artifactId>
+ <version>1.5.0</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.scala-lang</groupId>
+ <artifactId>scala-library</artifactId>
+ <version>2.9.0</version>
+ </dependency>
+ <dependency>
+ <groupId>org.scala-tools.sbinary</groupId>
+ <artifactId>sbinary_2.9.0</artifactId>
+ <version>0.4.0</version>
+ </dependency>
+
+ <!-- Dependencies that still need to be uploaded to Maven Central; when
+ done, the dependency versions should be moved into the parent pom -->
+ <dependency>
+ <groupId>org.mitre.medfacts</groupId>
+ <artifactId>medfacts-i2b2</artifactId>
+ <version>1.2</version>
+ <scope>system</scope>
+ <systemPath>${project.basedir}/lib/med-facts-i2b2-1.2-SNAPSHOT.jar</systemPath>
+ </dependency>
+ <dependency>
+ <groupId>org.mitre.medfacts</groupId>
+ <artifactId>medfacts-zoner</artifactId>
+ <version>1.1</version>
+ <scope>system</scope>
+ <systemPath>${project.basedir}/lib/med-facts-zoner-1.1.jar</systemPath>
+ </dependency>
+ <dependency>
+ <groupId>org.mitre.jcarafe.core</groupId>
+ <artifactId>jcarafe.core</artifactId>
+ <version>2.9.1</version>
+ <scope>system</scope>
+ <systemPath>${project.basedir}/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar</systemPath>
+ </dependency>
+ <dependency>
+ <groupId>org.mitre.jcarafe.ext</groupId>
+ <artifactId>jcarafe.ext</artifactId>
+ <version>2.9.1</version>
+ <scope>system</scope>
+ <systemPath>${project.basedir}/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar</systemPath>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-lvg</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-context-tokenizer</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-chunker</artifactId>
+ </dependency>
+ </dependencies>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.cleartk</groupId>
+ <artifactId>jcasgen-maven-plugin</artifactId>
+ <configuration>
+ <typeSystem>src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml</typeSystem>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+</project>
Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/Chi2FeatureSelection.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/Chi2FeatureSelection.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/Chi2FeatureSelection.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/Chi2FeatureSelection.java Fri Aug 2 16:48:14 2013
@@ -38,9 +38,12 @@ public class Chi2FeatureSelection<OUTCOM
protected Table<String, OUTCOME_T, Integer> featValueClassCount;
- public Chi2Scorer() {
+ private boolean yates = false;
+
+ public Chi2Scorer(boolean yate) {
this.classCounts = HashMultiset.<OUTCOME_T> create();
this.featValueClassCount = HashBasedTable.<String, OUTCOME_T, Integer> create();
+ this.yates = yate;
}
public void update(String featureName, OUTCOME_T outcome, int occurrences) {
@@ -88,13 +91,12 @@ public class Chi2FeatureSelection<OUTCOM
return chi2val;
}
- boolean yates = true;
for (int lbl = 0; lbl < numOfClass; lbl++) {
// for positive part of feature:
double expected = (outcomeCounts[lbl] / (double) n) * (posiFeatCount);
if (expected > 0) {
double diff = Math.abs(posiOutcomeCounts[lbl] - expected);
- if (yates) { // apply Yate's correction
+ if (this.yates ) { // apply Yate's correction
diff -= 0.5;
}
if (diff > 0)
@@ -106,7 +108,7 @@ public class Chi2FeatureSelection<OUTCOM
double observ = outcomeCounts[lbl] - posiOutcomeCounts[lbl];
if (expected > 0) {
double diff = Math.abs(observ - expected);
- if (yates) { // apply Yate's correction
+ if (this.yates) { // apply Yate's correction
diff -= 0.5;
}
if (diff > 0)
@@ -121,6 +123,8 @@ public class Chi2FeatureSelection<OUTCOM
private double chi2Threshold;
private Chi2Scorer<OUTCOME_T> chi2Function;
+
+ private boolean yates = false;
public Chi2FeatureSelection(String name) {
this(name, 0.0);
@@ -131,6 +135,17 @@ public class Chi2FeatureSelection<OUTCOM
this.chi2Threshold = threshold;
}
+ /**
+ * Constructor that can let use control the yate's correction
+ * @param name
+ * @param threshold
+ * @param yates : true for using yate's correction, false for turn off yate's correction
+ */
+ public Chi2FeatureSelection(String name, double threshold, boolean yates) {
+ super(name);
+ this.chi2Threshold = threshold;
+ this.yates = yates;
+ }
@Override
public boolean apply(Feature feature) {
return this.selectedFeatureNames.contains(this.getFeatureName(feature));
@@ -139,7 +154,7 @@ public class Chi2FeatureSelection<OUTCOM
@Override
public void train(Iterable<Instance<OUTCOME_T>> instances) {
// aggregate statistics for all features
- this.chi2Function = new Chi2Scorer<OUTCOME_T>();
+ this.chi2Function = new Chi2Scorer<OUTCOME_T>(this.yates);
for (Instance<OUTCOME_T> instance : instances) {
OUTCOME_T outcome = instance.getOutcome();
for (Feature feature : instance.getFeatures()) {
Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java Fri Aug 2 16:48:14 2013
@@ -38,6 +38,7 @@ import org.apache.ctakes.typesystem.type
import org.apache.ctakes.typesystem.type.syntax.Chunk;
import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textsem.SemanticArgument;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
@@ -45,7 +46,7 @@ import org.apache.ctakes.typesystem.type
/**
* @author shalgrim
- *
+ * tmiller says this is the MITRE stuff, ctakes 3.0
*/
public class HistoryAttributeClassifier {
@@ -69,6 +70,18 @@ public class HistoryAttributeClassifier
return classifyWithLogic(vfeat);
}
+
+ /**
+ *
+ * @param jCas - the jcas of the document
+ * @param arg - the node getting features added to it
+ * @return whether or not arg is a token preceded by "h/o"
+ */
+ public static Boolean precededByH_O(JCas jCas, Annotation arg) {
+ Boolean answer = false;
+
+ return answer;
+ }
public static Boolean classifyWithLogic(HashMap<String, Boolean> vfeat) {
@@ -80,9 +93,8 @@ public class HistoryAttributeClassifier
Boolean subsume_summary = (subsumectr>0);
if (vfeat.get(DISCUSSION_DEPPATH) || subsume_summary) {
return true;
- } else {
- return false;
}
+ return false;
}
@@ -109,19 +121,32 @@ public class HistoryAttributeClassifier
// 2) some other identified annotation subsumes this one?
- List<IdentifiedAnnotation> lsmentions = JCasUtil.selectPreceding(jCas, IdentifiedAnnotation.class, arg, 5);
- lsmentions.addAll(JCasUtil.selectFollowing(jCas, IdentifiedAnnotation.class, arg, 5));
+ List<IdentifiedAnnotation> lsmentions = JCasUtil.selectCovering(jCas, IdentifiedAnnotation.class, arg.getBegin(), arg.getEnd());
+ //lsmentions.addAll(JCasUtil.selectFollowing(jCas, IdentifiedAnnotation.class, arg, 5));
for (IdentifiedAnnotation annot : lsmentions) {
if ( annot.getBegin()>arg.getBegin()) {
+ // it's okay to break here b/c of the ordering?
break;
- } else {
- if ( annot.getEnd()<arg.getEnd()) {
- continue;
- } else if ( !DependencyUtility.equalCoverage(
- DependencyUtility.getNominalHeadNode(jCas, annot),
- DependencyUtility.getNominalHeadNode(jCas, arg)) ) {
- // the case that annot is a superset
- vfeat.put(SUBSUMED_ANNOT, true);
+ }
+
+ // INVARIANT: arg starts at or after annot begins
+ if ( annot.getEnd()<arg.getEnd()) {
+ // INVARIANT: arg ends at or after annot ends
+ continue;
+ } else if ( !DependencyUtility.equalCoverage(
+ DependencyUtility.getNominalHeadNode(jCas, annot),
+ DependencyUtility.getNominalHeadNode(jCas, arg)) ) {
+ // INVARIANT: arg start at or before annot starts
+ // INVARIANT: arg ends at or before annot ends
+ // INVARIANT: arg falls within bounds of annot
+ // plus there's that deal that they don't have the same head node
+ // but now we have to verify that annot is an EventMention or EntityMention
+ if ((annot instanceof EntityMention) || (annot instanceof EventMention)) {
+ // Here annot has boundaries at or exceeding those of arg
+ // They also have different head nodes (I guess)
+ // and annot is either an EntityMention of EventMention
+ vfeat.put(SUBSUMED_ANNOT, true);
+ break; // no reason to keep checking
}
}
}
Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java Fri Aug 2 16:48:14 2013
@@ -87,7 +87,6 @@ import org.cleartk.classifier.jar.Direct
import org.cleartk.classifier.jar.GenericJarClassifierFactory;
import org.cleartk.classifier.jar.JarClassifierBuilder;
import org.cleartk.classifier.liblinear.LIBLINEARStringOutcomeDataWriter;
-import org.cleartk.eval.AnnotationStatistics;
import org.cleartk.eval.Evaluation_ImplBase;
import org.cleartk.util.Options_ImplBase;
import org.kohsuke.args4j.Option;
@@ -113,7 +112,7 @@ import com.google.common.collect.Sets;
//import org.chboston.cnlp.ctakes.relationextractor.eval.RelationExtractorEvaluation;
//import org.chboston.cnlp.ctakes.relationextractor.ae.ModifierExtractorAnnotator;
-public class AssertionEvaluation extends Evaluation_ImplBase<File, Map<String, AnnotationStatistics>> {
+public class AssertionEvaluation extends Evaluation_ImplBase<File, Map<String, AnnotationStatisticsCompact>> {
private static Logger logger = Logger.getLogger(AssertionEvaluation.class);
@@ -352,20 +351,20 @@ private static Logger logger = Logger.ge
// run cross-validation
else if(options.crossValidationFolds != null) {
// run n-fold cross-validation
- List<Map<String, AnnotationStatistics>> foldStats = evaluation.crossValidation(trainFiles, options.crossValidationFolds);
- //AnnotationStatistics overallStats = AnnotationStatistics.addAll(foldStats);
- Map<String, AnnotationStatistics> overallStats = new TreeMap<String, AnnotationStatistics>();
+ List<Map<String, AnnotationStatisticsCompact>> foldStats = evaluation.crossValidation(trainFiles, options.crossValidationFolds);
+ //AnnotationStatisticsCompact overallStats = AnnotationStatisticsCompact.addAll(foldStats);
+ Map<String, AnnotationStatisticsCompact> overallStats = new TreeMap<String, AnnotationStatisticsCompact>();
for (String currentAnnotationType : annotationTypes)
{
- AnnotationStatistics currentAnnotationStatistics = new AnnotationStatistics();
- overallStats.put(currentAnnotationType, currentAnnotationStatistics);
+ AnnotationStatisticsCompact currentAnnotationStatisticsCompact = new AnnotationStatisticsCompact();
+ overallStats.put(currentAnnotationType, currentAnnotationStatisticsCompact);
}
- for (Map<String, AnnotationStatistics> singleFoldMap : foldStats)
+ for (Map<String, AnnotationStatisticsCompact> singleFoldMap : foldStats)
{
for (String currentAnnotationType : annotationTypes)
{
- AnnotationStatistics currentFoldStatistics = singleFoldMap.get(currentAnnotationType);
+ AnnotationStatisticsCompact currentFoldStatistics = singleFoldMap.get(currentAnnotationType);
overallStats.get(currentAnnotationType).addAll(currentFoldStatistics);
}
}
@@ -398,7 +397,7 @@ private static Logger logger = Logger.ge
}
logger.debug("testFiles.size() = " + testFiles.size());
CollectionReader testCollectionReader = evaluation.getCollectionReader(testFiles);
- Map<String, AnnotationStatistics> stats = evaluation.test(testCollectionReader, modelsDir);
+ Map<String, AnnotationStatisticsCompact> stats = evaluation.test(testCollectionReader, modelsDir);
AssertionEvaluation.printScore(stats, modelsDir.getAbsolutePath());
}
@@ -476,12 +475,12 @@ private static void printOptionsForDebug
logger.info(message);
}
-public static void printScore(Map<String, AnnotationStatistics> map, String directory)
+public static void printScore(Map<String, AnnotationStatisticsCompact> map, String directory)
{
- for (Map.Entry<String, AnnotationStatistics> currentEntry : map.entrySet())
+ for (Map.Entry<String, AnnotationStatisticsCompact> currentEntry : map.entrySet())
{
String annotationType = currentEntry.getKey();
- AnnotationStatistics stats = currentEntry.getValue();
+ AnnotationStatisticsCompact stats = currentEntry.getValue();
System.out.format("directory: \"%s\"; assertion type: %s%n%n%s%n%n",
directory,
@@ -491,11 +490,12 @@ public static void printScore(Map<String
try {
if (useEvaluationLogFile) {
evaluationLogFileOut.write(
- String.format("directory: \"%s\"; assertion type: %s%n%n%s%n%n",
- directory,
- annotationType.toUpperCase(),
- stats.toString())
+ String.format("%s\t%f\t%s",
+ annotationType,
+ options.featureSelectionThreshold,
+ stats.toTsv())
);
+ evaluationLogFileOut.flush();
}
} catch (IOException e) {
// TODO Auto-generated catch block
@@ -781,7 +781,7 @@ public static void printScore(Map<String
}
@Override
- protected Map<String, AnnotationStatistics> test(CollectionReader collectionReader, File directory)
+ protected Map<String, AnnotationStatisticsCompact> test(CollectionReader collectionReader, File directory)
throws Exception {
// AnalysisEngine classifierAnnotator = AnalysisEngineFactory.createPrimitive(AssertionCleartkAnalysisEngine.getDescription(
// GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
@@ -839,14 +839,14 @@ public static void printScore(Map<String
AnalysisEngine aggregate = builder.createAggregate();
- AnnotationStatistics polarityStats = new AnnotationStatistics();
- AnnotationStatistics conditionalStats = new AnnotationStatistics();
- AnnotationStatistics uncertaintyStats = new AnnotationStatistics();
- AnnotationStatistics subjectStats = new AnnotationStatistics();
- AnnotationStatistics genericStats = new AnnotationStatistics();
- AnnotationStatistics historyStats = new AnnotationStatistics(); // srh 3/6/13
+ AnnotationStatisticsCompact polarityStats = new AnnotationStatisticsCompact();
+ AnnotationStatisticsCompact conditionalStats = new AnnotationStatisticsCompact();
+ AnnotationStatisticsCompact uncertaintyStats = new AnnotationStatisticsCompact();
+ AnnotationStatisticsCompact subjectStats = new AnnotationStatisticsCompact();
+ AnnotationStatisticsCompact genericStats = new AnnotationStatisticsCompact();
+ AnnotationStatisticsCompact historyStats = new AnnotationStatisticsCompact(); // srh 3/6/13
- Map<String, AnnotationStatistics> map = new TreeMap<String, AnnotationStatistics>();
+ Map<String, AnnotationStatisticsCompact> map = new TreeMap<String, AnnotationStatisticsCompact>();
if (!options.ignorePolarity)
{
map.put("polarity", polarityStats);
@@ -921,8 +921,8 @@ public static void printScore(Map<String
if (!options.ignorePolarity)
{
polarityStats.add(goldEntitiesAndEvents, systemEntitiesAndEvents,
- AnnotationStatistics.<IdentifiedAnnotation>annotationToSpan(),
- AnnotationStatistics.<IdentifiedAnnotation>annotationToFeatureValue("polarity"));
+ AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToSpan(),
+ AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToFeatureValue("polarity"));
if(options.printErrors){
printErrors(jCas, goldEntitiesAndEvents, systemEntitiesAndEvents, "polarity", CONST.NE_POLARITY_NEGATION_PRESENT, Integer.class);
}
@@ -931,8 +931,8 @@ public static void printScore(Map<String
if (!options.ignoreConditional)
{
conditionalStats.add(goldEntitiesAndEvents, systemEntitiesAndEvents,
- AnnotationStatistics.<IdentifiedAnnotation>annotationToSpan(),
- AnnotationStatistics.<IdentifiedAnnotation>annotationToFeatureValue("conditional"));
+ AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToSpan(),
+ AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToFeatureValue("conditional"));
if(options.printErrors){
printErrors(jCas, goldEntitiesAndEvents, systemEntitiesAndEvents, "conditional", CONST.NE_CONDITIONAL_TRUE, Boolean.class);
}
@@ -941,8 +941,8 @@ public static void printScore(Map<String
if (!options.ignoreUncertainty)
{
uncertaintyStats.add(goldEntitiesAndEvents, systemEntitiesAndEvents,
- AnnotationStatistics.<IdentifiedAnnotation>annotationToSpan(),
- AnnotationStatistics.<IdentifiedAnnotation>annotationToFeatureValue("uncertainty"));
+ AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToSpan(),
+ AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToFeatureValue("uncertainty"));
if(options.printErrors){
printErrors(jCas, goldEntitiesAndEvents, systemEntitiesAndEvents, "uncertainty", CONST.NE_UNCERTAINTY_PRESENT, Integer.class);
}
@@ -951,8 +951,8 @@ public static void printScore(Map<String
if (!options.ignoreSubject)
{
subjectStats.add(goldEntitiesAndEvents, systemEntitiesAndEvents,
- AnnotationStatistics.<IdentifiedAnnotation>annotationToSpan(),
- AnnotationStatistics.<IdentifiedAnnotation>annotationToFeatureValue("subject"));
+ AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToSpan(),
+ AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToFeatureValue("subject"));
if(options.printErrors){
printErrors(jCas, goldEntitiesAndEvents, systemEntitiesAndEvents, "subject", null, CONST.ATTR_SUBJECT_PATIENT.getClass());
}
@@ -961,8 +961,8 @@ public static void printScore(Map<String
if (!options.ignoreGeneric)
{
genericStats.add(goldEntitiesAndEvents, systemEntitiesAndEvents,
- AnnotationStatistics.<IdentifiedAnnotation>annotationToSpan(),
- AnnotationStatistics.<IdentifiedAnnotation>annotationToFeatureValue("generic"));
+ AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToSpan(),
+ AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToFeatureValue("generic"));
if(options.printErrors){
printErrors(jCas, goldEntitiesAndEvents, systemEntitiesAndEvents, "generic", CONST.NE_GENERIC_TRUE, Boolean.class);
}
@@ -972,8 +972,8 @@ public static void printScore(Map<String
if (!options.ignoreHistory)
{
historyStats.add(goldEntitiesAndEvents, systemEntitiesAndEvents,
- AnnotationStatistics.<IdentifiedAnnotation>annotationToSpan(),
- AnnotationStatistics.<IdentifiedAnnotation>annotationToFeatureValue("historyOf"));
+ AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToSpan(),
+ AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToFeatureValue("historyOf"));
if(options.printErrors){
printErrors(jCas, goldEntitiesAndEvents, systemEntitiesAndEvents, "historyOf", CONST.NE_HISTORY_OF_PRESENT, Integer.class);
}
@@ -993,37 +993,37 @@ public static void printScore(Map<String
FeatureSelection<String> featureSelection;
if (currentAssertionAttribute.equals("polarity")) {
// TODO: parameterize the thresholds
- featureSelection = PolarityCleartkAnalysisEngine.createFeatureSelection(1f);
+ featureSelection = PolarityCleartkAnalysisEngine.createFeatureSelection(options.featureSelectionThreshold);
featureSelection.train(instances);
featureSelection.save(PolarityCleartkAnalysisEngine.createFeatureSelectionURI(directory));
}
else if (currentAssertionAttribute.equals("uncertainty")) {
// TODO: parameterize the thresholds
- featureSelection = UncertaintyCleartkAnalysisEngine.createFeatureSelection(1f);
+ featureSelection = UncertaintyCleartkAnalysisEngine.createFeatureSelection(options.featureSelectionThreshold);
featureSelection.train(instances);
featureSelection.save(UncertaintyCleartkAnalysisEngine.createFeatureSelectionURI(directory));
}
else if (currentAssertionAttribute.equals("conditional")) {
// TODO: parameterize the thresholds
- featureSelection = ConditionalCleartkAnalysisEngine.createFeatureSelection(1f);
+ featureSelection = ConditionalCleartkAnalysisEngine.createFeatureSelection(options.featureSelectionThreshold);
featureSelection.train(instances);
featureSelection.save(ConditionalCleartkAnalysisEngine.createFeatureSelectionURI(directory));
}
else if (currentAssertionAttribute.equals("subject")) {
// TODO: parameterize the thresholds
- featureSelection = SubjectCleartkAnalysisEngine.createFeatureSelection(1f);
+ featureSelection = SubjectCleartkAnalysisEngine.createFeatureSelection(options.featureSelectionThreshold);
featureSelection.train(instances);
featureSelection.save(SubjectCleartkAnalysisEngine.createFeatureSelectionURI(directory));
}
else if (currentAssertionAttribute.equals("generic")) {
// TODO: parameterize the thresholds
- featureSelection = GenericCleartkAnalysisEngine.createFeatureSelection(1f);
+ featureSelection = GenericCleartkAnalysisEngine.createFeatureSelection(options.featureSelectionThreshold);
featureSelection.train(instances);
featureSelection.save(GenericCleartkAnalysisEngine.createFeatureSelectionURI(directory));
}
else if (currentAssertionAttribute.equals("historyOf")) {
// TODO: parameterize the thresholds
- featureSelection = HistoryCleartkAnalysisEngine.createFeatureSelection(1f);
+ featureSelection = HistoryCleartkAnalysisEngine.createFeatureSelection(options.featureSelectionThreshold);
featureSelection.train(instances);
featureSelection.save(HistoryCleartkAnalysisEngine.createFeatureSelectionURI(directory));
}
@@ -1128,6 +1128,9 @@ private static void output(Object o) {
private static void printErrors(JCas jCas,
Collection<IdentifiedAnnotation> goldEntitiesAndEvents,
Collection<IdentifiedAnnotation> systemEntitiesAndEvents, String classifierType, Object trueCategory, Class<? extends Object> categoryClass) throws ResourceProcessException {
+
+ String documentId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+
Map<HashableAnnotation, IdentifiedAnnotation> goldMap = Maps.newHashMap();
for (IdentifiedAnnotation mention : goldEntitiesAndEvents) {
goldMap.put(new HashableAnnotation(mention), mention);
@@ -1176,17 +1179,17 @@ private static void printErrors(JCas jCa
// used for multi-class case:
System.out.println(classifierType+" Incorrectly labeled as " + systemLabel + " when the example was " + goldLabel + ": " + formatError(jCas, goldAnnotation));
}else if(systemLabel.equals(trueCategory)){
- System.out.println(classifierType+" FP: " + typeId + " " + formatError(jCas, systemAnnotation) + "| gold:|" + formatError(jCas, goldAnnotation));
+ System.out.println(classifierType+" FP: " + typeId + " " + formatError(jCas, systemAnnotation) + "| gold:|" + formatError(jCas, goldAnnotation) + " " + documentId);
}else{
- System.out.println(classifierType+" FN: " + typeId + " " + formatError(jCas, goldAnnotation)+ "| system:|" + formatError(jCas, systemAnnotation));
+ System.out.println(classifierType+" FN: " + typeId + " " + formatError(jCas, goldAnnotation)+ "| system:|" + formatError(jCas, systemAnnotation) + " " + documentId);
}
}else{
if(trueCategory == null){
// multi-class case -- probably don't want to print anything?
}else if(systemLabel.equals(trueCategory)){
- System.out.println(classifierType+" TP: " + typeId + " " + formatError(jCas, systemAnnotation) + "| gold:|" + formatError(jCas, goldAnnotation));
+ System.out.println(classifierType+" TP: " + typeId + " " + formatError(jCas, systemAnnotation) + "| gold:|" + formatError(jCas, goldAnnotation) + " " + documentId);
}else{
- System.out.println(classifierType+" TN: " + typeId + " " + formatError(jCas, systemAnnotation) + "| gold:|" + formatError(jCas, goldAnnotation));
+ System.out.println(classifierType+" TN: " + typeId + " " + formatError(jCas, systemAnnotation) + "| gold:|" + formatError(jCas, goldAnnotation) + " " + documentId);
}
}
}
Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java Fri Aug 2 16:48:14 2013
@@ -27,6 +27,7 @@ import java.util.Random;
import org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection;
import org.apache.ctakes.assertion.zoner.types.Zone;
+import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.structured.DocumentID;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation;
@@ -358,7 +359,18 @@ public abstract class AssertionCleartkAn
// }
- instance.add(new Feature("ENTITY_TYPE_" + entityOrEventMention.getTypeID()));
+ // 7/9/13 SRH trying to make it work just for anatomical site
+ int eemTypeId = entityOrEventMention.getTypeID();
+ if (eemTypeId == CONST.NE_TYPE_ID_ANATOMICAL_SITE) {
+ // 7/9/13 srh modified per tmiller so it's binary but not numeric feature
+ //instance.add(new Feature("ENTITY_TYPE_" + entityOrEventMention.getTypeID()));
+ instance.add(new Feature("ENTITY_TYPE_ANAT_SITE"));
+ } /* This hurts recall more than it helps precision
+ else if (eemTypeId == CONST.NE_TYPE_ID_DRUG) {
+ // 7/10 adding drug
+ instance.add(new Feature("ENTITY_TYPE_DRUG"));
+ }
+ */
for (SimpleFeatureExtractor extractor : this.entityFeatureExtractors) {
instance.addAll(extractor.extract(jCas, entityOrEventMention));
Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java Fri Aug 2 16:48:14 2013
@@ -72,7 +72,7 @@ public class ConditionalCleartkAnalysisE
}
}
public static FeatureSelection<String> createFeatureSelection(double threshold) {
- return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold);
+ return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold, false);
// return new MutualInformationFeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME);
}
Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java Fri Aug 2 16:48:14 2013
@@ -94,7 +94,7 @@ public class GenericCleartkAnalysisEngin
}
}
public static FeatureSelection<String> createFeatureSelection(double threshold) {
- return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold);
+ return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold, false);
// return new MutualInformationFeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME);
}
Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java Fri Aug 2 16:48:14 2013
@@ -97,7 +97,7 @@ public class HistoryCleartkAnalysisEngin
}
}
public static FeatureSelection<String> createFeatureSelection(double threshold) {
- return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold);
+ return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold, false);
// return new MutualInformationFeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME);
}
Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java Fri Aug 2 16:48:14 2013
@@ -93,7 +93,7 @@ public class PolarityCleartkAnalysisEngi
}
}
public static FeatureSelection<String> createFeatureSelection(double threshold) {
- return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold);
+ return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold, false);
// return new MutualInformationFeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME);
}
Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java Fri Aug 2 16:48:14 2013
@@ -97,7 +97,7 @@ public class SubjectCleartkAnalysisEngin
}
}
public static FeatureSelection<String> createFeatureSelection(double threshold) {
- return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold);
+ return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold, false);
// return new MutualInformationFeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME);
}
Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java Fri Aug 2 16:48:14 2013
@@ -79,7 +79,7 @@ public class UncertaintyCleartkAnalysisE
}
public static FeatureSelection<String> createFeatureSelection(double threshold) {
- return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold);
+ return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold, false);
// return new MutualInformationFeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME);
}
Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateChi2GridSearch.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateChi2GridSearch.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateChi2GridSearch.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateChi2GridSearch.java Fri Aug 2 16:48:14 2013
@@ -14,11 +14,11 @@ public class CrossValidateChi2GridSearch
AssertionEvaluation.useEvaluationLogFile = true;
- float[] threshs = {2f, 5f, 10f, 20f, 50f, 100f};
+ float[] threshs = {1f, 5f, 10f, 50f, 100f};
for (Float chi2threshold : threshs ) {
System.out.println("BEGIN Chi2 Grid Search with threshold = "+ Float.toString(chi2threshold));
- AssertionEvaluation.evaluationLogFileOut.write("BEGIN Chi2 Grid Search with threshold = "+ Float.toString(chi2threshold));
- AssertionEvaluation.evaluationLogFileOut.flush();
+// AssertionEvaluation.evaluationLogFileOut.write("BEGIN Chi2 Grid Search with threshold = "+ Float.toString(chi2threshold)+"\n");
+// AssertionEvaluation.evaluationLogFileOut.flush();
for (String attribute : AssertionConst.annotationTypes) {
Propchange: ctakes/branches/ctakes-3.1.0/ctakes-chunker/
------------------------------------------------------------------------------
Merged /ctakes/trunk/ctakes-chunker:r1506998-1509769
Modified: ctakes/branches/ctakes-3.1.0/ctakes-chunker-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-chunker-res/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-chunker-res/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-chunker-res/pom.xml Fri Aug 2 16:48:14 2013
@@ -24,7 +24,7 @@
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
- <version>3.1.0-SNAPSHOT</version>
+ <version>3.1.0</version>
</parent>
<artifactId>ctakes-chunker-res</artifactId>
<name>Apache cTAKES Resources ctakes-chunker-res</name>
Modified: ctakes/branches/ctakes-3.1.0/ctakes-chunker/desc/Chunker.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-chunker/desc/Chunker.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-chunker/desc/Chunker.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-chunker/desc/Chunker.xml Fri Aug 2 16:48:14 2013
@@ -37,7 +37,7 @@
<nameValuePair>
<name>ChunkerModelFile</name>
<value>
- <string>org/apache/ctakes/chunker/models/chunk-model.claims-1.5.zip
+ <string>org/apache/ctakes/chunker/models/chunker-model.zip
</string>
</value>
</nameValuePair>
@@ -92,7 +92,7 @@
<name>ChunkerModelFile</name>
<description></description>
<fileResourceSpecifier>
- <fileUrl>file:org/apache/ctakes/chunker/models/chunk-model.claims-1.5.zip
+ <fileUrl>file:org/apache/ctakes/chunker/models/chunker-model.zip
</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl
Modified: ctakes/branches/ctakes-3.1.0/ctakes-chunker/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-chunker/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-chunker/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-chunker/pom.xml Fri Aug 2 16:48:14 2013
@@ -1,69 +1,69 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
- 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.
-
--->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <artifactId>ctakes-chunker</artifactId>
- <name>Apache cTAKES chunker</name>
- <parent>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes</artifactId>
- <version>3.1.0-SNAPSHOT</version>
- </parent>
- <dependencies>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-chunker-res</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-type-system</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-core</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-utils</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-pos-tagger</artifactId>
- </dependency>
- <dependency>
- <groupId>log4j</groupId>
- <artifactId>log4j</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.opennlp</groupId>
- <artifactId>opennlp-maxent</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.opennlp</groupId>
- <artifactId>opennlp-tools</artifactId>
- </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- </dependency>
- </dependencies>
-</project>
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ 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.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <artifactId>ctakes-chunker</artifactId>
+ <name>Apache cTAKES chunker</name>
+ <parent>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes</artifactId>
+ <version>3.1.0</version>
+ </parent>
+ <dependencies>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-chunker-res</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-type-system</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-core</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-utils</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-pos-tagger</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.opennlp</groupId>
+ <artifactId>opennlp-maxent</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.opennlp</groupId>
+ <artifactId>opennlp-tools</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ </dependency>
+ </dependencies>
+</project>
Modified: ctakes/branches/ctakes-3.1.0/ctakes-clinical-pipeline/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-clinical-pipeline/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-clinical-pipeline/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-clinical-pipeline/pom.xml Fri Aug 2 16:48:14 2013
@@ -1,170 +1,170 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- 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. -->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <artifactId>ctakes-clinical-pipeline</artifactId>
- <name>Apache cTAKES ctakes-clinical-pipeline</name>
- <parent>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes</artifactId>
- <version>3.1.0-SNAPSHOT</version>
- </parent>
-
-
- <dependencies>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-type-system</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-core</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-utils</artifactId>
- </dependency>
- <dependency>
- <groupId>jdom</groupId>
- <artifactId>jdom</artifactId>
- </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-context-tokenizer</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-dictionary-lookup</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-preprocessor</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-lvg</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-chunker</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-ne-contexts</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-pos-tagger</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-assertion</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-dependency-parser</artifactId>
- </dependency>
- </dependencies>
- <profiles>
- <profile>
- <id>runCPE</id>
- <activation>
- <property>
- <name>runCPE</name>
- </property>
- </activation>
- <build>
- <plugins>
- <plugin>
- <groupId>org.codehaus.mojo</groupId>
- <artifactId>exec-maven-plugin</artifactId>
- <version>1.2.1</version>
- <executions>
- <execution>
- <!-- depends on other modules being on classpath -->
- <phase>compile</phase>
- <goals>
- <goal>java</goal>
- </goals>
- </execution>
- </executions>
- <configuration>
- <includeProjectDependencies>true</includeProjectDependencies>
- <includePluginDependencies>true</includePluginDependencies>
- <mainClass>org.apache.uima.tools.cpm.CpmFrame</mainClass>
- <arguments>
- <argument />
- </arguments>
- </configuration>
- <dependencies>
- <dependency>
- <groupId>gov.nih.nlm.nls.lvg</groupId>
- <artifactId>lvg2010dist</artifactId>
- <version>0.0.1</version>
- </dependency>
- </dependencies>
- </plugin>
- </plugins>
- </build>
- </profile>
-
- <profile>
- <id>runCVD</id>
- <activation>
- <property>
- <name>runCVD</name>
- </property>
- </activation>
- <build>
- <plugins>
- <plugin>
- <groupId>org.codehaus.mojo</groupId>
- <artifactId>exec-maven-plugin</artifactId>
- <version>1.2.1</version>
- <executions>
- <execution>
- <!-- depends on other modules being on classpath -->
- <phase>compile</phase>
- <goals>
- <goal>java</goal>
- </goals>
- </execution>
- </executions>
- <configuration>
- <includeProjectDependencies>true</includeProjectDependencies>
- <includePluginDependencies>true</includePluginDependencies>
-
- <mainClass>org.apache.uima.tools.cvd.CVD</mainClass>
- <!-- Have to specify at least one parameter otherwise, CVD thinks
- it's an invalid param because MVN passes null when joining to the mvn thread -->
- <arguments>
- <argument>-lookandfeel</argument>
- <argument>javax.swing.plaf.metal.MetalLookAndFeel</argument>
- </arguments>
- </configuration>
- <dependencies>
- <dependency>
- <groupId>gov.nih.nlm.nls.lvg</groupId>
- <artifactId>lvg2010dist</artifactId>
- <version>0.0.1</version>
- </dependency>
- </dependencies>
- </plugin>
- </plugins>
- </build>
- </profile>
- </profiles>
-</project>
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- 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. -->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <artifactId>ctakes-clinical-pipeline</artifactId>
+ <name>Apache cTAKES ctakes-clinical-pipeline</name>
+ <parent>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes</artifactId>
+ <version>3.1.0</version>
+ </parent>
+
+
+ <dependencies>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-type-system</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-core</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-utils</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>jdom</groupId>
+ <artifactId>jdom</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-context-tokenizer</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-dictionary-lookup</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-preprocessor</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-lvg</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-chunker</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-ne-contexts</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-pos-tagger</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-assertion</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-dependency-parser</artifactId>
+ </dependency>
+ </dependencies>
+ <profiles>
+ <profile>
+ <id>runCPE</id>
+ <activation>
+ <property>
+ <name>runCPE</name>
+ </property>
+ </activation>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>exec-maven-plugin</artifactId>
+ <version>1.2.1</version>
+ <executions>
+ <execution>
+ <!-- depends on other modules being on classpath -->
+ <phase>compile</phase>
+ <goals>
+ <goal>java</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <includeProjectDependencies>true</includeProjectDependencies>
+ <includePluginDependencies>true</includePluginDependencies>
+ <mainClass>org.apache.uima.tools.cpm.CpmFrame</mainClass>
+ <arguments>
+ <argument />
+ </arguments>
+ </configuration>
+ <dependencies>
+ <dependency>
+ <groupId>gov.nih.nlm.nls.lvg</groupId>
+ <artifactId>lvg2010dist</artifactId>
+ <version>0.0.1</version>
+ </dependency>
+ </dependencies>
+ </plugin>
+ </plugins>
+ </build>
+ </profile>
+
+ <profile>
+ <id>runCVD</id>
+ <activation>
+ <property>
+ <name>runCVD</name>
+ </property>
+ </activation>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>exec-maven-plugin</artifactId>
+ <version>1.2.1</version>
+ <executions>
+ <execution>
+ <!-- depends on other modules being on classpath -->
+ <phase>compile</phase>
+ <goals>
+ <goal>java</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <includeProjectDependencies>true</includeProjectDependencies>
+ <includePluginDependencies>true</includePluginDependencies>
+
+ <mainClass>org.apache.uima.tools.cvd.CVD</mainClass>
+ <!-- Have to specify at least one parameter otherwise, CVD thinks
+ it's an invalid param because MVN passes null when joining to the mvn thread -->
+ <arguments>
+ <argument>-lookandfeel</argument>
+ <argument>javax.swing.plaf.metal.MetalLookAndFeel</argument>
+ </arguments>
+ </configuration>
+ <dependencies>
+ <dependency>
+ <groupId>gov.nih.nlm.nls.lvg</groupId>
+ <artifactId>lvg2010dist</artifactId>
+ <version>0.0.1</version>
+ </dependency>
+ </dependencies>
+ </plugin>
+ </plugins>
+ </build>
+ </profile>
+ </profiles>
+</project>
Modified: ctakes/branches/ctakes-3.1.0/ctakes-constituency-parser-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-constituency-parser-res/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-constituency-parser-res/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-constituency-parser-res/pom.xml Fri Aug 2 16:48:14 2013
@@ -24,7 +24,7 @@
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
- <version>3.1.0-SNAPSHOT</version>
+ <version>3.1.0</version>
</parent>
<artifactId>ctakes-constituency-parser-res</artifactId>
<name>Apache cTAKES Resources constituency-parser</name>