You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@ctakes.apache.org by ch...@apache.org on 2012/10/04 21:56:15 UTC
svn commit: r1394229 - in /incubator/ctakes/trunk:
ctakes-drug-ner/desc/analysis_engine/ ctakes-drug-ner/resources/lookup/
ctakes-drug-ner/resources/tokenizer/ ctakes-drug-ner/src/main/resources/
ctakes-drug-ner/src/main/resources/org/ ctakes-drug-ner/...
Author: chenpei
Date: Thu Oct 4 19:56:12 2012
New Revision: 1394229
URL: http://svn.apache.org/viewvc?rev=1394229&view=rev
Log:
Have maven detect the models. (moving models to src/main/resources) will be automatically in the jar and classpath of the project.
First pass- updating the main projects first.
Added:
incubator/ctakes/trunk/ctakes-drug-ner/src/main/resources/
incubator/ctakes/trunk/ctakes-drug-ner/src/main/resources/org/
incubator/ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/
incubator/ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/
incubator/ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/
incubator/ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/lookup/
- copied from r1394192, incubator/ctakes/trunk/ctakes-drug-ner/resources/lookup/
incubator/ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/tokenizer/
- copied from r1394192, incubator/ctakes/trunk/ctakes-drug-ner/resources/tokenizer/
incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/
incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/
incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/
incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/
incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/padtermspotter/
incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/padtermspotter/lookup/
- copied from r1394192, incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/lookup/
incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/padtermspotter/lvg/
- copied from r1394192, incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/lvg/
incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/padtermspotter/negation/
- copied from r1394192, incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/negation/
incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/padtermspotter/sentenceDetector/
- copied from r1394192, incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/sentenceDetector/
incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/padtermspotter/tokenizer/
- copied from r1394192, incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/tokenizer/
incubator/ctakes/trunk/ctakes-preprocessor/src/main/resources/
incubator/ctakes/trunk/ctakes-preprocessor/src/main/resources/org/
incubator/ctakes/trunk/ctakes-preprocessor/src/main/resources/org/apache/
incubator/ctakes/trunk/ctakes-preprocessor/src/main/resources/org/apache/ctakes/
incubator/ctakes/trunk/ctakes-preprocessor/src/main/resources/org/apache/ctakes/preprocessor/
incubator/ctakes/trunk/ctakes-preprocessor/src/main/resources/org/apache/ctakes/preprocessor/cda/
- copied from r1394192, incubator/ctakes/trunk/ctakes-preprocessor/resources/cda/
incubator/ctakes/trunk/ctakes-preprocessor/src/main/resources/org/apache/ctakes/preprocessor/tokenizer/
- copied from r1394192, incubator/ctakes/trunk/ctakes-preprocessor/resources/tokenizer/
incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/
incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/
incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/
incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/
incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/
incubator/ctakes/trunk/ctakes-relation-extractor/src/main/resources/org/apache/ctakes/relationextractor/models/
- copied from r1394192, incubator/ctakes/trunk/ctakes-relation-extractor/resources/models/
incubator/ctakes/trunk/ctakes-side-effect/src/main/resources/
incubator/ctakes/trunk/ctakes-side-effect/src/main/resources/org/
incubator/ctakes/trunk/ctakes-side-effect/src/main/resources/org/apache/
incubator/ctakes/trunk/ctakes-side-effect/src/main/resources/org/apache/ctakes/
incubator/ctakes/trunk/ctakes-side-effect/src/main/resources/org/apache/ctakes/sideeffect/
- copied from r1394192, incubator/ctakes/trunk/ctakes-side-effect/resources/sideeffect/
incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/machine/
- copied from r1394192, incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/fsm/smoking/machine/
incubator/ctakes/trunk/ctakes-smoking-status/src/main/resources/
incubator/ctakes/trunk/ctakes-smoking-status/src/main/resources/org/
incubator/ctakes/trunk/ctakes-smoking-status/src/main/resources/org/apache/
incubator/ctakes/trunk/ctakes-smoking-status/src/main/resources/org/apache/ctakes/
incubator/ctakes/trunk/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/
incubator/ctakes/trunk/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/data/
- copied from r1394192, incubator/ctakes/trunk/ctakes-smoking-status/resources/ss/data/
Removed:
incubator/ctakes/trunk/ctakes-drug-ner/resources/lookup/
incubator/ctakes/trunk/ctakes-drug-ner/resources/tokenizer/
incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/core/
incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/lookup/
incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/lvg/
incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/negation/
incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/sentenceDetector/
incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/tokenizer/
incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/fsm/
incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/
incubator/ctakes/trunk/ctakes-preprocessor/resources/cda/
incubator/ctakes/trunk/ctakes-preprocessor/resources/tokenizer/
incubator/ctakes/trunk/ctakes-relation-extractor/resources/models/
incubator/ctakes/trunk/ctakes-side-effect/resources/sideeffect/
incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/
incubator/ctakes/trunk/ctakes-smoking-status/resources/ss/
incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/fsm/smoking/
incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/
incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/uima/libsvm/
Modified:
incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml
incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/NegationDxAnnotator.xml
incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/DxStatusAnnotator.xml
incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/NegationDxAnnotator.xml
incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/PAD_Hit.xml
incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml
incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/SubSectionBoundaryAnnotator.xml
incubator/ctakes/trunk/ctakes-preprocessor/desc/CdaCasInitializer.xml
incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/DegreeOfRelationExtractorAnnotator.xml
incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/EntityMentionPairRelationExtractorAnnotator.xml
incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/ModifierExtractorAnnotator.xml
incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml
incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorTrain.java
incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffect.xml
incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffectUMLS.xml
incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAnnotator.xml
incubator/ctakes/trunk/ctakes-smoking-status/README
incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml
incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/NonsmokerDictionaryLookupAnnotator.xml
incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/PcsClassifierAnnotator_libsvm.xml
incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml
incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context/negation/NegationContextAnalyzer.java
incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/machine/NegationFSM.java
Modified: incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml Thu Oct 4 19:56:12 2012
@@ -71,7 +71,7 @@
<name>LookupDescriptorFile</name>
<description/>
<fileResourceSpecifier>
- <fileUrl>file:lookup/LookupDesc_DrugNER.xml</fileUrl>
+ <fileUrl>file:org/apache/ctakes/drugner/lookup/LookupDesc_DrugNER.xml</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
@@ -106,7 +106,7 @@
<nameValuePair>
<name>IndexDirectory</name>
<value>
- <string>lookup/drug_index</string>
+ <string>org/apache/ctakes/drugner/lookup/drug_index</string>
</value>
</nameValuePair>
</configurationParameterSettings>
Modified: incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml Thu Oct 4 19:56:12 2012
@@ -143,7 +143,7 @@
<name>LookupDescriptorFile</name>
<description/>
<fileResourceSpecifier>
- <fileUrl>file:lookup/LookupDesc_DrugNER.xml</fileUrl>
+ <fileUrl>file:org/apache/ctakes/drugner/lookup/LookupDesc_DrugNER.xml</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
@@ -178,7 +178,7 @@
<nameValuePair>
<name>IndexDirectory</name>
<value>
- <string>lookup/rxnorm_index</string>
+ <string>org/apache/ctakes/drugner/lookup/rxnorm_index</string>
</value>
</nameValuePair>
</configurationParameterSettings>
Modified: incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/NegationDxAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/NegationDxAnnotator.xml?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/NegationDxAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/NegationDxAnnotator.xml Thu Oct 4 19:56:12 2012
@@ -149,7 +149,7 @@
<name>BoundaryDataFile</name>
<description>Represents tokens that signifies negation boundary</description>
<fileResourceSpecifier>
-<fileUrl>file:cni/negation/boundaryData.txt</fileUrl>
+<fileUrl>file:org/apache/ctakes/drugner/cni/negation/boundaryData.txt</fileUrl>
</fileResourceSpecifier>
<implementationName>edu.mayo.bmi.uima.common.resource.FileResourceImpl</implementationName>
</externalResource>
Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/DxStatusAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/DxStatusAnnotator.xml?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/DxStatusAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/DxStatusAnnotator.xml Thu Oct 4 19:56:12 2012
@@ -186,7 +186,7 @@
<name>BoundaryDataFile</name>
<description>Represents tokens that signifies negation boundary</description>
<fileResourceSpecifier>
-<fileUrl>file:negation/boundaryData.txt</fileUrl>
+<fileUrl>file:org/apache/ctakes/padtermspotter/negation/boundaryData.txt</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/NegationDxAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/NegationDxAnnotator.xml?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/NegationDxAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/NegationDxAnnotator.xml Thu Oct 4 19:56:12 2012
@@ -185,7 +185,7 @@
<name>BoundaryDataFile</name>
<description>Represents tokens that signifies negation boundary</description>
<fileResourceSpecifier>
-<fileUrl>file:negation/boundaryData.txt</fileUrl>
+<fileUrl>file:org/apache/ctakes/padtermspotter/negation/boundaryData.txt</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/PAD_Hit.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/PAD_Hit.xml?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/PAD_Hit.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/PAD_Hit.xml Thu Oct 4 19:56:12 2012
@@ -190,7 +190,7 @@
<name>StopWordsFileResource</name>
<description></description>
<fileResourceSpecifier>
-<fileUrl>file:lookup/radiology/StopWords.txt</fileUrl>
+<fileUrl>file:org/apache/ctakes/padtermspotter/lookup/radiology/StopWords.txt</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml Thu Oct 4 19:56:12 2012
@@ -81,7 +81,7 @@
<name>LookupDescriptorFile</name>
<description></description>
<fileResourceSpecifier>
-<fileUrl>file:lookup/radiology/LookupDesc_PAD.xml</fileUrl>
+<fileUrl>file:org/apache/ctakes/padtermspotter/lookup/radiology/LookupDesc_PAD.xml</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
@@ -89,7 +89,7 @@
<name>PAD_Location_FileResrc</name>
<description></description>
<fileResourceSpecifier>
-<fileUrl>file:lookup/radiology/pad_anatomical_sites.csv</fileUrl>
+<fileUrl>file:org/apache/ctakes/padtermspotter/lookup/radiology/pad_anatomical_sites.csv</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
@@ -97,7 +97,7 @@
<name>PAD_Terms_FileResrc</name>
<description></description>
<fileResourceSpecifier>
-<fileUrl>file:lookup/radiology/pad_disorders.csv</fileUrl>
+<fileUrl>file:org/apache/ctakes/padtermspotter/lookup/radiology/pad_disorders.csv</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/SubSectionBoundaryAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/SubSectionBoundaryAnnotator.xml?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/SubSectionBoundaryAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/SubSectionBoundaryAnnotator.xml Thu Oct 4 19:56:12 2012
@@ -65,7 +65,7 @@
<name>ExamTitleWordsFileResource</name>
<description></description>
<fileResourceSpecifier>
-<fileUrl>file:lookup/radiology/ExamTitleWords.txt</fileUrl>
+<fileUrl>file:org/apache/ctakes/padtermspotter/lookup/radiology/ExamTitleWords.txt</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
Modified: incubator/ctakes/trunk/ctakes-preprocessor/desc/CdaCasInitializer.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-preprocessor/desc/CdaCasInitializer.xml?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-preprocessor/desc/CdaCasInitializer.xml (original)
+++ incubator/ctakes/trunk/ctakes-preprocessor/desc/CdaCasInitializer.xml Thu Oct 4 19:56:12 2012
@@ -81,7 +81,7 @@ The CDA must conform to the DTD resource
<name>DtdFile</name>
<description></description>
<fileResourceSpecifier>
-<fileUrl>file:cda/NotesIIST_RTF.DTD</fileUrl>
+<fileUrl>file:org/apache/ctakes/preprocessor/cda/NotesIIST_RTF.DTD</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
@@ -89,7 +89,7 @@ The CDA must conform to the DTD resource
<name>HyphenFile</name>
<description></description>
<fileResourceSpecifier>
-<fileUrl>file:tokenizer/hyphenated.txt</fileUrl>
+<fileUrl>file:org/apache/ctakes/preprocessor/tokenizer/hyphenated.txt</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
Modified: incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/DegreeOfRelationExtractorAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/DegreeOfRelationExtractorAnnotator.xml?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/DegreeOfRelationExtractorAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/DegreeOfRelationExtractorAnnotator.xml Thu Oct 4 19:56:12 2012
@@ -107,7 +107,7 @@
<nameValuePair>
<name>org.cleartk.classifier.jar.GenericJarClassifierFactory.classifierJarPath</name>
<value>
- <string>resources/models/degree_of/model.jar</string>
+ <string>org/apache/ctakes/relationextractor/models/degree_of/model.jar</string>
</value>
</nameValuePair>
</configurationParameterSettings>
Modified: incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/EntityMentionPairRelationExtractorAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/EntityMentionPairRelationExtractorAnnotator.xml?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/EntityMentionPairRelationExtractorAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/EntityMentionPairRelationExtractorAnnotator.xml Thu Oct 4 19:56:12 2012
@@ -114,7 +114,7 @@
<nameValuePair>
<name>org.cleartk.classifier.jar.GenericJarClassifierFactory.classifierJarPath</name>
<value>
- <string>resources/models/em_pair/model.jar</string>
+ <string>org/apache/ctakes/relationextractor/models/em_pair/model.jar</string>
</value>
</nameValuePair>
<nameValuePair>
Modified: incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/ModifierExtractorAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/ModifierExtractorAnnotator.xml?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/ModifierExtractorAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/ModifierExtractorAnnotator.xml Thu Oct 4 19:56:12 2012
@@ -67,7 +67,7 @@
<nameValuePair>
<name>org.cleartk.classifier.jar.GenericJarClassifierFactory.classifierJarPath</name>
<value>
- <string>resources/models/modifier_extractor/model.jar</string>
+ <string>org/apache/ctakes/relationextractor/models/modifier_extractor/model.jar</string>
</value>
</nameValuePair>
</configurationParameterSettings>
Modified: incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml Thu Oct 4 19:56:12 2012
@@ -119,7 +119,7 @@
<nameValuePair>
<name>org.cleartk.classifier.jar.GenericJarClassifierFactory.classifierJarPath</name>
<value>
- <string>resources/models/em_pair/model.jar</string>
+ <string>org/apache/ctakes/relationextractor/models/em_pair/model.jar</string>
</value>
</nameValuePair>
<nameValuePair>
@@ -189,7 +189,7 @@
<nameValuePair>
<name>org.cleartk.classifier.jar.GenericJarClassifierFactory.classifierJarPath</name>
<value>
- <string>resources/models/modifier_extractor/model.jar</string>
+ <string>org/apache/ctakes/relationextractor/models/modifier_extractor/model.jar</string>
</value>
</nameValuePair>
</configurationParameterSettings>
@@ -475,7 +475,7 @@
<nameValuePair>
<name>org.cleartk.classifier.jar.GenericJarClassifierFactory.classifierJarPath</name>
<value>
- <string>resources/models/degree_of/model.jar</string>
+ <string>org/apache/ctakes/relationextractor/models/degree_of/model.jar</string>
</value>
</nameValuePair>
</configurationParameterSettings>
Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorTrain.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorTrain.java?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorTrain.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorTrain.java Thu Oct 4 19:56:12 2012
@@ -152,7 +152,7 @@ public class RelationExtractorTrain {
List<File> trainFiles = Arrays.asList(options.trainDirectory.listFiles());
// Initialize model directories
- File modelsDirBase = new File("resources/models");
+ File modelsDirBase = new File("org/apache/ctakes/relationextractor/models");
File modelsDirModExtractor = new File(modelsDirBase, "modifier_extractor");
File modelsDirDegreeOf = new File(modelsDirBase, "degree_of");
File modelsDirEMPair = new File(modelsDirBase, "em_pair");
Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffect.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffect.xml?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffect.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffect.xml Thu Oct 4 19:56:12 2012
@@ -97,7 +97,7 @@
<name>LookupDescriptorFile</name>
<description/>
<fileResourceSpecifier>
- <fileUrl>file:sideeffect/lookup/LookupDesc_sideEffect.xml</fileUrl>
+ <fileUrl>file:org/apache/ctakes/sideeffect/lookup/LookupDesc_sideEffect.xml</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
@@ -230,7 +230,7 @@
<name>CsvSEFile</name>
<description>supplemental NEs</description>
<fileResourceSpecifier>
- <fileUrl>file:sideeffect/lookup/additionalNE_dictionary.csv</fileUrl>
+ <fileUrl>file:org/apache/ctakes/sideeffect/lookup/additionalNE_dictionary.csv</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffectUMLS.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffectUMLS.xml?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffectUMLS.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffectUMLS.xml Thu Oct 4 19:56:12 2012
@@ -162,7 +162,7 @@
<name>LookupDescriptorFile</name>
<description/>
<fileResourceSpecifier>
- <fileUrl>file:sideeffect/lookup/LookupDesc_sideEffectUMLS.xml</fileUrl>
+ <fileUrl>file:org/apache/ctakes/sideeffect/lookup/LookupDesc_sideEffectUMLS.xml</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
@@ -311,7 +311,7 @@
<name>CsvSEFile</name>
<description>supplemental NEs</description>
<fileResourceSpecifier>
- <fileUrl>file:sideeffect/lookup/additionalNE_dictionary.csv</fileUrl>
+ <fileUrl>file:org/apache/ctakes/sideeffect/lookup/additionalNE_dictionary.csv</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAnnotator.xml?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAnnotator.xml Thu Oct 4 19:56:12 2012
@@ -241,7 +241,7 @@
<name>sideEffectDic</name>
<description>dictionary of drug side effect</description>
<fileResourceSpecifier>
- <fileUrl>file:sideeffect/lookup/sideEffect_dictionary.txt</fileUrl>
+ <fileUrl>file:org/apache/ctakes/sideeffect/lookup/sideEffect_dictionary.txt</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
Modified: incubator/ctakes/trunk/ctakes-smoking-status/README
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/README?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/README (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/README Thu Oct 4 19:56:12 2012
@@ -268,7 +268,7 @@ Debugging issues
#############
One of the next releases will look into addressing the following:
- - class 'edu.mayo.bmi.fsm.smoking.machine.NegationFSM.java' must inherit from 'core/org.apache.ctakes.core.fsm.machine.NegationFSM.java'
+ - class 'org.apache.ctakes.smokingstatus.machine.NegationFSM.java' must inherit from 'core/org.apache.ctakes.core.fsm.machine.NegationFSM.java'
- org.apache.ctakes.smokingstatus.context.negation.NegationContextAnalyzer - needs to use 'NE Contexts/org.apache.ctakes.necontexts.negation.NegationContextAnalyzer'
- ResolutionAnnotator.java references 'TypeSystemConst.NE_CERTAINTY_NEGATED' which has been commented out, uncomment in both places for next major release
- FIXED -Parameters probably need to be changed? /smoking status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml
Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml Thu Oct 4 19:56:12 2012
@@ -144,7 +144,7 @@ This param is optional. If not specifie
<name>negationContradictionWords</name>
<description/>
<fileResourceSpecifier>
- <fileUrl>file:ss/data/context/negationContradictionWords.txt</fileUrl>
+ <fileUrl>file:org/apache/ctakes/smokingstatus/data/context/negationContradictionWords.txt</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/NonsmokerDictionaryLookupAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/NonsmokerDictionaryLookupAnnotator.xml?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/NonsmokerDictionaryLookupAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/NonsmokerDictionaryLookupAnnotator.xml Thu Oct 4 19:56:12 2012
@@ -75,7 +75,7 @@
<name>LookupDescriptorFileNonSmoker</name>
<description></description>
<fileResourceSpecifier>
-<fileUrl>file:ss/data/SmokingStatusLookupConfig.xml</fileUrl>
+<fileUrl>file:org/apache/ctakes/smokingstatus/data/SmokingStatusLookupConfig.xml</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
@@ -83,7 +83,7 @@
<name>DictionaryFileNonSmoker</name>
<description></description>
<fileResourceSpecifier>
-<fileUrl>file:ss/data/nonsmoker.dictionary</fileUrl>
+<fileUrl>file:org/apache/ctakes/smokingstatus/data/nonsmoker.dictionary</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/PcsClassifierAnnotator_libsvm.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/PcsClassifierAnnotator_libsvm.xml?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/PcsClassifierAnnotator_libsvm.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/PcsClassifierAnnotator_libsvm.xml Thu Oct 4 19:56:12 2012
@@ -97,7 +97,7 @@
<name>PathOfModelResc</name>
<description></description>
<fileResourceSpecifier>
-<fileUrl>file:ss/data/PCS/pcs_libsvm-2.91.model</fileUrl>
+<fileUrl>file:org/apache/ctakes/smokingstatus/data/PCS/pcs_libsvm-2.91.model</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
@@ -105,7 +105,7 @@
<name>PCSKeyWordFileResc</name>
<description/>
<fileResourceSpecifier>
-<fileUrl>file:ss/data/PCS/keywords_PCS.txt</fileUrl>
+<fileUrl>file:org/apache/ctakes/smokingstatus/data/PCS/keywords_PCS.txt</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
@@ -113,7 +113,7 @@
<name>StopWordsFileResc</name>
<description></description>
<fileResourceSpecifier>
-<fileUrl>file:ss/data/PCS/stopwords_PCS.txt</fileUrl>
+<fileUrl>file:org/apache/ctakes/smokingstatus/data/PCS/stopwords_PCS.txt</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml Thu Oct 4 19:56:12 2012
@@ -79,7 +79,7 @@
<name>LookupDescriptorFile</name>
<description></description>
<fileResourceSpecifier>
-<fileUrl>file:ss/data/SmokingStatusLookupConfig.xml</fileUrl>
+<fileUrl>file:org/apache/ctakes/smokingstatus/data/SmokingStatusLookupConfig.xml</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
@@ -87,7 +87,7 @@
<name>DictionaryFileSmoker</name>
<description></description>
<fileResourceSpecifier>
-<fileUrl>file:ss/data/smoker.dictionary</fileUrl>
+<fileUrl>file:org/apache/ctakes/smokingstatus/data/smoker.dictionary</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
@@ -95,7 +95,7 @@
<name>DictionaryFileNonSmoker</name>
<description></description>
<fileResourceSpecifier>
-<fileUrl>file:ss/data/nonsmoker.dictionary</fileUrl>
+<fileUrl>file:org/apache/ctakes/smokingstatus/data/nonsmoker.dictionary</fileUrl>
</fileResourceSpecifier>
<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
</externalResource>
Modified: incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context/negation/NegationContextAnalyzer.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context/negation/NegationContextAnalyzer.java?rev=1394229&r1=1394228&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context/negation/NegationContextAnalyzer.java (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context/negation/NegationContextAnalyzer.java Thu Oct 4 19:56:12 2012
@@ -25,10 +25,10 @@ import org.apache.ctakes.core.fsm.output
import org.apache.ctakes.core.fsm.token.TextToken;
import org.apache.ctakes.necontexts.ContextHit;
import org.apache.ctakes.smokingstatus.context.NamedEntityContextAnalyzer;
+import org.apache.ctakes.smokingstatus.machine.NegationFSM;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.jcas.tcas.Annotation;
-import edu.mayo.bmi.fsm.smoking.machine.NegationFSM;
public class NegationContextAnalyzer extends NamedEntityContextAnalyzer {
private NegationFSM _negIndicatorFSM = new NegationFSM();
Modified: incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/machine/NegationFSM.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/machine/NegationFSM.java?rev=1394229&r1=1394192&r2=1394229&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/machine/NegationFSM.java (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/machine/NegationFSM.java Thu Oct 4 19:56:12 2012
@@ -16,7 +16,7 @@
* specific language governing permissions and limitations
* under the License.
*/
-package edu.mayo.bmi.fsm.smoking.machine;
+package org.apache.ctakes.smokingstatus.machine;
import java.util.HashMap;
import java.util.HashSet;