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From chen...@apache.org
Subject 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/...
Date Thu, 04 Oct 2012 19:56:15 GMT
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;



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