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From chen...@apache.org
Subject svn commit: r1636916 - in /ctakes/trunk/ctakes-assertion/desc/analysis_engine: GenericCleartkAnalysisEngine.xml HistoryCleartkAnalysisEngine.xml PolarityCleartkAnalysisEngine.xml SubjectCleartkAnalysisEngine.xml UncertaintyCleartkAnalysisEngine.xml
Date Wed, 05 Nov 2014 16:45:49 GMT
Author: chenpei
Date: Wed Nov  5 16:45:48 2014
New Revision: 1636916

URL: http://svn.apache.org/r1636916
Log:
CTAKES-326 - Added the descriptors for the new clearTK based Assertion annotators for backwards
compatibility and needed by current DefaultAggregate pipelines.

Added:
    ctakes/trunk/ctakes-assertion/desc/analysis_engine/GenericCleartkAnalysisEngine.xml  
(with props)
    ctakes/trunk/ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml  
(with props)
    ctakes/trunk/ctakes-assertion/desc/analysis_engine/PolarityCleartkAnalysisEngine.xml 
 (with props)
    ctakes/trunk/ctakes-assertion/desc/analysis_engine/SubjectCleartkAnalysisEngine.xml  
(with props)
    ctakes/trunk/ctakes-assertion/desc/analysis_engine/UncertaintyCleartkAnalysisEngine.xml
  (with props)

Added: ctakes/trunk/ctakes-assertion/desc/analysis_engine/GenericCleartkAnalysisEngine.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/desc/analysis_engine/GenericCleartkAnalysisEngine.xml?rev=1636916&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/desc/analysis_engine/GenericCleartkAnalysisEngine.xml (added)
+++ ctakes/trunk/ctakes-assertion/desc/analysis_engine/GenericCleartkAnalysisEngine.xml Wed
Nov  5 16:45:48 2014
@@ -0,0 +1,130 @@
+<?xml version="1.0" encoding="UTF-8"?><analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+    <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+    <primitive>true</primitive>
+    <annotatorImplementationName>org.apache.ctakes.assertion.medfacts.cleartk.GenericCleartkAnalysisEngine</annotatorImplementationName>
+    <analysisEngineMetaData>
+        <name>org.apache.ctakes.assertion.medfacts.cleartk.GenericCleartkAnalysisEngine</name>
+        <description>Descriptor automatically generated by uimaFIT</description>
+        <version>unknown</version>
+        <vendor>org.apache.ctakes.assertion.medfacts.cleartk</vendor>
+        <configurationParameters>
+            <configurationParameter>
+                <name>GoldViewName</name>
+                <description>view containing the manual identified annotations (especially
EntityMention and EventMention annotations); needed for training</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>PrintErrors</name>
+                <description>Print errors true/false</description>
+                <type>Boolean</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>ProbabilityOfKeepingADefaultExample</name>
+                <description>probability that a default example should be retained
for training</description>
+                <type>Float</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>PortionOfDataToUse</name>
+                <description>How much data to actually use during training (e.g. for
building learning curves)</description>
+                <type>Float</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>WhetherToDoFeatureSelection</name>
+                <description>the Chi-squared threshold at which features should be
removed</description>
+                <type>Float</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>FEATURE_CONFIG</name>
+                <description>Feature configuration to use (for experiments)</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>FeatureSelectionURI</name>
+                <description>provides a URI where the feature selection data will be
written</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>mapTrainFileToDomain</name>
+                <description>a map of filenames to their respective domains (i.e.,
directories that contain them)</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>classifierFactoryClassName</name>
+                <description>provides the full name of the ClassifierFactory class
to be used.</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>dataWriterFactoryClassName</name>
+                <description>provides the full name of the DataWriterFactory class
to be used.</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>isTraining</name>
+                <description>determines whether this annotator is writing training
data or using a classifier to annotate. Normally inferred automatically based on whether or
not a DataWriterFactory class has been set.</description>
+                <type>Boolean</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>classifierJarPath</name>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+        </configurationParameters>
+        <configurationParameterSettings>
+            <nameValuePair>
+                <name>PrintErrors</name>
+                <value>
+                    <boolean>false</boolean>
+                </value>
+            </nameValuePair>
+            <nameValuePair>
+                <name>classifierFactoryClassName</name>
+                <value>
+                    <string>org.cleartk.ml.jar.JarClassifierFactory</string>
+                </value>
+            </nameValuePair>
+            <nameValuePair>
+                <name>dataWriterFactoryClassName</name>
+                <value>
+                    <string>org.cleartk.ml.jar.DefaultDataWriterFactory</string>
+                </value>
+            </nameValuePair>
+            <nameValuePair>
+                <name>classifierJarPath</name>
+                <value>
+                    <string>org/apache/ctakes/assertion/models/generic/model.jar</string>
+                </value>
+            </nameValuePair>
+        </configurationParameterSettings>
+        <typePriorities/>
+        <fsIndexCollection/>
+        <capabilities/>
+        <operationalProperties>
+            <modifiesCas>true</modifiesCas>
+            <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+            <outputsNewCASes>false</outputsNewCASes>
+        </operationalProperties>
+    </analysisEngineMetaData>
+</analysisEngineDescription>

Propchange: ctakes/trunk/ctakes-assertion/desc/analysis_engine/GenericCleartkAnalysisEngine.xml
------------------------------------------------------------------------------
    svn:eol-style = native

Added: ctakes/trunk/ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml?rev=1636916&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml (added)
+++ ctakes/trunk/ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml Wed
Nov  5 16:45:48 2014
@@ -0,0 +1,130 @@
+<?xml version="1.0" encoding="UTF-8"?><analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+    <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+    <primitive>true</primitive>
+    <annotatorImplementationName>org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine</annotatorImplementationName>
+    <analysisEngineMetaData>
+        <name>org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine</name>
+        <description>Descriptor automatically generated by uimaFIT</description>
+        <version>unknown</version>
+        <vendor>org.apache.ctakes.assertion.medfacts.cleartk</vendor>
+        <configurationParameters>
+            <configurationParameter>
+                <name>GoldViewName</name>
+                <description>view containing the manual identified annotations (especially
EntityMention and EventMention annotations); needed for training</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>PrintErrors</name>
+                <description>Print errors true/false</description>
+                <type>Boolean</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>ProbabilityOfKeepingADefaultExample</name>
+                <description>probability that a default example should be retained
for training</description>
+                <type>Float</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>PortionOfDataToUse</name>
+                <description>How much data to actually use during training (e.g. for
building learning curves)</description>
+                <type>Float</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>WhetherToDoFeatureSelection</name>
+                <description>the Chi-squared threshold at which features should be
removed</description>
+                <type>Float</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>FEATURE_CONFIG</name>
+                <description>Feature configuration to use (for experiments)</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>FeatureSelectionURI</name>
+                <description>provides a URI where the feature selection data will be
written</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>mapTrainFileToDomain</name>
+                <description>a map of filenames to their respective domains (i.e.,
directories that contain them)</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>classifierFactoryClassName</name>
+                <description>provides the full name of the ClassifierFactory class
to be used.</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>dataWriterFactoryClassName</name>
+                <description>provides the full name of the DataWriterFactory class
to be used.</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>isTraining</name>
+                <description>determines whether this annotator is writing training
data or using a classifier to annotate. Normally inferred automatically based on whether or
not a DataWriterFactory class has been set.</description>
+                <type>Boolean</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>classifierJarPath</name>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+        </configurationParameters>
+        <configurationParameterSettings>
+            <nameValuePair>
+                <name>PrintErrors</name>
+                <value>
+                    <boolean>false</boolean>
+                </value>
+            </nameValuePair>
+            <nameValuePair>
+                <name>classifierFactoryClassName</name>
+                <value>
+                    <string>org.cleartk.ml.jar.JarClassifierFactory</string>
+                </value>
+            </nameValuePair>
+            <nameValuePair>
+                <name>dataWriterFactoryClassName</name>
+                <value>
+                    <string>org.cleartk.ml.jar.DefaultDataWriterFactory</string>
+                </value>
+            </nameValuePair>
+            <nameValuePair>
+                <name>classifierJarPath</name>
+                <value>
+                    <string>org/apache/ctakes/assertion/models/historyOf/model.jar</string>
+                </value>
+            </nameValuePair>
+        </configurationParameterSettings>
+        <typePriorities/>
+        <fsIndexCollection/>
+        <capabilities/>
+        <operationalProperties>
+            <modifiesCas>true</modifiesCas>
+            <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+            <outputsNewCASes>false</outputsNewCASes>
+        </operationalProperties>
+    </analysisEngineMetaData>
+</analysisEngineDescription>

Propchange: ctakes/trunk/ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml
------------------------------------------------------------------------------
    svn:eol-style = native

Added: ctakes/trunk/ctakes-assertion/desc/analysis_engine/PolarityCleartkAnalysisEngine.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/desc/analysis_engine/PolarityCleartkAnalysisEngine.xml?rev=1636916&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/desc/analysis_engine/PolarityCleartkAnalysisEngine.xml (added)
+++ ctakes/trunk/ctakes-assertion/desc/analysis_engine/PolarityCleartkAnalysisEngine.xml Wed
Nov  5 16:45:48 2014
@@ -0,0 +1,136 @@
+<?xml version="1.0" encoding="UTF-8"?><analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+    <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+    <primitive>true</primitive>
+    <annotatorImplementationName>org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine</annotatorImplementationName>
+    <analysisEngineMetaData>
+        <name>org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine</name>
+        <description>Descriptor automatically generated by uimaFIT</description>
+        <version>unknown</version>
+        <vendor>org.apache.ctakes.assertion.medfacts.cleartk</vendor>
+        <configurationParameters>
+            <configurationParameter>
+                <name>GoldViewName</name>
+                <description>view containing the manual identified annotations (especially
EntityMention and EventMention annotations); needed for training</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>PrintErrors</name>
+                <description>Print errors true/false</description>
+                <type>Boolean</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>ProbabilityOfKeepingADefaultExample</name>
+                <description>probability that a default example should be retained
for training</description>
+                <type>Float</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>PortionOfDataToUse</name>
+                <description>How much data to actually use during training (e.g. for
building learning curves)</description>
+                <type>Float</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>WhetherToDoFeatureSelection</name>
+                <description>the Chi-squared threshold at which features should be
removed</description>
+                <type>Float</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>FEATURE_CONFIG</name>
+                <description>Feature configuration to use (for experiments)</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>FeatureSelectionURI</name>
+                <description>provides a URI where the feature selection data will be
written</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>mapTrainFileToDomain</name>
+                <description>a map of filenames to their respective domains (i.e.,
directories that contain them)</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>classifierFactoryClassName</name>
+                <description>provides the full name of the ClassifierFactory class
to be used.</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>dataWriterFactoryClassName</name>
+                <description>provides the full name of the DataWriterFactory class
to be used.</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>isTraining</name>
+                <description>determines whether this annotator is writing training
data or using a classifier to annotate. Normally inferred automatically based on whether or
not a DataWriterFactory class has been set.</description>
+                <type>Boolean</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>classifierJarPath</name>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+        </configurationParameters>
+        <configurationParameterSettings>
+            <nameValuePair>
+                <name>PrintErrors</name>
+                <value>
+                    <boolean>false</boolean>
+                </value>
+            </nameValuePair>
+            <nameValuePair>
+                <name>classifierFactoryClassName</name>
+                <value>
+                    <string>org.cleartk.ml.jar.JarClassifierFactory</string>
+                </value>
+            </nameValuePair>
+            <nameValuePair>
+                <name>dataWriterFactoryClassName</name>
+                <value>
+                    <string>org.cleartk.ml.jar.DefaultDataWriterFactory</string>
+                </value>
+            </nameValuePair>
+            <nameValuePair>
+                <name>FEATURE_CONFIG</name>
+                <value>
+                    <string>DEP_REGEX</string>
+                </value>
+            </nameValuePair>
+            <nameValuePair>
+                <name>classifierJarPath</name>
+                <value>
+                    <string>org/apache/ctakes/assertion/models/polarity/sharpi2b2mipacqnegex/model.jar</string>
+                </value>
+            </nameValuePair>
+        </configurationParameterSettings>
+        <typePriorities/>
+        <fsIndexCollection/>
+        <capabilities/>
+        <operationalProperties>
+            <modifiesCas>true</modifiesCas>
+            <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+            <outputsNewCASes>false</outputsNewCASes>
+        </operationalProperties>
+    </analysisEngineMetaData>
+</analysisEngineDescription>

Propchange: ctakes/trunk/ctakes-assertion/desc/analysis_engine/PolarityCleartkAnalysisEngine.xml
------------------------------------------------------------------------------
    svn:eol-style = native

Added: ctakes/trunk/ctakes-assertion/desc/analysis_engine/SubjectCleartkAnalysisEngine.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/desc/analysis_engine/SubjectCleartkAnalysisEngine.xml?rev=1636916&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/desc/analysis_engine/SubjectCleartkAnalysisEngine.xml (added)
+++ ctakes/trunk/ctakes-assertion/desc/analysis_engine/SubjectCleartkAnalysisEngine.xml Wed
Nov  5 16:45:48 2014
@@ -0,0 +1,136 @@
+<?xml version="1.0" encoding="UTF-8"?><analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+    <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+    <primitive>true</primitive>
+    <annotatorImplementationName>org.apache.ctakes.assertion.medfacts.cleartk.SubjectCleartkAnalysisEngine</annotatorImplementationName>
+    <analysisEngineMetaData>
+        <name>org.apache.ctakes.assertion.medfacts.cleartk.SubjectCleartkAnalysisEngine</name>
+        <description>Descriptor automatically generated by uimaFIT</description>
+        <version>unknown</version>
+        <vendor>org.apache.ctakes.assertion.medfacts.cleartk</vendor>
+        <configurationParameters>
+            <configurationParameter>
+                <name>GoldViewName</name>
+                <description>view containing the manual identified annotations (especially
EntityMention and EventMention annotations); needed for training</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>PrintErrors</name>
+                <description>Print errors true/false</description>
+                <type>Boolean</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>ProbabilityOfKeepingADefaultExample</name>
+                <description>probability that a default example should be retained
for training</description>
+                <type>Float</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>PortionOfDataToUse</name>
+                <description>How much data to actually use during training (e.g. for
building learning curves)</description>
+                <type>Float</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>WhetherToDoFeatureSelection</name>
+                <description>the Chi-squared threshold at which features should be
removed</description>
+                <type>Float</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>FEATURE_CONFIG</name>
+                <description>Feature configuration to use (for experiments)</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>FeatureSelectionURI</name>
+                <description>provides a URI where the feature selection data will be
written</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>mapTrainFileToDomain</name>
+                <description>a map of filenames to their respective domains (i.e.,
directories that contain them)</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>classifierFactoryClassName</name>
+                <description>provides the full name of the ClassifierFactory class
to be used.</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>dataWriterFactoryClassName</name>
+                <description>provides the full name of the DataWriterFactory class
to be used.</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>isTraining</name>
+                <description>determines whether this annotator is writing training
data or using a classifier to annotate. Normally inferred automatically based on whether or
not a DataWriterFactory class has been set.</description>
+                <type>Boolean</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>classifierJarPath</name>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+        </configurationParameters>
+        <configurationParameterSettings>
+            <nameValuePair>
+                <name>PrintErrors</name>
+                <value>
+                    <boolean>false</boolean>
+                </value>
+            </nameValuePair>
+            <nameValuePair>
+                <name>classifierFactoryClassName</name>
+                <value>
+                    <string>org.cleartk.ml.jar.JarClassifierFactory</string>
+                </value>
+            </nameValuePair>
+            <nameValuePair>
+                <name>dataWriterFactoryClassName</name>
+                <value>
+                    <string>org.cleartk.ml.jar.DefaultDataWriterFactory</string>
+                </value>
+            </nameValuePair>
+            <nameValuePair>
+                <name>FEATURE_CONFIG</name>
+                <value>
+                    <string>DEP_REGEX</string>
+                </value>
+            </nameValuePair>
+            <nameValuePair>
+                <name>classifierJarPath</name>
+                <value>
+                    <string>org/apache/ctakes/assertion/models/subject/model.jar</string>
+                </value>
+            </nameValuePair>
+        </configurationParameterSettings>
+        <typePriorities/>
+        <fsIndexCollection/>
+        <capabilities/>
+        <operationalProperties>
+            <modifiesCas>true</modifiesCas>
+            <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+            <outputsNewCASes>false</outputsNewCASes>
+        </operationalProperties>
+    </analysisEngineMetaData>
+</analysisEngineDescription>

Propchange: ctakes/trunk/ctakes-assertion/desc/analysis_engine/SubjectCleartkAnalysisEngine.xml
------------------------------------------------------------------------------
    svn:eol-style = native

Added: ctakes/trunk/ctakes-assertion/desc/analysis_engine/UncertaintyCleartkAnalysisEngine.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/desc/analysis_engine/UncertaintyCleartkAnalysisEngine.xml?rev=1636916&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/desc/analysis_engine/UncertaintyCleartkAnalysisEngine.xml
(added)
+++ ctakes/trunk/ctakes-assertion/desc/analysis_engine/UncertaintyCleartkAnalysisEngine.xml
Wed Nov  5 16:45:48 2014
@@ -0,0 +1,136 @@
+<?xml version="1.0" encoding="UTF-8"?><analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+    <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+    <primitive>true</primitive>
+    <annotatorImplementationName>org.apache.ctakes.assertion.medfacts.cleartk.UncertaintyCleartkAnalysisEngine</annotatorImplementationName>
+    <analysisEngineMetaData>
+        <name>org.apache.ctakes.assertion.medfacts.cleartk.UncertaintyCleartkAnalysisEngine</name>
+        <description>Descriptor automatically generated by uimaFIT</description>
+        <version>unknown</version>
+        <vendor>org.apache.ctakes.assertion.medfacts.cleartk</vendor>
+        <configurationParameters>
+            <configurationParameter>
+                <name>GoldViewName</name>
+                <description>view containing the manual identified annotations (especially
EntityMention and EventMention annotations); needed for training</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>PrintErrors</name>
+                <description>Print errors true/false</description>
+                <type>Boolean</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>ProbabilityOfKeepingADefaultExample</name>
+                <description>probability that a default example should be retained
for training</description>
+                <type>Float</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>PortionOfDataToUse</name>
+                <description>How much data to actually use during training (e.g. for
building learning curves)</description>
+                <type>Float</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>WhetherToDoFeatureSelection</name>
+                <description>the Chi-squared threshold at which features should be
removed</description>
+                <type>Float</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>FEATURE_CONFIG</name>
+                <description>Feature configuration to use (for experiments)</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>FeatureSelectionURI</name>
+                <description>provides a URI where the feature selection data will be
written</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>mapTrainFileToDomain</name>
+                <description>a map of filenames to their respective domains (i.e.,
directories that contain them)</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>classifierFactoryClassName</name>
+                <description>provides the full name of the ClassifierFactory class
to be used.</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>dataWriterFactoryClassName</name>
+                <description>provides the full name of the DataWriterFactory class
to be used.</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>isTraining</name>
+                <description>determines whether this annotator is writing training
data or using a classifier to annotate. Normally inferred automatically based on whether or
not a DataWriterFactory class has been set.</description>
+                <type>Boolean</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>classifierJarPath</name>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+        </configurationParameters>
+        <configurationParameterSettings>
+            <nameValuePair>
+                <name>PrintErrors</name>
+                <value>
+                    <boolean>false</boolean>
+                </value>
+            </nameValuePair>
+            <nameValuePair>
+                <name>classifierFactoryClassName</name>
+                <value>
+                    <string>org.cleartk.ml.jar.JarClassifierFactory</string>
+                </value>
+            </nameValuePair>
+            <nameValuePair>
+                <name>dataWriterFactoryClassName</name>
+                <value>
+                    <string>org.cleartk.ml.jar.DefaultDataWriterFactory</string>
+                </value>
+            </nameValuePair>
+            <nameValuePair>
+                <name>FEATURE_CONFIG</name>
+                <value>
+                    <string>DEP_REGEX</string>
+                </value>
+            </nameValuePair>
+            <nameValuePair>
+                <name>classifierJarPath</name>
+                <value>
+                    <string>org/apache/ctakes/assertion/models/uncertainty/model.jar</string>
+                </value>
+            </nameValuePair>
+        </configurationParameterSettings>
+        <typePriorities/>
+        <fsIndexCollection/>
+        <capabilities/>
+        <operationalProperties>
+            <modifiesCas>true</modifiesCas>
+            <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+            <outputsNewCASes>false</outputsNewCASes>
+        </operationalProperties>
+    </analysisEngineMetaData>
+</analysisEngineDescription>

Propchange: ctakes/trunk/ctakes-assertion/desc/analysis_engine/UncertaintyCleartkAnalysisEngine.xml
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