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From james-mas...@apache.org
Subject svn commit: r1517920 - in /ctakes/branches/ctakes-3.1.0: ./ ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/ ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/
Date Tue, 27 Aug 2013 18:52:52 GMT
Author: james-masanz
Date: Tue Aug 27 18:52:51 2013
New Revision: 1517920

URL: http://svn.apache.org/r1517920
Log:
merge r1517867 from trunk into 3.1.0 branch

Modified:
    ctakes/branches/ctakes-3.1.0/   (props changed)
    ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/doc1_07543210_sample_unknown.txt.xml
    ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/doc2_07543210_sample_current.txt.xml
    ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/sample_note.xml
    ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/testpatient_plaintext_1.txt.xml
    ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/text1.txt.xml
    ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/doc1_07543210_sample_unknown.txt.xml
    ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/doc2_07543210_sample_current.txt.xml
    ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/sample_note.xml
    ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/testpatient_plaintext_1.txt.xml
    ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/text1.txt.xml

Propchange: ctakes/branches/ctakes-3.1.0/
------------------------------------------------------------------------------
  Merged /ctakes/trunk:r1517867

Modified: ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/doc1_07543210_sample_unknown.txt.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/doc1_07543210_sample_unknown.txt.xml?rev=1517920&r1=1517919&r2=1517920&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/doc1_07543210_sample_unknown.txt.xml
(original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/doc1_07543210_sample_unknown.txt.xml
Tue Aug 27 18:52:51 2013
@@ -11867,7 +11867,7 @@
     <org.apache.ctakes.typesystem.type.textsem.SignSymptomMention _indexed="1" _id="75459"
_ref_sofa="3" begin="3701" end="3705" id="27" _ref_ontologyConceptArr="75456" typeID="3" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.textsem.SignSymptomMention _indexed="1" _id="75498"
_ref_sofa="3" begin="3817" end="3821" id="29" _ref_ontologyConceptArr="75495" typeID="3" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="-1" uncertainty="0" conditional="false"
generic="false" historyOf="0"/>
     <org.apache.ctakes.typesystem.type.textsem.SignSymptomMention _indexed="1" _id="75537"
_ref_sofa="3" begin="4026" end="4030" id="30" _ref_ontologyConceptArr="75534" typeID="3" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
-    <org.apache.ctakes.typesystem.type.textsem.MedicationEventMention _indexed="1" _id="75574"
_ref_sofa="3" begin="1188" end="1195" id="8" _ref_ontologyConceptArr="75566" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
+    <org.apache.ctakes.typesystem.type.textsem.MedicationMention _indexed="1" _id="75574"
_ref_sofa="3" begin="1188" end="1195" id="8" _ref_ontologyConceptArr="75566" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.textsem.ContextAnnotation _indexed="1" _id="75601"
_ref_sofa="3" begin="2745" end="2747" id="14" typeID="0" segmentID="SIMPLE_SEGMENT" discoveryTechnique="0"
confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false" historyOf="0"
FocusText="10 lb" Scope="RIGHT"/>
     <org.apache.ctakes.typesystem.type.textsem.ContextAnnotation _indexed="1" _id="75620"
_ref_sofa="3" begin="3096" end="3098" id="16" typeID="0" segmentID="SIMPLE_SEGMENT" discoveryTechnique="0"
confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false" historyOf="0"
FocusText="pain" Scope="LEFT"/>
     <org.apache.ctakes.typesystem.type.textsem.ContextAnnotation _indexed="1" _id="75639"
_ref_sofa="3" begin="3129" end="3131" id="18" typeID="0" segmentID="SIMPLE_SEGMENT" discoveryTechnique="0"
confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false" historyOf="0"
FocusText="pain" Scope="LEFT"/>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/doc2_07543210_sample_current.txt.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/doc2_07543210_sample_current.txt.xml?rev=1517920&r1=1517919&r2=1517920&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/doc2_07543210_sample_current.txt.xml
(original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/doc2_07543210_sample_current.txt.xml
Tue Aug 27 18:52:51 2013
@@ -15303,8 +15303,8 @@
     <org.apache.ctakes.typesystem.type.textsem.SignSymptomMention _indexed="1" _id="97260"
_ref_sofa="3" begin="4865" end="4869" id="32" _ref_ontologyConceptArr="97257" typeID="3" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.textsem.SignSymptomMention _indexed="1" _id="97299"
_ref_sofa="3" begin="4981" end="4985" id="34" _ref_ontologyConceptArr="97296" typeID="3" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="-1" uncertainty="0" conditional="false"
generic="false" historyOf="0"/>
     <org.apache.ctakes.typesystem.type.textsem.SignSymptomMention _indexed="1" _id="97338"
_ref_sofa="3" begin="5190" end="5194" id="35" _ref_ontologyConceptArr="97335" typeID="3" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
-    <org.apache.ctakes.typesystem.type.textsem.MedicationEventMention _indexed="1" _id="97375"
_ref_sofa="3" begin="915" end="922" id="7" _ref_ontologyConceptArr="97367" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
-    <org.apache.ctakes.typesystem.type.textsem.MedicationEventMention _indexed="1" _id="97410"
_ref_sofa="3" begin="2307" end="2314" id="13" _ref_ontologyConceptArr="97402" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
+    <org.apache.ctakes.typesystem.type.textsem.MedicationMention _indexed="1" _id="97375"
_ref_sofa="3" begin="915" end="922" id="7" _ref_ontologyConceptArr="97367" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
+    <org.apache.ctakes.typesystem.type.textsem.MedicationMention _indexed="1" _id="97410"
_ref_sofa="3" begin="2307" end="2314" id="13" _ref_ontologyConceptArr="97402" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.textsem.ContextAnnotation _indexed="1" _id="97437"
_ref_sofa="3" begin="3909" end="3911" id="19" typeID="0" segmentID="SIMPLE_SEGMENT" discoveryTechnique="0"
confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false" historyOf="0"
FocusText="10 lb" Scope="RIGHT"/>
     <org.apache.ctakes.typesystem.type.textsem.ContextAnnotation _indexed="1" _id="97456"
_ref_sofa="3" begin="4260" end="4262" id="21" typeID="0" segmentID="SIMPLE_SEGMENT" discoveryTechnique="0"
confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false" historyOf="0"
FocusText="pain" Scope="LEFT"/>
     <org.apache.ctakes.typesystem.type.textsem.ContextAnnotation _indexed="1" _id="97475"
_ref_sofa="3" begin="4293" end="4295" id="23" typeID="0" segmentID="SIMPLE_SEGMENT" discoveryTechnique="0"
confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false" historyOf="0"
FocusText="pain" Scope="LEFT"/>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/sample_note.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/sample_note.xml?rev=1517920&r1=1517919&r2=1517920&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/sample_note.xml
(original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/sample_note.xml
Tue Aug 27 18:52:51 2013
@@ -757,9 +757,9 @@
     <org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation _indexed="1" _id="4843"
_ref_sofa="3" begin="254" end="261"/>
     <org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation _indexed="1" _id="4847"
_ref_sofa="3" begin="262" end="267"/>
     <org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation _indexed="1" _id="4851"
_ref_sofa="3" begin="269" end="282"/>
-    <org.apache.ctakes.typesystem.type.textsem.MedicationEventMention _indexed="1" _id="4863"
_ref_sofa="3" begin="167" end="174" id="0" _ref_ontologyConceptArr="4855" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
-    <org.apache.ctakes.typesystem.type.textsem.MedicationEventMention _indexed="1" _id="4898"
_ref_sofa="3" begin="194" end="203" id="1" _ref_ontologyConceptArr="4890" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
-    <org.apache.ctakes.typesystem.type.textsem.MedicationEventMention _indexed="1" _id="4933"
_ref_sofa="3" begin="254" end="261" id="4" _ref_ontologyConceptArr="4925" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
+    <org.apache.ctakes.typesystem.type.textsem.MedicationMention _indexed="1" _id="4863"
_ref_sofa="3" begin="167" end="174" id="0" _ref_ontologyConceptArr="4855" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
+    <org.apache.ctakes.typesystem.type.textsem.MedicationMention _indexed="1" _id="4898"
_ref_sofa="3" begin="194" end="203" id="1" _ref_ontologyConceptArr="4890" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
+    <org.apache.ctakes.typesystem.type.textsem.MedicationMention _indexed="1" _id="4933"
_ref_sofa="3" begin="254" end="261" id="4" _ref_ontologyConceptArr="4925" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode _indexed="1" _id="5039"
_ref_sofa="3" begin="0" end="10" nodeType="NN" nodeValue="IMPRESSION" leaf="true" _ref_parent="5122"
headIndex="0" index="0" tokenIndex="0"/>
     <org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode _indexed="1" _id="5052"
_ref_sofa="3" begin="10" end="11" nodeType="HYPH" nodeValue="/" leaf="true" _ref_parent="5122"
headIndex="0" index="1" tokenIndex="1"/>
     <org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode _indexed="1" _id="5065"
_ref_sofa="3" begin="11" end="17" nodeType="NN" nodeValue="REPORT" leaf="true" _ref_parent="5122"
headIndex="0" index="2" tokenIndex="2"/>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/testpatient_plaintext_1.txt.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/testpatient_plaintext_1.txt.xml?rev=1517920&r1=1517919&r2=1517920&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/testpatient_plaintext_1.txt.xml
(original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/testpatient_plaintext_1.txt.xml
Tue Aug 27 18:52:51 2013
@@ -1936,7 +1936,7 @@
     <org.apache.ctakes.typesystem.type.textsem.ProcedureMention _indexed="1" _id="12498"
_ref_sofa="3" begin="660" end="682" id="14" _ref_ontologyConceptArr="12495" typeID="5" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.textsem.SignSymptomMention _indexed="1" _id="12535"
_ref_sofa="3" begin="728" end="732" id="17" _ref_ontologyConceptArr="12532" typeID="3" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention _indexed="1" _id="12574"
_ref_sofa="3" begin="723" end="727" id="16" _ref_ontologyConceptArr="12571" typeID="6" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
-    <org.apache.ctakes.typesystem.type.textsem.MedicationEventMention _indexed="1" _id="12602"
_ref_sofa="3" begin="705" end="712" id="15" _ref_ontologyConceptArr="12594" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
+    <org.apache.ctakes.typesystem.type.textsem.MedicationMention _indexed="1" _id="12602"
_ref_sofa="3" begin="705" end="712" id="15" _ref_ontologyConceptArr="12594" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode _indexed="1" _id="12663"
_ref_sofa="3" begin="2" end="5" nodeType="NNP" nodeValue="Dr." leaf="true" _ref_parent="12707"
headIndex="0" index="0" tokenIndex="0"/>
     <org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode _indexed="1" _id="12676"
_ref_sofa="3" begin="6" end="16" nodeType="NNP" nodeValue="Nutritious" leaf="true" _ref_parent="12707"
headIndex="0" index="1" tokenIndex="1"/>
     <org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode _indexed="1" _id="12803"
_ref_sofa="3" begin="20" end="27" nodeType="JJ" nodeValue="Medical" leaf="true" _ref_parent="12903"
headIndex="0" index="0" tokenIndex="0"/>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/text1.txt.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/text1.txt.xml?rev=1517920&r1=1517919&r2=1517920&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/text1.txt.xml
(original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/text1.txt.xml
Tue Aug 27 18:52:51 2013
@@ -219,7 +219,7 @@
     <org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation _indexed="1" _id="1386"
_ref_sofa="3" begin="61" end="68"/>
     <org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation _indexed="1" _id="1390"
_ref_sofa="3" begin="69" end="75"/>
     <org.apache.ctakes.typesystem.type.textsem.SignSymptomMention _indexed="1" _id="1404"
_ref_sofa="3" begin="23" end="27" id="0" _ref_ontologyConceptArr="1401" typeID="3" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
-    <org.apache.ctakes.typesystem.type.textsem.MedicationEventMention _indexed="1" _id="1441"
_ref_sofa="3" begin="61" end="68" id="1" _ref_ontologyConceptArr="1433" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
+    <org.apache.ctakes.typesystem.type.textsem.MedicationMention _indexed="1" _id="1441"
_ref_sofa="3" begin="61" end="68" id="1" _ref_ontologyConceptArr="1433" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode _indexed="1" _id="1607"
_ref_sofa="3" begin="2" end="5" nodeType="DT" nodeValue="The" leaf="true" _ref_parent="1760"
headIndex="0" index="0" tokenIndex="0"/>
     <org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode _indexed="1" _id="1620"
_ref_sofa="3" begin="6" end="13" nodeType="NN" nodeValue="patient" leaf="true" _ref_parent="1760"
headIndex="0" index="1" tokenIndex="1"/>
     <org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode _indexed="1" _id="1633"
_ref_sofa="3" begin="14" end="22" nodeType="VBD" nodeValue="reported" leaf="true" _ref_parent="1777"
headIndex="0" index="2" tokenIndex="2"/>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/doc1_07543210_sample_unknown.txt.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/doc1_07543210_sample_unknown.txt.xml?rev=1517920&r1=1517919&r2=1517920&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/doc1_07543210_sample_unknown.txt.xml
(original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/doc1_07543210_sample_unknown.txt.xml
Tue Aug 27 18:52:51 2013
@@ -11809,7 +11809,7 @@
     <org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation _indexed="1" _id="75281"
_ref_sofa="3" begin="4409" end="4420"/>
     <org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation _indexed="1" _id="75285"
_ref_sofa="3" begin="4421" end="4429"/>
     <org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation _indexed="1" _id="75289"
_ref_sofa="3" begin="4441" end="4444"/>
-    <org.apache.ctakes.typesystem.type.textsem.MedicationEventMention _indexed="1" _id="75301"
_ref_sofa="3" begin="1188" end="1195" id="8" _ref_ontologyConceptArr="75293" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
+    <org.apache.ctakes.typesystem.type.textsem.MedicationMention _indexed="1" _id="75301"
_ref_sofa="3" begin="1188" end="1195" id="8" _ref_ontologyConceptArr="75293" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.textsem.SignSymptomMention _indexed="1" _id="75338"
_ref_sofa="3" begin="3114" end="3118" id="15" _ref_ontologyConceptArr="75335" typeID="3" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.textsem.SignSymptomMention _indexed="1" _id="75377"
_ref_sofa="3" begin="3139" end="3143" id="16" _ref_ontologyConceptArr="75374" typeID="3" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.textsem.SignSymptomMention _indexed="1" _id="75416"
_ref_sofa="3" begin="3483" end="3487" id="20" _ref_ontologyConceptArr="75413" typeID="3" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/doc2_07543210_sample_current.txt.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/doc2_07543210_sample_current.txt.xml?rev=1517920&r1=1517919&r2=1517920&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/doc2_07543210_sample_current.txt.xml
(original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/doc2_07543210_sample_current.txt.xml
Tue Aug 27 18:52:51 2013
@@ -15229,8 +15229,8 @@
     <org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation _indexed="1" _id="97082"
_ref_sofa="3" begin="5573" end="5584"/>
     <org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation _indexed="1" _id="97086"
_ref_sofa="3" begin="5585" end="5593"/>
     <org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation _indexed="1" _id="97090"
_ref_sofa="3" begin="5605" end="5608"/>
-    <org.apache.ctakes.typesystem.type.textsem.MedicationEventMention _indexed="1" _id="97102"
_ref_sofa="3" begin="915" end="922" id="7" _ref_ontologyConceptArr="97094" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
-    <org.apache.ctakes.typesystem.type.textsem.MedicationEventMention _indexed="1" _id="97137"
_ref_sofa="3" begin="2307" end="2314" id="13" _ref_ontologyConceptArr="97129" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
+    <org.apache.ctakes.typesystem.type.textsem.MedicationMention _indexed="1" _id="97102"
_ref_sofa="3" begin="915" end="922" id="7" _ref_ontologyConceptArr="97094" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
+    <org.apache.ctakes.typesystem.type.textsem.MedicationMention _indexed="1" _id="97137"
_ref_sofa="3" begin="2307" end="2314" id="13" _ref_ontologyConceptArr="97129" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.textsem.SignSymptomMention _indexed="1" _id="97174"
_ref_sofa="3" begin="4278" end="4282" id="20" _ref_ontologyConceptArr="97171" typeID="3" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.textsem.SignSymptomMention _indexed="1" _id="97213"
_ref_sofa="3" begin="4303" end="4307" id="21" _ref_ontologyConceptArr="97210" typeID="3" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.textsem.SignSymptomMention _indexed="1" _id="97252"
_ref_sofa="3" begin="4647" end="4651" id="25" _ref_ontologyConceptArr="97249" typeID="3" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/sample_note.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/sample_note.xml?rev=1517920&r1=1517919&r2=1517920&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/sample_note.xml
(original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/sample_note.xml
Tue Aug 27 18:52:51 2013
@@ -751,9 +751,9 @@
     <org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation _indexed="1" _id="4839"
_ref_sofa="3" begin="247" end="252"/>
     <org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation _indexed="1" _id="4843"
_ref_sofa="3" begin="254" end="267"/>
     <org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation _indexed="1" _id="4851"
_ref_sofa="3" begin="269" end="282"/>
-    <org.apache.ctakes.typesystem.type.textsem.MedicationEventMention _indexed="1" _id="4863"
_ref_sofa="3" begin="167" end="174" id="0" _ref_ontologyConceptArr="4855" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
-    <org.apache.ctakes.typesystem.type.textsem.MedicationEventMention _indexed="1" _id="4898"
_ref_sofa="3" begin="194" end="203" id="1" _ref_ontologyConceptArr="4890" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
-    <org.apache.ctakes.typesystem.type.textsem.MedicationEventMention _indexed="1" _id="4933"
_ref_sofa="3" begin="254" end="261" id="4" _ref_ontologyConceptArr="4925" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
+    <org.apache.ctakes.typesystem.type.textsem.MedicationMention _indexed="1" _id="4863"
_ref_sofa="3" begin="167" end="174" id="0" _ref_ontologyConceptArr="4855" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
+    <org.apache.ctakes.typesystem.type.textsem.MedicationMention _indexed="1" _id="4898"
_ref_sofa="3" begin="194" end="203" id="1" _ref_ontologyConceptArr="4890" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
+    <org.apache.ctakes.typesystem.type.textsem.MedicationMention _indexed="1" _id="4933"
_ref_sofa="3" begin="254" end="261" id="4" _ref_ontologyConceptArr="4925" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.refsem.OntologyConcept _id="4928" codingScheme="RXNORM"
code="C6666666" oid="C6666666#RXNORM"/>
     <uima.cas.FSArray _id="4925" size="1">
         <i>4928</i>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/testpatient_plaintext_1.txt.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/testpatient_plaintext_1.txt.xml?rev=1517920&r1=1517919&r2=1517920&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/testpatient_plaintext_1.txt.xml
(original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/testpatient_plaintext_1.txt.xml
Tue Aug 27 18:52:51 2013
@@ -1923,7 +1923,7 @@
     <org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation _indexed="1" _id="12424"
_ref_sofa="3" begin="692" end="695"/>
     <org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation _indexed="1" _id="12428"
_ref_sofa="3" begin="702" end="718"/>
     <org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation _indexed="1" _id="12432"
_ref_sofa="3" begin="713" end="732"/>
-    <org.apache.ctakes.typesystem.type.textsem.MedicationEventMention _indexed="1" _id="12448"
_ref_sofa="3" begin="705" end="712" id="15" _ref_ontologyConceptArr="12440" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
+    <org.apache.ctakes.typesystem.type.textsem.MedicationMention _indexed="1" _id="12448"
_ref_sofa="3" begin="705" end="712" id="15" _ref_ontologyConceptArr="12440" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention _indexed="1" _id="12493"
_ref_sofa="3" begin="50" end="64" id="0" _ref_ontologyConceptArr="12489" typeID="2" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.textsem.ProcedureMention _indexed="1" _id="12533"
_ref_sofa="3" begin="660" end="682" id="14" _ref_ontologyConceptArr="12530" typeID="5" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.textsem.SignSymptomMention _indexed="1" _id="12570"
_ref_sofa="3" begin="728" end="732" id="17" _ref_ontologyConceptArr="12567" typeID="3" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/text1.txt.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/text1.txt.xml?rev=1517920&r1=1517919&r2=1517920&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/text1.txt.xml
(original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/text1.txt.xml
Tue Aug 27 18:52:51 2013
@@ -216,7 +216,7 @@
     <org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation _indexed="1" _id="1374"
_ref_sofa="3" begin="23" end="44"/>
     <org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation _indexed="1" _id="1382"
_ref_sofa="3" begin="47" end="58"/>
     <org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation _indexed="1" _id="1386"
_ref_sofa="3" begin="61" end="75"/>
-    <org.apache.ctakes.typesystem.type.textsem.MedicationEventMention _indexed="1" _id="1402"
_ref_sofa="3" begin="61" end="68" id="1" _ref_ontologyConceptArr="1394" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
+    <org.apache.ctakes.typesystem.type.textsem.MedicationMention _indexed="1" _id="1402"
_ref_sofa="3" begin="61" end="68" id="1" _ref_ontologyConceptArr="1394" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.textsem.SignSymptomMention _indexed="1" _id="1439"
_ref_sofa="3" begin="23" end="27" id="0" _ref_ontologyConceptArr="1436" typeID="3" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" conditional="false" generic="false"
historyOf="0"/>
     <org.apache.ctakes.typesystem.type.refsem.UmlsConcept _id="1429" codingScheme="SNOMED"
code="100206" oid="100206#SNOMED" cui="Cui0206" tui="T_SS"/>
     <uima.cas.FSArray _id="1436" size="1">



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