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From vjapa...@apache.org
Subject svn commit: r1551254 [3/26] - in /ctakes/branches/ytex: ctakes-ytex-res/ ctakes-ytex-res/.settings/ ctakes-ytex-res/src/ ctakes-ytex-res/src/main/ ctakes-ytex-res/src/main/resources/ ctakes-ytex-res/src/main/resources/org/ ctakes-ytex-res/src/main/reso...
Date Mon, 16 Dec 2013 16:30:40 GMT
Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE beans PUBLIC "-//SPRING//DTD BEAN//EN" "http://www.springframework.org/dtd/spring-beans.dtd">
+
+<beans>
+	<bean name="kernelApplicationContext"
+		class="org.springframework.context.support.ClassPathXmlApplicationContext">
+		<constructor-arg>
+			<list>
+				<value>org/apache/ctakes/ytex/beans-datasource.xml</value>
+				<value>org/apache/ctakes/ytex/beans-kernel.hbm.xml</value>
+				<value>org/apache/ctakes/ytex/beans-kernel.xml</value>
+			</list>
+		</constructor-arg>
+	</bean>
+</beans>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/negex/negex_triggers.txt
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/negex/negex_triggers.txt?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/negex/negex_triggers.txt (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/negex/negex_triggers.txt Mon Dec 16 16:30:30 2013
@@ -0,0 +1,277 @@
+no increase		[PSEU]
+no suspicious change		[PSEU]
+no significant change		[PSEU]
+no change		[PSEU]
+no interval change		[PSEU]
+no definite change		[PSEU]
+no significant interval change		[PSEU]
+not extend		[PSEU]
+not cause		[PSEU]
+not drain		[PSEU]
+not certain if		[PSEU]
+not certain whether		[PSEU]
+gram negative		[PSEU]
+without difficulty		[PSEU]
+not necessarily		[PSEU]
+not only		[PSEU]
+no other	[PSEU]
+absence of		[PREN]
+cannot		[PREN]
+cannot see		[PREN]
+checked for		[PREN]
+declined		[PREN]
+declines		[PREN]
+denied		[PREN]
+denies		[PREN]
+denying		[PREN]
+evaluate for		[PREN]
+fails to reveal		[PREN]
+free of		[PREN]
+negative for		[PREN]
+never developed		[PREN]
+never had		[PREN]
+no		[PREN]
+no abnormal		[PREN]
+no cause of		[PREN]
+no complaints of		[PREN]
+no evidence		[PREN]
+no new evidence		[PREN]
+no other evidence		[PREN]
+no evidence to suggest		[PREN]
+no findings of		[PREN]
+no findings to indicate		[PREN]
+no mammographic evidence of		[PREN]
+no new		[PREN]
+no radiographic evidence of		[PREN]
+no sign of		[PREN]
+no significant		[PREN]
+no signs of		[PREN]
+no suggestion of		[PREN]
+no suspicious		[PREN]
+not		[PREN]
+not appear		[PREN]
+not appreciate		[PREN]
+not associated with		[PREN]
+not complain of		[PREN]
+not demonstrate		[PREN]
+not exhibit		[PREN]
+not feel		[PREN]
+not had		[PREN]
+not have		[PREN]
+not know of		[PREN]
+not known to have		[PREN]
+not reveal		[PREN]
+not see		[PREN]
+not to be		[PREN]
+patient was not		[PREN]
+rather than		[PREN]
+resolved		[PREN]
+test for		[PREN]
+to exclude		[PREN]
+unremarkable for		[PREN]
+with no		[PREN]
+without		[PREN]
+without any evidence of		[PREN]
+without evidence		[PREN]
+without indication of		[PREN]
+without sign of		[PREN]
+rules out		[PREN]
+rules him out		[PREN]
+rules her out		[PREN]
+rules the patient out		[PREN]
+rules out for		[PREN]
+rules him out for		[PREN]
+rules her out for		[PREN]
+rules the patient out for		[PREN]
+ruled out		[PREN]
+ruled him out		[PREN]
+ruled her out		[PREN]
+ruled the patient out		[PREN]
+ruled out for		[PREN]
+ruled him out for		[PREN]
+ruled her out for		[PREN]
+ruled the patient out for		[PREN]
+ruled out against		[PREN]
+ruled him out against		[PREN]
+ruled her out against		[PREN]
+ruled the patient out against		[PREN]
+did rule out		[PREN]
+did rule out for		[PREN]
+did rule out against		[PREN]
+did rule him out		[PREN]
+did rule her out		[PREN]
+did rule the patient out		[PREN]
+did rule him out for		[PREN]
+did rule her out for		[PREN]
+did rule him out against		[PREN]
+did rule her out against		[PREN]
+did rule the patient out for		[PREN]
+did rule the patient out against		[PREN]
+can rule out		[PREN]
+can rule out for		[PREN]
+can rule out against		[PREN]
+can rule him out		[PREN]
+can rule her out		[PREN]
+can rule the patient out		[PREN]
+can rule him out for		[PREN]
+can rule her out for		[PREN]
+can rule the patinet out for		[PREN]
+can rule him out against		[PREN]
+can rule her out against		[PREN]
+can rule the patinet out against		[PREN]
+adequate to rule out		[PREN]
+adequate to rule him out		[PREN]
+adequate to rule her out		[PREN]
+adequate to rule the patient out		[PREN]
+adequate to rule out for		[PREN]
+adequate to rule him out for		[PREN]
+adequate to rule her out for		[PREN]
+adequate to rule the patient out for		[PREN]
+adequate to rule the patient out against		[PREN]
+sufficient to rule out		[PREN]
+sufficient to rule him out		[PREN]
+sufficient to rule her out		[PREN]
+sufficient to rule the patient out		[PREN]
+sufficient to rule out for		[PREN]
+sufficient to rule him out for		[PREN]
+sufficient to rule her out for		[PREN]
+sufficient to rule the patient out for		[PREN]
+sufficient to rule out against		[PREN]
+sufficient to rule him out against		[PREN]
+sufficient to rule her out against		[PREN]
+sufficient to rule the patient out against		[PREN]
+resolution of	[PREN]
+rule out		[PREP]
+r/o		[PREP]
+ro		[PREP]
+rule him out		[PREP]
+rule her out		[PREP]
+rule the patient out		[PREP]
+rule out for		[PREP]
+rule him out for		[PREP]
+rule her out for		[PREP]
+rule the patinet out for		[PREP]
+be ruled out for		[PREP]
+should be ruled out for		[PREP]
+ought to be ruled out for		[PREP]
+may be ruled out for		[PREP]
+might be ruled out for		[PREP]
+could be ruled out for		[PREP]
+will be ruled out for		[PREP]
+can be ruled out for		[PREP]
+must be ruled out for		[PREP]
+is to be ruled out for		[PREP]
+what must be ruled out is		[PREP]
+suggestive of	[PREP]
+unlikely		[POST]
+free		[POST]
+was ruled out		[POST]
+is ruled out		[POST]
+are ruled out		[POST]
+have been ruled out		[POST]
+has been ruled out		[POST]
+is not demonstrated	[POST]
+have resolved	[POST]
+did not rule out		[POSP]
+not ruled out		[POSP]
+not been ruled out		[POSP]
+being ruled out		[POSP]
+be ruled out		[POSP]
+should be ruled out		[POSP]
+ought to be ruled out		[POSP]
+may be ruled out		[POSP]
+might be ruled out		[POSP]
+could be ruled out		[POSP]
+will be ruled out		[POSP]
+can be ruled out		[POSP]
+must be ruled out		[POSP]
+is to be ruled out		[POSP]
+but		[CONJ]
+however		[CONJ]
+nevertheless		[CONJ]
+yet		[CONJ]
+though		[CONJ]
+although		[CONJ]
+still		[CONJ]
+aside from		[CONJ]
+except		[CONJ]
+apart from		[CONJ]
+secondary to		[CONJ]
+as the cause of		[CONJ]
+as the source of		[CONJ]
+as the reason of		[CONJ]
+as the etiology of		[CONJ]
+as the origin of		[CONJ]
+as the cause for		[CONJ]
+as the source for		[CONJ]
+as the reason for		[CONJ]
+as the etiology for		[CONJ]
+as the origin for		[CONJ]
+as the secondary cause of		[CONJ]
+as the secondary source of		[CONJ]
+as the secondary reason of		[CONJ]
+as the secondary etiology of		[CONJ]
+as the secondary origin of		[CONJ]
+as the secondary cause for		[CONJ]
+as the secondary source for		[CONJ]
+as the secondary reason for		[CONJ]
+as the secondary etiology for		[CONJ]
+as the secondary origin for		[CONJ]
+as a cause of		[CONJ]
+as a source of		[CONJ]
+as a reason of		[CONJ]
+as a etiology of		[CONJ]
+as a cause for		[CONJ]
+as a source for		[CONJ]
+as a reason for		[CONJ]
+as a etiology for		[CONJ]
+as a secondary cause of		[CONJ]
+as a secondary source of		[CONJ]
+as a secondary reason of		[CONJ]
+as a secondary etiology of		[CONJ]
+as a secondary origin of		[CONJ]
+as a secondary cause for		[CONJ]
+as a secondary source for		[CONJ]
+as a secondary reason for		[CONJ]
+as a secondary etiology for		[CONJ]
+as a secondary origin for		[CONJ]
+as an cause of		[CONJ]
+as an source of		[CONJ]
+as an reason of		[CONJ]
+as an etiology of		[CONJ]
+as an origin of		[CONJ]
+as an cause for		[CONJ]
+as an source for		[CONJ]
+as an reason for		[CONJ]
+as an etiology for		[CONJ]
+as an origin for		[CONJ]
+as an secondary cause of		[CONJ]
+as an secondary source of		[CONJ]
+as an secondary reason of		[CONJ]
+as an secondary etiology of		[CONJ]
+as an secondary origin of		[CONJ]
+as an secondary cause for		[CONJ]
+as an secondary source for		[CONJ]
+as an secondary reason for		[CONJ]
+as an secondary etiology for		[CONJ]
+as an secondary origin for		[CONJ]
+cause of		[CONJ]
+cause for		[CONJ]
+causes of		[CONJ]
+causes for		[CONJ]
+source of		[CONJ]
+source for		[CONJ]
+sources of		[CONJ]
+sources for		[CONJ]
+reason of		[CONJ]
+reason for		[CONJ]
+reasons of		[CONJ]
+reasons for		[CONJ]
+etiology of		[CONJ]
+etiology for		[CONJ]
+trigger event for		[CONJ]
+origin of		[CONJ]
+origin for		[CONJ]
+origins of		[CONJ]
+origins for		[CONJ]
+other possibilities of		[CONJ]

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/negex/negex_triggers_orig.txt
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/negex/negex_triggers_orig.txt?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/negex/negex_triggers_orig.txt (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/negex/negex_triggers_orig.txt Mon Dec 16 16:30:30 2013
@@ -0,0 +1,272 @@
+no increase		[PSEU]
+no suspicious change		[PSEU]
+no significant change		[PSEU]
+no change		[PSEU]
+no interval change		[PSEU]
+no definite change		[PSEU]
+no significant interval change		[PSEU]
+not extend		[PSEU]
+not cause		[PSEU]
+not drain		[PSEU]
+not certain if		[PSEU]
+not certain whether		[PSEU]
+gram negative		[PSEU]
+without difficulty		[PSEU]
+not necessarily		[PSEU]
+not only		[PSEU]
+absence of		[PREN]
+cannot		[PREN]
+cannot see		[PREN]
+checked for		[PREN]
+declined		[PREN]
+declines		[PREN]
+denied		[PREN]
+denies		[PREN]
+denying		[PREN]
+evaluate for		[PREN]
+fails to reveal		[PREN]
+free of		[PREN]
+negative for		[PREN]
+never developed		[PREN]
+never had		[PREN]
+no		[PREN]
+no abnormal		[PREN]
+no cause of		[PREN]
+no complaints of		[PREN]
+no evidence		[PREN]
+no new evidence		[PREN]
+no other evidence		[PREN]
+no evidence to suggest		[PREN]
+no findings of		[PREN]
+no findings to indicate		[PREN]
+no mammographic evidence of		[PREN]
+no new		[PREN]
+no radiographic evidence of		[PREN]
+no sign of		[PREN]
+no significant		[PREN]
+no signs of		[PREN]
+no suggestion of		[PREN]
+no suspicious		[PREN]
+not		[PREN]
+not appear		[PREN]
+not appreciate		[PREN]
+not associated with		[PREN]
+not complain of		[PREN]
+not demonstrate		[PREN]
+not exhibit		[PREN]
+not feel		[PREN]
+not had		[PREN]
+not have		[PREN]
+not know of		[PREN]
+not known to have		[PREN]
+not reveal		[PREN]
+not see		[PREN]
+not to be		[PREN]
+patient was not		[PREN]
+rather than		[PREN]
+resolved		[PREN]
+test for		[PREN]
+to exclude		[PREN]
+unremarkable for		[PREN]
+with no		[PREN]
+without		[PREN]
+without any evidence of		[PREN]
+without evidence		[PREN]
+without indication of		[PREN]
+without sign of		[PREN]
+rules out		[PREN]
+rules him out		[PREN]
+rules her out		[PREN]
+rules the patient out		[PREN]
+rules out for		[PREN]
+rules him out for		[PREN]
+rules her out for		[PREN]
+rules the patient out for		[PREN]
+ruled out		[PREN]
+ruled him out		[PREN]
+ruled her out		[PREN]
+ruled the patient out		[PREN]
+ruled out for		[PREN]
+ruled him out for		[PREN]
+ruled her out for		[PREN]
+ruled the patient out for		[PREN]
+ruled out against		[PREN]
+ruled him out against		[PREN]
+ruled her out against		[PREN]
+ruled the patient out against		[PREN]
+did rule out		[PREN]
+did rule out for		[PREN]
+did rule out against		[PREN]
+did rule him out		[PREN]
+did rule her out		[PREN]
+did rule the patient out		[PREN]
+did rule him out for		[PREN]
+did rule her out for		[PREN]
+did rule him out against		[PREN]
+did rule her out against		[PREN]
+did rule the patient out for		[PREN]
+did rule the patient out against		[PREN]
+can rule out		[PREN]
+can rule out for		[PREN]
+can rule out against		[PREN]
+can rule him out		[PREN]
+can rule her out		[PREN]
+can rule the patient out		[PREN]
+can rule him out for		[PREN]
+can rule her out for		[PREN]
+can rule the patinet out for		[PREN]
+can rule him out against		[PREN]
+can rule her out against		[PREN]
+can rule the patinet out against		[PREN]
+adequate to rule out		[PREN]
+adequate to rule him out		[PREN]
+adequate to rule her out		[PREN]
+adequate to rule the patient out		[PREN]
+adequate to rule out for		[PREN]
+adequate to rule him out for		[PREN]
+adequate to rule her out for		[PREN]
+adequate to rule the patient out for		[PREN]
+adequate to rule the patient out against		[PREN]
+sufficient to rule out		[PREN]
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+sufficient to rule her out		[PREN]
+sufficient to rule the patient out		[PREN]
+sufficient to rule out for		[PREN]
+sufficient to rule him out for		[PREN]
+sufficient to rule her out for		[PREN]
+sufficient to rule the patient out for		[PREN]
+sufficient to rule out against		[PREN]
+sufficient to rule him out against		[PREN]
+sufficient to rule her out against		[PREN]
+sufficient to rule the patient out against		[PREN]
+rule out		[PREP]
+r/o		[PREP]
+ro		[PREP]
+rule him out		[PREP]
+rule her out		[PREP]
+rule the patient out		[PREP]
+rule out for		[PREP]
+rule him out for		[PREP]
+rule her out for		[PREP]
+rule the patinet out for		[PREP]
+be ruled out for		[PREP]
+should be ruled out for		[PREP]
+ought to be ruled out for		[PREP]
+may be ruled out for		[PREP]
+might be ruled out for		[PREP]
+could be ruled out for		[PREP]
+will be ruled out for		[PREP]
+can be ruled out for		[PREP]
+must be ruled out for		[PREP]
+is to be ruled out for		[PREP]
+what must be ruled out is		[PREP]
+unlikely		[POST]
+free		[POST]
+was ruled out		[POST]
+is ruled out		[POST]
+are ruled out		[POST]
+have been ruled out		[POST]
+has been ruled out		[POST]
+did not rule out		[POSP]
+not ruled out		[POSP]
+not been ruled out		[POSP]
+being ruled out		[POSP]
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+ought to be ruled out		[POSP]
+may be ruled out		[POSP]
+might be ruled out		[POSP]
+could be ruled out		[POSP]
+will be ruled out		[POSP]
+can be ruled out		[POSP]
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+is to be ruled out		[POSP]
+but		[CONJ]
+however		[CONJ]
+nevertheless		[CONJ]
+yet		[CONJ]
+though		[CONJ]
+although		[CONJ]
+still		[CONJ]
+aside from		[CONJ]
+except		[CONJ]
+apart from		[CONJ]
+secondary to		[CONJ]
+as the cause of		[CONJ]
+as the source of		[CONJ]
+as the reason of		[CONJ]
+as the etiology of		[CONJ]
+as the origin of		[CONJ]
+as the cause for		[CONJ]
+as the source for		[CONJ]
+as the reason for		[CONJ]
+as the etiology for		[CONJ]
+as the origin for		[CONJ]
+as the secondary cause of		[CONJ]
+as the secondary source of		[CONJ]
+as the secondary reason of		[CONJ]
+as the secondary etiology of		[CONJ]
+as the secondary origin of		[CONJ]
+as the secondary cause for		[CONJ]
+as the secondary source for		[CONJ]
+as the secondary reason for		[CONJ]
+as the secondary etiology for		[CONJ]
+as the secondary origin for		[CONJ]
+as a cause of		[CONJ]
+as a source of		[CONJ]
+as a reason of		[CONJ]
+as a etiology of		[CONJ]
+as a cause for		[CONJ]
+as a source for		[CONJ]
+as a reason for		[CONJ]
+as a etiology for		[CONJ]
+as a secondary cause of		[CONJ]
+as a secondary source of		[CONJ]
+as a secondary reason of		[CONJ]
+as a secondary etiology of		[CONJ]
+as a secondary origin of		[CONJ]
+as a secondary cause for		[CONJ]
+as a secondary source for		[CONJ]
+as a secondary reason for		[CONJ]
+as a secondary etiology for		[CONJ]
+as a secondary origin for		[CONJ]
+as an cause of		[CONJ]
+as an source of		[CONJ]
+as an reason of		[CONJ]
+as an etiology of		[CONJ]
+as an origin of		[CONJ]
+as an cause for		[CONJ]
+as an source for		[CONJ]
+as an reason for		[CONJ]
+as an etiology for		[CONJ]
+as an origin for		[CONJ]
+as an secondary cause of		[CONJ]
+as an secondary source of		[CONJ]
+as an secondary reason of		[CONJ]
+as an secondary etiology of		[CONJ]
+as an secondary origin of		[CONJ]
+as an secondary cause for		[CONJ]
+as an secondary source for		[CONJ]
+as an secondary reason for		[CONJ]
+as an secondary etiology for		[CONJ]
+as an secondary origin for		[CONJ]
+cause of		[CONJ]
+cause for		[CONJ]
+causes of		[CONJ]
+causes for		[CONJ]
+source of		[CONJ]
+source for		[CONJ]
+sources of		[CONJ]
+sources for		[CONJ]
+reason of		[CONJ]
+reason for		[CONJ]
+reasons of		[CONJ]
+reasons for		[CONJ]
+etiology of		[CONJ]
+etiology for		[CONJ]
+trigger event for		[CONJ]
+origin of		[CONJ]
+origin for		[CONJ]
+origins of		[CONJ]
+origins for		[CONJ]
+other possibilities of		[CONJ]

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/simSvcBeanRefContext.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/simSvcBeanRefContext.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/simSvcBeanRefContext.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/simSvcBeanRefContext.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE beans PUBLIC "-//SPRING//DTD BEAN//EN" "http://www.springframework.org/dtd/spring-beans.dtd">
+
+<beans>
+	<bean name="kernelApplicationContext"
+		class="org.springframework.context.support.ClassPathXmlApplicationContext">
+		<constructor-arg>
+			<list>
+				<value>org/apache/ctakes/ytex/beans-datasource.xml</value>
+				<value>org/apache/ctakes/ytex/beans-kernel.hbm.xml</value>
+				<value>org/apache/ctakes/ytex/beans-kernel.xml</value>
+				<value>org/apache/ctakes/ytex/beans-kernel-sim.xml</value>
+			</list>
+		</constructor-arg>
+	</bean>
+</beans>
\ No newline at end of file

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Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE beans PUBLIC "-//SPRING//DTD BEAN//EN" "http://www.springframework.org/dtd/spring-beans.dtd">
+
+<beans>
+	<bean name="ytexApplicationContext"
+		class="org.springframework.context.support.ClassPathXmlApplicationContext">
+		<constructor-arg>
+			<list>
+				<value>org/apache/ctakes/ytex/beans-datasource.xml</value>
+				<value>org/apache/ctakes/ytex/beans-kernel.xml</value>
+				<value>org/apache/ctakes/ytex/beans-kernel-sim.xml</value>
+				<value>org/apache/ctakes/ytex/uima/beans-uima.hbm.xml</value>
+				<value>org/apache/ctakes/ytex/uima/beans-uima-dao.xml</value>
+				<value>org/apache/ctakes/ytex/uima/beans-uima-mapper.xml</value>
+			</list>
+		</constructor-arg>
+	</bean>
+</beans>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-dao.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-dao.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-dao.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-dao.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:aop="http://www.springframework.org/schema/aop"
+	xmlns:tx="http://www.springframework.org/schema/tx"
+	xsi:schemaLocation="
+http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
+http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx-2.5.xsd
+http://www.springframework.org/schema/aop http://www.springframework.org/schema/aop/spring-aop-2.5.xsd">
+
+	<alias name="dataSource" alias="collectionReaderDataSource" />
+	<!-- ensure that the above transactional advice runs for any execution of 
+		an operation defined by the FooService interface -->
+	<aop:config>
+		<aop:pointcut id="ytexDaoOperation" expression="execution(* org.apache.ctakes.ytex.uima.dao.*Dao.*(..))" />
+		<aop:advisor advice-ref="txAdvice" pointcut-ref="ytexDaoOperation" />
+	</aop:config>
+
+	<bean id="documentDao" class="org.apache.ctakes.ytex.uima.dao.DocumentDaoImpl">
+		<property name="sessionFactory" ref="sessionFactory" />
+	</bean>
+	<bean id="namedEntityRegexDao" class="org.apache.ctakes.ytex.uima.dao.NamedEntityRegexDaoImpl">
+		<property name="sessionFactory" ref="sessionFactory" />
+	</bean>
+	<bean id="segmentRegexDao" class="org.apache.ctakes.ytex.uima.dao.SegmentRegexDaoImpl">
+		<property name="sessionFactory" ref="sessionFactory" />
+	</bean>
+
+</beans>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-mapper.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-mapper.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-mapper.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-mapper.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,122 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- spring bean in org.apache.ctakes.ytex.uima -->
+<beans xmlns="http://www.springframework.org/schema/beans"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:aop="http://www.springframework.org/schema/aop"
+	xmlns:tx="http://www.springframework.org/schema/tx"
+	xsi:schemaLocation="
+http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
+http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx-2.5.xsd
+http://www.springframework.org/schema/aop http://www.springframework.org/schema/aop/spring-aop-2.5.xsd">
+	<!-- ensure that the above transactional advice runs for any execution of 
+		an operation defined by the FooService interface -->
+	<aop:config>
+		<aop:pointcut id="mapperOperation" expression="execution(* org.apache.ctakes.ytex.uima.mapper.*.*(..))" />
+		<aop:advisor advice-ref="txAdvice" pointcut-ref="mapperOperation" />
+	</aop:config>
+	<bean id="ISO8601Converter" class="org.apache.ctakes.ytex.uima.mapper.ISO8601Converter"></bean>
+
+	<bean id="documentMapperService" class="org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl">
+		<property name="sessionFactory" ref="sessionFactory" />
+		<property name="transactionManager" ref="transactionManager" />
+		<property name="dataSource" ref="dataSource" />
+		<property name="dialectClassName" value="${hibernate.dialect}" />
+		<property name="dbSchema" value="${db.schema}" />
+		<property name="dbType" value="${db.type}" />
+		<property name="batchSize" value="${hibernate.jdbc.batch_size}" />
+		<property name="annoMappingInfos">
+			<set>
+				<bean class="org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo">
+					<property name="annoClassName" value="org.apache.ctakes.ytex.uima.types.Date" />
+					<property name="tableName" value="anno_date" />
+					<property name="columnMappingInfos">
+						<set>
+							<bean class="org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo">
+								<property name="annoFieldName" value="date" />
+								<property name="columnName" value="TSTAMP" />
+								<property name="converter" ref="ISO8601Converter" />
+								<property name="targetTypeName" value="java.sql.Timestamp" />
+							</bean>
+						</set>
+					</property>
+				</bean>
+				<bean class="org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo">
+					<property name="annoClassName"
+						value="org.mipacq.annotation.type.CoreferenceRelation" />
+					<property name="tableName" value="anno_link" />
+					<property name="columnMappingInfos">
+						<set>
+							<bean class="org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo">
+								<property name="annoFieldName" value="arg1" />
+								<property name="columnName" value="parent_anno_base_id" />
+								<property name="jxpath" value="argument/content" />
+							</bean>
+							<bean class="org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo">
+								<property name="annoFieldName" value="arg2" />
+								<property name="columnName" value="child_anno_base_id" />
+								<property name="jxpath" value="argument/content" />
+							</bean>
+						</set>
+					</property>
+				</bean>
+				<bean class="org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo">
+					<property name="annoClassName"
+						value="edu.mayo.bmi.uima.coref.type.MarkablePairSet" />
+					<property name="tableName" value="anno_link" />
+					<property name="columnMappingInfos">
+						<set>
+							<bean class="org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo">
+								<property name="annoFieldName" value="anaphor" />
+								<property name="columnName" value="parent_anno_base_id" />
+								<property name="jxpath" value="content" />
+							</bean>
+							<bean class="org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo">
+								<property name="annoFieldName" value="antecedentList" />
+								<property name="columnName" value="child_anno_base_id" />
+								<property name="jxpath" value="feature" />
+							</bean>
+						</set>
+					</property>
+				</bean>
+				<bean class="org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo">
+					<property name="annoClassName"
+						value="edu.mayo.bmi.uima.core.type.textsem.MedicationEventMention" />
+					<property name="tableName" value="anno_med_event" />
+					<property name="columnMappingInfos">
+						<set>
+							<bean class="org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo">
+								<property name="annoFieldName" value="medicationFrequency" />
+								<property name="columnName" value="freqNumber" />
+								<property name="jxpath" value="number" />
+							</bean>
+							<bean class="org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo">
+								<property name="annoFieldName" value="medicationFrequency" />
+								<property name="columnName" value="freqUnit" />
+								<property name="jxpath" value="unit" />
+							</bean>
+							<bean class="org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo">
+								<property name="annoFieldName" value="medicationStrength" />
+								<property name="columnName" value="strengthNumber" />
+								<property name="jxpath" value="number" />
+							</bean>
+							<bean class="org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo">
+								<property name="annoFieldName" value="medicationStrength" />
+								<property name="columnName" value="strengthUnit" />
+								<property name="jxpath" value="unit" />
+							</bean>
+							<bean class="org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo">
+								<property name="annoFieldName" value="medicationStatusChange" />
+								<property name="columnName" value="change" />
+								<property name="jxpath" value="value" />
+							</bean>
+							<bean class="org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo">
+								<property name="annoFieldName" value="medicationDosage" />
+								<property name="columnName" value="dosage" />
+								<property name="jxpath" value="value" />
+							</bean>
+						</set>
+					</property>
+				</bean>
+			</set>
+		</property>
+	</bean>
+</beans>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima.hbm.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima.hbm.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima.hbm.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima.hbm.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:aop="http://www.springframework.org/schema/aop"
+	xmlns:tx="http://www.springframework.org/schema/tx"
+	xsi:schemaLocation="
+http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
+http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx-2.5.xsd
+http://www.springframework.org/schema/aop http://www.springframework.org/schema/aop/spring-aop-2.5.xsd">
+	<bean id="sessionFactory"
+		class="org.springframework.orm.hibernate4.LocalSessionFactoryBean">
+		<property name="dataSource" ref="dataSource" />
+		<property name="mappingResources">
+			<list>
+				<!--  kernel persistent objects -->
+				<value>org/apache/ctakes/ytex/kernel/model/KernelEvaluation.hbm.xml</value>
+				<value>org/apache/ctakes/ytex/kernel/model/ClassifierEvaluation.hbm.xml</value>
+				<!--  umls persistent objects -->
+				<value>org/apache/ctakes/ytex/umls/model/UMLS.hbm.xml</value>
+				<value>org/apache/ctakes/ytex/umls/model/FWord.hbm.xml</value>
+				<!--  uima persistent objects -->
+				<value>org/apache/ctakes/ytex/uima/model/Document.hbm.xml</value>
+				<value>org/apache/ctakes/ytex/uima/model/NamedEntityRegex.hbm.xml</value>
+				<value>org/apache/ctakes/ytex/uima/model/SegmentRegex.hbm.xml</value>				
+			</list>
+		</property>
+		<property name="hibernateProperties" ref="hibernateProperties" />
+	</bean>
+</beans>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/model/Document.hbm.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/model/Document.hbm.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/model/Document.hbm.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/model/Document.hbm.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,77 @@
+<?xml version="1.0"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://www.hibernate.org/dtd/hibernate-mapping-3.0.dtd">
+<hibernate-mapping package="org.apache.ctakes.ytex.uima.model">
+	<class name="Document" table="document" discriminator-value="D">
+		<id name="documentID" column="document_id">
+			<generator class="org.hibernate.id.enhanced.TableGenerator">
+				<!-- <generator class="native"> -->
+				<param name="sequence">document_id_sequence</param>
+				<param name="increment_size">100</param>
+			</generator>
+		</id>
+		<property name="docText" column="doc_text" type="text" />
+		<property name="cas" column="cas" type="binary" />
+		<property name="analysisBatch" column="analysis_batch" />
+		<property name="instanceID" column="instance_id" />
+		<property name="instanceKey" column="instance_key" />
+		<bag name="documentAnnotations" inverse="true" cascade="delete">
+			<key column="document_id" />
+			<one-to-many class="DocumentAnnotation" />
+		</bag>
+	</class>
+	<class name="UimaType" table="ref_uima_type">
+		<cache usage="read-only" />
+		<id name="uimaTypeID" column="uima_type_id" />
+		<property name="uimaTypeName" column="uima_type_name" />
+		<property name="tableName" column="table_name" />
+	</class>
+	<class name="AnnotationContainmentLink" table="anno_contain">
+		<!-- <id name="annotationContainmentLinkId" column="anno_contain_id"> <generator 
+			class="native"> <param name="sequence">anno_contain_id_sequence</param> </generator> 
+			</id> -->
+		<composite-id>
+			<key-property name="parentAnnotationId" column="parent_anno_base_id" />
+			<key-property name="childAnnotationId" column="child_anno_base_id" />
+		</composite-id>
+		<property name="parentUimaTypeId" column="parent_uima_type_id" />
+		<property name="childUimaTypeId" column="child_uima_type_id" />
+	</class>
+	<class name="DocumentAnnotation" table="anno_base">
+		<id name="documentAnnotationID" column="anno_base_id">
+			<generator class="org.hibernate.id.enhanced.TableGenerator">
+				<param name="table_name">anno_base_sequence</param>
+				<param name="segment_value">anno_base_id_sequence</param>
+				<param name="increment_size">1000</param>
+			</generator>
+			<!-- <generator class="native"> <param name="sequence">anno_base_id_sequence</param> 
+				</generator> -->
+		</id>
+		<property name="begin" column="span_begin" />
+		<property name="end" column="span_end" />
+		<many-to-one name="uimaType" class="UimaType" column="uima_type_id"
+			not-null="true" />
+		<many-to-one name="document" class="Document" column="document_id"
+			not-null="true" />
+	</class>
+	<query name="getUimaTypeByName"><![CDATA[
+		from UimaType
+		where uimaTypeName = :uimaTypeName
+	]]></query>
+	<query name="getUimaTypes"><![CDATA[
+		from UimaType
+	]]></query>
+	<!-- insert anno_contain for a document annotations must pertain to the 
+		same document parent annotation spans a range that contains the child annotation 
+		if annotations span the exact same range, they must be of different types -->
+	<query name="insertAnnotationContainmentLinks"><![CDATA[
+		insert into AnnotationContainmentLink (parentAnnotationId, parentUimaTypeId, childAnnotationId, childUimaTypeId)
+		select p.documentAnnotationID, p.uimaType.uimaTypeID, c.documentAnnotationID, c.uimaType.uimaTypeID
+		from DocumentAnnotation p, DocumentAnnotation c
+		where p.begin <= c.begin
+		and p.end >= c.end
+		and p.documentAnnotationID <> c.documentAnnotationID
+		and not (p.begin = c.begin and p.end = c.end and p.uimaType.uimaTypeID = c.uimaType.uimaTypeID)
+		and p.document.documentID = :documentID
+		and c.document.documentID = :documentID
+	]]></query>
+</hibernate-mapping>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/model/NamedEntityRegex.hbm.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/model/NamedEntityRegex.hbm.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/model/NamedEntityRegex.hbm.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/model/NamedEntityRegex.hbm.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://www.hibernate.org/dtd/hibernate-mapping-3.0.dtd">
+<hibernate-mapping package="org.apache.ctakes.ytex.uima.model">
+	<class name="NamedEntityRegex" table="ref_named_entity_regex">
+		<id name="namedEntityRegexID" column="named_entity_regex_id">
+			<generator class="native">
+				<param name="sequence">named_entity_regex_id_sequence</param>
+			</generator>
+		</id>
+		<property name="code" column="code" />
+		<property name="codingScheme" column="coding_scheme" />
+		<property name="oid" column="oid" />
+		<property name="regex" column="regex" />
+		<property name="context" column="context" />
+	</class>
+</hibernate-mapping>
+	
+	

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/model/SegmentRegex.hbm.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/model/SegmentRegex.hbm.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/model/SegmentRegex.hbm.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/model/SegmentRegex.hbm.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,16 @@
+<?xml version="1.0"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://www.hibernate.org/dtd/hibernate-mapping-3.0.dtd">
+<hibernate-mapping package="org.apache.ctakes.ytex.uima.model">
+	<class name="SegmentRegex" table="ref_segment_regex">
+		<id name="SegmentRegexID" column="segment_regex_id">
+			<generator class="native">
+				<param name="sequence">segment_regex_id_sequence</param>
+			</generator>
+		</id>
+		<property name="regex" column="regex" />
+		<property name="segmentID" column="segment_id" />
+		<property name="limitToRegex" column="limit_to_regex" />
+	</class>
+</hibernate-mapping>
+	
+	

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/umls/model/FWord.hbm.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/umls/model/FWord.hbm.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/umls/model/FWord.hbm.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/umls/model/FWord.hbm.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,43 @@
+<?xml version="1.0"?>
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://www.hibernate.org/dtd/hibernate-mapping-3.0.dtd">
+<hibernate-mapping package="org.apache.ctakes.ytex.umls.model">
+	<class name="UmlsAuiFirstWord" table="umls_aui_fword">
+		<id name="aui" />
+		<property name="fword" />
+		<property name="fstem" />
+		<property name="stemmedStr" column="stem_str" />
+		<property name="tokenizedStr" column="tok_str" />
+	</class>
+	<query name="getFirstAuiStr"><![CDATA[
+		select aui,str
+		from MRCONSO
+		where length(aui) > 0
+		and length(str) < 200
+		and lat = 'ENG'
+		order by aui
+	]]></query>
+	<query name="getNextAuiStr"><![CDATA[
+		select aui,str
+		from MRCONSO
+		where aui > :aui
+		and length(aui) > 0
+		and length(str) < 200
+		and lat = 'ENG'
+		order by aui
+	]]></query>
+	<query name="getLastAui"><![CDATA[
+		select max(aui)
+		from UmlsAuiFirstWord
+	]]></query>
+	<query name="getRXNORMCuis"><![CDATA[
+		select distinct(cui)
+		from MRCONSO
+		where sab = 'RXNORM'
+	]]></query>
+	<query name="isRXNORMCui"><![CDATA[
+		select count(*)
+		from MRCONSO
+		where sab = 'RXNORM'
+		and cui = :cui
+	]]></query>
+</hibernate-mapping>

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/umls/model/UMLS.hbm.template.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/umls/model/UMLS.hbm.template.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/umls/model/UMLS.hbm.template.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/umls/model/UMLS.hbm.template.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,48 @@
+<?xml version="1.0"?>
+<!-- umls tables in a different schema no easy way known to me to override 
+	schema for specific tables at runtime use this template to create the hibernate 
+	mapping -->
+<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://www.hibernate.org/dtd/hibernate-mapping-3.0.dtd">
+<hibernate-mapping package="org.apache.ctakes.ytex.umls.model"
+	schema="@umls.schema@" @filter.umls.catalog@>
+	<!-- mrrel doesn't really have a primary key / unique index -->
+	<class name="MRREL" table="MRREL">
+		<id name="rui" column="rui" />
+		<property name="cui1"></property>
+		<property name="cui2"></property>
+		<property name="rel"></property>
+		<property name="sab"></property>
+		<property name="rela" />
+	</class>
+	<class name="MRCONSO" table="MRCONSO">
+		<id name="aui" column="aui" />
+		<property name="cui" />
+		<property name="lat" />
+		<property name="ts" />
+		<property name="lui" />
+		<property name="stt" />
+		<property name="sui" />
+		<property name="ispref" />
+		<property name="saui" />
+		<property name="scui" />
+		<property name="sdui" />
+		<property name="sab" />
+		<property name="tty" />
+		<property name="code" />
+		<property name="str" />
+		<property name="srl" />
+		<property name="suppress" />
+		<property name="cvf" />
+	</class>
+
+	<class name="MRSTY" table="MRSTY">
+		<composite-id>
+			<key-property name="cui"></key-property>
+			<key-property name="tui"></key-property>
+		</composite-id>
+		<property name="stn" />
+		<property name="sty" />
+		<property name="atui" />
+		<property name="cvf" />
+	</class>
+</hibernate-mapping>

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex-default.properties
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex-default.properties?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex-default.properties (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex-default.properties Mon Dec 16 16:30:30 2013
@@ -0,0 +1,8 @@
+ytex.conceptGraphName=sct-msh-csp-aod
+ytex.conceptPreload=true
+ytex.corpusName=
+ytex.conceptSetName=
+hibernate.jdbc.batch_size=100
+hibernate.order_inserts=true
+hibernate.order_updates=true
+db.name=

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex-umls.properties
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex-umls.properties?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex-umls.properties (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex-umls.properties Mon Dec 16 16:30:30 2013
@@ -0,0 +1,2 @@
+umls.schema=${db.schema}
+umls.catalog=${db.name}
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mssql.example
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mssql.example?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mssql.example (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mssql.example Mon Dec 16 16:30:30 2013
@@ -0,0 +1,28 @@
+# database (catalog) name
+db.name=YTEX_TEST
+
+# schema. default is dbo
+db.schema=test
+
+# jdbc url for database.  Replace localhost and YTEX_TEST 
+# with the values of db.host and db.name respectively
+db.url=jdbc:sqlserver://localhost;databaseName=YTEX_TEST;integratedSecurity=true
+
+# assume windows integrated authentication, change if necessary
+db.username=
+db.password=
+
+# the schema and catalog (database) where umls is installed
+# if not specified, will default to schema/database from ytex
+#umls.schema=dbo
+#umls.catalog=umls
+
+# you should not have to modify anything below
+db.type=mssql
+db.driver=com.microsoft.sqlserver.jdbc.SQLServerDriver
+db.initStatements=
+ytex.beanRefContext=classpath*:beanRefContext.xml
+hibernate.dialect=org.hibernate.dialect.SQLServerDialect
+
+# transaction isolation level
+db.isolationLevel=READ_UNCOMMITTED

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mysql.example
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mysql.example?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mysql.example (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mysql.example Mon Dec 16 16:30:30 2013
@@ -0,0 +1,30 @@
+# schema/database name 
+db.schema=ytex
+# username
+db.username=ytex
+# password
+db.password=ytex
+
+# jdbc url for database.  schema name must match db.schema
+db.url=jdbc:mysql://localhost:3306/ytex?autoReconnect=true
+
+# the schema where umls is installed
+# if not specified, will default to schema from ytex
+#umls.schema=umls
+
+
+# you should not have to modify anything below
+db.type=mysql
+db.driver=com.mysql.jdbc.Driver
+db.initStatements=
+ytex.beanRefContext=classpath*:beanRefContext.xml
+hibernate.dialect=org.hibernate.dialect.MySQLMyISAMDialect
+
+# transaction isolation level
+db.isolationLevel=READ_UNCOMMITTED
+
+# the parameters passed to mysql
+# if you have any additional parameters that must be passed to mysql 
+# (e.g. if you are using a non-standard port)
+# uncomment and modify the line below
+# mysql.line=--user=${db.username} --password=${db.password} --host=${db.host} ${db.schema} 

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.orcl.example
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.orcl.example?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.orcl.example (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.orcl.example Mon Dec 16 16:30:30 2013
@@ -0,0 +1,31 @@
+# jdbc url for database.  
+# Replace localhost:1521/XE with the host, port and service name/SID of your database
+# another format that works is e.g.: jdbc:oracle:thin:ytex/ytex@localhost:1521:XE
+db.url=jdbc:oracle:thin:@//localhost:1521/XE
+
+# oracle username and password
+# user needs connect, resource, and create view privileges
+db.username=ytex
+db.password=ytex
+
+# database schema 
+# typically identical to username
+# alternatively, the user must have access to the schema
+db.schema=ytex
+
+# the schema where umls is installed
+# if not specified, will default to schema from ytex
+#umls.schema=umls
+
+
+# you should not have to modify anything below
+# hibernate database dialect
+# specify Oracle8iDialect, Oracle9iDialect, or Oracle10gDialect
+# can use Oracle10gDialect for Oracle11
+hibernate.dialect=org.hibernate.dialect.Oracle10gDialect
+
+db.type=orcl
+db.driver=oracle.jdbc.driver.OracleDriver
+
+# transaction isolation level
+db.isolationLevel=READ_COMMITTED

Added: ctakes/branches/ytex/ctakes-ytex-uima/.classpath
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/.classpath?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/.classpath (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/.classpath Mon Dec 16 16:30:30 2013
@@ -0,0 +1,42 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

Added: ctakes/branches/ytex/ctakes-ytex-uima/.project
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/.project?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/.project (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/.project Mon Dec 16 16:30:30 2013
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>ctakes-ytex-uima</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+	</natures>
+</projectDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/.settings/org.eclipse.core.resources.prefs
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/.settings/org.eclipse.core.resources.prefs?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/.settings/org.eclipse.core.resources.prefs (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/.settings/org.eclipse.core.resources.prefs Mon Dec 16 16:30:30 2013
@@ -0,0 +1,7 @@
+eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
+encoding//src/main/resources=UTF-8
+encoding//src/test/java=UTF-8
+encoding//src/test/resources=UTF-8
+encoding//target/generated-sources/jcasgen=UTF-8
+encoding/<project>=UTF-8

Added: ctakes/branches/ytex/ctakes-ytex-uima/.settings/org.eclipse.jdt.core.prefs
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/.settings/org.eclipse.jdt.core.prefs?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/.settings/org.eclipse.jdt.core.prefs (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/.settings/org.eclipse.jdt.core.prefs Mon Dec 16 16:30:30 2013
@@ -0,0 +1,5 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.6

Added: ctakes/branches/ytex/ctakes-ytex-uima/.settings/org.eclipse.m2e.core.prefs
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/.settings/org.eclipse.m2e.core.prefs?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/.settings/org.eclipse.m2e.core.prefs (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/.settings/org.eclipse.m2e.core.prefs Mon Dec 16 16:30:30 2013
@@ -0,0 +1,4 @@
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

Added: ctakes/branches/ytex/ctakes-ytex-uima/LICENSE
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/LICENSE?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/LICENSE (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/LICENSE Mon Dec 16 16:30:30 2013
@@ -0,0 +1,202 @@
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
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+          of the NOTICE file are for informational purposes only and
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+          notices within Derivative Works that You distribute, alongside
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+
+      You may add Your own copyright statement to Your modifications and
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+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
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+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
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+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
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+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
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+   9. Accepting Warranty or Additional Liability. While redistributing
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+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
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+
+   Copyright [yyyy] [name of copyright owner]
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

Added: ctakes/branches/ytex/ctakes-ytex-uima/conceptGraph/test.gz
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/conceptGraph/test.gz?rev=1551254&view=auto
==============================================================================
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Added: ctakes/branches/ytex/ctakes-ytex-uima/conceptGraph/test.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/conceptGraph/test.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/conceptGraph/test.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/conceptGraph/test.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!DOCTYPE properties SYSTEM "http://java.sun.com/dtd/properties.dtd">
+<properties>
+<comment>created on Mon Nov 18 21:58:59 EST 2013</comment>
+<entry key="org.apache.ctakes.ytex.conceptGraphQuery">select child, parent from test_concepts</entry>
+<entry key="org.apache.ctakes.ytex.conceptGraphName">test</entry>
+<entry key="org.apache.ctakes.ytex.checkCycle">true</entry>
+</properties>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,209 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+-->
+<analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+  <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+  <analysisEngineMetaData>
+  	<description>
+  	Identical to ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml with the following changes:
+  	substitute ytex SegmentRegexAnnotator for SimpleSegmentAnnotator;
+  	substitute ytex SentenceDetectorAnnotator for SentenceDetectorAnnotator; 
+  	substitute ytex DictionaryLookupAnnotator for DictionaryLookupAnnotatorUMLS
+  	</description>
+  </analysisEngineMetaData>
+  <primitive>false</primitive>
+  <delegateAnalysisEngineSpecifiers>
+    <delegateAnalysisEngine key="Chunker">
+      <import location="../../../ctakes-chunker/desc/Chunker.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="TokenizerAnnotator">
+      <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
+      <import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
+      <import location="./DictionaryLookupAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="StatusAnnotator">
+      <import location="../../../ctakes-ne-contexts/desc/StatusAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="NegationAnnotator">
+      <import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="SentenceDetectorAnnotator">
+      <import location="./SentenceDetectorAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="LookupWindowAnnotator">
+      <import location="../../../ctakes-clinical-pipeline/desc/analysis_engine/LookupWindowAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="AdjustNounPhraseToIncludeFollowingNP">
+      <import location="../../../ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingNP.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="AdjustNounPhraseToIncludeFollowingPPNP">
+      <import location="../../../ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingPPNP.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="SegmentRegexAnnotator">
+      <import location="SegmentRegexAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="POSTagger">
+      <import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
+    </delegateAnalysisEngine>
+	<!-- 
+	<delegateAnalysisEngine key="ClearPOSTagger">
+	<import location="../../../ctakes-pos-tagger/desc/ClearNLPPOSTagger.xml"/>
+	</delegateAnalysisEngine>
+	 -->    
+    <delegateAnalysisEngine key="LvgAnnotator">
+      <import location="../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="AssertionAnnotator">
+      <import location="../../../ctakes-assertion/desc/AssertionMiniPipelineAnalysisEngine.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="DependencyParser">
+      <import location="../../../ctakes-dependency-parser/desc/analysis_engine/ClearNLPDependencyParserAE.xml"/>
+    </delegateAnalysisEngine>
+<delegateAnalysisEngine key="SemanticRoleLabeler">
+<import location="../../../ctakes-dependency-parser/desc/analysis_engine/ClearNLPSemanticRoleLabelerAE.xml"/>
+</delegateAnalysisEngine>    
+  </delegateAnalysisEngineSpecifiers>
+  <analysisEngineMetaData>
+    <name>AggregatePlaintextUMLSProcessor</name>
+    <description>Runs the complete pipeline for annotating clinical documents in plain text format using the built in UMLS (SNOMEDCT and RxNORM) dictionaries.  This uses the dictionary lookup/desc/DictionaryLookupAnnotatorUMLS.xml
+and requires an UMLS license.  Please update DictionaryLookupAnnotatorUMLS.xml file with your UMLS username and password.
+</description>
+    <version/>
+    <vendor/>
+    <configurationParameters searchStrategy="language_fallback">
+      <configurationParameter>
+        <name>ChunkCreatorClass</name>
+        <type>String</type>
+        <multiValued>false</multiValued>
+        <mandatory>true</mandatory>
+        <overrides>
+          <parameter>Chunker/ChunkCreatorClass</parameter>
+        </overrides>
+      </configurationParameter>
+    </configurationParameters>
+    <configurationParameterSettings>
+      <nameValuePair>
+        <name>ChunkCreatorClass</name>
+        <value>
+          <string>org.apache.ctakes.chunker.ae.PhraseTypeChunkCreator</string>
+        </value>
+      </nameValuePair>
+    </configurationParameterSettings>
+    <flowConstraints>
+      <fixedFlow>
+        <node>SegmentRegexAnnotator</node>
+        <node>SentenceDetectorAnnotator</node>
+        <node>TokenizerAnnotator</node>
+        <node>LvgAnnotator</node>
+        <node>ContextDependentTokenizerAnnotator</node>
+        <node>POSTagger</node>
+		<!-- <node>ClearPOSTagger</node>  -->        
+        <node>Chunker</node>
+        <node>AdjustNounPhraseToIncludeFollowingNP</node>
+        <node>AdjustNounPhraseToIncludeFollowingPPNP</node>
+        <node>LookupWindowAnnotator</node>
+        <node>DictionaryLookupAnnotatorDB</node>
+        <!-- 
+        <node>DependencyParser</node>
+		<node>SemanticRoleLabeler</node>        
+        <node>AssertionAnnotator</node>
+        	<node>StatusAnnotator</node>
+        	<node>NegationAnnotator</node>
+	        <node>ExtractionPrepAnnotator</node>
+         -->
+      </fixedFlow>
+    </flowConstraints>
+    <typePriorities>
+      <name>Ordering</name>
+      <description>For subiterator</description>
+      <version>1.0</version>
+      <priorityList>
+        <type>org.apache.ctakes.typesystem.type.textspan.Segment</type>
+        <type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+        <type>org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+      </priorityList>
+      <priorityList>
+        <type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+        <type>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
+      </priorityList>
+    </typePriorities>
+    <fsIndexCollection/>
+    <capabilities>
+      <capability>
+        <inputs/>
+        <outputs>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.NewlineToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.WordToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.VP</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.refsem.UmlsConcept</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.UCP</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.TimeAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.SymbolToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspanSegment</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.SBAR</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.RangeAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PunctuationToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.Property</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.Properties</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PRT</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PP</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.OntologyConcept</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.NumToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.Lemma</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.LST</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.INTJ</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.FractionAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.structured.DocumentID</type>
+          <type allAnnotatorFeatures="true">uima.tcas.DocumentAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.DateAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.CopySrcAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.CopyDestAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.ContractionToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.ContextAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.Chunk</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.CONJP</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+          <type allAnnotatorFeatures="true">uima.cas.AnnotationBase</type>
+          <type allAnnotatorFeatures="true">uima.tcas.Annotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.ADVP</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.ADJP</type>        
+        </outputs>
+        <languagesSupported/>
+      </capability>
+    </capabilities>
+    <operationalProperties>
+      <modifiesCas>true</modifiesCas>
+      <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+      <outputsNewCASes>false</outputsNewCASes>
+    </operationalProperties>
+  </analysisEngineMetaData>
+  <resourceManagerConfiguration/>
+</analysisEngineDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DBConsumer.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DBConsumer.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DBConsumer.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DBConsumer.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,148 @@
+<?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.ytex.uima.annotators.DBConsumer
+	</annotatorImplementationName>
+	<analysisEngineMetaData>
+		<name>DBConsumer</name>
+		<description />
+		<version>1.0</version>
+		<vendor />
+		<configurationParameters>
+			<configurationParameter>
+				<name>xmiOutputDirectory</name>
+				<description>if specified, will write CAS XMI for each document to
+					this directory
+				</description>
+				<type>String</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+			</configurationParameter>
+			<configurationParameter>
+				<name>analysisBatch</name>
+				<description>document.analysis_batch</description>
+				<type>String</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+			</configurationParameter>
+			<configurationParameter>
+				<name>storeDocText</name>
+				<description>store document text in document table? default true
+				</description>
+				<type>Boolean</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+			</configurationParameter>
+			<configurationParameter>
+				<name>storeCAS</name>
+				<description>store gzipped CAS XML in document table? default true
+				</description>
+				<type>Boolean</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+			</configurationParameter>
+			<configurationParameter>
+				<name>insertAnnotationContainmentLinks</name>
+				<description>should anno_contain entries be created for this
+					document? default true
+				</description>
+				<type>Boolean</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+			</configurationParameter>
+			<configurationParameter>
+				<name>typesToIgnore</name>
+				<description>uima types (fully qualified class names) that should
+					not be saved in the database.
+				</description>
+				<type>String</type>
+				<multiValued>true</multiValued>
+				<mandatory>false</mandatory>
+			</configurationParameter>
+		</configurationParameters>
+		<configurationParameterSettings>
+			<nameValuePair>
+				<name>xmiOutputDirectory</name>
+				<value>
+					<string />
+				</value>
+			</nameValuePair>
+			<nameValuePair>
+				<name>analysisBatch</name>
+				<value>
+					<string>test</string>
+				</value>
+			</nameValuePair>
+			<nameValuePair>
+				<name>storeDocText</name>
+				<value>
+					<boolean>true</boolean>
+				</value>
+			</nameValuePair>
+			<nameValuePair>
+				<name>storeCAS</name>
+				<value>
+					<boolean>true</boolean>
+				</value>
+			</nameValuePair>
+			<nameValuePair>
+				<name>insertAnnotationContainmentLinks</name>
+				<value>
+					<boolean>true</boolean>
+				</value>
+			</nameValuePair>
+			<nameValuePair>
+				<name>typesToIgnore</name>
+				<value>
+					<array>
+						<string>org.apache.ctakes.typesystem.type.syntax.ContractionToken
+						</string>
+						<string>org.apache.ctakes.typesystem.type.syntax.NewlineToken
+						</string>
+						<string>org.apache.ctakes.typesystem.type.syntax.PunctuationToken
+						</string>
+						<string>org.apache.ctakes.typesystem.type.syntax.SymbolToken
+						</string>
+						<string>org.apache.ctakes.typesystem.type.syntax.NP</string>
+						<string>org.apache.ctakes.typesystem.type.syntax.VP</string>
+						<string>org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation
+						</string>
+						<string>org.apache.ctakes.typesystem.type.textsem.DateAnnotation
+						</string>
+						<string>org.apache.ctakes.typesystem.type.textsem.FractionAnnotation
+						</string>
+						<string>org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation
+						</string>
+						<string>org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation
+						</string>
+						<string>org.apache.ctakes.typesystem.type.textsem.RangeAnnotation
+						</string>
+						<string>org.apache.ctakes.typesystem.type.textsem.TimeAnnotation
+						</string>
+					</array>
+				</value>
+			</nameValuePair>
+		</configurationParameterSettings>
+		<typeSystemDescription>
+			<imports>
+				<import name="org.apache.ctakes.ytex.types.TypeSystem" />
+			</imports>
+		</typeSystemDescription>
+		<typePriorities />
+		<fsIndexCollection />
+		<capabilities>
+			<capability>
+				<inputs />
+				<outputs />
+				<languagesSupported />
+			</capability>
+		</capabilities>
+		<operationalProperties>
+			<modifiesCas>false</modifiesCas>
+			<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+			<outputsNewCASes>false</outputsNewCASes>
+		</operationalProperties>
+	</analysisEngineMetaData>
+	<resourceManagerConfiguration />
+</analysisEngineDescription>



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