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From vjapa...@apache.org
Subject svn commit: r1560998 - in /ctakes/branches/ytex/ctakes-ytex-res: ./ .settings/ src/main/resources/org/apache/ctakes/ytex/ src/main/resources/org/apache/ctakes/ytex/web/
Date Fri, 24 Jan 2014 13:41:11 GMT
Author: vjapache
Date: Fri Jan 24 13:41:10 2014
New Revision: 1560998

URL: http://svn.apache.org/r1560998
Log:
ctakes-ytex-web initial import

Added:
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-kernel-simweb.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-security.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-web.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-ws.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/messages.properties
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search-msh.mysql.properties
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search-sct.mysql.properties
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search.mssql.properties
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search.mysql.properties
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search.orcl.properties
Modified:
    ctakes/branches/ytex/ctakes-ytex-res/.classpath
    ctakes/branches/ytex/ctakes-ytex-res/.project
    ctakes/branches/ytex/ctakes-ytex-res/.settings/org.eclipse.jdt.core.prefs
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.orcl.example

Modified: ctakes/branches/ytex/ctakes-ytex-res/.classpath
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/.classpath?rev=1560998&r1=1560997&r2=1560998&view=diff
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/.classpath (original)
+++ ctakes/branches/ytex/ctakes-ytex-res/.classpath Fri Jan 24 13:41:10 2014
@@ -25,6 +25,7 @@
 	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="org.eclipse.jst.component.nondependency" value=""/>
 		</attributes>
 	</classpathentry>
 	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">

Modified: ctakes/branches/ytex/ctakes-ytex-res/.project
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/.project?rev=1560998&r1=1560997&r2=1560998&view=diff
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/.project (original)
+++ ctakes/branches/ytex/ctakes-ytex-res/.project Fri Jan 24 13:41:10 2014
@@ -6,6 +6,11 @@
 	</projects>
 	<buildSpec>
 		<buildCommand>
+			<name>org.eclipse.wst.common.project.facet.core.builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
 			<name>org.eclipse.jdt.core.javabuilder</name>
 			<arguments>
 			</arguments>
@@ -15,9 +20,17 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.wst.validation.validationbuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.jem.workbench.JavaEMFNature</nature>
+		<nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+		<nature>org.eclipse.wst.common.project.facet.core.nature</nature>
 	</natures>
 </projectDescription>

Modified: ctakes/branches/ytex/ctakes-ytex-res/.settings/org.eclipse.jdt.core.prefs
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/.settings/org.eclipse.jdt.core.prefs?rev=1560998&r1=1560997&r2=1560998&view=diff
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/.settings/org.eclipse.jdt.core.prefs (original)
+++ ctakes/branches/ytex/ctakes-ytex-res/.settings/org.eclipse.jdt.core.prefs Fri Jan 24 13:41:10
2014
@@ -1,5 +1,8 @@
 eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
 org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
 org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
 org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
 org.eclipse.jdt.core.compiler.source=1.6

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-kernel-simweb.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-kernel-simweb.xml?rev=1560998&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-kernel-simweb.xml
(added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-kernel-simweb.xml
Fri Jan 24 13:41:10 2014
@@ -0,0 +1,38 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Configure a SemanticSimServiceBean for each concept graph we would like 
+	to compute semantic similarity for. SemanticSimServiceBean references a conceptSimilarityService

+	bean which computes similarity, and a conceptSearchService bean used to map 
+	words to concepts -->
+<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">
+	<!-- default SemanticSimServiceBean -->
+	<bean id="conceptSimilarityService" class="org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl"
+		init-method="init">
+		<property name="transactionManager" ref="transactionManager" />
+		<property name="conceptDao" ref="conceptDao" />
+		<property name="classifierEvaluationDao" ref="classifierEvaluationDao" />
+		<property name="cacheManager" ref="cacheManager" />
+		<property name="corpusName" value="${ytex.corpusName}" />
+		<property name="conceptGraphName" value="${ytex.conceptGraphName}" />
+		<property name="conceptSetName" value="${ytex.conceptSetName}" />
+		<property name="preload" value="false" />
+	</bean>
+	<bean id="semanticSimBean" class="org.apache.ctakes.ytex.web.search.SemanticSimServiceBean">
+		<property name="conceptSearchService" ref="umlsFirstWordService" />
+		<property name="conceptSimilarityService" ref="conceptSimilarityService" />
+		<property name="description" value="${ytex.conceptGraphName}" />
+	</bean>
+	<!-- snomed-ct SemanticSimServiceBean -->
+	<bean id="semanticSimRegistryBean" class="org.apache.ctakes.ytex.web.search.SemanticSimRegistryBean">
+		<property name="semanticSimServiceList">
+			<list>
+				<ref bean="semanticSimBean" />
+			</list>
+		</property>
+	</bean>
+</beans>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-security.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-security.xml?rev=1560998&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-security.xml
(added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-security.xml
Fri Jan 24 13:41:10 2014
@@ -0,0 +1,66 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+	<!--
+  - Sample namespace-based configuration
+  -
+  -->
+
+<beans:beans xmlns="http://www.springframework.org/schema/security"
+	xmlns:beans="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-3.0.xsd
+                        http://www.springframework.org/schema/security http://www.springframework.org/schema/security/spring-security-3.0.xsd">
+
+	<global-method-security pre-post-annotations="enabled">
+		<!--
+			AspectJ pointcut expression that locates our "post" method and
+			applies security that way <protect-pointcut expression="execution(*
+			bigbank.*Service.post*(..))" access="ROLE_TELLER"/>
+		-->
+	</global-method-security>
+
+	<http use-expressions="true">
+		<intercept-url pattern="/**" access="hasRole('ROLE_USER')" />
+		<!--
+			Disable web URI authorization, as we're using
+			<global-method-security> and have @Secured the services layer instead
+			<intercept-url pattern="/listAccounts.html" access="isRememberMe()"
+			/> <intercept-url pattern="/post.html"
+			access="hasRole('ROLE_TELLER')" />
+		-->
+		<form-login />
+		<logout />
+		<remember-me />
+		<!--
+			Uncomment to enable X509 client authentication support <x509 />
+		-->
+		<!-- Uncomment to limit the number of sessions a user can have -->
+			<!--
+		<session-management invalid-session-url="/timeout.jsp">
+				<concurrency-control max-sessions="1"
+				error-if-maximum-exceeded="true" />
+
+		</session-management>
+			-->
+
+	</http>
+
+	<!--
+		Usernames/Passwords are rod/koala dianne/emu scott/wombat peter/opal
+	-->
+	<authentication-manager>
+		<authentication-provider>
+			<password-encoder hash="md5" />
+			<user-service>
+				<user name="rod" password="a564de63c2d0da68cf47586ee05984d7"
+					authorities="ROLE_SUPERVISOR, ROLE_USER, ROLE_TELLER" />
+				<user name="dianne" password="65d15fe9156f9c4bbffd98085992a44e"
+					authorities="ROLE_USER,ROLE_TELLER" />
+				<user name="scott" password="2b58af6dddbd072ed27ffc86725d7d3a"
+					authorities="ROLE_USER" />
+				<user name="peter" password="22b5c9accc6e1ba628cedc63a72d57f8"
+					authorities="ROLE_USER" />
+			</user-service>
+		</authentication-provider>
+	</authentication-manager>
+
+</beans:beans>

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-web.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-web.xml?rev=1560998&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-web.xml
(added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-web.xml
Fri Jan 24 13:41:10 2014
@@ -0,0 +1,29 @@
+<?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">
+	<aop:config>
+		<aop:pointcut id="ytexSearchOperation" expression="execution(* org.apache.ctakes.ytex.web.search.*Service.*(..))"
/>
+		<aop:advisor advice-ref="txAdvice" pointcut-ref="ytexSearchOperation" />
+	</aop:config>
+	<bean id="searchProperties"
+		class="org.springframework.beans.factory.config.PropertiesFactoryBean">
+		<property name="location" value="classpath:/org/apache/ctakes/ytex/web/search.${db.type}.properties"
/>
+	</bean>
+	<bean id="documentSearchService" class="org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl">
+		<property name="dataSource" ref="dataSource" />
+		<property name="searchProperties" ref="searchProperties" />
+		<property name="ytexProperties" ref="ytexProperties" />
+		<property name="sessionFactory" ref="sessionFactory" />
+	</bean>
+	<bean id="umlsFirstWordService" class="org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl">
+		<property name="dataSource" ref="dataSource" />
+		<property name="ytexProperties" ref="ytexProperties" />
+		<property name="searchProperties" ref="searchProperties" />
+	</bean>
+	
+</beans>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-ws.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-ws.xml?rev=1560998&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-ws.xml
(added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-ws.xml
Fri Jan 24 13:41:10 2014
@@ -0,0 +1,24 @@
+<beans xmlns="http://www.springframework.org/schema/beans"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:jaxws="http://cxf.apache.org/jaxws"
+	xmlns:jaxrs="http://cxf.apache.org/jaxrs"
+	xsi:schemaLocation="
+http://www.springframework.org/schema/beans 
+http://www.springframework.org/schema/beans/spring-beans.xsd
+http://cxf.apache.org/jaxws http://cxf.apache.org/schemas/jaxws.xsd 
+http://cxf.apache.org/jaxrs
+http://cxf.apache.org/schemas/jaxrs.xsd">
+	<import resource="classpath:META-INF/cxf/cxf.xml" />
+	<import resource="classpath:META-INF/cxf/cxf-servlet.xml" />
+	<import resource="classpath:META-INF/cxf/cxf-extension-soap.xml" />
+	<bean id="conceptSimilarityWebService" class="org.apache.ctakes.ytex.ws.ConceptSimilarityWebServiceImpl">
+		<property name="semanticSimRegistryBean" ref="semanticSimRegistryBean" />
+	</bean>
+	<jaxws:endpoint id="conceptSimilarityWebServiceEndpoint"
+		implementor="#conceptSimilarityWebService" address="/conceptSimilarityWebService" />
+	<jaxrs:server id="conceptSimilarityRestServiceEndpoint"
+		address="/">
+		<jaxrs:serviceBeans>
+			<ref bean="conceptSimilarityWebService" />
+		</jaxrs:serviceBeans>
+	</jaxrs:server>
+</beans>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/messages.properties
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/messages.properties?rev=1560998&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/messages.properties
(added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/messages.properties
Fri Jan 24 13:41:10 2014
@@ -0,0 +1,12 @@
+LCH=Leacock-Chodorow (Taxonomy)
+INTRINSIC_LCH=Leacock-Chodorow (Intrinsic IC)
+LIN=Lin (Corpus IC)
+INTRINSIC_LIN=Lin (Intrinsic IC)
+PATH=Path (Taxonomy)
+INTRINSIC_PATH=Path (Intrinsic IC)
+JACCARD=Jaccard (Intrinsic IC)
+SOKAL=Sokal & Sneath (Intrinsic IC)
+PAGERANK=PageRank
+WUPALMER=Wu-Palmer (Taxonomy)
+RADA=Rada (Taxonomy)
+INTRINSIC_RADA=Rada (Intrinsic IC)
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search-msh.mysql.properties
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search-msh.mysql.properties?rev=1560998&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search-msh.mysql.properties
(added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search-msh.mysql.properties
Fri Jan 24 13:41:10 2014
@@ -0,0 +1,13 @@
+retrieveConceptByFword=\
+select distinct conceptString fword, descriptorUI conceptId, SUBSTRING(conceptString, 1,
30) text \
+from mesh_concept  \
+where conceptString = :term \
+limit 30
+
+conceptIdPattern=\A[CD]\d{6}\Z"
+
+retrieveTermByConceptId=\
+select min(conceptString) text \
+from mesh_concept c \
+where descriptorUI = :conceptId
+

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search-sct.mysql.properties
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search-sct.mysql.properties?rev=1560998&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search-sct.mysql.properties
(added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search-sct.mysql.properties
Fri Jan 24 13:41:10 2014
@@ -0,0 +1,21 @@
+retrieveConceptByFword=\
+select distinct term fword, conceptId, SUBSTRING(term, 1, 30) text \
+from sct2_concept c \
+inner join sct2_description d \
+    on c.id = d.conceptId  \
+    and d.term = :term \
+    and c.active = 1  \
+    and d.active = 1 \
+limit 30
+
+conceptIdPattern=\d+
+
+retrieveTermByConceptId=\
+select min(term) text \
+from sct2_concept c \
+inner join sct2_description d \
+    on c.id = d.conceptId  \
+    and c.active = 1  \
+    and d.active = 1 \
+    and d.typeId = 900000000000003001 \
+and c.id = cast(:conceptId as decimal)

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search.mssql.properties
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search.mssql.properties?rev=1560998&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search.mssql.properties
(added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search.mssql.properties
Fri Jan 24 13:41:10 2014
@@ -0,0 +1,47 @@
+retrieveConceptByFword=\
+select distinct top 30 fword, cui conceptId, SUBSTRING(tok_str, 1, 30) text \
+from @db.schema@.v_snomed_fword_lookup \
+where fword = :fword \
+and substring(tok_str, 1, :termlen) = :term \
+order by SUBSTRING(tok_str, 1, 30)
+
+# used by DocumentSearchDao
+retrieveDocumentByCUI=\
+select distinct top 100 document_id, \
+	cast(cui_text as char(256)) cui_text, \
+	cast(sentence_text as char(256)) sentence_text, \
+	patient_id, \
+	doc_date, \
+	cast(doc_title as char(256)) doc_title, \
+	document_type_name \
+from @db.schema@.v_document_cui_sent \
+where code = :code \
+and (:certainty is null or polarity = :certainty) \
+and (:patient_id is null or patient_id = :patient_id) \
+and (:from_doc_date is null or doc_date >= :from_doc_date) \
+and (:to_doc_date is null or doc_date <= :to_doc_date) \
+and (:document_type_name is null or document_type_name = :document_type_name)
+
+# map concept id to preferred term for concept id
+# try to get preferred term; if there isn't one, get the 'first' string
+retrieveTermByConceptId=\
+select coalesce(s2.term, s1.term) term \
+from \
+( \
+    select min(str) term \
+    from @umls.catalog@.@umls.schema@.MRCONSO \
+    where cui = :conceptId \
+    and lat = 'ENG' \
+) s1 \
+, \
+( \
+    select min(str) term \
+    from @umls.catalog@.@umls.schema@.MRCONSO \
+    where tty in ('PT', 'PN') \
+    and cui = :conceptId \
+    and lat = 'ENG' \
+) s2
+
+
+retrieveDocumentByID=select doc_text from @db.schema@.v_document where document_id = ?
+

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search.mysql.properties
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search.mysql.properties?rev=1560998&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search.mysql.properties
(added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search.mysql.properties
Fri Jan 24 13:41:10 2014
@@ -0,0 +1,48 @@
+retrieveConceptByFword=\
+select distinct fword, cui conceptId, SUBSTRING(tok_str, 1, 30) text \
+from v_snomed_fword_lookup \
+where fword = :fword \
+and substring(tok_str, 1, :termlen) = :term \
+order by tok_str \
+limit 30
+
+# used by DocumentSearchDao
+retrieveDocumentByCUI=\
+select distinct document_id, \
+	cast(cui_text as char(256)) cui_text, \
+	cast(sentence_text as char(256)) sentence_text, \
+	patient_id, \
+	doc_date, \
+	cast(doc_title as char(256)) doc_title, \
+	document_type_name \
+from v_document_cui_sent \
+where code = :code \
+and (:certainty is null or polarity = :certainty) \
+and (:patient_id is null or patient_id = :patient_id) \
+and (:from_doc_date is null or doc_date >= :from_doc_date) \
+and (:to_doc_date is null or doc_date <= :to_doc_date) \
+and (:document_type_name is null or document_type_name = :document_type_name) \
+limit 100 
+
+# map concept id to preferred term for concept id
+# try to get preferred term; if there isn't one, get the 'first' string
+retrieveTermByConceptId=\
+select coalesce(s2.term, s1.term) term \
+from \
+( \
+    select min(str) term \
+    from @umls.schema@.MRCONSO \
+    where cui = :conceptId \
+    and lat = 'ENG' \
+) s1 \
+, \
+( \
+    select min(str) term \
+    from @umls.schema@.MRCONSO \
+    where tty in ('PT', 'PN') \
+    and cui = :conceptId \
+    and lat = 'ENG' \
+) s2
+
+
+retrieveDocumentByID=select doc_text from v_document where document_id = ?

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search.orcl.properties
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search.orcl.properties?rev=1560998&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search.orcl.properties
(added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/search.orcl.properties
Fri Jan 24 13:41:10 2014
@@ -0,0 +1,50 @@
+retrieveConceptByFword=\
+select * from ( \
+	select distinct fword, cui conceptId, SUBSTR(tok_str, 1, 30) text \
+	from v_snomed_fword_lookup \
+	where fword = :fword \
+	and lower(SUBSTR(tok_str, 1, :termlen)) = :term \
+	order by SUBSTR(tok_str, 1, 30) \
+) where rownum < 30
+
+# used by DocumentSearchDao
+retrieveDocumentByCUI=\
+select * from ( \
+	select distinct document_id, \
+		cast(cui_text as varchar2(256)) cui_text, \
+		cast(sentence_text as varchar2(256)) sentence_text, \
+		patient_id, \
+		doc_date, \
+		cast(doc_title as varchar2(256)) doc_title, \
+		document_type_name \
+	from v_document_cui_sent \
+	where code = :code \
+	and (:certainty is null or polarity = :certainty) \
+	and (:patient_id is null or patient_id = :patient_id) \
+	and (:from_doc_date is null or doc_date >= :from_doc_date) \
+	and (:to_doc_date is null or doc_date <= :to_doc_date) \
+	and (:document_type_name is null or document_type_name = :document_type_name) \
+) where rownum < 100
+
+# map concept id to preferred term for concept id
+# try to get preferred term; if there isn't one, get the 'first' string
+retrieveTermByConceptId=\
+select coalesce(s2.term, s1.term) term \
+from \
+( \
+    select min(str) term \
+    from @umls.schema@.MRCONSO \
+    where cui = :conceptId \
+    and lat = 'ENG' \
+) s1 \
+, \
+( \
+    select min(str) term \
+    from @umls.schema@.MRCONSO \
+    where tty in ('PT', 'PN') \
+    and cui = :conceptId \
+    and lat = 'ENG' \
+) s2
+
+
+retrieveDocumentByID=select doc_text from v_document where document_id = ?

Modified: 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=1560998&r1=1560997&r2=1560998&view=diff
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.orcl.example
(original)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.orcl.example
Fri Jan 24 13:41:10 2014
@@ -1,17 +1,17 @@
 # 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
+# Replace localhost:1521:orcl 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:orcl
+db.url=jdbc:oracle:thin:@localhost:1521:orcl
 
 # oracle username and password
 # user needs connect, resource, and create view privileges
-db.username=ytex
-db.password=ytex
+db.username=ytex_test
+db.password=ytex_test
 
 # database schema 
 # typically identical to username
 # alternatively, the user must have access to the schema
-db.schema=ytex
+db.schema=ytex_test
 
 # the schema where umls is installed
 # if not specified, will default to schema from ytex



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