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From vjapa...@apache.org
Subject svn commit: r1555277 - in /ctakes/branches/ytex/ctakes-ytex/scripts: build-nonasf.xml dbannotationviewer.bat
Date Fri, 03 Jan 2014 23:16:47 GMT
Author: vjapache
Date: Fri Jan  3 23:16:47 2014
New Revision: 1555277

URL: http://svn.apache.org/r1555277
Log:
create script to generate the ctakes-ytex-resources.zip
script to launch dbannotationviewer 

Added:
    ctakes/branches/ytex/ctakes-ytex/scripts/build-nonasf.xml
    ctakes/branches/ytex/ctakes-ytex/scripts/dbannotationviewer.bat

Added: ctakes/branches/ytex/ctakes-ytex/scripts/build-nonasf.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex/scripts/build-nonasf.xml?rev=1555277&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex/scripts/build-nonasf.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex/scripts/build-nonasf.xml Fri Jan  3 23:16:47 2014
@@ -0,0 +1,56 @@
+<project name="build-nonasf" default="all">
+<description>
+<![CDATA[
+Create the ctakes-ytex-resources.zip that contains the following:
+* umls dictionary lookup table 
+* umls concept graphs
+* non asf compliant jars: hibernate, weka, mysql, ms sql
+
+Before running this:
+* run the maven build
+* need db with umls installed
+* run the data/build.xml (so we can generate the v_snomed_fword_lookup table)
+]]>
+</description>
+	<import file="build-classpath.xml" />
+	<property name="sqljdbc.home" value="c:/java/sqljdbc_4.0/enu" />
+	<target name="all" depends="create.conceptGraph.all,export.lookup,create.zip" />
+	<target name="create.zip">
+		<delete file="../target/ctakes-ytex-resources.zip" quiet="yes" /> 
+		<zip destfile="../target/ctakes-ytex-resources.zip">
+			<!-- dictionary lookup -->
+			<zipfileset prefix="resources" dir="${ytex.resources.home}" includes="org/apache/ctakes/ytex/dictionary/lookup/v_snomed_fword_lookup.txt"
/>
+			<!-- concept graphs -->
+			<zipfileset prefix="resources" dir="${ytex.resources.home}" includes="org/apache/ctakes/ytex/conceptGraph/*.gz"
/>
+			<!-- non-asf libraries -->
+			<zipfileset prefix="lib" dir="../target/nonasf-lib" includes="*.jar" />
+			<!-- mssql jdbc driver and authentication dlls -->
+			<zipfileset prefix="lib" dir="${sqljdbc.home}" includes="sqljdbc4.jar,auth/**/*.*"
/>
+			<!-- mssql jdbc readmes -->
+			<zipfileset prefix="lib/auth" dir="${sqljdbc.home}" includes="*.txt" />
+		</zip>
+	</target>
+	<target name="export.lookup">
+		<mkdir dir="${ytex.resources.home}/org/apache/ctakes/ytex/dictionary/lookup" />
+		<sql url="${db.url}" userid="${db.username}" password="${db.password}" driver="${db.driver}"
classpathref="${kernel.cp}" csvColumnSeparator="&#9;" showheaders="false" showtrailers="false"
print="true" output="${ytex.resources.home}/org/apache/ctakes/ytex/dictionary/lookup/v_snomed_fword_lookup.txt">
+			select cui, coalesce(tui, ''), fword, coalesce(fstem,''), tok_str, coalesce(stem_str,'')
from v_snomed_fword_lookup
+		</sql>
+	</target>
+	<target name="create.conceptGraph.all">
+		<antcall target="create.conceptGraph" />
+		<antcall target="create.conceptGraph">
+			<param name="cg.name" value="sct-rxnorm" />
+		</antcall>
+	</target>
+	<target name="create.conceptGraph">
+		<property name="cg.name" value="sct-msh-csp-aod" />
+		<java classname="org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl" classpathref="${kernel.cp}"
maxmemory="4g" fork="true">
+			<arg value="-name" />
+			<arg value="${cg.name}" />
+		</java>
+		<mkdir dir="${ytex.resources.home}/org/apache/ctakes/ytex/conceptGraph" />
+		<copy todir="${ytex.resources.home}">
+			<javaresource name="org/apache/ctakes/ytex/conceptGraph/${cg.name}.gz" classpathref="${kernel.cp}"
/>
+		</copy>
+	</target>
+</project>

Added: ctakes/branches/ytex/ctakes-ytex/scripts/dbannotationviewer.bat
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex/scripts/dbannotationviewer.bat?rev=1555277&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex/scripts/dbannotationviewer.bat (added)
+++ ctakes/branches/ytex/ctakes-ytex/scripts/dbannotationviewer.bat Fri Jan  3 23:16:47 2014
@@ -0,0 +1,4 @@
+@setlocal
+@call %~dp0../../setenv.bat
+java -cp %CLASSPATH% org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
+@endlocal
\ No newline at end of file



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