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YTEX is in the current cTAKES trunk (as of 1-May-2014) (https://svn.apache.org/repos/asf/ctakes/trunk) and will be included in cTAKES 3.2.  This This document describes additional installation steps required to take advantage of the following YTEX features:

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If you want to install the UMLS in your SQL Server, you may want to use a different database/schema from the YTEX database. If that is the case, you need permissions on the UMLS database/schema as well.

Installation

0) Build cTAKES Trunk

All of ytex has been moved into ctakes, it is currently in trunk (https://svn.apache.org/repos/asf/ctakes/trunk). You must build a ctakes distribution (that includes ytex).

• Open a command prompt
• Ensure that maven, svn, and the JDK 1.7 (64-bit version) are in your PATH variable
• cd to some directory where you want to check stuff out (I like c:\temp)
• run the following commands

rmdir /s /q ctakes
svn co https://svn.apache.org/repos/asf/ctakes/branches/ytex ctakes
cd ctakes
mvn clean install -DskipTests

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1) Install ctakes

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'as usual'

Go through the standard ctakes installation for the distribution you just created: See https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide. For the rest of this document, we assume ctakes is installed in CTAKES_HOME

1.5) Patch YTEX Distro (YTEX 3.2.0 only)

Not needed for YTEX 3.2.1.  Some of the install scripts need to be patched (fixed in trunk). Download and unzip  ytex-patch-3.2.0.zip 'over' your installation.  

Linux users: set the shell scripts to executable:

cd CTAKES_HOME/bin
chmod ug+x ant ctakes.profile *.sh

2) Unzip YTEX Libraries

Download and unzip ctakes-ytex-lib-3.1.2-SNAPSHOT.zip 'over' your installation. This contains non-APACHE 2.0 license compliant libraries:

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In this file, you specify the database connection parameters. Use CTAKESYou will find templates in CTAKES_HOME\resources\lib\ctakes-ytex-res-[version].jar, under org\apache\ctakes\ytex\ytex.properties.<db type>.example as a templateexample. If you have UMLS installed on your database, specify the umls.schema and umls.catalog properties (see the properties file for an explanation of what these are).

cd %CTAKES_HOME%\resources
mkdir org\apache\ctakes\ytex
@REM extract the mysql example.  change mysql to mssql (for MS SQL Server) or orcl (for Oracle)
jar xf ..\lib\ctakes-ytex-res-*.jar org/apache/ctakes/ytex/ytex.properties.mysql.example
copy org\apache\ctakes\ytex\ytex.properties.mysql.example org\apache\ctakes\ytex\ytex.properties
@REM edit the properties file
notepad org\apache\ctakes\ytex\ytex.properties

cd $CTAKES_HOME/resources
mkdir -p org/apache/ctakes/ytex
# extract the mysql example.  change mysql to mssql (for MS SQL Server) or orcl (for Oracle)
jar xf ../lib/ctakes-ytex-res-*.jar org/apache/ctakes/ytex/ytex.properties.mysql.example
cp org/apache/ctakes/ytex/ytex.properties.mysql.example org/apache/ctakes/ytex/ytex.properties
# edit the properties file
vi org\apache\ctakes\ytex\ytex.properties

6) Install the UMLS in your database (Optional)

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cd /d c:\java\apache-ctakes-3.1.2-SNAPSHOT%CTAKES_HOME%\bin\ctakes-ytex\scripts
..\..\ant.bat -f build-setup.xml all > setup.out 2>&1

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