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Please see information regarding new UMLS dictionary Authentication at cTAKES 4.0.0.1

About

These are instructions for installation of cTAKES for developers. With these instructions you can set up your development environment with cTAKES code so you can compile the code and change or extend it. If you simply want to be a user of the software, refer to the the cTAKES 4.0 User Install Guide.These install instructions do not supply knowledge of what the cTAKES components do. That is found in the cTAKES 4.0 Component Use Guide and the pages for the individual components.Guide.

These install instructions do not supply knowledge of what the cTAKES components do. That is found in the cTAKES 4.0 Component Use Guide and the pages for the individual components.

Getting the code

Subversion

Subversion is the default VCS used by cTAKES.

export CTAKES_DEV_HOME=~/projects/ctakes

cd ${CTAKES_DEV_HOME}
svn checkout https://svn.apache.org/repos/asf/ctakes/trunk
export CTAKES_SRC_HOME=${CTAKES_DEV_HOME}/trunk
cd ${CTAKES_SRC_HOME}

Build

The standard Maven command for building cTAKES is:

$  mvn clean package -DskipTests=true

If you would like to build with the same settings as the default Jenkins job (recommended only for committers), use:

$ rm -fr /tmp/ctakes-*
$ exports MAVEN_OPTS='-Xms3072m -Xmx4g -Xss128M  -XX:+CMSClassUnloadingEnabled -XX:-UseGCOverheadLimit -Dmaven.test.failure.ignore=false'
$  mvn --fail-at-end --errors --update-snapshots clean install sonar:sonar -DskipTests=false -Dsonar.scm.provider=svn -Dsonar.host.url=https://builds.apache.org/analysis

IDE based installs

Below are instructions for Eclipse and for IntelliJ

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• These steps assume a Windows or Ubuntu Linux install environment. You will need to extrapolate for any other environments.
• These steps were written using Mars aka Eclipse 4.5. You may need to adapt some steps for other versions of Eclipse.
• Recommend searching for "Eclipse IDE for Java Developers" and downloading the desired version 
• Within Eclipse, install the Maven SCM connector
  • File -> Import -> Maven -> Check out Maven Projects from SCM
  • Click Next.
  • Click the "m2e Marketplace" link (somewhat above the Cancel button)
  • You are now in the m2e Marketplace not the Eclipse Marketplace. 
  • Scroll to and select m2e-subversive
  • Click Next, Next, the radio button for Accept, Finish
  • restart Eclipse when prompted
    
• Within Eclipse, install the Subversive Connector
• Again, use  File -> Import -> Maven -> Check out Maven Projects from SCM
• The Install Connectors window will open.
• Select one of them and install it: (On Windows 7 Pro, "Native JavaHL 1.8.14 (64 bit" works
  • Click Finish
  • Accept the install by clicking:  Next, Next, the radio button for Accept, Finish.
• When prompted to restart Eclipse, Click Yes
   
•  You can set your UMLS userID and password to be passed to all Java programs you launch within Eclipse, using Windows->Preferences->Java->Installed JREs->(highlight the JRE you are using)->Edit->Default VM arguments:
             -Dctakes.umlsuser=YourUmlsUserIdGoesHere  "-Dctakes.umlspw=YourUmlsPasswordGoesHere"
• Check out cTAKES:  
• For a third time, Import-> Maven -> Check out Maven Projects from SCM
• For SCM URL, select svn and in the text field enter:  https://svn.apache.org/repos/asf/ctakes/trunk

• Click Finish. Eclipse will download all of the cTAKES sub-projects

  Info
  Due to the way Maven and Eclipse work together you will see two copies of the sub-projects in Eclipse. If you look into your workspace directories there is only one set of underlying files.

   
  

• If you don't have Eclipse set to Build Automatically, you'll need perform a build:

  • Select all projects, right click, and choose Maven->Update Projects. Click Select All, and click OK to start the maven build.

  • You can view the Progress pane by using the Eclipse menu option  Window->Show View->Progress

  • Performing a maven build includes running jcasgen as needed. 

• The dictionary for the Fast Dictionary Lookup was downloaded as part of the Maven build.
• If you want to use the full LVG or original dictionary lookup, merge resources from https://sourceforge.net/projects/ctakesresources/files/ctakes-resources-4.0-bin.zip/download into the relevant subproject.
• (Optional) UIMA plug-ins called "UIMA Eclipse tooling and runtime support" can be installed from update site: http://www.apache.org/dist/uima/eclipse-update-site 
  
  

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> set ctakes_umlsuser=<your user>
> set ctakes_umlspw=<your password>
> mvn clean test
> REM or running oneline command:
> mvn -Dctakes_umlsuser=<your user> -Dctakes_umlspw=<your password> clean test

$ export ctakes_umlsuser=<your user>
$ export ctakes_umlspw=<your password>
$ mvn clean test
$ # or running oneline command:
$ mvn -Dctakes_umlsuser=<your user> -Dctakes_umlspw=<your password> clean test

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