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cTAKES 3.0 Links

Apache cTAKES web site
Documentation:

These are instructions for installation of cTAKES for developers. With these instructions you can set up your development environment with cTAKES code, change or extend the code, compile the code, and deploy. If you simply want to be a user of the software, refer to the cTAKES 3.0 User Guide.

Knowledge about what the cTAKES components do is not supplied by the install instructions. This is found in the cTAKES 3.0 Component Use Guide. There is no training or documentation (except for code comments) on the code itself. You must familiarize yourself with the components and then study the code on your own to be able to extend it.

In order to modify/compile the source code for a cTAKES component, developers must utilize either an IDE, such as Eclipse, or another editor of your choice. Follow the appropriate sections here depending upon your developer preferences.

Once you have compiled the code you can process documents with the cTAKES components. The documents upon which you can run cTAKES will take many forms. An example of doing this is covered in the Processing Documents section.

The minimal install instructions below are short but require a lot of prerequisite setup on your own. If you need more help then follow the step by step instructions. The step by step instructions for Eclipse assume a Windows or Ubuntu Linux install environment. You will need to extrapolate for any other environments.

Eclipse minimal install instructions

Prerequisites: Java JDK 1.6+, Eclipse IDE 4.2+, subversive plugin (or svn equivalent with appropriate SVN team provider connectors), m2e plugin (or mvn equivalent)

  • Import Project > Maven > Checkout Maven Project from SCM and use: svn and https://svn.apache.org/repos/asf/incubator/ctakes/trunk
  • Select all projects.
  • Wait until Eclipse downloads and builds all of your projects (it may take up to 30 minutes depending on the machine).
    • The various build helpers should run jcasgen and builds the projects for you. There should not be any reason to run mvn install, etc.
  • (Optional) If you would like to launch the UIMA CVD or CPE GUI, run ctakes-clinical-pipeline/resources/launch/UIMA_<CVD | CPE>GUI--clinical_documents pipeline.launch
  • (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

Eclipse step by step install instructions

Preparing Java

Unable to render {include} The included page could not be found.

Preparing Eclipse

If you are going to use Eclipse for development then follow these instructions.

Step

Example

1. Download and install Eclipse 4.2+.

(optional) It is recommended that you start a new workspace to keep your cTAKES projects separate from other work.

No example

2. Subversion Eclipse plug-in (based on Subversive site). We will use the one called "Subversive - SVN Team Provider"

Help -> Install New Software...
Select the current Eclipse release (in the case of Eclipse 4 it is Juno) for the "Work with" field: 

Juno - http://download.eclipse.org/releases/juno

Expand the Collaboration category.
Select "Subversive SVN Team Provider".
Click Next.
Click Next.
Agree to the license agreement.
Click Finish.
Restart Eclipse.

3. Subversion team provider connectors 1.7+.

After restarting Eclipse a dialog will ask you to install an SVN Kit for the Team Provider.
Select SVN Kit 1.7 or greater.
Click Finish.
Click Next.
Click Next.
Agree to the license agreement.
Click Finish.
Accept the security warning (if one appears).
Restart Eclipse.



4. Maven is already part of Eclipse, but more integration to Maven commands is needed.

Help -> Install New Software...
Select the current Eclipse release (in the case of Eclipse 4 it is Juno) for the "Work with" field: 

Juno - http://download.eclipse.org/releases/juno

Expand the Collaboration category.
Select "m2e - Maven Integration for Eclipse".
Click Next.
Click Finish.
Restart Eclipse.

5. Maven SCM connector.

File -> Import ... -> Maven -> Check out Maven Projects from SCM.
Click Next.
Click the "m2e Marketplace" link.
You are now in the m2e Marketplace not the Eclipse Marketplace.
Scroll to and select m2e-subversive.
Click Finish.
Leave the defaults to install the "Maven SCM Handler for Subversive" and click Next.
Click Next.
Accept the license agreement.
Click Finish.
Accept the security warning (if one appears).
Restart Eclipse.



Compile the latest stable release in Eclipse

Step

Example

1. Import the cTAKES projects using Maven.

File -> Import ... -> Maven -> Check out Maven Projects from SCM.
Click Next.


2. For SCM URL use "svn" in the drop-down 

https://svn.apache.org/repos/asf/incubator/ctakes/tags/ctakes-3.0.0-incubating

in the text field.
Click Finish.
Eclipse will download and builds all of the cTAKES projects including running jcasgen as needed. It may take up to 30 minutes depending on your machine and Internet speed.


Process documents using cTAKES

Step

Example

1. Launching the UIMA CAS Visual Debugger (CVD) or the Collection Processing Engine (CPE) from Eclipse can now be accomplished in the ctakes-clinical-pipeline project: 

ctakes-clinical-pipeline/resources/launch/UIMA_<CVD | CPE>GUI--clinical_documents pipeline.launch

where you must select between CVD and CPE in the command. Other Run Configurations are also available in the Eclipse Run menu.


2. (Optional) Process data.

Now that you can launch the tools, the User Guide has steps to walk you through processing test data if you want to go there.

No example

(Optional) UIMA tools plug-in

Developers may be interested in the Eclipse plug-ins provided by the UIMA community. They include, for example, a UIMA component descriptor editor.

Step

Example

1. Find UIMA Eclipse plug-ins.

Help> Install New Software...> Add... button
Set a repository name and this site location 

http://www.apache.org/dist/uima/eclipse-update-site


Click OK.


2. Install UIMA Eclipse plug-ins.

Select the UIMA Eclipse tooling and runtime support.
Click Next.
Leave the defaults and click Next.
Accept the license agreement.
Click Finish.
Restart Eclipse.


3. (optional) Verify the installation of the UIMA Plug-ins. Go to Help -> About Eclipse -> Installation Details -> Plug-ins. You will see a dialog such as that i the next cell with plug-in names starting with "UIMA Eclipse:".


Command line minimal install instructions

Prerequisites: Java JDK 1.6+, SVN, Maven 3.0+

  • svn co https://svn.apache.org/repos/asf/incubator/ctakes/trunk ctakes-3.0
  • mvn clean compile package
    • Running the mvn package command will generate a binary distribution in /ctakes-distribution/target/ctakes-<release>-bin.tar.gz/zip
  • (Optional) If you would like to launch the UIMA CVD or CPE GUI
    • with MAVEN_OPTS="-Xmx1g" run mvn -PrunCVD compile

For further information see the Apache Source Code Repository page.

Command line step by step install instructions

Preparing Java

Unable to render {include} The included page could not be found.

Preparing command line tools

Step

Example

1. Install an SVN client.

Windows:
We used a binary package of Apache Subversion from SlikSVN.
Apache has a larger list here.
Download and run the MSI file.
Click Next.
Accept the license agreement.
Click Next.
Click Next.
Select Typical.
Select Install.
Wait
Click Finish.
Exit and restart any command prompts that were open.

Linux: 

sudo apt-get install subversion


Run svn --version to check the setup

Windows:


Linux: 

The following extra packages will be installed:
  libapr1 libaprutil1 libneon27-gnutls libsvn1
Suggested packages:
  subversion-tools db4.8-util
The following NEW packages will be installed:
  libapr1 libaprutil1 libneon27-gnutls libsvn1 subversion

...

Processing triggers for python-central ...
Processing triggers for man-db ...
Setting up libapr1 (1.4.2-7ubuntu2) ...
Setting up libaprutil1 (1.3.9+dfsg-5ubuntu3) ...
Setting up libneon27-gnutls (0.29.5-3) ...
Setting up libsvn1 (1.6.12dfsg-4ubuntu2) ...
Setting up subversion (1.6.12dfsg-4ubuntu2) ...

2. Install a Maven 3.0+ client.

Windows:
We downloaded Apache Maven file apache-maven-3.0.4-bin.zip. Install instructions are on the same page.
Unzip the file to the root drive.
C:\apache-maven-3.0.4 will be your MAVEN_HOME.

Linux:
We downloaded Apache Maven file apache-maven-3.0.4-bin.tar.gz. Install instructions are on the same page.
Unzip the file to /usr/local/apache-maven-3.0.4 which will be your MAVEN_HOME. 

cd /tmp
wget http://apache.mirrors.pair.com/maven/maven-3/3.0.4/binaries/apache-maven-3.0.4-bin.tar.gz
sudo tar -xvf apache-maven-3.0.4-bin.tar.gz -C /usr/local

Windows:


Linux:

3. Set the Maven environment variable values -
M2_HOME=<MAVEN_HOME>
M2=<MAVEN_HOME>/bin
PATH=<existing Path>;<MAVEN_HOME>
where MAVEN_HOME is the path you unzipped to.

Windows:
Right-click on Computer > Properties > Advanced System Settings > Advanced tab > Environment Variables button > New button for User variables. Once the values are entered click OK until you are out of the dialog series.

Linux: 

export M2_HOME=/usr/local/apache-maven-3.0.4
export M2=$M2_HOME/bin
export PATH=$PATH:$M2

Run mvn --version to check the setup

It is left to the user to make environment variables permanent in their development environment.

Windows:





Linux: 

tbleeker@system:~$ export
...
declare -x M2="/usr/local/apache-maven-3.0.4/bin"
declare -x M2_HOME="/usr/local/apache-maven-3.0.4"
declare -x PATH="/usr/lib/jvm/java-6-sun/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/apache-maven-3.0.4/bin"

Compile the latest stable release from command line

Step

Example

1. Checkout the cTAKES project.

Windows/Linux: 

cd /
svn co https://svn.apache.org/repos/asf/incubator/ctakes/tags/ctakes-3.0.0-incubating cTAKES-3.0

The parameter on the end will be created as a new directory in your current location.

For Linux, make sure that you have write access to the directory that you are in.

Windows: 

C:\>cd /
C:\>svn co https://svn.apache.org/repos/asf/incubator/ctakes/tags/ctakes-3.0.0-incubating cTAKES-3.0

 ...

A ctakes-3.0\ctakes-type-system\pom.xml
A ctakes-3.0\ctakes-type-system\.settings
A ctakes-3.0\ctakes-type-system\.settings\org.eclipse.jdt.core.prefs
A ctakes-3.0\ctakes-type-system\.settings\org.eclipse.core.resources.prefs
A ctakes-3.0\ctakes-type-system\desc
A ctakes-3.0\DISCLAIMER
Checked out revision 1433729.

C:\>cd cTAKES-3.0
C:\cTAKES-3.0>

Linux: 

tbleeker@system:~$ cd /
tbleeker@system:/$ svn co https://svn.apache.org/repos/asf/incubator/ctakes/tags/ctakes-3.0.0-incubating cTAKES-3.0

...

A ctakes-3.0/ctakes-type-system/pom.xml
A ctakes-3.0/ctakes-type-system/.settings
A ctakes-3.0/ctakes-type-system/.settings/org.eclipse.jdt.core.prefs
A ctakes-3.0/ctakes-type-system/.settings/org.eclipse.core.resources.prefs
A ctakes-3.0/ctakes-type-system/desc
A ctakes-3.0/DISCLAIMER
Checked out revision 1434842.

tbleeker@system:/$ cd cTAKES-3.0/
tbleeker@system:/cTAKES-3.0$

2. Compile the complete set.

Make sure you are in the proper directory.

Windows/Linux: 

mvn clean compile package

For Linux, make sure you are using the user that has access to the files in your cTAKES directory.

Windows/Linux: 

...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Apache cTAKES ..................................... SUCCESS [59.140s]
[INFO] Apache cTAKES common type system .................. SUCCESS [41.856s]
[INFO] Apache cTAKES utils ............................... SUCCESS [6.255s]
[INFO] Apache cTAKES core ................................ SUCCESS [17.940s]
[INFO] Apache cTAKES part-of-speech tagger ............... SUCCESS [5.148s]
[INFO] Apache cTAKES chunker ............................. SUCCESS [3.027s]
[INFO] Apache cTAKES document preprocessor ............... SUCCESS [4.118s]
[INFO] Apache cTAKES dictionary lookup ................... SUCCESS [1:14.740s]
[INFO] Apache cTAKES context dependent tokenizer ......... SUCCESS [5.975s]
[INFO] Apache cTAKES LVG lexical tools ................... SUCCESS [7.831s]
[INFO] Apache cTAKES named entity contexts ............... SUCCESS [4.743s]
[INFO] Apache cTAKES Constituency Parser ................. SUCCESS [9.516s]
[INFO] Apache cTAKES Dependency Parser ................... SUCCESS [32.386s]
[INFO] Apache cTAKES Assertion's zoner ................... SUCCESS [2.152s]
[INFO] Apache cTAKES Assertion ........................... SUCCESS [12.200s]
[INFO] Apache cTAKES ctakes-clinical-pipeline ............ SUCCESS [4.446s]
[INFO] Apache cTAKES Relation Extractor .................. SUCCESS [13.634s]
[INFO] Apache cTAKES CoReference Resolver ................ SUCCESS [8.923s]
[INFO] Apache cTAKES Drug NER ............................ SUCCESS [6.958s]
[INFO] Apache cTAKES Side Effects ........................ SUCCESS [7.566s]
[INFO] Apache cTAKES Smoking Status ...................... SUCCESS [8.377s]
[INFO] Apache cTAKES Pad Term Spotter .................... SUCCESS [9.048s]
[INFO] Apache cTAKES Temporal Information Extraction ..... SUCCESS [33.993s]
[INFO] Apache cTAKES Distribution ........................ SUCCESS [17:59.809s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 24:22.120s
[INFO] Finished at: Wed Jan 16 17:44:35 CST 2013
[INFO] Final Memory: 41M/181M
[INFO] ------------------------------------------------------------------------
...

Process documents using cTAKES

Step

Example

1. Launching the UIMA CAS Visual Debugger (CVD) or the Collection Processing Engine (CPE) from Eclipse can now be accomplished in the ctakes-clinical-pipeline project: 

export MAVEN_OPTS="-Xmx1g"
mvn -Prun<CVD | CPE> compile

where you must select between CVD and CPE in the command. Other Run Configurations are also available in the Eclipse Run menu.

No example

2. (Optional) Process data.

Now that you can launch the tools, the User Guide has steps to walk you through processing test data if you want to go there.

No example

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