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cTAKES 3.0 Links

Apache cTAKES web site
Documentation:

WARNING: Newer instructions

NOTE: The information here is largely for the ctakes 2.5 build process (eclipse based with some ant). ctakes 3.x under apache now uses a maven based build process. Please see the following web site for current build instructions: http://incubator.apache.org/ctakes/3.0.0/developer-guide-3.0

(should these instructions be copied into this wiki page?)
YES! The original contents were just a start to the page and it should be changed over into what it takes now for 3.0.
The user doc and the developer doc that started on the incubator site should both be moved here and the ain site should point to this doc. The same groups should be covered, meaning developers using Eclipse or the command line.

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 expert instructions below are short and require a lot of prerequisite setup on your own. If you need more help then follow the step by step instructions.

Expert install instructions (for Eclipse)

Prerequisites

Using Eclipse IDE

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

*Import Project > Maven > Checkout Maven Project from SCM
*Use: svn: 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 mins depending on the machine). The various build helpers should run jcasgen and builds the projects for you (there shouldn't be a need to run mvn install, etc.)
*(Optional) If you would like to launch the UIMA CVD/CPE GUI, run ctakes-clinical-pipeline/resources/launch/UIMA_

Unknown macro: {CVD/CPE}

GUI--clinical_documents pipeline.launch.

Using Command Line

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

*svn co https://svn.apache.org/repos/asf/incubator/ctakes/trunk ctakes
*mvn clean compile package
*(Optional) If you would like to launch the UIMA CVD/CPE GUI, run $ MAVEN_OPTS="-Xmx1g" mvn -PrunCVD compile
Notes: If you run the mvn package, it will generate a binary distribution in /ctakes-distribution/target/ctakes-

Unknown macro: {release}

-bin.tar.gz/zip.

For further information see the Apache Source Code Repository page.

Step by Step install instructions (for Eclipse)

Prerequisites

Preparing Java

Step

Example

1. All forms of development require the Java SDK 1.6+. You can get it from java.com.

Make sure you get the proper version and install the SDK not just the Java Runtime environment.

To check if you have the SDK, look in the lib directory of the Java install and see if the file tools.jar is there. If there is a lib directory and there is a file by that name then you have the SDK.

To check if you have the proper version. Enter the command:
Windows and Linux: 

java -version


on any command line to see what version you have now. 

C:\>java -version
java version "1.6.0_20"
Java(TM) SE Runtime Environment (build 1.6.0_20-b02)
Java HotSpot(TM) Client VM (build 16.3-b01, mixed mode, sharing)

2. It is possible that some commands and programs can find the Java runtime that you want to be used but it is best to set the JAVA_HOME environment variable. Set the value of JAVA_HOME to the absolute path of the root of the Java Runtime environment that you want UIMA and cTAKES to use.
Windows:
Right-click on Computer > Properties > Advanced System Settings > Advanced tab > Environment Variables button > New button for System variables. Once the values are entered click OK until you are out of the dialog series.
Linux: 

export JAVA_HOME=<path>

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Preparing Eclipse

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

Step

Example

1. Download and install Eclipse if you don't already have it.

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

No example

2. 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.

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3. Install UIMA Eclipse plug-ins.

Select the UIMA Eclipse tooling and runtime support.
Click *Next >*and finish the install.

Additional help can be found on the Apache site UIMA for Eclipse on apache.org.

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Note

These install instructions depend upon the installation of these plug-ins.



(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 on the right (next cell) with plug-in names starting with "UIMA Eclipse:".

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Compile the latest stable release in Eclipse

A tested and stable release is delivered as a ZIP file. The cTAKES source code is included in the file as well as UIMA.

Step

Example

1. Navigate to the source downloads for areleased version on SourceForge.net

Even without the full LVG data, cTAKES is about 790 MB when compressed.

2. Download the latest version.

Select the directory for the latest version and download the *ZIP*file.

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3.
Unzip the file you downloaded into a directory that you want to be the
cTAKES install location. It will expand to about 1.4GB.
Windows: 

c:\cTAKES-3.0


Linux: 

/usr/bin/cTAKES-3.0



This folder we will call <cTAKES_HOME>. You will need to refer to the directory later.

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4. Set UIMA_HOME. UIMA requires a special environment variable for its commands to run.

Use the absolute path to the <cTAKES_HOME> directory in the previous step as the value.

Windows:
Right-click on Computer> Properties> Advanced> *Environment Variables*button > *New*button for System variables. Keep clicking *OK*until you are out of the dialog series.
Linux:
Use the command export UIMA_HOME=<cTAKES_HOME> for example: 

export UIMA_HOME=/usr/bin/cTAKES-3.0

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5. Edit PATH. This will be used for any command line access to binaries.
Windows:
Right-click on Computer> Properties> Advanced> *Environment Variables*button. Edit the *Path*environment variable adding *;<cTAKES_HOME>\bin*to the end. Keep clicking *OK*until you are out of the dialog series.
Linux:
Use the command export PATH=%PATH%:<cTAKES_HOME>/bin for example 

export PATH=%PATH%:/usr/bin/cTAKES-3.0/bin

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6. In Eclipse use File > New > Java Project ...

Uncheck Use default location*and navigate to *<cTAKES_HOME>*for location Click *Next>*Click *Finish.

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7. Remove unnecessary JAR files.

Go to Project> Properties> Java Build Path> Libraries. Select all the entries except the JRE System Library and click the *Remove*button.

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8. Add cTAKES folders as class resources.

Select Add Class Folder. Check the two class folders cTAKESdesc*and *resources. Click OK.

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9. Add JAR files from <cTAKES_HOME>/lib.

Select Add Library*button > *User Library*list item > *Next >*button > *User Libraries*button > *New*button. Name the new user library *ctakes3.0lib*and click *OK. Click the Add JARs...*button and Navigate to <cTAKES_HOME>\lib*. Select all the JAR files and click Open. Click OK. Click Finish.

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10. Close the User Libraries dialog.

Click OK. Your Package Explorer should look something like this (next cell).

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11. If you have Eclipse set to build automatically it will do so and you may continue to run and debug from Eclipse.

You can also setup Eclipse to run Ant builds using the Ant files shipped as seen on the right (next cell).

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Compile a development release from SVN in Eclipse

If you know what you are doing with the cTAKES code and you must get the latest code currently under development (potentially unstable), then you need to use an SVN connection to retrieve the code.

Step

Example

1. Install subversion or a suitable plug-in for your IDE.

No example

2. Check-out the code to a local directory, such as: 

c:\cTAKES-3.0


This folder we will call <cTAKES_HOME>. You will need to refer to the directory later.
Pre-release versions are available from: 

svn checkout https://ohnlp.svn.sourceforge.net/svnroot/ohnlp/trunk/cTAKES


If you are checking out via Subclipse in Eclipse, make sure to check out each project separately.

 
...
A cTAKES\PAD term spotter\desc\type_system
A cTAKES\PAD term spotter\desc\type_system\PADSiteAndTerm.xml
A cTAKES\PAD term spotter\desc\analysis_engine
A cTAKES\PAD term spotter\desc\analysis_engine\Radiology_TermSpotterAnnotatorTAEStyleMap.xml
A cTAKES\PAD term spotter\desc\analysis_engine\Radiology_TermSpotterAnnotatorTAE.xml
A cTAKES\PAD term spotter\desc\analysis_engine\DxStatusAnnotator.xml
A cTAKES\PAD term spotter\desc\analysis_engine\NegationDxAnnotator.xml
A cTAKES\PAD term spotter\desc\analysis_engine\PAD_Hit.xml
A cTAKES\PAD term spotter\desc\analysis_engine\SubSectionBoundaryAnnotator.xml
A cTAKES\PAD term spotter\desc\analysis_engine\Radiology_DictionaryLookupCSVAnnotator.xml
A cTAKES\PAD term spotter\desc\collection_processing_engine
A cTAKES\PAD term spotter\desc\collection_processing_engine\Radiology_sample.xml
A cTAKES\PAD term spotter\desc\collection_reader
A cTAKES\PAD term spotter\desc\collection_reader\RadiologyRecordsCollectionReader.xml
A cTAKES\PAD term spotter\.settings
A cTAKES\PAD term spotter\.settings\org.eclipse.jdt.ui.prefs
Checked out revision 667.

3. In Eclipse use File > Import... > General > Existing Projects into Workspace

Use your local directory for the root directory. Leave all of the projects selected and click Finish.

It may be necessary to import each project one by one!

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4. Install UIMA 2.4. Make note of UIMA_HOME.

No example

5. Add UIMA JARs to the build path configuration in Eclipse. Add all JARs from: 

<UIMA_HOME>/lib
  • jVinci.jar
  • uima-adapter-soap.jar
  • uima-adapter-vinci.jar
  • uima-core.jar
  • uima-cpe.jar
  • uima-documentation-annotation.jar
  • uima-examples.jar
  • uima-bootstrap.jar
  • uima-tools.jar

6. Generate the common type system.

A bug in the ordering and generation currently requires that you go to your project properties> Java Build Path> *Order and Export*and move the *auto_generatesrc*directory to the top of the list.

Right-click on /cTAKESdesc/typesysytem/common_type_system.xml*and select *Open With> Component Descriptor Editor.
Click the *Type System*tab then the *JCasGen*button (in the center).

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Step by Step install instructions (for command line)

Preparing Command Line Tools

If you are going to use command line only to compile then you will need these tools.

Step

Example

1. Navigate to the Ant download site on apache.org and install Ant 1.7.1+

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2. Download Ant 1.7.1+. Unzip the file you downloaded to a local directory. We will call this <ANT_HOME> Follow the instructions for installing Ant on apache.org. This will include changing the PATH and ANT_HOME environment variables.

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The UIMA command to generate the type system through the command line (JCasGen) is not shipped with cTAKES at this time. The common type system has already been generated for you. If you need, for some reason, to generate this then you will need to use the method described for Eclipse or install the entire UIMA SDK.

Step

Example

1. Follow the first steps of the "Compile the latest stable release in Eclipse" (which do not require Eclipse) until you get to the part about creating a new project in Eclipse.

No example

2. Obtain the relevant build.xml file from SVN, placing it into <cTAKES_HOME>

It can be found at https://ohnlp.svn.sourceforge.net/svnroot/ohnlp/trunk/icTAKES/build.xml
Be aware there are multiple build.xml files in SVN. be sure to use the one listed above

No example

3. To compile cTAKES, change to the <cTAKES_HOME> directory and simply run: 

ant

No example

Process documents using cTAKES

You can now launch or debug the cTAKES components that you have built. You could run commands from a command prompt, as found in the [user install instructions], but you can launch them from within Eclipse now instead. Launching the CAS Visual Debugger (CVD) and the Collection processing engine (CPE) from Eclipse is as simple as following this step.

Step

Example

1. In Eclipse, launch the tools using their main program.

Find in the Eclipse project: src-> edu.mayo.bmi.ctakes.main> cTAKESCPEGUI.java*or *cTAKESCVDGUI.java. Then use the Run menu to run or debug as desired. Using the tools does not change from what is documented in the [user install instructions].

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