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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.

Eclipse

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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

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Eclipse step by step install instructions

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:

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java -version


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

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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:

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export JAVA_HOME=<path>


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:

Code Block
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:

Code Block
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

Code Block
https://svn.apache.org/repos/asf/incubator/ctakes/trunk

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:

Code Block
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

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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

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minimal install instructions

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

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For further information see the Apache Source Code Repository page.

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Command line step by step install instructions

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Preparing

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command line

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tools

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Step

Example

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

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.

Info

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.

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Step

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Example

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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.

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No example

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Install SVN

 

2. Create a directory for your cTAKES project.
Windows/Linux:

Code Block
mkdir cTAKES-3.0
cd cTAKES-3.0

We'll call this CTAKES_HOME


3. Checkout the cTAKES project.

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svn co https://svn.apache.org/repos/asf/incubator/ctakes/trunk ctakes-3.0

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4. Compile the complete set.

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mvn clean compile package



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No example

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

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ant

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Process documents using cTAKES