WARNING: Newer instructions |
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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?) |
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 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
Step |
Example |
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1. All forms of development require the Java SDK 1.6+. You can get it from java.com. java -version |
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. 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 |
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1. Download and install Eclipse 4.2+. |
No example |
2. Subversion Eclipse plug-in (based on Subversive site). We will use the one called "Subversive - SVN Team Provider" Juno - http://download.eclipse.org/releases/juno Expand the Collaboration category. |
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3. Subversion team provider connectors 1.7+. |
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4. Maven is already part of Eclipse, but more integration to Maven commands is needed. Juno - http://download.eclipse.org/releases/juno Expand the Collaboration category. |
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5. Maven SCM connector. |
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Compile the latest stable release in Eclipse
Step |
Example |
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1. Import the cTAKES projects using Maven. |
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2. For SCM URL use "svn" in the drop-down https://svn.apache.org/repos/asf/incubator/ctakes/trunk in the text field. |
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Process documents using cTAKES
Step |
Example |
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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. |
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2. (Optional) Process data. |
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 |
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1. Find UIMA Eclipse plug-ins. http://www.apache.org/dist/uima/eclipse-update-site |
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2. Install UIMA Eclipse plug-ins. |
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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:". |
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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, run $ MAVEN_OPTS="-Xmx1g" mvn -PrunCVD compile
For further information see the Apache Source Code Repository page.
Command line step by step install instructions
Preparing command line tools
Step |
Example |
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1. Install an SVN client. apt-get install subversion apt-get install libapache2-svn
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Windows: |
2. Install a Maven 3.0+ client. |
Run svn --version to check the setup
| Windows:
19
Linux:
23
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3. Set the Maven environment variable values - export M2_HOME=/usr/local/apache-maven/apache-maven-3.0.4 export M2=$M2_HOME/bin export PATH=$PATH:$M2 mvn --version Run mvn --version to check the setup |
Windows: |
3. Checkout the cTAKES project. svn co https://svn.apache.org/repos/asf/incubator/ctakes/trunk cTAKES-3.0 The parameter on the end will be created as a new directory in your current location. |
Windows: C:\>svn co https://svn.apache.org/repos/asf/incubator/ctakes/trunk 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: |
4. Compile the complete set. mvn clean compile package
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Windows: |