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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
...
Code Block | ||
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java -version |
...
Code Block | ||
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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:
Code Block | ||
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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
...
No example
...
Code Block |
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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.
...
...
...
Code Block |
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Juno - http://download.eclipse.org/releases/juno |
Expand the Collaboration category.
Select "m2e - Maven Integration for Eclipse".
Click Next.
Click Finish.
Restart Eclipse.
...
...
Compile the latest stable release in Eclipse
...
Step
...
Example
...
...
2. For SCM URL use "svn" in the drop-down
Code Block |
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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
...
Code Block |
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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.
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 Install 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)
Info |
---|
The following location is the main trunk of cTAKES. See how cTAKES treats the trunk, branches, and tags in the developer FAQs. |
- Import Project > Maven > Checkout Maven Project from SCM and use: svn and https://svn.apache.org/repos/asf/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 build the projects for you. There should not be any reason to run mvn install, etc.
- Merge the version-matching resources ZIP file from http://sourceforge.net/projects/ctakesresources/files/ into your ctakes-dictionary-lookup project.
- (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
Include Page | ||||
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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"
Expand the Collaboration category. | ||||||
3. Subversion team provider connectors 1.7+. | ||||||
4. Maven is already part of Eclipse, but more integration to Maven commands is needed.
Expand the Collaboration category. | ||||||
5. Maven SCM connector. |
Compile a release in Eclipse
Step | Example | ||||||||||||
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1. Import the cTAKES projects using Maven. | |||||||||||||
2. For SCM URL use "svn" in the drop-down and this in the text field
Click Finish.
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3. Download cTAKES 3.0 Dictionaries and models.
| Windows:
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4. Copy (or move) the resources to cTAKES_HOME.
| Windows:
Linux:
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5. Refresh Eclipse. | No example | ||||||||||||
6. Add ctakes-dictionary-lookup/resources as a folder to the classpath. | |||||||||||||
7. UMLS user ID and password.
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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. Navigate to:
where you must select between CVD and CPE in the command. Right-click on the launch file and select Run-As -> UIMA_<CVD | CPE>GUI-clinical_documents.
| ||||||||
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.
| ||||||
2. Install UIMA Eclipse plug-ins. | ||||||
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+
Info |
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The following location is the main trunk of cTAKES. See how cTAKES treats the trunk, branches, and tags in the developer FAQs. |
- svn co https://svn.apache.org/repos/asf/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
- Merge the version-matching resources ZIP file from http://sourceforge.net/projects/ctakesresources/files/ into your ctakes-dictionary-lookup project.
- (Optional) If you would like to launch the UIMA CVD or CPE GUI
- with MAVEN_OPTS="-Xmx2g -Xms1g" run mvn -PrunCVD compile
For further information see the Apache Source Code Repository page.
Command line step by step install instructions
Preparing Java
Include Page | ||||
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Preparing command line tools
Step | Example | ||||||||||||||
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1. Install an SVN client.
| Windows:
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2. Install a Maven 3.0+ client. Unzip the file to the root drive. Unzip the file to /usr/local/apache-maven-3.0.4 which will be your MAVEN_HOME.
| Windows: | ||||||||||||||
3. Set the Maven environment variable values -
| Windows:
|
Compile a release from command line
Step | Example | |||||||||||||||||||
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1. Checkout the cTAKES project.
The parameter on the end will be created as a new directory in your current location.
We will refer to the directory you specify at the end of the checkout command as <cTAKES_HOME>. | Windows:
Linux:
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2. Download cTAKES 3.0 Dictionaries and models.
| Windows:
| |||||||||||||||||||
3. Copy (or move) the resources to cTAKES_HOME.
| Windows:
Linux:
| |||||||||||||||||||
4. Compile the complete set.
| Windows/Linux:
|
...
...
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
...
Code Block | ||
---|---|---|
| ||
http://www.apache.org/dist/uima/eclipse-update-site
|
...
...
...
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, 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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Code Block |
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apt-get install subversion |
Info |
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Run svn --version to check the setup |
Linux:
Code Block |
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Suggested packages:
subversion-tools
The following NEW packages will be installed:
subversion
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 385kB of archives.
After this operation, 4,391kB of additional disk space will be used.
Get:1 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ lucid-updates/main subversion 1.6.6dfsg-2ubuntu1.3 \[385kB\]
Fetched 385kB in 0s (2,396kB/s)
Selecting previously deselected package subversion.
(Reading database ... 131403 files and directories currently installed.)
Unpacking subversion (from .../subversion_1.6.6dfsg-2ubuntu1.3_amd64.deb) ...
Processing triggers for man-db ...
Setting up subversion (1.6.6dfsg-2ubuntu1.3) ... |
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.
Code Block |
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cd /tmp
wget http://apache.mirrors.pair.com/maven/maven-3/3.0.4/binaries/apache-maven-3.0.4-bin.tar.gz
tar -xvf apache-maven-3.0.4-bin.tar.gz -C /usr/local |
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:
Code Block |
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export M2_HOME=/usr/local/apache-maven-3.0.4
export M2=$M2_HOME/bin
export PATH=$PATH:$M2 |
Info |
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Run mvn --version to check the setup |
Linux:
Code Block |
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tbleeker@system:~$ 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" |
Windows/Linux:
Code Block |
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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:
Code Block |
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C:\>cd \
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:
Code Block |
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tbleeker@system:~$ cd /
tbleeker@system:/$ 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 1434842.
tbleeker@system:/$ cd cTAKES-3.0/
tbleeker@system:/cTAKES-3.0$ |
Make sure you are in the proper directory.
Windows/Linux:
Code Block |
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mvn clean compile package |
Windows:
Code Block |
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[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 [759.831s140s] [INFO] Apache cTAKES namedcommon entitytype contextssystem .................. SUCCESS [441.743s856s] [INFO] Apache cTAKES Constituency Parser utils ............................... SUCCESS [96.516s255s] [INFO] Apache cTAKES Dependencycore Parser .................... SUCCESS [32.386s............ SUCCESS [17.940s] [INFO] Apache cTAKES Assertion's zonerpart-of-speech tagger ................... SUCCESS [25.152s148s] [INFO] Apache cTAKES Assertionchunker ............................. SUCCESS [123.200s027s] [INFO] Apache cTAKES ctakes-clinical-pipeline document preprocessor ............... SUCCESS [4.446s118s] [INFO] Apache cTAKES Relationdictionary Extractorlookup ................... SUCCESS [131:14.634s740s] [INFO] Apache cTAKES CoReferencecontext dependent Resolvertokenizer ................ SUCCESS [8.923s SUCCESS [5.975s] [INFO] Apache cTAKES DrugLVG lexical NERtools ............................ SUCCESS [67.958s831s] [INFO] Apache cTAKES Sidenamed entity Effectscontexts ........................ SUCCESS [74.566s743s] [INFO] Apache cTAKES SmokingConstituency StatusParser ...................... SUCCESS [89.377s516s] [INFO] Apache cTAKES PadDependency TermParser Spotter .................... SUCCESS [932.048s386s] [INFO] Apache cTAKES TemporalAssertion's Information Extraction zoner ................... SUCCESS [332.993s152s] [INFO] Apache cTAKES DistributionAssertion ........................... SUCCESS [17:5912.809s200s] [INFO] Apache cTAKES ctakes------------------------------------------------------------------------ [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] ---------------------------------------------------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] ------------------------------ |
...
| |||||
5. Add the resources as a folder to the classpath. | No example | ||||
6. UMLS user ID and password.
| No example |
Process documents using cTAKES
Step | Example | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1. Launching the UIMA CAS Visual Debugger (CVD) or the Collection Processing Engine (CPE) can now be accomplished in the ctakes-clinical-pipeline project:
Linux:
where you must select between CVD and CPE in the command. | |||||||||||
2. (Optional) Process data.
| No example |
Next Steps
The cTAKES 3.0 Component Use Guide will help you to understand, in great detail, each of the cTAKES components that have been installed. In some cases you can learn how to improve the components.
Also, before you go on to process text in production you will need to consider dictionaries and models. cTAKES does not distribute from Apache a complete dictionary capable of annotating production data. The models provided have been trained on data that may not match your data well enough to be effective. In most cases, you will need to modify the dictionaries and train models on your own data to be effective.