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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.
Warning |
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This page is still under construction. |
Eclipse minimal install instructions
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Step | Example |
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1. Checkout the cTAKES project.
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. |
Windows/Linux:
Code Block |
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| cd /
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. Note |
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For Linux, make sure that you have write access to the directory that you are in. |
| Windows:
Code Block |
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| C:\>cd /
C:\>svn co https://svn.apache.org/repos/asf/incubator/ctakes/trunk cTAKES-3.0
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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
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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$ |
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2. Download cTAKES 3.0 Dictionaries and models.
Info |
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Due to licensing considerations and easy of installability, one download from an external location was established with all the resources you will need. Licensing for these resources is found within the download. |
Info |
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Download time will be commensurate with 1GB of data. |
Windows: Go to cTAKES resources and download the ZIP file with a matching version from the ctakesresources project. Unzip the files into a temporary location such as C:\temp.
Linux: Obtain the URL of the version matching ZIP file from cTAKES resources, get the file, and unzip to a temporary location.
| Windows:
Linux:
Code Block |
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| cd /tmp
wget http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.0.1.zip
sudo unzip ctakes-resources-3.0.1.zip |
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3. Copy (or move) the resources to cTAKES_HOME. With Eclipse, cTAKES_HOME will be your workspace location followed by the project name "ctakes". Copy the contents of the temporary resources directory (and all sub-directories) to <cTAKES_HOME>/ctakes-dictionary-lookup/resources.
Info |
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There may be conflicts while taking this action. Overwrite the cTAKES_HOME files with those in the resources download. |
| Windows:
Code Block |
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| xcopy /s C:\temp\ctakes-resources-3.0.1\resources C:\cTAKES-3.0\ctakes-dictionary-lookup\resources |
Linux:
Code Block |
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| sudo cp -R /tmp/resources/* /cTAKES-3.0/ctakes-dictionary-lookup/resources |
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4. Compile the complete set.
Make sure you are in the proper directory.
Windows/Linux:
Code Block |
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| cd cTAKES-3.0
mvn clean compile package |
Note |
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For Linux, make sure you are using the user that has access to the files in your cTAKES directory. |
Info |
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Instead of "compile" you can use the maven target called "package" to compile and build all the cTAKES deliverables. Package is convenient in situations like running cTAKES outside of maven with custom processes/scripts because it will bundle up all of the 3rd party and transient dependencies. |
| Windows/Linux:
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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 [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] ------------------------------------------------------------------------
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5. Add the resources as a folder to the classpath. Make sure the current path or dot (.) is in your CLASSPATH environment variable accessible to the process maven is running in. | No example |
6. UMLS user ID and password. Usually the dictionaries are required to process data. If you plan to utilize the UMLS dictionaries you must pass your UMLS user ID and password to the pipeline. There are several ways to do this - select one. Note |
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If you do not have a UMLS username and password, you may request one at UMLS Terminology Services |
# Environment variable - Set or export environment variables. Refer to the Eclipse documentation above for more information. - Add the system properties to the Java arguments for the maven environment.
Add these parameters to the MAVEN_OPTS environment variable in the next section as you run the commands to process documents.
No Format |
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-Dctakes.umlsuser=<username> -Dctakes.umlspw=<password>
| Make the ID and password specific to you. - Change the UMLSUser and UMLSPW <nameValuePair> strings in these descriptor files with your UMLS username and password.
Refer to the Eclipse documentation above for more information.
| No example |
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