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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 and this in the text field

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

Click Finish.
Eclipse will download and build all of the cTAKES sub-projects including running jcasgen as needed.

3. Download cTAKES 3.0 Dictionaries and models.

Go to http://sourceforge.net/projects/ctakesresources/files/ and download the ZIP file with a matching version from the ctakesresources project.
Download time will be commensurate with 1GB of data.
Unzip the files into a temporary location.

Windows:

C:\temp\ctakes-resources-3.0.1\resources

Linux:

/tmp/ctakes-resources-3.0.1/resources

4. 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.

Windows:

xcopy /s C:\temp\ctakes-resources-3.0.1\resources C:\Users\<userID>\workspace\ctakes\ctakes-dictionary-lookup\resources

Linux:

copy /tmp/ctakes-resources-3.0.1/resources/* /usr/local/apache-ctakes-3.0.0-incubating/ctakes-dictionary-lookup/resources/*

5. Refresh Eclipse.

You must refresh your Eclipse projects to make sure that Eclipse knows about the new directories and data.

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6. Add the resources as a folder to the classpath.
You will need to repeat this step for ALL project that you wish to use the resources (nearly all of them do except for ctakes-relation-extractor). For example:

Open the properties on the top-level project ctake-clicical-pipeline. For Eclipse, do not select the one under the ctakes project but the sibling to that at the highest level. Select Java Build Path -> Libraries tab -> Add Class Folder ... button.
Select the resources directory under the ctakes-dictionary-lookup.
Click OK on all dialogs until you are out of the sequence.

7. 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.

1. Environment variable - Set or export environment variable
   
   

   No Format
   export ctakes.umlsuser=<username>, ctakes.umlspw=<password>

2. Add the system properties to the Java arguments for a run configuration (shown in the next cell). Navigate to ctakes-clinical-pipeline -> resources -> launch > UIMA_<CVD | CPE>GUI--clinical_documents pipeline.launch. Right-click on the launch file and select Run-As -> Run Configurations... In the Arguments tab enter these parameters in the VM. Click Apply.
   
   

   No Format
   -Dctakes.umlsuser=<username> -Dctakes.umlspw=<password>

3. Change the UMLSUser and UMLSPW <nameValuePair> strings in these descriptor files with your UMLS username and password.
   
   • Dictionary Lookup: <cTAKES_HOME>/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml* (optional) Drug NER: <cTAKES_HOME>/desc/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
     The following shows where in the files you would make the changes. (Do not change the <configurationParameters> by the same name.)
     

     Code Block
     language none
     <nameValuePair> <name>ctakes.umlsuser</name> <value> <string>YOUR_UMLS_USERNAME_HERE</string> </value> </nameValuePair> <nameValuePair> <name>ctakes.umlspw</name> <value> <string>YOUR_UMLS_PASSWORD_HERE</string> </value> </nameValuePair>

   • Now include the DictionaryLookupAnnotatorUMLS.xml Analysis Engine within your aggregate Analysis Engine or switch to the ones provided by cTAKES. cTAKES has provided duplicates of shipped Analysis Engine descriptors, put UMLS in the name, and placed DictionaryLookupAnnotatorUMLS.xml within them for these components:
     • Dictionary Lookup
     • Clinical Documents pipeline
     • Drug NER
     • Side Effect 
   • So you simply need to switch to using those descriptors. For example, if you were using AggregateCdaProcessor.xml in the Clinical Documents pipeline you would switch to using AggregateCdaUMLSProcessor.xml instead and you will now hook into the complete dictionaries.
     
     You can, of course, modify your own aggregate Analysis Engine files and place the DictionaryLookupAnnotatorUMLS.xml Analysis Engine within them.
     Since this is an in-memory database implementation, please be patient during the initial load as it could take approximately 20-30 seconds for the database to initialize.

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:

export MAVEN_OPTS="-Xmx2g -Xms1g"
mvn -Prun<CVD | CPE> compile

where you must select between CVD and CPE in the command. Other Run Configurations are also available in the Eclipse Run menu.

(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.

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