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Step

Example

1. Import the cTAKES projects using Maven.

File -> Import ... -> Maven -> Check out Maven Projects from SCM.
Click Next.


Note

The following location is the main trunk of cTAKES. Tags are used for release candidates and previous releases. You may need to make changes in a tag as well as the main trunk. Separate Eclipse workspaces are recommended for each checkout. The main trunk may be unstable at any given point.

2. For SCM URL use "svn" in the drop-down and this in the text field

Code Block
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.

Info

Due to the way Maven and Eclipse work together you will see two copies of the sub-projects in Eclipse. If you look into your workspace directories there is only one set of underlying files.



3. Download cTAKES 3.0 Dictionaries and models.

Info

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.

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:

Code Block
langnone
C:\temp\ctakes-resources-3.0.1\resources

Linux:

Code Block
langnone
/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.

Info

There may be conflicts while taking this action. Overwrite the cTAKES_HOME files with those in the resources download.

...



Windows:

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

Linux:

Code Block
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copy /tmp/ctakes-resources-3.0.1/resources/* /usr/local/apache-ctakes-3.0.0-incubating/resources/*

...

 5. Refresh Eclipse. 

 You must refresh your Eclipse projects to make sure that Eclipse knows about the new directories and data. 
 No example 
 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.
 Note
If you do not have a UMLS username and password, you may request one at UMLS Terminology Services

  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
      languagenone
            <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. 
 
 

...
 Step 
 Example 
 1. Install an SVN client. 
 Info
Run this command to check the setup. 
 svn --version


 Windows: 
 We used a binary package of Apache Subversion from SlikSVN. 
 Apache has a larger list here. 
 Download and run the MSI file. 
 Click Next. 
 Accept the license agreement. 
 Click Next. 
 Click Next. 
 Select Typical. 
 Select Install. 
 Wait 
 Click Finish. 
 Exit and restart any command prompts that were open. 

 Linux: 
 Code Block
sudo apt-get install subversion
 Windows: 
 

 Linux: 

 Code Block
The following extra packages will be installed:
  libapr1 libaprutil1 libneon27-gnutls libsvn1
Suggested packages:
  subversion-tools db4.8-util
The following NEW packages will be installed:
  libapr1 libaprutil1 libneon27-gnutls libsvn1 subversion

...

Processing triggers for python-central ...
Processing triggers for man-db ...
Setting up libapr1 (1.4.2-7ubuntu2) ...
Setting up libaprutil1 (1.3.9+dfsg-5ubuntu3) ...
Setting up libneon27-gnutls (0.29.5-3) ...
Setting up libsvn1 (1.6.12dfsg-4ubuntu2) ...
Setting up subversion (1.6.12dfsg-4ubuntu2) ...

 2. Install a Maven 3.0+ client. 

 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
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

 Windows: 
 

 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. 
 Info
Run this command to check the setup. 
 mvn --version


 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
export M2_HOME=/usr/local/apache-maven-3.0.4
export M2=$M2_HOME/bin
export PATH=$PATH:$M2
 Note
It is left to the user to make environment variables permanent in their development environment.
 Windows: 
 
 
 


 Linux: 

 Code Block
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"
...