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Comment: add example of setting UMLS user ID and password

...

Step

Example

1. Navigate to the cTAKES downloads page on the Apache site and download the binary package. Select a mirror site and press the Change button to modify the URL to your desired mirror location before doing the download or accept the default.

Windows:
Download the ZIP file.
Linux:
Use wget to obtain the *.TAR.GZ file.
wget <URL of the file from downloads>

Info

The download time will be commensurate with ~165MB of data.

Windows:

Linux:

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HTTP request sent, awaiting response... 200 OK
Length: 763500777 (728M) [application/x-gzip]
Saving to: `apache-ctakes-3.0.0-incubating-bin.tar.gz'

13% [===========>                                     ] 106,548,331 1.13M/s eta 11m 9s

2. (Optional but recommended) Verify the downloaded files against a file signature to ensure you have the proper and complete file.

No example

3. Unzip the file you downloaded into a directory that you want to be the cTAKES install location. The compressed files contain a single directory at the top level. This folder we will call <cTAKES_HOME>. You will need to refer to this directory later.

Windows:

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C:\apache-ctakes-3.0.0-incubating

Linux:

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/usr/local/apache-ctakes-3.0.0-incubating

Windows:

Linux:

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tar -xvf apache-ctakes-3.0.0-incubating-bin.tar.gz -C /usr/local

Optional steps - install UMLS resources

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and set UMLS password

Step

Example

4. Obtain a UMLS license if you don't already have one. You can request one at https://uts.nlm.nih.gov/license.html

No example

5. Edit the following files, adding in your UMLS user ID and password as parameters to the java command:

Windows:

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bin\runctakesCVD.bat
bin\runctakesCPE.bat

Linux:

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bin/runctakesCVD.sh
bin/runctakesCPE.sh

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java -Dctakes.umlsuser=YOUR_ID_HERE -Dctakes.umlspw=YOUR_PASSSWORD_HERE -cp ...

6

Step

Example

4. Download cTAKES 3.0 Dictionaries and models. These resources are required to operate cTAKES.

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.

Info

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:

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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

5 7. Copy (or move) the resources to cTAKES_HOME.
Copy the contents of the temporary resources directory (and all sub-directories) to <cTAKES_HOME>/resources.

Info

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



Windows:

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xcopy /s C:\temp\ctakes-resources-3.0.1\resources C:\apache-ctakes-3.0.0-incubating\resources

Linux:

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cp -R /tmp/resources/* /usr/local/apache-ctakes-3.0.0-incubating/resources

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