Page History

1. Open a command prompt and change to the cTAKES_HOME directory:

Windows:

cd \apache-ctakes-3.0.0-incubating\bin

Linux:

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

2. Start the collection processing engine by running this command:
The application may take a minute to start on slower hardware.

Windows:

runctakesCPE.bat

Linux:

runctakesCPE.sh

The application may take a minute to start on slower hardware.

3. This will bring up the Collection Processing Engine Configurator. In the Menu bar click File >Open CPE Descriptor

4. Navigate to the file

<cTAKES_HOME>/desc/ctakes-clinical-pipeline/desc/collection_processing_engine/test_plaintext.xml

Click Open.

No example

5. Click the Play button (green/blue play arrow near the bottom).

6. You should see that one document was processed. You did process a collection of documents. In this case the collection only contained one just to show how to do it. Close the results window.

7. Close the CPE application. You may be prompted to save changes. Since this was just a test you may click the No button.

8. Open a new command prompt and change to the <cTAKES_HOME>

9. To test the results there is a comparison tool that will help show that the results match expectations with the following syntax:

java -cp ctakes-utils-3.0.0.jar org.apache.ctakes.utils.xcas_comparison.Compare
<First File> <Second File> <diff-html>

Where: <First File> is the first file to compare; <Second File> is the second file to compare; <diff-html> is where the results are written to
Copy and paste the example at the right (next cell) which has had our
example files already substituted into a command prompt to run. In this
case we have shipped an example of what the output should be for you to
compare against.

Windows:

java -cp ctakes-utils-3.0.0.jar org.apache.ctakes.utils.xcas_comparison.Compare ^
"testdata\cdptest\testoutput\plaintext\sample_note_plaintext.xml" ^
"testdata\cdptest\testsampleoutput\plaintext\sample_note_plaintext.xml" ^
c:\stuff\diff-html.html

Linux:

java -cp ctakes-utils-3.0.0.jar org.apache.ctakes.utils.xcas_comparison.Compare \
"/usr/bin/cTAKES3.0/testdata/cdptest/testoutput/plaintext\sample_note_plaintext.xml" \
"/usr/bin/cTAKES3.0/testdata/cdptest/testsampleoutput/plaintext/sample_note_plaintext.xml" \
/tmp/diff-html.html

10. The resulting file will open for you. Look at the comparison to see the annotations resulting from this pipeline.
Windows:

c:\stuff\diff-html.html

Linux:

/tmp/diff-html.html