a simple script for wrapping metamaplite to process files
Requires installation of MetaMapLite.
Please edit MetaMapLiteRunner.py to include the appropriate path to your MetaMapLite installation.
Usage:
python MetaMapLiteRunner.py -l <logfilename> file1 fle2...
Each input file will create two output files:
- .mmi file is raw MetaMapLite output
- .csv is the simplified output
Both should contain only codes and should therefore be de-identified.
Note that although the extension is ".csv", the simplified output file is actually pipe deliminted.
#MetaMapLiteServerRunner.py
This version of the Runner uses an modified version of MetaMap Lite available at:
https://github.com/espinoj/public_mm_lite
This modified version provides the functionality for MetaMap to run as a daemon accepting input from either HTTP GET requests or via STDIN. To activate this feature the user should enter a single filename that is either http://localhost:<port> for HTTP Server Mode or stdin for stdin mode. In HTTP Server mode enter requests as http://localhost:<port>//process?filename=<filename> In stdin mode the server waits for filename input. Both formats will return json strings like {'status':'processed','procTime':48.0,'filename':'/tmp/7602_200017_03262020_101127.LDS.txt'}.
To use the MetaMapLiteServerRunner.py use the same switches available to MetaMapLiteRunner.py but add the -d switch to put it into daemon mode. Number of CPUs i.e., -c still work.