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💊 Extract DailyMed SPL

Extracting the indication from the SPLs (Structured Product Labeling) that are coming from DailyMed dataset.

Clone

This project has a git submodule where the data are stored on a hugging face git repository. This module uses git large file storage. Use the following to automatically extract and set up the submodule when cloning the repository

git lfs install

git clone --recurse-submodules https://github.com/MaastrichtU-IDS/extract-dailymed-spl

Otherwise, you can initialize, fetch and checkout the nested submodule with the following command

git submodule update --init --recursive

Install

Create and activate virtual env

python -m venv .venv
source .venv/bin/activate

Install

pip install -e .

Run

Parameters

usage: Dailymed Parser [-h] [-w WORKING_DIR] [-d DOWNLOAD] [-f] [-a DATE] [-s FILES] [-e EXTRACT] [-p PROCESS]

Downloads and parses Dailymed product labels

options:
  -h, --help            show this help message and exit
  -w WORKING_DIR, --working_dir WORKING_DIR
                        Directory to download files into
  -d DOWNLOAD, --download DOWNLOAD
                        Download content, if it hasn't already been downloaded.
  -f, --force           Replace files, even if they were previously downloaded
  -a DATE, --date DATE  Use data from specified date in format of YYYY-MM-DD
  -s FILES, --files FILES
                        Specify a comma-separated list of the files to download/process. options: all|prescription|otc
  -e EXTRACT, --extract EXTRACT
                        Extract XML files from download files
  -p PROCESS, --process PROCESS
                        Extract XML files from download files

python src/dm_parser.py