#!/bin/bash
# Run ci_extraction.R
# Usage: ./02_run_ci_extraction.sh --end_date=<YYYY-MM-DD> --offset=<days> --project_dir=kibos

end_date=$(date +'%Y-%m-%d')
offset=28
project_dir="kibos"

for arg in "$@"; do
    case $arg in
        --end_date=*)
            end_date="${arg#*=}"
            ;;
        --offset=*)
            offset="${arg#*=}"
            ;;
        --project_dir=*)
            project_dir="${arg#*=}"
            ;;
        *)
            echo "Unknown option: $arg"
            exit 1
            ;;
    esac
    shift
done

echo "Running ci_extraction.R for $project_dir with end_date $end_date and offset $offset."
cd r_app
Rscript 02_ci_extraction.R $end_date $offset $project_dir
cd ..