run_bagel_cli.sh

#!/usr/bin/bash

ldin=inputs/openneuro-jsonld/
ldout=outputs/openneuro-jsonld/

ds="$1"
ds_name="$2"
ds_portal=https://github.com/OpenNeuroDatasets-JSONLD/${ds}.git
workdir=`realpath ${ldin}/$ds`
container_dir=/${ds}
out=(${ldout}/${ds}.jsonld)

if [ "$ds_name" == "None" ]; then
    ds_name=$ds
fi

if [ ! -e ${ldout} ]; then
    mkdir -p ${ldout}
fi

echo $ds "$ds_name"
if [ ! -e ${out} ]; then
    echo Checking data dictionary for descriptions!
    python3 add_description.py ${workdir}/participants.json

    echo bagel pheno --pheno ${workdir}/participants.tsv --dictionary ${workdir}/participants.json --output ${workdir}/pheno.jsonld --name "$ds_name" --portal $ds_portal
    docker run --rm -v ${workdir}:${container_dir} neurobagel/bagelcli:latest pheno --pheno ${container_dir}/participants.tsv --dictionary ${container_dir}/participants.json --output ${container_dir}/pheno.jsonld --name "$ds_name" --portal $ds_portal
    docker run --rm -v ${workdir}:${container_dir} neurobagel/bagelcli:latest bids --jsonld-path ${container_dir}/pheno.jsonld --bids-dir ${container_dir} --output ${container_dir}/pheno_bids.jsonld

    echo Resetting dataset to HEAD
    git -C ${workdir} checkout HEAD -- participants.json
    
    cp ${workdir}/pheno_bids.jsonld ${out}
fi