diff --git a/datalad_get_single_dataset.sh b/datalad_get_single_dataset.sh new file mode 100755 index 0000000..1e105a7 --- /dev/null +++ b/datalad_get_single_dataset.sh @@ -0,0 +1,31 @@ +#!/bin/bash + +ds_id=$1 + +docker pull neurobagel/bagelcli:latest + +# Get the data +ds_portal="https://github.com/OpenNeuroDatasets-JSONLD/${ds_id}.git" +ds_git="git@github.com:OpenNeuroDatasets-JSONLD/${ds_id}" + +ldin="inputs/openneuro-jsonld/" +mkdir -p $ldin +ldout="outputs/openneuro-jsonld/" +mkdir -p $ldout + +workdir=$(realpath ${ldin}${ds_id}) +out="${ldout}${ds_id}.jsonld" + +datalad clone ${ds_git} ${workdir} +datalad get -d $workdir "${workdir}/participants.tsv" +datalad get -d $workdir "${workdir}/participants.json" +datalad get -d $workdir "${workdir}/dataset_description.json" + +# Get the dataset label +ds_name=$(python extract_bids_dataset_name.py --ds $workdir) +if [ "$ds_name" == "None" ] ; then ds_name=$ds_id ; else ds_name=$ds_name ; fi + +# Run the Neurobagel CLI +docker run --rm -v ${workdir}:${workdir} neurobagel/bagelcli pheno --pheno ${workdir}/participants.tsv --dictionary ${workdir}/participants.json --output ${workdir} --name "$ds_name" --portal $ds_portal +docker run --rm -v ${workdir}:${workdir} neurobagel/bagelcli bids --jsonld-path ${workdir}/pheno.jsonld --bids-dir ${workdir} --output ${workdir} +cp ${workdir}/pheno_bids.jsonld ${out}