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Using datalad to automate OpenNeuro CLI running #29

Merged
merged 13 commits into from
Sep 17, 2023
Merged

Using datalad to automate OpenNeuro CLI running #29

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5f860a1
sh to datalad clone/get specific dataset with id
maelleF Jul 20, 2023
92a6f16
add "datalad get <file>"
maelleF Jul 21, 2023
6b49948
change name of the file
maelleF Jul 21, 2023
a2c2ee4
add cmd to run_bagel_cli + change variable name
maelleF Jul 21, 2023
a1e388c
replace run_bagel_cli by commands/change var name
maelleF Jul 21, 2023
b25396d
add output directory for jsonld file/fix var name
maelleF Jul 21, 2023
577976a
Update datalad_get_single_dataset.sh
maelleF Jul 21, 2023
2a86260
Update datalad_get_single_dataset.sh
maelleF Jul 21, 2023
5bd74a3
change path
maelleF Jul 21, 2023
4e5b27e
bug fix on path
maelleF Jul 21, 2023
3fb12af
change var names
maelleF Jul 21, 2023
6b959b4
Update commands to work with containerized CLI
alyssadai Sep 16, 2023
755c52b
update comments and pull latest CLI image
alyssadai Sep 17, 2023
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26 changes: 26 additions & 0 deletions datalad_get_single_dataset.sh
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#!/bin/bash

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#step1
ds_id="ds004107"
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ds_portal="https://openneuro.org/datasets/${ds_id}"
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GIT="[email protected]:OpenNeuroDatasets-JSONLD/${ds_id}"
bagel_dir="/home/maellef/DataBase/NeuroBagel_test/"
ldout="${bagel_dir}outputs/openneuro-jsonld/"
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mkdir -p $ldout
out="${ldout}${ds_id}.jsonld"

workdir="${bagel_dir}${ds_id}"

datalad clone ${GIT} ${workdir}
datalad get -d $workdir "${workdir}/participants.tsv"
datalad get -d $workdir "${workdir}/participants.json"
datalad get -d $workdir "${workdir}/dataset_description.json"

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

#step2
bagel pheno --pheno ${workdir}/participants.tsv --dictionary ${workdir}/participants.json --output ${workdir} --name "$ds_name" --portal $ds_portal
bagel bids --jsonld-path ${workdir}/pheno.jsonld --bids-dir ${workdir} --output ${workdir}
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cp ${workdir}/pheno_bids.jsonld ${out}