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Added some test script I found

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yarikoptic committed Dec 19, 2019
1 parent 4e879cd commit f43063e79b45634d5f76765b4059100830275af6
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  1. +53 −0 tests/test_run.sh
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#!/bin/bash
#emacs: -*- mode: shell-script; c-basic-offset: 4; tab-width: 4; indent-tabs-mode: t -*-
#ex: set sts=4 ts=4 sw=4 noet:
#
# A sample script to test correct operation for a prototypical/recommended
# setup etc
#
# COPYRIGHT: Yaroslav Halchenko 2019
#
# LICENSE: MIT
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#

set -eu

INPUT=( ~/datalad/dbic/QA/sourcedata/sub-qa/ses-20180904/ )

STUDY=$(mktemp -u /tmp/reproin.XXXXXX)

#HEUDICONV=datalad containers-run containers/reproin

# This a study oriented scenario. Will override
# --locator

# requires datalad >= 0.12b*
datalad create -c text2git "$STUDY"
# requires datalad-neuroimaging
datalad create -c bids -d "$STUDY" "$STUDY/data/bids"

# Reuse our containers collection
# datalad install -d $STUDY/data/bids -s ///repronim/containers .containers

cd "$STUDY/data/bids"
HEUDICONV="docker run -it --workdir $PWD -v $HOME/datalad:$HOME/datalad -v $PWD:$PWD -u $(id -u):$(id -g) -e HOME=$HOME -v $HOME:$HOME 723a01d04689"

$HEUDICONV -f reproin --bids --datalad -o . --files "${INPUT[@]}"

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