From f43063e79b45634d5f76765b4059100830275af6 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Thu, 19 Dec 2019 18:32:44 -0500 Subject: [PATCH] Added some test script I found --- tests/test_run.sh | 53 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100755 tests/test_run.sh diff --git a/tests/test_run.sh b/tests/test_run.sh new file mode 100755 index 0000000..3dfa0ee --- /dev/null +++ b/tests/test_run.sh @@ -0,0 +1,53 @@ +#!/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[@]}"