cpp-lln-lab / template_datalad_fMRI

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[BUG]: automate configuration wil not set the sub-sub-modules' url in derivatives correctly #14

Closed marcobarilari closed 2 years ago

marcobarilari commented 2 years ago

Is there an existing issue for this?

Expected Behavior

both cpp_spm-preproc and cpp_spm-stats should hav the correct sibling

the script dataladSetUp.sh should point to a specific submod when resetting the URL here

if [ ! -z "${URL_DER_PREPROC}" ]; then
    cd "${preproc_dir}"
    datalad siblings add --name origin --url "${URL_DER_PREPROC}"
    cd ..
    datalad subdatasets --set-property url "${URL_DER_PREPROC}"
    cd "${root_dir}"
fi

datalad create -d . "${stats_dir}"

if [ ! -z "${URL_DER_STATS}" ]; then
    cd "${stats_dir}"
    datalad siblings add --name origin --url "${URL_DER_STATS}"
    cd ..
    datalad subdatasets --set-property url "${URL_DER_STATS}" 
    cd "${root_dir}"
fi

Current Behavior

the .gitmodules file:

[submodule "cpp_spm-preproc"]
    path = cpp_spm-preproc
    url = git@gin.g-node.org:/marcobarilari/analysis_high-res_pilot001_ses-001_derivatives-cpp_spm-stats.git
    datalad-id = 5839c7a6-cda3-417e-bd83-d0fa2e146504
[submodule "cpp_spm-stats"]
    path = cpp_spm-stats
    url = git@gin.g-node.org:/marcobarilari/analysis_high-res_pilot001_ses-001_derivatives-cpp_spm-stats.git
    datalad-id = 9cd016c0-2e39-48fc-99f9-6afaa4d8e9f9

Error message

No response

Environment

- OS:
- Matlab:
- SPM:

Anything else?

No response