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minor fix

This commit is contained in:
bpinsard 2024-02-09 21:21:54 -05:00
parent b0ad528b43
commit 58f1755587
1 changed files with 1 additions and 2 deletions
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3
docker/dicom_indexer/indexer/index_dicom.py
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@ -322,17 +322,16 @@ def init_bids(
source=bids_project_repo._attrs["ssh_url_to_repo"], source=bids_project_repo._attrs["ssh_url_to_repo"],
path=tmpdir, path=tmpdir,
) )
bids_project_ds.create(force=True)
shutil.copytree( shutil.copytree(
REPO_TEMPLATES_PATH / "bids", bids_project_ds.path, dirs_exist_ok=True REPO_TEMPLATES_PATH / "bids", bids_project_ds.path, dirs_exist_ok=True
) )
write_ci_env(bids_project_ds, gitlab_group_path) write_ci_env(bids_project_ds, gitlab_group_path)
bids_project_ds.create(force=True)
bids_project_ds.save(path=".", message="init structure and pipelines") bids_project_ds.save(path=".", message="init structure and pipelines")
bids_project_ds.install( bids_project_ds.install(
path="sourcedata/dicoms", path="sourcedata/dicoms",
source=dicom_study_repo._attrs["ssh_url_to_repo"], source=dicom_study_repo._attrs["ssh_url_to_repo"],
) )
# TODO: setup sensitive / non-sensitive S3 buckets
bids_project_ds.push(to="origin") bids_project_ds.push(to="origin")
# create dev branch and push for merge requests # create dev branch and push for merge requests
bids_project_ds.repo.checkout(BIDS_DEV_BRANCH, ["-b"]) bids_project_ds.repo.checkout(BIDS_DEV_BRANCH, ["-b"])