diff --git a/docker/dicom_indexer/indexer/index_dicom.py b/docker/dicom_indexer/indexer/index_dicom.py index ea1396b..13eae93 100644 --- a/docker/dicom_indexer/indexer/index_dicom.py +++ b/docker/dicom_indexer/indexer/index_dicom.py @@ -322,17 +322,16 @@ def init_bids( source=bids_project_repo._attrs["ssh_url_to_repo"], path=tmpdir, ) + bids_project_ds.create(force=True) shutil.copytree( REPO_TEMPLATES_PATH / "bids", bids_project_ds.path, dirs_exist_ok=True ) 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.install( path="sourcedata/dicoms", source=dicom_study_repo._attrs["ssh_url_to_repo"], ) - # TODO: setup sensitive / non-sensitive S3 buckets bids_project_ds.push(to="origin") # create dev branch and push for merge requests bids_project_ds.repo.checkout(BIDS_DEV_BRANCH, ["-b"]) diff --git a/docker/heudiconv/Dockerfile b/docker/heudiconv/Dockerfile index eec3a38..7d0c2f3 100644 --- a/docker/heudiconv/Dockerfile +++ b/docker/heudiconv/Dockerfile @@ -11,4 +11,4 @@ RUN curl -O -L https://gitlab.com/gitlab-org/cli/-/releases/v${GLAB_VERSION}/dow RUN ln -s /usr/bin/7zz /usr/bin/7z RUN pip install --no-cache-dir frozendict bids datalad -RUN pip install --no-cache-dir git+https://github.com/UNFmontreal/heudiconv@enh-custom-seqinfo +RUN pip install --no-cache-dir git+https://github.com/UNFmontreal/heudiconv@unf_prod