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Merge branch 'dicom_index'

This commit is contained in:
bpinsard 2024-02-09 21:22:09 -05:00
parent 4440e89eca 58f1755587
commit 15e29bfad5
2 changed files with 2 additions and 3 deletions
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3
docker/dicom_indexer/indexer/index_dicom.py
View File

@ -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"])

2
docker/heudiconv/Dockerfile
View File

@ -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 ln -s /usr/bin/7zz /usr/bin/7z
RUN pip install --no-cache-dir frozendict bids datalad 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