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corrected creation of ci-env.yml and more use of pathlib

This commit is contained in:
Milton Camacho 2024-01-31 20:58:41 +00:00
parent c336879fa5
commit 483cc64d53
1 changed files with 4 additions and 4 deletions
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8
docker/dicom_indexer/indexer/index_dicom.py
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@ -313,18 +313,18 @@ def init_bids(
def init_dicom_study( def init_dicom_study(
dicom_study_ds: dlad.Dataset, dicom_study_ds: dlad.Dataset,
gitlab_group_path: str, gitlab_group_path: pathlib.Path,
) -> None: ) -> None:
shutil.copytree( shutil.copytree(
"repo_templates/dicom_study", dicom_study_ds.path, dirs_exist_ok=True "repo_templates/dicom_study", dicom_study_ds.path, dirs_exist_ok=True
) )
env = { env = {
"variables": { "variables": {
"STUDY_PATH": gitlab_group_path, "STUDY_PATH": str(gitlab_group_path),
"BIDS_PATH": f"{gitlab_group_path}/bids", "BIDS_PATH": str(gitlab_group_path / "bids"),
} }
} }
with open(os.path.join(dicom_study_ds.path, "ci-env.yml"), "w") as outfile: with (pathlib.Path(dicom_study_ds.path) / "ci-env.yml").open("w") as outfile:
yaml.dump(env, outfile, default_flow_style=False) yaml.dump(env, outfile, default_flow_style=False)
dicom_study_ds.save(path=".", message="init structure and pipelines") dicom_study_ds.save(path=".", message="init structure and pipelines")
dicom_study_ds.push(to="origin") dicom_study_ds.push(to="origin")