diff --git a/docker/dicom_indexer/indexer/index_dicom.py b/docker/dicom_indexer/indexer/index_dicom.py index d1e872a..4ee4b7e 100644 --- a/docker/dicom_indexer/indexer/index_dicom.py +++ b/docker/dicom_indexer/indexer/index_dicom.py @@ -17,7 +17,7 @@ DEBUG = bool(os.environ.get("DEBUG", False)) GITLAB_REMOTE_NAME = os.environ.get("GITLAB_REMOTE_NAME", "origin") GITLAB_TOKEN = os.environ.get("GITLAB_TOKEN", None) GITLAB_BOT_USERNAME = os.environ.get("GITLAB_BOT_USERNAME", None) - +BIDS_DEV_BRANCH = os.environ.get("BIDS_DEV_BRANCH", "dev") S3_REMOTE_DEFAULT_PARAMETERS = [ "type=S3", @@ -291,7 +291,7 @@ def init_bids( ) -> None: bids_project_repo = get_or_create_gitlab_project(gl, f"{gitlab_group_path}/bids") with tempfile.TemporaryDirectory() as tmpdir: - bids_project_ds = datalad.api.install( + bids_project_ds = dlad.install( source=bids_project_repo._attrs["ssh_url_to_repo"], path=tmpdir, ) @@ -305,7 +305,7 @@ def init_bids( # TODO: setup sensitive / non-sensitive S3 buckets bids_project_ds.push(to="origin") # create dev branch and push for merge requests - bids_project_ds.gitrepo.checkout(BIDS_DEV_BRANCH, ["-b"]) + bids_project_ds.repo.checkout(BIDS_DEV_BRANCH, ["-b"]) bids_project_ds.push(to="origin") # set protected branches bids_project_repo.protectedbranches.create(data={"name": "convert/*"}) @@ -427,7 +427,9 @@ def export_to_s3( # git-annex initremote remotename ... remote_name = s3_url.hostname bucket_name, path = pathlib.Path(s3_url.path).parts - ds.repo.initremote( + + # TODO: change the bucket information to datadata information + ds.repo.init_remote( remote_name, S3_REMOTE_DEFAULT_PARAMETERS + [ @@ -437,11 +439,13 @@ def export_to_s3( ], ) ds.repo.set_preferred_content( - remote_name, + "wanted", "include=**.{7z,tar.gz,zip}", + remote=remote_name ) - ds.push(to=remote_name) + ds.push(to=remote_name, data='auto') + #It does not push the data to the S3 unless I set data="anything" which pushes everyhing including the deflated archived data def connect_gitlab(