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wip: dicom indexer

This commit is contained in:
Milton Camacho 2024-01-30 16:47:30 +00:00
parent b6053a4c47
commit 386a10de22
1 changed files with 10 additions and 6 deletions
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16
docker/dicom_indexer/indexer/index_dicom.py
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@ -17,7 +17,7 @@ DEBUG = bool(os.environ.get("DEBUG", False))
GITLAB_REMOTE_NAME = os.environ.get("GITLAB_REMOTE_NAME", "origin") GITLAB_REMOTE_NAME = os.environ.get("GITLAB_REMOTE_NAME", "origin")
GITLAB_TOKEN = os.environ.get("GITLAB_TOKEN", None) GITLAB_TOKEN = os.environ.get("GITLAB_TOKEN", None)
GITLAB_BOT_USERNAME = os.environ.get("GITLAB_BOT_USERNAME", 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 = [ S3_REMOTE_DEFAULT_PARAMETERS = [
"type=S3", "type=S3",
@ -291,7 +291,7 @@ def init_bids(
) -> None: ) -> None:
bids_project_repo = get_or_create_gitlab_project(gl, f"{gitlab_group_path}/bids") bids_project_repo = get_or_create_gitlab_project(gl, f"{gitlab_group_path}/bids")
with tempfile.TemporaryDirectory() as tmpdir: 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"], source=bids_project_repo._attrs["ssh_url_to_repo"],
path=tmpdir, path=tmpdir,
) )
@ -305,7 +305,7 @@ def init_bids(
# TODO: setup sensitive / non-sensitive S3 buckets # 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.gitrepo.checkout(BIDS_DEV_BRANCH, ["-b"]) bids_project_ds.repo.checkout(BIDS_DEV_BRANCH, ["-b"])
bids_project_ds.push(to="origin") bids_project_ds.push(to="origin")
# set protected branches # set protected branches
bids_project_repo.protectedbranches.create(data={"name": "convert/*"}) bids_project_repo.protectedbranches.create(data={"name": "convert/*"})
@ -427,7 +427,9 @@ def export_to_s3(
# git-annex initremote remotename ... # git-annex initremote remotename ...
remote_name = s3_url.hostname remote_name = s3_url.hostname
bucket_name, path = pathlib.Path(s3_url.path).parts 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, remote_name,
S3_REMOTE_DEFAULT_PARAMETERS S3_REMOTE_DEFAULT_PARAMETERS
+ [ + [
@ -437,11 +439,13 @@ def export_to_s3(
], ],
) )
ds.repo.set_preferred_content( ds.repo.set_preferred_content(
remote_name, "wanted",
"include=**.{7z,tar.gz,zip}", "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( def connect_gitlab(