517 lines
16 KiB
Python
517 lines
16 KiB
Python
import os
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import pydicom as dicom
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import argparse
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import pathlib
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import urllib.parse
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import datalad.api as dlad
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import shutil
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import gitlab
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import tempfile
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import logging
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import subprocess
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import yaml
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from contextlib import contextmanager
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DEBUG = bool(os.environ.get("DEBUG", False))
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if DEBUG:
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logging.basicConfig(level=logging.DEBUG)
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GITLAB_REMOTE_NAME = os.environ.get("GITLAB_REMOTE_NAME", "origin")
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GITLAB_TOKEN = os.environ.get("GITLAB_TOKEN", None)
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GITLAB_BOT_USERNAME = os.environ.get("GITLAB_BOT_USERNAME", None)
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BIDS_DEV_BRANCH = os.environ.get("BIDS_DEV_BRANCH", "dev")
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S3_REMOTE_DEFAULT_PARAMETERS = [
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"type=S3",
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"encryption=none",
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"autoenable=true",
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"port=443",
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"protocol=https",
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"chunk=1GiB",
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"requeststyle=path",
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]
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# TODO: rewrite for pathlib.Path input
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def sort_series(path: pathlib.Path) -> None:
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"""Sort series in separate folder
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Parameters
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----------
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path : str
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path to dicoms
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"""
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files = path.glob(os.path.join(path, "*"))
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for f in files:
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if not os.path.isfile(f):
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continue
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dic = dicom.read_file(f, stop_before_pixels=True)
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# series_number = dic.SeriesNumber
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series_instance_uid = dic.SeriesInstanceUID
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subpath = os.path.join(path, series_instance_uid)
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if not os.path.exists(subpath):
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os.mkdir(subpath)
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os.rename(f, os.path.join(subpath, f.name))
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def _build_arg_parser() -> argparse.ArgumentParser:
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p = argparse.ArgumentParser(
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description="dicom_indexer - indexes dicoms into datalad"
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)
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p.add_argument("input", help="path/url of the dicom.")
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p.add_argument(
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"--gitlab-url",
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type=str,
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default=os.environ.get("GITLAB_SERVER", None),
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help="http(s) url to the gitlab server where to push repos",
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)
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p.add_argument(
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"--gitlab-group-template",
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default="{ReferringPhysicianName}/{StudyDescription}",
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type=str,
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help="string with placeholder for dicom tags",
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)
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p.add_argument(
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"--session-name-tag",
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default="PatientName",
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type=str,
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help="dicom tags that contains the name of the session",
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)
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p.add_argument("--storage-remote", help="url to the datalad remote")
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p.add_argument(
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"--sort-series",
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type=bool,
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default=True,
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help="sort dicom series in separate folders",
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)
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p.add_argument(
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"--fake-dates",
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action="store_true",
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help="use fake dates for datalad dataset",
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)
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p.add_argument(
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"--p7z-opts",
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type=str,
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default="-mx5 -ms=off",
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help="option for 7z generated archives",
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)
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return p
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def main() -> None:
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parser = _build_arg_parser()
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args = parser.parse_args()
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if not GITLAB_REMOTE_NAME:
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raise RuntimeError("missing GITLAB_REMOTE_NAME env var")
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if not GITLAB_TOKEN:
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raise RuntimeError("missing GITLAB_TOKEN env var")
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if not GITLAB_BOT_USERNAME:
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raise RuntimeError("missing GITLAB_BOT_USERNAME env var")
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input = urllib.parse.urlparse(args.input)
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output_remote = urllib.parse.urlparse(args.storage_remote)
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gitlab_url = urllib.parse.urlparse(args.gitlab_url)
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with index_dicoms(
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input,
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sort_series=args.sort_series,
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fake_dates=args.fake_dates,
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p7z_opts=args.p7z_opts,
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) as dicom_session_ds:
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session_metas = extract_session_metas(dicom_session_ds)
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if (
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not input.scheme
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or input.scheme == "file"
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or args.force_export
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and output_remote
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):
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export_data(
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dicom_session_ds,
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output_remote,
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dicom_session_tag=args.session_name_tag,
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session_metas=session_metas,
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)
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setup_gitlab_repos(
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dicom_session_ds,
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gitlab_url=gitlab_url,
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dicom_session_tag=args.session_name_tag,
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session_metas=session_metas,
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gitlab_group_template=args.gitlab_group_template,
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)
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@contextmanager
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def index_dicoms(
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input: urllib.parse.ParseResult,
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sort_series: bool,
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fake_dates: bool,
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p7z_opts: str,
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) -> dlad.Dataset:
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"""Process incoming dicoms into datalad repo"""
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with tempfile.TemporaryDirectory(delete=not DEBUG) as tmpdirname:
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dicom_session_ds = dlad.create(tmpdirname, fake_dates=fake_dates)
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if not input.scheme or input.scheme == "file":
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archive = import_local_data(
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dicom_session_ds,
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pathlib.Path(input.path),
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sort_series=sort_series,
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p7z_opts=p7z_opts,
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)
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elif input.scheme in ["http", "https", "s3"]:
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archive = import_remote_data(dicom_session_ds, input_url)
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# index dicoms files
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dlad.add_archive_content(
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archive,
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dataset=dicom_session_ds,
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strip_leading_dirs=True,
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commit=False,
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)
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# cannot pass message above so commit now
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dicom_session_ds.save(message=f"index dicoms from archive {archive}") #
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# optimize git index after large import
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dicom_session_ds.repo.gc() # aggressive by default
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yield dicom_session_ds
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def export_data(
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dicom_session_ds: dlad.Dataset,
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output_remote: urllib.parse.ParseResult,
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dicom_session_tag: str,
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session_metas: dict,
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) -> None:
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if "ria" in output_remote.scheme:
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export_to_ria(
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dicom_session_ds,
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output_remote,
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dicom_session_tag=dicom_session_tag,
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session_metas=session_metas,
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)
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elif output_remote.scheme == "s3":
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export_to_s3(dicom_session_ds, output_remote, session_metas)
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def set_bot_privileges(gitlab_conn: gitlab.Gitlab, gitlab_group_path: pathlib.Path) -> None:
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# add maint permissions for the dicom bot user on the study repos
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study_group = get_or_create_gitlab_group(gitlab_conn, gitlab_group_path)
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bot_user = gitlab_conn.users.list(username=GITLAB_BOT_USERNAME)
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if not bot_user:
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raise RuntimeError(
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f"bot_user: {GITLAB_BOT_USERNAME} does not exists in gitlab instance"
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)
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bot_user = bot_user[0]
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if not any(m.id == bot_user.id for m in study_group.members.list()):
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study_group.members.create(
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{
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"user_id": bot_user.id,
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"access_level": gitlab.const.AccessLevel.MAINTAINER,
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}
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)
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def setup_gitlab_repos(
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dicom_session_ds: dlad.Dataset,
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gitlab_url: urllib.parse.ParseResult,
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session_metas: dict,
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dicom_session_tag: str,
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gitlab_group_template: str,
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) -> None:
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gitlab_conn = connect_gitlab(gitlab_url)
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# generate gitlab group/repo paths
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gitlab_group_path = pathlib.Path(gitlab_group_template.format(**session_metas))
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dicom_sourcedata_path = gitlab_group_path / "sourcedata/dicoms"
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dicom_session_path = dicom_sourcedata_path / session_metas["StudyInstanceUID"]
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dicom_study_path = dicom_sourcedata_path / "study"
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# create repo (should not exists unless rerun)
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dicom_session_repo = get_or_create_gitlab_project(gitlab_conn, dicom_session_path)
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dicom_session_ds.siblings(
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action="configure", # allow to overwrite existing config
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name=GITLAB_REMOTE_NAME,
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url=dicom_session_repo._attrs["ssh_url_to_repo"],
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)
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"""
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# prevent warnings
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dicom_session_ds.config.add(
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f"remote.{GITLAB_REMOTE_NAME}.annex-ignore",
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value='false',
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scope='local'
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)"""
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set_bot_privileges(gitlab_conn, gitlab_group_path)
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# and push
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dicom_session_ds.push(to=GITLAB_REMOTE_NAME)
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## add the session to the dicom study repo
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dicom_study_repo = get_or_create_gitlab_project(gitlab_conn, dicom_study_path)
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with tempfile.TemporaryDirectory(delete=not DEBUG) as tmpdir:
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dicom_study_ds = dlad.install(
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source=dicom_study_repo._attrs["ssh_url_to_repo"],
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path=tmpdir,
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)
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"""
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# prevent warnings when pushing
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dicom_study_ds.config.add(
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f"remote.origin.annex-ignore",
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value='false',
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scope='local'
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)"""
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if dicom_study_ds.repo.get_hexsha() is None or dicom_study_ds.id is None:
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dicom_study_ds.create(force=True)
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# add default study DS structure.
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init_dicom_study(dicom_study_ds, gitlab_group_path)
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# initialize BIDS project
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init_bids(gitlab_conn, dicom_study_repo, gitlab_group_path)
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# create subgroup for QC and derivatives repos
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get_or_create_gitlab_group(gitlab_conn, gitlab_group_path / "derivatives")
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get_or_create_gitlab_group(gitlab_conn, gitlab_group_path / "qc")
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dicom_study_ds.install(
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source=dicom_session_repo._attrs["ssh_url_to_repo"],
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path=session_metas.get(dicom_session_tag),
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)
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# Push to gitlab
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dicom_study_ds.push(to="origin")
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def init_bids(
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gl: gitlab.Gitlab,
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dicom_study_repo: dlad.Dataset,
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gitlab_group_path: pathlib.Path,
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) -> None:
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bids_project_repo = get_or_create_gitlab_project(gl, gitlab_group_path / "bids")
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with tempfile.TemporaryDirectory() as tmpdir:
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bids_project_ds = dlad.install(
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source=bids_project_repo._attrs["ssh_url_to_repo"],
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path=tmpdir,
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)
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bids_project_ds.create(force=True)
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shutil.copytree("repo_templates/bids", bids_project_ds.path, dirs_exist_ok=True)
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bids_project_ds.save(path=".", message="init structure and pipelines")
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bids_project_ds.install(
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path="sourcedata/dicoms",
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source=dicom_study_repo._attrs["ssh_url_to_repo"],
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)
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# TODO: setup sensitive / non-sensitive S3 buckets
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bids_project_ds.push(to="origin")
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# create dev branch and push for merge requests
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bids_project_ds.repo.checkout(BIDS_DEV_BRANCH, ["-b"])
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bids_project_ds.push(to="origin")
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# set protected branches
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bids_project_repo.protectedbranches.create(data={"name": "convert/*"})
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bids_project_repo.protectedbranches.create(data={"name": "dev"})
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def init_dicom_study(
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dicom_study_ds: dlad.Dataset,
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gitlab_group_path: str,
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) -> None:
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shutil.copytree(
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"repo_templates/dicom_study", dicom_study_ds.path, dirs_exist_ok=True
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)
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env = {
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"variables": {
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"STUDY_PATH": gitlab_group_path,
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"BIDS_PATH": f"{gitlab_group_path}/bids",
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}
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}
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with open(os.path.join(dicom_study_ds.path, "ci-env.yml"), "w") as outfile:
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yaml.dump(env, outfile, default_flow_style=False)
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dicom_study_ds.save(path=".", message="init structure and pipelines")
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dicom_study_ds.push(to="origin")
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SESSION_META_KEYS = [
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"StudyInstanceUID",
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"PatientID",
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"PatientName",
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"ReferringPhysicianName",
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"StudyDate",
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"StudyDescription",
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]
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def extract_session_metas(dicom_session_ds: dlad.Dataset) -> dict:
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all_files = dicom_session_ds.repo.get_files()
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for f in all_files:
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try:
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dic = dicom.read_file(dicom_session_ds.pathobj / f, stop_before_pixels=True)
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except Exception as e: # TODO: what exception occurs when non-dicom ?
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continue
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# return at first dicom found
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return {k: str(getattr(dic, k)).replace("^", "/") for k in SESSION_META_KEYS}
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raise InputError("no dicom found")
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def import_local_data(
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dicom_session_ds: dlad.Dataset,
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input_path: pathlib.Path,
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sort_series: bool = True,
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p7z_opts: str = "-mx5 -ms=off",
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):
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dest = input_path.name
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if input_path.is_dir():
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dest = dest + ".7z"
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# create 7z archive with 1block/file parameters
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cmd = ["7z", "u", str(dest), str(input_path)] + p7z_opts.split()
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subprocess.run(cmd, cwd=dicom_session_ds.path)
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elif input_path.is_file():
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dest = dicom_session_ds.pathobj / dest
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try: # try hard-linking to avoid copying
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os.link(str(input_path), str(dest))
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except OSError: # fallback if hard-linking not supported
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shutil.copyfile(str(input_path), str(dest))
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dicom_session_ds.save(dest, message="add dicoms archive")
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return dest
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def import_remote_data(
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dicom_session_ds: dlad.Dataset, input_url: urllib.parse.ParseResult
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):
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try:
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dest = pathlib.Path(url.path).name
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dicom_session_ds.repo.add_url_to_file(dest, url)
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except Exception:
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... # TODO: check how things can fail here and deal with it.
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return dest
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def export_to_ria(
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ds: dlad.Dataset,
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ria_url: urllib.parse.ParseResult,
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dicom_session_tag: str,
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session_metas: dict,
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export_ria_archive: bool = False,
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ria_archive_7zopts: str = "-mx5 -ms=off",
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):
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ria_name = pathlib.Path(ria_url.path).name
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ds.create_sibling_ria(
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ria_url.geturl(),
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name=ria_name,
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alias=session_metas[dicom_session_tag],
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existing="reconfigure",
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new_store_ok=True,
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)
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ds.push(to=ria_name, data="nothing")
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# keep the old ria-archive before add-archive-content, not used for now
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if export_ria_archive:
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ria_sibling_path = pathlib.Path(ds.siblings(name=ria_name)[0]["url"])
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archive_path = ria_sibling_path / "archives" / "archive.7z"
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ds.export_archive_ora(
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archive_path,
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opts=ria_archive_7zopts.split(),
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missing_content="error",
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)
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ds.repo.fsck(remote=f"{ria_url}-storage", fast=True) # index
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ds.push(to=ria_name, data="nothing")
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def export_to_s3(
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ds: dlad.Dataset,
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s3_url: urllib.parse.ParseResult,
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session_metas: dict,
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):
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# TODO: check if we can reuse a single bucket (or per study) with fileprefix
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# git-annex initremote remotename ...
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remote_name = s3_url.hostname
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_, bucket_name, *fileprefix = pathlib.Path(s3_url.path).parts
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fileprefix.append(session_metas["StudyInstanceUID"] + "/")
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ds.repo.init_remote(
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remote_name,
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S3_REMOTE_DEFAULT_PARAMETERS
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+ [
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f"host={s3_url.hostname}",
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f"bucket={bucket_name}",
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f"fileprefix={'/'.join(fileprefix)}",
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],
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)
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ds.repo.set_preferred_content(
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"wanted",
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"include=*7z or include=*.tar.gz or include=*zip",
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remote=remote_name,
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)
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ds.push(to=remote_name, data="auto")
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# It does not push the data to the S3 unless I set data="anything" which pushes everyhing including the deflated archived data
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def connect_gitlab(
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gitlab_url: urllib.parse.ParseResult, debug: bool = False
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) -> gitlab.Gitlab:
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"""
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Connection to Gitlab
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"""
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gl = gitlab.Gitlab(gitlab_url.geturl(), private_token=GITLAB_TOKEN)
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if debug:
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gl.enable_debug()
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gl.auth()
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return gl
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def get_or_create_gitlab_group(
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gl: gitlab.Gitlab,
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group_path: pathlib.Path,
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):
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"""fetch or create a gitlab group"""
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group_list = group_path.parts
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found = False
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for keep_groups in reversed(range(len(group_list) + 1)):
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tmp_repo_path = "/".join(group_list[0:keep_groups])
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logging.debug(tmp_repo_path)
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gs = gl.groups.list(search=tmp_repo_path)
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for g in gs:
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if g.full_path == tmp_repo_path:
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found = True
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break
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if found:
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break
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for nb_groups in range(keep_groups, len(group_list)):
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if nb_groups == 0:
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logging.debug(f"Creating group {group_list[nb_groups]}")
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g = gl.groups.create(
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{"name": group_list[nb_groups], "path": group_list[nb_groups]}
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)
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else:
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logging.debug(f"Creating group {group_list[nb_groups]} from {g.name}")
|
|
g = gl.groups.create(
|
|
{
|
|
"name": group_list[nb_groups],
|
|
"path": group_list[nb_groups],
|
|
"parent_id": g.id,
|
|
}
|
|
)
|
|
|
|
return g
|
|
|
|
|
|
def get_or_create_gitlab_project(gl: gitlab.Gitlab, project_path: pathlib.Path):
|
|
"""fetch or create a gitlab repo"""
|
|
project_name = project_path.parts
|
|
|
|
# Look for exact repo/project:
|
|
p = gl.projects.list(search=project_name[-1])
|
|
if p:
|
|
for curr_p in p:
|
|
if curr_p.path_with_namespace == str(project_path):
|
|
return curr_p
|
|
|
|
g = get_or_create_gitlab_group(gl, project_path.parent)
|
|
logging.debug(f"Creating project {project_name[-1]} from {g.name}")
|
|
p = gl.projects.create({"name": project_name[-1], "namespace_id": g.id})
|
|
return p
|
|
|
|
|
|
if __name__ == "__main__":
|
|
main()
|