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fix race condition init/heudiconv

This commit is contained in:
bpinsard 2024-02-14 10:26:37 -05:00
parent b67e0d1bad
commit 795ff1b709
1 changed files with 15 additions and 3 deletions
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16
docker/dicom_indexer/indexer/index_dicom.py
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@ -1,4 +1,5 @@
import os import os
import time
import pydicom as dicom import pydicom as dicom
import argparse import argparse
import pathlib import pathlib
@ -340,6 +341,17 @@ def init_bids(
bids_project_repo.protectedbranches.create(data={"name": "convert/*"}) bids_project_repo.protectedbranches.create(data={"name": "convert/*"})
bids_project_repo.protectedbranches.create(data={"name": "dev"}) bids_project_repo.protectedbranches.create(data={"name": "dev"})
### avoid race conditions for first session pushed ###
### otherwise heudiconv starts before the remotes are configured
time.sleep(5) # wait for config pipeline to be created
while True:
pipelines = bids_project_repo.pipelines.list(all=True)
no_pipe = all(p.status in ["success", "failed"] for p in pipelines)
if no_pipe:
break
time.sleep(1)
return bids_project_repo
def init_dicom_study( def init_dicom_study(
dicom_study_ds: dlad.Dataset, dicom_study_ds: dlad.Dataset,
@ -385,7 +397,7 @@ def extract_session_metas(dicom_session_ds: dlad.Dataset) -> dict:
except Exception as e: # TODO: what exception occurs when non-dicom ? except Exception as e: # TODO: what exception occurs when non-dicom ?
continue continue
metas = {k: str(getattr(dic, k)).replace("^", "/") for k in SESSION_META_KEYS} metas = {k: str(getattr(dic, k)).replace("^", "/") for k in SESSION_META_KEYS}
metas["StudyDescriptionPath"] = metas["StudyDescription"].split('/') metas["StudyDescriptionPath"] = metas["StudyDescription"].split("/")
# return at first dicom found # return at first dicom found
return metas return metas
raise InputError("no dicom found") raise InputError("no dicom found")
@ -465,7 +477,7 @@ def export_to_s3(
# git-annex initremote remotename ... # git-annex initremote remotename ...
remote_name = s3_url.hostname remote_name = s3_url.hostname
s3_path = s3_url.path s3_path = s3_url.path
if '{' in s3_path: if "{" in s3_path:
s3_path = s3_path.format(**session_metas) s3_path = s3_path.format(**session_metas)
_, bucket_name, *fileprefix = pathlib.Path(s3_path).parts _, bucket_name, *fileprefix = pathlib.Path(s3_path).parts
fileprefix.append(session_metas["StudyInstanceUID"] + "/") fileprefix.append(session_metas["StudyInstanceUID"] + "/")