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allow hic hubCheck "error" to pass
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daler committed Apr 20, 2024
1 parent ecdda0b commit e28ecb5
Showing 1 changed file with 10 additions and 2 deletions.
12 changes: 10 additions & 2 deletions ci/check_hubs.py
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@

for line in open(args.tsv):
line = line.strip()
if line.startswith('#') or not line:
if line.startswith("#") or not line:
continue

# Dest in trackhub demo is the second column of TSV, without the initial directory
Expand All @@ -59,7 +59,15 @@
# with "can't find database hg19 in hg.conf, should have a default
# named "db"". When checking the hub in the Genome Browser it seems
# fine. So allowing this as a "pass".
if line.startswith("can't find database") and "hic_hub" in str(dest):
#
# Some time later...
# hubCheck for those same tracks is now showing "can't find profile
# central in hg.conf" error. Aain the tracks look fine the browser,
# so we'll consider that OK as well.
if "hic_hub" in str(dest) and (
line.startswith("can't find database")
or line.startswith("can't find profile central in hg.conf")
):
warnings = True
elif not (line.startswith("Found") or line.startswith("warning:")):
error = True
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