65a21f5c7cdda8de27c2054ddffdd391284c3aa1 hiram Mon Jun 1 09:03:06 2026 -0700 switching entirely to genome-centdb hgcentral refs #31811 diff --git src/hg/utils/otto/userRequests/ottoLib.py src/hg/utils/otto/userRequests/ottoLib.py index 25e369027d2..7f658bde93b 100644 --- src/hg/utils/otto/userRequests/ottoLib.py +++ src/hg/utils/otto/userRequests/ottoLib.py @@ -81,34 +81,34 @@ result = subprocess.run( ["git", "-C", kentTree, "pull"], capture_output=True, text=True, ) if result.returncode != 0: print("ERROR: 'git pull' failed in %s:\n%s%s" % (kentTree, result.stdout, result.stderr), file=sys.stderr) return False out = result.stdout.strip() if out and out != "Already up to date.": print("# git pull in %s:\n%s" % (kentTree, out), file=sys.stderr) return True -def hgsql(query, db="hgcentraltest"): +def hgsql(query, db="hgcentral"): """Run hgsql -N -B and return rows as list of tuples (tab-split).""" out = subprocess.run( - ["/cluster/bin/x86_64/hgsql", "-N", "-B", "-e", query, db], + ["/cluster/bin/x86_64/hgsql", '-h', 'genome-centdb', "-N", "-B", "-e", query, db], check=True, capture_output=True, text=True, ).stdout return [tuple(line.split("\t")) for line in out.splitlines() if line] def loadDbDbClades(): """Read dbDb.name.clade.tsv -> {dbName: clade}.""" result = {} with open(cladeTsv) as fh: for line in fh: if line.startswith("#") or not line.strip(): continue name, clade = line.rstrip("\n").split("\t")[:2] result[name] = clade return result