From f7f30893fefe3830dfeb735c8cd49de2cc18eb5a Mon Sep 17 00:00:00 2001 From: Jeff Knaggs Date: Fri, 16 Oct 2020 12:17:58 +0100 Subject: [PATCH] Clobber (and warn about) existing output directories instead of raising exception. --- python/clockwork/db.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/python/clockwork/db.py b/python/clockwork/db.py index 3a89ba1..c7f0d90 100644 --- a/python/clockwork/db.py +++ b/python/clockwork/db.py @@ -5,6 +5,7 @@ import re import sys import tempfile +import shutil from operator import itemgetter from clockwork import ( db_connection, @@ -558,7 +559,9 @@ def make_qc_jobs_tsv( output_dir = iso_dir.pipeline_dir( row["sequence_replicate_number"], "qc", pipeline_version ) - assert not os.path.exists(output_dir) + if os.path.exists(output_dir): + print("Warning:", output_dir, "already exists. Removing.", file=sys.stderr) + shutil.rmtree(output_dir) try: os.makedirs(output_dir) except: