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Fix output discovery when directory doesn't exist
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This broke in 8b76a5a.
Checking if `directory` is a directory is what we had done previously.
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mvdbeek committed Mar 2, 2018
1 parent bd69278 commit d21d7d9
Showing 1 changed file with 11 additions and 10 deletions.
21 changes: 11 additions & 10 deletions lib/galaxy/tools/parameters/output_collect.py
Original file line number Diff line number Diff line change
Expand Up @@ -516,16 +516,17 @@ def walk_over_extra_files(target_dir, extra_file_collector, job_working_director
"""
matches = []
directory = discover_target_directory(target_dir, job_working_directory)
for filename in os.listdir(directory):
path = os.path.join(directory, filename)
if os.path.isdir(path) and extra_file_collector.recurse:
# The current directory is already validated, so use that as the next job_working_directory when recursing
for match in walk_over_extra_files(filename, extra_file_collector, directory, matchable):
yield match
else:
match = extra_file_collector.match(matchable, filename, path=path)
if match:
matches.append(match)
if os.path.isdir(directory):
for filename in os.listdir(directory):
path = os.path.join(directory, filename)
if os.path.isdir(path) and extra_file_collector.recurse:
# The current directory is already validated, so use that as the next job_working_directory when recursing
for match in walk_over_extra_files(filename, extra_file_collector, directory, matchable):
yield match
else:
match = extra_file_collector.match(matchable, filename, path=path)
if match:
matches.append(match)

for match in extra_file_collector.sort(matches):
yield match
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