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Continue gracefully in set_meta if unable to count number of dataset lines. #7641

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Merged
merged 2 commits into from
Apr 3, 2019
Merged

Continue gracefully in set_meta if unable to count number of dataset lines. #7641

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20026b5
Continue gracefully in set_meta if unable to count number of dataset …
blankenberg Apr 1, 2019
4ee0e7f
Add note about cause for try/except in line counting.
blankenberg Apr 3, 2019
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14 changes: 10 additions & 4 deletions lib/galaxy/datatypes/data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -802,10 +802,16 @@ def count_data_lines(self, dataset):
"""
data_lines = 0
with compression_utils.get_fileobj(dataset.file_name) as in_file:
for line in in_file:
line = line.strip()
if line and not line.startswith('#'):
data_lines += 1
# FIXME: Potential encoding issue can prevent the ability to iterate over lines
# causing set_meta process to fail otherwise OK jobs. A better solution than
# a silent try/except is desirable.
try:
for line in in_file:
line = line.strip()
if line and not line.startswith('#'):
data_lines += 1
except Exception:
pass
return data_lines

def set_peek(self, dataset, line_count=None, is_multi_byte=False, WIDTH=256, skipchars=None, line_wrap=True):
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