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Minor cleanup

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This commit is contained in:
mvdbeek
2020-02-11 19:38:42 +01:00
parent 6f7e8881f5
commit 95fba0f9b1
1 changed files with 21 additions and 22 deletions
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lib/galaxy/webapps/galaxy/api/users.py
+21 -22
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@@ -846,28 +846,27 @@ class UserAPIController(BaseAPIController, UsesTagsMixin, CreatesApiKeysMixin, B
trans.sa_session.flush()
counter = 0
lines_skipped = 0
f = open(new_len.file_name, 'w')
# LEN files have format:
# <chrom_name><tab><chrom_length>
for line in len_value.split('\n'):
# Splits at the last whitespace in the line
lst = line.strip().rsplit(None, 1)
if not lst or len(lst) < 2:
lines_skipped += 1
continue
chrom, length = lst[0], lst[1]
try:
length = int(length)
except ValueError:
lines_skipped += 1
continue
if chrom != escape(chrom):
build_dict['message'] = 'Invalid chromosome(s) with HTML detected and skipped.'
lines_skipped += 1
continue
counter += 1
f.write('%s\t%s\n' % (chrom, length))
f.close()
with open(new_len.file_name, 'w') as f:
# LEN files have format:
# <chrom_name><tab><chrom_length>
for line in len_value.split('\n'):
# Splits at the last whitespace in the line
lst = line.strip().rsplit(None, 1)
if not lst or len(lst) < 2:
lines_skipped += 1
continue
chrom, length = lst[0], lst[1]
try:
length = int(length)
except ValueError:
lines_skipped += 1
continue
if chrom != escape(chrom):
build_dict['message'] = 'Invalid chromosome(s) with HTML detected and skipped.'
lines_skipped += 1
continue
counter += 1
f.write('%s\t%s\n' % (chrom, length))
build_dict['len'] = new_len.id
build_dict['count'] = counter
else: