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Merge branch 'release_20.01' into dev

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This commit is contained in:
Nicola Soranzo
2020-02-12 01:11:09 +00:00
parent d31a4ed84d 32b2da2035
commit f831bd842e
1 changed files with 29 additions and 27 deletions
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lib/galaxy/webapps/galaxy/api/users.py
+29 -27
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@@ -779,19 +779,22 @@ class UserAPIController(BaseAPIController, UsesTagsMixin, CreatesApiKeysMixin, B
"""
user = self._get_user(trans, id)
dbkeys = json.loads(user.preferences['dbkeys']) if 'dbkeys' in user.preferences else {}
valid_dbkeys = {}
update = False
for key in dbkeys:
dbkey = dbkeys[key]
for key, dbkey in dbkeys.items():
if 'count' not in dbkey and 'linecount' in dbkey:
chrom_count_dataset = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(dbkey['linecount'])
if chrom_count_dataset.state == trans.app.model.Job.states.OK:
if chrom_count_dataset and not chrom_count_dataset.deleted and chrom_count_dataset.state == trans.app.model.HistoryDatasetAssociation.states.OK:
chrom_count = int(open(chrom_count_dataset.file_name).readline())
dbkey['count'] = chrom_count
valid_dbkeys[key] = dbkey
update = True
else:
valid_dbkeys[key] = dbkey
if update:
user.preferences['dbkeys'] = json.dumps(dbkeys)
user.preferences['dbkeys'] = json.dumps(valid_dbkeys)
dbkey_collection = []
for key, attributes in dbkeys.items():
for key, attributes in valid_dbkeys.items():
attributes['id'] = key
dbkey_collection.append(attributes)
return dbkey_collection
@@ -840,28 +843,27 @@ 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: