def get(self, message="", msg_level=None):
all_emails_except_current = yield Task(self._get_all_emails)
all_emails_except_current.remove(self.current_user.id)
avail_meta = SampleTemplate.metadata_headers() +\
get_table_cols("study")
self.render('list_studies.html',
availmeta=avail_meta,
all_emails_except_current=all_emails_except_current,
message=message,
msg_level=msg_level)
def get(self, message="", msg_level=None):
all_emails_except_current = yield Task(self._get_all_emails)
all_emails_except_current.remove(self.current_user.id)
avail_meta = SampleTemplate.metadata_headers() +\
get_table_cols("study")
self.render('list_studies.html',
availmeta=avail_meta,
all_emails_except_current=all_emails_except_current,
message=message,
msg_level=msg_level)
with TRN:
# a few notes: just getting the preps with duplicated values; ignoring
# column 'sample_id' and tables 'study_sample', 'prep_template',
# 'prep_template_sample'
sql = """SELECT table_name, array_agg(column_name::text)
FROM information_schema.columns
WHERE column_name IN %s
AND column_name != 'sample_id'
AND table_name LIKE 'prep_%%'
AND table_name NOT IN (
'prep_template', 'prep_template_sample')
GROUP BY table_name"""
# note that we are looking for those columns with duplicated names in
# the headers
headers = set(PrepTemplate.metadata_headers()) & \
set(SampleTemplate.metadata_headers())
if headers:
TRN.add(sql, [tuple(headers)])
overlapping = dict(TRN.execute_fetchindex())
else:
overlapping = None
if overlapping is not None:
# finding actual duplicates
for table_name, cols in overlapping.items():
# leaving print so when we patch in the main system we know that
# nothing was renamed or deal with that
print(table_name)
with TRN:
for c in cols:
with TRN:
# a few notes: just getting the preps with duplicated values; ignoring
# column 'sample_id' and tables 'study_sample', 'prep_template',
# 'prep_template_sample'
sql = """SELECT table_name, array_agg(column_name::text)
FROM information_schema.columns
WHERE column_name IN %s
AND column_name != 'sample_id'
AND table_name LIKE 'prep_%%'
AND table_name NOT IN (
'prep_template', 'prep_template_sample')
GROUP BY table_name"""
# note that we are looking for those columns with duplicated names in
# the headers
headers = set(PrepTemplate.metadata_headers()) & \
set(SampleTemplate.metadata_headers())
if headers:
TRN.add(sql, [tuple(headers)])
overlapping = dict(TRN.execute_fetchindex())
else:
overlapping = None
if overlapping is not None:
# finding actual duplicates
for table_name, cols in viewitems(overlapping):
# leaving print so when we patch in the main system we know that
# nothing was renamed or deal with that
print table_name
with TRN:
for c in cols:
