def post(self):
name = self.get_argument('name')
description = self.get_argument('description')
user = self.get_current_user()
# create list of studies
study_ids = {s.id for s in Study.get_public()}
userobj = User(user)
[study_ids.add(x) for x in userobj.private_studies]
[study_ids.add(x) for x in userobj.shared_studies]
studies = [Study(i) for i in study_ids]
analysis = Analysis.create(User(user), name, description)
self.render('select_studies.html', user=user, aid=analysis.id,
studies=studies)
def __call__(self, searchstr, user):
"""Runs a Study query and returns matching studies and samples
Parameters
----------
searchstr : str
Search string to use
user : str
User making the search. Needed for permissions checks.
Returns
-------
dict
Found samples in format
{study_id: [[samp_id1, meta1, meta2, ...],
[samp_id2, meta1, meta2, ...], ...}
list
metadata column names searched for
Notes
-----
Metadata information for each sample is in the same order as the
metadata columns list returned
Metadata column names and string searches are case-sensitive
"""
study_sql, sample_sql, meta_headers = \
self._parse_study_search_string(searchstr)
conn_handler = SQLConnectionHandler()
# get all studies containing the metadata headers requested
study_ids = {x[0] for x in conn_handler.execute_fetchall(study_sql)}
# strip to only studies user has access to
userobj = User(user)
study_ids = study_ids.intersection(Study.get_public() +
userobj.private_studies +
userobj.shared_studies)
results = {}
# run search on each study to get out the matching samples
for sid in study_ids:
study_res = conn_handler.execute_fetchall(sample_sql.format(sid))
if study_res:
# only add study to results if actually has samples in results
results[sid] = study_res
return results, meta_headers
def __call__(self, searchstr, user):
"""Runs a Study query and returns matching studies and samples
Parameters
----------
searchstr : str
Search string to use
user : str
User making the search. Needed for permissions checks.
Returns
-------
dict
Found samples in format
{study_id: [[samp_id1, meta1, meta2, ...],
[samp_id2, meta1, meta2, ...], ...}
list
metadata column names searched for
Notes
-----
Metadata information for each sample is in the same order as the
metadata columns list returned
Metadata column names and string searches are case-sensitive
"""
study_sql, sample_sql, meta_headers = \
self._parse_study_search_string(searchstr)
conn_handler = SQLConnectionHandler()
# get all studies containing the metadata headers requested
study_ids = {x[0] for x in conn_handler.execute_fetchall(study_sql)}
# strip to only studies user has access to
userobj = User(user)
study_ids = study_ids.intersection(Study.get_public() +
userobj.private_studies +
userobj.shared_studies)
results = {}
# run search on each study to get out the matching samples
for sid in study_ids:
study_res = conn_handler.execute_fetchall(sample_sql.format(sid))
if study_res:
# only add study to results if actually has samples in results
results[sid] = study_res
return results, meta_headers
def test_get_public(self):
Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
obs = Study.get_public()
self.assertEqual(obs, [1])
def get(self):
self.write(self.render_string('waiting.html'))
self.flush()
public_studies = [Study(s_id) for s_id in Study.get_public()]
self.render('public_studies.html', user=self.current_user,
public_studies=public_studies)
def test_get_public(self):
Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
obs = Study.get_public()
self.assertEqual(obs, [1])