def _build_study_info(user, search_type, study_proc=None, proc_samples=None):
"""Builds list of dicts for studies table, with all HTML formatted
Parameters
----------
user : User object
logged in user
search_type : choice, ['user', 'public']
what kind of search to perform
study_proc : dict of lists, optional
Dictionary keyed on study_id that lists all processed data associated
with that study. Required if proc_samples given.
proc_samples : dict of lists, optional
Dictionary keyed on proc_data_id that lists all samples associated with
that processed data. Required if study_proc given.
Returns
-------
infolist: list of dict of lists and dicts
study and processed data info for JSON serialiation for datatables
Each dict in the list is a single study, and contains the text
Notes
-----
Both study_proc and proc_samples must be passed, or neither passed.
"""
build_samples = False
# Logic check to make sure both needed parts passed
if study_proc is not None and proc_samples is None:
raise IncompetentQiitaDeveloperError(
'Must pass proc_samples when study_proc given')
elif proc_samples is not None and study_proc is None:
raise IncompetentQiitaDeveloperError(
'Must pass study_proc when proc_samples given')
elif study_proc is None:
build_samples = True
# get list of studies for table
if search_type == 'user':
user_study_set = user.user_studies.union(user.shared_studies)
if user.level == 'admin':
user_study_set = (user_study_set |
Study.get_by_status('sandbox') |
Study.get_by_status('private'))
study_set = user_study_set - Study.get_by_status('public')
elif search_type == 'public':
study_set = Study.get_by_status('public')
else:
raise ValueError('Not a valid search type')
if study_proc is not None:
study_set = study_set.intersection(study_proc)
if not study_set:
# No studies left so no need to continue
return []
return generate_study_list([s.id for s in study_set], build_samples,
public_only=(search_type == 'public'))
def _build_study_info(user, search_type, study_proc=None, proc_samples=None):
"""Builds list of dicts for studies table, with all HTML formatted
Parameters
----------
user : User object
logged in user
search_type : choice, ['user', 'public']
what kind of search to perform
study_proc : dict of lists, optional
Dictionary keyed on study_id that lists all processed data associated
with that study. Required if proc_samples given.
proc_samples : dict of lists, optional
Dictionary keyed on proc_data_id that lists all samples associated with
that processed data. Required if study_proc given.
Returns
-------
infolist: list of dict of lists and dicts
study and processed data info for JSON serialiation for datatables
Each dict in the list is a single study, and contains the text
Notes
-----
Both study_proc and proc_samples must be passed, or neither passed.
"""
build_samples = False
# Logic check to make sure both needed parts passed
if study_proc is not None and proc_samples is None:
raise IncompetentQiitaDeveloperError(
'Must pass proc_samples when study_proc given')
elif proc_samples is not None and study_proc is None:
raise IncompetentQiitaDeveloperError(
'Must pass study_proc when proc_samples given')
elif study_proc is None:
build_samples = True
# get list of studies for table
if search_type == 'user':
user_study_set = user.user_studies.union(user.shared_studies)
if user.level == 'admin':
user_study_set = (user_study_set |
Study.get_by_status('sandbox') |
Study.get_by_status('private'))
study_set = user_study_set - Study.get_by_status('public')
elif search_type == 'public':
study_set = Study.get_by_status('public')
else:
raise ValueError('Not a valid search type')
if study_proc is not None:
study_set = study_set.intersection(study_proc)
if not study_set:
# No studies left so no need to continue
return []
return generate_study_list([s.id for s in study_set], build_samples,
public_only=(search_type == 'public'))
def get(self, ignore):
user = self.get_argument('user')
visibility = self.get_argument('visibility')
echo = int(self.get_argument('sEcho'))
if user != self.current_user.id:
raise HTTPError(403, reason='Unauthorized search!')
if visibility not in ['user', 'public']:
raise HTTPError(400, reason='Not a valid visibility')
info = generate_study_list(self.current_user, visibility)
# linkifying data
len_info = len(info)
for i in range(len_info):
info[i]['shared'] = ", ".join([
study_person_linkifier(element)
for element in info[i]['shared']
])
ppid = [pubmed_linkifier([p]) for p in info[i]['publication_pid']]
pdoi = [doi_linkifier([p]) for p in info[i]['publication_doi']]
del info[i]['publication_pid']
del info[i]['publication_doi']
info[i]['pubs'] = ', '.join(ppid + pdoi)
info[i]['pi'] = study_person_linkifier(info[i]['pi'])
info[i]['ebi_info'] = info[i]['ebi_submission_status']
ebi_study_accession = info[i]['ebi_study_accession']
if ebi_study_accession:
info[i]['ebi_info'] = '%s (%s)' % (''.join([
EBI_LINKIFIER.format(a)
for a in ebi_study_accession.split(',')
]), info[i]['ebi_submission_status'])
# build the table json
results = {
"sEcho": echo,
"iTotalRecords": len_info,
"iTotalDisplayRecords": len_info,
"aaData": info
}
# return the json in compact form to save transmit size
self.write(dumps(results, separators=(',', ':')))
def get(self, ignore):
user = self.get_argument('user')
visibility = self.get_argument('visibility')
echo = int(self.get_argument('sEcho'))
if user != self.current_user.id:
raise HTTPError(403, reason='Unauthorized search!')
if visibility not in ['user', 'public']:
raise HTTPError(400, reason='Not a valid visibility')
info = generate_study_list(self.current_user, visibility)
# linkifying data
len_info = len(info)
for i in range(len_info):
info[i]['shared'] = ", ".join([study_person_linkifier(element)
for element in info[i]['shared']])
ppid = [pubmed_linkifier([p]) for p in info[i]['publication_pid']]
pdoi = [doi_linkifier([p]) for p in info[i]['publication_doi']]
del info[i]['publication_pid']
del info[i]['publication_doi']
info[i]['pubs'] = ', '.join(ppid + pdoi)
info[i]['pi'] = study_person_linkifier(info[i]['pi'])
info[i]['ebi_info'] = info[i]['ebi_submission_status']
ebi_study_accession = info[i]['ebi_study_accession']
if ebi_study_accession:
info[i]['ebi_info'] = '%s (%s)' % (
''.join([EBI_LINKIFIER.format(a)
for a in ebi_study_accession.split(',')]),
info[i]['ebi_submission_status'])
# build the table json
results = {
"sEcho": echo,
"iTotalRecords": len_info,
"iTotalDisplayRecords": len_info,
"aaData": info
}
# return the json in compact form to save transmit size
self.write(dumps(results, separators=(',', ':')))
proc_data_list = [ar for ar in study.artifacts()
if ar.artifact_type == 'BIOM']
proc_samples = {}
study_proc = {study.id: defaultdict(list)}
for proc_data in proc_data_list:
study_proc[study.id][proc_data.data_type].append(proc_data.id)
# there is only one prep template for each processed data
proc_samples[proc_data.id] = proc_data.prep_templates[0].keys()
study_info = _build_single_study_info(study, info, study_proc,
proc_samples)
infolist.append(study_info)
return infolist
=======
return generate_study_list([s.id for s in study_set],
public_only=(search_type == 'public'))
>>>>>>> 405cbef0c9f71c620da95a0c1ba6c7d3d588b3ed
class ListStudiesHandler(BaseHandler):
@authenticated
@coroutine
@execute_as_transaction
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,
