def get(self, ignore):
user = self.get_argument('user')
query = self.get_argument('query')
echo = int(self.get_argument('sEcho'))
if user != self.current_user.id:
raise HTTPError(403, 'Unauthorized search!')
if query:
# Search for samples matching the query
search = QiitaStudySearch()
try:
search(query, self.current_user)
study_proc, proc_samples, _ = search.filter_by_processed_data()
except ParseException:
self.clear()
self.set_status(400)
self.write('Malformed search query. Please read "search help" '
'and try again.')
return
except QiitaDBIncompatibleDatatypeError as e:
self.clear()
self.set_status(400)
searchmsg = ''.join(e)
self.write(searchmsg)
return
except Exception as e:
# catch any other error as generic server error
self.clear()
self.set_status(500)
self.write("Server error during search. Please try again "
"later")
LogEntry.create('Runtime',
str(e),
info={
'User': self.current_user.id,
'query': query
})
return
else:
study_proc = proc_samples = None
info = _build_study_info(self.current_user,
study_proc=study_proc,
proc_samples=proc_samples)
# 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')
query = self.get_argument('query')
echo = int(self.get_argument('sEcho'))
if user != self.current_user.id:
raise HTTPError(403, 'Unauthorized search!')
if query:
# Search for samples matching the query
search = QiitaStudySearch()
try:
search(query, self.current_user)
study_proc, proc_samples, _ = search.filter_by_processed_data()
except ParseException:
self.clear()
self.set_status(400)
self.write('Malformed search query. Please read "search help" '
'and try again.')
return
except QiitaDBIncompatibleDatatypeError as e:
self.clear()
self.set_status(400)
searchmsg = ''.join(e)
self.write(searchmsg)
return
except Exception as e:
# catch any other error as generic server error
self.clear()
self.set_status(500)
self.write("Server error during search. Please try again "
"later")
LogEntry.create('Runtime', str(e),
info={'User': self.current_user.id,
'query': query})
return
else:
study_proc = proc_samples = None
info = _build_study_info(self.current_user, study_proc=study_proc,
proc_samples=proc_samples)
# 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 test_filter_by_processed_data(self):
search = QiitaStudySearch()
results, meta_cols = search('study_id = 1', User('*****@*****.**'))
spid, pds, meta = search.filter_by_processed_data()
exp_spid = {1: {'18S': [1]}}
exp_pds = {1: [
'1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195', '1.SKB4.640189',
'1.SKB5.640181', '1.SKB6.640176', '1.SKB7.640196', '1.SKB8.640193',
'1.SKB9.640200', '1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
'1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190', '1.SKD7.640191',
'1.SKD8.640184', '1.SKD9.640182', '1.SKM1.640183', '1.SKM2.640199',
'1.SKM3.640197', '1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']}
exp_meta = pd.DataFrame.from_dict({x: 1 for x in exp_pds[1]},
orient='index')
exp_meta.rename(columns={0: 'study_id'}, inplace=True)
self.assertEqual(spid, exp_spid)
self.assertEqual(pds, exp_pds)
self.assertEqual(meta.keys(), [1])
assert_frame_equal(meta[1], exp_meta)
def get(self, ignore):
user = self.get_argument('user')
query = self.get_argument('query')
search_type = self.get_argument('search_type')
echo = int(self.get_argument('sEcho'))
if user != self.current_user.id:
raise HTTPError(403, 'Unauthorized search!')
if search_type not in ['user', 'public']:
raise HTTPError(400, 'Not a valid search type')
if query:
# Search for samples matching the query
search = QiitaStudySearch()
try:
search(query, self.current_user)
study_proc, proc_samples, _ = search.filter_by_processed_data()
except ParseException:
self.clear()
self.set_status(400)
self.write('Malformed search query. Please read "search help" '
'and try again.')
return
except QiitaDBIncompatibleDatatypeError as e:
self.clear()
self.set_status(400)
searchmsg = ''.join(e)
self.write(searchmsg)
return
except Exception as e:
# catch any other error as generic server error
self.clear()
self.set_status(500)
self.write("Server error during search. Please try again "
"later")
LogEntry.create('Runtime', str(e),
info={'User': self.current_user.id,
'query': query})
return
else:
study_proc = proc_samples = None
info = _build_study_info(self.current_user, search_type, study_proc,
proc_samples)
# 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')
query = self.get_argument('query')
search_type = self.get_argument('search_type')
echo = int(self.get_argument('sEcho'))
if user != self.current_user.id:
raise HTTPError(403, 'Unauthorized search!')
if search_type not in ['user', 'public']:
raise HTTPError(400, 'Not a valid search type')
if query:
# Search for samples matching the query
search = QiitaStudySearch()
try:
search(query, self.current_user)
study_proc, proc_samples, _ = search.filter_by_processed_data()
except ParseException:
self.clear()
self.set_status(400)
self.write('Malformed search query. Please read "search help" '
'and try again.')
return
except QiitaDBIncompatibleDatatypeError as e:
self.clear()
self.set_status(400)
searchmsg = ''.join(e)
self.write(searchmsg)
return
except Exception as e:
# catch any other error as generic server error
self.clear()
self.set_status(500)
self.write("Server error during search. Please try again "
"later")
LogEntry.create('Runtime',
str(e),
info={
'User': self.current_user.id,
'query': query
})
return
else:
study_proc = proc_samples = None
info = _build_study_info(self.current_user, search_type, study_proc,
proc_samples)
# 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=(',', ':')))
echo = int(self.get_argument('sEcho'))
if user != self.current_user.id:
<<<<<<< HEAD
raise HTTPError(403, 'Unauthorized search!')
=======
raise HTTPError(403, reason='Unauthorized search!')
if search_type not in ['user', 'public']:
raise HTTPError(400, reason='Not a valid search type')
>>>>>>> 405cbef0c9f71c620da95a0c1ba6c7d3d588b3ed
if query:
# Search for samples matching the query
search = QiitaStudySearch()
try:
search(query, self.current_user)
study_proc, proc_samples, _ = search.filter_by_processed_data()
except ParseException:
self.clear()
self.set_status(400)
self.write('Malformed search query. Please read "search help" '
'and try again.')
return
except QiitaDBIncompatibleDatatypeError as e:
self.clear()
self.set_status(400)
searchmsg = ''.join(e)
self.write(searchmsg)
return
except Exception as e:
# catch any other error as generic server error
self.clear()
