def post(self):
'''
parameters:
q
scopes
fields
email
jsoninput if true, input "q" is a json string, must be decoded as a list.
'''
kwargs = self.get_query_params()
self._examine_kwargs('POST', kwargs)
q = kwargs.pop('q', None)
jsoninput = kwargs.pop('jsoninput', None) in ('1', 'true')
if q:
# ids = re.split('[\s\r\n+|,]+', q)
try:
ids = json.loads(q) if jsoninput else split_ids(q)
if not isinstance(ids, list):
raise ValueError
except ValueError:
ids = None
res = {'success': False, 'error': 'Invalid input for "q" parameter.'}
if ids:
scopes = kwargs.pop('scopes', None)
fields = kwargs.pop('fields', None)
res = self.esq.mget_biothings(ids, fields=fields, scopes=scopes, **kwargs)
else:
res = {'success': False, 'error': "Missing required parameters."}
encode = not isinstance(res, str) # when res is a string, e.g. when rawquery is true, do not encode it as json
self.return_json(res, encode=encode)
self.ga_track(event=self._ga_event_object('POST', {'qsize': len(q) if q else 0}))
def str_to_list(val):
""" Cast Biothings-style str to list. """
try: # core splitting algorithm
lst = split_ids(str(val))
except ValueError as err:
raise OptionError(str(err))
return lst
def str_to_list(self, val, param=''):
if self.jsoninput:
try:
val = json.loads(val)
except Exception:
pass
if not isinstance(val, list):
try:
val = split_ids(val)
except ValueError as e:
raise BiothingParameterTypeError(str(e), param)
return val
def str_to_list(self, val, param=''):
if self.jsoninput:
try:
val = json.loads(val)
except Exception:
pass
if not isinstance(val, list):
try:
val = split_ids(str(val))
except ValueError as e:
raise OptionArgError(reason=str(e), param=param)
return val
def _typify(self, arg, argval, json_list_input=False):
''' Try to get the parameter's type from settings '''
# first see if this parameter has an alias
# do value translations, if they exist
if 'type' not in self.kwarg_settings[arg]:
return argval
if self.kwarg_settings[arg]['type'] == list:
ret = []
if json_list_input:
try:
ret = json.loads(argval)
if not isinstance(ret, list):
raise ValueError
except Exception:
ret = []
#raise BiothingParameterTypeError('Could not listify "{}" in parameter "{}" with "jsoninput" True'.format(argval, arg))
if not ret:
try:
ret = split_ids(argval)
except ValueError as e:
raise BiothingParameterTypeError(
"Could not split argument '{0}' due to the following error: '{1}'"
.format(arg, str(e)))
#ret = [x for x in re.split(getattr(self.web_settings, 'LIST_SPLIT_REGEX', '[\s\r\n+|,]+'), argval) if x]
ret = ret[:self.kwarg_settings[arg].get(
'max', getattr(self.web_settings, 'LIST_SIZE_CAP', 1000))]
elif self.kwarg_settings[arg]['type'] == int:
try:
ret = int(argval)
except ValueError:
raise BiothingParameterTypeError(
"Expected '{0}' parameter to have integer type. Couldn't convert '{1}' to integer"
.format(arg, argval))
elif self.kwarg_settings[arg]['type'] == float:
try:
ret = float(argval)
except ValueError:
raise BiothingParameterTypeError(
"Expected '{0}' parameter to have float type. Couldn't convert '{1}' to float"
.format(arg, argval))
elif self.kwarg_settings[arg]['type'] == bool:
ret = self._boolify(argval)
else:
ret = argval
return ret
def post(self):
'''
parameters:
q
scopes
fields
species
jsoninput if true, input "q" is a json string, must be decoded as a list.
'''
kwargs = self.get_query_params()
q = kwargs.pop('q', None)
jsoninput = kwargs.pop('jsoninput', None) in ('1', 'true')
if q:
# ids = re.split('[\s\r\n+|,]+', q)
try:
ids = json.loads(q) if jsoninput else split_ids(q)
if not isinstance(ids, list):
raise ValueError
except ValueError:
ids = None
res = {'success': False, 'error': 'Invalid input for "q" parameter.'}
if ids:
scopes = kwargs.pop('scopes', None)
if scopes:
scopes = [x.strip() for x in scopes.split(',')]
fields = kwargs.pop('fields', None)
res = yield Task(self.esq.mget_gene2, ids, fields=fields, scopes=scopes, **kwargs)
else:
res = {'success': False, 'error': "Missing required parameters."}
self.return_json(res)
self.ga_track(event={'category': 'v2_api',
'action': 'query_post',
'label': 'qsize',
'value': len(q) if q else 0})