def ls(self, table=None, verbose=False):
"""
Queries the database for a list of 'users' and/or 'dataset-types' and/or 'subjects' fields
:param table: the table (s) to query among: 'dataset-types','users'
and 'subjects'; if empty or None assumes all tables
:type table: str, list
:param verbose: [False] prints the list in the current window
:type verbose: bool
:return: list of names to query, list of full raw output in json serialized format
:rtype: list, list
"""
tlist = ('dataset-types', 'users', 'subjects')
field = ('name', 'username', 'nickname')
if not table:
table = tlist
table = [table] if isinstance(table, str) else table
full_out = []
list_out = []
for ind, tab in enumerate(tlist):
if tab in table:
full_out.append(self._alyxClient.get('/' + tab))
list_out.append([f[field[ind]] for f in full_out[-1]])
if verbose:
pprint(list_out)
if len(table) == 1:
return list_out[0], full_out[0]
else:
return list_out, full_out
def _ls(self, table=None, verbose=False):
"""
Queries the database for a list of 'users' and/or 'dataset-types' and/or 'subjects' fields
:param table: the table (s) to query among: 'dataset-types','users'
and 'subjects'; if empty or None assumes all tables
:type table: str
:param verbose: [False] prints the list in the current window
:type verbose: bool
:return: list of names to query, list of full raw output in json serialized format
:rtype: list, list
"""
assert (isinstance(table, str))
table_field_names = {
'dataset-types': 'name',
'datasets': 'name',
'users': 'username',
'subjects': 'nickname',
'labs': 'name'
}
if not table or table not in list(set(_ENDPOINTS.keys())):
raise KeyError("The attribute/endpoint: " + table +
" doesn't exist \n" + "possible values are " +
str(set(_ENDPOINTS.values())))
field_name = table_field_names[_ENDPOINTS[table]]
full_out = self.alyx.get('/' + _ENDPOINTS[table])
list_out = [f[field_name] for f in full_out]
if verbose:
pprint(list_out)
return list_out, full_out
def rest(self, url=None, action=None, id=None, data=None, **kwargs):
"""
alyx_client.rest(): lists endpoints
alyx_client.rest(endpoint): lists actions for endpoint
alyx_client.rest(endpoint, action): lists fields and URL
Example with a rest endpoint with all actions
>>> alyx.client.rest('subjects', 'list')
alyx.client.rest('subjects', 'list', field_filter1='filterval')
alyx.client.rest('subjects', 'create', data=sub_dict)
alyx.client.rest('subjects', 'read', id='nickname')
alyx.client.rest('subjects', 'update', id='nickname', data=sub_dict)
alyx.client.rest('subjects', 'partial_update', id='nickname', data=sub_ict)
alyx.client.rest('subjects', 'delete', id='nickname')
:param url: endpoint name
:param action: 'list', 'create', 'read', 'update', 'partial_update', 'delete'
:param id: lookup string for actions 'read', 'update', 'partial_update', and 'delete'
:param data: data dictionary for actions 'update', 'partial_update' and 'create'
:param ``**kwargs``: filter as per the REST documentation
:return: list of queried dicts ('list') or dict (other actions)
"""
# if endpoint is None, list available endpoints
if not url:
pprint([
k for k in self._rest_schemes.keys()
if not k.startswith('_') and k
])
return
# remove beginning slash if any
if url.startswith('/'):
url = url[1:]
# and split to the next slash or question mark
endpoint = re.findall("^/*[^?/]*", url)[0].replace('/', '')
# make sure the queryied endpoint exists, if not throw an informative error
if endpoint not in self._rest_schemes.keys():
av = [
k for k in self._rest_schemes.keys()
if not k.startswith('_') and k
]
raise ValueError('REST endpoint "' + endpoint +
'" does not exist. Available ' +
'endpoints are \n ' + '\n '.join(av))
endpoint_scheme = self._rest_schemes[endpoint]
# on a filter request, override the default action parameter
if '?' in url:
action = 'list'
# if action is None, list available actions for the required endpoint
if not action:
pprint(list(endpoint_scheme.keys()))
return
# make sure the the desired action exists, if not throw an informative error
if action not in endpoint_scheme.keys():
raise ValueError('Action "' + action + '" for REST endpoint "' +
endpoint + '" does ' +
'not exist. Available actions are: ' +
'\n ' +
'\n '.join(endpoint_scheme.keys()))
# the actions below require an id in the URL, warn and help the user
if action in ['read', 'update', 'partial_update', 'delete'] and not id:
logger_.warning('REST action "' + action +
'" requires an ID in the URL: ' +
endpoint_scheme[action]['url'])
return
# the actions below require a data dictionary, warn and help the user with fields list
if action in ['create', 'update', 'partial_update'] and not data:
pprint(endpoint_scheme[action]['fields'])
for act in endpoint_scheme[action]['fields']:
print("'" + act['name'] + "': ...,")
logger_.warning('REST action "' + action +
'" requires a data dict with above keys')
return
if action == 'list':
# list doesn't require id nor
assert (endpoint_scheme[action]['action'] == 'get')
# add to url data if it is a string
if id:
url = url + id
# otherwise, look for a dictionary of filter terms
elif kwargs:
for k in kwargs.keys():
if isinstance(kwargs[k], str):
query = kwargs[k]
elif isinstance(kwargs[k], list):
query = ','.join(kwargs[k])
else:
continue
url = url + f"?&{k}=" + query
return self.get('/' + url)
if action == 'read':
assert (endpoint_scheme[action]['action'] == 'get')
return self.get('/' + endpoint + '/' + id.split('/')[-1])
elif action == 'create':
assert (endpoint_scheme[action]['action'] == 'post')
return self.post('/' + endpoint, data=data)
elif action == 'delete':
assert (endpoint_scheme[action]['action'] == 'delete')
return self.delete('/' + endpoint + '/' + id.split('/')[-1])
elif action == 'partial_update':
assert (endpoint_scheme[action]['action'] == 'patch')
return self.patch('/' + endpoint + '/' + id.split('/')[-1],
data=data)
elif action == 'update':
assert (endpoint_scheme[action]['action'] == 'put')
return self.put('/' + endpoint + '/' + id.split('/')[-1],
data=data)
from ibllib.misc import pprint
from oneibl.one import ONE
one = ONE(base_url='https://test.alyx.internationalbrainlab.org')
# list all water administrations
wa = one.alyx.rest('water-administrations', 'list')
# to list administrations for one subject, it is better to use the subjects endpoint
sub_info = one.alyx.rest('subjects', 'read', 'ZM_346')
pprint(sub_info['water_administrations'])
# this is how to programmatically create a water administration
wa_ = {
'subject': 'ZM_346',
'date_time': '2018-11-25T12:34',
'water_administered': 25,
'water_type': 'Water 10% Sucrose',
'user': '******',
'session': 'f4b13ba2-1308-4673-820e-0e0a3e0f2d73',
'adlib': True
}
# do not use the example on anything else than alyx-dev
if one.alyx._base_url != 'https://dev.alyx.internationalbrainlab.org':
rep = one.alyx.rest('water-administrations', 'create', wa_)
## Init
from oneibl.one import ONE
from ibllib.misc import pprint
one = ONE(base_url='https://test.alyx.internationalbrainlab.org',
username='******',
password='******')
## Find an experiment
eid = one.search(users='olivier', date_range=['2018-08-24', '2018-08-24'])
pprint(eid)
one.search_terms()
## List dataset types for a session
eid = 'cf264653-2deb-44cb-aa84-89b82507028a'
one.list(eid)
## List #1
one.list()
## Load #1
dataset_types = [
'clusters.templateWaveforms', 'clusters.probes', 'clusters.depths'
]
eid = 'cf264653-2deb-44cb-aa84-89b82507028a'
wf, pr, d = one.load(eid, dataset_types=dataset_types)
## Load #2
my_data = one.load(eid, dataset_types=dataset_types, dclass_output=True)
from ibllib.misc import pprint
def rest(self, url=None, action=None, data=None, **kwargs):
"""
alyx_client.rest()
alyx_client.rest("sessions")
lab_info = alyx_client.rest('labs', 'read', 'mainenlab')
OR
lab_info = alyx_client.rest('labs', 'read',
'https://test.alyx.internationalbrainlab.org/labs/mainenlab')
:param url:
:param action:
:param data:
:return:
"""
# if endpoint is None, list available endpoints
if not url:
pprint([
k for k in self._rest_schemes.keys()
if not k.startswith('_') and k
])
return
# remove beginning slash if any
if url.startswith('/'):
url = url[1:]
# and split to the next slash or question mark
endpoint = re.findall("^/*[^?/]*", url)[0].replace('/', '')
# make sure the queryied endpoint exists, if not throw an informative error
if endpoint not in self._rest_schemes.keys():
av = [
k for k in self._rest_schemes.keys()
if not k.startswith('_') and k
]
raise ValueError('REST endpoint "' + endpoint +
'" does not exist. Available ' +
'endpoints are \n ' + '\n '.join(av))
endpoint_scheme = self._rest_schemes[endpoint]
# on a filter request, override the default action parameter
if '?' in url:
action = 'list'
# if action is None, list available actions for the required endpoint
if not action:
pprint(list(endpoint_scheme.keys()))
return
# make sure the the desired action exists, if not throw an informative error
if action not in endpoint_scheme.keys():
raise ValueError('Action "' + action + '" for REST endpoint "' +
endpoint + '" does ' +
'not exist. Available actions are: ' +
'\n ' +
'\n '.join(endpoint_scheme.keys()))
# if there is no data (except for list), show the user a list of fields
if action != 'list' and not data:
pprint(endpoint_scheme[action]['fields'])
for act in endpoint_scheme[action]['fields']:
print("'" + act['name'] + "': ...,")
return
if action == 'list':
assert (endpoint_scheme[action]['action'] == 'get')
# add to url data if it is a string
if data:
url = url + data
# otherwise, look for a dictionary of filter terms
elif kwargs:
for k in kwargs.keys():
if isinstance(kwargs[k], str):
query = kwargs[k]
elif isinstance(kwargs[k], list):
query = ','.join(kwargs[k])
else:
continue
url = url + f"?&{k}=" + query
return self.get('/' + url)
if action == 'read':
assert (endpoint_scheme[action]['action'] == 'get')
return self.get('/' + endpoint + '/' + data.split('/')[-1])
elif action == 'create':
assert (endpoint_scheme[action]['action'] == 'post')
return self.post('/' + endpoint, data)
elif action == 'delete':
assert (endpoint_scheme[action]['action'] == 'delete')
return self.delete('/' + endpoint + '/' + data.split('/')[-1])
elif action == 'partial_update':
assert (endpoint_scheme[action]['action'] == 'patch')
return self.patch('/' + url, data)
elif action == 'update':
assert (endpoint_scheme[action]['action'] == 'put')
return self.put('/' + url, data)
'''
Print water administration values from behavior data downloaded via ONE.
'''
# Author: Olivier Winter
from ibllib.misc import pprint
from oneibl.one import ONE
one = ONE(base_url='https://dev.alyx.internationalbrainlab.org')
# -- Get saved water administration --
# List all water administrations
wa = one.alyx.rest('water-administrations', 'list')
# To list administrations for one subject, it is better to use the subjects endpoint
subject_details = one.alyx.rest('subjects', 'read', 'ZM_346')
pprint(subject_details['water_administrations']
[0:2]) # Print the first 2 water admin.
## More Info about a session
d = one.session_data_info(eid)
print(d)
## Load #1
dataset_types = [
'clusters.templateWaveforms', 'clusters.probes', 'clusters.depths'
]
eid = '86e27228-8708-48d8-96ed-9aa61ab951db'
wf, pr, d = one.load(eid, dataset_types=dataset_types)
## Load #2
my_data = one.load(eid, dataset_types=dataset_types, dclass_output=True)
from ibllib.misc import pprint
pprint(my_data.local_path)
pprint(my_data.dataset_type)
## Load everything
eid, ses_info = one.search(subject='flowers')
my_data = one.load(eid[0])
pprint(my_data.dataset_type)
## Load
eid = '86e27228-8708-48d8-96ed-9aa61ab951db'
dataset_types = [
'clusters.probes', 'thisDataset.IveJustMadeUp', 'clusters.depths'
]
t, empty, cl = one.load(eid, dataset_types=dataset_types)
## List #1
'''
Print water administration values from behavior data downloaded via ONE.
'''
# Author: Olivier Winter
from ibllib.misc import pprint
from oneibl.one import ONE
one = ONE(base_url='https://test.alyx.internationalbrainlab.org')
# -- Get saved water administration --
# List all water administrations
wa = one.alyx.rest('water-administrations', 'list')
# To list administrations for one subject, it is better to use the subjects endpoint
subject_details = one.alyx.rest('subjects', 'read', 'ZM_346')
pprint(subject_details['water_administrations'])
