def _pipe_modules(self):
""" display modules
"""
self.project = expipe.require_project('project_test')
modules = display_ex.modules_view(self.project)
return modules
def module_teardown_setup_project_setup():
try:
expipe.delete_project(PROJECT_ID, remove_all_childs=True)
except NameError:
pass
project = expipe.require_project(PROJECT_ID)
from expipe_plugin_cinpla.main import CinplaPlugin
CinplaPlugin().attach_to_cli(cli)
# make surgery action
run_command(['register-surgery', pytest.RAT_ID,
'--weight', '500',
'--birthday', '21.05.2017',
'--procedure', 'implantation',
'-d', '21.01.2017T14:40',
'-a', 'mecl', 1.9,
'-a', 'mecr', 1.8])
# init adjusment
run_command(['adjust', pytest.RAT_ID,
'-a', 'mecl', 50,
'-a', 'mecr', 50,
'-d', 'now',
'--init'], inp='y')
yield project
def test_create_delete_project_and_childs():
module_contents = {'species': {'value': 'rat'}}
project = expipe.core.require_project(pytest.PROJECT_ID)
action = project.require_action(pytest.ACTION_ID)
action_module = action.create_module(pytest.MODULE_ID,
contents=module_contents,
overwrite=False)
project_module = project.create_module(pytest.MODULE_ID,
contents=module_contents,
overwrite=False)
expipe.delete_project(pytest.PROJECT_ID, remove_all_childs=True)
with pytest.raises(KeyError):
expipe.get_project(pytest.PROJECT_ID)
# remake project, then the "old" action and project_module should be deleted
project = expipe.require_project(pytest.PROJECT_ID)
with pytest.raises(KeyError):
project.actions[pytest.ACTION_ID]
project.modules[pytest.MODULE_ID]
# remake action, then the "old" action_module should be deleted
action = project.require_action(pytest.ACTION_ID)
with pytest.raises(KeyError):
action.modules[pytest.MODULE_ID]
def _pipe_entities(self):
""" display entities
"""
self.project = expipe.require_project('project_test')
entities = display_ex.entities_view(self.project)
return entities
def _pipe_actions(self):
""" display actions
"""
self.project = expipe.require_project('project_test')
actions = display_ex.actions_view(self.project)
return actions
def setup_project_action():
project = expipe.require_project(PROJECT_ID)
try:
project.delete_action(ACTION_ID)
except NameError:
pass
action = project.require_action(ACTION_ID)
yield project, action
def teardown_setup_project():
try:
expipe.delete_project(PROJECT_ID, remove_all_childs=True)
except NameError:
pass
project = expipe.require_project(PROJECT_ID)
action = project.require_action(ACTION_ID)
yield project, action
def _add_metadata_to_Expipe(self, type_register, module_name, meta_key):
"""_add_to_Exdir
"""
self.project = expipe.require_project('project_test')
if type_register == 'module':
self.project.require_module(
name=module_name,
contents={meta_key: {self.metadata[meta_key]}})
def test_module_array():
import numpy as np
quan = np.array([1, 2])
module_contents = {'quan': quan}
project = expipe.require_project(pytest.PROJECT_ID)
action = project.require_action(pytest.ACTION_ID)
project_module = project.create_module(pytest.MODULE_ID,
contents=module_contents,
overwrite=True)
mod_dict = project_module.to_dict()
assert isinstance(mod_dict['quan'], list)
assert all(a == b for a, b in zip(quan, mod_dict['quan']))
def test_module_quantities():
import quantities as pq
quan = [1, 2] * pq.s
module_contents = {'quan': quan}
project = expipe.require_project(pytest.PROJECT_ID)
action = project.require_action(pytest.ACTION_ID)
project_module = project.create_module(pytest.MODULE_ID,
contents=module_contents,
overwrite=True)
mod_dict = project_module.to_dict()
assert isinstance(mod_dict['quan'], pq.Quantity)
assert all(a == b for a, b in zip(quan, mod_dict['quan']))
def test_action_attr_list_dtype():
project = expipe.require_project(pytest.PROJECT_ID)
action = project.require_action(pytest.ACTION_ID)
for attr in ['entities', 'users', 'tags']:
with pytest.raises(TypeError):
setattr(action, attr, ['sub1', 'sub2', 1])
with pytest.raises(TypeError):
setattr(action, attr, ['sub1', 'sub2', ['s']])
setattr(action, attr, ['sub1', 'sub2'])
prop_list = getattr(action, attr)
with pytest.raises(TypeError):
prop_list.append(1)
with pytest.raises(TypeError):
prop_list.extend([1])
def test_action_messages_setter():
from datetime import datetime, timedelta
project = expipe.require_project(pytest.PROJECT_ID)
action = project.require_action(pytest.ACTION_ID)
message_manager = action.messages
assert len(message_manager) == 0
time = datetime(2017, 6, 1, 21, 42, 20)
text = "my message"
user = "******"
msg_1 = {'text': text, 'user': user, 'datetime': time}
messages = [msg_1]
msg_object = action.create_message(text=text, user=user, datetime=time)
assert isinstance(msg_object, expipe.core.Message)
assert msg_object.text == text
assert msg_object.user == user
assert msg_object.datetime == time
assert contain_same(messages, message_manager)
text = "my new message"
user = "******"
msg_2 = {'text': text, 'user': user, 'datetime': time}
messages.append(msg_2)
msg_object = action.create_message(text=text, user=user, datetime=time)
assert isinstance(msg_object, expipe.core.Message)
assert msg_object.text == text
assert msg_object.user == user
assert msg_object.datetime == time
assert contain_same(messages, message_manager)
text = "updated text"
user = "******"
time = datetime(2019, 6, 1, 21, 42, 20)
msg_object.text = text
msg_object.user = user
msg_object.datetime = time
assert msg_object.text == text
assert msg_object.user == user
assert msg_object.datetime == time
def _add_file_to_Expipe(self, name, target_dir, level_dir):
"""_add_to_Exdir
"""
self.project = expipe.require_project('project_test')
self.project.modules['project-module'] = {
"environment": {
"type": "laboratory"
},
"method": {
"type": "EM"
}
}
entity = self.project.create_entity('equipment')
action = self.project.create_action('acquisition')
action.type = 'Collection of dataset'
def test_fill_the_project():
import quantities as pq
from datetime import datetime, timedelta
module_contents = {'species': {'value': 'rat'}}
project = expipe.require_project(pytest.PROJECT_ID)
action = project.require_action(pytest.ACTION_ID)
quan = [1, 2] * pq.s
module_contents = {'quan': quan}
project_module = project.create_module(pytest.MODULE_ID,
contents=module_contents,
overwrite=True)
mod_dict = project_module.to_dict()
assert isinstance(mod_dict['quan'], pq.Quantity)
assert all(a == b for a, b in zip(quan, mod_dict['quan']))
def test_action_messages_dtype():
from datetime import datetime, timedelta
project = expipe.require_project(pytest.PROJECT_ID)
action = project.require_action(pytest.ACTION_ID)
time = datetime(2017, 6, 1, 21, 42, 20)
# string in date not ok
msg = {
'message': 'sub2',
'user': '******',
'datetime': str(time + timedelta(minutes=10))
}
with pytest.raises(TypeError):
action.create_message(msg)
# int not ok
msg = {
'message': 'sub2',
'user': 13,
'datetime': time + timedelta(minutes=10)
}
with pytest.raises(TypeError):
action.create_message(msg)
# int not ok
msg = {
'message': 12,
'user': "******",
'datetime': time + timedelta(minutes=10)
}
with pytest.raises(TypeError):
action.create_message(msg)
# None is not ok
msg = {
'message': "sub2",
'user': None,
'datetime': time + timedelta(minutes=10)
}
with pytest.raises(TypeError):
action.create_message(msg)
def test_module_list():
project = expipe.require_project(pytest.PROJECT_ID)
action = project.require_action(pytest.ACTION_ID)
list_cont = ['list I am', 1]
project_module = project.create_module(pytest.MODULE_ID,
contents=list_cont,
overwrite=True)
mod_dict = project_module.to_dict()
assert isinstance(mod_dict, list)
assert all(a == b for a, b in zip(list_cont, mod_dict))
module_contents = {'list': list_cont}
project_module = project.create_module(pytest.MODULE_ID,
contents=module_contents,
overwrite=True)
mod_dict = project_module.to_dict()
assert isinstance(mod_dict['list'], list)
assert all(a == b for a, b in zip(list_cont, mod_dict['list']))
module_contents = {'is_list': {'0': 'df', '1': 'd', '2': 's'}}
action_module = action.create_module(pytest.MODULE_ID,
contents=module_contents,
overwrite=True)
mod_dict = action_module.to_dict()
assert isinstance(mod_dict['is_list'], dict)
module_contents = {'almost_list1': {'0': 'df', '1': 'd', 'd': 's'}}
action_module = action.create_module(pytest.MODULE_ID,
contents=module_contents,
overwrite=True)
mod_dict = action_module.to_dict()
assert isinstance(mod_dict['almost_list1'], dict)
assert module_contents == mod_dict, '{}, {}'.format(
module_contents, mod_dict)
module_contents = {'is_list': {0: 'df', 1: 'd', 2: 's'}}
action_module = action.create_module(pytest.MODULE_ID,
contents=module_contents,
overwrite=True)
mod_dict = action_module.to_dict()
assert isinstance(mod_dict['is_list'], dict)
def test_change_message():
from datetime import datetime, timedelta
project = expipe.require_project(pytest.PROJECT_ID)
action = project.require_action(pytest.ACTION_ID)
message_manager = action.messages
time = datetime(2017, 6, 1, 21, 42, 20)
# add two messages
msg_1 = {'text': 'sub1', 'user': '******', 'datetime': time}
msg_2 = {
'text': 'sub2',
'user': '******',
'datetime': time + timedelta(minutes=10)
}
action.create_message(text=msg_1["text"],
user=msg_1["user"],
datetime=msg_1["datetime"])
action.create_message(text=msg_2["text"],
user=msg_2["user"],
datetime=msg_2["datetime"])
# assert all([m1 == m2.to_dict() for m1, m2 in zip([msg_1, msg_2], message_manager)])
# change one of them
msg_3 = {
'text': 'sub3',
'user': '******',
'datetime': time + timedelta(minutes=20)
}
for i, message in enumerate(message_manager):
if message.user == "usr2":
message.text = msg_3["text"]
message.user = msg_3["user"]
message.datetime = msg_3["datetime"]
assert contain_same([msg_1, msg_3], message_manager)
# -*- coding: utf-8 -*-
"""
Created on Wed May 5 12:08:57 2021
@author: Benjamin
"""
import expipe
import os
project = expipe.require_project("test")
action = project.require_action("something")
from datetime import datetime
action.tags = ['place cell', 'familiar environment']
action.datetime = datetime.now()
action.location = 'here'
action.type = 'Recording'
action.subjects = ['rat1']
action.users = ['Peter', 'Mary']
tracking = action.require_module("tracking", template="tracking")
import quantities as pq
tracking_contents = {'box_shape': {'value': 'square'}}
tracking_module = action.require_module(name="tracking",
contents=tracking_contents)
elphys_contents = {
'depth': 2 * pq.um,
}
elphys_module = action.require_module(name="electrophysiology",
contents=elphys_contents)
def test_create_project():
expipe.require_project(pytest.PROJECT_ID)