def test_get_default():
value = 42
assert get_default(value, 1, int) == value
assert get_default(value, 'hello', str) == 'hello'
assert isinstance(get_default(value, 1, int), int)
assert isinstance(get_default(value, 'hello', str), str)
assert get_default('...', 42, str) == 42
assert get_default('---', 42, str, na_value='---') == 42
assert isinstance(get_default('---', 42, str, na_value='---'), int)
def test_detail_scatter_fix(fig, SCdata):
"""This test is to confirm the plt.scatter() fix continues to work.
Error changed to Index error in matplotlib#11383"""
from utils import get_default
ax = fig.add_subplot(111)
star = "Kepler-617"
df, _ = SCdata
df0 = df[df.Star == star]
df = df.sample(5)
df.append([df0])
teffs = df["teff"].values
for teff in teffs:
color = get_default(teff, 5777, float)
with pytest.raises((TypeError, IndexError)):
ax.scatter([0], [1], c=color)
# This checks that the new version with color in [] does not raise an error.
ax.scatter([0], [1], c=[color])
def detail_plot(df, tlow, thigh):
hz1 = get_default(df['hz1'].values[0], -2, float)
hz2 = get_default(df['hz2'].values[0], -1, float)
color = get_default(df['teff'].values[0], 5777, float)
tlow = get_default(max(2500, tlow), 2500, int)
thigh = get_default(min(8500, thigh), 8500, int)
R = df.iloc[0]['radius']
r = [
planetary_radius(mi, ri)
for mi, ri in df.loc[:, ['plMass', 'plRadius']].values
]
smas = df['sma'].values
max_smas = max(smai for smai in smas
if isinstance(smai, (int, float)) and not np.isnan(smai))
Rs = max(500, 500 * R)
rs = [max(80, 30 * ri) for ri in r]
fig, ax = plt.subplots(1, figsize=(14, 2))
ax.scatter([0], [1],
s=Rs,
c=[color],
vmin=tlow,
vmax=thigh,
cmap=cm.autumn)
no_sma = []
if 0 < hz1 < hz2:
x = np.linspace(hz1, hz2, 10)
y = np.linspace(0.9, 1.1, 10)
z = np.array([[xi] * 10 for xi in x[::-1]]).T
plt.contourf(x, y, z, 300, alpha=0.8, cmap=cm.summer)
for i, sma in enumerate(smas):
if np.isnan(sma):
no_sma.append('{} has no SMA'.format(df['plName'].values[i]))
continue
if sma < hz1:
dist = hz1 - sma
ax.scatter(sma, [1],
s=rs[i],
c=[dist],
vmin=0,
vmax=hz1,
cmap=cm.autumn)
elif hz1 <= sma <= hz2:
ax.scatter(sma, [1], s=rs[i], c='k', alpha=0.8)
else:
dist = sma - hz2
ax.scatter(sma, [1],
s=rs[i],
c=[dist],
vmin=hz2,
vmax=max_smas,
cmap=cm.winter_r)
for planet in ss_planets.keys():
s = ss_planets[planet][0]
r = 30 * ss_planets[planet][1] / 2.
r /= float(ss_planets['Jupiter'][1])
ax.scatter(s, [0.95], s=r * 10, c='g')
ax.text(s - 0.01, 0.97, planet, color='white')
ax.set_xlim(0.0, max_smas * 1.2)
ax.set_ylim(0.9, 1.1)
ax.set_xlabel('Semi-major axis [AU]')
ax.yaxis.set_major_formatter(plt.NullFormatter())
ax.set_yticks([])
ax.spines['left'].set_visible(False)
ax.set_facecolor('black')
plt.tight_layout()
for i, text in enumerate(no_sma):
ax.text(max_smas * 0.8, 1.05 - i * 0.02, text, color='white')
return fig_to_html(fig)
import logging
import utils
DEFAULT = utils.get_default()
class MonitorLog(object):
def __init__(self):
self.log_path = DEFAULT['monitor_log']
self.log_level = logging.DEBUG
self.logger = logging.getLogger('MonitorLog')
self.logger.setLevel(self.log_level)
self.fmt = logging.Formatter("%(asctime)s %(levelname)s %(message)s","%Y-%m-%d %H:%M:%S")
def file_log(self):
fh = logging.FileHandler(self.log_path)
fh.setLevel(self.log_level)
fh.setFormatter(self.fmt)
self.logger.addHandler(fh)
return fh.stream,self.logger
def stream_log(self):
ch = logging.StreamHandler()
ch.setLevel(self.log_level)
ch.setFormatter(self.fmt)
self.logger.addHandler(ch)
return self.logger
monitor_obj = MonitorLog()
STREAM,FILE_LOG = monitor_obj.file_log()
STREAM_LOG = monitor_obj.stream_log()
if __name__ == '__main__':
STREAM_LOG.info("info")
STREAM_LOG.debug("debug")
def detail_plot(df, tlow, thigh):
hz1 = get_default(df['datetime'].values[0], -2, float)
hz2 = get_default(df['outcome_datetime'].values[0], -1, float)
color = get_default(df['los'].values[0], 5777, float)
tlow = get_default(max(2500, tlow), 2500, int)
thigh = get_default(min(8500, thigh), 8500, int)
R = df.iloc[0]['los']
r = [ri for ri in df.loc[:, ['los']].values]
LOSs = df['los'].values
max_LOSs = max([
losi for losi in LOSs
if isinstance(losi, (int, float)) and not np.isnan(losi)
])
Rs = max(500, 500 * R)
rs = [max(80, 30 * ri) for ri in r]
fig, ax = plt.subplots(1, figsize=(14, 2))
ax.scatter([0], [1],
s=Rs,
c=[color],
vmin=tlow,
vmax=thigh,
cmap=cm.autumn)
no_los = []
if 0 < hz1 < hz2:
x = np.linspace(hz1, hz2, 10)
y = np.linspace(0.9, 1.1, 10)
z = np.array([[xi] * 10 for xi in x[::-1]]).T
plt.contourf(x, y, z, 300, alpha=0.8, cmap=cm.summer)
for i, los in enumerate(LOSs):
if np.isnan(los):
no_los.append('{} has no LOS'.format(df['plName'].values[i]))
continue
if los < hz1:
dist = hz1 - los
ax.scatter(los, [1],
s=rs[i],
c=[dist],
vmin=0,
vmax=hz1,
cmap=cm.autumn)
elif hz1 <= los <= hz2:
ax.scatter(los, [1], s=rs[i], c='k', alpha=0.8)
else:
dist = los - hz2
ax.scatter(los, [1],
s=rs[i],
c=[dist],
vmin=hz2,
vmax=max_LOSs,
cmap=cm.winter_r)
for intake in ss_intake.keys():
s = ss_intake[intake][0]
r = 30 * ss_intake[intake][1] / 2.
r /= float(ss_intake['Jupiter'][1])
ax.scatter(s, [0.95], s=r * 10, c='g')
ax.text(s - 0.01, 0.97, intake, color='white')
ax.set_xlim(0.0, max_LOSs * 1.2)
ax.set_ylim(0.9, 1.1)
ax.set_xlabel('Date')
ax.yaxis.set_major_formatter(plt.NullFormatter())
ax.set_yticks([])
ax.spines['left'].set_visible(False)
# ax.set_facecolor('black')
plt.tight_layout()
for i, text in enumerate(no_los):
ax.text(max_LOSs * 0.8, 1.05 - i * 0.02, text, color='white')
return fig_to_html(fig)
def add_action(n_clicks_add, n_clicks_delete, monitoring_dropdown_value,
restriction_dropdown_value, administration_dropdown_value,
new_data, data, selected_rows):
ctx = dash.callback_context
triggered_component = ctx.triggered[0]['prop_id'].split('.')[0]
if monitoring_dropdown_value == 'Weighing':
data = action.Weighing.fetch(as_dict=True)
columns = [{"name": i, "id": i} for i in action.Weighing.heading.names]
data_add_action_table = [{
c['id']: utils.get_default(action.Weighing, c['id'])
for c in columns
}]
elif monitoring_dropdown_value == 'HealthStatus':
data = action.Weighing.HealthStatus.fetch(as_dict=True)
columns = [{
"name": i,
"id": i
} for i in action.Weighing.HealthStatus.heading.names]
data_add_action_table = [{
c['id']: utils.get_default(action.Weighing.HealthStatus, c['id'])
for c in columns
}]
elif restriction_dropdown_value == 'WaterRestriction':
data = action.WaterRestriction.fetch(as_dict=True)
columns = [{
"name": i,
"id": i
} for i in action.WaterRestriction.heading.names]
data_add_action_table = [{
c['id']: utils.get_default(action.WaterRestriction, c['id'])
for c in columns
}]
elif restriction_dropdown_value == 'FoodRestriction':
data = action.FoodRestriction.fetch(as_dict=True)
columns = [{
"name": i,
"id": i
} for i in action.FoodRestriction.heading.names]
data_add_action_table = [{
c['id']: utils.get_default(action.FoodRestriction, c['id'])
for c in columns
}]
elif administration_dropdown_value == 'WaterAdministration':
data = action.WaterAdministration.fetch(as_dict=True)
columns = [{
"name": i,
"id": i
} for i in action.WaterAdministration.heading.names]
data_add_action_table = [{
c['id']: utils.get_default(action.WaterAdministration, c['id'])
for c in columns
}]
elif administration_dropdown_value == 'FoodAdministration':
data = action.FoodAdministration.fetch(as_dict=True)
columns = [{
"name": i,
"id": i
} for i in action.FoodAdministration.heading.names]
data_add_action_table = [{
c['id']: utils.get_default(action.FoodAdministration, c['id'])
for c in columns
}]
if triggered_component == 'add-action-button':
entry = {k: v for k, v in new_data[0].items() if v != ''}
if monitoring_dropdown_value == 'Weighing':
action.Weighing.insert1(entry)
data = action.Weighing.fetch(as_dict=True)
elif monitoring_dropdown_value == 'HealthStatus':
for c in columns:
if c['name'] in [
'fur', 'mobility', 'stress', 'suture_implant'
]:
c = c.update(presentation="dropdown")
action.Weighing.HealthStatus.insert1(entry)
data = action.Weighing.HealthStatus.fetch(as_dict=True)
elif restriction_dropdown_value == 'WaterRestriction':
action.WaterRestriction.insert1(entry)
data = action.WaterRestriction.fetch(as_dict=True)
elif restriction_dropdown_value == 'FoodRestriction':
action.FoodRestriction.insert1(entry)
data = action.FoodRestriction.fetch(as_dict=True)
elif administration_dropdown_value == 'WaterAdministration':
action.WaterAdministration.insert1(entry)
data = action.WaterAdministration.fetch(as_dict=True)
elif administration_dropdown_value == 'FoodAdministration':
action.FoodAdministration.insert1(entry)
data = action.FoodAdministration.fetch(as_dict=True)
if triggered_component == 'delete-action-button' and selected_rows:
print(selected_rows)
if monitoring_dropdown_value == 'Weighing':
entry = {
'subject_id': data[selected_rows[0]]['subject_id'],
'weighing_time': data[selected_rows[0]]['weighing_time']
}
(action.Weighing & entry).delete()
data = action.Weighing.fetch(as_dict=True)
elif monitoring_dropdown_value == 'HealthStatus':
entry = {
'subject_id': data[selected_rows[0]]['subject_id'],
'computer_name': data[selected_rows[0]]['computer_name']
}
(action.Weighing.HealthStatus & entry).delete()
data = action.Weighing.HealthStatus.fetch(as_dict=True)
elif restriction_dropdown_value == 'WaterRestriction':
entry = {
'subject_id':
data[selected_rows[0]]['subject_id'],
'water_restr_start_time':
data[selected_rows[0]]['water_restr_start_time']
}
(action.WaterRestriction & entry).delete()
data = action.WaterRestriction.fetch(as_dict=True)
elif restriction_dropdown_value == 'FoodRestriction':
entry = {
'subject_id':
data[selected_rows[0]]['subject_id'],
'food_restr_start_time':
data[selected_rows[0]]['food_restr_start_time']
}
(action.FoodRestriction & entry).delete()
data = action.FoodRestriction.fetch(as_dict=True)
elif administration_dropdown_value == 'WaterAdministration':
entry = {
'subject_id': data[selected_rows[0]]['subject_id'],
'water_admin_time': data[selected_rows[0]]['water_admin_time']
}
(action.WaterAdministration & entry).delete()
data = action.WaterAdministration.fetch(as_dict=True)
elif administration_dropdown_value == 'FoodAdministration':
entry = {
'subject_id': data[selected_rows[0]]['subject_id'],
'food_admin_time': data[selected_rows[0]]['food_admin_time']
}
(action.FoodAdministration & entry).delete()
data = action.FoodAdministration.fetch(as_dict=True)
return data, columns, data_add_action_table, columns
def add_acquisition(n_clicks_add, n_clicks_delete, general_dropdown_value,
task_dropdown_value, instruments_dropdown_value, new_data,
data, selected_rows):
ctx = dash.callback_context
triggered_component = ctx.triggered[0]['prop_id'].split('.')[0]
if general_dropdown_value == 'Session':
data = acquisition.Session.fetch(as_dict=True)
columns = [{
"name": i,
"id": i
} for i in acquisition.Session.heading.names]
data_add_acquisition_table = [{
c['id']: utils.get_default(acquisition.Session, c['id'])
for c in columns
}]
elif general_dropdown_value == 'User':
data = acquisition.Session.User.fetch(as_dict=True)
columns = [{
"name": i,
"id": i
} for i in acquisition.Session.User.heading.names]
data_add_acquisition_table = [{
c['id']: utils.get_default(acquisition.Session.User, c['id'])
for c in columns
}]
elif general_dropdown_value == 'Reward':
data = acquisition.Session.Reward.fetch(as_dict=True)
columns = [{
"name": i,
"id": i
} for i in acquisition.Session.Reward.heading.names]
data_add_acquisition_table = [{
c['id']: utils.get_default(acquisition.Session.Reward, c['id'])
for c in columns
}]
elif task_dropdown_value == 'Scara':
data = acquisition.Session.Scara.fetch(as_dict=True)
columns = [{
"name": i,
"id": i
} for i in acquisition.Session.Scara.heading.names]
data_add_acquisition_table = [{
c['id']: utils.get_default(acquisition.Session.Scara, c['id'])
for c in columns
}]
elif instruments_dropdown_value == 'Camera':
data = acquisition.Session.Camera.fetch(as_dict=True)
columns = [{
"name": i,
"id": i
} for i in acquisition.Session.Camera.heading.names]
data_add_acquisition_table = [{
c['id']: utils.get_default(acquisition.Session.Camera, c['id'])
for c in columns
}]
elif instruments_dropdown_value == 'TwoPhoton':
data = acquisition.Session.TwoPhoton.fetch(as_dict=True)
columns = [{
"name": i,
"id": i
} for i in acquisition.Session.TwoPhoton.heading.names]
data_add_acquisition_table = [{
c['id']: utils.get_default(acquisition.Session.TwoPhoton, c['id'])
for c in columns
}]
elif instruments_dropdown_value == 'Inscopix':
data = acquisition.Session.Inscopix.fetch(as_dict=True)
columns = [{
"name": i,
"id": i
} for i in acquisition.Session.Inscopix.heading.names]
data_add_acquisition_table = [{
c['id']: utils.get_default(acquisition.Session.Inscopix, c['id'])
for c in columns
}]
elif instruments_dropdown_value == 'Nvoke':
data = acquisition.Session.Nvoke.fetch(as_dict=True)
columns = [{
"name": i,
"id": i
} for i in acquisition.Session.Nvoke.heading.names]
data_add_acquisition_table = [{
c['id']: utils.get_default(acquisition.Session.Nvoke, c['id'])
for c in columns
}]
elif instruments_dropdown_value == 'Optogenetics':
data = acquisition.Session.Optogenetics.fetch(as_dict=True)
columns = [{
"name": i,
"id": i
} for i in acquisition.Session.Optogenetics.heading.names]
data_add_acquisition_table = [{
c['id']: utils.get_default(acquisition.Session.Optogenetics,
c['id'])
for c in columns
}]
elif instruments_dropdown_value == 'Ephys':
data = acquisition.Session.Ephys.fetch(as_dict=True)
columns = [{
"name": i,
"id": i
} for i in acquisition.Session.Ephys.heading.names]
data_add_acquisition_table = [{
c['id']: utils.get_default(acquisition.Session.Ephys, c['id'])
for c in columns
}]
elif instruments_dropdown_value == 'Calibration':
data = acquisition.Session.Calibration.fetch(as_dict=True)
columns = [{
"name": i,
"id": i
} for i in acquisition.Session.Calibration.heading.names]
data_add_acquisition_table = [{
c['id']: utils.get_default(acquisition.Session.Calibration,
c['id'])
for c in columns
}]
if triggered_component == 'add-acquisition-button':
entry = {k: v for k, v in new_data[0].items() if v != ''}
if general_dropdown_value == 'Session':
acquisition.Session.insert1(entry)
data = acquisition.Session.fetch(as_dict=True)
elif general_dropdown_value == 'User':
acquisition.Session.User.insert1(entry)
data = acquisition.Session.User.fetch(as_dict=True)
elif general_dropdown_value == 'Reward':
acquisition.Session.Reward.insert1(entry)
data = acquisition.Session.Reward.fetch(as_dict=True)
elif task_dropdown_value == 'Scara':
acquisition.Session.Scara.insert1(entry)
data = acquisition.Session.Scara.fetch(as_dict=True)
elif instruments_dropdown_value == 'Camera':
acquisition.Session.Camera.insert1(entry)
data = acquisition.Session.Camera.fetch(as_dict=True)
elif instruments_dropdown_value == 'TwoPhoton':
acquisition.Session.TwoPhoton.insert1(entry)
data = acquisition.Session.TwoPhoton.fetch(as_dict=True)
elif instruments_dropdown_value == 'Inscopix':
acquisition.Session.Inscopix.insert1(entry)
data = acquisition.Session.Inscopix.fetch(as_dict=True)
elif instruments_dropdown_value == 'Nvoke':
acquisition.Session.Nvoke.insert1(entry)
data = acquisition.Session.Nvoke.fetch(as_dict=True)
elif instruments_dropdown_value == 'Optogenetics':
acquisition.Session.Optogenetics.insert1(entry)
data = acquisition.Session.Optogenetics.fetch(as_dict=True)
elif instruments_dropdown_value == 'Ephys':
acquisition.Session.Ephys.insert1(entry)
data = acquisition.Session.Ephys.fetch(as_dict=True)
elif instruments_dropdown_value == 'Calibration':
acquisition.Session.Calibration.insert1(entry)
data = acquisition.Session.Calibration.fetch(as_dict=True)
if triggered_component == 'delete-acquisition-button' and selected_rows:
print(selected_rows)
if general_dropdown_value == 'Session':
entry = {
'subject_id': data[selected_rows[0]]['subject_id'],
'session_start_time':
data[selected_rows[0]]['session_start_time']
}
(acquisition.Session & entry).delete()
data = acquisition.Session.fetch(as_dict=True)
elif general_dropdown_value == 'User':
entry = {
'subject_id': data[selected_rows[0]]['subject_id'],
'session_start_time':
data[selected_rows[0]]['session_start_time'],
'user': data[selected_rows[0]]['user']
}
(acquisition.Session.User & entry).delete()
data = acquisition.Session.User.fetch(as_dict=True)
elif general_dropdown_value == 'Reward':
entry = {
'subject_id': data[selected_rows[0]]['subject_id'],
'session_start_time':
data[selected_rows[0]]['session_start_time'],
'reward_name': data[selected_rows[0]]['reward_name']
}
(acquisition.Session.Reward & entry).delete()
data = acquisition.Session.Reward.fetch(as_dict=True)
elif task_dropdown_value == 'Scara':
entry = {
'subject_id': data[selected_rows[0]]['subject_id'],
'session_start_time':
data[selected_rows[0]]['session_start_time']
}
(acquisition.Scara & entry).delete()
data = acquisition.Scara.fetch(as_dict=True)
elif instruments_dropdown_value == 'Camera':
entry = {
'subject_id': data[selected_rows[0]]['subject_id'],
'session_start_time':
data[selected_rows[0]]['session_start_time'],
'camera_index': data[selected_rows[0]]['camera_index']
}
(acquisition.Session.Camera & entry).delete()
data = acquisition.Session.Camera.fetch(as_dict=True)
elif instruments_dropdown_value == 'TwoPhoton':
entry = {
'subject_id': data[selected_rows[0]]['subject_id'],
'session_start_time':
data[selected_rows[0]]['session_start_time'],
'two_photon_name': data[selected_rows[0]]['two_photon_name']
}
(acquisition.Session.TwoPhoton & entry).delete()
data = acquisition.Session.TwoPhoton.fetch(as_dict=True)
elif instruments_dropdown_value == 'Inscopix':
entry = {
'subject_id': data[selected_rows[0]]['subject_id'],
'session_start_time':
data[selected_rows[0]]['session_start_time']
}
(acquisition.Session.Inscopix & entry).delete()
data = acquisition.Session.Inscopix.fetch(as_dict=True)
elif instruments_dropdown_value == 'Nvoke':
entry = {
'subject_id': data[selected_rows[0]]['subject_id'],
'session_start_time':
data[selected_rows[0]]['session_start_time']
}
(acquisition.Session.Nvoke & entry).delete()
data = acquisition.Session.Nvoke.fetch(as_dict=True)
elif instruments_dropdown_value == 'Optogenetics':
entry = {
'subject_id': data[selected_rows[0]]['subject_id'],
'session_start_time':
data[selected_rows[0]]['session_start_time']
}
(acquisition.Session.Optogenetics & entry).delete()
data = acquisition.Session.Optogenetics.fetch(as_dict=True)
elif instruments_dropdown_value == 'Ephys':
entry = {
'subject_id': data[selected_rows[0]]['subject_id'],
'session_start_time':
data[selected_rows[0]]['session_start_time']
}
(acquisition.Session.Ephys & entry).delete()
data = acquisition.Session.Ephys.fetch(as_dict=True)
elif instruments_dropdown_value == 'Calibration':
entry = {
'subject_id': data[selected_rows[0]]['subject_id'],
'session_start_time':
data[selected_rows[0]]['session_start_time']
}
(acquisition.Session.Calibration & entry).delete()
data = acquisition.Session.Calibration.fetch(as_dict=True)
return data, columns, data_add_acquisition_table, columns
def execute(self, *args, **options):
if os.path.basename(sys.argv[0]) == 'snodas':
self.snodas_command_error()
return 1
if options.get('version'):
print('snodas version {}'.format(self.get_version()))
return 2
self.verbosity = options.get('verbosity')
self.output_file = utils.get_default(
options,
'output_file',
self.default_conf_file(),
)
self.vprint(2, 'Config file path will be {}'.format(self.output_file))
conf_exists = os.path.isfile(self.output_file)
if options.get('no_configure') and conf_exists:
self.vprint(1,'Reusing existing configuration from {}'.format(self.output_file))
self.settings = utils.load_conf_file(self.output_file)
elif options.get('no_configure') and not conf_exists:
print('ERROR: no-configure option specified '
'but configuration file does not exist.')
return 3
elif conf_exists and not options.get('overwrite_conf'):
print('ERROR: configuration file already exists '
'and overwrite-conf option not specified.')
return 4
else:
self.vprint(1, 'Generating configuration from install options')
self.settings = self.extract_settings_from_options(options)
self.print_conf()
if options.get('make_env'):
self.vprint(1, 'creating conda env')
self.create_conda_env(options)
else:
self.vprint(
1,
'conda env creation skipped; '
'installing to active python instance',
)
self.vprint(1, 'Installing project')
self.install(options)
if not options.get('no_configure'):
self.write_conf_file()
# print next steps for user
self.vprint(1, '\nInstallation successful!')
self.vprint(
1,
('\nNext, activate the new conda env for the project:\n\n'
'`activate {}`\n\n'
'(`source` is required in a sh-like shell).\n\n'
'Then, setup any required services for this instance:\n\n:'
'`snodas createdb [options] # creates a postgres DB`\n'
'`snodas setupiis [options] # creates a site in IIS`\n\n'
'Once the services are configured, '
'you can run a webserver or celery:\n\n'
'`snodas runserver [options]'
'To learn what options apply to each command, try:\n\n'
'`snodas help <command>`'
).format(self.settings['INSTANCE_NAME'])
)
def extract_settings_from_options(self, options):
settings = {}
settings['ENV'] = options.get('env') or utils.get_env_name()
if not settings['ENV']:
raise InstallError(
'Could not extract env name from path and none specified.'
)
pyfile = settings['ENV'] + '.py'
if not os.path.isfile(utils.get_settings_file(pyfile)):
warnings.warn(
'Could not find settings file for env named {}'
.format(pyfile),
)
settings['DEBUG'] = (
settings['ENV'] == 'development' or options.get('DEBUG')
)
settings['INSTANCE_NAME'] = utils.get_default(
options,
'instance_name',
utils.get_instance_name(),
)
if not settings['INSTANCE_NAME']:
raise InstallError(
'Could not extract instance name from path and none specified.'
)
settings['SECRET_KEY'] = utils.get_default(
options,
'secret_key',
utils.generate_secret_key(options.get('secret_key_length'))
)
settings['DATABASE_NAME'] = utils.get_default(
options,
'db_name',
settings['INSTANCE_NAME'],
)
settings['DATABASE_USER'] = utils.get_default(
options,
'db_user',
settings['DATABASE_NAME'],
)
settings['DATABASE_PASSWORD'] = utils.get_default(
options,
'db_password',
get_password('Please enter the database user password: '******'DATABASE_HOST'] = utils.get_default(options, 'db_host', None)
settings['DATABASE_PORT'] = utils.get_default(options, 'db_port', None)
settings['SITE_DOMAIN_NAME'] = utils.get_default(
options,
'domain',
input('Enter in the domain name for this project instance: '),
)
settings['SUBDOMAINS'] = []
settings['ADDITIONAL_SETTINGS_FILES'] = utils.get_default(
options,
'additional_settings_file',
[],
)
return settings
# if c['name'] in ['sex', 'strain']:
# c.update(presentation="dropdown")
# add subject table style
add_acquisition_style = copy.deepcopy(table_style_template)
add_acquisition_style['style_table'].update({
'minHeight': '80px',
'height': '80px',
'maxHeight': '80px',
})
add_acquisition_table = dash_table.DataTable(id='add-acquisition-table',
columns=columns,
data=[{
c['id']: utils.get_default(
acquisition.Session,
c['id'])
for c in columns
}],
**add_acquisition_style,
editable=True)
## ----------------------------- add acquisition button ---------------------------------
add_acquisition_button = html.Button(children='Add an acquisition record',
id='add-acquisition-button',
n_clicks=0,
style={'marginBottom': '0.5em'})
## ------------------------- deletion confirm dialogue ------------------------------
delete_acquisition_confirm = dcc.ConfirmDialog(
id='delete-acquisition-confirm',
# for c in columns:
# if c['name'] in ['sex', 'strain']:
# c.update(presentation="dropdown")
# add subject table style
add_action_style = copy.deepcopy(table_style_template)
add_action_style['style_table'].update({
'minHeight': '80px',
'height': '80px',
'maxHeight': '80px',
})
add_action_table = dash_table.DataTable(id='add-action-table',
columns=columns,
data=[{
c['id']: utils.get_default(
action.Weighing, c['id'])
for c in columns
}],
**add_action_style,
editable=True)
## ----------------------------- add action button ---------------------------------
add_action_button = html.Button(children='Add an action record',
id='add-action-button',
n_clicks=0,
style={'marginBottom': '0.5em'})
## ------------------------- deletion confirm dialogue ------------------------------
delete_action_confirm = dcc.ConfirmDialog(
id='delete-action-confirm',
message='Are you sure you want to delete the record?',