def exit():
# stop any active threads
exit_threads.set() # stop detached run thread
Robot.get_instance().stop() # stops attached run thread
func = request.environ.get('werkzeug.server.shutdown')
if func is None:
sys.exit()
func()
return 'Server shutting down...'
def _detached_progress():
robot = Robot.get_instance()
while not exit_threads.is_set():
res = robot._driver.smoothie_player.progress(timeout=20)
if not res.get('file'):
return
percentage = '{}%'.format(round(res.get('percentage', 0) * 100, 2))
def _seconds_to_string(sec):
hours = int(sec / (60 * 60))
hours = str(hours) if hours > 9 else '0{}'.format(hours)
minutes = int(sec / 60) % 60
minutes = str(minutes) if minutes > 9 else '0{}'.format(minutes)
seconds = sec % 60
seconds = str(seconds) if seconds > 9 else '0{}'.format(seconds)
return (hours, minutes, seconds)
h, m, s = _seconds_to_string(res.get('elapsed_time'))
progress_data = 'Protocol {} Complete - Elapsed Time {}:{}:{}'.format(
percentage, h, m, s)
if res.get('estimated_time'):
h, m, s = _seconds_to_string(res.get('estimated_time'))
progress_data += ' - Estimated Time Left {}:{}:{}'.format(h, m, s)
d = {
'caller': 'ui',
'mode': 'live',
'name': 'command-run',
'command_description': progress_data
}
notify(d)
def _run_commands(should_home_first=True):
robot = Robot.get_instance()
start_time = time.time()
api_response = {'errors': [], 'warnings': []}
try:
robot.resume()
robot.run(caller='ui')
if len(robot._commands) == 0:
error = \
"This protocol does not contain any commands for the robot."
api_response['errors'] = [error]
except Exception as e:
api_response['errors'] = [str(e)]
api_response['warnings'] = robot.get_warnings() or []
api_response['name'] = 'run exited'
end_time = time.time()
emit_notifications(api_response['warnings'], 'warning')
emit_notifications(api_response['errors'], 'danger')
seconds = end_time - start_time
minutes, seconds = divmod(seconds, 60)
hours, minutes = divmod(minutes, 60)
run_time = "%d:%02d:%02d" % (hours, minutes, seconds)
result = "Run complete in {}".format(run_time)
emit_notifications([result], 'success')
socketio.emit('event', {'name': 'run-finished'})
def _run_detached():
try:
robot = Robot.get_instance()
p = player.SmoothiePlayer_2_0_0()
d = {'caller': 'ui', 'mode': 'live', 'name': 'command-run'}
d.update({'command_description': 'Simulating, please wait...'})
notify(d)
robot.smoothie_drivers['simulate'].record_start(p)
robot.simulate()
robot.smoothie_drivers['simulate'].record_stop()
d.update(
{'command_description': 'Saving file to robot, please wait...'})
notify(d)
robot._driver.play(p)
d.update({
'command_description':
'Protocol running, unplug USB at any time.'
})
notify(d)
d.update(
{'command_description': 'To stop, unplug USB and power robot OFF'})
notify(d)
_detached_progress()
except Exception as e:
emit_notifications([str(e)], 'danger')
socketio.emit('event', {'name': 'run-finished'})
def _get_all_pipettes():
robot = Robot.get_instance()
pipette_list = []
for _, p in robot.get_instruments():
if isinstance(p, instruments.Pipette):
pipette_list.append(p)
return sorted(pipette_list, key=lambda p: p.name.lower())
def setUp(self):
Robot.reset_for_tests()
self.robot = Robot.get_instance()
self.robot.connect()
self.trash = containers.load('point', 'A1', 'trash')
self.tiprack = containers.load('tiprack-200ul', 'B2', 'p200-rack')
self.trough = containers.load('trough-12row', 'B2', 'trough')
self.plate = containers.load('96-flat', 'A2', 'magbead')
self.p200 = instruments.Pipette(
name="p200",
trash_container=self.trash,
tip_racks=[self.tiprack],
min_volume=10, # These are variable
axis="b",
channels=1)
self.p1000 = instruments.Pipette(
name="p1000",
trash_container=self.trash,
tip_racks=[self.tiprack],
min_volume=100, # These are variable
axis="a",
channels=1)
def test_containers_create(self):
import os
import json
from opentrons import Robot
container_name = 'plate_for_testing_containers_create'
containers.create(name=container_name,
grid=(8, 12),
spacing=(9, 9),
diameter=4,
depth=8,
volume=1000)
p = containers.load(container_name, 'A1')
self.assertEquals(len(p), 96)
self.assertEquals(len(p.rows), 12)
self.assertEquals(len(p.cols), 8)
self.assertEquals(p.get_parent(), Robot.get_instance().deck['A1'])
self.assertEquals(p['C3'], p[18])
self.assertEquals(p['C3'].max_volume(), 1000)
for i, w in enumerate(p):
self.assertEquals(w, p[i])
# remove the file if we only created it for this test
should_delete = False
with open(environment.get_path('CONTAINERS_FILE')) as f:
created_containers = json.load(f)
del created_containers['containers'][p.get_name()]
if not len(created_containers['containers'].keys()):
should_delete = True
if should_delete:
os.remove(environment.get_path('CONTAINERS_FILE'))
def setUp(self):
Robot.reset_for_tests()
self.robot = Robot.get_instance()
self.robot.connect()
self.trash = containers.load('point', 'A1', 'trash')
self.tiprack = containers.load('tiprack-200ul', 'B2', 'p200-rack')
self.trough = containers.load('trough-12row', 'B2', 'trough')
self.plate = containers.load('96-flat', 'A2', 'magbead')
self.p200 = instruments.Pipette(
name="p200",
trash_container=self.trash,
tip_racks=[self.tiprack],
min_volume=10, # These are variable
axis="b",
channels=1
)
self.p1000 = instruments.Pipette(
name="p1000",
trash_container=self.trash,
tip_racks=[self.tiprack],
min_volume=100, # These are variable
axis="a",
channels=1
)
def update_step_list():
global current_protocol_step_list
robot = Robot.get_instance()
if current_protocol_step_list is None:
create_step_list()
try:
for step in current_protocol_step_list:
t_axis = str(step['axis']).upper()
instrument = robot._instruments[t_axis]
step.update({
'top':
instrument.positions['top'],
'bottom':
instrument.positions['bottom'],
'blow_out':
instrument.positions['blow_out'],
'drop_tip':
instrument.positions['drop_tip'],
'max_volume':
instrument.max_volume,
'calibrated':
_check_if_instrument_calibrated(instrument)
})
for placeable_step in step['placeables']:
c = _get_container_from_step(placeable_step)
if c:
placeable_step.update(
{'calibrated': _check_if_calibrated(instrument, c)})
except Exception as e:
emit_notifications([str(e)], 'danger')
return current_protocol_step_list
def get_unallocated_slot(self):
"""
:return: str name of a slot without any children (first occurence)
"""
robot = Robot.get_instance()
for slot in robot._deck.get_children_list():
if not slot.has_children():
return slot.get_name()
raise JSONProcessorRuntimeError(
'Unable to find any unallocated slots in robot deck')
def get_unallocated_slot(self):
"""
:return: str name of a slot without any children (first occurence)
"""
robot = Robot.get_instance()
for slot in robot._deck.get_children_list():
if not slot.has_children():
return slot.get_name()
raise JSONProcessorRuntimeError(
'Unable to find any unallocated slots in robot deck'
)
def _get_all_containers():
"""
Returns all containers currently on the deck
"""
all_containers = list()
robot = Robot.get_instance()
for slot in robot._deck:
if slot.has_children():
all_containers += slot.get_children_list()
return _sort_containers(all_containers)
def drop_tip():
robot = Robot.get_instance()
try:
axis = request.json.get("axis")
instrument = robot._instruments[axis.upper()]
instrument.return_tip(enqueue=False)
except Exception as e:
emit_notifications([str(e)], 'danger')
return flask.jsonify({'status': 'error', 'data': str(e)})
return flask.jsonify({'status': 'success', 'data': ''})
def disconnectRobot():
status = 'success'
data = None
robot = Robot.get_instance()
try:
robot.disconnect()
emit_notifications(["Successfully disconnected"], 'info')
except Exception as e:
status = 'error'
data = str(e)
emit_notifications([data], 'danger')
return flask.jsonify({'status': status, 'data': data})
def test_remove_child(self):
robot = Robot.get_instance()
robot.reset()
slot = 'B1'
plate = containers.load('96-flat', slot, 'plate')
self.assertEquals(len(robot.containers()), 1)
plate.get_parent().remove_child(plate.get_name())
self.assertEquals(len(robot.containers()), 0)
plate = containers.load('96-flat', slot, 'plate')
self.assertEquals(len(robot.containers()), 1)
robot.deck[slot].remove_child(plate.get_name())
self.assertEquals(len(robot.containers()), 0)
def setUp(self):
self.robot = Robot.get_instance()
# set this to True if testing with a robot connected
# testing while connected allows the response handlers
# and serial handshakes to be tested
self.motor = self.robot._driver
options = {"limit_switches": True, "config": {"alpha_steps_per_mm": 80.0, "beat_steps_per_mm": 80.0}}
myport = self.robot.VIRTUAL_SMOOTHIE_PORT
self.robot.disconnect()
success = self.robot.connect(port=myport, options=options)
self.assertTrue(success)
def load(container_name, slot, label=None):
"""
Examples
--------
>>> from opentrons import containers
>>> containers.load('96-flat', 'A1')
<Deck>/<Slot A1>/<Container 96-flat>
>>> containers.load('96-flat', 'A2', 'plate')
<Deck>/<Slot A2>/<Container plate>
>>> containers.load('non-existent-type', 'A2') # doctest: +ELLIPSIS
Exception: Container type "non-existent-type" not found in file ...
"""
from opentrons import Robot
if not label:
label = container_name
protocol = Robot.get_instance()
return protocol.add_container(container_name, slot, label)
def load(container_name, slot, label=None):
"""
Examples
--------
>>> from opentrons import containers
>>> containers.load('96-flat', 'A1')
<Deck>/<Slot A1>/<Container 96-flat>
>>> containers.load('96-flat', 'A2', 'plate')
<Deck>/<Slot A2>/<Container plate>
>>> containers.load('non-existent-type', 'A2') # doctest: +ELLIPSIS
Exception: Container type "non-existent-type" not found in file ...
"""
from opentrons import Robot
if not label:
label = container_name
protocol = Robot.get_instance()
return protocol.add_container(container_name, slot, label)
def jog():
robot = Robot.get_instance()
coords = request.json
status = 'success'
result = ''
try:
if coords.get("a") or coords.get("b"):
result = robot._driver.move_plunger(mode="relative", **coords)
else:
result = robot.move_head(mode="relative", **coords)
except Exception as e:
result = str(e)
status = 'error'
emit_notifications([result], 'danger')
return flask.jsonify({'status': status, 'data': result})
def setUp(self):
Robot.reset_for_tests()
self.robot = Robot.get_instance()
self.robot.connect()
self.plate = containers.load('96-flat', 'A1', 'plate')
self.p200 = instruments.Pipette(name="p200", axis="b")
self.p200.delete_calibration_data()
well = self.plate[0]
pos = well.from_center(x=0, y=0, z=0, reference=self.plate)
self.location = (self.plate, pos)
well_deck_coordinates = well.center(well.get_deck())
dest = well_deck_coordinates + Vector(1, 2, 3)
self.robot.move_head(x=dest['x'], y=dest['y'], z=dest['z'])
self.p200.calibrate_position(self.location)
def setUp(self):
Robot.reset_for_tests()
self.robot = Robot.get_instance()
self.robot.connect()
self.plate = containers.load('96-flat', 'A1', 'plate')
self.p200 = instruments.Pipette(name="p200", axis="b")
self.p200.delete_calibration_data()
well = self.plate[0]
pos = well.from_center(x=0, y=0, z=0, reference=self.plate)
self.location = (self.plate, pos)
well_deck_coordinates = well.center(well.get_deck())
dest = well_deck_coordinates + Vector(1, 2, 3)
self.robot.move_head(x=dest['x'], y=dest['y'], z=dest['z'])
self.p200.calibrate_position(self.location)
def setUp(self):
self.robot = Robot.get_instance()
# set this to True if testing with a robot connected
# testing while connected allows the response handlers
# and serial handshakes to be tested
options = {
'firmware': 'edge-1c222d9NOMSD',
'limit_switches': True,
'config': {
'alpha_steps_per_mm': 80.0,
'beta_steps_per_mm': 80.0
}
}
self.robot.disconnect()
self.robot.connect(options=options)
self.motor = self.robot._driver
def connectRobot():
port = request.json.get('port')
options = request.json.get('options', {'limit_switches': False})
status = 'success'
data = None
robot = Robot.get_instance()
try:
robot.connect(port, options=options)
except Exception as e:
# any robot version incompatibility will be caught here
robot.disconnect()
status = 'error'
data = str(e)
if "versions are incompatible" in data:
data += ". To upgrade, go to docs.opentrons.com"
emit_notifications([data], 'danger')
return flask.jsonify({'status': status, 'data': data})
def _calibrate_placeable(container_name, parent_slot, axis_name):
robot = Robot.get_instance()
deck = robot._deck
this_container = deck[parent_slot].get_child_by_name(container_name)
axis_name = axis_name.upper()
if not this_container:
raise ValueError('Container {0} not found in slot {1}'.format(
container_name, parent_slot))
if axis_name not in robot._instruments:
raise ValueError('Axis {} is not initialized'.format(axis_name))
instrument = robot._instruments[axis_name]
well = this_container[0]
pos = well.from_center(x=0, y=0, z=-1, reference=this_container)
location = (this_container, pos)
instrument.calibrate_position(location)
return instrument.calibration_data
def move_to_container():
robot = Robot.get_instance()
slot = request.json.get("slot")
name = request.json.get("label")
axis = request.json.get("axis")
try:
instrument = robot._instruments[axis.upper()]
container = robot._deck[slot].get_child_by_name(name)
well_x, well_y, well_z = tuple(
instrument.calibrator.convert(container[0],
container[0].bottom()[1]))
_, _, robot_max_z = robot._driver.get_dimensions()
# move to max Z to avoid collisions while calibrating
robot.move_head(z=robot_max_z)
robot.move_head(x=well_x, y=well_y)
robot.move_head(z=well_z)
except Exception as e:
emit_notifications([str(e)], 'danger')
return flask.jsonify({'status': 'error', 'data': str(e)})
return flask.jsonify({'status': 'success', 'data': ''})
def move_to_slot():
robot = Robot.get_instance()
status = 'success'
result = ''
try:
slot = request.json.get("slot")
slot = robot._deck[slot]
slot_x, slot_y, _ = slot.from_center(x=-1,
y=0,
z=0,
reference=robot._deck)
_, _, robot_max_z = robot._driver.get_dimensions()
robot.move_head(z=robot_max_z)
robot.move_head(x=slot_x, y=slot_y)
except Exception as e:
result = str(e)
status = 'error'
emit_notifications([result], 'danger')
return flask.jsonify({'status': status, 'data': result})
def setUp(self):
self.robot = Robot.get_instance()
# set this to True if testing with a robot connected
# testing while connected allows the response handlers
# and serial handshakes to be tested
self.motor = self.robot._driver
options = {
'limit_switches': True,
'config': {
'alpha_steps_per_mm': 80.0,
'beat_steps_per_mm': 80.0
}
}
myport = self.robot.VIRTUAL_SMOOTHIE_PORT
self.robot.disconnect()
success = self.robot.connect(port=myport, options=options)
self.assertTrue(success)
def upload_jupyter():
global robot, filename, last_modified, current_protocol_step_list
robot = Robot.get_instance()
try:
jupyter_robot = dill.loads(request.data)
# These attributes need to be persisted from existing robot
jupyter_robot._driver = robot._driver
jupyter_robot.smoothie_drivers = robot.smoothie_drivers
jupyter_robot.can_pop_command = robot.can_pop_command
Singleton._instances[Robot] = jupyter_robot
robot = jupyter_robot
# Reload instrument calibrations
[
instr.load_persisted_data()
for _, instr in jupyter_robot.get_instruments()
]
[
instr.update_calibrator()
for _, instr in jupyter_robot.get_instruments()
]
current_protocol_step_list = None
calibrations = update_step_list()
filename = 'JUPYTER UPLOAD'
last_modified = dt.datetime.now().strftime('%a %b %d %Y')
upload_data = {
'calibrations': calibrations,
'fileName': 'Jupyter Upload',
'lastModified': last_modified
}
app.logger.info('Successfully deserialized robot for jupyter upload')
socketio.emit('event', {'data': upload_data, 'name': 'jupyter-upload'})
except Exception as e:
app.logger.exception('Failed to properly deserialize jupyter upload')
print(e)
return flask.jsonify({'status': 'success', 'data': None})
def _start_connection_watcher():
robot = Robot.get_instance()
connection_state_watcher, watcher_should_run = BACKGROUND_TASKS.get(
'CONNECTION_STATE_WATCHER', (None, None))
if connection_state_watcher and watcher_should_run:
watcher_should_run.set()
watcher_should_run = threading.Event()
def watch_connection_state(should_run):
while not should_run.is_set():
socketio.emit('event', {
'type': 'connection_status',
'is_connected': robot.is_connected()
})
socketio.sleep(1.5)
connection_state_watcher = socketio.start_background_task(
watch_connection_state, (watcher_should_run))
BACKGROUND_TASKS['CONNECTION_STATE_WATCHER'] = (connection_state_watcher,
watcher_should_run)
def load_python(stream):
global robot
robot = Robot.get_instance()
code = helpers.convert_byte_stream_to_str(stream)
api_response = {'errors': [], 'warnings': []}
robot.reset()
patched_robot, restore_patched_robot = (
helpers.get_upload_proof_robot(robot))
try:
try:
exec(code, globals())
except Exception as e:
tb = e.__traceback__
stack_list = traceback.extract_tb(tb)
_, line, name, text = stack_list[-1]
if 'exec' in text:
text = None
raise Exception('Error in protocol file line {} : {}\n{}'.format(
line, str(e), text or ''))
robot = restore_patched_robot()
# robot.simulate()
if len(robot._commands) == 0:
error = (
"This protocol does not contain any commands for the robot.")
api_response['errors'] = [error]
except Exception as e:
app.logger.error(e)
api_response['errors'] = [str(e)]
finally:
robot = restore_patched_robot()
api_response['warnings'] = robot.get_warnings() or []
return api_response
def setUp(self):
Robot.reset_for_tests()
self.robot = Robot.get_instance()
def get_versions():
robot = Robot.get_instance()
return flask.jsonify({'versions': robot.versions()})
def protocol(self):
robot = Robot.get_instance()
robot.get_serial_ports_list()
robot.connect()
robot.home()
tiprack = containers.load(
'tiprack-200ul', # container type
'A1', # slot
'tiprack' # user-defined name
)
plate = containers.load(
'96-flat',
'B1',
'plate'
)
trash = containers.load(
'point',
'C2',
'trash'
)
trough = containers.load(
'trough-12row',
'B2',
'trough'
)
p200 = instruments.Pipette(
name="p200",
trash_container=trash,
tip_racks=[tiprack],
max_volume=200,
min_volume=0.5,
axis="b",
channels=1
)
calibration_data = """
{
"b": {
"blowout": 28.0,
"bottom": 26.0,
"droptip": 32.0,
"resting": 0,
"theContainers": {
"plate": {
"rel_x": 181.696,
"rel_y": 0.700999999999965,
"rel_z": 9.600999999999999,
"x": 202.195,
"y": 370.304,
"z": 125.7
},
"tiprack": {
"rel_x": 0.0,
"rel_y": 0.0,
"rel_z": 0.0,
"x": 20.499,
"y": 369.603,
"z": 116.099
},
"trough": {
"rel_x": 0.0,
"rel_y": 0.0,
"rel_z": 0.0,
"x": 20.499,
"y": 269.603,
"z": 116.099
},
"trash": {
"rel_x": 212.701,
"rel_y": -200.801,
"rel_z": -58.399,
"x": 233.2,
"y": 171.305,
"z": 57.7
}
},
"tip_rack_origin": "tiprack",
"tip_racks": [
{
"container": "tiprack"
}
],
"top": 13.0,
"trash_container": {
"container": "trash"
},
"volume": 200
}
}
"""
import_calibration_json(calibration_data, robot, True)
robot.clear_commands()
# distribute
p200.pick_up_tip(tiprack[0])
p200.aspirate(96 * 2, trough[0])
for i in range(96):
p200.dispense(2, plate[i]).touch_tip()
p200.drop_tip(tiprack[0])
p200.pick_up_tip(tiprack[1])
for i in range(96):
p200.aspirate(2, plate[95 - i])
p200.dispense(trough[0])
p200.drop_tip(tiprack[1])
import os
from opentrons import containers
from opentrons.labware import instruments
from opentrons import Robot
from opentrons.drivers.motor import CNCDriver
from helpers.calibration import import_json_calibration
robot = Robot.get_instance()
robot._driver = CNCDriver()
plate = containers.load("96-flat", "A2", "magbead")
trash = containers.load("point", "A1", "trash")
tiprack = containers.load("tiprack-200ul", "B2", "p200-rack")
# tipracks need a Well height equal to the tip length
for tip in tiprack:
tip.properties["height"] = 80
p200 = instruments.Pipette(
name="p200",
trash_container=trash,
tip_racks=[tiprack],
max_volume=200,
min_volume=0.1, # These are variable
axis="b",
channels=1,
)
import os
from opentrons import containers
from opentrons.labware import instruments
from opentrons import Robot
from opentrons.drivers.motor import SmoothieDriver1
from helpers.calibration import import_json_calibration
robot = Robot.get_instance()
robot._driver = SmoothieDriver1()
plate = containers.load('96-flat', 'A2', 'magbead')
trash = containers.load('point', 'A1', 'trash')
tiprack = containers.load('tiprack-200ul', 'B2', 'p200-rack')
# tipracks need a Well height equal to the tip length
for tip in tiprack:
tip.properties['height'] = 80
p200 = instruments.Pipette(
name="p200",
trash_container=trash,
tip_racks=[tiprack],
max_volume=200,
min_volume=0.1, # These are variable
axis="b",
channels=1)
json_file_path = os.path.join(os.path.dirname(__file__),
def get_coordinates():
robot = Robot.get_instance()
return flask.jsonify(
{'coords': robot._driver.get_position().get("target")})
def setUp(self):
Robot.reset_for_tests()
self.robot = Robot.get_instance()
self.robot.connect()
self.protocol = None
def diagnostics():
robot = Robot.get_instance()
return flask.jsonify({'diagnostics': robot.diagnostics()})