def _setup_container(container_name):
try:
container = database.load_container(container_name)
# Database.load_container throws ValueError when a container name is not
# found.
except ValueError:
# First must populate "get persisted container" list
old_container_loading.load_all_containers_from_disk()
# Load container from old json file
container = old_container_loading.get_persisted_container(
container_name)
# Rotate coordinates to fit the new deck map
rotated_container = database_migration.rotate_container_for_alpha(
container)
# Save to the new database
database.save_new_container(rotated_container, container_name)
container.properties['type'] = container_name
container_x, container_y, container_z = container._coordinates
if not fflags.split_labware_definitions():
# infer z from height
if container_z == 0 and 'height' in container[0].properties:
container_z = container[0].properties['height']
from opentrons.util.vector import Vector
container._coordinates = Vector(container_x, container_y, container_z)
return container
def get_version():
'''Get the Opentrons-defined database version'''
if fflags.split_labware_definitions():
# warnings.warn('database operations no longer have an effect')
pass
db_conn = sqlite3.connect(database_path)
return _get_db_version(db_conn)
def calibrate_container_with_delta(pose_tree,
container,
delta_x,
delta_y,
delta_z,
save,
new_container_name=None):
delta = Point(delta_x, delta_y, delta_z)
new_coordinates = change_base(
pose_tree, src=container, dst=container.parent) + delta
pose_tree = update(pose_tree, container, new_coordinates)
if ff.split_labware_definitions():
for well in container.wells():
well._coordinates = well._coordinates + delta
else:
container._coordinates = container._coordinates + delta
if save and new_container_name:
database.save_new_container(container, new_container_name)
elif save:
database.overwrite_container(container)
return pose_tree
def get_grid(self):
"""
Calculates the grid inferring row/column structure
from indexes. Currently only Letter+Number names are supported
"""
columns = OrderedDict()
if ff.split_labware_definitions():
# implementing this for compatibility, but new refactors and
# features should use `ordering` directly
for i, col in enumerate(self.ordering):
col_idx = str(i + 1)
columns[col_idx] = OrderedDict()
for well in col:
row_idx = well[0]
columns[col_idx][row_idx] = (row_idx, col_idx)
else:
index_pattern = r'^([A-Za-z]+)([0-9]+)$'
for name in self.children_by_name:
match = re.match(index_pattern, name)
if match:
row, col = match.groups(0)
if col not in columns:
columns[col] = OrderedDict()
columns[col][row] = (row, col)
return columns
def test_invalid_container_name():
if ff.split_labware_definitions():
error_type = FileNotFoundError
else:
error_type = ValueError
with pytest.raises(error_type):
database.load_container("fake_container")
def load_module(module_name: str) -> Container:
if fflags.split_labware_definitions():
raise NotImplementedError
else:
db_conn = sqlite3.connect(database_path)
res = _load_module_dict_from_db(db_conn, module_name)
return res
def list_all_containers() -> List[str]:
if fflags.split_labware_definitions():
# warnings.warn('list_all_containers is deprecated, please use list_all_labware') # noqa
res = list_all_labware()
else:
db_conn = sqlite3.connect(database_path)
res = _list_all_containers_by_name(db_conn)
return res
def delete_container(container_name) -> bool:
if fflags.split_labware_definitions():
raise NotImplementedError # What should delete do in the new system?
else:
db_conn = sqlite3.connect(database_path)
_delete_container_object_in_db(db_conn, container_name)
res = True # old delete fn does not return anything
return res
def test_container_parse():
robot.reset()
plate = containers_load(robot, '96-flat', '1')
if ff.split_labware_definitions():
expected = {'x': 0, 'y': 0, 'z': 0}
else:
expected = {'x': 14.34, 'y': 11.24, 'z': 10.50}
assert database._parse_container_obj(plate) == expected
def load_container(container_name: str) -> Container:
if fflags.split_labware_definitions():
# warnings.warn('save_new_container is deprecated, please use save_labware') # noqa
res = load_labware(container_name)
else:
db_conn = sqlite3.connect(database_path)
res = _load_container_object_from_db(db_conn, container_name)
return res
def save_new_container(container: Container, container_name: str) -> bool:
if fflags.split_labware_definitions():
# warnings.warn('save_new_container is deprecated, please use save_labware') # noqa
res = save_labware(container, container_name)
else:
db_conn = sqlite3.connect(database_path)
_create_container_obj_in_db(db_conn, container, container_name)
res = True # old create fn does not return anything
return res
def overwrite_container(container: Container) -> bool:
if fflags.split_labware_definitions():
# warnings.warn('overwrite_container is deprecated, please use save_labware_offset') # noqa
res = save_labware_offset(container)
else:
log.debug("Overwriting container definition: {}".format(
container.get_type()))
db_conn = sqlite3.connect(database_path)
_update_container_object_in_db(db_conn, container)
res = True # old overwrite fn does not return anything
return res
def test_container_from_container_load():
robot.reset()
plate = containers_load(robot, '96-flat', '1')
if ff.split_labware_definitions():
actual = plate[0]._coordinates + plate[0].top()[1]
expected = Vector(14.34, 74.24, 10.50)
else:
actual = plate._coordinates
expected = Vector(14.34, 11.24, 10.50)
assert plate.get_type() == '96-flat'
assert actual == expected
def add_container_to_pose_tracker(self, location, container: Container):
"""
Add container and child wells to pose tracker. Sets container.parent
(slot) as pose tracker parent
"""
self.poses = pose_tracker.add(
self.poses, container, container.parent,
pose_tracker.Point(*container._coordinates))
for well in container:
center_x, center_y, center_z = well.top()[1]
offset_x, offset_y, offset_z = well._coordinates
if not fflags.split_labware_definitions():
center_z = 0
self.poses = pose_tracker.add(
self.poses, well, container,
pose_tracker.Point(center_x + offset_x, center_y + offset_y,
center_z + offset_z))
def test_well_from_center_new(split_labware_def):
print("Split labware definitions? {}".format(
ff.split_labware_definitions()))
deck = Deck()
slot = Slot()
plate = generate_plate(wells=4,
cols=2,
spacing=(10, 10),
offset=(0, 0),
radius=5,
height=20)
deck.add(slot, 'A1', (0, 0, 0))
slot.add(plate)
assert plate['B2'].center() == (5, 5, 10)
assert plate['B2'].from_center(x=0.0, y=0.0, z=2.0) == (5, 5, 30)
assert plate['B2'].from_center(r=1.0, theta=pi / 2, h=5.0) == (5, 10, 60)
assert plate['B2'].top()[1] == (5, 5, 20)
assert plate['B2'].bottom()[1] == (5, 5, 0)
from collections import OrderedDict
import json
import os
import shutil
import unittest
from opentrons.data_storage import old_container_loading
from opentrons.containers.placeable import Container, Well
from opentrons.util import environment
from opentrons.config import feature_flags as ff
if not ff.split_labware_definitions():
class PersistedContainersTestCase(unittest.TestCase):
@classmethod
def setUpClass(cls):
# here we are copying containers from data and
# re-defining APP_DATA_DIR. This way we can
# load a few more custom containers
old_container_loading.persisted_containers_dict.clear()
os.environ['APP_DATA_DIR'] = os.path.join(
os.path.dirname(__file__), 'opentrons-data')
environment.refresh()
source = os.path.join(os.path.dirname(__file__), 'data')
containers_dir = environment.get_path('CONTAINERS_DIR')
shutil.rmtree(containers_dir)
shutil.copytree(source, containers_dir)
@classmethod
def get_children_list(self):
if ff.split_labware_definitions():
return [self[i] for i in list(chain.from_iterable(self.ordering))]
else:
return super(Container, self).get_children_list()
def set_version(version):
if fflags.split_labware_definitions():
# warnings.warn('database operations no longer have an effect')
pass
db_conn = sqlite3.connect(database_path)
db_queries.set_user_version(db_conn, version)
def change_database(db_path: str):
global database_path
if fflags.split_labware_definitions():
# warnings.warn('database operations no longer have an effect')
pass
database_path = db_path