def provision_assay_plate(name, plate_type='4titude 4ti-0223', id=None):
"""
Provision a new assay plate.
Parameters
----------
name : str
The name of the container
plate_type : str, optional, default='4titude 4ti-0223'
The name of the plate type used to retrieve the `container_type` from library
id : str, optional, default=None
Unless `id` is specified, a unique container ID will be autogenerated.
"""
if id == None:
id = generate_uuid
# Define the container
container_type = container_types[plate_type]
container = Container(name="assay-plate",
id=id,
container_type=container_type)
# Initialize well properties for this container
for well in container.all_wells():
well.set_volume(Unit(0.0, 'microliters')) # well starts empty
return container
def test_set_properties(self):
c = Container(None, dummy_type)
c.well(0).set_properties({"Concentration": "40:nanogram/microliter"})
self.assertIsInstance(c.well(0).properties, dict)
self.assertEqual(["Concentration"], c.well(0).properties.keys())
self.assertEqual(["40:nanogram/microliter"],
c.well(0).properties.values())
def test_add_properties(self):
c = Container(None, dummy_type)
c.well(0).add_properties({"nickname": "dummy"})
self.assertEqual(len(c.well(0).properties.keys()), 1)
c.well(0).set_properties({"concentration": "12:nanogram/microliter"})
self.assertEqual(len(c.well(0).properties.keys()), 2)
c.well(0).add_properties({"property1": "2", "ratio": "1:10"})
self.assertEqual(len(c.well(0).properties.keys()), 4)
self.assertRaises(AssertionError,
c.well(0).add_properties, ["property", "value"])
def test_add_properties_wellgroup(self):
c = Container(None, dummy_type)
group = c.wells_from(0, 3).set_properties({
"property1": "value1",
"property2": "value2"
})
c.well(0).add_properties({"property4": "value4"})
self.assertEqual(len(c.well(0).properties.keys()), 3)
for well in group:
self.assertTrue("property1" in well.properties)
self.assertTrue("property2" in well.properties)
def dummy_pathological():
return Container(
None,
ContainerType(
name="dummy",
well_count=384,
well_depth_mm=None,
well_volume_ul=Unit(200, "microliter"),
well_coating=None,
sterile=False,
is_tube=False,
cover_types=[],
seal_types=None,
capabilities=[],
shortname="dummy",
col_count=96,
dead_volume_ul=Unit(15, "microliter"),
safe_min_volume_ul=Unit(30, "microliter"),
),
)
def dummy_96():
return Container(
None,
ContainerType(
name="dummy",
well_count=96,
well_depth_mm=None,
well_volume_ul=Unit(200, "microliter"),
well_coating=None,
sterile=False,
is_tube=False,
cover_types=["universal"],
seal_types=None,
capabilities=["cover"],
shortname="dummy",
col_count=12,
dead_volume_ul=Unit(15, "microliter"),
safe_min_volume_ul=Unit(30, "microliter")
)
)
def dummy_reservoir_row():
return Container(
None,
ContainerType(
name="dummy",
well_count=8,
well_depth_mm=None,
well_volume_ul=Unit(200, "microliter"),
well_coating=None,
sterile=False,
is_tube=False,
cover_types=None,
seal_types=None,
capabilities=None,
shortname="dummy",
col_count=1,
dead_volume_ul=Unit(15, "microliter"),
safe_min_volume_ul=Unit(30, "microliter"),
),
)
def dummy_echo():
return Container(
None,
ContainerType(
name="dummy",
well_count=384,
well_depth_mm=None,
well_volume_ul=Unit(65, "microliter"),
well_coating=None,
sterile=False,
is_tube=False,
cover_types=[],
seal_types=None,
capabilities=[],
shortname="dummy",
col_count=96,
dead_volume_ul=Unit(15, "microliter"),
safe_min_volume_ul=Unit(15, "microliter"),
true_max_vol_ul=Unit(135, "microliter"),
vendor="Labcyte"
)
)
def ref_kit_container(protocol,
name,
container,
kit_id,
discard=True,
store=None):
'''
Still in use to allow booking of agar plates on the fly
'''
kit_item = Container(None, protocol.container_type(container))
if store:
protocol.refs[name] = Ref(name, {
"reserve": kit_id,
"store": {
"where": store
}
}, kit_item)
else:
protocol.refs[name] = Ref(name, {
"reserve": kit_id,
"discard": discard
}, kit_item)
return (kit_item)
def test_set_volume_through_group(self):
c = Container(None, dummy_type)
c.all_wells().set_volume("30:microliter")
for w in c.all_wells():
self.assertEqual(30, w.volume.value)
def test_set_volume(self):
c = Container(None, dummy_type)
c.well(0).set_volume("20:microliter")
self.assertEqual(20, c.well(0).volume.value)
self.assertEqual("microliter", c.well(0).volume.unit)
self.assertIs(None, c.well(1).volume)
def setUp(self):
self.c = Container(None, dummy_type)
well_depth_mm=Unit(11.15, 'millimeter'),
well_volume_ul=Unit(300, 'milliliter'),
well_coating='polystyrene',
sterile=False,
capabilities=capabilities,
shortname='4ti-0223',
col_count=12,
dead_volume_ul=Unit(20, 'milliliter'),
safe_min_volume_ul=Unit(50, 'milliliter'))
# Generate a unique container ID
import uuid
id = str(uuid.uuid4())
# Define the container
container = Container(name="assay-plate", id=id, container_type=container_type)
#
# Assay Parameters
#
Lstated = [
Unit(x, "moles/liter") for x in [
20.0e-6, 9.15e-6, 4.18e-6, 1.91e-6, 0.875e-6, 0.4e-6, 0.183e-6,
0.0837e-6, 0.0383e-6, 0.0175e-6, 0.008e-6, 0
]
] # gefitinib concentration
Pstated = Unit(0.5e-6, "moles/liter")
well_volume = Unit(100, "milliliter")
receptor_name = 'Src'
ligand_name = 'gefitinib'
def make_containers(self, dummy_type):
self.c = Container(None, dummy_type)
self.c2 = Container(None, dummy_type)
def make_another_container(self, dummy_type):
self.c2 = Container(None, dummy_type)
def make_wells(self, dummy_type):
self.container = Container(id=None, container_type=dummy_type)
self.well = self.container.well(0)
