# pylint: disable=C0330,C0103,R0913
"""This module contains a generic class for a well."""
from synbiopython.lab_automation.containers.WellContent import WellContent
from synbiopython.lab_automation.picklist.Transfer import TransferError
from ..tools import unit_factors
[docs]class Well:
"""Generic class for a well.
:param plate: The plate on which the well is located
:param row: The well's row (a number, starting from 0)
:param column: The well's column (a number, starting from 0)
:param name: The well's name, for instance "A1"
:param data: A dictionary storing data on the well, used in algorithms and reports.
"""
capacity = None
dead_volume_per_transfer_class = None
def __init__(self, plate, row, column, name, data=None):
self.plate = plate
self.row = row
self.column = column
self.name = name
self.data = data or {}
self.sources = []
self.content = WellContent()
@property
def volume(self):
"""Return volume."""
return self.content.volume
[docs] def iterate_sources_tree(self):
"""Iterate through the tree of sources."""
for source in self.sources:
if isinstance(source, Well):
for parent in source.iterate_sources_tree():
yield parent
else:
yield source
yield self
[docs] def add_content(self, components_quantities, volume=None, unit_volume="L"):
"""Add content to well.
:param components_quantities: Dictionary of components and quantities
(default: gram). Example `{"Compound_1": 5}`.
:param volume: Volume (default: liter).
:param unit_volume: Unit of volume (default: liter). Options: liter (L),
milliliter (mL), microliter (uL), nanoliter (nL).
"""
volume = volume * unit_factors[unit_volume]
if volume > 0:
final_volume = self.content.volume + volume
if (self.capacity is not None) and (final_volume > self.capacity):
raise TransferError(
"Transfer of %.2e L to %s brings volume over capacity."
% (volume, self)
)
self.content.volume = final_volume
for component, quantity in components_quantities.items():
if component not in self.content.quantities:
self.content.quantities[component] = 0
self.content.quantities[component] += quantity
[docs] def subtract_content(self, components_quantities, volume=0):
"""Subtract content from well."""
if volume > 0:
if volume > self.volume:
raise TransferError(
(
"Subtraction of %.2e L from %s is impossible."
" Current volume: %.2e L"
)
% (volume, self, self.volume)
)
self.content.volume -= volume
for component, quantity in components_quantities.items():
if self.content.quantities[component] == quantity:
self.content.quantities.pop(component)
else:
self.content.quantities[component] -= quantity
[docs] def empty_completely(self):
"""Empty the well."""
self.content.quantities = {}
self.content.volume = 0
@property
def coordinates(self):
"""Return (well.row, well.column)."""
return (self.row, self.column)
@property
def is_empty(self):
"""Return true if the well's volume is 0."""
return self.volume == 0
def __repr__(self):
return "(%s-%s)" % (self.plate.name, self.name)
[docs] def pretty_summary(self):
"""Return a summary string of the well."""
data = "\n ".join(
[""] + [("%s: %s" % (key, value)) for key, value in self.data.items()]
)
content = "\n ".join(
[""]
+ [
("%s: %s" % (key, value))
for key, value in self.content.quantities.items()
]
)
return (
"{self}\n"
" Volume: {self.volume}\n"
" Content: {content}\n"
" Metadata: {data}"
).format(self=self, content=content, data=data)
[docs] def to_dict(self):
"""Convert well to dict"""
return dict(
[
["name", self.name],
["content", self.content.to_dict()],
["row", self.row],
["column", self.column],
]
+ list(self.data.items())
)
[docs] def index_in_plate(self, direction="row"):
"""Return the index of the well in the plate."""
return self.plate.wellname_to_index(self.name, direction=direction)
[docs] def is_after(self, other, direction="row"):
"""Return whether this well is located strictly after the other well.
Example: iterate over all free wells after the last non-free well:
>>> direction = 'row'
>>> last_occupied_well = plate.last_nonempty_well(direction=direction)
>>> free_wells = (w for w in plate.iter_wells(direction=direction)
>>> if w.is_after(last_occupied_well))
>>> for well in free_wells: ...
"""
well_index = self.index_in_plate(direction=direction)
other_index = other.index_in_plate(direction=direction)
return well_index > other_index
def __lt__(self, other):
return str(self) < str(other)