Source code for synbiopython.lab_automation.containers.Well

# 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 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 = name = 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)" % (,
[docs] def pretty_summary(self): """Return a summary string of the well.""" data = "\n ".join( [""] + [("%s: %s" % (key, value)) for key, value in] ) 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",], ["content", self.content.to_dict()], ["row", self.row], ["column", self.column], ] + list( )
[docs] def index_in_plate(self, direction="row"): """Return the index of the well in the plate.""" return self.plate.wellname_to_index(, 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)