semaphoresolutions / s4-clarity-lib

A modern Python library for BaseSpace Clarity LIMS.

S4-Clarity Library

Used in numerous labs around the world, the S4-Clarity library provides an easy-to-use integration with the BaseSpace Clarity LIMS API. The package includes:

• Classes representing familiar Clarity API entities that provide read-write access to most properties.
• Helper methods that simplify common operations.
• Base classes for scripts that integrate with Clarity: EPPs, DSAs, and shell scripts.
• Utilities that help with Clarity-related tasks, such as managing config slices, or automating the completion of a Step.

The S4-Clarity library lets developers interact with the Clarity API in fewer lines of code. With HTTP and XML boilerplate out of the way, you'll have your integration built in no time at all.

from s4.clarity.scripts import TriggeredStepEPP

LibraryVolume = 2.0
MolWeightBasePair = 660 * 1e6  # micrograms / mol
AssumedBasePairs = 400.0
TargetMolarity = 4.0
Overage = 4


class Normalization (TriggeredStepEPP):
    def on_record_details_enter(self):
        self.prefetch(self.PREFETCH_INPUTS, self.PREFETCH_OUTPUTS)

        for iomap in self.step.details.iomaps:
            library_concentration = iomap.input["Concentration"]
            library_molarity = library_concentration / (AssumedBasePairs * MolWeightBasePair)
            iomap.output["Concentration"] = library_concentration
            iomap.output["Molarity (nM)"] = library_molarity
            iomap.output["Library Vol (uL)"] = LibraryVolume
            iomap.output["Tris HCl (uL)"] = LibraryVolume * (library_molarity / TargetMolarity - 1)

        self.lims.artifacts.batch_update(self.step.details.outputs)


if __name__ == "__main__":
    Normalization.main()

Installation

To install s4-clarity, simply use pip:

$ pip install s4-clarity

s4-clarity-lib's Issues

broken in python 3.10 because the attribute MutableMapping has been removed from the module collections

`Python 3.10.6 (main, Aug 5 2022, 16:21:03) [Clang 13.0.0 (clang-1300.0.29.30)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
Python shell history and tab completion are enabled.

from s4.clarity.scripts import TriggeredStepEPP
Traceback (most recent call last):
File "", line 1, in
File "/opt/pkg/lib/python3.10/site-packages/s4/clarity/init.py", line 12, in
from ._internal.lazy_property import lazy_property
File "/opt/pkg/lib/python3.10/site-packages/s4/clarity/_internal/init.py", line 6, in
from .fields import FieldsMixin
File "/opt/pkg/lib/python3.10/site-packages/s4/clarity/_internal/fields.py", line 163, in
class FieldsDict(collections.MutableMapping):
AttributeError: module 'collections' has no attribute 'MutableMapping'`

container.artifact_at raises KeyError instead of returning None for empty, valid wells

docs suggest that container.artifact_at should return none if the well is empty:

def artifact_at(self, well):
        """
        :param well: String matching "Y:X" where Y is a column index and X is a row index.
            The string may use letters or numbers depending on the container type.
        :type well: str

        :rtype: Artifact or None

currently, artifact_at will throw a KeyError instead. This is the correct behavior for an invalid well.

artifact_at should consult self.container_type.row_major_order_wells to decide if it should throw a KeyError (preferably an InvalidWellError?) or return None

Typing dependency breaks deployments in AWS lambda

The explicit dependency on typing is no longer required given typing is part of the python Standard Library. When deploying this package in AWS lambda via the serverless application model, the order of dependency loading generates an error type object 'Callable' has no attribute '_abc_registry'. Is it possible to remove the explicit dependency on Typing for Python versions >= 3.5