UA-Lims-Tools

Provides 2 sets of tools for use with clarity and it's endpoints: ClarityTools and StepTools.

Motivation

To create a set of tools to assist in script writing for Clarity.

Features

Use ClarityTools as a means of interfacing with Clarity and it's endpoints.

• get_samples will get all samples from a list of uris passed in.

• get_arts_from_samples will get all artifact uris for the list of uris passed.

• get_udfs will find all the udfs that should be attached to target.

• set_reagent_label will set the reagent_label for all artifacts passed.

• step_router will route a list of artifact_uris to a specified step.Use StepTools as a way of interacting with a Clarity step.*

• get_artifacts will return all artifacts from the step.

• get_process_data will retrieve the process data for the current step.

• get_artifact_map creates a mapping of input artifacts to output artifacts.

• set_artifact_udf sets the udfs of all analytes in the step.

• get_artifacts_previous_step will map the current steps artifact uris to an ancestor artifact from the step passed to it.

• get_assays will find the assays within the current protocol.## Code Example

python from ua_lims_tools import ua_lims_tools clarity_api = ua_lims_tools.ClarityApi() step_api = ua_lims_tools.StepTools()

Installation

bash pip install ua-lims-tools

Tests

From the root of the repo run: python -m unittest ua_clarity_tools.tests.test_ua_clarity_tools

How to Use

Examples of syntax for each method

python clarity_api = ua_lims_tools.ClarityApi() samples = clarity_api.get_samples(uris)

• get_samples gets the samples from the passed in uris.
• Arguments: uris is a list of sample endpoints to get.
• Returns: a list of Sample dataclass objects with gotten sample's data.

Credits

sterns1 raflopjr RyanJohannesBland

LicenseMIT