Provides 2 sets of tools for use with clarity and it's endpoints: ClarityTools and StepTools.
To create a set of tools to assist in script writing for Clarity.
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()
bash pip install ua-lims-tools
bash pip install --update nose cd ./repo cd ./tests nosetests test_lims_tools.py
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.