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API that interacts with Illumina's Clarity LIMS software at a higher level than requests.

Project description


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

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.


sterns1 raflopjr RyanJohannesBland


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