Skip to main content
Join the official 2019 Python Developers SurveyStart the survey!

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

Project description

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

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.

Credits

sterns1 raflopjr RyanJohannesBland

LicenseMIT

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for ua-clarity-tools, version 1.0.0
Filename, size File type Python version Upload date Hashes
Filename, size ua_clarity_tools-1.0.0-py3-none-any.whl (11.3 kB) File type Wheel Python version py3 Upload date Hashes View hashes
Filename, size ua_clarity_tools-1.0.0.tar.gz (10.3 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page