Metadata-Version: 2.1
Name: ua_clarity_tools
Version: 1.1.3
Summary: API that interacts with Illumina's Clarity LIMS software at a higher level than requests.
Home-page: https://github.com/UACoreFacilitiesIT/UA-Clarity-Tools
Author: Stephen Stern, Rafael Lopez, Ryan Johannes-Bland
Author-email: sterns1@email.arizona.edu
License: MIT
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](https://github.com/sterns1)
        [raflopjr](https://github.com/raflopjr)
        [RyanJohannesBland](https://github.com/RyanJohannesBland)
        
        ## LicenseMIT
Platform: UNKNOWN
Description-Content-Type: text/markdown
