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Python SDK for Illumina Connected Analytics

Project description

libica

Python SDK to programmatically call Illumina Connected Analytics (ICA) BioInformatics web services i.e. SDK for API https://ica-docs.readme.io/reference

  • Workflow Execution Service (WES)
  • Task Execution Service (TES)
  • Genomic Data Store (GDS)
  • Developer Console Service (DCS)
  • Event Notification Service (ENS)

Overview:

TL;DR

  • Install through pip like so:
pip install libica
  • Export ICA base URL and JWT Bearer token:
export ICA_BASE_URL=<baseUrl>
export ICA_ACCESS_TOKEN=<tok>
  • Generate Bearer JWT token using ICA CLI like so:
ica tokens create --help
  • Somewhere in your Python code:
import os
from libica.openapi import libwes
from libica.openapi.libwes import WorkflowList, WorkflowCompact

ica_base_url = os.getenv("ICA_BASE_URL")
ica_access_token = os.getenv("ICA_ACCESS_TOKEN")

configuration = libwes.Configuration(
    host=ica_base_url,
    api_key={
        'Authorization': ica_access_token
    },
    api_key_prefix={
        'Authorization': "Bearer"
    },
)

with libwes.ApiClient(configuration) as api_client:

    wfl_api: libwes.WorkflowsApi = libwes.WorkflowsApi(api_client)
    try:
        page_token = None
        while True:
            wfl_list: WorkflowList = wfl_api.list_workflows(page_size=100, page_token=page_token)
            # print(wfl_list)
            for item in wfl_list.items:
                wfl: WorkflowCompact = item
                print(wfl.id)
                print(wfl.name)
            page_token = wfl_list.next_page_token
            if not wfl_list.next_page_token:
                break
    except libwes.ApiException as e:
        print(e)

More examples available at:

Development

  • Setup virtual environment and activate it

  • Install dependencies

make install
  • To run unit tests suite
make unit
make autounit
  • To bring up mock API μ-services
make up
  • To run integration tests suite (required services fully up)
make it
  • To run full test suite (required services fully up)
make test
  • Most of the dev pipelines are in Makefile workflow

License

MIT License and DISCLAIMER

License: MIT

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