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Initial support for OrcaBus API #21

Merged
merged 13 commits into from
Oct 7, 2024
Merged

Initial support for OrcaBus API #21

merged 13 commits into from
Oct 7, 2024

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pdiakumis
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A few enhancements for handling OrcaBus workflow runs. Most of these will likely be replaced in the near future by better wrappers based on the OrcaBus OpenAPI spec.

  • new functions:

    • envvar_defined: better replacement for envvar_undefined to check AWS/ICA env vars
    • jwt_exp: checks JWT expiry date
    • jwt_validate: validates JWT
    • orca_jwt: retrieves orcabus/token-service-jwt from AWS Secrets Manager
    • orca_libid2workflows: generates tibble with workflows for a given libid
    • orca_prid2wfpayload: generates workflow payload for give prid
    • orca_query_url: query given endpoint (name could've been simply query_url)
    • orca_workflow_list: generates tibble with list of workflows (can specify type of workflow to return)
  • deprecated functions:

    • awsvault_profile: now just using AWS env vars (e.g. via granted)
    • envvar_undefined: replaced with envvar_defined
  • refactored functions:

    • meta_rnasum: handle newer umccrise field from v1.1.0 onwards
  • pre-commit: bump 0.4.2 -> 0.4.3

  • dependencies: import httr2, jose, paws for OrcaBus queries

@pdiakumis pdiakumis merged commit 69a6982 into main Oct 7, 2024
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@pdiakumis pdiakumis deleted the pd_dev branch October 7, 2024 00:28
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