Change seqrepo dataproxy env vars to all use SEQREPO_DATAPROXY_URI

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#540 opened on Apr 9, 2025 8 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty: 2/5
Estimated time: 1-3 hours
Newbie friendliness: 78/100

Issue type: Refactor
Clarity: Clearly specified
Activity status: Quiet
Tech stack: python
Domain: testing, tooling

Research direction

Start by inspecting conftest.py and hgvs_tools.py, focusing on their current SEQREPO_REST_URL and SEQREPO_URI environment-variable references. Update both references to use SEQREPO_DATAPROXY_URI, then run the relevant vrs-python tests to confirm the environment-variable changes work for filesystem and HTTP seqrepo endpoints.

Written by the indexing model from the issue text.

Description

biocommons.seqrepo uses SEQREPO_DATAPROXY_URI to point to a filesystem or HTTP endpoint for a seqrepo instance.

Change SEQREPO_REST_URL in vrs-python conftest.py to use SEQREPO_DATAPROXY_URI
Change SEQREPO_URI in vrs-python hgvs_tools.py to use SEQREPO_DATAPROXY_URI

See https://github.com/biocommons/biocommons.seqrepo/issues/183

Dominant language: Python
Stars: 63
Forks: 43
Avg merge: 1h 2m
Merged PRs (30d): 1

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