galaxyproject / galaxyproject/brc-analytics

Gate UCSC GTF auto-discovery

Open
#1,057 2 comments 0 reactions 0 assignees View on GitHub
Dominant language
TypeScript
Stars
7
Forks
11
Avg merge
2d 12h
Merged PRs (30d)
16

Description

## Description

Today we query UCSC at runtime, accept every /genes/*.gtf.gz, and derive labels via simple regex (RefSeq, Gene, Augustus, VEuPath, etc.).
UCSC added community GTFs (VEuPathDB) and we now show duplicate entries with raw filenames. Need a guard before showing new sources.

## Options

- Drop anything we can’t label (if getGeneModelLabel falls back to filename, skip).
- Introduce configurable gating (allow/block lists, curated patterns, etc.) so only approved sources make it through regardless of where that logic lives.
- Longer-term: maintain a first-class list of supported GTF sources and have the UI/API read from that rather than blindly trusting UCSC responses.

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by tracing the runtime UCSC query and the getGeneModelLabel fallback mentioned in the issue. Decide which gating approach is approved before changing behavior, then verify that unsupported sources are excluded and approved sources do not produce duplicate or raw-filename entries in the UI/API.

Written by the indexing model from the issue text.

Assessment

Tech stack
typescript
Domain
full-stack
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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