Issues

• Curator Desk daily-update workflow is invalid and has never run successfully

  waldronlab/bioanalyzer-backend#137 · Filter by author RonaldRonnie opened on Sep 24, 2026

• LLM_PROVIDER is ignored by the analysis pipeline: provider is hardcoded to Gemini

  waldronlab/bioanalyzer-backend#136 · Filter by author RonaldRonnie opened on Sep 24, 2026

• v2 RAG pipeline only re-ranks the already-truncated 8k context, ignores summary settings, and never reads the cache

  waldronlab/bioanalyzer-backend#135 · Filter by author RonaldRonnie opened on Sep 24, 2026

• NCBI rate limiting is per-thread sleep(), so concurrent requests exceed NCBI's limit

  waldronlab/bioanalyzer-backend#134 · Filter by author RonaldRonnie opened on Sep 24, 2026

• Exception messages logged without mask_exception_message() in LLM/network code paths

  waldronlab/bioanalyzer-backend#133 · Filter by author RonaldRonnie opened on Sep 24, 2026

• API has no authentication; /qa and /analyze-url let any caller spend LLM budget and choose the model

  waldronlab/bioanalyzer-backend#132 · Filter by author RonaldRonnie opened on Sep 24, 2026

• Structured extraction runs at temperature 0.7, so results aren't reproducible

  waldronlab/bioanalyzer-backend#131 · Filter by author RonaldRonnie opened on Sep 24, 2026

• Remove leftover taxa_level field from URL-analysis schemas

  waldronlab/bioanalyzer-backend#130 · Filter by author RonaldRonnie opened on Sep 24, 2026

• [bot] Repoint semantic-sql base URL to the semanticsql CDN before raw-bucket retirement

  waldronlab/bioanalyzer-backend#124 · Filter by author kltm opened on Aug 18, 2026
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• Proposal: A Production-Grade Ontology Grounding Engine for BioAnalyzer

  waldronlab/bioanalyzer-backend#121 · Filter by author RonaldRonnie opened on Aug 10, 2026
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• Caching

  waldronlab/bioanalyzer-backend#78 · Filter by author jwokaty opened on Feb 19, 2026