Commit History
18 days ago
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feat: the five knowledge endpoints, gradio_ui and frozen descriptor (s2)
avoigt1121 +1: Claude Opus 5.5- src/endpoints/: drugs_for_targets, trials_for_genes, annotate_genes, pathways_for_genes, targets_for_disease on the s1 core. Inputs validated before any call; every row and nested block (ChEMBL mechanisms, UniProt protein, HGNC mapping, disease resolution) stamped; deterministic "According to <source> (queried <date>)" narratives; unresolved inputs and structured source errors instead of guesses. - Loaded tool set narrowed 12 -> 8 once real responses were seen (HGNC gives Ensembl + UniProt ids; one batched UniProt search; Reactome's mapping is already lowest-level). The other 4 stay approved, unloaded. - 8 pinned output schemas, written from the recorded responses. - scripts/record_fixtures.py: the only live step. 11 cassettes recorded 2026-10-20 through ToolUniverse 1.5.6 (123 calls): the Phase 0 lookups Q1-Q9 plus the C1 SORD2P case and two edge cases. All Phase 0 expectations replay. - gradio_ui.py: machine gate first in every handler (x-orchestrator-token), ty…3ed6b66
19 days ago
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feat: governed ToolUniverse core for the knowledge specialist (s1)
avoigt1121 +1: Claude Opus 5.5The repo from the pdac-spatial-agent template, plus the core every endpoint will sit on (ADR-0001, accepted 2026-10-20): - config/tools_allowlist.yaml: the memo's 28 tools by exact 1.5.6 name; the 12 the five endpoints use are the only ones loaded. - config/sources.yaml: 8 sources with hosts, licences checked 2026-10-20 (Reactome is CC0, not CC BY 4.0; DGIdb unconfirmed, so no DGIdb endpoint), TTLs, rate limits, timeouts, coverage notes. - src/tu_client.py, the only importer of tooluniverse: loads with keep_default_tools=False and load_workspace=False, refuses startup on any model-provider key, a version other than 1.5.6, an extra or forbidden tool, or ToolUniverse's own cache being on. load_workspace=False matters: with any workspace present, 1.5.6 seeds a profile that loads all 2,691 tools and reads workspace and ~/.tooluniverse .env files (found by these tests). - provenance (10 fields per row), pinned output schemas (drift = no rows), SQLite cache that keeps retr…377417d