discover-shed-tool: normalize tool-id-shaped queries before declaring miss#321
Merged
jmchilton merged 1 commit intoJun 18, 2026
Merged
Conversation
… miss A tool-id token (`integron_finder`, `iuc/integron_finder`) — what a template `_plan_context` candidate hands the discover step — scores zero in `tool-search` while the human name (`integron finder`) hits the real `iuc/integron_finder` wrapper. Without normalization the loop emits a false `miss` and wrongly fall-throughs to authoring a tool that already exists. - index.md §1: strip `owner/`, split `_`/`-` into words, try human name + bare word; `miss` only honest after variants tried. Strengthen the caveat. - eval.md: add property "a miss survives query-variant normalization". - re-cast claude bundle (verify clean). - refinement journals: discover-shed-tool (applied fix) + advance-galaxy-draft-step (the test-pipeline finding; upstream _plan_context-hint question stays open). Surfaced by /test-pipeline interview-to-galaxy UC1 MRSA re-run. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Problem
A tool-id token — what a template
_plan_contextcandidate hands the per-step loop's discover step — does not lexically match in the Tool Shed index:gxwf tool-search integron_finder→No hitsgxwf tool-search "integron finder"→ 34.60, resolves to the realiuc/integron_finder(changeset5429646e486d, 2.0.5+galaxy1)So a discover-shed-tool run that feeds the raw underscored/owner-prefixed token into
tool-searchemits a falsemissand wrongly fall-throughs toauthor-galaxy-tool-wrapper— authoring a wrapper for a tool that already exists. Themisspasses every static check. ISEScan masked the class of bug because its bare token (isescan) happens to score.Fix
index.md§1 (Search): normalize a tool-id-shaped need before searching — stripowner/prefix, split_/-into words, try the human name and the bare significant word; amissis only honest after the variants are tried. Strengthened the caveats bullet with the concrete failure mode.eval.md: new property "a miss survives query-variant normalization" — amissan obvious name-variant would have turned into a hit is a failure (closes the false-missloophole).verify clean: 5 refs, no drift). Validator: 0 errors.discover-shed-tool(the applied fix) andadvance-galaxy-draft-step(the test-pipeline finding; the upstream question of whether the template should write a human tool name into_plan_contextstays open).Surfaced by a
/test-pipeline interview-to-galaxyre-run on the UC1 MRSA case.🤖 Generated with Claude Code