mims-harvard ToolUniverse Code Optimization
Always run Skill(skill="simplify") after writing or modifying code.
Pre-Commit Checklist
-
return_schemahasoneOf: [{data+metadata}, {error}] - Test examples use real IDs (no DUMMY/PLACEHOLDER)
-
try:hasexcept:at exact same indentation level - No trailing commas in JSON (
python3 -c "import json; json.load(open('f.json'))") - New tool class registered in
_lazy_registry_static.pyanddefault_config.py -
ruff check src/tooluniverse/<file>.pypasses -
python -c "from tooluniverse.<module> import <Class>"passes -
python -m tooluniverse.cli run <Tool> '<real_args_json>'returns expected data - Ran
Skill(skill="simplify")on all modified files
Key Fix Categories
| Category | Signal | Reference |
|---|---|---|
| Silent param ignored | API accepts but drops filter | code-patterns.md — Client-Side Filter |
| Wrong API field/endpoint | 0 results or 404 | api-fixes.md — Quick Lookup Table |
| Schema invalid | null type, missing oneOf | code-patterns.md — Schema Patterns |
| Undisclosed normalization | Auto-transform hidden from user | code-patterns.md — Normalization Disclosure |
| try/except indent | SyntaxError at runtime | code-patterns.md — try/except section |
| Truncation buried | Data count hidden in notes | code-patterns.md — Truncation |
| Hosted model API (NIM) | async 404 on poll, JSON-wrapped output, 200+inner-failure, "not found for account" | code-patterns.md — Hosted Model-API Tools |
| R subprocess tool | '\.' unrecognized escape from Rscript -e |
code-patterns.md — R-subprocess Tools |
References
- references/api-fixes.md — Per-API bug fixes (GtoPdb, CIViC, GTEx, ENCODE, CPIC, etc.)
- references/code-patterns.md — Reusable Python patterns (schema, filtering, pagination, normalization)
Git & PR Workflow
git fetch origin && git stash && git rebase origin/main && git stash pop
git push --force-with-lease origin fix/round-XX-bugs
gh pr view <N> --json mergeable # must be MERGEABLE before done
- Never push to
maindirectly - Never have multiple open fix PRs
- Commit messages: "Feature" or "Fix" — never "Bug"
- No AI attribution in commits
- Repo:
mims-harvard/ToolUniverse— verify withgit remote -v