[Forge] Instrument all tool calls with DB logging
Goal
Wrap every tool function in tools.py with a decorator/wrapper that logs to tool_calls table (inputs, outputs, timing, success/failure). Update research_topic() and any tools used in orchestrator.
Acceptance Criteria
☐ After an analysis, tool_calls shows which tools were invoked, inputs, outputs, timing.
Approach
Read AGENTS.md and relevant source files
Understand existing code patterns before modifying
Implement changes following existing conventions (f-string HTML, SQLite, Bedrock Claude)
Test: curl affected pages, verify rendering, run scidex status
Commit atomically with descriptive messageWork Log
2026-04-01 19:38 PT — Slot 12
- Started task: Instrument all tool calls with DB logging
- Read AGENTS.md, tools.py, scidex_orchestrator.py
- Checked database:
tool_calls table does not exist yet
- Found 9 tool functions to instrument:
- pubmed_search, pubmed_abstract
- semantic_scholar_search
- get_gene_info, get_disease_info
- search_trials
- enrichr_analyze
- open_targets_associations
- research_topic (convenience wrapper)
1. Create tool_calls table schema
2. Create decorator to log inputs, outputs, timing, success/failure
3. Apply decorator to all tool functions
4. Test with a sample analysis
Verification
2026-04-26 04:20 PT — Verification
All acceptance criteria are satisfied on main (commit
30f121046):
Evidence:
tool_calls table exists in PostgreSQL with 32,784 rows across 133 distinct tools- 143
@log_tool_call decorators applied throughout scidex/forge/tools.py
research_topic() is decorated at line 6760 (@log_tool_call def research_topic(...))scidex_orchestrator.py imports tools from tools module (line 58) — all instrumented- Live DB query confirms
tool_research_topic entries with inputs, outputs, timing:
skill_id: tool_research_topic
input_json: {"args": ["mitochondrial transfer mechanisms query"], "kwargs": {}}
output_json: {"topic": "...", "pubmed_papers": [...], "semantic_scholar_papers": [...], "total_evidence": N}
duration_ms: 2895, status: success
- 16
tool_pubmed_search, 9 tool_search_trials, 6 tool_paper_corpus_search calls logged with analysis_id
Conclusion: Already implemented — this task was superseded by prior work in
scidex/forge/tools.py and
scidex/agora/scidex_orchestrator.py that applied
@log_tool_call to all Forge tools including
research_topic().