AI Functions Reference

Complete list of tools (@ai_function()) exposed to the LLM. The unified agent has access to all tools and decides per-turn which to use.

PathfinderAgent (Unified)

Catalog / Discovery

  • list_sites — List VEuPathDB sites (RAG + WDK)

  • get_record_types — Record types for the site

  • get_record_type_details — Details for one record type (RAG)

  • list_searches — Searches for a record type

  • search_for_searches — Semantic search for searches

  • get_search_parameters — Parameter specs for a search

  • get_dependent_vocab — Refresh dependent parameter options

  • lookup_phyletic_codes — Look up phyletic pattern codes for organisms

  • search_example_plans — Search example strategies (RAG + WDK)

Graph Building / Editing

  • create_step — Create a search, transform, or combine step

  • list_current_steps — List steps with WDK IDs and counts

  • validate_graph_structure — Validate structure and single-output

  • ensure_single_output — Combine loose roots into one output

  • delete_step — Delete a step

  • undo_last_change — Undo last graph mutation

  • rename_step — Rename a step

  • update_step — Update step parameters

  • add_step_filter — Add filter to a step

  • add_step_analysis — Add analysis to a step

  • add_step_report — Add report to a step

  • explain_operator — Explain combine operator (UNION, etc.)

  • search_searches_by_keywords — Keyword search for available searches

Execution / Outputs

  • get_result_count — Get result count for a built step

  • get_download_url — Get download URL for results

  • get_sample_records — Get sample records from a step

Strategy Metadata

  • save_strategy — Save strategy to WDK

  • rename_strategy — Rename the strategy

  • clear_strategy — Clear the graph

  • get_strategy_summary — Summary of current strategy

Delegation

  • delegate_strategy_subtasks — Spawn sub-kanis for multi-step build

Research

  • web_search — DuckDuckGo web search

  • literature_search — Scientific literature search

Validation & Optimization

  • run_control_tests — Run positive/negative control gene lists

  • optimize_search_parameters — Optimize parameters (Bayesian, grid, random)

  • lookup_gene_records — Look up genes by text

  • resolve_gene_ids_to_records — Resolve gene IDs to records

Artifacts

  • save_planning_artifact — Save artifact (title, summary, parameters, proposed_strategy_plan)

Workbench / Gene Sets

  • create_workbench_gene_set — Create a gene set in the workbench

  • run_gene_set_enrichment — Run enrichment analysis on a gene set

  • list_workbench_gene_sets — List available gene sets

Export

  • export_gene_set — Export a gene set as CSV or TXT

Session

  • set_conversation_title — Set conversation title

  • report_reasoning — Report reasoning to the user

SubtaskAgent (Sub-kani)

Has catalog, graph building / editing, execution / outputs, strategy metadata, and research tools – the same core tools as PathfinderAgent. Does not have delegation, validation & optimization, workbench, export, or artifact tools.

Detailed Tool Docs

See AI Tools for full module reference (unified_registry, registry, research_registry, execution_tools).