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Use when adding, renaming, or removing an MCP tool in gencc-link. Walks through the tool module, facade registration, the capabilities TOOLS tuple, tests, and the README/connection-guide tables.
Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.
Use when adding, renaming, or modifying this backend's FastAPI routes, dependencies, middleware, or response behavior.
Use when CI fails on a PR or main in gencc-link. Walks through reproducing make ci-local locally and root-causing without bypassing checks.
Use when changing the GenCC SQLite schema. Coordinates schema.sql, the ingest builder/aggregates, and the repository together, then rebuilds the database and updates tests and fixtures.
Use when preparing a versioned release of gencc-link. Walks through the pre-release checklist — ci-local green, CHANGELOG, version bump, valid docker config — then tagging and watching the release workflow.
Based on SOC occupation classification
| name | mcp-tool-change |
| description | Use when adding, renaming, or removing an MCP tool in gencc-link. Walks through the tool module, facade registration, the capabilities TOOLS tuple, tests, and the README/connection-guide tables. |
Use this skill when changing the MCP tool surface (additions, renames, removals, description rewrites). GenCC-Link exposes exactly 10 tools today; the tool list is part of the public contract.
Pick the tool module. Tools are grouped by concern under
gencc_link/mcp/tools/:
discovery.py (get_server_capabilities, get_gencc_diagnostics)genes.py (search_genes, get_gene_curations)diseases.py (search_diseases, get_disease_curations)assertions.py (get_gene_disease_assertion, find_curations,
resolve_identifier)submitters.py (list_submitters)
Add the tool to the matching register_*_tools(mcp) function (create a new
group only if it genuinely does not fit an existing one).Register in the facade. If you added a new register_*_tools group, wire
it into gencc_link/mcp/facade.py create_gencc_mcp().
Update the capabilities TOOLS tuple. Edit
gencc_link/mcp/capabilities.py — the TOOLS tuple is the canonical
inventory returned by get_server_capabilities and the gencc://capabilities
resource. Order matters; keep it consistent with the README table.
Tune the description and envelope. Write the tool description for an AI
client choosing a tool: what it does, when to use it, input/output shape, and
what it does NOT do. Keep READ_ONLY_OPEN_WORLD annotations
(gencc_link/mcp/annotations.py), the run_mcp_tool envelope
(gencc_link/mcp/envelope.py), response_mode shaping
(gencc_link/services/shaping.py), and _meta.next_commands
(gencc_link/mcp/next_commands.py).
Error mapping. If the tool can raise a new exception, ensure it maps to a
typed error code (invalid_input, not_found, ambiguous_query,
data_unavailable, upstream_unavailable, rate_limited, internal_error)
in gencc_link/exceptions.py / the envelope classifier.
Tests. Add or update tests under tests/ covering the tool's behavior,
its presence in the capabilities inventory, response_mode shaping, and error
masking. Run make test (optionally -k <tool_name>).
Docs / tables. Update the tool tables in README.md,
docs/MCP_CONNECTION_GUIDE.md, and docs/usage.md. Mention the tool in
docs/architecture.md if it changes the tool grouping.
Preserved names. Existing tool names are part of the public contract.
Renaming or removing a tool requires a CHANGELOG.md entry and a migration
note.
CI. Run make ci-local.