synapse-mcp: Instructions file for Claude Code

CLAUDE.md

synapse-mcp CLAUDE.md is an instructions file for Claude Code from Sage-Bionetworks/synapse-mcp. It costs 1,295 tokens per session, scanned A, original, MIT.

Repository instructions for a Python server that lets AI assistants use Synapse, a platform for managing and sharing scientific research data. It covers the server's tools, development commands, and rules for adding tools.

In plain words
What is it for?
Use them to install dependencies, run tests, evaluate tool selection, start the server, or add a Synapse service tool with the required naming and tagging rules.
Why use it?
They provide the project setup and conventions needed to extend the server safely, including the distinction between read-only and write or destructive operations.

Instructions file for Claude Code

Written for Claude Code: the file is CLAUDE.md. Also seen: mentions CLAUDE.md.

This is Sage-Bionetworks/synapse-mcp's own configuration. It tells Claude Code how to work on synapse-mcp itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything synapse-mcp configures →

Reuse

Borrowing it

Nothing to install: this file belongs to Sage-Bionetworks/synapse-mcp. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file
curl -O https://raw.githubusercontent.com/Sage-Bionetworks/synapse-mcp/main/CLAUDE.md
Clone the repo
git clone --depth 1 https://github.com/Sage-Bionetworks/synapse-mcp

Made for: Claude Code.

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Per session 1,295 This file is loaded in full into every session.
When invoked 1,295 The same file — it is already loaded in full.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.01295 $0.01295
Opus 5 $0.00647 $0.00647
Sonnet 5 $0.00259 $0.00259
Haiku 4.5 $0.00129 $0.00129

Measured 9d ago against content hash 5a2421f28819, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-09, from the pricing page.

Security

Grade A, and why

synapse-mcp CLAUDE.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

CLAUDE.md · 59 lines

How it starts

The opening of the file, as written. The whole thing — 59 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Project

FastMCP-based server that exposes Synapse (synapse.org) capabilities to LLMs over MCP. Tool catalog is 72 tools (48 read-only, 24 write/destructive) spanning entity, wiki, team, user, activity, evaluation, submission, schema, organization, form, curation, utility, and search domains.

Stack

  • Python 3.11 (CI runs on 3.10)
  • FastMCP 3.2.3 (fastmcp)
  • synapseclient 4.12.0
  • pytest with anyio (asyncio backend) — see tests/CLAUDE.md
  • astral/uv for local dev

Commands

  • Install deps: uv sync
  • Run the full test suite: uv run pytest
  • Run a single test file: uv run pytest tests/test_tool_service.py
  • Run the BM25 eval with its printed summary: uv run pytest tests/evals/test_tool_selection.py -s
  • Run the server over stdio: uv run synapse-mcp
  • Run the server over HTTP on :9000 (matches the VS Code launch config): uv run synapse-mcp --http --host 127.0.0.1 --port 9000

Tool authoring

Every tool is declared via @service_tool (from synapse_mcp.services), never @mcp.tool directly — because the decorator enforces naming, docstring, and tagging conventions at registration time. See doc/tool-authoring.md for the full convention.

  • Tool name must start with one of: get_ list_ search_ create_ update_ delete_ submit_ check_ validate_ register_ — decorator raises ValueError at import otherwise.
  • First sentence of description= must name the concrete Synapse object passed as synapse_object= (head-noun matched, plural allowed) — because LLMs pick tools by reading that sentence first, and a typo'd object name makes selection accuracy drop.
  • Synonyms live in synonyms=(...); siblings live in siblings=(...). Never embed them in prose — because the Related terms: / Distinct from: lines the decorator renders keep the primary description scannable for humans while still feeding the BM25 index.
  • Tool function bodies stay thin: validate ID with validate_synapse_id(...), delegate to a service-class method, return — because business logic lives in services/ under @error_boundary. Any logic that escapes the tool wrapper becomes a 500 to the LLM.
  • ID-accepting parameters must include a concrete example in the description: syn123456 for entity IDs, numeric strings for team/evaluation/submission/user IDs, URI form for JSON schema $id — because LLMs infer argument shape from example values, not just parameter names.
  • Tool functions put ctx: Context last, EXCEPT when every business arg is optional (defaulted): then ctx comes first, because Python forbids a non-default arg after a defaulted one (e.g. get_entity_provenance(ctx, entity_id=None, ...)). Service methods take ctx: Context first, then business args — no self, since services are @staticmethod. Don't swap the service/tool convention.

Read the full file on GitHub · 59 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 9d ago First seen · 59 lines · 1,295 tokens per session scan A 5a2421f28819

Subscribe to this mod's changes

synapse-mcp CLAUDE.md is an instructions file published in the GitHub repository Sage-Bionetworks/synapse-mcp (3 stars, last pushed 18d ago), licensed MIT. It adds 1,295 tokens to every session, about $0.0065 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

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