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May 5, 2026
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Grpinto branch#3
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@grpinto grpinto commented May 5, 2026

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grpinto and others added 2 commits May 4, 2026 19:12
Adds a BioContextAI Registry-compatible MCP server that exposes
dataset search and download from CellxGene Discover so any
MCP-capable agent (Claude Desktop, Cursor, mcp-cli + Ollama, ...)
can fetch single-cell datasets by disease, tissue, or ontology
term. The server complements (instead of duplicating) the existing
MaxMLang/cxg-census-mcp and biocontext-ai/anndata-mcp registry
servers.

- New src/patpy/mcp/ package with a multi-source plugin
  architecture (DataSource protocol) and a CellxGene Discover REST
  source with pagination, retries, 24 h on-disk index cache, and
  streaming download with SHA-256 verification.
- New mcp/ directory with a schema-validated meta.yaml ready to be
  PR'd into biocontext-ai/registry, plus a Dockerfile and
  .dockerignore.
- Documentation in docs/mcp.md (linked from docs/index.md and a
  new section in README.md) covering install, agent config
  snippets, and a chaining recipe with cxg-census-mcp and
  anndata-mcp.
- Test suite under tests/: server tool registration check,
  twelve discover-client unit tests with a hand-rolled fake
  session, and registry-schema validation against the upstream
  schema.json (committed offline as a fixture).

Co-authored-by: Cursor <cursoragent@cursor.com>
@grpinto grpinto merged commit 50db219 into main May 5, 2026
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grpinto added a commit that referenced this pull request May 5, 2026
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