@pipeworx/mcp-civic 0.1.0

package/LICENSE

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+MIT License
+
+Copyright (c) 2026 Mojibake Inc.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

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+# @pipeworx/civic
+
+Expert-curated clinical interpretation of cancer variants from CIViC — which
+somatic alterations are clinically actionable, in which disease, with which
+therapy, and the graded published evidence behind each claim.
+
+Part of [Pipeworx](https://pipeworx.io) — an MCP gateway connecting AI agents to 1679+ live data sources.
+
+## Tools
+
+- `civic_search_genes(query, limit?)` — cancer genes and fusions by name, with
+  variant / evidence / assertion counts and the CIViC feature id.
+- `civic_gene_variants(gene, variant_name?, limit?)` — the curated variants of a
+  gene, with associated diseases and therapies.
+- `civic_variant_evidence(molecular_profile | variant_id, evidence_type?, disease?, therapy?, limit?)`
+  — individual evidence items with type, level A-E, direction, significance,
+  1-5 star rating and the PubMed/ASCO source.
+- `civic_assertions(molecular_profile? | disease? | therapy?, limit?)` — the
+  AMP/ASCO/CAP-tiered rollups, with FDA companion-test and regulatory-approval
+  flags, ACMG codes and NCCN guideline.
+
+## Auth
+
+Keyless. Public GraphQL endpoint; CIViC's content is CC0.
+
+## Data sources
+
+- <https://civicdb.org/api/graphql> — POST, `{query, variables}`.
+
+Things that will otherwise cost you an afternoon:
+
+- **An explicitly null variable is a FILTER, not an absent filter — and it
+  returns HTTP 200.** Measured 2026-09-17: `evidenceItems(molecularProfileName:
+  "BRAF V600E")` reports 249 matches; adding `variantId: null` reports **0**,
+  `diseaseName: null` reports 245, `therapyName: null` reports 313. Unset
+  filters must be omitted from the variables map entirely. `omitNulls()` in
+  `src/index.ts` exists for exactly this and removing it produces a silent zero.
+- **`browseVariants.totalCount` and `browseFeatures.totalCount` ignore their own
+  filter arguments.** `browseVariants(featureName: "BRAF")` and an unfiltered
+  `browseVariants` both report 5029, the whole catalogue. `evidenceItems` and
+  `assertions` DO filter their totalCount. This pack only reports the count for
+  the two that mean it.
+- **`description` on the `BrowseFeature` type 500s the entire query.** It is in
+  the schema and it is not callable. The gene summary lives on the `Gene` type,
+  which is why `civic_search_genes` makes a second call.
+- **`genes` takes `entrezSymbols`/`entrezIds`, not `name`.** Free-text gene
+  search is `browseFeatures(featureName:)` (substring, unranked — this pack
+  re-ranks exact matches first) or `featureTypeahead(queryTerm:)`.
+- Evidence and assertion `status` can be `SUBMITTED` as well as `ACCEPTED`;
+  a submitted item has not been through CIViC review yet.
+
+## Quick Start
+
+Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
+
+```json
+{
+  "mcpServers": {
+    "civic": {
+      "url": "https://gateway.pipeworx.io/civic/mcp"
+    }
+  }
+}
+```
+
+### What this endpoint actually serves
+
+`tools/list` at `https://gateway.pipeworx.io/civic/mcp` returns the tools in the table
+above **plus the shared Pipeworx meta-tools** — `ask_pipeworx`,
+`discover_tools`, `search_within`, `remember`/`recall` and the rest of the
+gateway-wide set. So the tool count you see is larger than this table: a
+single-pack endpoint currently lists roughly 30 shared tools alongside the
+pack's own. The connection's `initialize` response states its exact scope, and
+is the authoritative answer for a given day.
+
+This is deliberate, not multiplexing by accident. The meta-tools are what let a
+scoped connection answer a question this pack does not cover — via
+`ask_pipeworx`, which routes across the whole catalog — without you adding a
+second MCP server. There is currently no way to mount a pack endpoint without
+them; if the extra schemas cost you more context than the routing is worth,
+connect to the full gateway once rather than to several pack endpoints.
+
+Or connect to the full Pipeworx gateway to get every pack's tools listed
+directly, instead of just this one's:
+
+```json
+{
+  "mcpServers": {
+    "pipeworx": {
+      "url": "https://gateway.pipeworx.io/mcp"
+    }
+  }
+}
+```
+
+Both URLs reach the same gateway and the same 1679+ data sources. The
+only difference is which pack's tools are listed **directly**; `ask_pipeworx`
+reaches all of them from either one.
+
+## No MCP client? Call it over HTTP
+
+```bash
+curl -X POST https://gateway.pipeworx.io/v1/tools/civic_search_genes \
+  -H 'Content-Type: application/json' \
+  -d '{"query":"BRAF","limit":5}'
+```
+
+No account needed for the first calls. Inspect any tool: `GET https://gateway.pipeworx.io/v1/tools/civic_search_genes`. Find one: `POST https://gateway.pipeworx.io/v1/tools/search_packs` with `{"query":"..."}`.
+
+## Standalone (no gateway account)
+
+This package also runs as a local stdio MCP server — no Pipeworx account, no
+gateway round-trip:
+
+```json
+{
+  "mcpServers": {
+    "civic": {
+      "command": "npx",
+      "args": ["-y", "@pipeworx/mcp-civic"]
+    }
+  }
+}
+```
+
+Or run it directly to confirm it starts:
+
+```bash
+npx -y @pipeworx/mcp-civic
+```
+
+It speaks MCP over stdin/stdout and answers `initialize`/`tools/list`/`tools/call`
+for **only** this pack's tools — none of the shared meta-tools the gateway
+connection above adds. Same source, same tools, no ask_pipeworx routing.
+
+## Using with ask_pipeworx
+
+Instead of calling tools directly, you can ask questions in plain English —
+this works on the pack endpoint above as well as on the full gateway:
+
+```
+ask_pipeworx({ question: "your question about Civic data" })
+```
+
+The gateway picks the right tool and fills the arguments automatically.
+
+## More
+
+- [Docs and guides](https://pipeworx.io/docs)
+- [pipeworx.io](https://pipeworx.io)
+
+## License
+
+MIT

package/bin/cli.js

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+#!/usr/bin/env node
+//
+// Entry point for `npx @pipeworx/mcp-<slug>`.
+//
+// Packs ship as raw TypeScript (no build step — see publish-pack.sh for why:
+// tsx sidesteps every extensionless-import / bare-JSON-import edge case a
+// per-pack tsc build would have to solve one pack at a time). This file
+// registers tsx's ESM loader programmatically, then hands off to src/server.ts,
+// which wraps the pack's {tools, callTool} export in a stdio MCP server.
+//
+// Copied verbatim into every published pack repo by scripts/publish-pack.sh —
+// edit this file, not a per-pack copy.
+import { register } from 'tsx/esm/api';
+
+register();
+
+await import('../src/server.ts');

package/package.json

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+{
+  "name": "@pipeworx/mcp-civic",
+  "version": "0.1.0",
+  "description": "CIViC — Clinical Interpretation of Variants in Cancer.",
+  "type": "module",
+  "main": "src/index.ts",
+  "types": "src/index.ts",
+  "bin": {
+    "mcp-civic": "bin/cli.js"
+  },
+  "keywords": ["mcp", "mcp-server", "model-context-protocol", "pipeworx", "civic"],
+  "license": "MIT",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/pipeworx-io/mcp-civic.git"
+  },
+  "scripts": {
+    "typecheck": "tsc --noEmit"
+  },
+  "dependencies": {
+    "@modelcontextprotocol/sdk": "^1.30.0",
+    "tsx": "^4.19.0"
+  },
+  "devDependencies": {
+    "typescript": "^5.9.3",
+    "@cloudflare/workers-types": "^4.20260405.1"
+  },
+  "pipeworx": {
+    "sourceHash": "v1-ad48a207126f5b01153eb26d3decaf8fc1d694495c8c00c5e1589d1b95b7eca8",
+    "sourceCommit": "839ab210d969ef7f822cd747ea516f6bb49e9231"
+  }
+}

package/server.json

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+{
+  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
+  "name": "io.github.pipeworx-io/civic",
+  "title": "Civic",
+  "description": "CIViC — Clinical Interpretation of Variants in Cancer.",
+  "version": "0.1.0",
+  "websiteUrl": "https://pipeworx.io/packs/civic",
+  "repository": {
+    "url": "https://github.com/pipeworx-io/mcp-civic",
+    "source": "github"
+  },
+  "remotes": [
+    {
+      "type": "streamable-http",
+      "url": "https://gateway.pipeworx.io/civic/mcp"
+    }
+  ]
+}