@cyanheads/pubchem-mcp-server 0.1.19 → 0.1.21

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Files changed (7) hide show
  1. package/README.md +12 -3
  2. package/dist/services/pubchem/pubchem-client.d.ts.map +1 -1
  3. package/dist/services/pubchem/pubchem-client.js +13 -7
  4. package/dist/services/pubchem/pubchem-client.js.map +1 -1
  5. package/manifest.json +44 -0
  6. package/package.json +19 -7
  7. package/server.json +3 -3
package/README.md CHANGED
@@ -1,12 +1,21 @@
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  <div align="center">
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  <h1>@cyanheads/pubchem-mcp-server</h1>
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- <p><b>MCP server for the PubChem chemical database. Search compounds, fetch properties, safety data, bioactivity, cross-references, and entity summaries. STDIO & Streamable HTTP</b></p>
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- <p><b>8 Tools</b></p>
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+ <p><b>MCP server for the PubChem chemical database. Search compounds, fetch properties, safety data, bioactivity, cross-references, and entity summaries. STDIO & Streamable HTTP.</b>
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+ <div>8 Tools</div>
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+ </p>
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  </div>
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  <div align="center">
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- [![Version](https://img.shields.io/badge/Version-0.1.19-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-^1.3.0-f472b6.svg?style=flat-square)](https://bun.sh/)
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+ [![Version](https://img.shields.io/badge/Version-0.1.21-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubchem-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubchem-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubchem-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-^1.3.0-f472b6.svg?style=flat-square)](https://bun.sh/)
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+
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+ </div>
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+
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+ <div align="center">
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+
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+ [![Install in Claude Desktop](https://img.shields.io/badge/Install_in-Claude_Desktop-D97757?style=for-the-badge&logo=anthropic&logoColor=white)](https://github.com/cyanheads/pubchem-mcp-server/releases/latest/download/pubchem-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=pubchem-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvcHViY2hlbS1tY3Atc2VydmVyIl19) [![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=for-the-badge&logo=visualstudiocode&logoColor=white)](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22pubchem-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads/pubchem-mcp-server%22%5D%7D)
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+
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+ [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-67E8F9?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
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  </div>
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package/dist/services/pubchem/pubchem-client.d.ts.map CHANGED
@@ -1 +1 @@
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+ {"version":3,"file":"pubchem-client.d.ts","sourceRoot":"","sources":["../../../src/services/pubchem/pubchem-client.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAIH,OAAO,KAAK,EAGV,cAAc,EAEd,sBAAsB,EACtB,iBAAiB,EAQlB,MAAM,YAAY,CAAC;AA8MpB,qBAAa,aAAa;IACxB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAA+C;IACvE,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAoD;IAC7E,OAAO,CAAC,QAAQ,CAAC,WAAW,CAAsB;YAIpC,SAAS;YAgDT,WAAW;IA2BzB,wEAAwE;YAC1D,SAAS;IAWvB,qDAAqD;YACvC,WAAW;IAgBzB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAI7C,cAAc,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAQjD,gBAAgB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAMrD,eAAe,CAAC,OAAO,EAAE,MAAM,EAAE,UAAU,UAAQ,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAOvE,iBAAiB,CACf,IAAI,EAAE,cAAc,GAAG,gBAAgB,GAAG,YAAY,EACtD,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,QAAQ,GAAG,KAAK,EAC3B,SAAS,CAAC,EAAE,MAAM,GACjB,OAAO,CAAC,MAAM,EAAE,CAAC;IA2Bd,aAAa,CACjB,IAAI,EAAE,MAAM,EAAE,EACd,UAAU,EAAE,MAAM,EAAE,GACnB,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG;QAAE,GAAG,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IA0BtD,WAAW,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAYjD,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,GAAE,OAAO,GAAG,OAAiB,GAAG,OAAO,CAAC,WAAW,CAAC;IAKxE,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,CAAC,MAAM,GAAG,MAAM,CAAC,EAAE,CAAC;IAiBrE,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,KAAK,CAAC;QAAE,MAAM,CAAC,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IA8B9E,aAAa,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,iBAAiB,GAAG,IAAI,CAAC;IAgE7D,iBAAiB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,sBAAsB,GAAG,IAAI,CAAC;IAwEtE,eAAe,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,cAAc,EAAE,CAAC;IAY7D,OAAO,CAAC,eAAe;IA0EjB,oBAAoB,CAAC,UAAU,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAgB1E,gBAAgB,CACpB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,MAAM,GAAG,MAAM,GAC1B,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC;CAiC3C;AAMD,wBAAgB,iBAAiB,IAAI,IAAI,CAExC;AAED,wBAAgB,gBAAgB,IAAI,aAAa,CAIhD"}
package/dist/services/pubchem/pubchem-client.js CHANGED
@@ -4,7 +4,7 @@
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  * @module services/pubchem/pubchem-client
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  */
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  import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
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- import { httpStatusToErrorCode } from '@cyanheads/mcp-ts-core/utils';
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+ import { httpErrorFromResponse } from '@cyanheads/mcp-ts-core/utils';
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  const isNotFound = (error) => error instanceof McpError && error.code === JsonRpcErrorCode.NotFound;
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  // ── Rate Limiter ─────────────────────────────────────────────────────
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  /** Sliding-window rate limiter. Queues requests exceeding maxPerSecond. */
@@ -207,14 +207,17 @@ export class PubChemClient {
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  return (await response.json());
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  }
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  const text = await response.text();
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- const message = parseFaultMessage(text) ?? text.slice(0, 300);
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+ const fault = parseFaultMessage(text) ?? text.slice(0, 300);
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  // Retry once on 5xx
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  if (response.status >= 500 && attempt < 1) {
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  await sleep(1000 * 2 ** attempt);
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  continue;
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  }
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- const code = httpStatusToErrorCode(response.status) ?? JsonRpcErrorCode.InternalError;
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- throw new McpError(code, message, { url, status: response.status });
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+ throw await httpErrorFromResponse(response, {
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+ captureBody: false,
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+ service: 'PubChem',
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+ data: { fault, url },
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+ });
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  }
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  catch (error) {
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  // HTTP errors are already classified — surface them, don't retry.
@@ -243,9 +246,12 @@ export class PubChemClient {
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  const response = await fetch(url, { signal: controller.signal });
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  if (!response.ok) {
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  const text = await response.text();
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- const message = parseFaultMessage(text) ?? text.slice(0, 300);
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- const code = httpStatusToErrorCode(response.status) ?? JsonRpcErrorCode.InternalError;
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- throw new McpError(code, message, { url, status: response.status });
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+ const fault = parseFaultMessage(text) ?? text.slice(0, 300);
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+ throw await httpErrorFromResponse(response, {
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+ captureBody: false,
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+ service: 'PubChem',
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+ data: { fault, url },
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+ });
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  }
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  return await response.arrayBuffer();
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  }
package/dist/services/pubchem/pubchem-client.js.map CHANGED
@@ -1 +1 @@
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package/manifest.json ADDED
@@ -0,0 +1,44 @@
1
+ {
2
+ "manifest_version": "0.3",
3
+ "name": "pubchem-mcp-server",
4
+ "version": "0.1.21",
5
+ "description": "Search PubChem compounds, properties, safety data, bioactivity, cross-references, and entity summaries via MCP.",
6
+ "author": {
7
+ "name": "cyanheads"
8
+ },
9
+ "repository": {
10
+ "type": "git",
11
+ "url": "https://github.com/cyanheads/pubchem-mcp-server"
12
+ },
13
+ "homepage": "https://github.com/cyanheads/pubchem-mcp-server#readme",
14
+ "license": "Apache-2.0",
15
+ "server": {
16
+ "type": "node",
17
+ "entry_point": "dist/index.js",
18
+ "mcp_config": {
19
+ "command": "node",
20
+ "args": ["${__dirname}/dist/index.js"],
21
+ "env": {
22
+ "MCP_TRANSPORT_TYPE": "stdio",
23
+ "MCP_AUTH_MODE": "none",
24
+ "NODE_ENV": "production"
25
+ }
26
+ }
27
+ },
28
+ "compatibility": {
29
+ "runtimes": {
30
+ "node": ">=24.0.0"
31
+ }
32
+ },
33
+ "tools_generated": true,
34
+ "prompts_generated": true,
35
+ "user_config": {
36
+ "MCP_LOG_LEVEL": {
37
+ "title": "Log Level",
38
+ "description": "Minimum log level for output (debug, info, warn, error).",
39
+ "type": "string",
40
+ "default": "info",
41
+ "required": false
42
+ }
43
+ }
44
+ }
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@cyanheads/pubchem-mcp-server",
3
- "version": "0.1.19",
3
+ "version": "0.1.21",
4
4
  "description": "MCP server for the PubChem chemical database. Search compounds, fetch properties, safety data, bioactivity, cross-references, and entity summaries. STDIO & Streamable HTTP.",
5
5
  "mcpName": "io.github.cyanheads/pubchem-mcp-server",
6
6
  "type": "module",
@@ -9,15 +9,22 @@
9
9
  "bin": {
10
10
  "pubchem-mcp-server": "dist/index.js"
11
11
  },
12
- "files": ["dist/", "README.md", "LICENSE", "server.json", "Dockerfile"],
12
+ "files": ["dist/", "README.md", "LICENSE", "server.json", "manifest.json", "Dockerfile"],
13
13
  "scripts": {
14
14
  "build": "bun scripts/build.ts",
15
15
  "rebuild": "bun scripts/clean.ts && bun scripts/build.ts",
16
16
  "clean": "bun scripts/clean.ts",
17
17
  "devcheck": "bun scripts/devcheck.ts",
18
+ "audit:refresh": "rm -f bun.lock && bun install && bun audit",
18
19
  "tree": "bun scripts/tree.ts",
20
+ "list-skills": "bun scripts/list-skills.ts",
19
21
  "format": "biome check --write --unsafe .",
20
22
  "lint:mcp": "bun scripts/lint-mcp.ts",
23
+ "lint:packaging": "bun scripts/lint-packaging.ts",
24
+ "bundle": "bun run build && npx -y @anthropic-ai/mcpb pack . dist/pubchem-mcp-server.mcpb",
25
+ "changelog:build": "bun scripts/build-changelog.ts",
26
+ "changelog:check": "bun scripts/build-changelog.ts --check",
27
+ "publish-mcp": "mcp-publisher publish",
21
28
  "test": "vitest run",
22
29
  "start:stdio": "node dist/index.js",
23
30
  "start:http": "MCP_TRANSPORT_TYPE=http node dist/index.js"
@@ -35,6 +42,10 @@
35
42
  "mcp",
36
43
  "mcp-server",
37
44
  "model-context-protocol",
45
+ "typescript",
46
+ "bun",
47
+ "stdio",
48
+ "streamable-http",
38
49
  "pubchem",
39
50
  "chemistry",
40
51
  "compounds",
@@ -60,16 +71,17 @@
60
71
  "access": "public"
61
72
  },
62
73
  "dependencies": {
63
- "@cyanheads/mcp-ts-core": "^0.9.1",
64
- "pino-pretty": "^13.1.3"
74
+ "@cyanheads/mcp-ts-core": "^0.9.13",
75
+ "pino-pretty": "^13.1.3",
76
+ "zod": "^4.4.3"
65
77
  },
66
78
  "devDependencies": {
67
- "@biomejs/biome": "^2.4.15",
68
- "@types/node": "^25.8.0",
79
+ "@biomejs/biome": "^2.4.16",
80
+ "@types/node": "^25.9.1",
69
81
  "depcheck": "^1.4.7",
70
82
  "ignore": "^7.0.5",
71
83
  "tsc-alias": "^1.8.17",
72
84
  "typescript": "^6.0.3",
73
- "vitest": "^4.1.6"
85
+ "vitest": "^4.1.7"
74
86
  }
75
87
  }
package/server.json CHANGED
@@ -6,7 +6,7 @@
6
6
  "url": "https://github.com/cyanheads/pubchem-mcp-server",
7
7
  "source": "github"
8
8
  },
9
- "version": "0.1.19",
9
+ "version": "0.1.21",
10
10
  "remotes": [
11
11
  {
12
12
  "type": "streamable-http",
@@ -19,7 +19,7 @@
19
19
  "registryBaseUrl": "https://registry.npmjs.org",
20
20
  "identifier": "@cyanheads/pubchem-mcp-server",
21
21
  "runtimeHint": "bun",
22
- "version": "0.1.19",
22
+ "version": "0.1.21",
23
23
  "packageArguments": [
24
24
  { "type": "positional", "value": "run" },
25
25
  { "type": "positional", "value": "start:stdio" }
@@ -42,7 +42,7 @@
42
42
  "registryBaseUrl": "https://registry.npmjs.org",
43
43
  "identifier": "@cyanheads/pubchem-mcp-server",
44
44
  "runtimeHint": "bun",
45
- "version": "0.1.19",
45
+ "version": "0.1.21",
46
46
  "packageArguments": [
47
47
  { "type": "positional", "value": "run" },
48
48
  { "type": "positional", "value": "start:http" }