@cyanheads/pubchem-mcp-server 1.0.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/LICENSE +201 -0
- package/README.md +236 -0
- package/dist/config/index.d.ts +98 -0
- package/dist/config/index.js +326 -0
- package/dist/index.d.ts +24 -0
- package/dist/index.js +214 -0
- package/dist/mcp-server/server.d.ts +21 -0
- package/dist/mcp-server/server.js +124 -0
- package/dist/mcp-server/tools/fetchAssaySummary/index.d.ts +7 -0
- package/dist/mcp-server/tools/fetchAssaySummary/index.js +7 -0
- package/dist/mcp-server/tools/fetchAssaySummary/logic.d.ts +71 -0
- package/dist/mcp-server/tools/fetchAssaySummary/logic.js +96 -0
- package/dist/mcp-server/tools/fetchAssaySummary/registration.d.ts +12 -0
- package/dist/mcp-server/tools/fetchAssaySummary/registration.js +68 -0
- package/dist/mcp-server/tools/fetchCompoundProperties/index.d.ts +7 -0
- package/dist/mcp-server/tools/fetchCompoundProperties/index.js +7 -0
- package/dist/mcp-server/tools/fetchCompoundProperties/logic.d.ts +131 -0
- package/dist/mcp-server/tools/fetchCompoundProperties/logic.js +100 -0
- package/dist/mcp-server/tools/fetchCompoundProperties/registration.d.ts +13 -0
- package/dist/mcp-server/tools/fetchCompoundProperties/registration.js +52 -0
- package/dist/mcp-server/tools/fetchCompoundXrefs/index.d.ts +7 -0
- package/dist/mcp-server/tools/fetchCompoundXrefs/index.js +7 -0
- package/dist/mcp-server/tools/fetchCompoundXrefs/logic.d.ts +89 -0
- package/dist/mcp-server/tools/fetchCompoundXrefs/logic.js +145 -0
- package/dist/mcp-server/tools/fetchCompoundXrefs/registration.d.ts +13 -0
- package/dist/mcp-server/tools/fetchCompoundXrefs/registration.js +52 -0
- package/dist/mcp-server/tools/fetchSubstanceDetails/index.d.ts +7 -0
- package/dist/mcp-server/tools/fetchSubstanceDetails/index.js +7 -0
- package/dist/mcp-server/tools/fetchSubstanceDetails/logic.d.ts +69 -0
- package/dist/mcp-server/tools/fetchSubstanceDetails/logic.js +97 -0
- package/dist/mcp-server/tools/fetchSubstanceDetails/registration.d.ts +13 -0
- package/dist/mcp-server/tools/fetchSubstanceDetails/registration.js +79 -0
- package/dist/mcp-server/tools/getCompoundImage/index.d.ts +7 -0
- package/dist/mcp-server/tools/getCompoundImage/index.js +7 -0
- package/dist/mcp-server/tools/getCompoundImage/logic.d.ts +42 -0
- package/dist/mcp-server/tools/getCompoundImage/logic.js +68 -0
- package/dist/mcp-server/tools/getCompoundImage/registration.d.ts +12 -0
- package/dist/mcp-server/tools/getCompoundImage/registration.js +57 -0
- package/dist/mcp-server/tools/searchAssaysByTarget/index.d.ts +7 -0
- package/dist/mcp-server/tools/searchAssaysByTarget/index.js +7 -0
- package/dist/mcp-server/tools/searchAssaysByTarget/logic.d.ts +35 -0
- package/dist/mcp-server/tools/searchAssaysByTarget/logic.js +64 -0
- package/dist/mcp-server/tools/searchAssaysByTarget/registration.d.ts +12 -0
- package/dist/mcp-server/tools/searchAssaysByTarget/registration.js +62 -0
- package/dist/mcp-server/tools/searchCompoundByIdentifier/index.d.ts +7 -0
- package/dist/mcp-server/tools/searchCompoundByIdentifier/index.js +7 -0
- package/dist/mcp-server/tools/searchCompoundByIdentifier/logic.d.ts +35 -0
- package/dist/mcp-server/tools/searchCompoundByIdentifier/logic.js +59 -0
- package/dist/mcp-server/tools/searchCompoundByIdentifier/registration.d.ts +12 -0
- package/dist/mcp-server/tools/searchCompoundByIdentifier/registration.js +51 -0
- package/dist/mcp-server/tools/searchCompoundsByFormula/index.d.ts +7 -0
- package/dist/mcp-server/tools/searchCompoundsByFormula/index.js +7 -0
- package/dist/mcp-server/tools/searchCompoundsByFormula/logic.d.ts +38 -0
- package/dist/mcp-server/tools/searchCompoundsByFormula/logic.js +75 -0
- package/dist/mcp-server/tools/searchCompoundsByFormula/registration.d.ts +12 -0
- package/dist/mcp-server/tools/searchCompoundsByFormula/registration.js +62 -0
- package/dist/mcp-server/tools/searchCompoundsBySimilarity/index.d.ts +7 -0
- package/dist/mcp-server/tools/searchCompoundsBySimilarity/index.js +7 -0
- package/dist/mcp-server/tools/searchCompoundsBySimilarity/logic.d.ts +41 -0
- package/dist/mcp-server/tools/searchCompoundsBySimilarity/logic.js +82 -0
- package/dist/mcp-server/tools/searchCompoundsBySimilarity/registration.d.ts +12 -0
- package/dist/mcp-server/tools/searchCompoundsBySimilarity/registration.js +62 -0
- package/dist/mcp-server/tools/searchCompoundsByStructure/index.d.ts +7 -0
- package/dist/mcp-server/tools/searchCompoundsByStructure/index.js +7 -0
- package/dist/mcp-server/tools/searchCompoundsByStructure/logic.d.ts +41 -0
- package/dist/mcp-server/tools/searchCompoundsByStructure/logic.js +78 -0
- package/dist/mcp-server/tools/searchCompoundsByStructure/registration.d.ts +13 -0
- package/dist/mcp-server/tools/searchCompoundsByStructure/registration.js +63 -0
- package/dist/mcp-server/transports/auth/core/authContext.d.ts +33 -0
- package/dist/mcp-server/transports/auth/core/authContext.js +24 -0
- package/dist/mcp-server/transports/auth/core/authTypes.d.ts +17 -0
- package/dist/mcp-server/transports/auth/core/authTypes.js +5 -0
- package/dist/mcp-server/transports/auth/core/authUtils.d.ts +18 -0
- package/dist/mcp-server/transports/auth/core/authUtils.js +45 -0
- package/dist/mcp-server/transports/auth/index.d.ts +10 -0
- package/dist/mcp-server/transports/auth/index.js +9 -0
- package/dist/mcp-server/transports/auth/strategies/jwt/jwtMiddleware.d.ts +27 -0
- package/dist/mcp-server/transports/auth/strategies/jwt/jwtMiddleware.js +149 -0
- package/dist/mcp-server/transports/auth/strategies/oauth/oauthMiddleware.d.ts +20 -0
- package/dist/mcp-server/transports/auth/strategies/oauth/oauthMiddleware.js +124 -0
- package/dist/mcp-server/transports/httpErrorHandler.d.ts +26 -0
- package/dist/mcp-server/transports/httpErrorHandler.js +73 -0
- package/dist/mcp-server/transports/httpTransport.d.ts +21 -0
- package/dist/mcp-server/transports/httpTransport.js +208 -0
- package/dist/mcp-server/transports/stdioTransport.d.ts +42 -0
- package/dist/mcp-server/transports/stdioTransport.js +63 -0
- package/dist/services/pubchem/pubchemApiClient.d.ts +52 -0
- package/dist/services/pubchem/pubchemApiClient.js +120 -0
- package/dist/types-global/errors.d.ts +127 -0
- package/dist/types-global/errors.js +126 -0
- package/dist/utils/index.d.ts +12 -0
- package/dist/utils/index.js +20 -0
- package/dist/utils/internal/errorHandler.d.ts +176 -0
- package/dist/utils/internal/errorHandler.js +335 -0
- package/dist/utils/internal/index.d.ts +9 -0
- package/dist/utils/internal/index.js +9 -0
- package/dist/utils/internal/logger.d.ts +148 -0
- package/dist/utils/internal/logger.js +430 -0
- package/dist/utils/internal/requestContext.d.ts +83 -0
- package/dist/utils/internal/requestContext.js +72 -0
- package/dist/utils/metrics/index.d.ts +7 -0
- package/dist/utils/metrics/index.js +7 -0
- package/dist/utils/metrics/tokenCounter.d.ts +35 -0
- package/dist/utils/metrics/tokenCounter.js +110 -0
- package/dist/utils/network/fetchWithTimeout.d.ts +21 -0
- package/dist/utils/network/fetchWithTimeout.js +59 -0
- package/dist/utils/network/index.d.ts +6 -0
- package/dist/utils/network/index.js +5 -0
- package/dist/utils/parsing/dateParser.d.ts +73 -0
- package/dist/utils/parsing/dateParser.js +107 -0
- package/dist/utils/parsing/index.d.ts +8 -0
- package/dist/utils/parsing/index.js +8 -0
- package/dist/utils/parsing/jsonParser.d.ts +82 -0
- package/dist/utils/parsing/jsonParser.js +126 -0
- package/dist/utils/scheduling/index.d.ts +6 -0
- package/dist/utils/scheduling/index.js +6 -0
- package/dist/utils/scheduling/scheduler.d.ts +72 -0
- package/dist/utils/scheduling/scheduler.js +152 -0
- package/dist/utils/security/idGenerator.d.ts +137 -0
- package/dist/utils/security/idGenerator.js +215 -0
- package/dist/utils/security/index.d.ts +9 -0
- package/dist/utils/security/index.js +9 -0
- package/dist/utils/security/rateLimiter.d.ts +108 -0
- package/dist/utils/security/rateLimiter.js +179 -0
- package/dist/utils/security/sanitization.d.ts +184 -0
- package/dist/utils/security/sanitization.js +453 -0
- package/package.json +108 -0
package/package.json
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{
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"name": "@cyanheads/pubchem-mcp-server",
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"version": "1.0.1",
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"description": "A Model Context Protocol (MCP) server providing comprehensive LLM tools for the PubChem PUG REST API.",
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"main": "dist/index.js",
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"files": [
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"dist"
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],
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"bin": {
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"pubchem-mcp-server": "dist/index.js"
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},
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"exports": "./dist/index.js",
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"types": "dist/index.d.ts",
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"type": "module",
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"repository": {
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"type": "git",
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"url": "git+https://github.com/cyanheads/pubchem-mcp-server.git"
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},
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"bugs": {
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"url": "https://github.com/cyanheads/pubchem-mcp-server/issues"
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},
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"homepage": "https://github.com/cyanheads/pubchem-mcp-server#readme",
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"scripts": {
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"build": "tsc && node --loader ts-node/esm scripts/make-executable.ts dist/index.js",
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"start": "node dist/index.js",
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"start:stdio": "MCP_LOG_LEVEL=debug MCP_TRANSPORT_TYPE=stdio node dist/index.js",
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"start:http": "MCP_LOG_LEVEL=debug MCP_TRANSPORT_TYPE=http node dist/index.js",
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"start:agent": "MCP_LOG_LEVEL=debug node dist/agent/cli/boot.js",
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"rebuild": "ts-node --esm scripts/clean.ts && npm run build",
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"docs:generate": "typedoc --tsconfig ./tsconfig.typedoc.json",
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"depcheck": "npx depcheck",
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"tree": "ts-node --esm scripts/tree.ts",
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"fetch-spec": "ts-node --esm scripts/fetch-openapi-spec.ts",
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"format": "prettier --write \"**/*.{ts,js,json,md,html,css}\"",
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"inspector": "npx mcp-inspector --config mcp.json --server pubchem-mcp-server",
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"db:duckdb-example": "MCP_LOG_LEVEL=debug tsc && node dist/storage/duckdbExample.js"
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},
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"dependencies": {
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"@duckdb/node-api": "^1.3.1-alpha.23",
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"@hono/node-server": "^1.14.4",
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"@modelcontextprotocol/sdk": "^1.13.2",
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"@supabase/supabase-js": "^2.50.2",
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"@types/node": "^24.0.7",
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"@types/sanitize-html": "^2.16.0",
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"@types/validator": "13.15.2",
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"chrono-node": "^2.8.0",
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"dotenv": "^16.5.0",
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"hono": "^4.8.3",
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"ignore": "^7.0.5",
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"jose": "^6.0.11",
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"limiter": "^3.0.0",
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"node-cron": "^4.1.1",
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"openai": "^5.8.2",
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"partial-json": "^0.1.7",
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"sanitize-html": "^2.17.0",
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"tiktoken": "^1.0.21",
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"ts-node": "^10.9.2",
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"typescript": "^5.8.3",
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"validator": "13.15.15",
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"winston": "^3.17.0",
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"winston-transport": "^4.9.0",
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"zod": "^3.25.67"
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},
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"keywords": [
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"mcp",
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"mcp-server",
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"model-context-protocol",
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"ai-agent",
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"llm",
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"pubchem",
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"chemistry",
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"cheminformatics",
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"api-wrapper",
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"typescript",
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],
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"author": "cyanheads <casey@caseyjhand.com> (https://github.com/cyanheads/pubchem-mcp-server#readme)",
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"license": "Apache-2.0",
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"publishConfig": {
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"access": "public"
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},
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"funding": [
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{
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"type": "github",
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"url": "https://github.com/sponsors/cyanheads"
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},
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{
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"type": "buy_me_a_coffee",
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"url": "https://www.buymeacoffee.com/cyanheads"
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}
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],
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"engines": {
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"node": ">=20.0.0"
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},
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"devDependencies": {
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"@types/js-yaml": "^4.0.9",
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"@types/node-cron": "^3.0.11",
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"axios": "^1.10.0",
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"depcheck": "^1.4.7",
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"js-yaml": "^4.1.0",
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"prettier": "^3.6.2",
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"typedoc": "^0.28.7"
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}
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}
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