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Data Aggregator for VS Code

io.github.musharna/data-aggregator-mcp

Find & fetch research datasets across 17 archives, omics registries, and literature sources.

client:VS Code transport:stdio runtime:pypi

Install Data Aggregator in VS Code

.vscode/mcp.json

{
  "inputs": [
    {
      "type": "promptString",
      "id": "ncbi-api-key",
      "description": "NCBI_API_KEY",
      "password": true
    },
    {
      "type": "promptString",
      "id": "llm-api-base",
      "description": "LLM_API_BASE",
      "password": true
    },
    {
      "type": "promptString",
      "id": "llm-api-key",
      "description": "LLM_API_KEY",
      "password": true
    },
    {
      "type": "promptString",
      "id": "llm-model",
      "description": "LLM_MODEL",
      "password": true
    },
    {
      "type": "promptString",
      "id": "embedding-api-base",
      "description": "EMBEDDING_API_BASE",
      "password": true
    },
    {
      "type": "promptString",
      "id": "embedding-api-key",
      "description": "EMBEDDING_API_KEY",
      "password": true
    },
    {
      "type": "promptString",
      "id": "embedding-model",
      "description": "EMBEDDING_MODEL",
      "password": true
    },
    {
      "type": "promptString",
      "id": "data-gov-api-key",
      "description": "DATA_GOV_API_KEY",
      "password": true
    },
    {
      "type": "promptString",
      "id": "unpaywall-email",
      "description": "UNPAYWALL_EMAIL",
      "password": true
    },
    {
      "type": "promptString",
      "id": "ncbi-email",
      "description": "NCBI_EMAIL",
      "password": true
    },
    {
      "type": "promptString",
      "id": "dataverse-base-url",
      "description": "DATAVERSE_BASE_URL",
      "password": true
    },
    {
      "type": "promptString",
      "id": "cache-ttl-seconds",
      "description": "CACHE_TTL_SECONDS",
      "password": true
    }
  ],
  "servers": {
    "data-aggregator-mcp": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "data-aggregator-mcp"
      ],
      "env": {
        "NCBI_API_KEY": "${input:ncbi-api-key}",
        "LLM_API_BASE": "${input:llm-api-base}",
        "LLM_API_KEY": "${input:llm-api-key}",
        "LLM_MODEL": "${input:llm-model}",
        "EMBEDDING_API_BASE": "${input:embedding-api-base}",
        "EMBEDDING_API_KEY": "${input:embedding-api-key}",
        "EMBEDDING_MODEL": "${input:embedding-model}",
        "DATA_GOV_API_KEY": "${input:data-gov-api-key}",
        "UNPAYWALL_EMAIL": "${input:unpaywall-email}",
        "NCBI_EMAIL": "${input:ncbi-email}",
        "DATAVERSE_BASE_URL": "${input:dataverse-base-url}",
        "CACHE_TTL_SECONDS": "${input:cache-ttl-seconds}"
      }
    }
  }
}

VS Code prompts for each input the first time the server starts, so no secret is written to the file. VS Code docs

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