scholarx 0.20.0

Universal Research Paper API — single entry point for arXiv, PMC, bioRxiv, medRxiv, PsyArXiv, OSF, and Semantic Scholar

Scholarx

CLI or API | MCP | Agent

Version: 0.20.0

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Overview

Scholarx is a production-grade Agent and Model Context Protocol (MCP) server designed to interface directly with Universal Research Paper API — single entry point for arXiv, PMC, bioRxiv, medRxiv, PsyArXiv, OSF, and Semantic Scholar.

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Key Features

• Consolidated Action-Routed MCP Tools: Minimizes token overhead and eliminates tool bloat in LLM contexts by grouping methods into optimized, togglable tool modules.
• Enterprise-Grade Security: Comprehensive support for Eunomia policies, OIDC token delegation, and granular execution context tracking.
• Integrated Graph Agent: Built-in Pydantic AI agent supporting the Agent Control Protocol (ACP) and standard Web interfaces (AG-UI).
• Native Telemetry & Tracing: Out-of-the-box OpenTelemetry exports and native Langfuse tracing.

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CLI or API

This agent wraps the Universal Research Paper API — single entry point for arXiv, PMC, bioRxiv, medRxiv, PsyArXiv, OSF, and Semantic Scholar API. You can interact with it programmatically or via its integrated execution entrypoints.

Detailed instructions on how to use the underlying API wrappers, extended schema bindings, and developer SDK references are maintained in docs/index.md.

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MCP

This server utilizes dynamic Action-Routed tools to optimize token overhead and maximize IDE compatibility.

Available MCP Tools

Tool Module	Toggle Env Var	Enabled by Default	Description & Nested Methods
Search	SEARCH_TOOL	True	Register search-related tools. Action-routed methods: author, get, recent.
Discovery	DISCOVERY_TOOL	True	Register discovery-related tools. Action-routed methods: categories.
Storage	STORAGE_TOOL	True	Register paper storage tools. Action-routed methods: bulk_download, download, download_url, queue, status, stored.

Detailed tool schemas, parameter shapes, and validation constraints are preserved in docs/mcp.md.

Dynamic Tool Selection & Visibility

This MCP server supports dynamic toolset selection and visibility filtering at runtime. This allows you to restrict the set of exposed tools in order to prevent blowing up the LLM's context window.

You can configure tool filtering via multiple input channels:

• CLI Arguments: Pass --tools or --toolsets (or their disabled counterparts --disabled-tools and --disabled-toolsets) during startup.
• Environment Variables: Define standard environment variables:
  • MCP_ENABLED_TOOLS / MCP_DISABLED_TOOLS
  • MCP_ENABLED_TAGS / MCP_DISABLED_TAGS
• HTTP SSE Request Headers: Pass custom headers during transport initialization:
  • x-mcp-enabled-tools / x-mcp-disabled-tools
  • x-mcp-enabled-tags / x-mcp-disabled-tags
• HTTP SSE Request Query Parameters: Append query parameters directly to your transport connection URL:
  • ?tools=tool1,tool2
  • ?tags=tag1

When query strings or parameters are supplied, an LLM-free Knowledge Graph resolution layer (using DynamicToolOrchestrator) matches query intents against known tool tags, names, or descriptions, with safe fallback and automated 24-hour background cache refreshing.

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MCP Configuration Examples

stdio Transport (Recommended for local IDEs e.g., Cursor, Claude Desktop)

Configure your IDE's mcp.json to launch the MCP server via uvx:

{
  "mcpServers": {
    "scholarx": {
      "command": "uvx",
      "args": [
        "--from",
        "scholarx",
        "scholarx-mcp"
      ],
      "env": {
        "SCHOLARX_STORAGE_DIR": "your_scholarx_storage_dir_here",
        "DEBUG": "your_debug_here",
        "PYTHONUNBUFFERED": "your_pythonunbuffered_here",
        "SERVICENOW_INSTANCE": "your_servicenow_instance_here",
        "SERVICENOW_USERNAME": "your_servicenow_username_here",
        "OSF_TOKEN": "your_osf_token_here",
        "S2_API_KEY": "your_s2_api_key_here",
        "NCBI_API_KEY": "your_ncbi_api_key_here",
        "SERVICENOW_PASSWORD": "your_servicenow_password_here"
      }
    }
  }
}

Streamable-HTTP Transport (Recommended for production deployments)

Configure your client's mcp.json to launch the Streamable-HTTP server via uvx with explicit host and port definition:

{
  "mcpServers": {
    "scholarx": {
      "command": "uvx",
      "args": [
        "--from",
        "scholarx",
        "scholarx-mcp"
      ],
      "env": {
        "TRANSPORT": "streamable-http",
        "HOST": "0.0.0.0",
        "PORT": "8000",
        "SCHOLARX_STORAGE_DIR": "your_scholarx_storage_dir_here",
        "DEBUG": "your_debug_here",
        "PYTHONUNBUFFERED": "your_pythonunbuffered_here",
        "SERVICENOW_INSTANCE": "your_servicenow_instance_here",
        "SERVICENOW_USERNAME": "your_servicenow_username_here",
        "OSF_TOKEN": "your_osf_token_here",
        "S2_API_KEY": "your_s2_api_key_here",
        "NCBI_API_KEY": "your_ncbi_api_key_here",
        "SERVICENOW_PASSWORD": "your_servicenow_password_here"
      }
    }
  }
}

Alternatively, connect to a pre-deployed remote or local Streamable-HTTP instance:

{
  "mcpServers": {
    "scholarx": {
      "url": "http://localhost:8004/scholarx/mcp"
    }
  }
}

Deploying the Streamable-HTTP server via Docker:

docker run -d \
  --name scholarx-mcp \
  -p 8004:8004 \
  -e TRANSPORT=streamable-http \
  -e PORT=8004 \
  -e SCHOLARX_STORAGE_DIR="your_value" \
  -e DEBUG="your_value" \
  -e PYTHONUNBUFFERED="your_value" \
  -e SERVICENOW_INSTANCE="your_value" \
  -e SERVICENOW_USERNAME="your_value" \
  -e OSF_TOKEN="your_value" \
  -e S2_API_KEY="your_value" \
  -e NCBI_API_KEY="your_value" \
  -e SERVICENOW_PASSWORD="your_value" \
  knucklessg1/scholarx:latest

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Agent

This repository features a fully integrated Pydantic AI Graph Agent. It communicates over the Agent Control Protocol (ACP) and interacts seamlessly with the Agent Web UI (AG-UI) and Terminal interface.

Running the Agent CLI

To start the interactive command-line agent:

# Set credentials
export SCHOLARX_STORAGE_DIR="your_value"
export DEBUG="your_value"
export PYTHONUNBUFFERED="your_value"
export SERVICENOW_INSTANCE="your_value"
export SERVICENOW_USERNAME="your_value"
export OSF_TOKEN="your_value"
export S2_API_KEY="your_value"
export NCBI_API_KEY="your_value"
export SERVICENOW_PASSWORD="your_value"

# Run the agent server
scholarx-agent --provider openai --model-id gpt-4o

Docker Compose Orchestration

The following docker/agent.compose.yml configures the Agent, Web UI, and Terminal Interface together:

version: '3.8'

services:
  scholarx-mcp:
    image: knucklessg1/scholarx:latest
    container_name: scholarx-mcp
    hostname: scholarx-mcp
    restart: always
    env_file:
      - ../.env
    environment:
      - PYTHONUNBUFFERED=1
      - HOST=0.0.0.0
      - PORT=8004
      - TRANSPORT=streamable-http
    ports:
      - "8004:8004"
    healthcheck:
      test: ["CMD", "python3", "-c", "import urllib.request; urllib.request.urlopen('http://localhost:8004/health')"]
      interval: 30s
      timeout: 10s
      retries: 3
      start_period: 10s
    logging:
      driver: json-file
      options:
        max-size: "10m"
        max-file: "3"

  scholarx-agent:
    image: knucklessg1/scholarx:latest
    container_name: scholarx-agent
    hostname: scholarx-agent
    restart: always
    depends_on:
      - scholarx-mcp
    env_file:
      - ../.env
    command: [ "scholarx-agent" ]
    environment:
      - PYTHONUNBUFFERED=1
      - HOST=0.0.0.0
      - PORT=9600
      - MCP_URL=http://scholarx-mcp:8004/mcp
      - PROVIDER=${PROVIDER:-openai}
      - MODEL_ID=${MODEL_ID:-gpt-4o}
      - ENABLE_WEB_UI=True
      - ENABLE_OTEL=True
    ports:
      - "9600:9600"
    healthcheck:
      test: ["CMD", "python3", "-c", "import urllib.request; urllib.request.urlopen('http://localhost:9600/health')"]
      interval: 30s
      timeout: 10s
      retries: 3
      start_period: 10s
    logging:
      driver: json-file
      options:
        max-size: "10m"
        max-file: "3"

Detailed graph node architecture explanations, custom skill configurations, and agentic trace guides are available in docs/agent.md.

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Security & Governance

Built directly upon the enterprise-ready agent-utilities core, standard security parameters are fully supported:

Access Control & Policy Enforcement

• Eunomia Policies: Fine-grained, policy-driven tool authorization. Supports none, local embedded (mcp_policies.json), or centralized remote modes.
• OIDC Token Delegation: Compliant with RFC 8693 token exchange for flowing authenticating user credentials from Web UI / ACP → Agent → MCP.
• Scoped Credentials: Execution context runs restricted to the specific caller identity.

Runtime Security Grid

Feature	Functionality	Enablement
Tool Guard	Sensitivity inspection with human-in-the-loop validation	Enabled by default
Prompt Injection Defense	Input scanning, repetition monitoring, and recursive loop blocks	Enabled by default
Context Safety Guard	Stuck-loop detectors and contextual overflow preemptive alerts	Enabled by default

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Environment Variables

The application can be configured using the following environment variables:

Variable	Type	Default	Description
HOST	String	0.0.0.0	Host IP address to bind the servers to.
PORT	Integer	8004	Port number to run the servers on.
TRANSPORT	String	stdio	MCP transport type (stdio, streamable-http, sse).
AUTH_TYPE	String	none	Authentication type for access control (none, basic, custom).
DEFAULT_AGENT_NAME	String	ScholarX Agent	Custom display name for the Pydantic AI Graph Agent.
ENABLE_OTEL	Boolean	True	Enable OpenTelemetry tracing and exports.
EUNOMIA_TYPE	String	none	Eunomia policy evaluation mode (none, embedded, remote).
EUNOMIA_POLICY_FILE	String	mcp_policies.json	Path to the local Eunomia policy configuration file.
EUNOMIA_REMOTE_URL	String		Centralized Eunomia server endpoint.
SCHOLARX_STORAGE_DIR	String	~/.local/share/scholarx/papers	Directory path where downloaded PDF papers are cached.
DEBUG	Boolean	False	Enable verbose debugging mode.
PYTHONUNBUFFERED	Integer	1	Forces stdout and stderr to be unbuffered.
SERVICENOW_INSTANCE	String		ServiceNow instance base URL.
SERVICENOW_USERNAME	String		ServiceNow account username.
SERVICENOW_PASSWORD	String		ServiceNow account password.
OSF_TOKEN	String		API Access Token for OSF integration.
S2_API_KEY	String		Semantic Scholar API Key to bypass public rate limits.
NCBI_API_KEY	String		NCBI API Key for PubMed Central (PMC) queries.
SEARCHTOOL	Boolean	True	Toggle to enable/disable Search MCP tool category.
DISCOVERYTOOL	Boolean	True	Toggle to enable/disable Discovery MCP tool category.
STORAGETOOL	Boolean	True	Toggle to enable/disable Storage MCP tool category.

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Installation

Install the Python package locally:

# Using uv (highly recommended)
uv pip install scholarx[all]

# Using standard pip
python -m pip install scholarx[all]

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Repository Owners

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Contribute

Contributions are welcome! Please ensure code quality by executing local checks before submitting pull requests:

• Format code using ruff format .
• Lint code using ruff check .
• Validate type-safety with mypy .
• Execute test suites using pytest