Sqlite Literature Management Fastmcp Mcp Server

Universal Source Management System

A lightweight FastMCP server for managing literature, notes, entity links, and reading-list resources in a local SQLite database.

Current Scope

This repository provides:

• Local SQLite-backed source management
• Notes attached to sources
• Entity links between sources and named concepts
• Read-only database inspection tools
• MCP resources for source lookup and reading lists
• Normalized identifier storage with a transitional JSON cache

It does not integrate with MCP Memory Server or an external memory graph.

Quick Start

1. Create a database from the current schema:

sqlite3 sources.db `
- `source://by-identifier//`
- `reading-list://unread`
- `reading-list://reading`
- `entity://`

## Schema Notes

The current schema centers on four tables:

- `sources`
- `source_identifiers`
- `source_notes`
- `source_entity_links`

`sources.identifiers` is still kept as a transitional JSON cache, but identifier lookups now use `source_identifiers`.

Supported identifier types:

- `semantic_scholar`
- `doi`
- `arxiv`
- `openalex`
- `pmid`
- `isbn`
- `url`

Supported entity relation types:

- `discusses`
- `introduces`
- `extends`
- `evaluates`
- `applies`
- `critiques`
- `supports`
- `contradicts`
- `refutes`

Lightweight provenance fields live on `sources`:

- `provider`
- `discovered_via`
- `discovered_at`

The schema now uses `PRAGMA user_version = 3`.

## Migration

If you have a version 0 or version 1 database, apply:

```bash
sqlite3 /path/to/sources.db < migrations/2026-03-09__normalize-identifiers.sql
sqlite3 /path/to/sources.db < migrations/2026-03-09__expand-entity-relation-types.sql

If you already migrated to version 2, apply:

sqlite3 /path/to/sources.db < migrations/2026-03-09__expand-entity-relation-types.sql

These migrations:

• adds source_identifiers
• backfills identifier rows from the legacy JSON column
• adds provenance fields
• expands source_entity_links.relation_type to include supports, contradicts, and refutes
• updates PRAGMA user_version to 3

The server checks PRAGMA user_version on connection and will reject older databases until they are migrated.

Package Layout

The implementation is organized under sqlite_lit_server/:

• app.py creates the FastMCP instance and registers tools/resources
• db.py owns connection setup and schema-version checks
• repository.py keeps SQL-heavy lookup logic close to the data layer
• tools_admin.py, tools_sources.py, and tools_entities.py hold the MCP tools
• resources.py defines the MCP resources

sqlite-paper-fastmcp-server.py remains as a thin compatibility shim.

Batch Import Sources

add_sources is the batch import entrypoint for new sources. It accepts one argument named sources, where each item is:

[title, source_type, identifier_type, identifier_value, initial_note]

initial_note must be either null or an object with both title and content.

Supported source_type values:

• paper
• webpage
• book
• video
• blog

Supported identifier_type values:

• semantic_scholar
• doi
• arxiv
• openalex
• pmid
• isbn
• url

Duplicate handling:

• Exact identifier matches return Source already exists together with the existing source payload.
• Title-based fuzzy matches return Potential duplicates found. Please verify or use add_identifiers if these are the same source.
• Successful batch writes return one result per input item in the same order as the request.

Example MCP/JSON payload:

{
  "sources": [
    [
      "Attention Is All You Need",
      "paper",
      "arxiv",
      "1706.03762",
      {
        "title": "Initial thoughts",
        "content": "Transformers start here."
      }
    ],
    [
      "OpenAlex Import",
      "paper",
      "openalex",
      "W1234567890",
      null
    ]
  ]
}

Example Python call:

add_sources([
    (
        "Attention Is All You Need",
        "paper",
        "arxiv",
        "1706.03762",
        {
            "title": "Initial thoughts",
            "content": "Transformers start here.",
        },
    ),
    (
        "OpenAlex Import",
        "paper",
        "openalex",
        "W1234567890",
        None,
    ),
])

The same tool payloads work whether you start the server locally or through Docker with docker compose run --rm sqlite-lit-mcp.

Batch Write Conventions

Plural write tools accept lists and return a per-input result list in the same order. Related batch tools include:

• add_notes
• add_identifiers
• update_status
• link_to_entities

Example Usage

Add another identifier:

add_identifiers([
    (
        "Attention Is All You Need",
        "paper",
        "arxiv",
        "1706.03762",
        "semantic_scholar",
        "204e3073870fae3d05bcbc2f6a8e263d9b72e776",
    ),
])

Read a source resource:

source://by-identifier/arxiv/1706.03762

Source & license

This open-source MCP server is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: zongmin-yu
• Source: zongmin-yu/sqlite-literature-management-fastmcp-mcp-server
• License: MIT

Install and usage instructions live in the source repository linked above.