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.

Related MCP server: ClickUp Operator

Quick Start

1. Create a database from the current schema:

sqlite3 sources.db < create_sources_db.sql

2. Install the FastMCP server with your database path:

fastmcp install sqlite-paper-fastmcp-server.py --name "Source Manager" -e SQLITE_DB_PATH=/path/to/sources.db

3. Optional: use the checked-in demo fixture at examples/sources.db.

Docker

This server can be packaged as a containerized stdio MCP server.

Build the image:

docker build -t sqlite-lit-mcp .

Run it with a persistent SQLite volume:

mkdir -p data
docker run --rm -i \
  -e SQLITE_DB_PATH=/data/sources.db \
  -v "$(pwd)/data:/data" \
  sqlite-lit-mcp

Notes:

• The image defaults SQLITE_DB_PATH to /data/sources.db.

• If the database file does not exist, the container initializes it from create_sources_db.sql.

• If you are mounting an older database, apply the required migrations under migrations/ before starting the server.

• This repo runs as a stdio MCP server, so there is no HTTP port to expose by default.

With Docker Compose:

docker compose run --rm sqlite-lit-mcp

Current Tool Surface

Implemented tools:

• read_query

• list_tables

• describe_table

• get_table_stats

• get_database_info

• vacuum_database

• add_sources

• add_notes

• update_status

• add_identifiers

• link_to_entities

• get_source_entities

• update_entity_links

• remove_entity_links

• get_entity_sources

Implemented resources:

• source://<id>

• source://by-identifier/<type>/<value>

• reading-list://unread

• reading-list://reading

• entity://<entity_name>

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:

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