atomic-server

Status: Alpha. Not ready for production time. Prone to changes and corrupt databases when upgrading. Changelog

The easiest way to share Atomic Data on the web. atomic-server is a graph database server for storing and sharing typed linked data. Demo on atomicdata.dev

• No runtime dependencies, fast, runs on all platforms
• Embedded HTTP / HTTPS / HTTP2.0 server. Built-in LetsEncrypt handshake.
• Serialization to JSON, JSON-AD, and various Linked Data / RDF formats (RDF/XML, N-Triples / Turtle / JSON-LD).
• Dynamic schema validation / type checking using Atomic Schema
• Event-sourced versioning / history powered by Atomic Commits
• Pagination, sorting and filtering using Atomic Collections
• Authorization (read / write permissions) and Hierarchical structures powered by Atomic Hierarchy
• Invite / sharing system with Atomic Invites
• Supports querying, sorting and filtering using Atomic Collections
• Uses atomic-data-browser as a GUI / front-end, which offers dynamic forms, tables, authentication and more.

Powered by Rust, atomic-lib, actix-web, sled and more.

When should you use this

• You want to make (high-value) datasets as easily accessible as possible
• You want to specify and share a common vocabulary / ontology / schema for some specific domain or dataset. Example classes here.
• You want to use and share linked data, but don't want to deal with most of the complexities of RDF, SPARQL, Triple Stores, Named Graphs and Blank Nodes.
• You are interested in re-decentralizing the web or want want to work with tech that improves data ownership and interoperability.
• You like living on the edge (this application is not production ready)

CLI commands

FLAGS:
    -h, --help       Prints help information
    -i, --init       Recreates the `/setup` Invite for creating a new Root User. Also re-runs various populate commands,
                     and re-builds the index.
    -r, --reindex    Rebuilds the index (can take a while for large stores).
    -V, --version    Prints version information

SUBCOMMANDS:
    export    Create a JSON-AD backup of the store.
    help      Prints this message or the help of the given subcommand(s)
    import    Import a JSON-AD backup to the store. Overwrites Resources with same @id.

When not to use this

• If you need stability or reliability, look further (for now).
• You're dealing with non-public / private data. As of now, this server does not have methods to prevent access to content.
• Complex query requirements. Check out NEO4j, Apache Jena or maybe TerminusDB.

Installation & getting started

You can run atomic-server in four ways:

• From a published binary (probably the quickest)
• Using docker
• Using Cargo from crates.io: cargo install atomic-server
• Manually from source

When you're running atomic-server, go to Initial setup and configuration

Run using docker

The dockerfile is located in the project root, above this server folder.

• Run: docker run -p 80:80 -p 443:443 -v atomic-storage:/atomic-storage joepmeneer/atomic-server
• If you want to update, run docker pull joepmeneer/atomic-server and docker should fetch the latest version.

Install from source

# Clone this repoo
git clone git@github.com:joepio/atomic-data-rust.git
cd atomic-data-rust/server
# Optional, but recommended: Create a new .env using the template.
cp default.env .env
# Run the server. It creates a store in ~/.config/atomic/db by default
cargo run
# Or tun the extra-cool desktop version with a presence in your app tray
cargo run --features desktop

Troubleshooting compiling from source:

# If pkg-config or libssl-dev is not installed, make sure to install them
sudo apt-get install -y pkg-config libssl-dev --fix-missing

Initial setup and configuration

• The server loads the .env from the current path by default. Use the default.env from this repo as a template and for reference.
• If you want to run Atomic Server on your own domain, you'll probably want to set ATOMIC_DOMAIN, ATOMIC_HTTPS and ATOMIC_EMAIL in the .env (see HTTPS setup below).
• After running the server, check the logs and take note of the Agent Subject and Private key. You should use these in the atomic-cli and atomic-data-browser clients for authorization.
• A directory is made: ~/.config/atomic, which stores your newly created Agent keys, your data, the HTTPS certificates and a folder for public static files.
• Visit http://localhost/setup to register your first (admin) user. You can use an existing Agent, or create a new one.

HTTPS Setup

You'll probably want to make your Atomic Data available through HTTPS. You can use the embedded HTTPS / TLS setup powered by LetsEncrypt, acme_lib and rustls. To setup HTTPS, we'll need to set some environment variables. Open .env and set:

ATOMIC_EMAIL=youremail@example.com
ATOMIC_DOMAIN=example.com
ATOMIC_HTTPS=true

Run the server: cargo run. Make sure the server is accessible at ATOMIC_DOMAIN at port 80, because Let's Encrypt will send an HTTP request to this server's /.well-known directory to check the keys. It will now initialize the certificate. Read the logs, watch for errors.

HTTPS certificates are automatically renewed when the server is restarted, and the certs are 4 weeks or older.

Usage

There are three ways to interact with this server:

• GUI: Use the atomic-data-browser JS frontend by visiting localhost.
• API: Check out ./example_requests.http for various HTTP requests to the server. Also, read the docs. You can also try the react boilerplate to build your own front-end app using @tomic/lib and @tomic/react.
• CLI: The atomic-cli terminal app

Use atomic-cli as client

atomic-cli is a useful terminal tool for interacting with atomic-server. It makes it easy to query and edit Atomic Data from the command line. Check it out.

API

You can fetch individual items by sending a GET request to their URL.

# Fetch as JSON-AD (de facto standard for Atomic Data)
curl -i -H "Accept: application/ad+json" https://atomicdata.dev/properties/shortname
# Fetch as JSON-LD
curl -i -H "Accept: application/ld+json" https://atomicdata.dev/properties/shortname
# Fetch as JSON
curl -i -H "Accept: application/json" https://atomicdata.dev/properties/shortname
# Fetch as Turtle / N3
curl -i -H "Accept: text/turtle" https://atomicdata.dev/properties/shortname

Check out ./example_requests.http for more things that you can do.

Testing

# This also makes sure that cli and server work, plus it test the db feature
cargo test --all

Performance benchmarking

# Install drill
cargo install drill
drill -b benchmark.yml --stats

FAQ

I lost the key / secret to my Root Agent, and the /setup invite is no longer usable! What now?

You can run atomic-server --init to recreate the /setup invite. It will be reset to 1 usage.

How do I migrate my data to a new domain?

There are no helper functions for this, but you could atomic-server export your JSON-AD, and find + replace your old domain with the new one. This could especially be helpful if you're running at localhost and want to move to a live server.

How do I reset my database?

Remove the db folder in your atomic config: rm -rf ~/.config/atomic/db.

How do I make my data private, yet available online?

This is not yet possible. See #13.

Collections are empty / TPF is not working

You might have a problem with your index. Try reindexing using atomic-server --reindex.