atomic-server

https://user-images.githubusercontent.com/2183313/139728539-d69b899f-6f9b-44cb-a1b7-bbab68beac0c.mp4

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

Atomic-server is a graph database server for storing and sharing Atomic Data. Demo on atomicdata.dev

• ⚛️ Dynamic schema validation / type checking using Atomic Schema. Combines safety of structured data with the
• 🚀 Fast (1ms responses on my laptop)
• 🪶 Lightweight (15MB binary, no runtime dependencies)
• 💻 Runs everywhere (linux, windows, mac, arm)
• 🌐 Embedded server with support for HTTP / HTTPS / HTTP2.0 and Built-in LetsEncrypt handshake.
• 🎛️ Browser GUI included powered by atomic-data-browser. Features dynamic forms, tables, authentication, theming and more.
• 💾 Event-sourced versioning / history powered by Atomic Commits
• 🔄 Synchronization using websockets: communicates state changes with a client. Send a wss request to /ws to open a webscocket.
• 🧰 Many serialization options: to JSON, JSON-AD, and various Linked Data / RDF formats (RDF/XML, N-Triples / Turtle / JSON-LD).
• 🔎 Full-text search with fuzzy search and various operators, often <3ms responses.
• 📖 Pagination, sorting and filtering using Atomic Collections
• 🔐 Authorization (read / write permissions) and Hierarchical structures powered by Atomic Hierarchy
• 📲 Invite and sharing system with Atomic Invites

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

README Contents

• When should you use this
• When not to use this
• Installation & getting started
• Initial setup and configuration
• Usage
• Testing
• Performance benchmarking
• FAQ & Troubleshooting

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)

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 as binary

After installing from cargo install atomic-server or as a binary, run atomic-server. Run atomic-server --help to learn more about the available commands, such as export, import and various flags.

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

```sh

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

If you don't need HTTPS (or don't have OpenSSL available on your device)

cargo run --no-default-features ```

Troubleshooting compiling from source:

```sh

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

• You can configure the server by passing arguments (see atomic-server --help), or by setting ENV variables.
• The server loads the .env from the current path by default. Create a .env file from the default template in your current directory with atomic-server setup-env.
• 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.

You can do this by passing these flags:

Run the server: atomic-server --https --email some@example.com --domain example.com.

You can also set these things using a .env or by setting them some other way.

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. They are stored in your .config/atomic/ dir.

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.

```sh

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. Also, read the Atomic Data Docs to learn more about Collections, Commits, JSON-AD and other concepts used here.

Testing

```sh

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

cargo test --all ```

Performance benchmarking

```sh

Install drill

cargo install drill drill -b benchmark.yml --stats ```

FAQ & Troubleshooting

Can / should I create backups?

Yes! You should. Especially before installing a newer Atomic-Server version, it might be imcompatible with the previous database model and could corrupt the database. Run atomic-server export to create a backup in your ~/.config/atomic/backups folder. Import them using atomic-server import -p ~/.config/atomic/backups/${date}.json.

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

You can run atomic-server --initialize 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.

I get a failed to retrieve error when opening

Try re-initializing atomic server atomic-server --initialize.