Nanopub Services

The nanopub services are a collection of Docker containers that include a nanopub server, a query/API service based on Virtuoso and grlc, and a Linked Data Fragments server.

Setup

The nanopublication services can be setup by following these four steps. It assumes that your server has a recent version of Docker installed.

Step 1: Clone this repository

Clone this repository in the server where you want to deploy the nanopub services:

$ git clone https://github.com/peta-pico/nanopub-services.git
$ cd nanopub-services

Step 2: Setup the data directory

The data will be stored in a directory called data in your nanopub-services directory (around 32 GB, and growing). If the data should be stored somewhere else, e.g. because of performance or space reasons, you should make a symbolic link like this (run this and the following commands in the nanopub-services directory):

$ ln -s /location/where/data/should/be/stored data

These services will automatically sync with the network, but to speed things up, you can download and extract pre-built database packages:

$ wget https://zenodo.org/record/5515280/files/mongodb0.tar.gz
$ tar -xvzf mongodb0.tar.gz && rm mongodb0.tar.gz

$ wget https://zenodo.org/record/5515280/files/virtuoso.tar.gz
$ tar -xvzf virtuoso.tar.gz && rm virtuoso.tar.gz

Step 3: Configure web server and services

Configure your web server to forward three subdomains to the three public-facing nanopub services server, grlc, and ldf. See the configuration template for Nginx and Apache. Replace YOUR.SERVER.DOMAIN with your actual server domain (e.g. example.com or mygroup.example.com).

The services themselves also need some small configuration. For that, make a copy of the docker-compose.override template:

$ cp docker-compose.override.yml.template docker-compose.override.yml

In the file docker-compose.override.yml replace http://server.np.YOUR.SERVER.DOMAIN with the actual URL for the server container on your web server (e.g. http://server.np.example.com/), and similarly with ldf. These URLs need to end with a slash /, and they need to match the domains defined above. For grlc, you also need to specify the server, but here just the plain server name without http:// and without a final slash.

(If you need to do any other changes to the configuration found in docker-compose.yml, just add them to the file docker-compose.override.yml. Directly editing docker-compose.yml can lead to problems when updating.)

Step 4: Start services

Now you should be able to start the services with Docker Compose:

$ docker-compose up -d

You should now be able to access the services via the subdomains defined above (you might have to restart your web server, e.g. with service nginx restart or service apache2 restart).

Updating

Run this to update the services:

$ ./update.sh

This will shutdown the services, update everything, and start them up again. If you see the message "Successfully updated" in the end, then probably everything went well.

Services

Nanopub Server

A service to publish and individually retrieve nanopublications.

grlc Nanopub API

The grlc-based nanopub-api running on all the published nanopublications.

Nanopub LDF Server

A service providing Linked Data Fragments (LDF) access to all the published nanopublications.