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.
The nanopublication services can be setup by following these four steps. It assumes that your server has a recent version of Docker installed.
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
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
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.)
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).
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.
A service to publish and individually retrieve nanopublications.
The grlc-based nanopub-api running on all the published nanopublications.
A service providing Linked Data Fragments (LDF) access to all the published nanopublications.