Nanopub Query

Nanopub Query is the second-generation query service for nanopublications.

Available Instances

You can check out Nanopub Query at these instances:

• https://query.knowledgepixels.com/
• https://query.np.trustyuri.net/
• https://query.np.kpxl.org/

Repos and Triples

Each nanopublications is loaded into different repos in the form of RDF4J triple stores. There are these general repos:

• meta: Stores some specific "admin-graph metadata" of the nanopublications (see below), but not the nanopublications themselves
• full: Stores all nanopublications in full and their admin-graph metadata (this is not scalable on the long term, so will be deprecated in the medium-term future)
• last30d: Stores all nanopublications of the last 30 days and their admin-graph metadata
• text: Stores all nanopublications for full-text search
• admin: Stores some further admin info, such as the full pubkeys for their hash values
• empty: Empty repo from which other repos can be accessed via the SPARQL service keyword

On top of that, there are these specific repos:

• pubkey: For each public key used to sign a nanopublication, a separate repo is created
• type: For each nanopub type, a separate repo is created too

Two admin graphs (npa:graph and npa:networkGraph) are created with metadata about the nanopublications. The admin triple table shows the details.

General Setup

Get pre-packaged data (optional):

$ wget https://zenodo.org/records/14260335/files/rdf4j-20241202.tar.gz
$ tar -xzf rdf4j-20241202.tar.gz

Init directories:

$ ./init-dirs.sh

Check docker-compose.yml and make any adjustments in a new file docker-compose.override.yml.

Connection to Publishing Layer

In the near future, Nanopub Query will get its initial nanopublications and regular updates via the Nanopub Registry, which isn't yet available.

So, currently, it relies on a small autofetch script to get the initial nanopublications, and then needs to connect to a nanopub-server instance to get regular updates.

To receive updates from such a nanopub-server instance, e.g. via signed-nanopub-services, that nanopub-server needs to be configured to send new nanopublications to the Nanopub Query instance like this:

services:
  server:
    environment:
      - 'NPS_POST_NEW_NANOPUBS_TO=https://query.example1.com/ https://query.example2.com/'

Deadlock Problem Workaround

There is a deadlock problem with RDF4J (details), which requires some specific web server configuration to work around it. Specifically, concurrent requests per repo have to be avoided, with a configuration like in this nginx example.

Launch

Start with Docker Compose:

$ sudo docker compose up -d

License

Copyright (C) 2024 Knowledge Pixels

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see https://www.gnu.org/licenses/.