Instantiate the IDP Registry backend

Prerequisites

• Docker Desktop

OR

• Docker Engine and Docker Compose

Create a new context for the remote deployment

docker context create ermes --description "ermes" --docker "host=ssh://<user>@ermes"

Set the new context as default

docker context use ermes

Volumes

We now need to create two separate volumes for the two different triplestores. The volumes will be used to store the data of the triplestores. The volumes will be created on the remote machine and will be mounted on the containers on startup.

GraphDB volume:

docker volume create -d local kg-graphdb

Virtuoso volume:

docker volume create -d local kg-virtuoso

Use docker-compose to start the containers

This should download the two remote images (graphdb and virtuoso) and start the containers on the remote machine.

Configuration options can be passed to the containers from the docker-compose.yml file.

docker compose -f docker-compose-kg.yml -p idp-kg up -d

Show logs

docker logs -f kg-graphdb    # For a single container
docker compose logs -f docker-compose-kg.yml logs -f # For all containers

Import pre-saved data into the volumes

If you want to import the pre-saved data into the created volumes, you can use the following commands:

./docker-volume-snapshot.sh restore /projects/volumes_dump/GraphDB.tar.gz kg-graphdb

./docker-volume-snapshot.sh restore /projects/volumes_dump/Virtuoso.tar.gz kg-virtuoso

Import to a remote volume without copying the file to the remote machine

pv <dump>.tar.gz | docker run --rm -v <volume name>:/destination -i busybox tar xzf - -C /destination

Export from a remote volume without copying the file to the local machine

docker run --rm -v <volume name>:/dest -i busybox tar -czvf - -C /dest . > <dump>.tar.gz

Import triples into the triplestores

GraphDB

• Open the GraphDB Workbench at http://localhost:7201
• Create a new repository, just set the name, the rest leave it as default
• Open the repository and go to the Import tab
• Import the triples from the file ./data/*.ttl
• For each of the ttl file, click import and select target graphs Named graphs
• Set the name of the graph to https://idpcentral.org/registry/<name of resource>
• The name of the resource can be one of ped, mobidb or disprot
• Click Import
• Now if you go to the Explore/Graphs overview you should see the imported graphs

Virtuoso

• Open the Virtuoso interface at http://localhost:8890
• Click on Conductor
• Login with the default credentials dba/dba (password can be changed in the docker-compose.yml file)
• Go to Linked Data -> Quad Store Upload
• Upload the file ./data/*.ttl
• For each of the ttl file, set the Named Graph IRI to https://idpcentral.org/registry/<name of resource>
• Click Upload
• Now if you go to the Linked Data -> Graphs -> Graphs you should see the imported graphs

Export volume data as a tar.gz file

./docker-volume-snapshot.sh create kg-graphdb GraphDB.tar.gz 

./docker-volume-snapshot.sh create kg-virtuoso Virtuoso.tar.gz