Virtuoso-httpd docker image with data loader

This repository is made to create a docker image that can run both Virtuoso and Apache web server in one container. It also facilitate data import into Virtuoso using custom-made bash script. The docker image also includes SNORQL, a SPARQL explorer interface to facilitate querying the knowledge graph.

The WikiPathways SPARQL endpoint and SNORQL UI run on http://81.169.200.64:8895/sparql and http://81.169.200.64:8085.

Step 1 - Clone this repository

git clone https://github.com/wikipathways/virtuoso-httpd-docker.git

cd virtuoso-httpd-docker

Step 2 - Build the docker image

docker build -t virtuoso-httpd .

Step 3 - Run the docker container

Before running the container, make sure to create two folders: the first "PATH_TO_VIRTUOSO_DATA_FOLDER" is to store Virtuoso databases so you don't lose the graphs after importing them when the docker image is stopped (i.e. persistence). The second folder "PATH_TO_VIRTUOSO_IMPORT_FOLDER" is the location of RDF files that need to be imported into Virtuoso (the data loading tool will look for RDF files in this location which is mapped to /import inside the docker image).

Also, don't forget to replace "PASSWORD_HERE" with the password you set for Virtuoso.

For the first time you run the container, the password you should use is "dba". Then, you can change it from the web interface "http://localhost:8890" and replace it in the next run for the container.

Also, if you don't know the default graph URI, don't include it in your run command. Otherwise, the queries will not work against the endpoint.

docker run --rm --name wikipathways-virtuoso-httpd \
    -p 8895:8890 -p 1115:1111 \
    -p 8085:80 -p 449:443 \
    -e DBA_PASSWORD=PASSWORD_HERE \
    -e SPARQL_UPDATE=true \
    -e SNORQL_ENDPOINT=https://sparql.wikipathways.org/sparql \
    -e SNORQL_EXAMPLES_REPO=https://github.com/wikipathways/SPARQLQueries \
    -e SNORQL_TITLE="WikiPathways Snorql UI" \
    -v /home/MarvinMartens/WikiPathways/import:/import \
    -v /home/MarvinMartens/WikiPathways/data:/data \
    -d virtuoso-httpd

Step 4 (Optional) - Loading data

If you need to import RDF data into Virtuoso, just make sure the RDF file is in the directory you already mapped to /import in the run command (step 3). Then run the following command from terminal (make sure to change to file name and the graph IRI where you want to load the data under in Virtuoso):

docker exec -i virtuoso-httpd bash -c "/load.sh FILE_TO_IMPORT GRAPH_IRI /data/load.log dba"

Troubleshooting

If the SPARQL endpoint is down, try to stop and start the Docker container using

sudo docker stop wp-virtuoso-httpd
sudo docker start wp-virtuoso-httpd

If the RDF is not working correctly, try reloading the data or data of the previous month using the documentation at https://github.com/marvinm2/WikiPathwaysLoader