Improve federated SPARQL query testing to use docker and add virtuoso test #789
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…d a blazegraph triplestore to test federating querying to the bioregistry SPARQL mapping service. Added a simpler SPARQL query to test federated querying, since the original query using VALUES fails on Virtuoso The docker stack is now started in the tests github action A section to describe how to run the tests has been added at the bottom of the README, you might want to move it to a more consistent place
…from workflow, and improve readme docs for tests
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@cthoyt I improved the federated query testing to use docker and added virtuoso
The
docker compose upstarts a virtuoso, blazegraph and bioregistry. There is a little catch with virtuoso, you need to run an additional command the first time you start it to enable federated queriesI added an expandable section under installations to explain how to start the stack with docker and enable federated query in virtuoso
I also added a step to start the docker compose stack directly with
docker compose up -din the GitHub action workflow for ubuntu (the images we use are not available on ARM windows apparently), all tests are passing: https://github.com/vemonet/bioregistry/actions/runs/4525145166According to the GitHub action workflow run logs the
test_sparql.pytests are passing on ubuntu, and skipped as expected on windows:Note that the original query you use with VALUES fails on Virtuoso, so I added a simpler SPARQL query to test the most basic federated querying works, then we can iterate to fix issues related to specific query patterns
The csv parsing was failing due to virtuoso adding double quotes, so I used python built-in
csv.DictReader()to parse it. And virtuoso was not acceptingapplication/xml, so I usedapplication/sparql-results+xmlwhich works on blazegraph and virtuoso