wikipathways / WikiPathwaysCurator

Unit tests that validate the WikiPathways content and support the curation of the knowledge base.

Unit tests for curating WikiPathways using SPARQL.

This code base runs a number of SPARQL queries wrapped in JUnit files to detect issues in the GPML content, by assessing the WPRDF.

License

MIT license

Running the tests

First, you need to copy WikiPathways RDF file into a local folder, e.g. /tmp/doesntexist/, and then you can run the tests with by setting a few options:

mvn install -DOPSWPRDF=/tmp/doesntexist -DSUBSETPREFIX=wp9

Or run a specific test:

mvn install -DOPSWPRDF=/tmp/doesntexist -DSUBSETPREFIX=wp9 -Dtest=nl.unimaas.bigcat.wikipathways.curator.EnsemblGenes

Selection subsets of tests

JUnit was used to define groups of tests, which can be included and excluded on runtime. For this, the junit5.excludeGroups and junit5.groups options can be used. For example, to only run the VoID header file tests, do:

mvn install -DOPSWPRDF=/tmp/doesntexist -DSUBSETPREFIX=wp9 -Djunit5.groups=void

SPARQL end point

If you wish to run the tests agains a SPARQL end point (e.g. http://sparql.wikipathways.org/), then you run:

mvn install -DSPARQLEP=https://sparql.wikipathways.org/sparql

If you have the data loaded into a local Blazegraph installation, then the command looks like:

mvn install -DSPARQLEP=http://localhost:9999/blazegraph/sparql