Phyloreferencing Test Suite

Usage

py.test tests/

Description

This test suite is designed to be used to validate the outputs of the phylo2owl.py script. It does this in two ways:

1. By comparing an output file with its expected output, and reporting an error if they differ.
2. By validating an output OWL file against a set of SHACL shapes.

You can examine previous runs of this test suite on Travis-CI.

Test scripts

• conftest.py: A py.test configuration file that sets up the fixtures.
• test_execute.py: Test whether the phylo2owl.py script can be executed at all.
• test_alt_inputs.py: Test whether alternate input formats (NEXUS and NeXML) produce the expected outputs.
• test_owl_output.py: Test whether the OWL produced by phylo2owl.py is identical to the expected output, and whether it is syntactically correct RDF/XML.
• test_shacl.py: Test whether every expected output OWL file can be validated against a generic Node shape, as well as any file-specific SHACL shapes that have been written.
• test_shacl_shapes.py: A self-contained file that deliberately constructs phylogenies that should fail the generic Node shape, and then tests to make sure they actually do.