Write tests for validating

[nsbgn]

We need some tests for validating that our ontologies and workflow files are sane. This issue will track the tests that make sense to have.

• Check whether the files are consistent with the workflow schema.
• Every tool must have a corresponding description.
• Every tool in a scenario workflow must exist in the tools ontology.
• Check whether blank nodes are never used in multiple tools.
• All blank nodes should only ever be reused in the same supertool workflow.
• Every signature should have at least one input and one output.
• Every abstract tool should either be implemented by a concrete tool, or it should be a supertool, or it should be implemented by a supertool. An abstract tool is a tool that has a semantics in terms of a CCD signature; a supertool might not have a CCD signature, in which case it must implement an abstract tool.
• Every node (indicated by wf:edge) in a workflow should have a tool (indicated by wf:applicationOf).

[nsbgn]

The above tests are now implemented in [test.py] using the nose2 testing framework. I also tried pytest and plain unittest, but I found that these were more of a hassle to use for generating separate tests for each node/workflow (which helps to know where the error occurs). unittest's TestCase.subTest came close, but would have required more boilerplate. In the end, I wrote the @nodes decorator to make use of node2's test generator functionality, which ends up looking like this:

@nodes(graph.subjects(RDF.type, TOOLS.ToolCombination))
def test_supertool_blank_nodes_never_reused(self, tool: Node):
    for step in graph.objects(tool, WF.edge):
        self.assertEqual([tool], list(graph.subjects(WF.edge, step)))

This seems to me the cleanest way to go about it. Please feel free to add tests in the same style, since clearly, there are a great number of tests we could possibly do and it is hard to know which are important.

In fact, it's probably wise to use a dedicated RDF schema validator for this purpose, as I mentioned in the comment at the top of the test file; cf. https://www.w3.org/2012/12/rdf-val/SOTA; http://book.validatingrdf.com/; https://shex.io/shex-primer/; https://www.w3.org/TR/shacl/. We can do that later, but for now, this should suffice.

148 out of the 627 tests currently fail. I will look into the reason later.