possibly another problem with the last version of the CL ontology

[gp]

Hello,

I am slowly feeling like the messenger of bad news, hope nobody will shoot me!

Some older script of mine started to make problems recently (basically the program crashes), I could boil down the problem to the following lines:

import owlready2 as owl

clIRI = "http://purl.obolibrary.org/obo/cl.owl"
cl = owl.get_ontology(clIRI).load()
hasExactSynonym = cl.search_one(label='has_exact_synonym')
allSynonyms = {el[1]:el[0] for el in hasExactSynonym.get_relations()}

When I replace the github repo with some cached version of the CL onto I have on my system, the problem disappears, so I suspect there was a recent update of the CL onto which causes the problem.

This is with owlready2 0.15 and 0.16

Let me know if I can help further...
GP

[Jiba]

Hi,

I've just tested your program, but it does not crash with Owlready 0.16. However, I get the following warning :

* Owlready2 * Warning: ignoring cyclic subclass of/subproperty of, involving:
  http://purl.obolibrary.org/obo/CL_0000000
  http://purl.obolibrary.org/obo/GO_0005623

It means that there is an inheritance cycle. It is not supported by Owlready and thus ignored. Since these two classes are also declared as equivalent, it should be safe.

Was this warning the problem you encountered?

Jiba

[gp]

Interesting,
I could reproduce the problem with both python 3.6 and 3.7
These are installation done with anaconda on a windows platform.

This is the last line of the above script which causes the problem.

Could someone reproduce the issue on the same platform?

Cheers,
GP