Updated to new RO term and relaxed error handling for missing ext rel

[dustine32]

For #572.

I also changed how missing extension relation errors are handled. This change now skips translating only the offending extension (e.g. RO:0002491(GO:0098768)) whereas the old code would skip translating the entire annotation model for the gene. The error is still being reported out.

[kltm]

@dustine32 Just to clarify, previously, as it was a raise, an error would cause it to fail and return non-zero, whereas this would mean that it adds to a complaint queue that gets output? Does it return a non-zero status?

[dustine32]

Sorry @kltm, one correction to what I said above. The "before" code used to skip translating the entire model (so, all annotations for a gene) if a single extension relation was not in the relations lookup.

To (hopefully) answer your question, the raise errors.GocamgenException in the "before" code would be caught at a higher level here: https://github.com/biolink/ontobio/blob/f00b3d76a3c909ab720d6c13849771bc9a764f6b/ontobio/rdfgen/gocamgen/gocam_builder.py#L89-L90 Essentially this raise is a "bail out of translating model" that should then cause the gpad2gocams process to simply move on to translating the next model in a GPAD. This raise by itself shouldn't stop the process with a non-zero status and, ideally, the gpad2gocams cmd will always return 0 status. The new error handling in this PR shouldn't return a non-zero status either. Hope this helps!

[kltm]

Okay, makes sense to me--thank you for the explanation.

[dustine32]

@kltm Whoa, awesome!