problems parsing output from latest obographs library

[balhoff]

In GO, we are trying to update to the latest obographs in ROBOT. We have been using owltools, which uses an older obographs release. We noticed this change, which currently upsets the ontobio JSON reader:

owltools:

{
      "definedClassId" : "http://purl.obolibrary.org/obo/GO_0101013",
      "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0005248", "http://purl.obolibrary.org/obo/GO_0008381" ],
      "restrictions" : [ ]
}

robot:

{
      "definedClassId" : "http://purl.obolibrary.org/obo/GO_0101013",
      "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0005248", "http://purl.obolibrary.org/obo/GO_0008381" ]
}

owltools outputs an empty restrictions array, but the newer obographs leaves it out. As pointed out by @cmungall in my issue at obographs, all properties in a JSON schema are optional unless marked required. So ontobio should be able to handle a missing restrictions and treat it as an empty list. I think there are other properties that will trigger this, so the same fix should be applied to all list handling.

cc @kltm @sierra-moxon

[kltm]

Shadowed as "draft" item in: https://github.com/orgs/geneontology/projects/135 Tagging @pgaudet

[balhoff]

For the ontology build we need to move to the latest version of ROBOT, to stay compatible with the latest Protege, and also to take advantage of new OBO format features which impact several different open issues in the ontology repo. Currently we use owltools for this step (the JSON change is actually in older versions of ROBOT as well), but to help manage technical debt we would like to eliminate owltools from the ontology build.