BioMixer unable to expand concept mappings

[jvendetti]

End user reported that the BioMixer visualization software doesn't allow you to expand mappings for concepts. I was able to reproduce this on Biblioportal:

1. Go to Bibliportal and navigate to any ontology, e.g., BIBFRAME.
2. Open the Classes tab and select the "Agent" class (or any class with mappings).
3. Click the Visualization tab on the right-hand side.
4. Select "mappings neighborhood" from the BioMixer menu bar.

Notice that no mappings are displayed. The Chrome developer console shows the following error, shortened for the sake of brevity:

Thu Apr 04 14:04:51 GMT-700 2019 
SEVERE: Could not expand mapping neighbourhood for http://xmlns.com/foaf/0.1/Agent
Class$S1758: Could not expand mapping neighbourhood for http://xmlns.com/foaf/0.1/Agent
	at Unknown.Zs(0.js@270:74)
	at Unknown.new CE(0.js@87:1021)
	at Unknown._.ke(0.js@435:672)
	at Unknown._.le(0.js@374:794)
	at Unknown._.Nf(0.js@331:1201)
	at Unknown.Fka(0.js@262:672)
	at Unknown._.Wd(0.js@222:227)
	at Unknown.eval(0.js@131:226)
	at Unknown.eval(0.js@235:1284)
	at Unknown.anonymous(http://data.biblio.ontoportal.org:8080/ontologies/BIBFRAME/classes/http%3A%2F%2Fxmlns.com%2Ffoaf%2F0.1%2FAgent/mappings/?format=jsonp&apikey=6700f7bc-5209-43b6-95da-44336cbc0a3a&callback=__gwt_jsonp__.P16.onSuccess@19:1)
Caused by: Class$S1402: failed to transform '{"0":{"id":null, "source":"LOOM", "classes":[{"@id":"http://xmlns.com/foaf/0.1/Agent", "@type":"http://www.w3.org/2002/07/owl#Class", 

I was able to expand the concepts using BioMixer. This problem seems specific to mappings.

[graybeal]

A quick take with limited time:

That failure to transform message is pretty big if you paste the whole thing (I pasted my example below, for AdminMetadata). Scroll right to see the whole JSON for the response.

And it looks like it's an incomplete list of mappings—in the case I had, there was one mapping, to ri:AdminMetadata, but at the end of that mapping—when there should have been an identifier for that mapping, in

{"@vocab":"http://data.bioontology.org/metadata/"}}], "process":null, "@id":"", "@type":"http://data.bioontology.org/metadata/Mapping"}}'

the identifier for the mapping is null. Whereas I think normally in the REST JSON response, there would be an identifier there. So the message further down

Caused by: Class$S98: (TypeError) : Cannot read property 'b' of null

seems consistent with the fact there was no ID for that mapping.

Caused by: Class$S1402: failed to transform '{"0":{"id":null, "source":"LOOM", "classes":[{"@id":"http://id.loc.gov/ontologies/bibframe/AdminMetadata", "@type":"http://www.w3.org/2002/07/owl#Class", "links":{"self":"https://data.biblio.ontoportal.org/ontologies/BIBFRAME/classes/http%3A%2F%2Fid.loc.gov%2Fontologies%2Fbibframe%2FAdminMetadata", "ontology":"https://data.biblio.ontoportal.org/ontologies/BIBFRAME", "children":"https://data.biblio.ontoportal.org/ontologies/BIBFRAME/classes/http%3A%2F%2Fid.loc.gov%2Fontologies%2Fbibframe%2FAdminMetadata/children", "parents":"https://data.biblio.ontoportal.org/ontologies/BIBFRAME/classes/http%3A%2F%2Fid.loc.gov%2Fontologies%2Fbibframe%2FAdminMetadata/parents", "descendants":"https://data.biblio.ontoportal.org/ontologies/BIBFRAME/classes/http%3A%2F%2Fid.loc.gov%2Fontologies%2Fbibframe%2FAdminMetadata/descendants", "ancestors":"https://data.biblio.ontoportal.org/ontologies/BIBFRAME/classes/http%3A%2F%2Fid.loc.gov%2Fontologies%2Fbibframe%2FAdminMetadata/ancestors", "instances":"https://data.biblio.ontoportal.org/ontologies/BIBFRAME/classes/http%3A%2F%2Fid.loc.gov%2Fontologies%2Fbibframe%2FAdminMetadata/instances", "tree":"https://data.biblio.ontoportal.org/ontologies/BIBFRAME/classes/http%3A%2F%2Fid.loc.gov%2Fontologies%2Fbibframe%2FAdminMetadata/tree", "notes":"https://data.biblio.ontoportal.org/ontologies/BIBFRAME/classes/http%3A%2F%2Fid.loc.gov%2Fontologies%2Fbibframe%2FAdminMetadata/notes", "mappings":"https://data.biblio.ontoportal.org/ontologies/BIBFRAME/classes/http%3A%2F%2Fid.loc.gov%2Fontologies%2Fbibframe%2FAdminMetadata/mappings", "ui":"http://http://biblio.ontoportal.org/ontologies/BIBFRAME?p=classes&conceptid=http%3A%2F%2Fid.loc.gov%2Fontologies%2Fbibframe%2FAdminMetadata", "@context":{"self":"http://www.w3.org/2002/07/owl#Class", "ontology":"http://data.bioontology.org/metadata/Ontology", "children":"http://www.w3.org/2002/07/owl#Class", "parents":"http://www.w3.org/2002/07/owl#Class", "descendants":"http://www.w3.org/2002/07/owl#Class", "ancestors":"http://www.w3.org/2002/07/owl#Class", "instances":"http://data.bioontology.org/metadata/Instance", "tree":"http://www.w3.org/2002/07/owl#Class", "notes":"http://data.bioontology.org/metadata/Note", "mappings":"http://data.bioontology.org/metadata/Mapping", "ui":"http://www.w3.org/2002/07/owl#Class"}}, "@context":{"@vocab":"http://data.bioontology.org/metadata/"}},{"@id":"ri:AdminMetadata", "@type":"http://www.w3.org/2002/07/owl#Class", "links":{"self":"https://data.biblio.ontoportal.org/ontologies/MODS-RDF/classes/ri%3AAdminMetadata", "ontology":"https://data.biblio.ontoportal.org/ontologies/MODS-RDF", "children":"https://data.biblio.ontoportal.org/ontologies/MODS-RDF/classes/ri%3AAdminMetadata/children", "parents":"https://data.biblio.ontoportal.org/ontologies/MODS-RDF/classes/ri%3AAdminMetadata/parents", "descendants":"https://data.biblio.ontoportal.org/ontologies/MODS-RDF/classes/ri%3AAdminMetadata/descendants", "ancestors":"https://data.biblio.ontoportal.org/ontologies/MODS-RDF/classes/ri%3AAdminMetadata/ancestors", "instances":"https://data.biblio.ontoportal.org/ontologies/MODS-RDF/classes/ri%3AAdminMetadata/instances", "tree":"https://data.biblio.ontoportal.org/ontologies/MODS-RDF/classes/ri%3AAdminMetadata/tree", "notes":"https://data.biblio.ontoportal.org/ontologies/MODS-RDF/classes/ri%3AAdminMetadata/notes", "mappings":"https://data.biblio.ontoportal.org/ontologies/MODS-RDF/classes/ri%3AAdminMetadata/mappings", "ui":"http://http://biblio.ontoportal.org/ontologies/MODS-RDF?p=classes&conceptid=ri%3AAdminMetadata", "@context":{"self":"http://www.w3.org/2002/07/owl#Class", "ontology":"http://data.bioontology.org/metadata/Ontology", "children":"http://www.w3.org/2002/07/owl#Class", "parents":"http://www.w3.org/2002/07/owl#Class", "descendants":"http://www.w3.org/2002/07/owl#Class", "ancestors":"http://www.w3.org/2002/07/owl#Class", "instances":"http://data.bioontology.org/metadata/Instance", "tree":"http://www.w3.org/2002/07/owl#Class", "notes":"http://data.bioontology.org/metadata/Note", "mappings":"http://data.bioontology.org/metadata/Mapping", "ui":"http://www.w3.org/2002/07/owl#Class"}}, "@context":{"@vocab":"http://data.bioontology.org/metadata/"}}], "process":null, "@id":"", "@type":"http://data.bioontology.org/metadata/Mapping"}}'
	at Unknown.Zs(0.js@270:74)
	at Unknown.new kLa(0.js@179:794)
	at Unknown._.le(0.js@377:794)
	at Unknown._.Nf(0.js@331:1201)
	at Unknown.Fka(0.js@262:672)
	at Unknown._.Wd(0.js@222:227)
	at Unknown.eval(0.js@131:226)
	at Unknown.eval(0.js@235:1284)
Caused by: Class$S98: (TypeError) : Cannot read property 'b' of null
	at Unknown._.ch(0.js@255:990)
	at Unknown._.le(0.js@332:794)
	at Unknown._.Nf(0.js@331:1201)
	at Unknown.Fka(0.js@262:672)
	at Unknown._.Wd(0.js@222:227)
	at Unknown.eval(0.js@131:226)
	at Unknown.eval(0.js@235:1284)