biomixer_url config variable gets passed as conceptid parameter in some ajax calls, resulting in (undefined method notes' for nil:NilClass):

[alexskr]

I am observing odd behavior where the value of biomixer_url configuration variable is being passed as the conceptid parameter in some of the AJAX calls. This results in a NoMethodError (undefined method 'notes' for nil:NilClass): error. This issue began appearing with the release of UI v7.0.0

Log:

Started GET "/ontologies/RXNORM/?p=classes&lang=en&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F1299852" for 192.168.65.1 at 2024-12-03 21:30:51 +0000
Processing by OntologiesController#show as HTML
  Parameters: {"p"=>"classes", "lang"=>"en", "conceptid"=>"http://purl.bioontology.org/ontology/RXNORM/1299852", "id"=>"RXNORM"}
  Rendering layout layouts/ontology_viewer.html.haml
  Rendering ontologies/visualize.html.haml within layouts/ontology_viewer
  Rendered concepts/_details.html.haml (Duration: 1309.6ms | Allocations: 30887)
  Rendered concepts/_biomixer.html.erb (Duration: 0.1ms | Allocations: 27)
  Rendered notes/_list.html.haml (Duration: 0.2ms | Allocations: 244)
  Rendered mappings/_mapping_table.html.haml (Duration: 0.0ms | Allocations: 78)
  Rendered mappings/_concept_mappings.html.haml (Duration: 0.7ms | Allocations: 277)
  Rendered concepts/_show.html.haml (Duration: 1325.7ms | Allocations: 40086)
  Rendered ontologies/visualize.html.haml within layouts/ontology_viewer (Duration: 1360.2ms | Allocations: 70424)
  Rendered application/_ga_tracking.html.haml (Duration: 0.0ms | Allocations: 16)
  Rendered layouts/_topnav.html.haml (Duration: 4.0ms | Allocations: 1361)
  Rendered layouts/_notices.html.haml (Duration: 0.1ms | Allocations: 35)
  Rendered layouts/_header.html.erb (Duration: 1169.2ms | Allocations: 212000)
  Rendered application/_kgcl_dialogs.html.haml (Duration: 0.0ms | Allocations: 15)
  Rendered layouts/_footer.html.haml (Duration: 22.2ms | Allocations: 6198)
  Rendered layouts/_ontology_viewer.html.haml (Duration: 1263.4ms | Allocations: 268527)
  Rendered layout layouts/ontology_viewer.html.haml (Duration: 2624.7ms | Allocations: 339111)
Completed 200 OK in 2923ms (Views: 2625.8ms | ActiveRecord: 0.0ms | Allocations: 376347)

Started GET "/ontologies/RXNORM/biomixer.stage.bioontology.org/?mode=embed&embed_mode=paths_to_root&ontology_acronym=RXNORM&full_concept_id=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F1299852&userapikey=&restURLPrefix=stagedata.bioontology.org" for 192.168.65.1 at 2024-12-03 21:30:54 +0000
Processing by OntologiesController#show as HTML
  Parameters: {"mode"=>"embed", "embed_mode"=>"paths_to_root", "ontology_acronym"=>"RXNORM", "full_concept_id"=>"http://purl.bioontology.org/ontology/RXNORM/1299852", "userapikey"=>"", "restURLPrefix"=>"stagedata.bioontology.org", "acronym"=>"RXNORM", "purl_conceptid"=>"biomixer.stage.bioontology.org"}
Redirected to http://localhost:3000/ontologies/RXNORM?p=classes&mode=embed&embed_mode=paths_to_root&ontology_acronym=RXNORM&full_concept_id=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F1299852&restURLPrefix=stagedata.bioontology.org&conceptid=biomixer.stage.bioontology.org
Completed 301 Moved Permanently in 2ms (ActiveRecord: 0.0ms | Allocations: 250)


Started GET "/ontologies/RXNORM?p=classes&mode=embed&embed_mode=paths_to_root&ontology_acronym=RXNORM&full_concept_id=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F1299852&restURLPrefix=stagedata.bioontology.org&conceptid=biomixer.stage.bioontology.org" for 192.168.65.1 at 2024-12-03 21:30:54 +0000
Started GET "/ajax/classes/treeview?ontology=RXNORM&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F1299852&lang=en" for 192.168.65.1 at 2024-12-03 21:30:54 +0000
Processing by OntologiesController#show as HTML
  Parameters: {"p"=>"classes", "mode"=>"embed", "embed_mode"=>"paths_to_root", "ontology_acronym"=>"RXNORM", "full_concept_id"=>"http://purl.bioontology.org/ontology/RXNORM/1299852", "restURLPrefix"=>"stagedata.bioontology.org", "conceptid"=>"biomixer.stage.bioontology.org", "id"=>"RXNORM"}
Processing by ConceptsController#show_tree as HTML
  Parameters: {"ontology"=>"RXNORM", "conceptid"=>"http://purl.bioontology.org/ontology/RXNORM/1299852", "lang"=>"en"}
Completed 500 Internal Server Error in 27ms (ActiveRecord: 0.0ms | Allocations: 39591)

NoMethodError (undefined method `notes' for nil:NilClass):

app/controllers/ontologies_controller.rb:147:in `classes'
app/controllers/ontologies_controller.rb:295:in `show'
  Rendered ontologies/_treeview.html.haml (Duration: 63.0ms | Allocations: 126535)
Completed 200 OK in 84ms (Views: 63.8ms | ActiveRecord: 0.0ms | Allocations: 162400)

From: /app/app/controllers/ontologies_controller.rb @ line 145 :

    140:     end
    141:
    142:     @current_purl = @concept.purl if Rails.configuration.settings.purl[:enabled]
    143:
    144:     unless @concept.id == "bp_fake_root"
 => 145:       binding.irb
    146:       @notes = @concept.explore.notes
    147:       @mappings = get_concept_mappings(@concept)
    148:       @delete_mapping_permission = check_delete_mapping_permission(@mappings)
    149:     end
    150:

irb(#<OntologiesController:0x0000...):004> @concept
=> #<OpenStruct links=nil, context=nil, errors=["The input class id 'biomixer.stage.bioontology.org' is not a valid IRI"], status=400, children=[]>