property_tree raises SystemStackError for ontologies with a self-referential property parent

[alexskr]

property_tree raises SystemStackError for ontologies with a self-referential property parent

Summary

Rendering the property tree for certain ontologies crashes with SystemStackError (stack level too deep). The trigger is a property whose parents list contains its own IRI (a subPropertyOf pointing at itself). Ontology#property_tree builds the tree client-side and appends each property under every parent, so a self-referential parent produces a self-child edge. Property#to_hash then recurses on itself indefinitely until the stack is exhausted.

Confirmed in production (data.bioontology.org) for:

• NIFSTD — http://www.w3.org/2004/02/skos/core#definition (parents: ["skos:note", "skos:definition"])
• IOBC — http://www.w3.org/2004/02/skos/core#altLabel, http://purl.org/dc/elements/1.1/creator, http://www.w3.org/2004/02/skos/core#definition

Both ontologies contain only self-loops — no multi-node cycles.

Impact

Any UI request that renders the property tree for an affected ontology returns 500 Internal Server Error. Observed via ConceptsController#property_tree in bioportal_web_ui:

Processing by ConceptsController#property_tree as */*
  Parameters: {"apikey"=>"", "ontology"=>"NIFSTD", "no_context"=>"true", "concept"=>{}}
Completed 500 Internal Server Error in 6048ms
SystemStackError (stack level too deep):
app/controllers/concepts_controller.rb:135:in `property_tree'

Client stack trace (truncated, ~3000 frames):

lib/ontologies_api_client/models/property.rb:47:in `to_hash'
lib/ontologies_api_client/models/property.rb:47:in `block in to_hash'
lib/ontologies_api_client/models/property.rb:47:in `map'
lib/ontologies_api_client/models/property.rb:47:in `to_hash'
... (repeats until stack exhausted)
lib/ontologies_api_client/base.rb:100:in `map'
lib/ontologies_api_client/base.rb:100:in `marshal_dump'
lib/ontologies_api_client/base.rb:85:in `to_hash'

Root cause

lib/ontologies_api_client/models/ontology.rb, property_tree:

prop.parents.each { |par| properties[par].children << prop if properties[par] }

When par == prop.id this appends the property to its own children. Property#to_hash (lib/ontologies_api_client/models/property.rb) then maps over children recursively with no cycle guard:

hash[:children] = self.children.map { |p| p.to_hash }

Steps to reproduce

LinkedData::Client.config { |c| c.rest_url = "https://data.bioontology.org"; c.apikey = ENV["API_KEY"] }
ont = LinkedData::Client::Models::Ontology.find_by_acronym("NIFSTD").first
ont.property_tree.to_hash   # => SystemStackError

Confirm the offending data directly:

p = ont.explore.properties.find { |x| x.id == "http://www.w3.org/2004/02/skos/core#definition" }
p.parents.include?(p.id)    # => true

Proposed fix

Two layers:

1. property_tree — skip self-referential parents so the constructed tree is acyclic for all consumers (jstree rendering, to_hash, …):

   prop.parents.each do |par|
     next if par == prop.id
     properties[par].children << prop if properties[par]
   end

2. Property#to_hash — carry a visited set as defense-in-depth, which also covers hypothetical multi-node cycles (mutual subPropertyOf, A→B→A) that the self-edge check alone would not catch.

Verified end-to-end against production after the fix: NIFSTD serializes 1950 tree nodes and IOBC 86, with no SystemStackError.

Notes

The self-referential parent is a data artifact in the affected ontologies, but the client should not crash on it. A regression test that builds a Property with a self-referential child and asserts to_hash terminates would guard against future regressions without requiring a live API call.

Affected version: 2.9.0.