`GET /classes/:cls/paths_to_root` returns HTTP 500 for SKOS concepts that have parents

[matthewhorridge]

Summary

The paths_to_root endpoint returns 500 Internal Server Error for SKOS concepts that have at least one parent (skos:broader). Every other class-hierarchy endpoint (/tree, /parents, /ancestors, /descendants) works for the same concept, and /paths_to_root works for OWL/OBO classes. A concept with no parents (a top concept) returns 200 [], so the crash is in the code path that walks parents.

Observed on stagedata.bioontology.org.

Steps to reproduce

Any SKOS concept that has a parent. Example — INJURYTYPES / "Sprain":

curl -H "Authorization: apikey token=$APIKEY" \
  "https://stagedata.bioontology.org/ontologies/INJURYTYPES/classes/http%3A%2F%2Fwww.fairdatacollective.com%2Ftemplate-vocabulary%2FSprain/paths_to_root?include=prefLabel,hasChildren"

Returns:

HTTP/1.1 500 Internal Server Error
Content-Type: text/html;charset=utf-8

<h1>Internal Server Error</h1>

Scope

include=prefLabel,hasChildren, valid apikey, raw HTTP:

Ontology	Type	Concept	/paths_to_root
INJURYTYPES	SKOS	Sprain	500
PLOSTHES	SKOS	Atmosphere / Separation processes	500
I2SV	SKOS	Axiology	500
ISO639-1	SKOS	iu (a top concept, no parents)	200 []
UBERON	OWL	(any deep class)	200
GO	OBO	general transcription…	200

Endpoint matrix for one failing SKOS concept (INJURYTYPES / Sprain):

Endpoint	Result
/tree	200 (22 KB)
/parents	200
/ancestors	200
/descendants	200
/paths_to_root	500

So the failure is specific to /paths_to_root on SKOS concepts that have parents.

?display=all on the same endpoint returns a clean 422 {"errors":["all not allowed in include parameter for this endpoint"]}, so the route and parameter handling are reached; the 500 happens when the endpoint computes the paths.

Relevant source: ontologies_linked_data lib/ontologies_linked_data/concerns/concepts/concept_tree.rb (paths_to_root) and models/class.rb (traverse_path_to_root).

Suggested next step

The server log / backtrace for one of these 500s would pin the exact line.

[matthewhorridge]

For reference: the bioportal_web_ui "Show parent paths" feature (ncbo/bioportal_web_ui#540) works around this by reconstructing the paths from the /parents links when /paths_to_root fails. Once this endpoint is fixed for SKOS, that fallback can be dropped in favour of the single /paths_to_root call.