Class tree performance: remove per-node N+1 queries (build + serialize)

[alexskr]

Removes two independent per-node N+1 SPARQL patterns on the class tree endpoint. Follow-up to #297 (batch hasChildren resolution). Two separate commits, one per fix.

Query counts measured against staging AG (goo queries per /classes/:cls/tree).

Commit 1 — tree build: per-node concept-scheme query · Fixes #303

load_is_in_scheme runs per node during build and calls get_main_concept_scheme → all_concepts_schemes (a SPARQL query). Two issues:

• No skos? guard — isInActiveScheme is SKOS-only and only serialized for SKOS, but non-SKOS (OWL/OBO) submissions still ran a skos:ConceptScheme query per node that always returns nothing. Now skipped for them.
• No memoization — for genuine SKOS the scheme set is fixed per request but was re-queried per node. Now memoized on the submission.

Ontology	Type	Build queries before → after
IOBC	OWL	669 → 92
AGROVOC	SKOS	264 → 58

Files: concerns/concepts/concept_in_scheme.rb, concerns/ontology_submissions/skos/skos_submission_schemes.rb

Commit 2 — JSON serialize: per-node naturalLanguage query · Fixes #304

serializers/json.rb get_languages runs once per serialized object and calls submission.bring :naturalLanguage. goo's bring re-queries every call, so a response of N objects sharing a submission issued N queries. Guarded with bring? (the codebase convention) so it loads once per request.

This is not tree-specific — get_languages runs for every multi-class response (search, /children, /descendants, collections), so this helps broadly. It is also the dominant N+1 on large trees.

Ontology	Type	Nodes	Serialize queries before → after
DDSS	OWL	2945	2830 → 0
AGROVOC	SKOS (multilingual)	173	60 → 0

File: serializers/json.rb

Testing

Syntax-checked; query counts verified against staging AG (numbers above). No triplestore-backed unit run yet — please run the class-tree controller tests against a backend before merge, ideally on both a SKOS and an OWL ontology.

[codecov]

Codecov Report

❌ Patch coverage is 75.00000% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 81.36%. Comparing base (a8a8dfb) to head (1c316d2).

Files with missing lines	Patch %	Lines
lib/ontologies_linked_data/serializers/json.rb	0.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff            @@
##           develop     #302   +/-   ##
========================================
  Coverage    81.36%   81.36%           
========================================
  Files          101      101           
  Lines         6848     6849    +1     
========================================
+ Hits          5572     5573    +1     
  Misses        1276     1276           

Flag	Coverage Δ
ag	81.28% <75.00%> (+0.03%)	⬆️
fs	81.34% <75.00%> (+<0.01%)	⬆️
gd	81.28% <75.00%> (+0.04%)	⬆️
unittests	81.36% <75.00%> (+<0.01%)	⬆️
vo	81.29% <75.00%> (+0.01%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[mdorf]

Reviewed the approach — it's sound and near-optimal for the goal. The fixes work because classes loaded .in(submission) share one submission instance, so the memoization and bring? guards collapse to one query per request. No correctness regression found.

Checked and cleared: the [nil]→[] change in load_is_in_scheme for non-SKOS can't affect the roots delete_if (ontology_submission.rb:814) — that filter only runs unless concept_schemes.empty?, while the altered branch only runs when schemes is empty. Mutually exclusive.

One observable change to document: for OWL/OBO ontologies, isInActiveScheme in the tree JSON goes from [null] to [] (it's in extra_include unconditionally and is serialized). That's a correctness improvement, but worth noting in the description and sanity-checking against the web UI.

Main gap — tests: needs a triplestore-backed class-tree test on both a SKOS and an OWL ontology, asserting correct output (ideally a query-count assertion so the N+1 can't silently return).