From b67edaf3d4f3159e8450a9559966d9a5da667b92 Mon Sep 17 00:00:00 2001
From: Michael Dorf <mdorf@stanford.edu>
Date: Thu, 16 Jul 2026 14:49:52 -0700
Subject: [PATCH] Batch load SKOS root classes

---
 Gemfile.lock                                  |  2 +-
 .../skos/skos_submission_roots.rb             | 10 ++----
 .../models/ontology_submission.rb             | 19 +++++++---
 test/models/test_skos_submission.rb           | 35 ++++++++++++++++++-
 4 files changed, 52 insertions(+), 14 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 8f0ebcbe..3e9a7246 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -8,7 +8,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: cc806c845c79b707e7a10f44e4959caa15939b8b
+  revision: 752fb6b3fe2ec0ba9417397f3283baeac7a9abfc
   branch: development
   specs:
     goo (0.0.2)
diff --git a/lib/ontologies_linked_data/concerns/ontology_submissions/skos/skos_submission_roots.rb b/lib/ontologies_linked_data/concerns/ontology_submissions/skos/skos_submission_roots.rb
index 624c792d..f6b8437f 100644
--- a/lib/ontologies_linked_data/concerns/ontology_submissions/skos/skos_submission_roots.rb
+++ b/lib/ontologies_linked_data/concerns/ontology_submissions/skos/skos_submission_roots.rb
@@ -3,18 +3,12 @@ module Models
     module SKOS
       module RootsFetcher
 
-        def skos_roots(concept_schemes, page, paged, pagesize)
-          classes = []
+        def skos_root_ids(concept_schemes, page, paged, pagesize)
           class_ids, count = roots_by_has_top_concept(concept_schemes, page, paged, pagesize)
 
           class_ids, count = roots_by_top_concept_of(concept_schemes, page, paged, pagesize) if class_ids.empty?
 
-          class_ids.each do |id|
-            classes << LinkedData::Models::Class.find(id).in(self).disable_rules.first
-          end
-
-          classes = Goo::Base::Page.new(page, pagesize, count, classes) if paged
-          classes
+          [class_ids, count]
         end
 
         private
diff --git a/lib/ontologies_linked_data/models/ontology_submission.rb b/lib/ontologies_linked_data/models/ontology_submission.rb
index 8ce7e246..f43ba5a8 100644
--- a/lib/ontologies_linked_data/models/ontology_submission.rb
+++ b/lib/ontologies_linked_data/models/ontology_submission.rb
@@ -711,9 +711,11 @@ def roots(extra_include = [], page = nil, pagesize = nil, concept_schemes: [], c
 
         skos = self.skos?
         classes = []
+        class_ids = []
+        root_count = 0
 
         if skos
-          classes = skos_roots(concept_schemes, page, paged, pagesize)
+          class_ids, root_count = skos_root_ids(concept_schemes, page, paged, pagesize)
           extra_include += LinkedData::Models::Class.concept_is_in_attributes
         else
           self.ontology.bring(:flat)
@@ -744,7 +746,12 @@ def roots(extra_include = [], page = nil, pagesize = nil, concept_schemes: [], c
           end
         end
 
-        where = LinkedData::Models::Class.in(self).models(classes).include(:prefLabel, :definition, :synonym, :obsolete)
+        where = if skos
+                  LinkedData::Models::Class.in(self).ids(class_ids) unless class_ids.empty?
+                else
+                  LinkedData::Models::Class.in(self).models(classes)
+                end
+        where.include(:prefLabel, :definition, :synonym, :obsolete) if where
 
         if extra_include
           %i[prefLabel definition synonym obsolete childrenCount].each do |x|
@@ -767,9 +774,13 @@ def roots(extra_include = [], page = nil, pagesize = nil, concept_schemes: [], c
             load_children = [:children]
           end
 
-          where.include(extra_include) if extra_include.length > 0
+          where.include(extra_include) if where && extra_include.length > 0
         end
-        where.all
+        if where
+          loaded_classes = where.all
+          classes = loaded_classes if skos
+        end
+        classes = Goo::Base::Page.new(page, pagesize, root_count, classes) if skos && paged
 
         LinkedData::Models::Class.partially_load_children(classes, 99, self) if load_children.length > 0
 
diff --git a/test/models/test_skos_submission.rb b/test/models/test_skos_submission.rb
index 5ab2e16a..601c9565 100644
--- a/test/models/test_skos_submission.rb
+++ b/test/models/test_skos_submission.rb
@@ -104,6 +104,40 @@ def test_roots_of_multiple_scheme
                           'http://www.ebi.ac.uk/efo/EFO_0000324'].sort
   end
 
+  def test_roots_batch_loads_skos_classes
+    sub = before_suite
+    concept_schemes = ['http://www.ebi.ac.uk/efo/skos/EFO_GWAS_view_2',
+                       'http://www.ebi.ac.uk/efo/skos/EFO_GWAS_view']
+
+    roots = nil
+    queries = count_sparql_queries do
+      roots = sub.roots(concept_schemes: concept_schemes)
+    end
+
+    assert_equal 6, roots.length
+    assert_operator queries, :<=, 3,
+      "loading #{roots.length} SKOS roots issued #{queries} SPARQL queries -- " \
+      'looks like per-root class hydration'
+  end
+
+  def test_roots_batch_load_preserves_skos_pagination
+    sub = before_suite
+    concept_scheme = 'http://www.ebi.ac.uk/efo/skos/EFO_GWAS_view'
+
+    roots = sub.roots([], 1, 2, concept_schemes: [concept_scheme])
+
+    assert_instance_of Goo::Base::Page, roots
+    assert_equal 2, roots.length
+    assert_equal 2, roots.total_pages
+  end
+
+  def test_roots_with_no_skos_ids_returns_empty
+    sub = before_suite
+    roots = sub.roots(concept_schemes: ['http://example.org/missing-scheme'])
+
+    assert_empty roots
+  end
+
   def test_roots_of_scheme_collection
     sub = before_suite
 
@@ -241,4 +275,3 @@ def test_concept_schemes_query_memoized_per_submission
       'submission instance -- per-submission memoization (#302/#303) regressed'
   end
 end
-