Fix complicated has_many through with nested where condition

#40779 will be caused if (1) having nested where condition for through
association, and (2) through scope has references values, and (3) the
model has no association which is the same name with table name.

In that case, the join root will be found by the table name but the join
root isn't related with association reflection.

This changes to return the table klass from join dependency tree, it
works regardless of whether the join root or join association children.

Fixes #40779.

activerecord/lib/active_record/associations/association_scope.rb

@@ -131,11 +131,14 @@ def add_constraints(scope, owner, chain)
               if scope_chain_item == chain_head.scope
                 scope.merge! item.except(:where, :includes, :unscope, :order)
               elsif !item.references_values.empty?
-                join_dependency = item.construct_join_dependency(
-                  item.eager_load_values | item.includes_values, Arel::Nodes::OuterJoin
-                )
-                scope.joins!(*item.joins_values, join_dependency)
-                scope.left_outer_joins!(*item.left_outer_joins_values)
+                scope.joins_values |= item.joins_values
+                scope.left_outer_joins_values |= item.left_outer_joins_values
+
+                associations = item.eager_load_values | item.includes_values
+
+                unless associations.empty?
+                  scope.joins_values << item.construct_join_dependency(associations, Arel::Nodes::OuterJoin)
+                end
               end
 
               reflection.all_includes do

activerecord/lib/active_record/relation/query_methods.rb

@@ -1140,7 +1140,7 @@ def build_where_clause(opts, rest = []) # :nodoc:
           self.references_values |= references unless references.empty?
 
           parts = predicate_builder.build_from_hash(opts) do |table_name|
-            lookup_reflection_from_join_dependencies(table_name)
+            lookup_table_klass_from_join_dependencies(table_name)
           end
         when Arel::Nodes::Node
           parts = [opts]
@@ -1153,9 +1153,9 @@ def build_where_clause(opts, rest = []) # :nodoc:
       alias :build_having_clause :build_where_clause
 
     private
-      def lookup_reflection_from_join_dependencies(table_name)
+      def lookup_table_klass_from_join_dependencies(table_name)
         each_join_dependencies do |join|
-          return join.reflection if table_name == join.table_name
+          return join.base_klass if table_name == join.table_name
         end
         nil
       end
@@ -1366,7 +1366,7 @@ def arel_column(field)
         elsif field.match?(/\A\w+\.\w+\z/)
           table, column = field.split(".")
           predicate_builder.resolve_arel_attribute(table, column) do
-            lookup_reflection_from_join_dependencies(table)
+            lookup_table_klass_from_join_dependencies(table)
           end
         else
           yield field

activerecord/lib/active_record/table_metadata.rb

@@ -33,10 +33,13 @@ def associated_table(table_name)
         return self
       end
 
-      reflection ||= yield table_name if block_given?
+      if reflection
+        association_klass = reflection.klass unless reflection.polymorphic?
+      elsif block_given?
+        association_klass = yield table_name
+      end
 
-      if reflection && !reflection.polymorphic?
-        association_klass = reflection.klass
+      if association_klass
         arel_table = association_klass.arel_table
         arel_table = arel_table.alias(table_name) if arel_table.name != table_name
         TableMetadata.new(association_klass, arel_table, reflection)

activerecord/test/cases/associations/has_many_through_associations_test.rb

@@ -66,6 +66,14 @@ def test_through_association_with_left_joins
     assert_equal [comments(:eager_other_comment1)], authors(:mary).comments.merge(Post.left_joins(:comments))
   end
 
+  def test_through_association_with_through_scope_and_nested_where
+    company = Company.create!(name: "special")
+    developer = SpecialDeveloper.create!
+    SpecialContract.create!(company: company, special_developer: developer)
+
+    assert_equal [developer], company.special_developers.where.not("contracts.id": nil)
+  end
+
   def test_preload_with_nested_association
     posts = Post.where(id: [authors(:david).id, authors(:mary).id]).
       preload(:author, :author_favorites_with_scope).order(:id).to_a

activerecord/test/models/company.rb

@@ -13,6 +13,8 @@ class Company < AbstractCompany
   has_one :dummy_account, foreign_key: "firm_id", class_name: "Account"
   has_many :contracts
   has_many :developers, through: :contracts
+  has_many :special_contracts, -> { includes(:special_developer).where.not("developers.id": nil) }
+  has_many :special_developers, through: :special_contracts
 
   alias_attribute :new_name, :name
   attribute :metadata, :json

activerecord/test/models/contract.rb

@@ -30,3 +30,9 @@ def update_metadata
 class NewContract < Contract
   validates :company_id, presence: true
 end
+
+class SpecialContract < ActiveRecord::Base
+  self.table_name = "contracts"
+  belongs_to :company
+  belongs_to :special_developer, foreign_key: "developer_id"
+end

activerecord/test/models/developer.rb

@@ -114,6 +114,11 @@ def track_instance_count
 class SubDeveloper < Developer
 end
 
+class SpecialDeveloper < ActiveRecord::Base
+  self.table_name = "developers"
+  has_many :special_contracts, foreign_key: "developer_id"
+end
+
 class SymbolIgnoredDeveloper < ActiveRecord::Base
   self.table_name = "developers"
   self.ignored_columns = [:first_name, :last_name]