Sync: BioPortal v6.6.1 release

Gemfile.lock

@@ -27,7 +27,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_cron.git
-  revision: ffd62d61f36b9c58fef65afa082d200747a33893
+  revision: 8d67188e7f21014234359b71bb93a9d1256c320c
   branch: master
   specs:
     ncbo_cron (0.0.1)
@@ -56,7 +56,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 098c1e1b00a04a5b0f3c9eb335f95e12bc7e7829
+  revision: 5a4f4d39aeb3ec567038b88ea962b796b2715915
   branch: master
   specs:
     ontologies_linked_data (0.0.1)
@@ -73,7 +73,7 @@ GIT
       rack
       rack-test
       rsolr
-      rubyzip
+      rubyzip (~> 3.0)
 
 GIT
   remote: https://github.com/ncbo/sparql-client.git
@@ -146,7 +146,7 @@ GEM
     docile (1.4.1)
     domain_name (0.6.20240107)
     ed25519 (1.4.0)
-    faraday (2.13.2)
+    faraday (2.13.4)
       faraday-net_http (>= 2.0, < 3.5)
       json
       logger
@@ -167,7 +167,7 @@ GEM
     ffi (1.17.2-x86_64-darwin)
     ffi (1.17.2-x86_64-linux-gnu)
     ffi (1.17.2-x86_64-linux-musl)
-    gapic-common (1.0.0)
+    gapic-common (1.0.1)
       faraday (>= 1.9, < 3.a)
       faraday-retry (>= 1.0, < 3.a)
       google-cloud-env (~> 2.2)
@@ -213,22 +213,31 @@ GEM
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
-    grpc (1.73.0)
+    grpc (1.74.0)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.73.0-aarch64-linux)
+    grpc (1.74.0-aarch64-linux-gnu)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.73.0-arm64-darwin)
+    grpc (1.74.0-aarch64-linux-musl)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.73.0-x86-linux)
+    grpc (1.74.0-arm64-darwin)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.73.0-x86_64-darwin)
+    grpc (1.74.0-x86-linux-gnu)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.73.0-x86_64-linux)
+    grpc (1.74.0-x86-linux-musl)
+      google-protobuf (>= 3.25, < 5.0)
+      googleapis-common-protos-types (~> 1.0)
+    grpc (1.74.0-x86_64-darwin)
+      google-protobuf (>= 3.25, < 5.0)
+      googleapis-common-protos-types (~> 1.0)
+    grpc (1.74.0-x86_64-linux-gnu)
+      google-protobuf (>= 3.25, < 5.0)
+      googleapis-common-protos-types (~> 1.0)
+    grpc (1.74.0-x86_64-linux-musl)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
     haml (5.2.2)
@@ -240,15 +249,15 @@ GEM
       domain_name (~> 0.5)
     i18n (1.14.7)
       concurrent-ruby (~> 1.0)
-    json (2.13.0)
+    json (2.13.2)
     json-schema (2.8.1)
       addressable (>= 2.4)
     json_pure (2.8.1)
     jwt (2.10.2)
       base64
     kgio (2.11.4)
     language_server-protocol (3.17.0.5)
-    libxml-ruby (5.0.4)
+    libxml-ruby (5.0.5)
     lint_roller (1.1.0)
     logger (1.7.0)
     macaddr (1.7.2)
@@ -262,15 +271,15 @@ GEM
     mime-types (3.7.0)
       logger
       mime-types-data (~> 3.2025, >= 3.2025.0507)
-    mime-types-data (3.2025.0715)
+    mime-types-data (3.2025.0819)
     mini_mime (1.1.5)
     minitest (5.25.5)
     minitest-hooks (1.5.2)
       minitest (> 5.3)
     minitest-stub_any_instance (1.0.3)
     mlanett-redis-lock (0.2.7)
       redis
-    multi_json (1.15.0)
+    multi_json (1.17.0)
     net-ftp (0.3.8)
       net-protocol
       time
@@ -337,7 +346,7 @@ GEM
     redcarpet (3.6.1)
     redis (5.4.1)
       redis-client (>= 0.22.0)
-    redis-client (0.25.1)
+    redis-client (0.25.2)
       connection_pool
     redis-rack-cache (2.2.1)
       rack-cache (>= 1.10, < 2)
@@ -367,12 +376,12 @@ GEM
       rubocop-ast (>= 1.45.1, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 4.0)
-    rubocop-ast (1.45.1)
+    rubocop-ast (1.46.0)
       parser (>= 3.3.7.2)
       prism (~> 1.4)
     ruby-progressbar (1.13.0)
     ruby-xxHash (0.4.0.2)
-    rubyzip (2.4.1)
+    rubyzip (3.0.1)
     rufus-scheduler (2.0.24)
       tzinfo (>= 0.3.22)
     signet (0.20.0)
@@ -387,7 +396,7 @@ GEM
     simplecov-cobertura (3.0.0)
       rexml
       simplecov (~> 0.19)
-    simplecov-html (0.13.1)
+    simplecov-html (0.13.2)
     simplecov_json_formatter (0.1.4)
     sinatra (1.4.8)
       rack (~> 1.5)

controllers/classes_controller.rb

@@ -8,15 +8,22 @@ class ClassesController < ApplicationController
       ont, submission = get_ontology_and_submission
       cls_count = submission.class_count(LOGGER)
       error 403, "Unable to display classes due to missing metrics for #{submission.id.to_s}. Please contact the administrator." if cls_count < 0
+
+      attributes, page, size, order_by_hash, bring_unmapped_needed = settings_params(LinkedData::Models::Class)
       check_last_modified_segment(LinkedData::Models::Class, [ont.acronym])
-      page, size = page_params
-      ld = LinkedData::Models::Class.goo_attrs_to_load(includes_param)
-      unmapped = ld.delete(:properties)
-      page_data = LinkedData::Models::Class.in(submission).include(ld).page(page,size).page_count_set(cls_count).all
 
-      if unmapped && page_data.length > 0
-        LinkedData::Models::Class.in(submission).models(page_data).include(:unmapped).all
+      index = LinkedData::Models::Class.in(submission)
+      if order_by_hash
+        index = index.order_by(order_by_hash)
+        cls_count = nil
+        # Add index here when, indexing fixed
+        # index_name = 'classes_sort_by_date'
+        # index = index.index_as(index_name)
+        # index = index.with_index(index_name)
       end
+
+      page_data = index
+      page_data = page_data.include(attributes).page(page, size).page_count_set(cls_count).all
       reply page_data
     end
 
@@ -28,7 +35,8 @@ class ClassesController < ApplicationController
       load_attrs = LinkedData::Models::Class.goo_attrs_to_load(includes_param)
       unmapped = load_attrs.delete(:properties)
       page, size = page_params
-      roots = submission.roots(load_attrs, page, size)
+
+      roots = submission.roots(load_attrs, page, size, concept_schemes: concept_schemes, concept_collections: concept_collections)
 
       if unmapped && roots.length > 0
         LinkedData::Models::Class.in(submission).models(roots).include(:unmapped).all
@@ -44,13 +52,16 @@ class ClassesController < ApplicationController
       check_last_modified_segment(LinkedData::Models::Class, [ont.acronym])
       load_attrs = LinkedData::Models::Class.goo_attrs_to_load(includes_param)
       unmapped = load_attrs.delete(:properties)
-      sort = params["sort"].eql?('true') || params["sort"].eql?('1')  # default = false
-      roots = nil
+      load_attrs += LinkedData::Models::Class.concept_is_in_attributes if submission.skos?
+
+      request_display(load_attrs.join(','))
+
+      sort = params["sort"].eql?('true') || params["sort"].eql?('1') # default = false
 
       if sort
-        roots = submission.roots_sorted(load_attrs)
+        roots = submission.roots_sorted(load_attrs, concept_schemes: concept_schemes, concept_collections: concept_collections)
       else
-        roots = submission.roots(load_attrs)
+        roots = submission.roots(load_attrs, concept_schemes: concept_schemes, concept_collections: concept_collections)
       end
 
       if unmapped && roots.length > 0
@@ -66,25 +77,28 @@ class ClassesController < ApplicationController
       ld = LinkedData::Models::Class.goo_attrs_to_load(includes_param)
 
       load_children = ld.delete :children
-      if !load_children
+      unless load_children
         load_children = ld.select { |x| x.instance_of?(Hash) && x.include?(:children) }
         if load_children
           ld = ld.select { |x| !(x.instance_of?(Hash) && x.include?(:children)) }
         end
       end
 
       unmapped = ld.delete(:properties) ||
-          (includes_param && includes_param.include?(:all))
+                 (includes_param && includes_param.include?(:all))
+
+      ld << :memberOf if includes_param.include?(:all)
+
       cls = get_class(submission, ld)
       if unmapped
         LinkedData::Models::Class.in(submission)
-            .models([cls]).include(:unmapped).all
+                                 .models([cls]).include(:unmapped).all
       end
       if includes_param.include?(:hasChildren)
         cls.load_has_children
       end
-      if !load_children.nil? and load_children.length >0
-        LinkedData::Models::Class.partially_load_children([cls],500,cls.submission)
+      if !load_children.nil? and load_children.length > 0
+        LinkedData::Models::Class.partially_load_children([cls], 500, cls.submission)
         if includes_param.include?(:hasChildren)
           cls.children.each do |c|
             c.load_has_children
@@ -104,35 +118,27 @@ class ClassesController < ApplicationController
       reply cls.paths_to_root
     end
 
-    # Get a tree view
+    # Get a tree view (returns the tree from the roots classes to the specified class)
     get '/:cls/tree' do
       params ||= @params
       includes_param_check
-      sort = params["sort"].eql?('true') || params["sort"].eql?('1')  # default = false
+      sort = params["sort"].eql?('true') || params["sort"].eql?('1') # default = false
       # We override include values other than the following, user-provided include ignored
-      display_attrs = "prefLabel,hasChildren,children,obsolete,subClassOf"
-      params["display"] = display_attrs
-      params["serialize_nested"] = true # Override safety check and cause children to serialize
-
-      # Make sure Rack gets updated
-      req = Rack::Request.new(env)
-      req.update_param("display", display_attrs)
-      req.update_param("serialize_nested", true)
-
       ont, submission = get_ontology_and_submission
       check_last_modified_segment(LinkedData::Models::Class, [ont.acronym])
       cls = get_class(submission)
-      root_tree = nil
-      roots = nil
-
+      display_attrs = [:prefLabel, :hasChildren, :children, :obsolete, :subClassOf]
+      display_attrs += LinkedData::Models::Class.concept_is_in_attributes if submission.skos?
+      request_display(display_attrs.join(','))
+      extra_include = [:hasChildren, :isInActiveScheme, :isInActiveCollection]
       if sort
-        root_tree = cls.tree_sorted
-        #add the other roots to the response
-        roots = submission.roots_sorted(extra_include=[:hasChildren])
+        roots = submission.roots_sorted(extra_include, concept_schemes: concept_schemes, concept_collections: concept_collections)
+        root_tree = cls.tree_sorted(concept_schemes: concept_schemes, concept_collections: concept_collections, roots: roots)
+        # add the other roots to the response
       else
-        root_tree = cls.tree
-        #add the other roots to the response
-        roots = submission.roots(extra_include=[:hasChildren])
+        roots = submission.roots(extra_include, concept_schemes: concept_schemes, concept_collections: concept_collections)
+        root_tree = cls.tree(concept_schemes: concept_schemes, concept_collections: concept_collections, roots: roots)
+        # add the other roots to the response
       end
 
       # if this path' root does not get returned by the submission.roots call, manually add it
@@ -143,7 +149,7 @@ class ClassesController < ApplicationController
         if r.id == root_tree.id
           roots[i] = root_tree
         else
-          roots[i].instance_variable_set("@children",[])
+          roots[i].instance_variable_set("@children", [])
           roots[i].loaded_attributes << :children
         end
       end
@@ -159,7 +165,7 @@ class ClassesController < ApplicationController
       error 404 if cls.nil?
       ancestors = cls.ancestors
       LinkedData::Models::Class.in(submission).models(ancestors)
-          .include(:prefLabel,:synonym,:definition).all
+                               .include(:prefLabel, :synonym, :definition).all
       reply ancestors
     end
 
@@ -169,13 +175,13 @@ class ClassesController < ApplicationController
       ont, submission = get_ontology_and_submission
       check_last_modified_segment(LinkedData::Models::Class, [ont.acronym])
       page, size = page_params
-      cls = get_class(submission,load_attrs=[])
+      cls = get_class(submission, load_attrs = [])
       error 404 if cls.nil?
       ld = LinkedData::Models::Class.goo_attrs_to_load(includes_param)
       unmapped = ld.delete(:properties)
-      page_data = cls.retrieve_descendants(page,size)
+      page_data = cls.retrieve_descendants(page, size)
       LinkedData::Models::Class.in(submission).models(page_data)
-          .include(:prefLabel,:synonym,:definition).all
+                               .include(:prefLabel, :synonym, :definition).all
       if unmapped
         LinkedData::Models::Class.in(submission).models(page_data).include(:unmapped).all
       end
@@ -192,20 +198,12 @@ class ClassesController < ApplicationController
       cls = get_class(submission)
       error 404 if cls.nil?
       ld = LinkedData::Models::Class.goo_attrs_to_load(includes_param)
-      unmapped = ld.delete(:properties)
-      aggregates = LinkedData::Models::Class.goo_aggregates_to_load(ld)
-      page_data_query = LinkedData::Models::Class.where(parents: cls).in(submission).include(ld)
-      page_data_query.aggregate(*aggregates) unless aggregates.empty?
-      page_data = page_data_query.page(page,size).all
-      if unmapped
-        LinkedData::Models::Class.in(submission).models(page_data).include(:unmapped).all
-      end
-      page_data.delete_if { |x| x.id.to_s == cls.id.to_s }
-      if ld.include?(:hasChildren)
-        page_data.each do |c|
-          c.load_has_children
-        end
-      end
+      ld += LinkedData::Models::Class.concept_is_in_attributes if submission.skos?
+      request_display(ld.join(','))
+
+      page_data = submission.children(cls, includes_param: includes_param, concept_schemes: concept_schemes,
+                                      concept_collections: concept_collections, page: page, size: size)
+
       reply page_data
     end
 
@@ -236,6 +234,7 @@ class ClassesController < ApplicationController
     end
 
     private
+
     def includes_param_check
       if includes_param
         if includes_param.include?(:all)
@@ -248,5 +247,15 @@ def includes_param_check
       end
     end
 
+    def request_display(attrs)
+
+      params["display"] = attrs
+      params["serialize_nested"] = true # Override safety check and cause children to serialize
+
+      # Make sure Rack gets updated
+      req = Rack::Request.new(env)
+      req.update_param("display", attrs)
+      req.update_param("serialize_nested", true)
+    end
   end
 end