Merge pull request #141 from ncbo/develop

Merge Develop to Master, release v5.29.0

Gemfile

@@ -41,12 +41,12 @@ gem 'haml', '~> 5.2.2' # pin see https://github.com/ncbo/ontologies_api/pull/107
 gem 'redcarpet'
 
 # NCBO
-gem 'goo', github: 'ncbo/goo', branch: 'master'
-gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'master'
-gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'master'
-gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'master'
-gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'master'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
+gem 'goo', github: 'ncbo/goo', branch: 'develop'
+gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'develop'
+gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'develop'
+gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'develop'
+gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop'
+gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'
 
 group :development do
   # bcrypt_pbkdf and ed35519 is required for capistrano deployments when using ed25519 keys; see https://github.com/miloserdow/capistrano-deploy/issues/42

Gemfile.lock

@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 75436fe8e387febc53e34ee31ff0e6dd837a9d3f
-  branch: master
+  revision: 4ea0e70a4361fc694700e11f1012129452278c7d
+  branch: develop
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -15,8 +15,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_annotator.git
-  revision: 63c986880aa88c9384043e6611a682434a14aba7
-  branch: master
+  revision: fe0783c542479ed0a12da5663ef28e1673e80eba
+  branch: develop
   specs:
     ncbo_annotator (0.0.1)
       goo
@@ -26,8 +26,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_cron.git
-  revision: 46bd8e7eb7cfde6d173bdf55808a8e28d6700f1e
-  branch: master
+  revision: b5bc460250aa8a61e5825615e1337fb1dc46f335
+  branch: develop
   specs:
     ncbo_cron (0.0.1)
       dante
@@ -42,8 +42,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_ontology_recommender.git
-  revision: 013abea4af3b10910ec661dbb358a4b6cae198a4
-  branch: master
+  revision: d047de0a9650df321db47300eba8ff8c195e0854
+  branch: develop
   specs:
     ncbo_ontology_recommender (0.0.1)
       goo
@@ -53,8 +53,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: ec3236a71ff172579923245646d0ea058844794e
-  branch: master
+  revision: a973d62ca8be3a6cd86677d9bed24f361f580882
+  branch: develop
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -73,8 +73,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/sparql-client.git
-  revision: d418d56a6c9ff5692f925b45739a2a1c66bca851
-  branch: master
+  revision: 55e7dbf858eb571c767bc67868f9af61663859cb
+  branch: develop
   specs:
     sparql-client (1.0.1)
       json_pure (>= 1.4)
@@ -108,13 +108,13 @@ GEM
     airbrussh (1.5.1)
       sshkit (>= 1.6.1, != 1.7.0)
     ast (2.4.2)
-    backports (3.24.1)
+    backports (3.25.0)
     base64 (0.2.0)
     bcrypt (3.1.20)
     bcrypt_pbkdf (1.1.0)
     bigdecimal (1.4.2)
     builder (3.2.4)
-    capistrano (3.18.0)
+    capistrano (3.18.1)
       airbrussh (>= 1.0.0)
       i18n
       rake (>= 10.0.0)
@@ -153,45 +153,45 @@ GEM
       grpc (~> 1.59)
     get_process_mem (0.2.7)
       ffi (~> 1.0)
-    google-analytics-data (0.5.0)
+    google-analytics-data (0.6.0)
       google-analytics-data-v1beta (>= 0.11, < 2.a)
       google-cloud-core (~> 1.6)
-    google-analytics-data-v1beta (0.11.2)
+    google-analytics-data-v1beta (0.12.0)
       gapic-common (>= 0.21.1, < 2.a)
       google-cloud-errors (~> 1.0)
-    google-cloud-core (1.6.1)
+    google-cloud-core (1.7.0)
       google-cloud-env (>= 1.0, < 3.a)
       google-cloud-errors (~> 1.0)
     google-cloud-env (2.1.1)
       faraday (>= 1.0, < 3.a)
-    google-cloud-errors (1.3.1)
-    google-protobuf (3.25.2-aarch64-linux)
-    google-protobuf (3.25.2-arm64-darwin)
-    google-protobuf (3.25.2-x86_64-darwin)
-    google-protobuf (3.25.2-x86_64-linux)
-    googleapis-common-protos (1.4.0)
-      google-protobuf (~> 3.14)
-      googleapis-common-protos-types (~> 1.2)
-      grpc (~> 1.27)
-    googleapis-common-protos-types (1.11.0)
+    google-cloud-errors (1.4.0)
+    google-protobuf (3.25.3-aarch64-linux)
+    google-protobuf (3.25.3-arm64-darwin)
+    google-protobuf (3.25.3-x86_64-darwin)
+    google-protobuf (3.25.3-x86_64-linux)
+    googleapis-common-protos (1.5.0)
       google-protobuf (~> 3.18)
-    googleauth (1.10.0)
+      googleapis-common-protos-types (~> 1.7)
+      grpc (~> 1.41)
+    googleapis-common-protos-types (1.13.0)
+      google-protobuf (~> 3.18)
+    googleauth (1.11.0)
       faraday (>= 1.0, < 3.a)
       google-cloud-env (~> 2.1)
       jwt (>= 1.4, < 3.0)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
-    grpc (1.61.0-aarch64-linux)
+    grpc (1.62.0-aarch64-linux)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.61.0-arm64-darwin)
+    grpc (1.62.0-arm64-darwin)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.61.0-x86_64-darwin)
+    grpc (1.62.0-x86_64-darwin)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.61.0-x86_64-linux)
+    grpc (1.62.0-x86_64-linux)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
     haml (5.2.2)
@@ -206,10 +206,11 @@ GEM
     json-schema (2.8.1)
       addressable (>= 2.4)
     json_pure (2.7.1)
-    jwt (2.7.1)
+    jwt (2.8.1)
+      base64
     kgio (2.11.4)
     language_server-protocol (3.17.0.3)
-    libxml-ruby (5.0.2)
+    libxml-ruby (5.0.3)
     logger (1.6.0)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
@@ -221,7 +222,7 @@ GEM
     method_source (1.0.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0206)
+    mime-types-data (3.2024.0305)
     mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-stub_any_instance (1.0.3)
@@ -271,7 +272,7 @@ GEM
       rack (>= 0.4)
     rack-cors (1.0.6)
       rack (>= 1.6.0)
-    rack-mini-profiler (3.3.0)
+    rack-mini-profiler (3.3.1)
       rack (>= 1.2.0)
     rack-protection (1.5.5)
       rack
@@ -286,7 +287,7 @@ GEM
     redcarpet (3.6.0)
     redis (5.1.0)
       redis-client (>= 0.17.0)
-    redis-client (0.19.1)
+    redis-client (0.21.0)
       connection_pool
     redis-rack-cache (2.2.1)
       rack-cache (>= 1.10, < 2)
@@ -303,26 +304,26 @@ GEM
     rsolr (2.5.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.60.2)
+    rubocop (1.62.1)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
       parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
       rexml (>= 3.2.5, < 4.0)
-      rubocop-ast (>= 1.30.0, < 2.0)
+      rubocop-ast (>= 1.31.1, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.30.0)
-      parser (>= 3.2.1.0)
+    rubocop-ast (1.31.2)
+      parser (>= 3.3.0.4)
     ruby-progressbar (1.13.0)
     ruby-xxHash (0.4.0.2)
     ruby2_keywords (0.0.5)
     rubyzip (2.3.2)
     rufus-scheduler (2.0.24)
       tzinfo (>= 0.3.22)
-    signet (0.18.0)
+    signet (0.19.0)
       addressable (~> 2.8)
       faraday (>= 0.17.5, < 3.a)
       jwt (>= 1.5, < 3.0)
@@ -374,6 +375,7 @@ PLATFORMS
   aarch64-linux
   arm64-darwin-22
   arm64-darwin-23
+  x86_64-darwin-18
   x86_64-darwin-23
   x86_64-linux
 

docker-compose.yml

@@ -95,7 +95,7 @@ services:
       - 4store
 
   solr-ut:
-    image: ontoportal/solr-ut:0.0.2
+    image: ontoportal/solr-ut:0.1.0
     healthcheck:
       test: ["CMD-SHELL", "curl -sf http://localhost:8983/solr/term_search_core1/admin/ping?wt=json | grep -iq '\"status\":\"OK\"}' || exit 1"]
       start_period: 3s
@@ -114,7 +114,7 @@ services:
       retries: 5
 
   agraph-ut:
-    image: franzinc/agraph:v8.0.1
+    image: franzinc/agraph:v8.1.0
     platform: linux/amd64
     environment:
       - AGRAPH_SUPER_USER=test

helpers/application_helper.rb

@@ -21,9 +21,10 @@ def populate_from_params(obj, params)
 
         # Make sure everything is loaded
         if obj.is_a?(LinkedData::Models::Base)
-          obj.bring_remaining unless !obj.exist?
+          obj.bring_remaining if obj.exist?
+          no_writable_attributes = obj.class.attributes(:all) - obj.class.attributes
+          params = params.reject  {|k,v| no_writable_attributes.include? k.to_sym}
         end
-
         params.each do |attribute, value|
           next if value.nil?
 
@@ -346,8 +347,7 @@ def uri_as_needed(id)
       # If the setting is enabled, replace the URL prefix with the proper id prefix
       # EX: http://stagedata.bioontology.org/ontologies/BRO would become http://data.bioontology.org/ontologies/BRO
       def replace_url_prefix(id)
-        id = id.sub(LinkedData.settings.rest_url_prefix, LinkedData.settings.id_url_prefix) if LinkedData.settings.replace_url_prefix && id.start_with?(LinkedData.settings.rest_url_prefix)
-        id
+        LinkedData::Models::Base.replace_url_prefix_to_id(id)
       end
 
       def retrieve_latest_submissions(options = {})

helpers/batch_helper.rb

@@ -20,9 +20,8 @@ def batch_class_lookup(class_id_by_ontology, goo_include)
         class_id_to_ontology = Hash.new
         class_id_by_ontology.keys.each do |ont_id_orig|
           ont_id = ont_id_orig
-          if LinkedData.settings.replace_url_prefix && ont_id_orig.to_s.start_with?(LinkedData.settings.rest_url_prefix)
-            ont_id = ont_id_orig.sub(LinkedData.settings.rest_url_prefix, LinkedData.settings.id_url_prefix)
-          end
+          ont_id = LinkedData::Models::Base.replace_url_prefix_to_id(ont_id_orig.to_s)
+
           if all_latest_by_id[ont_id]
             latest_submissions << all_latest_by_id[ont_id]
             all_class_ids << class_id_by_ontology[ont_id_orig]
@@ -43,10 +42,7 @@ def batch_class_lookup(class_id_by_ontology, goo_include)
           ont_classes.each do |cls|
             if class_id_to_ontology[cls.id.to_s]
               ont_id_orig = class_id_to_ontology[cls.id.to_s]
-              ont_id = ont_id_orig
-              if LinkedData.settings.replace_url_prefix && ont_id_orig.to_s.start_with?(LinkedData.settings.rest_url_prefix)
-                ont_id = ont_id_orig.sub(LinkedData.settings.rest_url_prefix, LinkedData.settings.id_url_prefix)
-              end
+              ont_id = LinkedData::Models::Base.replace_url_prefix_to_id(ont_id_orig.to_s)
               if all_latest_by_id[ont_id]
                 cls.submission = all_latest_by_id[ont_id]
                 to_reply << cls

helpers/search_helper.rb

@@ -46,8 +46,8 @@ module SearchHelper
           "labelSuggestNgram" => MATCH_TYPE_LABEL,
           MATCH_TYPE_LABELGENERATED => MATCH_TYPE_LABELGENERATED,
           "labelGeneratedExact" => MATCH_TYPE_LABELGENERATED,
-          "labellabelGeneratedSuggestEdge" => MATCH_TYPE_LABELGENERATED,
-          "labellabelGeneratedSuggestNgram" => MATCH_TYPE_LABELGENERATED,
+          "labelGeneratedSuggestEdge" => MATCH_TYPE_LABELGENERATED,
+          "labelGeneratedSuggestNgram" => MATCH_TYPE_LABELGENERATED,
           "notation" => "notation",
           "cui" => "cui",
           "semanticType" => "semanticType"
@@ -57,6 +57,7 @@ module SearchHelper
       QUERYLESS_FIELDS_PARAMS = {
           "ontologies" => nil,
           "notation" => "notation",
+          "oboId" => "oboId",
           "cui" => "cui",
           "semantic_types" => "semanticType",
           ONTOLOGY_TYPES_PARAM => "ontologyType",
@@ -65,6 +66,7 @@ module SearchHelper
       }
 
       QUERYLESS_FIELDS_STR = QUERYLESS_FIELDS_PARAMS.values.compact.join(" ")
+      QUERYLESS_FIELDS_STR_NO_IDS = QUERYLESS_FIELDS_STR.gsub(/(notation|oboId)\s/, '')
 
       def get_term_search_query(text, params={})
         validate_params_solr_population(ALLOWED_INCLUDES_PARAMS)
@@ -98,7 +100,7 @@ def get_term_search_query(text, params={})
 
         if params[EXACT_MATCH_PARAM] == "true"
           query = "\"#{solr_escape(text)}\""
-          params["qf"] = "resource_id^20 prefLabelExact^10 synonymExact #{QUERYLESS_FIELDS_STR}"
+          params["qf"] = "resource_id^20 notation^20 oboId^20 prefLabelExact^10 synonymExact #{QUERYLESS_FIELDS_STR_NO_IDS}"
           params["hl.fl"] = "resource_id prefLabelExact synonymExact #{QUERYLESS_FIELDS_STR}"
         elsif params[SUGGEST_PARAM] == "true" || text[-1] == '*'
           text.gsub!(/\*+$/, '')
@@ -113,9 +115,9 @@ def get_term_search_query(text, params={})
           else
             query = solr_escape(text)
           end
-
-          params["qf"] = "resource_id^100 prefLabelExact^90 prefLabel^70 synonymExact^50 synonym^10 #{QUERYLESS_FIELDS_STR}"
+          params["qf"] = "resource_id^100 notation^100 oboId^100 prefLabelExact^90 prefLabel^70 synonymExact^50 synonym^10 #{QUERYLESS_FIELDS_STR_NO_IDS}"
           params["qf"] << " property" if params[INCLUDE_PROPERTIES_PARAM] == "true"
+          params["bq"] = "idAcronymMatch:true^80"
           params["hl.fl"] = "resource_id prefLabelExact prefLabel synonymExact synonym #{QUERYLESS_FIELDS_STR}"
           params["hl.fl"] = "#{params["hl.fl"]} property" if params[INCLUDE_PROPERTIES_PARAM] == "true"
         end

test/controllers/test_ontologies_controller.rb

@@ -291,6 +291,8 @@ def test_on_demand_ontology_pull
       del.delete if del
       stop_server
       LinkedData.settings.enable_security = false
+      del = User.find("blocked").first
+      del.delete if del
     end
   end