Merge remote-tracking branch 'origin/development' into feature/add-on…

…toportal-api-configs

Gemfile.lock

@@ -57,7 +57,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: f0098d7030541cf65e29f898c3315e2a2b9df95e
+  revision: 552fbe5faed5bb195396251066ef0e7b930939a0
   branch: development
   specs:
     ontologies_linked_data (0.0.1)
@@ -121,7 +121,7 @@ GEM
       i18n
       rake (>= 10.0.0)
       sshkit (>= 1.9.0)
-    capistrano-bundler (2.1.0)
+    capistrano-bundler (2.1.1)
       capistrano (~> 3.1)
     capistrano-locally (0.3.0)
       capistrano (~> 3.0)
@@ -138,7 +138,7 @@ GEM
     dante (0.2.0)
     date (3.3.4)
     declarative (0.0.20)
-    docile (1.4.0)
+    docile (1.4.1)
     domain_name (0.6.20240107)
     ed25519 (1.3.0)
     faraday (1.10.3)
@@ -164,7 +164,7 @@ GEM
     faraday-patron (1.0.0)
     faraday-rack (1.0.0)
     faraday-retry (1.0.3)
-    ffi (1.16.3)
+    ffi (1.17.0)
     gapic-common (0.21.1)
       faraday (>= 1.9, < 3.a)
       faraday-retry (>= 1.0, < 3.a)
@@ -178,27 +178,26 @@ GEM
     google-analytics-data (0.6.0)
       google-analytics-data-v1beta (>= 0.11, < 2.a)
       google-cloud-core (~> 1.6)
-    google-analytics-data-v1beta (0.12.0)
+    google-analytics-data-v1beta (0.13.0)
       gapic-common (>= 0.21.1, < 2.a)
       google-cloud-errors (~> 1.0)
     google-apis-analytics_v3 (0.16.0)
       google-apis-core (>= 0.15.0, < 2.a)
-    google-apis-core (0.15.0)
+    google-apis-core (0.15.1)
       addressable (~> 2.5, >= 2.5.1)
       googleauth (~> 1.9)
-      httpclient (>= 2.8.1, < 3.a)
+      httpclient (>= 2.8.3, < 3.a)
       mini_mime (~> 1.0)
+      mutex_m
       representable (~> 3.0)
       retriable (>= 2.0, < 4.a)
-      rexml
-    google-cloud-core (1.7.0)
+    google-cloud-core (1.7.1)
       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 (1.4.0)
-    google-protobuf (3.25.3)
-    google-protobuf (3.25.3-x86_64-linux)
+    google-protobuf (3.25.4)
     googleapis-common-protos (1.6.0)
       google-protobuf (>= 3.18, < 5.a)
       googleapis-common-protos-types (~> 1.7)
@@ -212,16 +211,13 @@ GEM
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
-    grpc (1.65.1)
-      google-protobuf (>= 3.25, < 5.0)
-      googleapis-common-protos-types (~> 1.0)
-    grpc (1.65.1-x86_64-linux)
+    grpc (1.65.2-x86_64-linux)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
     haml (5.2.2)
       temple (>= 0.8.0)
       tilt
-    hashdiff (1.1.0)
+    hashdiff (1.1.1)
     htmlentities (4.3.4)
     http-accept (1.7.0)
     http-cookie (1.0.6)
@@ -251,14 +247,15 @@ GEM
     method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0702)
+    mime-types-data (3.2024.0806)
     mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-stub_any_instance (1.0.3)
     mlanett-redis-lock (0.2.7)
       redis
     multi_json (1.15.0)
     multipart-post (2.4.1)
+    mutex_m (0.2.0)
     net-http-persistent (4.0.2)
       connection_pool (~> 2.2)
     net-imap (0.4.14)
@@ -344,7 +341,7 @@ GEM
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
     retriable (3.1.2)
-    rexml (3.3.2)
+    rexml (3.3.4)
       strscan
     rsolr (2.6.0)
       builder (>= 2.1.2)
@@ -409,7 +406,6 @@ GEM
       hashdiff (>= 0.4.0, < 2.0.0)
 
 PLATFORMS
-  ruby
   x86_64-linux
 
 DEPENDENCIES

controllers/agents_controller.rb

@@ -1,8 +1,29 @@
 class AgentsController < ApplicationController
 
-  %w[/agents /Agents].each do |namespace|
-    namespace namespace do
-      # Display all agents
+  get '/ontologies/:acronym/agents' do
+    ont = Ontology.find(params["acronym"]).first
+    latest = ont.latest_submission(status: :any)
+    latest.bring(*OntologySubmission.agents_attrs)
+    properties_agents= {}
+    OntologySubmission.agents_attrs.each do |attr|
+      properties_agents[attr] = Array(latest.send(attr))
+    end
+
+    agents =  []
+    properties_agents.each do |key, value|
+      agents.concat(value.map{ |agent| agent.bring_remaining})
+    end
+    agents.uniq!
+
+    if includes_param.include?(:all) || includes_param.include?(:usages)
+      LinkedData::Models::Agent.load_agents_usages(agents)
+    end
+
+    reply agents
+  end
+
+  %w[agents Agents].each do |namespace|
+    namespace "/#{namespace}" do
       get do
         check_last_modified_collection(LinkedData::Models::Agent)
         query = LinkedData::Models::Agent.where
@@ -147,4 +168,4 @@ def update_agent(agent, params)
     end
   end
 
-end
+end

controllers/home_controller.rb

@@ -13,11 +13,15 @@ class HomeController < ApplicationController
       expires 3600, :public
       last_modified @@root_last_modified ||= Time.now.httpdate
       routes = routes_list
+
       #TODO: delete when ccv will be on production
       routes.delete("/ccv")
       if LinkedData.settings.enable_resource_index == false
         routes.delete("/resource_index")
       end
+
+      routes.delete('/Agents')
+
       routes_hash = {}
       context = {}
       routes.each do |route|

controllers/properties_controller.rb

@@ -24,7 +24,7 @@ class PropertiesController < ApplicationController
     get '/:property' do
       prop = params[:property]
       ont, submission = get_ontology_and_submission
-      p = ont.property(prop, submission)
+      p = ont.property(prop, submission, display_all_attributes: false)
       error 404, "Property #{prop} not found in ontology #{ont.id.to_s}" if p.nil?
       reply 200, p
     end
@@ -51,7 +51,7 @@ class PropertiesController < ApplicationController
     get '/:property/tree' do
       prop = params[:property]
       ont, submission = get_ontology_and_submission
-      p = ont.property(prop, submission)
+      p = ont.property(prop, submission, display_all_attributes: false)
       error 404, "Property #{prop} not found in ontology #{ont.id.to_s}" if p.nil?
       root_tree = p.tree
 
@@ -79,7 +79,7 @@ class PropertiesController < ApplicationController
     get '/:property/ancestors' do
       prop = params[:property]
       ont, submission = get_ontology_and_submission
-      p = ont.property(prop, submission)
+      p = ont.property(prop, submission, display_all_attributes: false)
       error 404, "Property #{prop} not found in ontology #{ont.id.to_s}" if p.nil?
       ancestors = p.ancestors
       p.class.in(submission).models(ancestors).include(:label, :definition).all
@@ -91,7 +91,7 @@ class PropertiesController < ApplicationController
     get '/:property/descendants' do
       prop = params[:property]
       ont, submission = get_ontology_and_submission
-      p = ont.property(prop, submission)
+      p = ont.property(prop, submission, display_all_attributes: false)
       error 404, "Property #{prop} not found in ontology #{ont.id.to_s}" if p.nil?
       descendants = p.descendants
       p.class.in(submission).models(descendants).include(:label, :definition).all
@@ -103,7 +103,7 @@ class PropertiesController < ApplicationController
     get '/:property/parents' do
       prop = params[:property]
       ont, submission = get_ontology_and_submission
-      p = ont.property(prop, submission)
+      p = ont.property(prop, submission, display_all_attributes: false)
       error 404, "Property #{prop} not found in ontology #{ont.id.to_s}" if p.nil?
 
       p.bring(:parents)
@@ -120,7 +120,7 @@ class PropertiesController < ApplicationController
     get '/:property/children' do
       prop = params[:property]
       ont, submission = get_ontology_and_submission
-      p = ont.property(prop, submission)
+      p = ont.property(prop, submission, display_all_attributes: false)
       error 404, "Property #{prop} not found in ontology #{ont.id.to_s}" if p.nil?
 
       p.bring(:children)

controllers/search_controller.rb

@@ -63,7 +63,7 @@ class SearchController < ApplicationController
           page_size: page_size,
           sort: sort
         })
-        
+
         total_found = page_data.aggregate
         ontology_rank = LinkedData::Models::Ontology.rank
         docs = {}
@@ -153,11 +153,17 @@ class SearchController < ApplicationController
 
         fq = "agentType_t:#{type}" if type
 
-        qf = [
-          "acronymSuggestEdge^25  nameSuggestEdge^15 emailSuggestEdge^15 identifiersSuggestEdge^10 ", # start of the word first
-          "identifiers_texts^20 acronym_text^15  name_text^10 email_text^10 ", # full word match
-          "acronymSuggestNgram^2 nameSuggestNgram^1.5 email_text^1" # substring match last
-        ].join(' ')
+        if params[:qf]
+          qf = params[:qf]
+        else
+          qf = [
+            "acronymSuggestEdge^25  nameSuggestEdge^15 emailSuggestEdge^15 identifiersSuggestEdge^10 ", # start of the word first
+            "identifiers_texts^20 acronym_text^15  name_text^10 email_text^10 ", # full word match
+            "acronymSuggestNgram^2 nameSuggestNgram^1.5 email_text^1" # substring match last
+          ].join(' ')
+        end
+
+
 
         if params[:sort]
           sort = "#{params[:sort]} asc, score desc"
@@ -230,6 +236,9 @@ def process_search(params = nil)
         doc[:submission] = submission
         doc[:ontology_rank] = (ontology_rank[doc[:submissionAcronym]] && !ontology_rank[doc[:submissionAcronym]].empty?) ? ontology_rank[doc[:submissionAcronym]][:normalizedScore] : 0.0
         doc[:properties] = MultiJson.load(doc.delete(:propertyRaw)) if include_param_contains?(:properties)
+
+        doc = filter_attrs_by_language(doc)
+
         instance = doc[:provisional] ? LinkedData::Models::ProvisionalClass.read_only(doc) : LinkedData::Models::Class.read_only(doc)
         docs.push(instance)
       end

docker-compose.yml

@@ -31,6 +31,7 @@ services:
     environment:
       <<: *env
       BUNDLE_APP_CONFIG: /srv/ontoportal/ontologies_api/.bundle
+
     profiles:
       - 4store
     depends_on:
@@ -48,7 +49,7 @@ services:
       - "9393:9393"
     volumes:
       # bundle volume for hosting gems installed by bundle; it speeds up gem install in local development
-      - app_api:/srv/ontoportal/ontologies_api
+      - .:/srv/ontoportal/ontologies_api
       - repository:/srv/ontoportal/data/repository
 
   ncbo_cron: