From 169afb7c1002f9db2b3276af36d552575cc80ba2 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Wed, 18 Oct 2023 04:24:05 +0200
Subject: [PATCH 01/18] use $DEBUG_API_CLIENT instead of $DEBUG for debugging 
 request

---
 lib/ontologies_api_client/http.rb | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/ontologies_api_client/http.rb b/lib/ontologies_api_client/http.rb
index 8b736eb..ecb809c 100644
--- a/lib/ontologies_api_client/http.rb
+++ b/lib/ontologies_api_client/http.rb
@@ -61,7 +61,7 @@ def self.get(path, params = {}, options = {})
         invalidate_cache = params.delete(:invalidate_cache) || false
 
         begin
-          puts "Getting: #{path} with #{params}" if $DEBUG
+          puts "Getting: #{path} with #{params}" if $DEBUG_API_CLIENT
           begin
             response = conn.get do |req|
               req.url path
@@ -87,7 +87,7 @@ def self.get(path, params = {}, options = {})
             obj = recursive_struct(load_json(response.body))
           end
         rescue StandardError => e
-          puts "Problem getting #{path}" if $DEBUG
+          puts "Problem getting #{path}" if $DEBUG_API_CLIENT
           raise e
         end
         obj
@@ -143,7 +143,7 @@ def self.patch(path, obj)
       end
 
       def self.delete(id)
-        puts "Deleting #{id}" if $DEBUG
+        puts "Deleting #{id}" if $DEBUG_API_CLIENT
         response = conn.delete id
         raise StandardError, response.body if response.status >= 500
 

From 38e4299d8cad25aef71779704d9eff1aabbca1ce Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Sun, 17 Dec 2023 00:31:29 +0100
Subject: [PATCH 02/18] add  $API_CLIENT_INVALIDATE_CACHE option to disable
 cache

---
 lib/ontologies_api_client/http.rb | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/lib/ontologies_api_client/http.rb b/lib/ontologies_api_client/http.rb
index ecb809c..d3df241 100644
--- a/lib/ontologies_api_client/http.rb
+++ b/lib/ontologies_api_client/http.rb
@@ -2,7 +2,7 @@
 require 'multi_json'
 require 'digest'
 require 'ostruct'
-
+require 'benchmark'
 ##
 # This monkeypatch makes OpenStruct act like Struct objects
 class OpenStruct
@@ -58,18 +58,20 @@ def self.get(path, params = {}, options = {})
         raw = options[:raw] || false # return the unparsed body of the request
         params = params.delete_if { |k, v| v == nil || v.to_s.empty? }
         params[:ncbo_cache_buster] = Time.now.to_f if raw # raw requests don't get cached to ensure body is available
-        invalidate_cache = params.delete(:invalidate_cache) || false
-
+        invalidate_cache = params.delete(:invalidate_cache) || $API_CLIENT_INVALIDATE_CACHE || false
         begin
-          puts "Getting: #{path} with #{params}" if $DEBUG_API_CLIENT
           begin
-            response = conn.get do |req|
-              req.url path
-              req.params = params.dup
-              req.options[:timeout] = 60
-              req.headers.merge(headers)
-              req.headers[:invalidate_cache] = invalidate_cache
+            response = nil
+            time = Benchmark.realtime do
+              response = conn.get do |req|
+                req.url path
+                req.params = params.dup
+                req.options[:timeout] = 60
+                req.headers.merge(headers)
+                req.headers[:invalidate_cache] = invalidate_cache
+              end
             end
+            puts "Getting: #{path} with #{params} (#{time}s)" if $DEBUG_API_CLIENT
           rescue Exception => e
             params = Faraday::Utils.build_query(params)
             path << "?" unless params.empty? || path.include?("?")

From fe41668785affb77cc6d8a133da800819529447f Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Mon, 18 Dec 2023 06:33:58 +0100
Subject: [PATCH 03/18] save and re-use the top_level_links http response as
 the result do not change

---
 Gemfile.lock                            | 3 ++-
 lib/ontologies_api_client/collection.rb | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 2d0a48c..77dace9 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -54,6 +54,7 @@ GEM
 
 PLATFORMS
   x86_64-darwin-21
+  x86_64-darwin-23
   x86_64-linux
 
 DEPENDENCIES
@@ -63,4 +64,4 @@ DEPENDENCIES
   test-unit
 
 BUNDLED WITH
-   2.3.23
+   2.4.21
diff --git a/lib/ontologies_api_client/collection.rb b/lib/ontologies_api_client/collection.rb
index 97ccc0f..7e6b476 100644
--- a/lib/ontologies_api_client/collection.rb
+++ b/lib/ontologies_api_client/collection.rb
@@ -25,7 +25,7 @@ def method_missing(meth, *args, &block)
         ##
         # Get all top-level links for the API
         def top_level_links
-          HTTP.get(LinkedData::Client.settings.rest_url)
+          @top_level_links||= HTTP.get(LinkedData::Client.settings.rest_url)
         end
 
         ##

From ab9048ec0dd2b4b5ef1aef9d40fa0df61282b5ef Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Mon, 18 Dec 2023 06:35:33 +0100
Subject: [PATCH 04/18] deprecate the find method in favor of get method for
 better performance

---
 lib/ontologies_api_client/collection.rb      | 8 ++++----
 lib/ontologies_api_client/models/ontology.rb | 5 ++++-
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/lib/ontologies_api_client/collection.rb b/lib/ontologies_api_client/collection.rb
index 7e6b476..6e0e36f 100644
--- a/lib/ontologies_api_client/collection.rb
+++ b/lib/ontologies_api_client/collection.rb
@@ -75,16 +75,16 @@ def where(params = {}, &block)
 
         ##
         # Find a resource by id
+        # @deprecated replace with "get"
         def find(id, params = {})
-          found = where do |obj|
-            obj.id.eql?(id)
-          end
-          found.first
+          [get(id, params)]
         end
 
         ##
         # Get a resource by id (this will retrieve it from the REST service)
         def get(id, params = {})
+          path = collection_path
+          id = "#{path}/#{id}" unless id.include?(path)
           HTTP.get(id, params)
         end
 
diff --git a/lib/ontologies_api_client/models/ontology.rb b/lib/ontologies_api_client/models/ontology.rb
index 5db6ed4..0aeb365 100644
--- a/lib/ontologies_api_client/models/ontology.rb
+++ b/lib/ontologies_api_client/models/ontology.rb
@@ -108,7 +108,7 @@ def self.find_by(attrs, *args)
         # Override to search for views as well by default
         # Views get hidden on the REST service unless the `include_views`
         # parameter is set to `true`
-        def find(id, params = {})
+        def self.find(id, params = {})
           params[:include_views] = params[:include_views] || true
           super(id, params)
         end
@@ -119,6 +119,9 @@ def self.include_params
           "acronym,administeredBy,group,hasDomain,name,notes,projects,reviews,summaryOnly,viewingRestriction"
         end
 
+        def self.find_by_acronym(acronym, params = {})
+          [find(acronym, params)]
+        end
       end
     end
   end

From 674193220f93d99587e6d3a969adcb384caf0a61 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Mon, 18 Dec 2023 06:36:32 +0100
Subject: [PATCH 05/18] disable the refresh_cache on each update call

---
 lib/ontologies_api_client/collection.rb      | 2 +-
 lib/ontologies_api_client/models/ontology.rb | 4 ----
 lib/ontologies_api_client/read_write.rb      | 2 +-
 3 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/lib/ontologies_api_client/collection.rb b/lib/ontologies_api_client/collection.rb
index 6e0e36f..77572bf 100644
--- a/lib/ontologies_api_client/collection.rb
+++ b/lib/ontologies_api_client/collection.rb
@@ -77,7 +77,7 @@ def where(params = {}, &block)
         # Find a resource by id
         # @deprecated replace with "get"
         def find(id, params = {})
-          [get(id, params)]
+          get(id, params)
         end
 
         ##
diff --git a/lib/ontologies_api_client/models/ontology.rb b/lib/ontologies_api_client/models/ontology.rb
index 0aeb365..5a62a01 100644
--- a/lib/ontologies_api_client/models/ontology.rb
+++ b/lib/ontologies_api_client/models/ontology.rb
@@ -52,10 +52,6 @@ def admin?(user)
           return administeredBy.any? {|u| u == user.id}
         end
 
-        def invalidate_cache(cache_refresh_all = true)
-          self.class.all(invalidate_cache: true, include_views: true)
-          super(cache_refresh_all)
-        end
 
         # ACL with administrators
         def full_acl
diff --git a/lib/ontologies_api_client/read_write.rb b/lib/ontologies_api_client/read_write.rb
index 721c669..3549bb0 100644
--- a/lib/ontologies_api_client/read_write.rb
+++ b/lib/ontologies_api_client/read_write.rb
@@ -90,7 +90,7 @@ def invalidate_cache(cache_refresh_all = true)
         HTTP.get(self.id, invalidate_cache: true) if self.id
         session = Thread.current[:session]
         session[:last_updated] = Time.now.to_f if session
-        refresh_cache
+        # refresh_cache
       end
 
       def refresh_cache

From 4eb424539f114a96c4af7cee2800ca25af88afd7 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Sun, 14 Apr 2024 15:18:14 +0200
Subject: [PATCH 06/18] Refactor: update cache code and add tests (#15)

* add tests for the api cache code

* refactor the cache middleware code

* remove unused function in the cache middleware
---
 Gemfile                                       |   3 +-
 Gemfile.lock                                  |  14 ++
 config/config.test.rb                         |   3 +-
 .../middleware/faraday-object-cache.rb        | 213 ++++++++----------
 test/middleware/test_cache.rb                 | 141 ++++++++++++
 5 files changed, 259 insertions(+), 115 deletions(-)
 create mode 100644 test/middleware/test_cache.rb

diff --git a/Gemfile b/Gemfile
index acdf917..b7f6653 100644
--- a/Gemfile
+++ b/Gemfile
@@ -4,4 +4,5 @@ gemspec
 
 gem 'rake'
 gem 'pry'
-gem 'test-unit'
\ No newline at end of file
+gem 'test-unit'
+gem 'webmock', require: false
\ No newline at end of file
diff --git a/Gemfile.lock b/Gemfile.lock
index 77dace9..413fd8c 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -20,8 +20,14 @@ GEM
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
       tzinfo (~> 2.0)
+    addressable (2.8.6)
+      public_suffix (>= 2.0.2, < 6.0)
+    bigdecimal (3.1.7)
     coderay (1.1.3)
     concurrent-ruby (1.1.10)
+    crack (1.0.0)
+      bigdecimal
+      rexml
     excon (0.95.0)
     faraday (2.0.1)
       faraday-net_http (~> 2.0)
@@ -32,6 +38,7 @@ GEM
     faraday-multipart (1.0.4)
       multipart-post (~> 2)
     faraday-net_http (2.1.0)
+    hashdiff (1.1.0)
     i18n (1.12.0)
       concurrent-ruby (~> 1.0)
     lz4-ruby (0.3.3)
@@ -44,13 +51,19 @@ GEM
     pry (0.14.1)
       coderay (~> 1.1)
       method_source (~> 1.0)
+    public_suffix (5.0.5)
     rake (13.0.6)
+    rexml (3.2.6)
     ruby2_keywords (0.0.5)
     spawnling (2.1.5)
     test-unit (3.5.7)
       power_assert
     tzinfo (2.0.5)
       concurrent-ruby (~> 1.0)
+    webmock (3.23.0)
+      addressable (>= 2.8.0)
+      crack (>= 0.3.2)
+      hashdiff (>= 0.4.0, < 2.0.0)
 
 PLATFORMS
   x86_64-darwin-21
@@ -62,6 +75,7 @@ DEPENDENCIES
   pry
   rake
   test-unit
+  webmock
 
 BUNDLED WITH
    2.4.21
diff --git a/config/config.test.rb b/config/config.test.rb
index af6837b..a5d6166 100644
--- a/config/config.test.rb
+++ b/config/config.test.rb
@@ -3,7 +3,8 @@
 # be set via ENV variable UT_APIKEY
 abort('UT_APIKEY env variable is not set. Canceling tests') unless ENV.include?('UT_APIKEY')
 abort('UT_APIKEY env variable is set to an empty value. Canceling tests') unless ENV['UT_APIKEY'].size > 5
-
+$API_CLIENT_INVALIDATE_CACHE = false
+$DEBUG_API_CLIENT = false
 LinkedData::Client.config do |config|
   config.rest_url   = 'https://data.bioontology.org'
   config.apikey     = ENV['UT_APIKEY']
diff --git a/lib/ontologies_api_client/middleware/faraday-object-cache.rb b/lib/ontologies_api_client/middleware/faraday-object-cache.rb
index f5e06d3..4e9eb65 100644
--- a/lib/ontologies_api_client/middleware/faraday-object-cache.rb
+++ b/lib/ontologies_api_client/middleware/faraday-object-cache.rb
@@ -8,107 +8,47 @@ class ObjectCacheResponse < Faraday::Response
     attr_accessor :parsed_body
   end
 
-  ##
-  # This middleware causes Faraday to return an actual object instead of a response
-  # This is done so that the object is cached instead of the unparsed json body.
-  # Otherwise, we have to re-parse the json on every cache hit, which is extrememly costly
-  # when compared to unmarshaling an object.
   class ObjectCache < Faraday::Middleware
     def initialize(app, *arguments)
       super(app)
+      options = arguments.last.is_a?(Hash) ? arguments.pop : {}
+      @logger = options.delete(:logger)
+      @store = options[:store] || ActiveSupport::Cache.lookup_store(nil, options)
+    end
 
-      if arguments.last.is_a? Hash
-        options = arguments.pop
-        @logger = options.delete(:logger)
-      else
-        options = arguments
-      end
 
-      @store = options[:store] || ActiveSupport::Cache.lookup_store(store, options)
+    def last_modified_key_id(request_key)
+      "LM::#{request_key}"
+    end
+
+    def last_retrieved_key_id(request_key)
+      "LR::#{request_key}"
     end
 
     def call(env)
       invalidate_cache = env[:request_headers].delete(:invalidate_cache)
 
-      # Add if newer than last modified statement to headers
       request_key = cache_key_for(create_request(env))
-      last_modified_key = "LM::#{request_key}"
-      last_retrieved_key = "LR::#{request_key}"
+      last_modified_key = last_modified_key_id(request_key)
+      last_retrieved_key = last_retrieved_key_id(request_key)
 
-      # If we invalidate the cache, then it forces a clean request
       if invalidate_cache
-        cache_delete(request_key)
-        cache_delete(last_modified_key)
-        cache_delete(last_retrieved_key)
+        delete_cache_entries(request_key, last_modified_key, last_retrieved_key)
         env[:request_headers]["Cache-Control"] = "no-cache"
         puts "Invalidated key #{request_key}" if enable_debug(request_key)
       end
 
-      # If we made the last request within the expiry
       if cache_exist?(last_retrieved_key) && cache_exist?(request_key)
         puts "Not expired: #{env[:url].to_s}, key #{request_key}" if enable_debug(request_key)
-        cached_item = cache_read(request_key)
-        ld_obj = cached_item.is_a?(Hash) && cached_item.key?(:ld_obj) ? cached_item[:ld_obj] : cached_item
-        env[:status] = 304
-        cached_response = ObjectCacheResponse.new(env)
-        cached_response.parsed_body = ld_obj
-        return cached_response
+        return retrieve_cached_response(request_key)
       end
 
-      last_modified = cache_read(last_modified_key)
       headers = env[:request_headers]
-      puts "last modified: " + last_modified.to_s if last_modified && enable_debug(request_key)
-      headers['If-Modified-Since'] = last_modified if last_modified
+      headers['If-Modified-Since'] = cache_read(last_modified_key) if cache_read(last_modified_key)
 
       @app.call(env).on_complete do |response_env|
-        # Only cache get and head requests
         if [:get, :head].include?(response_env[:method])
-          puts "Response status for key #{request_key}: " + response_env[:status].to_s if enable_debug(request_key)
-          last_modified = response_env[:response_headers]["Last-Modified"]
-          # Generate key using header hash
-          key = request_key
-
-          # If the last retrieve time is less than expiry
-          if response_env[:status] == 304 && cache_exist?(key)
-            stored_obj = cache_read(key)
-
-            # Update if last modified is different
-            if stored_obj[:last_modified] != last_modified
-              puts "Updating cache #{response_env[:url].to_s}, key #{request_key}" if enable_debug(request_key)
-              stored_obj[:last_modified] = last_modified
-              cache_write(last_modified_key, last_modified)
-              cache_write(key, stored_obj)
-            end
-
-            ld_obj = stored_obj[:ld_obj]
-          else
-            if response_env[:body].nil? || response_env[:body].empty?
-              # We got here with an empty body, meaning the object wasn't
-              # in the cache (weird). So re-do the request.
-              puts "REDOING REQUEST, NO CACHE ENTRY for #{response_env[:url].to_s}, key #{request_key}" if enable_debug(request_key)
-              env[:request_headers].delete("If-Modified-Since")
-              response_env = @app.call(env).env
-              puts "REDOING REQUEST expiry: #{response_env[:response_headers]["Cache-Control"]}, last_modified: #{last_modified} for key #{request_key}" if enable_debug(request_key)
-            end
-
-            ld_obj = LinkedData::Client::HTTP.object_from_json(response_env[:body])
-            # This stmt was missing in the old code, resulting in repeated calls to REST because object failed to cache
-            last_modified = response_env[:response_headers]["Last-Modified"]
-            expiry = response_env[:response_headers]["Cache-Control"].to_s.split("max-age=").last.to_i
-            puts "Before storing object: expiry: #{expiry}, last_modified: #{last_modified} for key #{request_key}" if enable_debug(request_key)
-
-            if expiry > 0 && last_modified
-              # This request is cacheable, store it
-              puts "Storing object: #{response_env[:url].to_s}, key #{request_key}" if enable_debug(request_key)
-              stored_obj = {last_modified: last_modified, ld_obj: ld_obj}
-              cache_write(last_modified_key, last_modified)
-              cache_write(last_retrieved_key, true, expires_in: expiry)
-              cache_write(key, stored_obj)
-            end
-          end
-
-          response = ObjectCacheResponse.new(response_env)
-          response.parsed_body = ld_obj
+          response = process_response(response_env, request_key)
           return response
         end
       end
@@ -117,8 +57,83 @@ def call(env)
     private
 
     def enable_debug(key)
-      return true if LinkedData::Client.settings.debug_client && (LinkedData::Client.settings.debug_client_keys.empty? || LinkedData::Client.settings.debug_client_keys.include?(key))
-      false
+      LinkedData::Client.settings.debug_client && (LinkedData::Client.settings.debug_client_keys.empty? || LinkedData::Client.settings.debug_client_keys.include?(key))
+    end
+
+    def delete_cache_entries(*keys)
+      keys.each { |key| cache_delete(key) }
+    end
+
+    def retrieve_cached_response(request_key)
+      cached_item = cache_read(request_key)
+      ld_obj = cached_item.is_a?(Hash) && cached_item.key?(:ld_obj) ? cached_item[:ld_obj] : cached_item
+      env = { status: 304 }
+      cached_response = ObjectCacheResponse.new(env)
+      cached_response.parsed_body = ld_obj
+      cached_response.env.response_headers = { "x-rack-cache" => 'hit' }
+      cached_response
+    end
+
+    def process_response(response_env, request_key)
+      last_modified = response_env[:response_headers]["Last-Modified"]
+      key = request_key
+      cache_state = "miss"
+
+      if response_env[:status] == 304 && cache_exist?(key)
+        cache_state = "fresh"
+        ld_obj = update_cache(request_key, last_modified)
+      else
+        ld_obj = cache_response(response_env, request_key)
+      end
+
+      response = ObjectCacheResponse.new(response_env)
+      response.parsed_body = ld_obj
+      response.env.response_headers["x-rack-cache"] = cache_state
+      response
+    end
+
+    def update_cache(request_key, last_modified)
+      stored_obj = cache_read(request_key)
+      if stored_obj[:last_modified] != last_modified
+        stored_obj[:last_modified] = last_modified
+        cache_write(last_modified_key_id(request_key), last_modified)
+        cache_write(request_key, stored_obj)
+      end
+      stored_obj
+    end
+
+    def cache_response(response_env, request_key)
+      last_modified = response_env[:response_headers]["Last-Modified"]
+
+      if response_env[:body].nil? || response_env[:body].empty?
+        # We got here with an empty body, meaning the object wasn't
+        # in the cache (weird). So re-do the request.
+        puts "REDOING REQUEST, NO CACHE ENTRY for #{response_env[:url].to_s}, key #{request_key}" if enable_debug(request_key)
+        response_env[:request_headers].delete("If-Modified-Since")
+
+        response_env = @app.call(response_env).env
+        puts "REDOING REQUEST expiry: #{response_env[:response_headers]["Cache-Control"]}, last_modified: #{last_modified} for key #{request_key}" if enable_debug(request_key)
+      end
+
+
+      return nil if response_env[:body].nil? || response_env[:body].empty?
+
+      ld_obj = LinkedData::Client::HTTP.object_from_json(response_env[:body])
+
+      expiry = response_env[:response_headers]["Cache-Control"].to_s.split("max-age=").last.to_i
+
+      if expiry > 0 && last_modified
+        store_cache(request_key, ld_obj, last_modified, expiry)
+      end
+
+      ld_obj
+    end
+
+    def store_cache(request_key, ld_obj, last_modified, expiry)
+      stored_obj = { last_modified: last_modified, ld_obj: ld_obj }
+      cache_write(last_modified_key_id(request_key), last_modified)
+      cache_write(last_retrieved_key_id(request_key), true, expires_in: expiry)
+      cache_write(request_key, stored_obj)
     end
 
     def cache_write(key, obj, *args)
@@ -132,12 +147,6 @@ def cache_write(key, obj, *args)
       if result
         return result
       else
-        # This should still get stored in memcache
-        # keep it in memory, though, because
-        # marshal/unmarshal is too slow.
-        # This way memcache will act as a backup
-        # and you load from there if it isn't
-        # in memory yet.
         @large_object_cache ||= {}
         @large_object_cache[key] = obj
         cache_write_compressed(key, obj, *args)
@@ -147,11 +156,10 @@ def cache_write(key, obj, *args)
 
     def cache_read(key)
       obj = @store.read(key)
-      return if obj.nil?
+      return unless obj
+
       if obj.is_a?(CompressedMemcache)
-        # Try to get from the large object cache
         large_obj = @large_object_cache[key] if @large_object_cache
-        # Fallback to the memcache version
         large_obj ||= cache_read_compressed(key)
         obj = large_obj
       end
@@ -162,13 +170,14 @@ def cache_exist?(key)
       @store.exist?(key)
     end
 
-    class CompressedMemcache; attr_accessor :key; end
+    class CompressedMemcache
+      attr_accessor :key
+    end
 
-    ##
-    # Compress cache entry
     def cache_write_compressed(key, obj, *args)
       compressed = LZ4::compress(Marshal.dump(obj))
-      return if compressed.nil?
+      return unless compressed
+
       placeholder = CompressedMemcache.new
       placeholder.key = "#{key}::#{(Time.now.to_f * 1000).to_i}::LZ4"
       begin
@@ -181,8 +190,6 @@ def cache_write_compressed(key, obj, *args)
       end
     end
 
-    ##
-    # Read compressed cache entry
     def cache_read_compressed(key)
       obj = @store.read(key)
       if obj.is_a?(CompressedMemcache)
@@ -190,7 +197,6 @@ def cache_read_compressed(key)
           uncompressed = LZ4::uncompress(@store.read(obj.key))
           obj = Marshal.load(uncompressed)
         rescue StandardError => e
-          # There is a problem with the stored value, let's remove it so we don't get the error again
           @store.delete(key)
           @store.delete(obj.key)
           raise e
@@ -203,35 +209,16 @@ def cache_delete(key)
       @store.delete(key)
     end
 
-    # Internal: Generates a String key for a given request object.
-    # The request object is folded into a sorted Array (since we can't count
-    # on hashes order on Ruby 1.8), encoded as JSON and digested as a `SHA1`
-    # string.
-    #
-    # Returns the encoded String.
     def cache_key_for(request)
       array = request.stringify_keys.to_a.sort
       Digest::SHA1.hexdigest(Marshal.dump(array))
     end
 
-    # Internal: Creates a new 'Hash' containing the request information.
-    #
-    # env - the environment 'Hash' from the Faraday stack.
-    #
-    # Returns a 'Hash' containing the ':method', ':url' and 'request_headers'
-    # entries.
     def create_request(env)
       request = env.to_hash.slice(:method, :url, :request_headers)
       request[:request_headers] = request[:request_headers].dup
       request
     end
-
-    def clean_request_headers(request)
-      request[:request_headers].delete("If-Modified-Since")
-      request[:request_headers].delete("Expect")
-      request
-    end
-
   end
 end
 
diff --git a/test/middleware/test_cache.rb b/test/middleware/test_cache.rb
new file mode 100644
index 0000000..ddea7a9
--- /dev/null
+++ b/test/middleware/test_cache.rb
@@ -0,0 +1,141 @@
+require_relative  '../test_case'
+require 'faraday'
+require 'active_support'
+require 'active_support/cache'
+require_relative '../../lib/ontologies_api_client/middleware/faraday-object-cache'
+require 'pry'
+require 'benchmark'
+require 'webmock'
+
+class FaradayObjectCacheTest < LinkedData::Client::TestCase
+  def setup
+    WebMock.disable!
+    apikey = LinkedData::Client.settings.apikey
+    @url = "#{LinkedData::Client.settings.rest_url}/ontologies/SNOMEDCT?apikey=#{apikey}"
+
+    @cache_store = ActiveSupport::Cache::MemoryStore.new
+    @app = Faraday.new(url: @url) do |faraday|
+      faraday.use Faraday::ObjectCache, store: @cache_store
+      faraday.adapter :excon
+    end
+  end
+
+  def test_cache_hit_for_get_request
+    body1, body2 = nil
+    # First request should not hit the cache
+    time1 = Benchmark.realtime do
+      response1 = @app.get
+      assert_equal 200, response1.status
+      assert uncached?(response1)
+
+      body1 = JSON.parse(response1.body)
+    end
+
+    time2 = Benchmark.realtime do
+      # Second request should hit the cache
+      response2 = @app.get
+      assert_equal 304, response2.status
+      assert cached?(response2)
+      body2 = response2.parsed_body.to_hash.stringify_keys
+    end
+
+    assert time2 < time1
+
+    body2.each do |k,v|
+      k = "@id" if k.eql?('id')
+      k = "@type" if k.eql?('type')
+
+      next if k.eql?('context') || k.eql?('links')
+
+      assert_equal v, body1[k]
+    end
+  end
+
+
+  def test_cache_invalidation
+    # Make a request and cache the response
+    response1 = @app.get
+    assert_equal 200, response1.status
+
+    response1 = @app.get
+    assert_equal 304, response1.status
+    assert cached?(response1)
+
+    # Invalidate the cache
+    response2 = @app.get do |req|
+      req.headers['invalidate_cache'] = true
+    end
+    assert_equal 200, response2.status
+    assert uncached?(response2)
+  end
+
+  def test_cache_expiration
+    WebMock.enable!
+    WebMock.stub_request(:get, @url)
+           .to_return(headers: { 'Cache-Control': "max-age=1" , 'Last-Modified': Time.now.httpdate}, body: {result: 'hello'}.to_json)
+
+
+    # Make a request and cache the response with a short expiry time
+    response1 = @app.get
+    assert_equal 200, response1.status
+
+    # Wait for the cache to expire
+    sleep 2
+
+    response2 = @app.get
+
+    assert_equal 200, response2.status
+    assert uncached?(response2)
+
+    sleep 2
+
+    WebMock.stub_request(:get, @url)
+           .to_return(headers: { 'Cache-Control': "max-age=100" , 'Last-Modified': Time.now.httpdate}, body: {result: 'hello'}.to_json)
+    @app.get
+
+
+    # Wait for the cache to expire
+    sleep 2
+
+    response2 = @app.get
+
+    assert cached?(response2)
+
+    WebMock.disable!
+  end
+
+  def test_cache_last_modified
+    WebMock.enable!
+    # Make a request with Last-Modified header
+    WebMock.stub_request(:get, @url)
+           .to_return(headers: { 'Cache-Control': "max-age=1", 'Last-Modified': 3.days.ago.to_time.httpdate}, body: {result: 'hello'}.to_json, status: 304)
+
+    @app.get
+
+    response2 = @app.get
+    assert cached?(response2)
+
+    sleep 1
+
+    WebMock.stub_request(:get, @url)
+           .to_return(headers: { 'Cache-Control': "max-age=10", 'Last-Modified': 1.days.ago.to_time.httpdate}, body: {result: 'hello'}.to_json, status: 304)
+
+    response2 = @app.get
+    assert refreshed?(response2)
+    WebMock.disable!
+  end
+
+
+  private
+  def cached?(response)
+    response.env.response_headers['x-rack-cache'].eql?('hit')
+  end
+
+  def uncached?(response)
+    response.env.response_headers['x-rack-cache'].eql?('miss')
+  end
+
+  def refreshed?(response)
+    response.env.response_headers['x-rack-cache'].eql?('fresh')
+  end
+end

From abea6c217c0ee93bcfd80c47c2af52747365d491 Mon Sep 17 00:00:00 2001
From: Syphax Bouazzouni <gs_bouazzouni@esi.dz>
Date: Sat, 25 May 2024 08:29:55 +0200
Subject: [PATCH 07/18] fix refactored cache code not getting the ld_obj when
 updating the cache

---
 config/config.test.rb                                       | 6 +++---
 .../middleware/faraday-object-cache.rb                      | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/config/config.test.rb b/config/config.test.rb
index a5d6166..9185c5d 100644
--- a/config/config.test.rb
+++ b/config/config.test.rb
@@ -7,8 +7,8 @@
 $DEBUG_API_CLIENT = false
 LinkedData::Client.config do |config|
   config.rest_url   = 'https://data.bioontology.org'
-  config.apikey     = ENV['UT_APIKEY']
-#  config.apikey     = 'xxxxx-xxxxx-xxxxxxxxxx'
+  config.apikey = '8b5b7825-538d-40e0-9e9e-5ab9274a9aeb'
   config.links_attr = 'links'
-  config.cache      = false
+  config.cache = true
+  config.debug_client = false
 end
diff --git a/lib/ontologies_api_client/middleware/faraday-object-cache.rb b/lib/ontologies_api_client/middleware/faraday-object-cache.rb
index 4e9eb65..080c416 100644
--- a/lib/ontologies_api_client/middleware/faraday-object-cache.rb
+++ b/lib/ontologies_api_client/middleware/faraday-object-cache.rb
@@ -99,7 +99,7 @@ def update_cache(request_key, last_modified)
         cache_write(last_modified_key_id(request_key), last_modified)
         cache_write(request_key, stored_obj)
       end
-      stored_obj
+      stored_obj.is_a?(Hash) && stored_obj.key?(:ld_obj) ? stored_obj[:ld_obj] : stored_obj
     end
 
     def cache_response(response_env, request_key)

From db35d02e3cc63099ac0e92d83193884db8e987f6 Mon Sep 17 00:00:00 2001
From: Syphax Bouazzouni <gs_bouazzouni@esi.dz>
Date: Sun, 1 Sep 2024 23:56:56 +0200
Subject: [PATCH 08/18] add unit tests of the expected behavior of the
 federation

---
 config/config.test.rb          |  31 +++++++--
 test/models/test_federation.rb | 122 +++++++++++++++++++++++++++++++++
 test/test_case.rb              |   2 +
 3 files changed, 149 insertions(+), 6 deletions(-)
 create mode 100644 test/models/test_federation.rb

diff --git a/config/config.test.rb b/config/config.test.rb
index 9185c5d..1200719 100644
--- a/config/config.test.rb
+++ b/config/config.test.rb
@@ -1,14 +1,33 @@
-# config.rb is required for testing
-# unit test makes calls to bioportal api so it needs a valid API key which can
-# be set via ENV variable UT_APIKEY
-abort('UT_APIKEY env variable is not set. Canceling tests') unless ENV.include?('UT_APIKEY')
-abort('UT_APIKEY env variable is set to an empty value. Canceling tests') unless ENV['UT_APIKEY'].size > 5
 $API_CLIENT_INVALIDATE_CACHE = false
 $DEBUG_API_CLIENT = false
+
 LinkedData::Client.config do |config|
-  config.rest_url   = 'https://data.bioontology.org'
+  config.rest_url = 'https://data.bioontology.org/'
   config.apikey = '8b5b7825-538d-40e0-9e9e-5ab9274a9aeb'
   config.links_attr = 'links'
   config.cache = true
   config.debug_client = false
+  config.debug_client_keys = []
+  config.federated_portals = {
+    bioportal: {
+      api: 'https://data.agroportal.lirmm.fr/',
+      apikey: '1de0a270-29c5-4dda-b043-7c3580628cd5',
+      color: '#234979',
+    },
+    ecoportal: {
+      api: 'https://data.ecoportal.lifewatch.eu/',
+      apikey: "43a437ba-a437-4bf0-affd-ab520e584719",
+      color: '#0f4e8a',
+    },
+    # earthportal: {
+    #   api: 'https://earthportal.eu:8443/',
+    #   apikey: "c9147279-954f-41bd-b068-da9b0c441288",
+    #   color: '#1e2251',
+    # },
+    biodivportal: {
+      api: 'https://data.biodivportal.gfbio.org/',
+      apikey: "47a57aa3-7b54-4f34-b695-dbb5f5b7363e",
+      color: '#1e2251',
+    }
+  }
 end
diff --git a/test/models/test_federation.rb b/test/models/test_federation.rb
new file mode 100644
index 0000000..4890af5
--- /dev/null
+++ b/test/models/test_federation.rb
@@ -0,0 +1,122 @@
+require_relative '../test_case'
+require 'pry'
+require 'benchmark'
+require 'webmock'
+require 'request_store'
+
+class FederationTest < LinkedData::Client::TestCase
+
+  def test_federated_ontologies_all
+    ontologies = []
+    time1 = Benchmark.realtime do
+      ontologies = LinkedData::Client::Models::Ontology.all(display_links: false, display_context: false)
+    end
+
+    ontologies_federate_all = []
+    time2 = Benchmark.realtime do
+      ontologies_federate_all = LinkedData::Client::Models::Ontology.all(federate: true, display_links: false, display_context: false)
+    end
+
+    puts ""
+    puts "AgroPortal ontologies: #{ontologies.length} in #{time1}s"
+    puts "Federated ontologies: #{ontologies_federate_all.length} in #{time2}s"
+
+    refute_equal ontologies.length, ontologies_federate_all.length
+
+    ontologies_federate_all.group_by{|x| x.id.split('/')[0..-2].join('/')}.each do |portal, onts|
+      puts "#{portal} ontologies: #{onts.length}"
+    end
+
+    ontologies_federate_all_cache = []
+    time2 = Benchmark.realtime do
+      ontologies_federate_all_cache = LinkedData::Client::Models::Ontology.all(federate: true, display_links: false, display_context: false)
+    end
+
+
+    puts "Federated ontologies with cache: #{ontologies_federate_all_cache.length} in #{time2}s"
+
+    assert_equal ontologies_federate_all_cache.size, ontologies_federate_all.size
+
+    ontologies_federate_two = []
+    time2 = Benchmark.realtime do
+      ontologies_federate_two = LinkedData::Client::Models::Ontology.all(federate: [:ecoportal, :biodivportal], display_links: false, display_context: false)
+    end
+
+    puts "Federated ontologies  with two portal only with cache: #{ontologies_federate_two.length} in #{time2}s"
+
+    refute_equal ontologies_federate_two.size, ontologies_federate_all.size
+
+    federated_portals =  ontologies_federate_two.map{|x| x.id.split('/')[0..-2].join('/')}.uniq
+    assert_equal 3, federated_portals.size
+    assert %w[bioontology ecoportal biodivportal].all? { |p| federated_portals.any?{|id| id[p]}  }
+  end
+
+  def test_federated_submissions_all
+    onts = []
+    time1 = Benchmark.realtime do
+      onts = LinkedData::Client::Models::OntologySubmission.all
+    end
+
+    onts_federate = []
+    time2 = Benchmark.realtime do
+      onts_federate = LinkedData::Client::Models::OntologySubmission.all(federate: true)
+    end
+
+    puts ""
+    puts "AgroPortal submissions: #{onts.length} in #{time1}s"
+    puts "Federated submissions: #{onts_federate.length} in #{time2}s"
+
+    refute_equal onts.length, onts_federate.length
+
+    onts_federate.group_by{|x| x.id.split('/')[0..-4].join('/')}.each do |portal, onts|
+      puts "#{portal} submissions: #{onts.length}"
+    end
+
+    onts_federate = []
+    time2 = Benchmark.realtime do
+      onts_federate = LinkedData::Client::Models::OntologySubmission.all(federate: true)
+    end
+    puts "Federated submissions with cache: #{onts_federate.length} in #{time2}s"
+
+  end
+
+  def test_federation_middleware
+    ontologies_federate_one = LinkedData::Client::Models::Ontology.all(federate: [:ecoportal, :biodivportal], display_links: false, display_context: false)
+
+    RequestStore.store[:federated_portals] = [:ecoportal, :biodivportal] #saved globally
+
+    ontologies_federate_two = LinkedData::Client::Models::Ontology.all(display_links: false, display_context: false)
+    assert_equal ontologies_federate_one.size, ontologies_federate_two.size
+  end
+
+
+  def test_federation_error
+    WebMock.enable!
+    LinkedData::Client::Models::Ontology.all(invalidate_cache: true)
+    WebMock.stub_request(:get, "#{LinkedData::Client.settings.rest_url.chomp('/')}/ontologies?include=all&display_links=false&display_context=false")
+           .to_return(body: "Internal server error", status: 500)
+
+    ontologies_federate_one = LinkedData::Client::Models::Ontology.all(federate: [:ecoportal, :biodivportal], display_links: false, display_context: false, invalidate_cache: true)
+
+    assert_equal "Problem retrieving #{LinkedData::Client.settings.rest_url}/ontologies", ontologies_federate_one.first.errors
+
+    WebMock.disable!
+  end
+
+  def test_federated_analytics
+    RequestStore.store[:federated_portals] = [:ecoportal,:biodivportal]
+    analytics = LinkedData::Client::Analytics.last_month
+    refute_empty analytics.onts
+  end
+
+
+  def test_federation_ssl_error
+    WebMock.enable!
+    WebMock.stub_request(:get, "#{LinkedData::Client.settings.rest_url.chomp('/')}")
+           .to_raise(Faraday::SSLError)
+    ontologies_federate_one = LinkedData::Client::Models::Ontology.all(display_links: false, display_context: false, invalidate_cache: true)
+
+    refute_nil ontologies_federate_one.first.errors
+    WebMock.disable!
+  end
+end
\ No newline at end of file
diff --git a/test/test_case.rb b/test/test_case.rb
index cd9fe2e..0f2f907 100644
--- a/test/test_case.rb
+++ b/test/test_case.rb
@@ -1,7 +1,9 @@
 require 'test-unit'
 require_relative '../lib/ontologies_api_client'
 require_relative '../config/config'
+require 'webmock'
 
+WebMock.allow_net_connect!
 module LinkedData
   module Client
     class TestCase < Test::Unit::TestCase

From 9d5bb868fa1eef9fe3336a1354f42a0555725f14 Mon Sep 17 00:00:00 2001
From: Syphax Bouazzouni <gs_bouazzouni@esi.dz>
Date: Sun, 1 Sep 2024 23:58:16 +0200
Subject: [PATCH 09/18] add caching debuging message option to see the cached
 and missed calls

---
 lib/ontologies_api_client/http.rb                    | 12 +++++++++---
 .../middleware/faraday-object-cache.rb               |  5 +++--
 test/middleware/test_cache.rb                        | 10 +++++++---
 3 files changed, 19 insertions(+), 8 deletions(-)

diff --git a/lib/ontologies_api_client/http.rb b/lib/ontologies_api_client/http.rb
index d3df241..ebd8750 100644
--- a/lib/ontologies_api_client/http.rb
+++ b/lib/ontologies_api_client/http.rb
@@ -3,6 +3,7 @@
 require 'digest'
 require 'ostruct'
 require 'benchmark'
+require 'active_support/cache'
 ##
 # This monkeypatch makes OpenStruct act like Struct objects
 class OpenStruct
@@ -48,22 +49,27 @@ def self.conn
             rails = Kernel.const_get("Rails")
             store = rails.cache if rails.cache
           end
-          LinkedData::Client.config_connection(cache_store: store)
+          LinkedData::Client.config_connection(cache_store: store || ActiveSupport::Cache::MemoryStore.new)
         end
         LinkedData::Client.settings.conn
       end
 
+      def self.federated_conn
+        LinkedData::Client.settings.federated_conn
+      end
+
       def self.get(path, params = {}, options = {})
         headers = options[:headers] || {}
         raw = options[:raw] || false # return the unparsed body of the request
         params = params.delete_if { |k, v| v == nil || v.to_s.empty? }
         params[:ncbo_cache_buster] = Time.now.to_f if raw # raw requests don't get cached to ensure body is available
         invalidate_cache = params.delete(:invalidate_cache) || $API_CLIENT_INVALIDATE_CACHE || false
+        connection = options[:connection] || conn
         begin
           begin
             response = nil
             time = Benchmark.realtime do
-              response = conn.get do |req|
+              response = connection.get do |req|
                 req.url path
                 req.params = params.dup
                 req.options[:timeout] = 60
@@ -71,7 +77,7 @@ def self.get(path, params = {}, options = {})
                 req.headers[:invalidate_cache] = invalidate_cache
               end
             end
-            puts "Getting: #{path} with #{params} (#{time}s)" if $DEBUG_API_CLIENT
+            puts "Getting: #{path} with #{params} (t: #{time}s - cache: #{response.headers["X-Rack-Cache"]})" if $DEBUG_API_CLIENT
           rescue Exception => e
             params = Faraday::Utils.build_query(params)
             path << "?" unless params.empty? || path.include?("?")
diff --git a/lib/ontologies_api_client/middleware/faraday-object-cache.rb b/lib/ontologies_api_client/middleware/faraday-object-cache.rb
index 080c416..f8ea13f 100644
--- a/lib/ontologies_api_client/middleware/faraday-object-cache.rb
+++ b/lib/ontologies_api_client/middleware/faraday-object-cache.rb
@@ -1,4 +1,5 @@
 require 'digest/sha1'
+require 'active_support'
 require 'active_support/cache'
 require 'lz4-ruby'
 require_relative '../http'
@@ -70,7 +71,7 @@ def retrieve_cached_response(request_key)
       env = { status: 304 }
       cached_response = ObjectCacheResponse.new(env)
       cached_response.parsed_body = ld_obj
-      cached_response.env.response_headers = { "x-rack-cache" => 'hit' }
+      cached_response.env.response_headers = { "X-Rack-Cache" => 'hit' }
       cached_response
     end
 
@@ -88,7 +89,7 @@ def process_response(response_env, request_key)
 
       response = ObjectCacheResponse.new(response_env)
       response.parsed_body = ld_obj
-      response.env.response_headers["x-rack-cache"] = cache_state
+      response.env.response_headers["X-Rack-Cache"] = cache_state
       response
     end
 
diff --git a/test/middleware/test_cache.rb b/test/middleware/test_cache.rb
index ddea7a9..943b55c 100644
--- a/test/middleware/test_cache.rb
+++ b/test/middleware/test_cache.rb
@@ -20,6 +20,10 @@ def setup
     end
   end
 
+  def teardown
+    WebMock.disable!
+  end
+
   def test_cache_hit_for_get_request
     body1, body2 = nil
     # First request should not hit the cache
@@ -128,14 +132,14 @@ def test_cache_last_modified
 
   private
   def cached?(response)
-    response.env.response_headers['x-rack-cache'].eql?('hit')
+    response.env.response_headers['X-Rack-Cache'].eql?('hit')
   end
 
   def uncached?(response)
-    response.env.response_headers['x-rack-cache'].eql?('miss')
+    response.env.response_headers['X-Rack-Cache'].eql?('miss')
   end
 
   def refreshed?(response)
-    response.env.response_headers['x-rack-cache'].eql?('fresh')
+    response.env.response_headers['X-Rack-Cache'].eql?('fresh')
   end
 end

From 1daf74f9be56cb273f8830d3d58d69cf776686d7 Mon Sep 17 00:00:00 2001
From: Syphax Bouazzouni <gs_bouazzouni@esi.dz>
Date: Sun, 1 Sep 2024 23:59:35 +0200
Subject: [PATCH 10/18] update the initialization of the http connection to
 have multiple by API

---
 lib/ontologies_api_client/config.rb | 25 +++++++++++++++++--------
 1 file changed, 17 insertions(+), 8 deletions(-)

diff --git a/lib/ontologies_api_client/config.rb b/lib/ontologies_api_client/config.rb
index 25805a8..fbf6cfb 100644
--- a/lib/ontologies_api_client/config.rb
+++ b/lib/ontologies_api_client/config.rb
@@ -37,8 +37,22 @@ def config(&block)
 
     def config_connection(options = {})
       return if @settings_run_connection
-      store = options[:cache_store]
-      @settings.conn = Faraday.new(@settings.rest_url) do |faraday|
+      store = options[:cache_store] || ActiveSupport::Cache::MemoryStore.new
+      @settings.conn = faraday_connection(@settings.rest_url, @settings.apikey, store)
+      @settings.federated_conn = @settings.federated_portals.map do |portal_name, portal_info|
+        [portal_name, faraday_connection(portal_info[:api], portal_info[:apikey], store)]
+      end.to_h
+
+      @settings_run_connection = true
+    end
+
+    def connection_configured?
+      @settings_run_connection
+    end
+
+    private
+    def faraday_connection(url, apikey, store)
+      Faraday.new(url.to_s.chomp('/')) do |faraday|
         if @settings.enable_long_request_log
           require_relative 'middleware/faraday-long-requests'
           faraday.use :long_requests
@@ -69,15 +83,10 @@ def config_connection(options = {})
         faraday.adapter :excon
         faraday.headers = {
           "Accept" => "application/json",
-          "Authorization" => "apikey token=#{@settings.apikey}",
+          "Authorization" => "apikey token=#{apikey}",
           "User-Agent" => "NCBO API Ruby Client v0.1.0"
         }
       end
-      @settings_run_connection = true
-    end
-
-    def connection_configured?
-      @settings_run_connection
     end
   end
 end
\ No newline at end of file

From 63d00f0f38372087afa06cbc98b2c5ef0f8f6785 Mon Sep 17 00:00:00 2001
From: Syphax Bouazzouni <gs_bouazzouni@esi.dz>
Date: Mon, 2 Sep 2024 00:00:48 +0200
Subject: [PATCH 11/18] create the RequestFederation to implement federated_get
 function

---
 lib/ontologies_api_client.rb                  |  1 +
 .../request_federation.rb                     | 45 +++++++++++++++++++
 ontologies_api_client.gemspec                 |  4 +-
 3 files changed, 49 insertions(+), 1 deletion(-)
 create mode 100644 lib/ontologies_api_client/request_federation.rb

diff --git a/lib/ontologies_api_client.rb b/lib/ontologies_api_client.rb
index 739639a..43c4f6d 100644
--- a/lib/ontologies_api_client.rb
+++ b/lib/ontologies_api_client.rb
@@ -1,6 +1,7 @@
 require 'oj'
 require 'multi_json'
 require 'spawnling'
+require 'request_store'
 
 require_relative 'ontologies_api_client/config'
 require_relative 'ontologies_api_client/http'
diff --git a/lib/ontologies_api_client/request_federation.rb b/lib/ontologies_api_client/request_federation.rb
new file mode 100644
index 0000000..458af90
--- /dev/null
+++ b/lib/ontologies_api_client/request_federation.rb
@@ -0,0 +1,45 @@
+require 'active_support/core_ext/hash'
+
+module LinkedData
+  module Client
+    module RequestFederation
+
+      def self.included(base)
+        base.extend(ClassMethods)
+      end
+
+      module ClassMethods
+        def federated_get(params = {}, &link)
+          portals = request_portals(params)
+
+          connections = Parallel.map(portals, in_threads: portals.size) do |conn|
+            begin
+              HTTP.get(link.call(conn.url_prefix.to_s.chomp('/')), params, connection: conn)
+            rescue StandardError => e
+              [OpenStruct.new(errors: "Problem retrieving #{link.call(conn.url_prefix.to_s.chomp('/')) || conn.url_prefix}")]
+            end
+          end
+
+          connections.flatten
+        end
+
+        def request_portals(params = {})
+          federate = params.delete(:federate) || ::RequestStore.store[:federated_portals]
+
+          portals = [LinkedData::Client::HTTP.conn]
+
+          if federate.is_a?(Array)
+            portals += LinkedData::Client::HTTP.federated_conn
+                                               .select { |portal_name, _| federate.include?(portal_name) || federate.include?(portal_name.to_s) }
+                                               .values
+          elsif !federate.blank? # all
+            portals += LinkedData::Client::HTTP.federated_conn.values
+          end
+
+          portals
+        end
+      end
+
+    end
+  end
+end
diff --git a/ontologies_api_client.gemspec b/ontologies_api_client.gemspec
index fad13e4..b2ae8c2 100644
--- a/ontologies_api_client.gemspec
+++ b/ontologies_api_client.gemspec
@@ -12,7 +12,7 @@ Gem::Specification.new do |gem|
   gem.require_paths = ["lib"]
   gem.version       = "2.2.0"
 
-  gem.add_dependency('activesupport')
+  gem.add_dependency('activesupport', '~> 7.0.4')
   gem.add_dependency('excon')
   gem.add_dependency('faraday')
   gem.add_dependency('faraday-excon', '~> 2.0.0')
@@ -20,5 +20,7 @@ Gem::Specification.new do |gem|
   gem.add_dependency('lz4-ruby')
   gem.add_dependency('multi_json')
   gem.add_dependency('oj')
+  gem.add_dependency('parallel')
+  gem.add_dependency('request_store')
   gem.add_dependency('spawnling', '2.1.5')
 end

From 1161610ca3ed7463bb34ea107a8ab063a98bb749 Mon Sep 17 00:00:00 2001
From: Syphax Bouazzouni <gs_bouazzouni@esi.dz>
Date: Mon, 2 Sep 2024 00:02:24 +0200
Subject: [PATCH 12/18] update collections calls to use federated_get() instead
 of get()

---
 Gemfile.lock                            | 35 +++++++++++++++----------
 lib/ontologies_api_client/base.rb       | 13 ++++++---
 lib/ontologies_api_client/collection.rb | 15 ++++++++---
 3 files changed, 41 insertions(+), 22 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 413fd8c..dd5fb94 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -2,7 +2,7 @@ PATH
   remote: .
   specs:
     ontologies_api_client (2.2.0)
-      activesupport
+      activesupport (~> 7.0.4)
       excon
       faraday
       faraday-excon (~> 2.0.0)
@@ -10,12 +10,14 @@ PATH
       lz4-ruby
       multi_json
       oj
+      parallel
+      request_store
       spawnling (= 2.1.5)
 
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (7.0.4)
+    activesupport (7.0.8.1)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -24,11 +26,11 @@ GEM
       public_suffix (>= 2.0.2, < 6.0)
     bigdecimal (3.1.7)
     coderay (1.1.3)
-    concurrent-ruby (1.1.10)
+    concurrent-ruby (1.2.3)
     crack (1.0.0)
       bigdecimal
       rexml
-    excon (0.95.0)
+    excon (0.110.0)
     faraday (2.0.1)
       faraday-net_http (~> 2.0)
       ruby2_keywords (>= 0.0.4)
@@ -39,26 +41,31 @@ GEM
       multipart-post (~> 2)
     faraday-net_http (2.1.0)
     hashdiff (1.1.0)
-    i18n (1.12.0)
+    i18n (1.14.4)
       concurrent-ruby (~> 1.0)
     lz4-ruby (0.3.3)
-    method_source (1.0.0)
-    minitest (5.16.3)
+    method_source (1.1.0)
+    minitest (5.22.3)
     multi_json (1.15.0)
-    multipart-post (2.2.3)
-    oj (3.13.23)
-    power_assert (2.0.2)
-    pry (0.14.1)
+    multipart-post (2.4.0)
+    oj (3.16.3)
+      bigdecimal (>= 3.0)
+    parallel (1.24.0)
+    power_assert (2.0.3)
+    pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.0.5)
-    rake (13.0.6)
+    rack (3.0.10)
+    rake (13.2.1)
+    request_store (1.7.0)
+      rack (>= 1.4)
     rexml (3.2.6)
     ruby2_keywords (0.0.5)
     spawnling (2.1.5)
-    test-unit (3.5.7)
+    test-unit (3.6.2)
       power_assert
-    tzinfo (2.0.5)
+    tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     webmock (3.23.0)
       addressable (>= 2.8.0)
diff --git a/lib/ontologies_api_client/base.rb b/lib/ontologies_api_client/base.rb
index ff4aba6..a4404df 100644
--- a/lib/ontologies_api_client/base.rb
+++ b/lib/ontologies_api_client/base.rb
@@ -132,11 +132,16 @@ def create_attributes(attributes)
           attr_exists = self.public_methods(false).include?(attr)
           unless attr_exists
             self.class.class_eval do
-              define_method attr.to_sym do
-                instance_variable_get("@#{attr}")
+              unless method_defined?(attr.to_sym)
+                define_method attr.to_sym do
+                  instance_variable_get("@#{attr}")
+                end
               end
-              define_method "#{attr}=" do |val|
-                instance_variable_set("@#{attr}", val)
+
+              unless method_defined?("#{attr}=".to_sym)
+                define_method "#{attr}=" do |val|
+                  instance_variable_set("@#{attr}", val)
+                end
               end
             end
           end
diff --git a/lib/ontologies_api_client/collection.rb b/lib/ontologies_api_client/collection.rb
index 77572bf..a4d34c2 100644
--- a/lib/ontologies_api_client/collection.rb
+++ b/lib/ontologies_api_client/collection.rb
@@ -1,11 +1,15 @@
 require_relative 'config'
 require_relative 'http'
+require_relative 'request_federation'
+require 'parallel'
 
 module LinkedData
   module Client
     module Collection
 
+
       def self.included(base)
+        base.include LinkedData::Client::RequestFederation
         base.extend(ClassMethods)
       end
 
@@ -24,8 +28,8 @@ def method_missing(meth, *args, &block)
 
         ##
         # Get all top-level links for the API
-        def top_level_links
-          @top_level_links||= HTTP.get(LinkedData::Client.settings.rest_url)
+        def top_level_links(link = LinkedData::Client.settings.rest_url)
+          HTTP.get(link)
         end
 
         ##
@@ -36,11 +40,14 @@ def uri_from_context(object, media_type)
           end
         end
 
+
         ##
         # Get the first collection of resources for a given type
         def entry_point(media_type, params = {})
-          params = {include: @include_attrs}.merge(params)
-          HTTP.get(uri_from_context(top_level_links, media_type), params)
+          params = { include: @include_attrs, display_links: false, display_context: false}.merge(params)
+          federated_get(params) do |url|
+            uri_from_context(top_level_links(url), media_type) rescue nil
+          end
         end
 
         ##

From f651f9f920a55492629ad08a83dde4ed65278def Mon Sep 17 00:00:00 2001
From: Syphax Bouazzouni <gs_bouazzouni@esi.dz>
Date: Mon, 2 Sep 2024 00:02:51 +0200
Subject: [PATCH 13/18] update the special case of analytics to handle
 federated calls

---
 lib/ontologies_api_client/analytics.rb | 35 +++++++++++++++++++-------
 1 file changed, 26 insertions(+), 9 deletions(-)

diff --git a/lib/ontologies_api_client/analytics.rb b/lib/ontologies_api_client/analytics.rb
index cbb85ac..b6a78cc 100644
--- a/lib/ontologies_api_client/analytics.rb
+++ b/lib/ontologies_api_client/analytics.rb
@@ -1,6 +1,9 @@
+require_relative 'request_federation'
+
 module LinkedData::Client
   class Analytics
     HTTP = LinkedData::Client::HTTP
+    include LinkedData::Client::RequestFederation
 
     attr_accessor :onts, :date
 
@@ -10,18 +13,32 @@ def self.all(params = {})
 
     def self.last_month
       data = self.new
-      data.date = last_month = DateTime.now - 1.month
+      last_month = DateTime.now.prev_month
       year_num = last_month.year
       month_num = last_month.month
-      analytics = get(:analytics, {year: year_num, month: month_num}).to_h
-      analytics.delete(:links)
-      analytics.delete(:context)
+      params = { year: year_num, month: month_num }
+
+      responses = federated_get(params) do |url|
+        "#{url}/analytics"
+      end
+
+      portals = request_portals
       onts = []
-      analytics.keys.each do |ont|
-        views = analytics[ont][:"#{year_num}"][:"#{month_num}"]
-        onts << {ont: ont, views: views}
+      responses.each_with_index do |portal_views, index|
+        next nil if portal_views&.errors
+
+        portal_views = portal_views.to_h
+
+        url = portals[index].url_prefix.to_s.chomp('/')
+        portal_views.delete(:links)
+        portal_views.delete(:context)
+        portal_views.keys.map do |ont|
+          views = portal_views[ont][:"#{year_num}"][:"#{month_num}"]
+          onts << { ont: "#{url}/ontologies/#{ont}", views: views }
+        end
       end
-      data.onts = onts
+
+      data.onts = onts.flatten.compact
       data
     end
 
@@ -29,7 +46,7 @@ def self.last_month
 
     def self.get(path, params = {})
       path = path.to_s
-      path = "/"+path unless path.start_with?("/")
+      path = "/" + path unless path.start_with?("/")
       HTTP.get(path, params)
     end
 

From ccf38c2054689d3f99d86cc1827126c380c9d90a Mon Sep 17 00:00:00 2001
From: Syphax <gs_bouazzouni@esi.dz>
Date: Mon, 9 Sep 2024 16:42:26 +0200
Subject: [PATCH 14/18] in parallel calls save main thread states a cross
 threads

---
 lib/ontologies_api_client/config.rb           | 19 +++++++++++--------
 .../request_federation.rb                     |  4 +++-
 2 files changed, 14 insertions(+), 9 deletions(-)

diff --git a/lib/ontologies_api_client/config.rb b/lib/ontologies_api_client/config.rb
index fbf6cfb..e2d063e 100644
--- a/lib/ontologies_api_client/config.rb
+++ b/lib/ontologies_api_client/config.rb
@@ -38,7 +38,7 @@ def config(&block)
     def config_connection(options = {})
       return if @settings_run_connection
       store = options[:cache_store] || ActiveSupport::Cache::MemoryStore.new
-      @settings.conn = faraday_connection(@settings.rest_url, @settings.apikey, store)
+      @settings.conn = faraday_connection(@settings.rest_url, @settings.apikey, store, current_portal: true)
       @settings.federated_conn = @settings.federated_portals.map do |portal_name, portal_info|
         [portal_name, faraday_connection(portal_info[:api], portal_info[:apikey], store)]
       end.to_h
@@ -51,21 +51,24 @@ def connection_configured?
     end
 
     private
-    def faraday_connection(url, apikey, store)
+    def faraday_connection(url, apikey, store, current_portal: false)
       Faraday.new(url.to_s.chomp('/')) do |faraday|
+
         if @settings.enable_long_request_log
           require_relative 'middleware/faraday-long-requests'
           faraday.use :long_requests
         end
 
-        require_relative 'middleware/faraday-user-apikey'
-        faraday.use :user_apikey
+        if current_portal
+          require_relative 'middleware/faraday-user-apikey'
+          faraday.use :user_apikey
 
-        require_relative 'middleware/faraday-slices'
-        faraday.use :ncbo_slices
+          require_relative 'middleware/faraday-slices'
+          faraday.use :ncbo_slices
 
-        require_relative 'middleware/faraday-last-updated'
-        faraday.use :last_updated
+          require_relative 'middleware/faraday-last-updated'
+          faraday.use :last_updated
+        end
 
         if @settings.cache
           begin
diff --git a/lib/ontologies_api_client/request_federation.rb b/lib/ontologies_api_client/request_federation.rb
index 458af90..ff1c9e3 100644
--- a/lib/ontologies_api_client/request_federation.rb
+++ b/lib/ontologies_api_client/request_federation.rb
@@ -11,11 +11,13 @@ def self.included(base)
       module ClassMethods
         def federated_get(params = {}, &link)
           portals = request_portals(params)
+          main_thread_locals = Thread.current.keys.map { |key| [key, Thread.current[key]] }.to_h
 
           connections = Parallel.map(portals, in_threads: portals.size) do |conn|
+            main_thread_locals.each { |key, value| Thread.current[key] = value }
             begin
               HTTP.get(link.call(conn.url_prefix.to_s.chomp('/')), params, connection: conn)
-            rescue StandardError => e
+            rescue Exception => e
               [OpenStruct.new(errors: "Problem retrieving #{link.call(conn.url_prefix.to_s.chomp('/')) || conn.url_prefix}")]
             end
           end

From 0598e0068e545a5be9bbb501b0155c8bb2d9afb5 Mon Sep 17 00:00:00 2001
From: Bilel Kihal <61744974+Bilelkihal@users.noreply.github.com>
Date: Mon, 14 Oct 2024 10:57:42 +0200
Subject: [PATCH 15/18] Feature: Aggretate federated search results (#18)

* handle ssl error exception when federated call to a collection

* federate search endpoint and merge results

* fix activesupport gem version issue

* fix search params to keep federated and non federated calls work

* put collections mergin only for class search

* pass federation errors in federated search results

* remove unused parallel dependency in class.rb

* clean class.rb federation code

* update the activesupport gem version

* remove uncompleted federated search test

* use the key "collection" instead of "results" in federated search result hash to maintain the endpoint expected schema

* add test for federated search
---
 Gemfile.lock                                  |  1 +
 lib/ontologies_api_client/models/class.rb     | 22 ++++++++++++++++++-
 .../request_federation.rb                     |  2 ++
 test/models/test_federation.rb                | 19 +++++++++++++++-
 4 files changed, 42 insertions(+), 2 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index dd5fb94..b147d35 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -73,6 +73,7 @@ GEM
       hashdiff (>= 0.4.0, < 2.0.0)
 
 PLATFORMS
+  ruby
   x86_64-darwin-21
   x86_64-darwin-23
   x86_64-linux
diff --git a/lib/ontologies_api_client/models/class.rb b/lib/ontologies_api_client/models/class.rb
index e249887..6362c98 100644
--- a/lib/ontologies_api_client/models/class.rb
+++ b/lib/ontologies_api_client/models/class.rb
@@ -1,11 +1,14 @@
 require "cgi"
 require_relative "../base"
+require_relative "../request_federation"
 
 module LinkedData
   module Client
     module Models
+
       class Class < LinkedData::Client::Base
         HTTP = LinkedData::Client::HTTP
+        include LinkedData::Client::RequestFederation
         @media_type = %w[http://www.w3.org/2002/07/owl#Class http://www.w3.org/2004/02/skos/core#Concept]
         @include_attrs = "prefLabel,definition,synonym,obsolete,hasChildren,inScheme,memberOf"
         @include_attrs_full = "prefLabel,definition,synonym,obsolete,properties,hasChildren,childre,inScheme,memberOf"
@@ -61,10 +64,27 @@ def self.find(id, ontology, params = {})
 
         def self.search(*args)
           query = args.shift
+
           params = args.shift || {}
+
           params[:q] = query
+
           raise ArgumentError, "You must provide a search query: Class.search(query: 'melanoma')" if query.nil? || !query.is_a?(String)
-          HTTP.post("/search", params)
+
+
+          search_result = federated_get(params) do |url|
+            "#{url}/search"
+          end
+          merged_collections = {collection: [], errors: []}
+          search_result.each do |result|
+            if result.collection
+              merged_collections[:collection].concat(result.collection)
+            elsif result.errors
+              merged_collections[:errors] << result.errors
+            end
+          end
+          merged_collections
+
         end
 
         def expanded?
diff --git a/lib/ontologies_api_client/request_federation.rb b/lib/ontologies_api_client/request_federation.rb
index ff1c9e3..b57d3db 100644
--- a/lib/ontologies_api_client/request_federation.rb
+++ b/lib/ontologies_api_client/request_federation.rb
@@ -25,6 +25,8 @@ def federated_get(params = {}, &link)
           connections.flatten
         end
 
+
+
         def request_portals(params = {})
           federate = params.delete(:federate) || ::RequestStore.store[:federated_portals]
 
diff --git a/test/models/test_federation.rb b/test/models/test_federation.rb
index 4890af5..600f2bf 100644
--- a/test/models/test_federation.rb
+++ b/test/models/test_federation.rb
@@ -119,4 +119,21 @@ def test_federation_ssl_error
     refute_nil ontologies_federate_one.first.errors
     WebMock.disable!
   end
-end
\ No newline at end of file
+
+  def test_federated_search
+    query = 'test'
+
+    time1 = Benchmark.realtime do
+      @search_results = LinkedData::Client::Models::Class.search(query)[:collection]
+    end
+
+    time2 = Benchmark.realtime do
+      @federated_search_results = LinkedData::Client::Models::Class.search(query, {federate: 'true'})[:collection]
+    end
+
+    puts "Search results: #{@search_results .length} in #{time1}s"
+    puts "Federated search results: #{@federated_search_results.length} in #{time2}s"
+
+    refute_equal @search_results.length, @federated_search_results.length
+  end
+end

From 8788515be8be4101fba62dc4561b3d14b12d40a0 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Wed, 16 Oct 2024 23:47:24 +0200
Subject: [PATCH 16/18] Feature: Add rails performance gem and save API calls
 as custom events  (#20)

* add rails performance gem

* save as a custom event the API calls

* disable by default the rail performance monitoring

* use directly RailsPerformance::Models::CustomRecord instead of measure
---
 Gemfile.lock                      | 60 +++++++++++++++++++++++++++++--
 lib/ontologies_api_client/http.rb | 14 ++++++++
 ontologies_api_client.gemspec     |  1 +
 3 files changed, 72 insertions(+), 3 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index b147d35..0e45725 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -11,13 +11,27 @@ PATH
       multi_json
       oj
       parallel
+      rails_performance
       request_store
       spawnling (= 2.1.5)
 
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (7.0.8.1)
+    actionpack (7.0.4)
+      actionview (= 7.0.4)
+      activesupport (= 7.0.4)
+      rack (~> 2.0, >= 2.2.0)
+      rack-test (>= 0.6.3)
+      rails-dom-testing (~> 2.0)
+      rails-html-sanitizer (~> 1.0, >= 1.2.0)
+    actionview (7.0.4)
+      activesupport (= 7.0.4)
+      builder (~> 3.1)
+      erubi (~> 1.4)
+      rails-dom-testing (~> 2.0)
+      rails-html-sanitizer (~> 1.1, >= 1.2.0)
+    activesupport (7.0.4)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -25,11 +39,16 @@ GEM
     addressable (2.8.6)
       public_suffix (>= 2.0.2, < 6.0)
     bigdecimal (3.1.7)
+    browser (5.3.1)
+    builder (3.3.0)
     coderay (1.1.3)
     concurrent-ruby (1.2.3)
+    connection_pool (2.4.1)
     crack (1.0.0)
       bigdecimal
       rexml
+    crass (1.0.6)
+    erubi (1.13.0)
     excon (0.110.0)
     faraday (2.0.1)
       faraday-net_http (~> 2.0)
@@ -43,11 +62,16 @@ GEM
     hashdiff (1.1.0)
     i18n (1.14.4)
       concurrent-ruby (~> 1.0)
+    loofah (2.22.0)
+      crass (~> 1.0.2)
+      nokogiri (>= 1.12.0)
     lz4-ruby (0.3.3)
     method_source (1.1.0)
     minitest (5.22.3)
     multi_json (1.15.0)
     multipart-post (2.4.0)
+    nokogiri (1.15.6-x86_64-linux)
+      racc (~> 1.4)
     oj (3.16.3)
       bigdecimal (>= 3.0)
     parallel (1.24.0)
@@ -56,8 +80,36 @@ GEM
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.0.5)
-    rack (3.0.10)
+    racc (1.8.1)
+    rack (2.2.9)
+    rack-test (2.1.0)
+      rack (>= 1.3)
+    rails-dom-testing (2.2.0)
+      activesupport (>= 5.0.0)
+      minitest
+      nokogiri (>= 1.6)
+    rails-html-sanitizer (1.6.0)
+      loofah (~> 2.21)
+      nokogiri (~> 1.14)
+    rails_performance (1.2.2)
+      browser
+      railties
+      redis
+      redis-namespace
+    railties (7.0.4)
+      actionpack (= 7.0.4)
+      activesupport (= 7.0.4)
+      method_source
+      rake (>= 12.2)
+      thor (~> 1.0)
+      zeitwerk (~> 2.5)
     rake (13.2.1)
+    redis (5.3.0)
+      redis-client (>= 0.22.0)
+    redis-client (0.22.2)
+      connection_pool
+    redis-namespace (1.11.0)
+      redis (>= 4)
     request_store (1.7.0)
       rack (>= 1.4)
     rexml (3.2.6)
@@ -65,12 +117,14 @@ GEM
     spawnling (2.1.5)
     test-unit (3.6.2)
       power_assert
+    thor (1.3.2)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     webmock (3.23.0)
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
+    zeitwerk (2.6.18)
 
 PLATFORMS
   ruby
@@ -86,4 +140,4 @@ DEPENDENCIES
   webmock
 
 BUNDLED WITH
-   2.4.21
+   2.4.22
diff --git a/lib/ontologies_api_client/http.rb b/lib/ontologies_api_client/http.rb
index ebd8750..36dc67a 100644
--- a/lib/ontologies_api_client/http.rb
+++ b/lib/ontologies_api_client/http.rb
@@ -4,6 +4,7 @@
 require 'ostruct'
 require 'benchmark'
 require 'active_support/cache'
+require 'rails_performance' if defined?(Rails)
 ##
 # This monkeypatch makes OpenStruct act like Struct objects
 class OpenStruct
@@ -77,6 +78,8 @@ def self.get(path, params = {}, options = {})
                 req.headers[:invalidate_cache] = invalidate_cache
               end
             end
+
+            monitor_request(params, path, response, time)
             puts "Getting: #{path} with #{params} (t: #{time}s - cache: #{response.headers["X-Rack-Cache"]})" if $DEBUG_API_CLIENT
           rescue Exception => e
             params = Faraday::Utils.build_query(params)
@@ -164,6 +167,17 @@ def self.object_from_json(json)
 
       private
 
+      def self.monitor_request(params, path, response, time)
+        RailsPerformance::Models::CustomRecord.new(
+          tag_name: "Getting: #{path} with #{params} - cache: (#{response.headers["X-Rack-Cache"]})",
+          namespace_name: "API call #{path}",
+          status: response.status,
+          duration: time,
+          datetime: Time.current.strftime(RailsPerformance::FORMAT),
+          datetimei: Time.current.to_i).save if defined?(Rails) && RailsPerformance.enabled
+      end
+
+
       def self.custom_req(obj, file, file_attribute, req)
         req.headers['Content-Type'] = 'application/json'
 
diff --git a/ontologies_api_client.gemspec b/ontologies_api_client.gemspec
index b2ae8c2..63cc247 100644
--- a/ontologies_api_client.gemspec
+++ b/ontologies_api_client.gemspec
@@ -23,4 +23,5 @@ Gem::Specification.new do |gem|
   gem.add_dependency('parallel')
   gem.add_dependency('request_store')
   gem.add_dependency('spawnling', '2.1.5')
+  gem.add_dependency('rails_performance')
 end

From 65ac0d61fa363144906b761426e90c6b4a9b2c35 Mon Sep 17 00:00:00 2001
From: Bilel Kihal <61744974+Bilelkihal@users.noreply.github.com>
Date: Sat, 26 Oct 2024 09:29:36 +0200
Subject: [PATCH 17/18] Fix: Return search results as an object instead of a
 hash (#21)

* return search results as an object instad of a hash

* update test federated search to use search results as an object instead of a hash

* fix tests timeout by using the dev server of biodivportal

---------

Co-authored-by: Syphax <gs_bouazzouni@esi.dz>
---
 config/config.test.rb                     | 2 +-
 lib/ontologies_api_client/models/class.rb | 2 +-
 test/models/test_federation.rb            | 6 +++---
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/config/config.test.rb b/config/config.test.rb
index 1200719..f259b60 100644
--- a/config/config.test.rb
+++ b/config/config.test.rb
@@ -25,7 +25,7 @@
     #   color: '#1e2251',
     # },
     biodivportal: {
-      api: 'https://data.biodivportal.gfbio.org/',
+      api: 'https://data.biodivportal.gfbio.dev/',
       apikey: "47a57aa3-7b54-4f34-b695-dbb5f5b7363e",
       color: '#1e2251',
     }
diff --git a/lib/ontologies_api_client/models/class.rb b/lib/ontologies_api_client/models/class.rb
index 6362c98..41895d5 100644
--- a/lib/ontologies_api_client/models/class.rb
+++ b/lib/ontologies_api_client/models/class.rb
@@ -83,7 +83,7 @@ def self.search(*args)
               merged_collections[:errors] << result.errors
             end
           end
-          merged_collections
+          OpenStruct.new(merged_collections)
 
         end
 
diff --git a/test/models/test_federation.rb b/test/models/test_federation.rb
index 600f2bf..5a9a147 100644
--- a/test/models/test_federation.rb
+++ b/test/models/test_federation.rb
@@ -124,14 +124,14 @@ def test_federated_search
     query = 'test'
 
     time1 = Benchmark.realtime do
-      @search_results = LinkedData::Client::Models::Class.search(query)[:collection]
+      @search_results = LinkedData::Client::Models::Class.search(query).collection
     end
 
     time2 = Benchmark.realtime do
-      @federated_search_results = LinkedData::Client::Models::Class.search(query, {federate: 'true'})[:collection]
+      @federated_search_results = LinkedData::Client::Models::Class.search(query, {federate: 'true'}).collection
     end
 
-    puts "Search results: #{@search_results .length} in #{time1}s"
+    puts "Search results: #{@search_results.length} in #{time1}s"
     puts "Federated search results: #{@federated_search_results.length} in #{time2}s"
 
     refute_equal @search_results.length, @federated_search_results.length

From b161ff6a54314b5abc9abc507433c12015b5e8f7 Mon Sep 17 00:00:00 2001
From: Syphax <gs_bouazzouni@esi.dz>
Date: Mon, 28 Oct 2024 11:39:21 +0100
Subject: [PATCH 18/18] Revert "Feature: Add rails performance gem and save API
 calls as custom events  (#20)"

This reverts commit 8788515be8be4101fba62dc4561b3d14b12d40a0.
---
 Gemfile.lock                      | 60 ++-----------------------------
 lib/ontologies_api_client/http.rb | 14 --------
 ontologies_api_client.gemspec     |  1 -
 3 files changed, 3 insertions(+), 72 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 0e45725..b147d35 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -11,27 +11,13 @@ PATH
       multi_json
       oj
       parallel
-      rails_performance
       request_store
       spawnling (= 2.1.5)
 
 GEM
   remote: https://rubygems.org/
   specs:
-    actionpack (7.0.4)
-      actionview (= 7.0.4)
-      activesupport (= 7.0.4)
-      rack (~> 2.0, >= 2.2.0)
-      rack-test (>= 0.6.3)
-      rails-dom-testing (~> 2.0)
-      rails-html-sanitizer (~> 1.0, >= 1.2.0)
-    actionview (7.0.4)
-      activesupport (= 7.0.4)
-      builder (~> 3.1)
-      erubi (~> 1.4)
-      rails-dom-testing (~> 2.0)
-      rails-html-sanitizer (~> 1.1, >= 1.2.0)
-    activesupport (7.0.4)
+    activesupport (7.0.8.1)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -39,16 +25,11 @@ GEM
     addressable (2.8.6)
       public_suffix (>= 2.0.2, < 6.0)
     bigdecimal (3.1.7)
-    browser (5.3.1)
-    builder (3.3.0)
     coderay (1.1.3)
     concurrent-ruby (1.2.3)
-    connection_pool (2.4.1)
     crack (1.0.0)
       bigdecimal
       rexml
-    crass (1.0.6)
-    erubi (1.13.0)
     excon (0.110.0)
     faraday (2.0.1)
       faraday-net_http (~> 2.0)
@@ -62,16 +43,11 @@ GEM
     hashdiff (1.1.0)
     i18n (1.14.4)
       concurrent-ruby (~> 1.0)
-    loofah (2.22.0)
-      crass (~> 1.0.2)
-      nokogiri (>= 1.12.0)
     lz4-ruby (0.3.3)
     method_source (1.1.0)
     minitest (5.22.3)
     multi_json (1.15.0)
     multipart-post (2.4.0)
-    nokogiri (1.15.6-x86_64-linux)
-      racc (~> 1.4)
     oj (3.16.3)
       bigdecimal (>= 3.0)
     parallel (1.24.0)
@@ -80,36 +56,8 @@ GEM
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.0.5)
-    racc (1.8.1)
-    rack (2.2.9)
-    rack-test (2.1.0)
-      rack (>= 1.3)
-    rails-dom-testing (2.2.0)
-      activesupport (>= 5.0.0)
-      minitest
-      nokogiri (>= 1.6)
-    rails-html-sanitizer (1.6.0)
-      loofah (~> 2.21)
-      nokogiri (~> 1.14)
-    rails_performance (1.2.2)
-      browser
-      railties
-      redis
-      redis-namespace
-    railties (7.0.4)
-      actionpack (= 7.0.4)
-      activesupport (= 7.0.4)
-      method_source
-      rake (>= 12.2)
-      thor (~> 1.0)
-      zeitwerk (~> 2.5)
+    rack (3.0.10)
     rake (13.2.1)
-    redis (5.3.0)
-      redis-client (>= 0.22.0)
-    redis-client (0.22.2)
-      connection_pool
-    redis-namespace (1.11.0)
-      redis (>= 4)
     request_store (1.7.0)
       rack (>= 1.4)
     rexml (3.2.6)
@@ -117,14 +65,12 @@ GEM
     spawnling (2.1.5)
     test-unit (3.6.2)
       power_assert
-    thor (1.3.2)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     webmock (3.23.0)
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
-    zeitwerk (2.6.18)
 
 PLATFORMS
   ruby
@@ -140,4 +86,4 @@ DEPENDENCIES
   webmock
 
 BUNDLED WITH
-   2.4.22
+   2.4.21
diff --git a/lib/ontologies_api_client/http.rb b/lib/ontologies_api_client/http.rb
index 36dc67a..ebd8750 100644
--- a/lib/ontologies_api_client/http.rb
+++ b/lib/ontologies_api_client/http.rb
@@ -4,7 +4,6 @@
 require 'ostruct'
 require 'benchmark'
 require 'active_support/cache'
-require 'rails_performance' if defined?(Rails)
 ##
 # This monkeypatch makes OpenStruct act like Struct objects
 class OpenStruct
@@ -78,8 +77,6 @@ def self.get(path, params = {}, options = {})
                 req.headers[:invalidate_cache] = invalidate_cache
               end
             end
-
-            monitor_request(params, path, response, time)
             puts "Getting: #{path} with #{params} (t: #{time}s - cache: #{response.headers["X-Rack-Cache"]})" if $DEBUG_API_CLIENT
           rescue Exception => e
             params = Faraday::Utils.build_query(params)
@@ -167,17 +164,6 @@ def self.object_from_json(json)
 
       private
 
-      def self.monitor_request(params, path, response, time)
-        RailsPerformance::Models::CustomRecord.new(
-          tag_name: "Getting: #{path} with #{params} - cache: (#{response.headers["X-Rack-Cache"]})",
-          namespace_name: "API call #{path}",
-          status: response.status,
-          duration: time,
-          datetime: Time.current.strftime(RailsPerformance::FORMAT),
-          datetimei: Time.current.to_i).save if defined?(Rails) && RailsPerformance.enabled
-      end
-
-
       def self.custom_req(obj, file, file_attribute, req)
         req.headers['Content-Type'] = 'application/json'
 
diff --git a/ontologies_api_client.gemspec b/ontologies_api_client.gemspec
index 63cc247..b2ae8c2 100644
--- a/ontologies_api_client.gemspec
+++ b/ontologies_api_client.gemspec
@@ -23,5 +23,4 @@ Gem::Specification.new do |gem|
   gem.add_dependency('parallel')
   gem.add_dependency('request_store')
   gem.add_dependency('spawnling', '2.1.5')
-  gem.add_dependency('rails_performance')
 end