Merge branch 'master' into ecoportal-ontoportal-reset

Gemfile

@@ -4,4 +4,5 @@ gemspec
 
 gem 'rake'
 gem 'pry'
-gem 'test-unit'
+gem 'test-unit'
+gem 'webmock', require: false

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

config/config.test.rb

@@ -3,11 +3,12 @@
 # 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']
-#  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

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
 
         ##

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.is_a?(Hash) && stored_obj.key?(:ld_obj) ? stored_obj[:ld_obj] : 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
@@ -181,16 +190,13 @@ 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)
         begin
           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