cheminee 0.1.34 → 0.1.35

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: a816e24d54c16eac05470a3ab784eae20281fc29178fc12f362ef1a23b1d9ae0
-  data.tar.gz: ad426021b133d06f6fc33637d1d69a99de6602119ea4d65abd3ce0a5791d5494
+  metadata.gz: b489a78e92999967bac81cd48a4b6470ecbc181bead072db956d786f4b684289
+  data.tar.gz: '02818840a73cb71be8e156cd231aafcf6756b2d969bb027bb2e1b3b9a011db7b'
 SHA512:
-  metadata.gz: cb6654c25f54f5b54baca4b998fc5ad47264a4cdb4fa74f61d0c1dbcd91c96e6ac313e4b9fb66aeb8a01f01eb69338e4e485798d697f5413d702cdbfe4dbbf6e
-  data.tar.gz: a8c8032f8fc977069b621922b8f814becf537b2ae7a1c62721f26646a804873aaaba1c12b2332589db1fab844ac56fafbaf08463d2299f631867aa0206f58bce
+  metadata.gz: 362e1a903b2bfcda17583fd21ebb5833f44266f84d72bc9a8a5afdc505e9d0a7337af2c0c0535525c1a67836618375c159cd55de04bac6b30216d4e810b3ae2b
+  data.tar.gz: 23497cef82cb992182ef2c632998163513d280aeb9d17a35dc0108c3d36b09d6c1fc7c316a9b88653aff7584c08c4dc247dc8575f53fc8902be95d1ad0ef5ed3

data/Gemfile.lock

@@ -1,8 +1,10 @@
 PATH
   remote: .
   specs:
-    cheminee (0.1.34)
-      typhoeus (~> 1.0, >= 1.0.1)
+    cheminee (0.1.35)
+      faraday (>= 1.0.1, < 3.0)
+      faraday-multipart
+      marcel
 
 GEM
   remote: https://rubygems.org/
@@ -11,11 +13,22 @@ GEM
     byebug (11.1.3)
     coderay (1.1.3)
     diff-lcs (1.5.1)
-    ethon (0.16.0)
-      ffi (>= 1.15.0)
-    ffi (1.17.0-x86_64-linux-gnu)
+    faraday (2.12.0)
+      faraday-net_http (>= 2.0, < 3.4)
+      json
+      logger
+    faraday-multipart (1.0.4)
+      multipart-post (~> 2)
+    faraday-net_http (3.3.0)
+      net-http
     jaro_winkler (1.5.6)
+    json (2.7.2)
+    logger (1.6.1)
+    marcel (1.0.4)
     method_source (1.1.0)
+    multipart-post (2.4.1)
+    net-http (0.4.1)
+      uri
     parallel (1.26.3)
     parser (3.3.5.0)
       ast (~> 2.4.1)
@@ -54,9 +67,8 @@ GEM
       unicode-display_width (>= 1.4.0, < 1.6)
     ruby-progressbar (1.13.0)
     stringio (3.1.1)
-    typhoeus (1.4.1)
-      ethon (>= 0.9.0)
     unicode-display_width (1.5.0)
+    uri (0.13.1)
 
 PLATFORMS
   x86_64-linux

data/README.md

@@ -7,7 +7,7 @@ Cheminée: The Chemical Structure Search Engine
 This SDK is automatically generated by the [OpenAPI Generator](https://openapi-generator.tech) project:
 
 - API version: 1.0
-- Package version: 0.1.34
+- Package version: 0.1.35
 - Generator version: 7.9.0-SNAPSHOT
 - Build package: org.openapitools.codegen.languages.RubyClientCodegen
 For more information, please visit [https://github.com/rdkit-rs/cheminee](https://github.com/rdkit-rs/cheminee)
@@ -25,16 +25,16 @@ gem build cheminee.gemspec
 Then either install the gem locally:
 
 ```shell
-gem install ./cheminee-0.1.34.gem
+gem install ./cheminee-0.1.35.gem
 ```
 
-(for development, run `gem install --dev ./cheminee-0.1.34.gem` to install the development dependencies)
+(for development, run `gem install --dev ./cheminee-0.1.35.gem` to install the development dependencies)
 
 or publish the gem to a gem hosting service, e.g. [RubyGems](https://rubygems.org/).
 
 Finally add this to the Gemfile:
 
-    gem 'cheminee', '~> 0.1.34'
+    gem 'cheminee', '~> 0.1.35'
 
 ### Install from Git
 

data/cheminee.gemspec

@@ -28,7 +28,9 @@ Gem::Specification.new do |s|
   s.required_ruby_version = ">= 3.0"
   s.metadata    = {}
 
-  s.add_runtime_dependency 'typhoeus', '~> 1.0', '>= 1.0.1'
+  s.add_runtime_dependency 'faraday', '>= 1.0.1', '< 3.0'
+  s.add_runtime_dependency 'faraday-multipart'
+  s.add_runtime_dependency 'marcel'
 
   s.add_development_dependency 'rspec', '~> 3.6', '>= 3.6.0'
 

data/lib/cheminee/api_client.rb

@@ -15,7 +15,9 @@ require 'json'
 require 'logger'
 require 'tempfile'
 require 'time'
-require 'typhoeus'
+require 'faraday'
+require 'faraday/multipart' if Gem::Version.new(Faraday::VERSION) >= Gem::Version.new('2.0')
+require 'marcel'
 
 
 module Cheminee
@@ -46,39 +48,45 @@ module Cheminee
     # Call an API with given options.
     #
     # @return [Array<(Object, Integer, Hash)>] an array of 3 elements:
-    #   the data deserialized from response body (may be a Tempfile or nil), response status code and response headers.
+    #   the data deserialized from response body (could be nil), response status code and response headers.
     def call_api(http_method, path, opts = {})
-      request = build_request(http_method, path, opts)
-      tempfile = download_file(request) if opts[:return_type] == 'File'
-      response = request.run
+      stream = nil
+      begin
+        response = connection(opts).public_send(http_method.to_sym.downcase) do |req|
+          request = build_request(http_method, path, req, opts)
+          stream = download_file(request) if opts[:return_type] == 'File' || opts[:return_type] == 'Binary'
+        end
 
-      if @config.debugging
-        @config.logger.debug "HTTP response body ~BEGIN~\n#{response.body}\n~END~\n"
-      end
+        if config.debugging
+          config.logger.debug "HTTP response body ~BEGIN~\n#{response.body}\n~END~\n"
+        end
 
-      unless response.success?
-        if response.timed_out?
-          fail ApiError.new('Connection timed out')
-        elsif response.code == 0
-          # Errors from libcurl will be made visible here
-          fail ApiError.new(:code => 0,
-                            :message => response.return_message)
-        else
-          fail ApiError.new(:code => response.code,
-                            :response_headers => response.headers,
-                            :response_body => response.body),
-               response.status_message
+        unless response.success?
+          if response.status == 0 && response.respond_to?(:return_message)
+            # Errors from libcurl will be made visible here
+            fail ApiError.new(code: 0,
+                              message: response.return_message)
+          else
+            fail ApiError.new(code: response.status,
+                              response_headers: response.headers,
+                              response_body: response.body),
+                 response.reason_phrase
+          end
         end
+      rescue Faraday::TimeoutError
+        fail ApiError.new('Connection timed out')
+      rescue Faraday::ConnectionFailed
+        fail ApiError.new('Connection failed')
       end
 
-      if opts[:return_type] == 'File'
-        data = tempfile
+      if opts[:return_type] == 'File' || opts[:return_type] == 'Binary'
+        data = deserialize_file(response, stream)
       elsif opts[:return_type]
         data = deserialize(response, opts[:return_type])
       else
         data = nil
       end
-      return data, response.code, response.headers
+      return data, response.status, response.headers
     end
 
     # Builds the HTTP request
@@ -89,46 +97,33 @@ module Cheminee
     # @option opts [Hash] :query_params Query parameters
     # @option opts [Hash] :form_params Query parameters
     # @option opts [Object] :body HTTP body (JSON/XML)
-    # @return [Typhoeus::Request] A Typhoeus Request
-    def build_request(http_method, path, opts = {})
+    # @return [Faraday::Request] A Faraday Request
+    def build_request(http_method, path, request, opts = {})
       url = build_request_url(path, opts)
       http_method = http_method.to_sym.downcase
 
       header_params = @default_headers.merge(opts[:header_params] || {})
       query_params = opts[:query_params] || {}
       form_params = opts[:form_params] || {}
-      follow_location = opts[:follow_location] || true
-
-
-      # set ssl_verifyhosts option based on @config.verify_ssl_host (true/false)
-      _verify_ssl_host = @config.verify_ssl_host ? 2 : 0
-
-      req_opts = {
-        :method => http_method,
-        :headers => header_params,
-        :params => query_params,
-        :params_encoding => @config.params_encoding,
-        :timeout => @config.timeout,
-        :ssl_verifypeer => @config.verify_ssl,
-        :ssl_verifyhost => _verify_ssl_host,
-        :sslcert => @config.cert_file,
-        :sslkey => @config.key_file,
-        :verbose => @config.debugging,
-        :followlocation => follow_location
-      }
 
-      # set custom cert, if provided
-      req_opts[:cainfo] = @config.ssl_ca_cert if @config.ssl_ca_cert
+      update_params_for_auth! header_params, query_params, opts[:auth_names]
 
       if [:post, :patch, :put, :delete].include?(http_method)
         req_body = build_request_body(header_params, form_params, opts[:body])
-        req_opts.update :body => req_body
-        if @config.debugging
-          @config.logger.debug "HTTP request body param ~BEGIN~\n#{req_body}\n~END~\n"
+        if config.debugging
+          config.logger.debug "HTTP request body param ~BEGIN~\n#{req_body}\n~END~\n"
         end
       end
+      request.headers = header_params
+      request.body = req_body
 
-      Typhoeus::Request.new(url, req_opts)
+      # Overload default options only if provided
+      request.options.params_encoder = config.params_encoder if config.params_encoder
+      request.options.timeout        = config.timeout        if config.timeout
+
+      request.url url
+      request.params = query_params
+      request
     end
 
     # Builds the HTTP request body
@@ -139,13 +134,16 @@ module Cheminee
     # @return [String] HTTP body data in the form of string
     def build_request_body(header_params, form_params, body)
       # http form
-      if header_params['Content-Type'] == 'application/x-www-form-urlencoded' ||
-          header_params['Content-Type'] == 'multipart/form-data'
+      if header_params['Content-Type'] == 'application/x-www-form-urlencoded'
+        data = URI.encode_www_form(form_params)
+      elsif header_params['Content-Type'] == 'multipart/form-data'
         data = {}
         form_params.each do |key, value|
           case value
-          when ::File, ::Array, nil
-            # let typhoeus handle File, Array and nil parameters
+          when ::File, ::Tempfile
+            data[key] = Faraday::FilePart.new(value.path, Marcel::MimeType.for(Pathname.new(value.path)))
+          when ::Array, nil
+            # let Faraday handle Array and nil parameters
             data[key] = value
           else
             data[key] = value.to_s
@@ -159,49 +157,95 @@ module Cheminee
       data
     end
 
-    # Save response body into a file in (the defined) temporary folder, using the filename
-    # from the "Content-Disposition" header if provided, otherwise a random filename.
-    # The response body is written to the file in chunks in order to handle files which
-    # size is larger than maximum Ruby String or even larger than the maximum memory a Ruby
-    # process can use.
-    #
-    # @see Configuration#temp_folder_path
-    #
-    # @return [Tempfile] the tempfile generated
     def download_file(request)
-      tempfile = nil
-      encoding = nil
-      request.on_headers do |response|
-        content_disposition = response.headers['Content-Disposition']
-        if content_disposition && content_disposition =~ /filename=/i
-          filename = content_disposition[/filename=['"]?([^'"\s]+)['"]?/, 1]
-          prefix = sanitize_filename(filename)
-        else
-          prefix = 'download-'
-        end
-        prefix = prefix + '-' unless prefix.end_with?('-')
-        encoding = response.body.encoding
-        tempfile = Tempfile.open(prefix, @config.temp_folder_path, encoding: encoding)
-      end
-      request.on_body do |chunk|
-        chunk.force_encoding(encoding)
-        tempfile.write(chunk)
+      stream = []
+
+      # handle streaming Responses
+      request.options.on_data = Proc.new do |chunk, overall_received_bytes|
+        stream << chunk
       end
-      # run the request to ensure the tempfile is created successfully before returning it
-      request.run
-      if tempfile
-        tempfile.close
-        @config.logger.info "Temp file written to #{tempfile.path}, please copy the file to a proper folder "\
-                            "with e.g. `FileUtils.cp(tempfile.path, '/new/file/path')` otherwise the temp file "\
-                            "will be deleted automatically with GC. It's also recommended to delete the temp file "\
-                            "explicitly with `tempfile.delete`"
+
+      stream
+    end
+
+    def deserialize_file(response, stream)
+      body     = response.body
+      encoding = body.encoding
+
+      # reconstruct content
+      content = stream.join
+      content = content.unpack('m').join if response.headers['Content-Transfer-Encoding'] == 'binary'
+      content = content.force_encoding(encoding)
+
+      # return byte stream
+      return content if @config.return_binary_data == true
+
+      # return file instead of binary data
+      content_disposition = response.headers['Content-Disposition']
+      if content_disposition && content_disposition =~ /filename=/i
+        filename = content_disposition[/filename=['"]?([^'"\s]+)['"]?/, 1]
+        prefix = sanitize_filename(filename)
       else
-        fail ApiError.new("Failed to create the tempfile based on the HTTP response from the server: #{request.inspect}") 
+        prefix = 'download-'
       end
+      prefix = prefix + '-' unless prefix.end_with?('-')
+
+      tempfile = Tempfile.open(prefix, @config.temp_folder_path, encoding: encoding)
+      tempfile.write(content)
+      tempfile.close
 
+      config.logger.info "Temp file written to #{tempfile.path}, please copy the file to a proper folder "\
+                          "with e.g. `FileUtils.cp(tempfile.path, '/new/file/path')` otherwise the temp file "\
+                          "will be deleted automatically with GC. It's also recommended to delete the temp file "\
+                          "explicitly with `tempfile.delete`"
       tempfile
     end
 
+    def connection(opts)
+      opts[:header_params]['Content-Type'] == 'multipart/form-data' ? connection_multipart : connection_regular
+    end
+
+    def connection_multipart
+      @connection_multipart ||= build_connection do |conn|
+        conn.request :multipart
+        conn.request :url_encoded
+      end
+    end
+
+    def connection_regular
+      @connection_regular ||= build_connection
+    end
+
+    def build_connection
+      Faraday.new(url: config.base_url, ssl: ssl_options, proxy: config.proxy) do |conn|
+        basic_auth(conn)
+        config.configure_middleware(conn)
+        yield(conn) if block_given?
+        conn.adapter(Faraday.default_adapter)
+        config.configure_connection(conn)
+      end
+    end
+
+    def ssl_options
+      {
+        ca_file: config.ssl_ca_file,
+        verify: config.ssl_verify,
+        verify_mode: config.ssl_verify_mode,
+        client_cert: config.ssl_client_cert,
+        client_key: config.ssl_client_key
+      }
+    end
+
+    def basic_auth(conn)
+      if config.username && config.password
+        if Gem::Version.new(Faraday::VERSION) >= Gem::Version.new('2.0')
+          conn.request(:authorization, :basic, config.username, config.password)
+        else
+          conn.request(:basic_auth, config.username, config.password)
+        end
+      end
+    end
+
     # Check if the given MIME is a JSON MIME.
     # JSON MIME examples:
     #   application/json

data/lib/cheminee/configuration.rb

@@ -116,40 +116,39 @@ module Cheminee
     # @note Do NOT set it to false in production code, otherwise you would face multiple types of cryptographic attacks.
     #
     # @return [true, false]
-    attr_accessor :verify_ssl
+    attr_accessor :ssl_verify
 
     ### TLS/SSL setting
-    # Set this to false to skip verifying SSL host name
-    # Default to true.
+    # Any `OpenSSL::SSL::` constant (see https://ruby-doc.org/stdlib-2.5.1/libdoc/openssl/rdoc/OpenSSL/SSL.html)
     #
     # @note Do NOT set it to false in production code, otherwise you would face multiple types of cryptographic attacks.
     #
-    # @return [true, false]
-    attr_accessor :verify_ssl_host
+    attr_accessor :ssl_verify_mode
 
     ### TLS/SSL setting
     # Set this to customize the certificate file to verify the peer.
     #
     # @return [String] the path to the certificate file
-    #
-    # @see The `cainfo` option of Typhoeus, `--cert` option of libcurl. Related source code:
-    # https://github.com/typhoeus/typhoeus/blob/master/lib/typhoeus/easy_factory.rb#L145
-    attr_accessor :ssl_ca_cert
+    attr_accessor :ssl_ca_file
 
     ### TLS/SSL setting
     # Client certificate file (for client certificate)
-    attr_accessor :cert_file
+    attr_accessor :ssl_client_cert
 
     ### TLS/SSL setting
     # Client private key file (for client certificate)
-    attr_accessor :key_file
+    attr_accessor :ssl_client_key
+
+    ### Proxy setting
+    # HTTP Proxy settings
+    attr_accessor :proxy
 
-    # Set this to customize parameters encoding of array parameter with multi collectionFormat.
-    # Default to nil.
+    # Set this to customize parameters encoder of array parameter.
+    # Default to nil. Faraday uses NestedParamsEncoder when nil.
     #
-    # @see The params_encoding option of Ethon. Related source code:
-    # https://github.com/typhoeus/ethon/blob/master/lib/ethon/easy/queryable.rb#L96
-    attr_accessor :params_encoding
+    # @see The params_encoder option of Faraday. Related source code:
+    # https://github.com/lostisland/faraday/tree/main/lib/faraday/encoders
+    attr_accessor :params_encoder
 
 
     attr_accessor :inject_format
@@ -167,12 +166,17 @@ module Cheminee
       @api_key = {}
       @api_key_prefix = {}
       @client_side_validation = true
-      @verify_ssl = true
-      @verify_ssl_host = true
-      @cert_file = nil
-      @key_file = nil
-      @timeout = 0
-      @params_encoding = nil
+      @ssl_verify = true
+      @ssl_verify_mode = nil
+      @ssl_ca_file = nil
+      @ssl_client_cert = nil
+      @ssl_client_key = nil
+      @middlewares = Hash.new { |h, k| h[k] = [] }
+      @configure_connection_blocks = []
+      @timeout = 60
+      # return data as binary instead of file
+      @return_binary_data = false
+      @params_encoder = nil
       @debugging = false
       @ignore_operation_servers = false
       @inject_format = false
@@ -296,6 +300,86 @@ module Cheminee
       url
     end
 
+    # Configure Faraday connection directly.
+    #
+    # ```
+    # c.configure_faraday_connection do |conn|
+    #   conn.use Faraday::HttpCache, shared_cache: false, logger: logger
+    #   conn.response :logger, nil, headers: true, bodies: true, log_level: :debug do |logger|
+    #     logger.filter(/(Authorization: )(.*)/, '\1[REDACTED]')
+    #   end
+    # end
+    #
+    # c.configure_faraday_connection do |conn|
+    #   conn.adapter :typhoeus
+    # end
+    # ```
+    #
+    # @param block [Proc] `#call`able object that takes one arg, the connection
+    def configure_faraday_connection(&block)
+      @configure_connection_blocks << block
+    end
+
+    def configure_connection(conn)
+      @configure_connection_blocks.each do |block|
+        block.call(conn)
+      end
+    end
+
+    # Adds middleware to the stack
+    def use(*middleware)
+      set_faraday_middleware(:use, *middleware)
+    end
+
+    # Adds request middleware to the stack
+    def request(*middleware)
+      set_faraday_middleware(:request, *middleware)
+    end
+
+    # Adds response middleware to the stack
+    def response(*middleware)
+      set_faraday_middleware(:response, *middleware)
+    end
+
+    # Adds Faraday middleware setting information to the stack
+    #
+    # @example Use the `set_faraday_middleware` method to set middleware information
+    #   config.set_faraday_middleware(:request, :retry, max: 3, methods: [:get, :post], retry_statuses: [503])
+    #   config.set_faraday_middleware(:response, :logger, nil, { bodies: true, log_level: :debug })
+    #   config.set_faraday_middleware(:use, Faraday::HttpCache, store: Rails.cache, shared_cache: false)
+    #   config.set_faraday_middleware(:insert, 0, FaradayMiddleware::FollowRedirects, { standards_compliant: true, limit: 1 })
+    #   config.set_faraday_middleware(:swap, 0, Faraday::Response::Logger)
+    #   config.set_faraday_middleware(:delete, Faraday::Multipart::Middleware)
+    #
+    # @see https://github.com/lostisland/faraday/blob/v2.3.0/lib/faraday/rack_builder.rb#L92-L143
+    def set_faraday_middleware(operation, key, *args, &block)
+      unless [:request, :response, :use, :insert, :insert_before, :insert_after, :swap, :delete].include?(operation)
+        fail ArgumentError, "Invalid faraday middleware operation #{operation}. Must be" \
+                            " :request, :response, :use, :insert, :insert_before, :insert_after, :swap or :delete."
+      end
+
+      @middlewares[operation] << [key, args, block]
+    end
+    ruby2_keywords(:set_faraday_middleware) if respond_to?(:ruby2_keywords, true)
+
+    # Set up middleware on the connection
+    def configure_middleware(connection)
+      return if @middlewares.empty?
+
+      [:request, :response, :use, :insert, :insert_before, :insert_after, :swap].each do |operation|
+        next unless @middlewares.key?(operation)
+
+        @middlewares[operation].each do |key, args, block|
+          connection.builder.send(operation, key, *args, &block)
+        end
+      end
+
+      if @middlewares.key?(:delete)
+        @middlewares[:delete].each do |key, _args, _block|
+          connection.builder.delete(key)
+        end
+      end
+    end
 
   end
 end

data/lib/cheminee/version.rb

@@ -11,5 +11,5 @@ Generator version: 7.9.0-SNAPSHOT
 =end
 
 module Cheminee
-  VERSION = '0.1.34'
+  VERSION = '0.1.35'
 end

metadata

@@ -1,35 +1,63 @@
 --- !ruby/object:Gem::Specification
 name: cheminee
 version: !ruby/object:Gem::Version
-  version: 0.1.34
+  version: 0.1.35
 platform: ruby
 authors:
 - Xavier Lange
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-09-23 00:00:00.000000000 Z
+date: 2024-09-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: typhoeus
+  name: faraday
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.1
+    - - "<"
       - !ruby/object:Gem::Version
-        version: '1.0'
+        version: '3.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
     - - ">="
       - !ruby/object:Gem::Version
         version: 1.0.1
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+- !ruby/object:Gem::Dependency
+  name: faraday-multipart
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '1.0'
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: marcel
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.0.1
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -126,7 +154,7 @@ files:
 - lib/cheminee/version.rb
 - openapi-generator-config.json
 - openapi.json
-- pkg/cheminee-0.1.34.gem
+- pkg/cheminee-0.1.35.gem
 - spec/api/default_api_spec.rb
 - spec/api_client_spec.rb
 - spec/configuration_spec.rb