cheminee 0.1.12 → 0.1.14

data/lib/cheminee/api/default_api.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.1.0-SNAPSHOT
+OpenAPI Generator version: 7.3.0-SNAPSHOT
 
 =end
 
@@ -149,7 +149,7 @@ module Cheminee
     # Get extended information about an index
     # @param index [String] 
     # @param [Hash] opts the optional parameters
-    # @return [Array<IndexMeta>]
+    # @return [IndexSchema]
     def v1_indexes_index_get(index, opts = {})
       data, _status_code, _headers = v1_indexes_index_get_with_http_info(index, opts)
       data
@@ -158,7 +158,7 @@ module Cheminee
     # Get extended information about an index
     # @param index [String] 
     # @param [Hash] opts the optional parameters
-    # @return [Array<(Array<IndexMeta>, Integer, Hash)>] Array<IndexMeta> data, response status code and response headers
+    # @return [Array<(IndexSchema, Integer, Hash)>] IndexSchema data, response status code and response headers
     def v1_indexes_index_get_with_http_info(index, opts = {})
       if @api_client.config.debugging
         @api_client.config.logger.debug 'Calling API: DefaultApi.v1_indexes_index_get ...'
@@ -185,7 +185,7 @@ module Cheminee
       post_body = opts[:debug_body]
 
       # return_type
-      return_type = opts[:debug_return_type] || 'Array<IndexMeta>'
+      return_type = opts[:debug_return_type] || 'IndexSchema'
 
       # auth_names
       auth_names = opts[:debug_auth_names] || []
@@ -278,26 +278,99 @@ module Cheminee
       return data, status_code, headers
     end
 
+    # Perform basic query search against index
+    # @param index [String] 
+    # @param query [String] 
+    # @param [Hash] opts the optional parameters
+    # @option opts [Integer] :limit 
+    # @return [Array<QuerySearchHit>]
+    def v1_indexes_index_search_basic_get(index, query, opts = {})
+      data, _status_code, _headers = v1_indexes_index_search_basic_get_with_http_info(index, query, opts)
+      data
+    end
+
+    # Perform basic query search against index
+    # @param index [String] 
+    # @param query [String] 
+    # @param [Hash] opts the optional parameters
+    # @option opts [Integer] :limit 
+    # @return [Array<(Array<QuerySearchHit>, Integer, Hash)>] Array<QuerySearchHit> data, response status code and response headers
+    def v1_indexes_index_search_basic_get_with_http_info(index, query, opts = {})
+      if @api_client.config.debugging
+        @api_client.config.logger.debug 'Calling API: DefaultApi.v1_indexes_index_search_basic_get ...'
+      end
+      # verify the required parameter 'index' is set
+      if @api_client.config.client_side_validation && index.nil?
+        fail ArgumentError, "Missing the required parameter 'index' when calling DefaultApi.v1_indexes_index_search_basic_get"
+      end
+      # verify the required parameter 'query' is set
+      if @api_client.config.client_side_validation && query.nil?
+        fail ArgumentError, "Missing the required parameter 'query' when calling DefaultApi.v1_indexes_index_search_basic_get"
+      end
+      # resource path
+      local_var_path = '/v1/indexes/{index}/search/basic'.sub('{' + 'index' + '}', CGI.escape(index.to_s))
+
+      # query parameters
+      query_params = opts[:query_params] || {}
+      query_params[:'query'] = query
+      query_params[:'limit'] = opts[:'limit'] if !opts[:'limit'].nil?
+
+      # header parameters
+      header_params = opts[:header_params] || {}
+      # HTTP header 'Accept' (if needed)
+      header_params['Accept'] = @api_client.select_header_accept(['application/json; charset=utf-8'])
+
+      # form parameters
+      form_params = opts[:form_params] || {}
+
+      # http body (model)
+      post_body = opts[:debug_body]
+
+      # return_type
+      return_type = opts[:debug_return_type] || 'Array<QuerySearchHit>'
+
+      # auth_names
+      auth_names = opts[:debug_auth_names] || []
+
+      new_options = opts.merge(
+        :operation => :"DefaultApi.v1_indexes_index_search_basic_get",
+        :header_params => header_params,
+        :query_params => query_params,
+        :form_params => form_params,
+        :body => post_body,
+        :auth_names => auth_names,
+        :return_type => return_type
+      )
+
+      data, status_code, headers = @api_client.call_api(:GET, local_var_path, new_options)
+      if @api_client.config.debugging
+        @api_client.config.logger.debug "API called: DefaultApi#v1_indexes_index_search_basic_get\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
+      end
+      return data, status_code, headers
+    end
+
     # Perform substructure search against index
     # @param index [String] 
-    # @param smile [String] 
+    # @param smiles [String] 
     # @param [Hash] opts the optional parameters
     # @option opts [Integer] :result_limit 
     # @option opts [Integer] :tautomer_limit 
+    # @option opts [String] :extra_query 
     # @return [Array<StructureSearchHit>]
-    def v1_indexes_index_search_substructure_get(index, smile, opts = {})
-      data, _status_code, _headers = v1_indexes_index_search_substructure_get_with_http_info(index, smile, opts)
+    def v1_indexes_index_search_substructure_get(index, smiles, opts = {})
+      data, _status_code, _headers = v1_indexes_index_search_substructure_get_with_http_info(index, smiles, opts)
       data
     end
 
     # Perform substructure search against index
     # @param index [String] 
-    # @param smile [String] 
+    # @param smiles [String] 
     # @param [Hash] opts the optional parameters
     # @option opts [Integer] :result_limit 
     # @option opts [Integer] :tautomer_limit 
+    # @option opts [String] :extra_query 
     # @return [Array<(Array<StructureSearchHit>, Integer, Hash)>] Array<StructureSearchHit> data, response status code and response headers
-    def v1_indexes_index_search_substructure_get_with_http_info(index, smile, opts = {})
+    def v1_indexes_index_search_substructure_get_with_http_info(index, smiles, opts = {})
       if @api_client.config.debugging
         @api_client.config.logger.debug 'Calling API: DefaultApi.v1_indexes_index_search_substructure_get ...'
       end
@@ -305,18 +378,19 @@ module Cheminee
       if @api_client.config.client_side_validation && index.nil?
         fail ArgumentError, "Missing the required parameter 'index' when calling DefaultApi.v1_indexes_index_search_substructure_get"
       end
-      # verify the required parameter 'smile' is set
-      if @api_client.config.client_side_validation && smile.nil?
-        fail ArgumentError, "Missing the required parameter 'smile' when calling DefaultApi.v1_indexes_index_search_substructure_get"
+      # verify the required parameter 'smiles' is set
+      if @api_client.config.client_side_validation && smiles.nil?
+        fail ArgumentError, "Missing the required parameter 'smiles' when calling DefaultApi.v1_indexes_index_search_substructure_get"
       end
       # resource path
       local_var_path = '/v1/indexes/{index}/search/substructure'.sub('{' + 'index' + '}', CGI.escape(index.to_s))
 
       # query parameters
       query_params = opts[:query_params] || {}
-      query_params[:'smile'] = smile
+      query_params[:'smiles'] = smiles
       query_params[:'result_limit'] = opts[:'result_limit'] if !opts[:'result_limit'].nil?
       query_params[:'tautomer_limit'] = opts[:'tautomer_limit'] if !opts[:'tautomer_limit'].nil?
+      query_params[:'extra_query'] = opts[:'extra_query'] if !opts[:'extra_query'].nil?
 
       # header parameters
       header_params = opts[:header_params] || {}
@@ -408,25 +482,25 @@ module Cheminee
     end
 
     # Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
-    # @param smile [Array<Smile>] 
+    # @param smiles [Array<Smiles>] 
     # @param [Hash] opts the optional parameters
-    # @return [Array<StandardizedSmile>]
-    def v1_standardize_post(smile, opts = {})
-      data, _status_code, _headers = v1_standardize_post_with_http_info(smile, opts)
+    # @return [Array<StandardizedSmiles>]
+    def v1_standardize_post(smiles, opts = {})
+      data, _status_code, _headers = v1_standardize_post_with_http_info(smiles, opts)
       data
     end
 
     # Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
-    # @param smile [Array<Smile>] 
+    # @param smiles [Array<Smiles>] 
     # @param [Hash] opts the optional parameters
-    # @return [Array<(Array<StandardizedSmile>, Integer, Hash)>] Array<StandardizedSmile> data, response status code and response headers
-    def v1_standardize_post_with_http_info(smile, opts = {})
+    # @return [Array<(Array<StandardizedSmiles>, Integer, Hash)>] Array<StandardizedSmiles> data, response status code and response headers
+    def v1_standardize_post_with_http_info(smiles, opts = {})
       if @api_client.config.debugging
         @api_client.config.logger.debug 'Calling API: DefaultApi.v1_standardize_post ...'
       end
-      # verify the required parameter 'smile' is set
-      if @api_client.config.client_side_validation && smile.nil?
-        fail ArgumentError, "Missing the required parameter 'smile' when calling DefaultApi.v1_standardize_post"
+      # verify the required parameter 'smiles' is set
+      if @api_client.config.client_side_validation && smiles.nil?
+        fail ArgumentError, "Missing the required parameter 'smiles' when calling DefaultApi.v1_standardize_post"
       end
       # resource path
       local_var_path = '/v1/standardize'
@@ -448,10 +522,10 @@ module Cheminee
       form_params = opts[:form_params] || {}
 
       # http body (model)
-      post_body = opts[:debug_body] || @api_client.object_to_http_body(smile)
+      post_body = opts[:debug_body] || @api_client.object_to_http_body(smiles)
 
       # return_type
-      return_type = opts[:debug_return_type] || 'Array<StandardizedSmile>'
+      return_type = opts[:debug_return_type] || 'Array<StandardizedSmiles>'
 
       # auth_names
       auth_names = opts[:debug_auth_names] || []

data/lib/cheminee/api_client.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.1.0-SNAPSHOT
+OpenAPI Generator version: 7.3.0-SNAPSHOT
 
 =end
 
@@ -46,9 +46,10 @@ module Cheminee
     # Call an API with given options.
     #
     # @return [Array<(Object, Integer, Hash)>] an array of 3 elements:
-    #   the data deserialized from response body (could be nil), response status code and response headers.
+    #   the data deserialized from response body (may be a Tempfile or 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
 
       if @config.debugging
@@ -70,7 +71,9 @@ module Cheminee
         end
       end
 
-      if opts[:return_type]
+      if opts[:return_type] == 'File'
+        data = tempfile
+      elsif opts[:return_type]
         data = deserialize(response, opts[:return_type])
       else
         data = nil
@@ -125,9 +128,7 @@ module Cheminee
         end
       end
 
-      request = Typhoeus::Request.new(url, req_opts)
-      download_file(request) if opts[:return_type] == 'File'
-      request
+      Typhoeus::Request.new(url, req_opts)
     end
 
     # Builds the HTTP request body
@@ -165,6 +166,8 @@ module Cheminee
     # process can use.
     #
     # @see Configuration#temp_folder_path
+    #
+    # @return [Tempfile] the tempfile generated
     def download_file(request)
       tempfile = nil
       encoding = nil
@@ -179,21 +182,24 @@ module Cheminee
         prefix = prefix + '-' unless prefix.end_with?('-')
         encoding = response.body.encoding
         tempfile = Tempfile.open(prefix, @config.temp_folder_path, encoding: encoding)
-        @tempfile = tempfile
       end
       request.on_body do |chunk|
         chunk.force_encoding(encoding)
         tempfile.write(chunk)
       end
-      request.on_complete do |response|
-        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`"
-        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`"
+      else
+        fail ApiError.new("Failed to create the tempfile based on the HTTP response from the server: #{request.inspect}") 
       end
+
+      tempfile
     end
 
     # Check if the given MIME is a JSON MIME.
@@ -214,11 +220,6 @@ module Cheminee
     # @param [String] return_type some examples: "User", "Array<User>", "Hash<String, Integer>"
     def deserialize(response, return_type)
       body = response.body
-
-      # handle file downloading - return the File instance processed in request callbacks
-      # note that response body is empty when the file is written in chunks in request on_body callback
-      return @tempfile if return_type == 'File'
-
       return nil if body.nil? || body.empty?
 
       # return response body directly for String return type

data/lib/cheminee/api_error.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.1.0-SNAPSHOT
+OpenAPI Generator version: 7.3.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/configuration.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.1.0-SNAPSHOT
+OpenAPI Generator version: 7.3.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/models/bulk_request.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.1.0-SNAPSHOT
+OpenAPI Generator version: 7.3.0-SNAPSHOT
 
 =end
 
@@ -168,7 +168,7 @@ module Cheminee
       else # model
         # models (e.g. Pet) or oneOf
         klass = Cheminee.const_get(type)
-        klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
+        klass.respond_to?(:openapi_any_of) || klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
       end
     end
 

data/lib/cheminee/models/bulk_request_doc.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.1.0-SNAPSHOT
+OpenAPI Generator version: 7.3.0-SNAPSHOT
 
 =end
 
@@ -15,7 +15,7 @@ require 'time'
 
 module Cheminee
   class BulkRequestDoc
-    attr_accessor :smile
+    attr_accessor :smiles
 
     # This value can store an arbitrary JSON object like '{}'
     attr_accessor :extra_data
@@ -23,7 +23,7 @@ module Cheminee
     # Attribute mapping from ruby-style variable name to JSON key.
     def self.attribute_map
       {
-        :'smile' => :'smile',
+        :'smiles' => :'smiles',
         :'extra_data' => :'extra_data'
       }
     end
@@ -36,7 +36,7 @@ module Cheminee
     # Attribute type mapping.
     def self.openapi_types
       {
-        :'smile' => :'String',
+        :'smiles' => :'String',
         :'extra_data' => :'Object'
       }
     end
@@ -63,10 +63,10 @@ module Cheminee
         h[k.to_sym] = v
       }
 
-      if attributes.key?(:'smile')
-        self.smile = attributes[:'smile']
+      if attributes.key?(:'smiles')
+        self.smiles = attributes[:'smiles']
       else
-        self.smile = nil
+        self.smiles = nil
       end
 
       if attributes.key?(:'extra_data')
@@ -79,8 +79,8 @@ module Cheminee
     def list_invalid_properties
       warn '[DEPRECATED] the `list_invalid_properties` method is obsolete'
       invalid_properties = Array.new
-      if @smile.nil?
-        invalid_properties.push('invalid value for "smile", smile cannot be nil.')
+      if @smiles.nil?
+        invalid_properties.push('invalid value for "smiles", smiles cannot be nil.')
       end
 
       invalid_properties
@@ -90,7 +90,7 @@ module Cheminee
     # @return true if the model is valid
     def valid?
       warn '[DEPRECATED] the `valid?` method is obsolete'
-      return false if @smile.nil?
+      return false if @smiles.nil?
       true
     end
 
@@ -99,7 +99,7 @@ module Cheminee
     def ==(o)
       return true if self.equal?(o)
       self.class == o.class &&
-          smile == o.smile &&
+          smiles == o.smiles &&
           extra_data == o.extra_data
     end
 
@@ -112,7 +112,7 @@ module Cheminee
     # Calculates hash code according to all attributes.
     # @return [Integer] Hash code
     def hash
-      [smile, extra_data].hash
+      [smiles, extra_data].hash
     end
 
     # Builds the object from hash
@@ -177,7 +177,7 @@ module Cheminee
       else # model
         # models (e.g. Pet) or oneOf
         klass = Cheminee.const_get(type)
-        klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
+        klass.respond_to?(:openapi_any_of) || klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
       end
     end
 

data/lib/cheminee/models/create_index_error.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.1.0-SNAPSHOT
+OpenAPI Generator version: 7.3.0-SNAPSHOT
 
 =end
 
@@ -166,7 +166,7 @@ module Cheminee
       else # model
         # models (e.g. Pet) or oneOf
         klass = Cheminee.const_get(type)
-        klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
+        klass.respond_to?(:openapi_any_of) || klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
       end
     end
 

data/lib/cheminee/models/get_indexes_response_error.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.1.0-SNAPSHOT
+OpenAPI Generator version: 7.3.0-SNAPSHOT
 
 =end
 
@@ -166,7 +166,7 @@ module Cheminee
       else # model
         # models (e.g. Pet) or oneOf
         klass = Cheminee.const_get(type)
-        klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
+        klass.respond_to?(:openapi_any_of) || klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
       end
     end
 

data/lib/cheminee/models/index_meta.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.1.0-SNAPSHOT
+OpenAPI Generator version: 7.3.0-SNAPSHOT
 
 =end
 
@@ -182,7 +182,7 @@ module Cheminee
       else # model
         # models (e.g. Pet) or oneOf
         klass = Cheminee.const_get(type)
-        klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
+        klass.respond_to?(:openapi_any_of) || klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
       end
     end