cheminee 0.0.14

data/lib/cheminee/models/structure_search_hit.rb

@@ -0,0 +1,281 @@
+=begin
+#Cheminée
+
+#Cheminée: The Chemical Structure Search Engine
+
+The version of the OpenAPI document: 1.0
+
+Generated by: https://openapi-generator.tech
+OpenAPI Generator version: 7.3.0-SNAPSHOT
+
+=end
+
+require 'date'
+require 'time'
+
+module Cheminee
+  class StructureSearchHit
+    attr_accessor :extra_data
+
+    attr_accessor :smiles
+
+    attr_accessor :score
+
+    attr_accessor :query
+
+    attr_accessor :used_tautomers
+
+    # Attribute mapping from ruby-style variable name to JSON key.
+    def self.attribute_map
+      {
+        :'extra_data' => :'extra_data',
+        :'smiles' => :'smiles',
+        :'score' => :'score',
+        :'query' => :'query',
+        :'used_tautomers' => :'used_tautomers'
+      }
+    end
+
+    # Returns all the JSON keys this model knows about
+    def self.acceptable_attributes
+      attribute_map.values
+    end
+
+    # Attribute type mapping.
+    def self.openapi_types
+      {
+        :'extra_data' => :'Object',
+        :'smiles' => :'String',
+        :'score' => :'Float',
+        :'query' => :'String',
+        :'used_tautomers' => :'Boolean'
+      }
+    end
+
+    # List of attributes with nullable: true
+    def self.openapi_nullable
+      Set.new([
+        :'extra_data',
+      ])
+    end
+
+    # Initializes the object
+    # @param [Hash] attributes Model attributes in the form of hash
+    def initialize(attributes = {})
+      if (!attributes.is_a?(Hash))
+        fail ArgumentError, "The input argument (attributes) must be a hash in `Cheminee::StructureSearchHit` initialize method"
+      end
+
+      # check to see if the attribute exists and convert string to symbol for hash key
+      attributes = attributes.each_with_object({}) { |(k, v), h|
+        if (!self.class.attribute_map.key?(k.to_sym))
+          fail ArgumentError, "`#{k}` is not a valid attribute in `Cheminee::StructureSearchHit`. Please check the name to make sure it's valid. List of attributes: " + self.class.attribute_map.keys.inspect
+        end
+        h[k.to_sym] = v
+      }
+
+      if attributes.key?(:'extra_data')
+        self.extra_data = attributes[:'extra_data']
+      else
+        self.extra_data = nil
+      end
+
+      if attributes.key?(:'smiles')
+        self.smiles = attributes[:'smiles']
+      else
+        self.smiles = nil
+      end
+
+      if attributes.key?(:'score')
+        self.score = attributes[:'score']
+      else
+        self.score = nil
+      end
+
+      if attributes.key?(:'query')
+        self.query = attributes[:'query']
+      else
+        self.query = nil
+      end
+
+      if attributes.key?(:'used_tautomers')
+        self.used_tautomers = attributes[:'used_tautomers']
+      else
+        self.used_tautomers = nil
+      end
+    end
+
+    # Show invalid properties with the reasons. Usually used together with valid?
+    # @return Array for valid properties with the reasons
+    def list_invalid_properties
+      warn '[DEPRECATED] the `list_invalid_properties` method is obsolete'
+      invalid_properties = Array.new
+      if @smiles.nil?
+        invalid_properties.push('invalid value for "smiles", smiles cannot be nil.')
+      end
+
+      if @score.nil?
+        invalid_properties.push('invalid value for "score", score cannot be nil.')
+      end
+
+      if @query.nil?
+        invalid_properties.push('invalid value for "query", query cannot be nil.')
+      end
+
+      if @used_tautomers.nil?
+        invalid_properties.push('invalid value for "used_tautomers", used_tautomers cannot be nil.')
+      end
+
+      invalid_properties
+    end
+
+    # Check to see if the all the properties in the model are valid
+    # @return true if the model is valid
+    def valid?
+      warn '[DEPRECATED] the `valid?` method is obsolete'
+      return false if @smiles.nil?
+      return false if @score.nil?
+      return false if @query.nil?
+      return false if @used_tautomers.nil?
+      true
+    end
+
+    # Checks equality by comparing each attribute.
+    # @param [Object] Object to be compared
+    def ==(o)
+      return true if self.equal?(o)
+      self.class == o.class &&
+          extra_data == o.extra_data &&
+          smiles == o.smiles &&
+          score == o.score &&
+          query == o.query &&
+          used_tautomers == o.used_tautomers
+    end
+
+    # @see the `==` method
+    # @param [Object] Object to be compared
+    def eql?(o)
+      self == o
+    end
+
+    # Calculates hash code according to all attributes.
+    # @return [Integer] Hash code
+    def hash
+      [extra_data, smiles, score, query, used_tautomers].hash
+    end
+
+    # Builds the object from hash
+    # @param [Hash] attributes Model attributes in the form of hash
+    # @return [Object] Returns the model itself
+    def self.build_from_hash(attributes)
+      return nil unless attributes.is_a?(Hash)
+      attributes = attributes.transform_keys(&:to_sym)
+      transformed_hash = {}
+      openapi_types.each_pair do |key, type|
+        if attributes.key?(attribute_map[key]) && attributes[attribute_map[key]].nil?
+          transformed_hash["#{key}"] = nil
+        elsif type =~ /\AArray<(.*)>/i
+          # check to ensure the input is an array given that the attribute
+          # is documented as an array but the input is not
+          if attributes[attribute_map[key]].is_a?(Array)
+            transformed_hash["#{key}"] = attributes[attribute_map[key]].map { |v| _deserialize($1, v) }
+          end
+        elsif !attributes[attribute_map[key]].nil?
+          transformed_hash["#{key}"] = _deserialize(type, attributes[attribute_map[key]])
+        end
+      end
+      new(transformed_hash)
+    end
+
+    # Deserializes the data based on type
+    # @param string type Data type
+    # @param string value Value to be deserialized
+    # @return [Object] Deserialized data
+    def self._deserialize(type, value)
+      case type.to_sym
+      when :Time
+        Time.parse(value)
+      when :Date
+        Date.parse(value)
+      when :String
+        value.to_s
+      when :Integer
+        value.to_i
+      when :Float
+        value.to_f
+      when :Boolean
+        if value.to_s =~ /\A(true|t|yes|y|1)\z/i
+          true
+        else
+          false
+        end
+      when :Object
+        # generic object (usually a Hash), return directly
+        value
+      when /\AArray<(?<inner_type>.+)>\z/
+        inner_type = Regexp.last_match[:inner_type]
+        value.map { |v| _deserialize(inner_type, v) }
+      when /\AHash<(?<k_type>.+?), (?<v_type>.+)>\z/
+        k_type = Regexp.last_match[:k_type]
+        v_type = Regexp.last_match[:v_type]
+        {}.tap do |hash|
+          value.each do |k, v|
+            hash[_deserialize(k_type, k)] = _deserialize(v_type, v)
+          end
+        end
+      else # model
+        # models (e.g. Pet) or oneOf
+        klass = Cheminee.const_get(type)
+        klass.respond_to?(:openapi_any_of) || klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
+      end
+    end
+
+    # Returns the string representation of the object
+    # @return [String] String presentation of the object
+    def to_s
+      to_hash.to_s
+    end
+
+    # to_body is an alias to to_hash (backward compatibility)
+    # @return [Hash] Returns the object in the form of hash
+    def to_body
+      to_hash
+    end
+
+    # Returns the object in the form of hash
+    # @return [Hash] Returns the object in the form of hash
+    def to_hash
+      hash = {}
+      self.class.attribute_map.each_pair do |attr, param|
+        value = self.send(attr)
+        if value.nil?
+          is_nullable = self.class.openapi_nullable.include?(attr)
+          next if !is_nullable || (is_nullable && !instance_variable_defined?(:"@#{attr}"))
+        end
+
+        hash[param] = _to_hash(value)
+      end
+      hash
+    end
+
+    # Outputs non-array value in the form of hash
+    # For object, use to_hash. Otherwise, just return the value
+    # @param [Object] value Any valid value
+    # @return [Hash] Returns the value in the form of hash
+    def _to_hash(value)
+      if value.is_a?(Array)
+        value.compact.map { |v| _to_hash(v) }
+      elsif value.is_a?(Hash)
+        {}.tap do |hash|
+          value.each { |k, v| hash[k] = _to_hash(v) }
+        end
+      elsif value.respond_to? :to_hash
+        value.to_hash
+      else
+        value
+      end
+    end
+
+  end
+
+end

data/lib/cheminee/models/substructure_search_hit.rb

@@ -0,0 +1,265 @@
+=begin
+#Cheminée
+
+#Cheminée: The Chemical Structure Search Engine
+
+The version of the OpenAPI document: 1.0
+
+Generated by: https://openapi-generator.tech
+OpenAPI Generator version: 7.1.0-SNAPSHOT
+
+=end
+
+require 'date'
+require 'time'
+
+module Cheminee
+  class SubstructureSearchHit
+    attr_accessor :extra_data
+
+    attr_accessor :smiles
+
+    attr_accessor :score
+
+    attr_accessor :query
+
+    # Attribute mapping from ruby-style variable name to JSON key.
+    def self.attribute_map
+      {
+        :'extra_data' => :'extra_data',
+        :'smiles' => :'smiles',
+        :'score' => :'score',
+        :'query' => :'query'
+      }
+    end
+
+    # Returns all the JSON keys this model knows about
+    def self.acceptable_attributes
+      attribute_map.values
+    end
+
+    # Attribute type mapping.
+    def self.openapi_types
+      {
+        :'extra_data' => :'Object',
+        :'smiles' => :'String',
+        :'score' => :'Float',
+        :'query' => :'String'
+      }
+    end
+
+    # List of attributes with nullable: true
+    def self.openapi_nullable
+      Set.new([
+        :'extra_data',
+      ])
+    end
+
+    # Initializes the object
+    # @param [Hash] attributes Model attributes in the form of hash
+    def initialize(attributes = {})
+      if (!attributes.is_a?(Hash))
+        fail ArgumentError, "The input argument (attributes) must be a hash in `Cheminee::SubstructureSearchHit` initialize method"
+      end
+
+      # check to see if the attribute exists and convert string to symbol for hash key
+      attributes = attributes.each_with_object({}) { |(k, v), h|
+        if (!self.class.attribute_map.key?(k.to_sym))
+          fail ArgumentError, "`#{k}` is not a valid attribute in `Cheminee::SubstructureSearchHit`. Please check the name to make sure it's valid. List of attributes: " + self.class.attribute_map.keys.inspect
+        end
+        h[k.to_sym] = v
+      }
+
+      if attributes.key?(:'extra_data')
+        self.extra_data = attributes[:'extra_data']
+      else
+        self.extra_data = nil
+      end
+
+      if attributes.key?(:'smiles')
+        self.smiles = attributes[:'smiles']
+      else
+        self.smiles = nil
+      end
+
+      if attributes.key?(:'score')
+        self.score = attributes[:'score']
+      else
+        self.score = nil
+      end
+
+      if attributes.key?(:'query')
+        self.query = attributes[:'query']
+      else
+        self.query = nil
+      end
+    end
+
+    # Show invalid properties with the reasons. Usually used together with valid?
+    # @return Array for valid properties with the reasons
+    def list_invalid_properties
+      warn '[DEPRECATED] the `list_invalid_properties` method is obsolete'
+      invalid_properties = Array.new
+      if @smiles.nil?
+        invalid_properties.push('invalid value for "smiles", smiles cannot be nil.')
+      end
+
+      if @score.nil?
+        invalid_properties.push('invalid value for "score", score cannot be nil.')
+      end
+
+      if @query.nil?
+        invalid_properties.push('invalid value for "query", query cannot be nil.')
+      end
+
+      invalid_properties
+    end
+
+    # Check to see if the all the properties in the model are valid
+    # @return true if the model is valid
+    def valid?
+      warn '[DEPRECATED] the `valid?` method is obsolete'
+      return false if @smiles.nil?
+      return false if @score.nil?
+      return false if @query.nil?
+      true
+    end
+
+    # Checks equality by comparing each attribute.
+    # @param [Object] Object to be compared
+    def ==(o)
+      return true if self.equal?(o)
+      self.class == o.class &&
+          extra_data == o.extra_data &&
+          smiles == o.smiles &&
+          score == o.score &&
+          query == o.query
+    end
+
+    # @see the `==` method
+    # @param [Object] Object to be compared
+    def eql?(o)
+      self == o
+    end
+
+    # Calculates hash code according to all attributes.
+    # @return [Integer] Hash code
+    def hash
+      [extra_data, smiles, score, query].hash
+    end
+
+    # Builds the object from hash
+    # @param [Hash] attributes Model attributes in the form of hash
+    # @return [Object] Returns the model itself
+    def self.build_from_hash(attributes)
+      return nil unless attributes.is_a?(Hash)
+      attributes = attributes.transform_keys(&:to_sym)
+      transformed_hash = {}
+      openapi_types.each_pair do |key, type|
+        if attributes.key?(attribute_map[key]) && attributes[attribute_map[key]].nil?
+          transformed_hash["#{key}"] = nil
+        elsif type =~ /\AArray<(.*)>/i
+          # check to ensure the input is an array given that the attribute
+          # is documented as an array but the input is not
+          if attributes[attribute_map[key]].is_a?(Array)
+            transformed_hash["#{key}"] = attributes[attribute_map[key]].map { |v| _deserialize($1, v) }
+          end
+        elsif !attributes[attribute_map[key]].nil?
+          transformed_hash["#{key}"] = _deserialize(type, attributes[attribute_map[key]])
+        end
+      end
+      new(transformed_hash)
+    end
+
+    # Deserializes the data based on type
+    # @param string type Data type
+    # @param string value Value to be deserialized
+    # @return [Object] Deserialized data
+    def self._deserialize(type, value)
+      case type.to_sym
+      when :Time
+        Time.parse(value)
+      when :Date
+        Date.parse(value)
+      when :String
+        value.to_s
+      when :Integer
+        value.to_i
+      when :Float
+        value.to_f
+      when :Boolean
+        if value.to_s =~ /\A(true|t|yes|y|1)\z/i
+          true
+        else
+          false
+        end
+      when :Object
+        # generic object (usually a Hash), return directly
+        value
+      when /\AArray<(?<inner_type>.+)>\z/
+        inner_type = Regexp.last_match[:inner_type]
+        value.map { |v| _deserialize(inner_type, v) }
+      when /\AHash<(?<k_type>.+?), (?<v_type>.+)>\z/
+        k_type = Regexp.last_match[:k_type]
+        v_type = Regexp.last_match[:v_type]
+        {}.tap do |hash|
+          value.each do |k, v|
+            hash[_deserialize(k_type, k)] = _deserialize(v_type, v)
+          end
+        end
+      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)
+      end
+    end
+
+    # Returns the string representation of the object
+    # @return [String] String presentation of the object
+    def to_s
+      to_hash.to_s
+    end
+
+    # to_body is an alias to to_hash (backward compatibility)
+    # @return [Hash] Returns the object in the form of hash
+    def to_body
+      to_hash
+    end
+
+    # Returns the object in the form of hash
+    # @return [Hash] Returns the object in the form of hash
+    def to_hash
+      hash = {}
+      self.class.attribute_map.each_pair do |attr, param|
+        value = self.send(attr)
+        if value.nil?
+          is_nullable = self.class.openapi_nullable.include?(attr)
+          next if !is_nullable || (is_nullable && !instance_variable_defined?(:"@#{attr}"))
+        end
+
+        hash[param] = _to_hash(value)
+      end
+      hash
+    end
+
+    # Outputs non-array value in the form of hash
+    # For object, use to_hash. Otherwise, just return the value
+    # @param [Object] value Any valid value
+    # @return [Hash] Returns the value in the form of hash
+    def _to_hash(value)
+      if value.is_a?(Array)
+        value.compact.map { |v| _to_hash(v) }
+      elsif value.is_a?(Hash)
+        {}.tap do |hash|
+          value.each { |k, v| hash[k] = _to_hash(v) }
+        end
+      elsif value.respond_to? :to_hash
+        value.to_hash
+      else
+        value
+      end
+    end
+
+  end
+
+end

data/lib/cheminee/version.rb

@@ -0,0 +1,15 @@
+=begin
+#Cheminée
+
+#Cheminée: The Chemical Structure Search Engine
+
+The version of the OpenAPI document: 1.0
+
+Generated by: https://openapi-generator.tech
+OpenAPI Generator version: 7.3.0-SNAPSHOT
+
+=end
+
+module Cheminee
+  VERSION = '0.0.14'
+end

data/lib/cheminee.rb

@@ -0,0 +1,57 @@
+=begin
+#Cheminée
+
+#Cheminée: The Chemical Structure Search Engine
+
+The version of the OpenAPI document: 1.0
+
+Generated by: https://openapi-generator.tech
+OpenAPI Generator version: 7.3.0-SNAPSHOT
+
+=end
+
+# Common files
+require 'cheminee/api_client'
+require 'cheminee/api_error'
+require 'cheminee/version'
+require 'cheminee/configuration'
+
+# Models
+require 'cheminee/models/bulk_request'
+require 'cheminee/models/bulk_request_doc'
+require 'cheminee/models/create_index_error'
+require 'cheminee/models/get_indexes_response_error'
+require 'cheminee/models/index_meta'
+require 'cheminee/models/index_schema'
+require 'cheminee/models/list_index_response_err'
+require 'cheminee/models/post_index_bulk_response_error'
+require 'cheminee/models/post_index_bulk_response_ok'
+require 'cheminee/models/post_index_bulk_response_ok_status'
+require 'cheminee/models/query_response_error'
+require 'cheminee/models/query_search_hit'
+require 'cheminee/models/schema'
+require 'cheminee/models/smiles'
+require 'cheminee/models/standardized_smiles'
+require 'cheminee/models/structure_response_error'
+require 'cheminee/models/structure_search_hit'
+
+# APIs
+require 'cheminee/api/default_api'
+
+module Cheminee
+  class << self
+    # Customize default settings for the SDK using block.
+    #   Cheminee.configure do |config|
+    #     config.username = "xxx"
+    #     config.password = "xxx"
+    #   end
+    # If no block given, return the default Configuration object.
+    def configure
+      if block_given?
+        yield(Configuration.default)
+      else
+        Configuration.default
+      end
+    end
+  end
+end

data/openapi-generator-config.json

@@ -0,0 +1,7 @@
+{
+  "gemName": "cheminee",
+  "gemAuthor": "Xavier Lange",
+  "gemAuthorEmail": "xrlange@gmail.com",
+  "gemHomepage": "https://github.com/rdkit-rs/cheminee-ruby",
+  "gemRequiredRubyVersion": ">= 3.0"
+}

data/openapi.json

@@ -0,0 +1,77 @@
+{
+  "openapi": "3.0.0",
+  "info": {
+    "title": "Cheminée",
+    "description": "Cheminée: The Chemical Structure Search Engine",
+    "version": "1.0",
+    "contact": {
+      "url": "https://github.com/rdkit-rs/cheminee"
+    }
+  },
+  "servers": [
+    {
+      "url": "http://localhost:3000/api/v1"
+    }
+  ],
+  "tags": [],
+  "paths": {
+    "/standardize": {
+      "post": {
+        "requestBody": {
+          "content": {
+            "application/json; charset=utf-8": {
+              "schema": {
+                "type": "array",
+                "items": {
+                  "$ref": "#/components/schemas/Smile"
+                }
+              }
+            }
+          },
+          "required": true
+        },
+        "responses": {
+          "200": {
+            "description": "",
+            "content": {
+              "application/json; charset=utf-8": {
+                "schema": {
+                  "type": "array",
+                  "items": {
+                    "$ref": "#/components/schemas/StandardizedSmile"
+                  }
+                }
+              }
+            }
+          }
+        }
+      }
+    }
+  },
+  "components": {
+    "schemas": {
+      "Smile": {
+        "type": "object",
+        "required": [
+          "smile"
+        ],
+        "properties": {
+          "smile": {
+            "type": "string"
+          }
+        }
+      },
+      "StandardizedSmile": {
+        "type": "object",
+        "properties": {
+          "smile": {
+            "type": "string"
+          },
+          "error": {
+            "type": "string"
+          }
+        }
+      }
+    }
+  }
+}