pharmaobservatory 0.1.6 → 0.1.7

data/lib/pharmaobservatory/models/rare_disease_genes_row.rb

@@ -0,0 +1,399 @@
+=begin
+#Pharma Observatory Public REST API
+
+#Read-only REST API over the Pharma Observatory biomedical data platform. Reference: https://pharmaobservatory.com/api-reference
+
+The version of the OpenAPI document: 1.0.0
+
+Generated by: https://openapi-generator.tech
+Generator version: 7.13.0
+
+=end
+
+require 'date'
+require 'time'
+
+module PharmaObservatory
+  # One row of the rare_disease_genes dataset: one row per disease-gene assertion (Orphadata Product 6). A grouped request returns the group columns and the measures instead, as additional properties.
+  class RareDiseaseGenesRow
+    # The identifier of the disease-gene assertion.
+    attr_accessor :gene_assertion_id
+
+    # The ORPHA code of the disease, the digits in the web page address (/rare-diseases/558). The entry key of the rare_diseases object type.
+    attr_accessor :orpha_code
+
+    # The gene symbol as Orphadata gives it.
+    attr_accessor :gene_symbol
+
+    # The gene's full name.
+    attr_accessor :gene_name
+
+    # The gene type Orphadata records (for example gene_with_protein_product).
+    attr_accessor :gene_type
+
+    # The association Orphadata asserts between the gene and the disease, for example a disease-causing germline mutation or a modifying germline mutation.
+    attr_accessor :association_type
+
+    # assessed when Orphanet has assessed the association, not_yet_assessed otherwise.
+    attr_accessor :association_status
+
+    # True for an assessed disease-causing mutation assertion.
+    attr_accessor :is_known_causal
+
+    # The Ensembl gene id Orphadata gives for the gene.
+    attr_accessor :ensembl_id
+
+    # The NCBI Gene id Orphadata gives for the gene.
+    attr_accessor :ncbi_gene_id
+
+    # The Ensembl gene id of the matching row in the targets dataset; null when the gene has no row there.
+    attr_accessor :target_id
+
+    # How the gene's Ensembl and NCBI identifiers resolved against the gene spine.
+    attr_accessor :gene_resolution_status
+
+    # True when the identifiers on the assertion disagree with the gene spine.
+    attr_accessor :gene_identifier_conflict
+
+    # The Orphadata Science release the row was read from.
+    attr_accessor :source_release
+
+    # The URL of the source file the row was read from.
+    attr_accessor :source_url
+
+    # The licence of the Orphadata Science file.
+    attr_accessor :license_name
+
+    # The attribution line the source requires; quote it with any figure taken from the row.
+    attr_accessor :attribution
+
+    # Attribute mapping from ruby-style variable name to JSON key.
+    def self.attribute_map
+      {
+        :'gene_assertion_id' => :'gene_assertion_id',
+        :'orpha_code' => :'orpha_code',
+        :'gene_symbol' => :'gene_symbol',
+        :'gene_name' => :'gene_name',
+        :'gene_type' => :'gene_type',
+        :'association_type' => :'association_type',
+        :'association_status' => :'association_status',
+        :'is_known_causal' => :'is_known_causal',
+        :'ensembl_id' => :'ensembl_id',
+        :'ncbi_gene_id' => :'ncbi_gene_id',
+        :'target_id' => :'target_id',
+        :'gene_resolution_status' => :'gene_resolution_status',
+        :'gene_identifier_conflict' => :'gene_identifier_conflict',
+        :'source_release' => :'source_release',
+        :'source_url' => :'source_url',
+        :'license_name' => :'license_name',
+        :'attribution' => :'attribution'
+      }
+    end
+
+    # Returns attribute mapping this model knows about
+    def self.acceptable_attribute_map
+      attribute_map
+    end
+
+    # Returns all the JSON keys this model knows about
+    def self.acceptable_attributes
+      acceptable_attribute_map.values
+    end
+
+    # Attribute type mapping.
+    def self.openapi_types
+      {
+        :'gene_assertion_id' => :'String',
+        :'orpha_code' => :'String',
+        :'gene_symbol' => :'String',
+        :'gene_name' => :'String',
+        :'gene_type' => :'String',
+        :'association_type' => :'String',
+        :'association_status' => :'String',
+        :'is_known_causal' => :'Boolean',
+        :'ensembl_id' => :'String',
+        :'ncbi_gene_id' => :'String',
+        :'target_id' => :'String',
+        :'gene_resolution_status' => :'String',
+        :'gene_identifier_conflict' => :'Boolean',
+        :'source_release' => :'String',
+        :'source_url' => :'String',
+        :'license_name' => :'String',
+        :'attribution' => :'String'
+      }
+    end
+
+    # List of attributes with nullable: true
+    def self.openapi_nullable
+      Set.new([
+        :'gene_assertion_id',
+        :'orpha_code',
+        :'gene_symbol',
+        :'gene_name',
+        :'gene_type',
+        :'association_type',
+        :'association_status',
+        :'is_known_causal',
+        :'ensembl_id',
+        :'ncbi_gene_id',
+        :'target_id',
+        :'gene_resolution_status',
+        :'gene_identifier_conflict',
+        :'source_release',
+        :'source_url',
+        :'license_name',
+        :'attribution'
+      ])
+    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 `PharmaObservatory::RareDiseaseGenesRow` initialize method"
+      end
+
+      # check to see if the attribute exists and convert string to symbol for hash key
+      acceptable_attribute_map = self.class.acceptable_attribute_map
+      attributes = attributes.each_with_object({}) { |(k, v), h|
+        if (!acceptable_attribute_map.key?(k.to_sym))
+          fail ArgumentError, "`#{k}` is not a valid attribute in `PharmaObservatory::RareDiseaseGenesRow`. Please check the name to make sure it's valid. List of attributes: " + acceptable_attribute_map.keys.inspect
+        end
+        h[k.to_sym] = v
+      }
+
+      if attributes.key?(:'gene_assertion_id')
+        self.gene_assertion_id = attributes[:'gene_assertion_id']
+      end
+
+      if attributes.key?(:'orpha_code')
+        self.orpha_code = attributes[:'orpha_code']
+      end
+
+      if attributes.key?(:'gene_symbol')
+        self.gene_symbol = attributes[:'gene_symbol']
+      end
+
+      if attributes.key?(:'gene_name')
+        self.gene_name = attributes[:'gene_name']
+      end
+
+      if attributes.key?(:'gene_type')
+        self.gene_type = attributes[:'gene_type']
+      end
+
+      if attributes.key?(:'association_type')
+        self.association_type = attributes[:'association_type']
+      end
+
+      if attributes.key?(:'association_status')
+        self.association_status = attributes[:'association_status']
+      end
+
+      if attributes.key?(:'is_known_causal')
+        self.is_known_causal = attributes[:'is_known_causal']
+      end
+
+      if attributes.key?(:'ensembl_id')
+        self.ensembl_id = attributes[:'ensembl_id']
+      end
+
+      if attributes.key?(:'ncbi_gene_id')
+        self.ncbi_gene_id = attributes[:'ncbi_gene_id']
+      end
+
+      if attributes.key?(:'target_id')
+        self.target_id = attributes[:'target_id']
+      end
+
+      if attributes.key?(:'gene_resolution_status')
+        self.gene_resolution_status = attributes[:'gene_resolution_status']
+      end
+
+      if attributes.key?(:'gene_identifier_conflict')
+        self.gene_identifier_conflict = attributes[:'gene_identifier_conflict']
+      end
+
+      if attributes.key?(:'source_release')
+        self.source_release = attributes[:'source_release']
+      end
+
+      if attributes.key?(:'source_url')
+        self.source_url = attributes[:'source_url']
+      end
+
+      if attributes.key?(:'license_name')
+        self.license_name = attributes[:'license_name']
+      end
+
+      if attributes.key?(:'attribution')
+        self.attribution = attributes[:'attribution']
+      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
+      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'
+      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 &&
+          gene_assertion_id == o.gene_assertion_id &&
+          orpha_code == o.orpha_code &&
+          gene_symbol == o.gene_symbol &&
+          gene_name == o.gene_name &&
+          gene_type == o.gene_type &&
+          association_type == o.association_type &&
+          association_status == o.association_status &&
+          is_known_causal == o.is_known_causal &&
+          ensembl_id == o.ensembl_id &&
+          ncbi_gene_id == o.ncbi_gene_id &&
+          target_id == o.target_id &&
+          gene_resolution_status == o.gene_resolution_status &&
+          gene_identifier_conflict == o.gene_identifier_conflict &&
+          source_release == o.source_release &&
+          source_url == o.source_url &&
+          license_name == o.license_name &&
+          attribution == o.attribution
+    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
+      [gene_assertion_id, orpha_code, gene_symbol, gene_name, gene_type, association_type, association_status, is_known_causal, ensembl_id, ncbi_gene_id, target_id, gene_resolution_status, gene_identifier_conflict, source_release, source_url, license_name, attribution].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 = PharmaObservatory.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