pharmaobservatory 0.1.3 → 0.1.4

data/lib/pharmaobservatory/models/biomarker_sample_coverage_row.rb

@@ -0,0 +1,322 @@
+=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 biomarker_sample_coverage dataset: one row per protein variant and GDC data release. A grouped request returns the group columns and the measures instead, as additional properties.
+  class BiomarkerSampleCoverageRow
+    # The route key of the gene the variants belong to, the entry key for the biomarkers object type.
+    attr_accessor :route_key
+
+    # The gene symbol.
+    attr_accessor :gene_symbol
+
+    # The variant's own biomarker key.
+    attr_accessor :variant_biomarker_id
+
+    # The variant's own route key (the id its web page uses).
+    attr_accessor :variant_route_key
+
+    # The protein change, for example p.V600E.
+    attr_accessor :amino_acid_change
+
+    # The Genomic Data Commons data release the match was made against.
+    attr_accessor :gdc_data_release
+
+    # How the variant matched: resolved_single_ssm, no_exact_ssm, multiple_exact_ssms or source_error.
+    attr_accessor :normalization_status
+
+    # Somatic mutations in the catalogue that encode the same protein change.
+    attr_accessor :match_count
+
+    # The reason for the status, in words.
+    attr_accessor :resolution_reason
+
+    # Research projects with an observed frequency for the variant in biomarker_sample_prevalence.
+    attr_accessor :measured_project_count
+
+    # Attribute mapping from ruby-style variable name to JSON key.
+    def self.attribute_map
+      {
+        :'route_key' => :'route_key',
+        :'gene_symbol' => :'gene_symbol',
+        :'variant_biomarker_id' => :'variant_biomarker_id',
+        :'variant_route_key' => :'variant_route_key',
+        :'amino_acid_change' => :'amino_acid_change',
+        :'gdc_data_release' => :'gdc_data_release',
+        :'normalization_status' => :'normalization_status',
+        :'match_count' => :'match_count',
+        :'resolution_reason' => :'resolution_reason',
+        :'measured_project_count' => :'measured_project_count'
+      }
+    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
+      {
+        :'route_key' => :'String',
+        :'gene_symbol' => :'String',
+        :'variant_biomarker_id' => :'String',
+        :'variant_route_key' => :'String',
+        :'amino_acid_change' => :'String',
+        :'gdc_data_release' => :'String',
+        :'normalization_status' => :'String',
+        :'match_count' => :'Integer',
+        :'resolution_reason' => :'String',
+        :'measured_project_count' => :'Integer'
+      }
+    end
+
+    # List of attributes with nullable: true
+    def self.openapi_nullable
+      Set.new([
+        :'route_key',
+        :'gene_symbol',
+        :'variant_biomarker_id',
+        :'variant_route_key',
+        :'amino_acid_change',
+        :'gdc_data_release',
+        :'normalization_status',
+        :'match_count',
+        :'resolution_reason',
+        :'measured_project_count'
+      ])
+    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::BiomarkerSampleCoverageRow` 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::BiomarkerSampleCoverageRow`. 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?(:'route_key')
+        self.route_key = attributes[:'route_key']
+      end
+
+      if attributes.key?(:'gene_symbol')
+        self.gene_symbol = attributes[:'gene_symbol']
+      end
+
+      if attributes.key?(:'variant_biomarker_id')
+        self.variant_biomarker_id = attributes[:'variant_biomarker_id']
+      end
+
+      if attributes.key?(:'variant_route_key')
+        self.variant_route_key = attributes[:'variant_route_key']
+      end
+
+      if attributes.key?(:'amino_acid_change')
+        self.amino_acid_change = attributes[:'amino_acid_change']
+      end
+
+      if attributes.key?(:'gdc_data_release')
+        self.gdc_data_release = attributes[:'gdc_data_release']
+      end
+
+      if attributes.key?(:'normalization_status')
+        self.normalization_status = attributes[:'normalization_status']
+      end
+
+      if attributes.key?(:'match_count')
+        self.match_count = attributes[:'match_count']
+      end
+
+      if attributes.key?(:'resolution_reason')
+        self.resolution_reason = attributes[:'resolution_reason']
+      end
+
+      if attributes.key?(:'measured_project_count')
+        self.measured_project_count = attributes[:'measured_project_count']
+      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 &&
+          route_key == o.route_key &&
+          gene_symbol == o.gene_symbol &&
+          variant_biomarker_id == o.variant_biomarker_id &&
+          variant_route_key == o.variant_route_key &&
+          amino_acid_change == o.amino_acid_change &&
+          gdc_data_release == o.gdc_data_release &&
+          normalization_status == o.normalization_status &&
+          match_count == o.match_count &&
+          resolution_reason == o.resolution_reason &&
+          measured_project_count == o.measured_project_count
+    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
+      [route_key, gene_symbol, variant_biomarker_id, variant_route_key, amino_acid_change, gdc_data_release, normalization_status, match_count, resolution_reason, measured_project_count].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