pharmaobservatory 0.1.2 → 0.1.4

data/lib/pharmaobservatory/models/biomarker_sample_prevalence_row.rb

@@ -0,0 +1,436 @@
+=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_prevalence dataset: one row per protein variant, GDC research cohort and data release. A grouped request returns the group columns and the measures instead, as additional properties.
+  class BiomarkerSamplePrevalenceRow
+    # 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 identifier of the somatic mutation in the Genomic Data Commons.
+    attr_accessor :gdc_ssm_id
+
+    # The Genomic Data Commons research project (cohort) the counts come from.
+    attr_accessor :gdc_project_id
+
+    # The name of the research project.
+    attr_accessor :gdc_project_name
+
+    # The condition key (a MeSH, Medical Subject Headings, descriptor id) the project's disease maps to, where one is mapped.
+    attr_accessor :condition_id
+
+    # The mapped condition's MeSH heading.
+    attr_accessor :condition_name
+
+    # The disease types the source states for the project.
+    attr_accessor :source_disease_types
+
+    # The primary sites the source states for the project.
+    attr_accessor :source_primary_sites
+
+    # Cases in the cohort with the exact variant.
+    attr_accessor :affected_case_count
+
+    # Cases in the cohort profiled for somatic mutations, the denominator of the observed frequency.
+    attr_accessor :ssm_profiled_case_count
+
+    # All cases in the project.
+    attr_accessor :all_case_count
+
+    # Affected cases over mutation-profiled cases in this cohort.
+    attr_accessor :observed_frequency
+
+    # Lower bound of the 95 percent confidence interval of the observed frequency.
+    attr_accessor :frequency_ci95_low
+
+    # Upper bound of the 95 percent confidence interval of the observed frequency.
+    attr_accessor :frequency_ci95_high
+
+    # The Genomic Data Commons data release the counts come from.
+    attr_accessor :gdc_data_release
+
+    # What the figure states; an observed frequency in a named cohort.
+    attr_accessor :claim_type
+
+    # 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_ssm_id' => :'gdc_ssm_id',
+        :'gdc_project_id' => :'gdc_project_id',
+        :'gdc_project_name' => :'gdc_project_name',
+        :'condition_id' => :'condition_id',
+        :'condition_name' => :'condition_name',
+        :'source_disease_types' => :'source_disease_types',
+        :'source_primary_sites' => :'source_primary_sites',
+        :'affected_case_count' => :'affected_case_count',
+        :'ssm_profiled_case_count' => :'ssm_profiled_case_count',
+        :'all_case_count' => :'all_case_count',
+        :'observed_frequency' => :'observed_frequency',
+        :'frequency_ci95_low' => :'frequency_ci95_low',
+        :'frequency_ci95_high' => :'frequency_ci95_high',
+        :'gdc_data_release' => :'gdc_data_release',
+        :'claim_type' => :'claim_type'
+      }
+    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_ssm_id' => :'String',
+        :'gdc_project_id' => :'String',
+        :'gdc_project_name' => :'String',
+        :'condition_id' => :'String',
+        :'condition_name' => :'String',
+        :'source_disease_types' => :'Array<String>',
+        :'source_primary_sites' => :'Array<String>',
+        :'affected_case_count' => :'Integer',
+        :'ssm_profiled_case_count' => :'Integer',
+        :'all_case_count' => :'Integer',
+        :'observed_frequency' => :'Float',
+        :'frequency_ci95_low' => :'Float',
+        :'frequency_ci95_high' => :'Float',
+        :'gdc_data_release' => :'String',
+        :'claim_type' => :'String'
+      }
+    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_ssm_id',
+        :'gdc_project_id',
+        :'gdc_project_name',
+        :'condition_id',
+        :'condition_name',
+        :'source_disease_types',
+        :'source_primary_sites',
+        :'affected_case_count',
+        :'ssm_profiled_case_count',
+        :'all_case_count',
+        :'observed_frequency',
+        :'frequency_ci95_low',
+        :'frequency_ci95_high',
+        :'gdc_data_release',
+        :'claim_type'
+      ])
+    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::BiomarkerSamplePrevalenceRow` 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::BiomarkerSamplePrevalenceRow`. 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_ssm_id')
+        self.gdc_ssm_id = attributes[:'gdc_ssm_id']
+      end
+
+      if attributes.key?(:'gdc_project_id')
+        self.gdc_project_id = attributes[:'gdc_project_id']
+      end
+
+      if attributes.key?(:'gdc_project_name')
+        self.gdc_project_name = attributes[:'gdc_project_name']
+      end
+
+      if attributes.key?(:'condition_id')
+        self.condition_id = attributes[:'condition_id']
+      end
+
+      if attributes.key?(:'condition_name')
+        self.condition_name = attributes[:'condition_name']
+      end
+
+      if attributes.key?(:'source_disease_types')
+        if (value = attributes[:'source_disease_types']).is_a?(Array)
+          self.source_disease_types = value
+        end
+      end
+
+      if attributes.key?(:'source_primary_sites')
+        if (value = attributes[:'source_primary_sites']).is_a?(Array)
+          self.source_primary_sites = value
+        end
+      end
+
+      if attributes.key?(:'affected_case_count')
+        self.affected_case_count = attributes[:'affected_case_count']
+      end
+
+      if attributes.key?(:'ssm_profiled_case_count')
+        self.ssm_profiled_case_count = attributes[:'ssm_profiled_case_count']
+      end
+
+      if attributes.key?(:'all_case_count')
+        self.all_case_count = attributes[:'all_case_count']
+      end
+
+      if attributes.key?(:'observed_frequency')
+        self.observed_frequency = attributes[:'observed_frequency']
+      end
+
+      if attributes.key?(:'frequency_ci95_low')
+        self.frequency_ci95_low = attributes[:'frequency_ci95_low']
+      end
+
+      if attributes.key?(:'frequency_ci95_high')
+        self.frequency_ci95_high = attributes[:'frequency_ci95_high']
+      end
+
+      if attributes.key?(:'gdc_data_release')
+        self.gdc_data_release = attributes[:'gdc_data_release']
+      end
+
+      if attributes.key?(:'claim_type')
+        self.claim_type = attributes[:'claim_type']
+      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_ssm_id == o.gdc_ssm_id &&
+          gdc_project_id == o.gdc_project_id &&
+          gdc_project_name == o.gdc_project_name &&
+          condition_id == o.condition_id &&
+          condition_name == o.condition_name &&
+          source_disease_types == o.source_disease_types &&
+          source_primary_sites == o.source_primary_sites &&
+          affected_case_count == o.affected_case_count &&
+          ssm_profiled_case_count == o.ssm_profiled_case_count &&
+          all_case_count == o.all_case_count &&
+          observed_frequency == o.observed_frequency &&
+          frequency_ci95_low == o.frequency_ci95_low &&
+          frequency_ci95_high == o.frequency_ci95_high &&
+          gdc_data_release == o.gdc_data_release &&
+          claim_type == o.claim_type
+    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_ssm_id, gdc_project_id, gdc_project_name, condition_id, condition_name, source_disease_types, source_primary_sites, affected_case_count, ssm_profiled_case_count, all_case_count, observed_frequency, frequency_ci95_low, frequency_ci95_high, gdc_data_release, claim_type].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