pharmaobservatory 0.1.1 → 0.1.3

data/lib/pharmaobservatory/models/biomarkers_row.rb

@@ -0,0 +1,498 @@
+=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 biomarkers dataset: one row per biomarker (a gene, protein variant or other feature). A grouped request returns the group columns and the measures instead, as additional properties.
+  class BiomarkersRow
+    # The biomarker key.
+    attr_accessor :biomarker_id
+
+    # The biomarker's route key, the id the web page uses and the one entry key every biomarker dataset takes (the gene symbol for a gene biomarker).
+    attr_accessor :route_key
+
+    # gene, protein_variant or another feature kind.
+    attr_accessor :biomarker_kind
+
+    # Whether the biomarker's identity is confirmed.
+    attr_accessor :identity_status
+
+    # The biomarker's display name.
+    attr_accessor :display_name
+
+    # The parent biomarker (a variant's gene).
+    attr_accessor :parent_biomarker_id
+
+    # The gene symbol.
+    attr_accessor :gene_symbol
+
+    # The amino-acid change, for a variant.
+    attr_accessor :amino_acid_change
+
+    # The target's Ensembl gene id.
+    attr_accessor :target_id
+
+    # The HGNC gene id.
+    attr_accessor :hgnc_id
+
+    # The UniProt accession.
+    attr_accessor :uniprot_accession
+
+    # Feature code for a non-gene feature.
+    attr_accessor :feature_code
+
+    # Feature type for a non-gene feature.
+    attr_accessor :feature_type
+
+    # Strongest evidence tier: 1 FDA companion diagnostic through 6 no evidence.
+    attr_accessor :evidence_tier
+
+    # The tier's name.
+    attr_accessor :evidence_tier_label
+
+    # FDA companion diagnostic assertions.
+    attr_accessor :n_fda_cdx_assertions
+
+    # FDA biomarker qualification project assertions.
+    attr_accessor :n_fda_bqp_assertions
+
+    # Cancer Genome Interpreter actionable rows.
+    attr_accessor :n_cancer_actionable_cgi
+
+    # Open Targets target-disease associations.
+    attr_accessor :n_ot_association
+
+    # Trials that name the biomarker.
+    attr_accessor :n_trial_mention
+
+    # Publication variant mentions.
+    attr_accessor :n_publication_variant_mentions
+
+    # Whether clinical validation evidence exists.
+    attr_accessor :has_clinical_validation_evidence
+
+    # Whether analytical validation evidence exists.
+    attr_accessor :has_analytical_validation_evidence
+
+    # Papers naming an assay provider for the biomarker.
+    attr_accessor :n_assay_provider_papers
+
+    # Assay-provider suppliers named.
+    attr_accessor :n_assay_provider_suppliers
+
+    # Of those, diagnostic providers.
+    attr_accessor :n_diagnostic_provider_suppliers
+
+    # Attribute mapping from ruby-style variable name to JSON key.
+    def self.attribute_map
+      {
+        :'biomarker_id' => :'biomarker_id',
+        :'route_key' => :'route_key',
+        :'biomarker_kind' => :'biomarker_kind',
+        :'identity_status' => :'identity_status',
+        :'display_name' => :'display_name',
+        :'parent_biomarker_id' => :'parent_biomarker_id',
+        :'gene_symbol' => :'gene_symbol',
+        :'amino_acid_change' => :'amino_acid_change',
+        :'target_id' => :'target_id',
+        :'hgnc_id' => :'hgnc_id',
+        :'uniprot_accession' => :'uniprot_accession',
+        :'feature_code' => :'feature_code',
+        :'feature_type' => :'feature_type',
+        :'evidence_tier' => :'evidence_tier',
+        :'evidence_tier_label' => :'evidence_tier_label',
+        :'n_fda_cdx_assertions' => :'n_fda_cdx_assertions',
+        :'n_fda_bqp_assertions' => :'n_fda_bqp_assertions',
+        :'n_cancer_actionable_cgi' => :'n_cancer_actionable_cgi',
+        :'n_ot_association' => :'n_ot_association',
+        :'n_trial_mention' => :'n_trial_mention',
+        :'n_publication_variant_mentions' => :'n_publication_variant_mentions',
+        :'has_clinical_validation_evidence' => :'has_clinical_validation_evidence',
+        :'has_analytical_validation_evidence' => :'has_analytical_validation_evidence',
+        :'n_assay_provider_papers' => :'n_assay_provider_papers',
+        :'n_assay_provider_suppliers' => :'n_assay_provider_suppliers',
+        :'n_diagnostic_provider_suppliers' => :'n_diagnostic_provider_suppliers'
+      }
+    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
+      {
+        :'biomarker_id' => :'String',
+        :'route_key' => :'String',
+        :'biomarker_kind' => :'String',
+        :'identity_status' => :'String',
+        :'display_name' => :'String',
+        :'parent_biomarker_id' => :'String',
+        :'gene_symbol' => :'String',
+        :'amino_acid_change' => :'String',
+        :'target_id' => :'String',
+        :'hgnc_id' => :'String',
+        :'uniprot_accession' => :'String',
+        :'feature_code' => :'String',
+        :'feature_type' => :'String',
+        :'evidence_tier' => :'Integer',
+        :'evidence_tier_label' => :'String',
+        :'n_fda_cdx_assertions' => :'Integer',
+        :'n_fda_bqp_assertions' => :'Integer',
+        :'n_cancer_actionable_cgi' => :'Integer',
+        :'n_ot_association' => :'Integer',
+        :'n_trial_mention' => :'Integer',
+        :'n_publication_variant_mentions' => :'Integer',
+        :'has_clinical_validation_evidence' => :'Boolean',
+        :'has_analytical_validation_evidence' => :'Boolean',
+        :'n_assay_provider_papers' => :'Integer',
+        :'n_assay_provider_suppliers' => :'Integer',
+        :'n_diagnostic_provider_suppliers' => :'Integer'
+      }
+    end
+
+    # List of attributes with nullable: true
+    def self.openapi_nullable
+      Set.new([
+        :'biomarker_id',
+        :'route_key',
+        :'biomarker_kind',
+        :'identity_status',
+        :'display_name',
+        :'parent_biomarker_id',
+        :'gene_symbol',
+        :'amino_acid_change',
+        :'target_id',
+        :'hgnc_id',
+        :'uniprot_accession',
+        :'feature_code',
+        :'feature_type',
+        :'evidence_tier',
+        :'evidence_tier_label',
+        :'n_fda_cdx_assertions',
+        :'n_fda_bqp_assertions',
+        :'n_cancer_actionable_cgi',
+        :'n_ot_association',
+        :'n_trial_mention',
+        :'n_publication_variant_mentions',
+        :'has_clinical_validation_evidence',
+        :'has_analytical_validation_evidence',
+        :'n_assay_provider_papers',
+        :'n_assay_provider_suppliers',
+        :'n_diagnostic_provider_suppliers'
+      ])
+    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::BiomarkersRow` 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::BiomarkersRow`. 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?(:'biomarker_id')
+        self.biomarker_id = attributes[:'biomarker_id']
+      end
+
+      if attributes.key?(:'route_key')
+        self.route_key = attributes[:'route_key']
+      end
+
+      if attributes.key?(:'biomarker_kind')
+        self.biomarker_kind = attributes[:'biomarker_kind']
+      end
+
+      if attributes.key?(:'identity_status')
+        self.identity_status = attributes[:'identity_status']
+      end
+
+      if attributes.key?(:'display_name')
+        self.display_name = attributes[:'display_name']
+      end
+
+      if attributes.key?(:'parent_biomarker_id')
+        self.parent_biomarker_id = attributes[:'parent_biomarker_id']
+      end
+
+      if attributes.key?(:'gene_symbol')
+        self.gene_symbol = attributes[:'gene_symbol']
+      end
+
+      if attributes.key?(:'amino_acid_change')
+        self.amino_acid_change = attributes[:'amino_acid_change']
+      end
+
+      if attributes.key?(:'target_id')
+        self.target_id = attributes[:'target_id']
+      end
+
+      if attributes.key?(:'hgnc_id')
+        self.hgnc_id = attributes[:'hgnc_id']
+      end
+
+      if attributes.key?(:'uniprot_accession')
+        self.uniprot_accession = attributes[:'uniprot_accession']
+      end
+
+      if attributes.key?(:'feature_code')
+        self.feature_code = attributes[:'feature_code']
+      end
+
+      if attributes.key?(:'feature_type')
+        self.feature_type = attributes[:'feature_type']
+      end
+
+      if attributes.key?(:'evidence_tier')
+        self.evidence_tier = attributes[:'evidence_tier']
+      end
+
+      if attributes.key?(:'evidence_tier_label')
+        self.evidence_tier_label = attributes[:'evidence_tier_label']
+      end
+
+      if attributes.key?(:'n_fda_cdx_assertions')
+        self.n_fda_cdx_assertions = attributes[:'n_fda_cdx_assertions']
+      end
+
+      if attributes.key?(:'n_fda_bqp_assertions')
+        self.n_fda_bqp_assertions = attributes[:'n_fda_bqp_assertions']
+      end
+
+      if attributes.key?(:'n_cancer_actionable_cgi')
+        self.n_cancer_actionable_cgi = attributes[:'n_cancer_actionable_cgi']
+      end
+
+      if attributes.key?(:'n_ot_association')
+        self.n_ot_association = attributes[:'n_ot_association']
+      end
+
+      if attributes.key?(:'n_trial_mention')
+        self.n_trial_mention = attributes[:'n_trial_mention']
+      end
+
+      if attributes.key?(:'n_publication_variant_mentions')
+        self.n_publication_variant_mentions = attributes[:'n_publication_variant_mentions']
+      end
+
+      if attributes.key?(:'has_clinical_validation_evidence')
+        self.has_clinical_validation_evidence = attributes[:'has_clinical_validation_evidence']
+      end
+
+      if attributes.key?(:'has_analytical_validation_evidence')
+        self.has_analytical_validation_evidence = attributes[:'has_analytical_validation_evidence']
+      end
+
+      if attributes.key?(:'n_assay_provider_papers')
+        self.n_assay_provider_papers = attributes[:'n_assay_provider_papers']
+      end
+
+      if attributes.key?(:'n_assay_provider_suppliers')
+        self.n_assay_provider_suppliers = attributes[:'n_assay_provider_suppliers']
+      end
+
+      if attributes.key?(:'n_diagnostic_provider_suppliers')
+        self.n_diagnostic_provider_suppliers = attributes[:'n_diagnostic_provider_suppliers']
+      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 &&
+          biomarker_id == o.biomarker_id &&
+          route_key == o.route_key &&
+          biomarker_kind == o.biomarker_kind &&
+          identity_status == o.identity_status &&
+          display_name == o.display_name &&
+          parent_biomarker_id == o.parent_biomarker_id &&
+          gene_symbol == o.gene_symbol &&
+          amino_acid_change == o.amino_acid_change &&
+          target_id == o.target_id &&
+          hgnc_id == o.hgnc_id &&
+          uniprot_accession == o.uniprot_accession &&
+          feature_code == o.feature_code &&
+          feature_type == o.feature_type &&
+          evidence_tier == o.evidence_tier &&
+          evidence_tier_label == o.evidence_tier_label &&
+          n_fda_cdx_assertions == o.n_fda_cdx_assertions &&
+          n_fda_bqp_assertions == o.n_fda_bqp_assertions &&
+          n_cancer_actionable_cgi == o.n_cancer_actionable_cgi &&
+          n_ot_association == o.n_ot_association &&
+          n_trial_mention == o.n_trial_mention &&
+          n_publication_variant_mentions == o.n_publication_variant_mentions &&
+          has_clinical_validation_evidence == o.has_clinical_validation_evidence &&
+          has_analytical_validation_evidence == o.has_analytical_validation_evidence &&
+          n_assay_provider_papers == o.n_assay_provider_papers &&
+          n_assay_provider_suppliers == o.n_assay_provider_suppliers &&
+          n_diagnostic_provider_suppliers == o.n_diagnostic_provider_suppliers
+    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
+      [biomarker_id, route_key, biomarker_kind, identity_status, display_name, parent_biomarker_id, gene_symbol, amino_acid_change, target_id, hgnc_id, uniprot_accession, feature_code, feature_type, evidence_tier, evidence_tier_label, n_fda_cdx_assertions, n_fda_bqp_assertions, n_cancer_actionable_cgi, n_ot_association, n_trial_mention, n_publication_variant_mentions, has_clinical_validation_evidence, has_analytical_validation_evidence, n_assay_provider_papers, n_assay_provider_suppliers, n_diagnostic_provider_suppliers].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