pharmaobservatory 0.1.3 → 0.1.4

data/lib/pharmaobservatory/models/biomarker_relations_row.rb

@@ -0,0 +1,421 @@
+=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_relations dataset: one row per biomarker, related entity, source relation label and paper. A grouped request returns the group columns and the measures instead, as additional properties.
+  class BiomarkerRelationsRow
+    # The biomarker's own route key, the entry key for the biomarkers object type (the gene symbol for a gene, the variant key for a protein variant).
+    attr_accessor :route_key
+
+    # The biomarker's key.
+    attr_accessor :biomarker_id
+
+    # Whether the row describes a gene or a protein variant.
+    attr_accessor :biomarker_kind
+
+    # The gene symbol.
+    attr_accessor :gene_symbol
+
+    # The protein change, for a variant.
+    attr_accessor :amino_acid_change
+
+    # The kind of the related entity (gene, drug or condition).
+    attr_accessor :related_entity_kind
+
+    # The related entity's key in its own vocabulary (a gene symbol, a drug id such as unii:..., or a condition key).
+    attr_accessor :related_entity_id
+
+    # The related entity's name.
+    attr_accessor :related_display_name
+
+    # The source's relation label, as the source states it.
+    attr_accessor :relation_type
+
+    # The PubMed id of the paper the relation was extracted from.
+    attr_accessor :pmid
+
+    # The paper's title.
+    attr_accessor :title
+
+    # The journal's National Library of Medicine (NLM) id.
+    attr_accessor :journal_nlm_id
+
+    # The journal's title.
+    attr_accessor :journal_title
+
+    # The paper's publication year.
+    attr_accessor :pub_year
+
+    # Source assertions of this relation in the paper.
+    attr_accessor :n_source_assertions
+
+    # Papers that carry this biomarker, related entity and relation label.
+    attr_accessor :n_relation_papers
+
+    # The evidence type (a text-mined relation, never a clinical claim).
+    attr_accessor :evidence_type
+
+    # The source of the evidence.
+    attr_accessor :source
+
+    # The order the web page lists the relation in within its kind.
+    attr_accessor :display_order
+
+    # Attribute mapping from ruby-style variable name to JSON key.
+    def self.attribute_map
+      {
+        :'route_key' => :'route_key',
+        :'biomarker_id' => :'biomarker_id',
+        :'biomarker_kind' => :'biomarker_kind',
+        :'gene_symbol' => :'gene_symbol',
+        :'amino_acid_change' => :'amino_acid_change',
+        :'related_entity_kind' => :'related_entity_kind',
+        :'related_entity_id' => :'related_entity_id',
+        :'related_display_name' => :'related_display_name',
+        :'relation_type' => :'relation_type',
+        :'pmid' => :'pmid',
+        :'title' => :'title',
+        :'journal_nlm_id' => :'journal_nlm_id',
+        :'journal_title' => :'journal_title',
+        :'pub_year' => :'pub_year',
+        :'n_source_assertions' => :'n_source_assertions',
+        :'n_relation_papers' => :'n_relation_papers',
+        :'evidence_type' => :'evidence_type',
+        :'source' => :'source',
+        :'display_order' => :'display_order'
+      }
+    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',
+        :'biomarker_id' => :'String',
+        :'biomarker_kind' => :'String',
+        :'gene_symbol' => :'String',
+        :'amino_acid_change' => :'String',
+        :'related_entity_kind' => :'String',
+        :'related_entity_id' => :'String',
+        :'related_display_name' => :'String',
+        :'relation_type' => :'String',
+        :'pmid' => :'String',
+        :'title' => :'String',
+        :'journal_nlm_id' => :'String',
+        :'journal_title' => :'String',
+        :'pub_year' => :'Integer',
+        :'n_source_assertions' => :'Integer',
+        :'n_relation_papers' => :'Integer',
+        :'evidence_type' => :'String',
+        :'source' => :'String',
+        :'display_order' => :'Integer'
+      }
+    end
+
+    # List of attributes with nullable: true
+    def self.openapi_nullable
+      Set.new([
+        :'route_key',
+        :'biomarker_id',
+        :'biomarker_kind',
+        :'gene_symbol',
+        :'amino_acid_change',
+        :'related_entity_kind',
+        :'related_entity_id',
+        :'related_display_name',
+        :'relation_type',
+        :'pmid',
+        :'title',
+        :'journal_nlm_id',
+        :'journal_title',
+        :'pub_year',
+        :'n_source_assertions',
+        :'n_relation_papers',
+        :'evidence_type',
+        :'source',
+        :'display_order'
+      ])
+    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::BiomarkerRelationsRow` 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::BiomarkerRelationsRow`. 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?(:'biomarker_id')
+        self.biomarker_id = attributes[:'biomarker_id']
+      end
+
+      if attributes.key?(:'biomarker_kind')
+        self.biomarker_kind = attributes[:'biomarker_kind']
+      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?(:'related_entity_kind')
+        self.related_entity_kind = attributes[:'related_entity_kind']
+      end
+
+      if attributes.key?(:'related_entity_id')
+        self.related_entity_id = attributes[:'related_entity_id']
+      end
+
+      if attributes.key?(:'related_display_name')
+        self.related_display_name = attributes[:'related_display_name']
+      end
+
+      if attributes.key?(:'relation_type')
+        self.relation_type = attributes[:'relation_type']
+      end
+
+      if attributes.key?(:'pmid')
+        self.pmid = attributes[:'pmid']
+      end
+
+      if attributes.key?(:'title')
+        self.title = attributes[:'title']
+      end
+
+      if attributes.key?(:'journal_nlm_id')
+        self.journal_nlm_id = attributes[:'journal_nlm_id']
+      end
+
+      if attributes.key?(:'journal_title')
+        self.journal_title = attributes[:'journal_title']
+      end
+
+      if attributes.key?(:'pub_year')
+        self.pub_year = attributes[:'pub_year']
+      end
+
+      if attributes.key?(:'n_source_assertions')
+        self.n_source_assertions = attributes[:'n_source_assertions']
+      end
+
+      if attributes.key?(:'n_relation_papers')
+        self.n_relation_papers = attributes[:'n_relation_papers']
+      end
+
+      if attributes.key?(:'evidence_type')
+        self.evidence_type = attributes[:'evidence_type']
+      end
+
+      if attributes.key?(:'source')
+        self.source = attributes[:'source']
+      end
+
+      if attributes.key?(:'display_order')
+        self.display_order = attributes[:'display_order']
+      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 &&
+          biomarker_id == o.biomarker_id &&
+          biomarker_kind == o.biomarker_kind &&
+          gene_symbol == o.gene_symbol &&
+          amino_acid_change == o.amino_acid_change &&
+          related_entity_kind == o.related_entity_kind &&
+          related_entity_id == o.related_entity_id &&
+          related_display_name == o.related_display_name &&
+          relation_type == o.relation_type &&
+          pmid == o.pmid &&
+          title == o.title &&
+          journal_nlm_id == o.journal_nlm_id &&
+          journal_title == o.journal_title &&
+          pub_year == o.pub_year &&
+          n_source_assertions == o.n_source_assertions &&
+          n_relation_papers == o.n_relation_papers &&
+          evidence_type == o.evidence_type &&
+          source == o.source &&
+          display_order == o.display_order
+    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, biomarker_id, biomarker_kind, gene_symbol, amino_acid_change, related_entity_kind, related_entity_id, related_display_name, relation_type, pmid, title, journal_nlm_id, journal_title, pub_year, n_source_assertions, n_relation_papers, evidence_type, source, display_order].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