pharmaobservatory 0.1.7 → 0.1.8

data/lib/pharmaobservatory/models/biomarker_traversal_status_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_traversal_status dataset: one row per biomarker and traversal. A grouped request returns the group columns and the measures instead, as additional properties.
+  class BiomarkerTraversalStatusRow
+    # The biomarker's route key, the entry key for the biomarkers object type.
+    attr_accessor :route_key
+
+    # The biomarker's own key.
+    attr_accessor :biomarker_id
+
+    # What kind of biomarker the row describes.
+    attr_accessor :biomarker_kind
+
+    # The traversal.
+    attr_accessor :traversal_key
+
+    # The order the web page lists the traversals in, one to nine.
+    attr_accessor :display_order
+
+    # The traversal's display name.
+    attr_accessor :traversal_name
+
+    # applicable: measured for this kind of biomarker. inapplicable: does not apply to this kind. not_measured: applies in principle but the corpus is not mined for this kind yet.
+    attr_accessor :applicability_state
+
+    # How the traversal reads for this biomarker. direct: its own rows. parent_gene: the variant's gene rows. parent_and_exact: the gene's rows plus the exact variant's. child_variants: the gene's variant children. source_linked: shown when a source assertion resolves to it. bridge_deferred: depends on a bridge that has not landed. none: no traversal.
+    attr_accessor :context_mode
+
+    # The code behind the applicability state and context mode; state_detail is its sentence.
+    attr_accessor :reason_code
+
+    # The sentence the web page prints for the reason code.
+    attr_accessor :state_detail
+
+    # 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',
+        :'traversal_key' => :'traversal_key',
+        :'display_order' => :'display_order',
+        :'traversal_name' => :'traversal_name',
+        :'applicability_state' => :'applicability_state',
+        :'context_mode' => :'context_mode',
+        :'reason_code' => :'reason_code',
+        :'state_detail' => :'state_detail'
+      }
+    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',
+        :'traversal_key' => :'String',
+        :'display_order' => :'Integer',
+        :'traversal_name' => :'String',
+        :'applicability_state' => :'String',
+        :'context_mode' => :'String',
+        :'reason_code' => :'String',
+        :'state_detail' => :'String'
+      }
+    end
+
+    # List of attributes with nullable: true
+    def self.openapi_nullable
+      Set.new([
+        :'route_key',
+        :'biomarker_id',
+        :'biomarker_kind',
+        :'traversal_key',
+        :'display_order',
+        :'traversal_name',
+        :'applicability_state',
+        :'context_mode',
+        :'reason_code',
+        :'state_detail'
+      ])
+    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::BiomarkerTraversalStatusRow` 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::BiomarkerTraversalStatusRow`. 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?(:'traversal_key')
+        self.traversal_key = attributes[:'traversal_key']
+      end
+
+      if attributes.key?(:'display_order')
+        self.display_order = attributes[:'display_order']
+      end
+
+      if attributes.key?(:'traversal_name')
+        self.traversal_name = attributes[:'traversal_name']
+      end
+
+      if attributes.key?(:'applicability_state')
+        self.applicability_state = attributes[:'applicability_state']
+      end
+
+      if attributes.key?(:'context_mode')
+        self.context_mode = attributes[:'context_mode']
+      end
+
+      if attributes.key?(:'reason_code')
+        self.reason_code = attributes[:'reason_code']
+      end
+
+      if attributes.key?(:'state_detail')
+        self.state_detail = attributes[:'state_detail']
+      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 &&
+          traversal_key == o.traversal_key &&
+          display_order == o.display_order &&
+          traversal_name == o.traversal_name &&
+          applicability_state == o.applicability_state &&
+          context_mode == o.context_mode &&
+          reason_code == o.reason_code &&
+          state_detail == o.state_detail
+    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, traversal_key, display_order, traversal_name, applicability_state, context_mode, reason_code, state_detail].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

data/lib/pharmaobservatory/models/company_assets_row.rb

@@ -40,9 +40,15 @@ module PharmaObservatory
     # The drug's name.
     attr_accessor :drug_name
 
-    # Highest phase the sponsor reached on the drug: 0 early phase 1 through 6 for phase 4 (marketed); -1 when unstated.
+    # Highest phase the sponsor reached on the drug on the 0 to 4 scale: 0 not reported, 1 through 4 for phase 1 through phase 4 (4 is marketed); a split phase folds up to its higher phase.
     attr_accessor :max_phase
 
+    # The furthest phase reached with the split phases kept: Early 1, Phase 1, Phase 1/2, Phase 2, Phase 2/3, Phase 3, Phase 4, or Not reported. max_phase is the same value folded onto 0 to 4 (a split phase counts as its higher phase).
+    attr_accessor :max_phase_label
+
+    # The finest phase rank behind max_phase_label: 6 Phase 4, 5 Phase 3, 4 Phase 2/3, 3 Phase 2, 2 Phase 1/2, 1 Phase 1, 0 Early 1, -1 not reported. Sort on it to order programs by furthest phase with the split phases kept; max_phase is the same value folded onto 0 to 4.
+    attr_accessor :max_phase_fine_rank
+
     # Distinct trials this sponsor leads on the drug. Counted once per trial within the sponsor organization, so it is not additive across a company's organizations.
     attr_accessor :n_trials
 
@@ -67,6 +73,8 @@ module PharmaObservatory
         :'drug_id' => :'drug_id',
         :'drug_name' => :'drug_name',
         :'max_phase' => :'max_phase',
+        :'max_phase_label' => :'max_phase_label',
+        :'max_phase_fine_rank' => :'max_phase_fine_rank',
         :'n_trials' => :'n_trials',
         :'n_active' => :'n_active',
         :'last_year' => :'last_year',
@@ -96,6 +104,8 @@ module PharmaObservatory
         :'drug_id' => :'String',
         :'drug_name' => :'String',
         :'max_phase' => :'Integer',
+        :'max_phase_label' => :'String',
+        :'max_phase_fine_rank' => :'Integer',
         :'n_trials' => :'Integer',
         :'n_active' => :'Integer',
         :'last_year' => :'Integer',
@@ -115,6 +125,8 @@ module PharmaObservatory
         :'drug_id',
         :'drug_name',
         :'max_phase',
+        :'max_phase_label',
+        :'max_phase_fine_rank',
         :'n_trials',
         :'n_active',
         :'last_year',
@@ -174,6 +186,14 @@ module PharmaObservatory
         self.max_phase = attributes[:'max_phase']
       end
 
+      if attributes.key?(:'max_phase_label')
+        self.max_phase_label = attributes[:'max_phase_label']
+      end
+
+      if attributes.key?(:'max_phase_fine_rank')
+        self.max_phase_fine_rank = attributes[:'max_phase_fine_rank']
+      end
+
       if attributes.key?(:'n_trials')
         self.n_trials = attributes[:'n_trials']
       end
@@ -220,6 +240,8 @@ module PharmaObservatory
           drug_id == o.drug_id &&
           drug_name == o.drug_name &&
           max_phase == o.max_phase &&
+          max_phase_label == o.max_phase_label &&
+          max_phase_fine_rank == o.max_phase_fine_rank &&
           n_trials == o.n_trials &&
           n_active == o.n_active &&
           last_year == o.last_year &&
@@ -235,7 +257,7 @@ module PharmaObservatory
     # Calculates hash code according to all attributes.
     # @return [Integer] Hash code
     def hash
-      [sponsor_org_id, sponsor_name, sponsor_company_id, sponsor_company_name, sponsor_group_id, sponsor_group_name, drug_id, drug_name, max_phase, n_trials, n_active, last_year, withdrawn].hash
+      [sponsor_org_id, sponsor_name, sponsor_company_id, sponsor_company_name, sponsor_group_id, sponsor_group_name, drug_id, drug_name, max_phase, max_phase_label, max_phase_fine_rank, n_trials, n_active, last_year, withdrawn].hash
     end
 
     # Builds the object from hash