pharmaobservatory 0.1.11 → 0.1.13

data/lib/pharmaobservatory/models/company_competitors_row.rb

@@ -14,7 +14,7 @@ require 'date'
 require 'time'
 
 module PharmaObservatory
-  # One row of the company_competitors dataset: one row per ordered company pair: a company and one of its top 25 competitors. A grouped request returns the group columns and the measures instead, as additional properties.
+  # One row of the company_competitors dataset: one row per ordered company pair: a company and one of the top 25 companies of each competitor_class by program overlap. A grouped request returns the group columns and the measures instead, as additional properties.
   class CompanyCompetitorsRow
     # Company level: the company the row is about; the entry key for the companies object type.
     attr_accessor :company_id
@@ -40,7 +40,13 @@ module PharmaObservatory
     # Display name of the competitor's group.
     attr_accessor :competitor_group_name
 
-    # The competitor's rank for the company by competitor_score (1 is the highest).
+    # The competitor's class: industry, or non_industry (not classed as industry by the sponsor-class rule: academic, hospital, government, nonprofit, and any record the rule does not reach). competitor_rank restarts at 1 within each class, so filter or sort on this column first.
+    attr_accessor :competitor_class
+
+    # How many companies of this competitor_class were candidates (a shared target, or an indication overlap above the similarity floor) before the top 25 were kept. The same value on every row of one company and class.
+    attr_accessor :n_class_candidates
+
+    # The competitor's rank within its competitor_class for the company by competitor_score (1 is the highest).
     attr_accessor :competitor_rank
 
     # 100 times the weighted mean of the four similarities below, rounded to four places.
@@ -91,6 +97,9 @@ module PharmaObservatory
     # Up to 3 shared mechanisms written as a gene symbol and an action, by combined phase then combined trials. An empty list when none.
     attr_accessor :top_shared_mechanisms
 
+    # Distinct trials on which the company and the competitor are both named as sponsors, counted over their subtrees; 0 when none. A consortium trial (more than 25 sponsor companies) is left out.
+    attr_accessor :n_cosponsored_trials
+
     # Attribute mapping from ruby-style variable name to JSON key.
     def self.attribute_map
       {
@@ -102,6 +111,8 @@ module PharmaObservatory
         :'competitor_company_name' => :'competitor_company_name',
         :'competitor_group_id' => :'competitor_group_id',
         :'competitor_group_name' => :'competitor_group_name',
+        :'competitor_class' => :'competitor_class',
+        :'n_class_candidates' => :'n_class_candidates',
         :'competitor_rank' => :'competitor_rank',
         :'competitor_score' => :'competitor_score',
         :'target_sim' => :'target_sim',
@@ -118,7 +129,8 @@ module PharmaObservatory
         :'n_competitor_indications' => :'n_competitor_indications',
         :'top_shared_targets' => :'top_shared_targets',
         :'top_shared_indications' => :'top_shared_indications',
-        :'top_shared_mechanisms' => :'top_shared_mechanisms'
+        :'top_shared_mechanisms' => :'top_shared_mechanisms',
+        :'n_cosponsored_trials' => :'n_cosponsored_trials'
       }
     end
 
@@ -143,6 +155,8 @@ module PharmaObservatory
         :'competitor_company_name' => :'String',
         :'competitor_group_id' => :'String',
         :'competitor_group_name' => :'String',
+        :'competitor_class' => :'String',
+        :'n_class_candidates' => :'Integer',
         :'competitor_rank' => :'Integer',
         :'competitor_score' => :'Float',
         :'target_sim' => :'Float',
@@ -159,7 +173,8 @@ module PharmaObservatory
         :'n_competitor_indications' => :'Integer',
         :'top_shared_targets' => :'Array<String>',
         :'top_shared_indications' => :'Array<String>',
-        :'top_shared_mechanisms' => :'Array<String>'
+        :'top_shared_mechanisms' => :'Array<String>',
+        :'n_cosponsored_trials' => :'Integer'
       }
     end
 
@@ -174,6 +189,8 @@ module PharmaObservatory
         :'competitor_company_name',
         :'competitor_group_id',
         :'competitor_group_name',
+        :'competitor_class',
+        :'n_class_candidates',
         :'competitor_rank',
         :'competitor_score',
         :'target_sim',
@@ -190,7 +207,8 @@ module PharmaObservatory
         :'n_competitor_indications',
         :'top_shared_targets',
         :'top_shared_indications',
-        :'top_shared_mechanisms'
+        :'top_shared_mechanisms',
+        :'n_cosponsored_trials'
       ])
     end
 
@@ -242,6 +260,14 @@ module PharmaObservatory
         self.competitor_group_name = attributes[:'competitor_group_name']
       end
 
+      if attributes.key?(:'competitor_class')
+        self.competitor_class = attributes[:'competitor_class']
+      end
+
+      if attributes.key?(:'n_class_candidates')
+        self.n_class_candidates = attributes[:'n_class_candidates']
+      end
+
       if attributes.key?(:'competitor_rank')
         self.competitor_rank = attributes[:'competitor_rank']
       end
@@ -315,6 +341,10 @@ module PharmaObservatory
           self.top_shared_mechanisms = value
         end
       end
+
+      if attributes.key?(:'n_cosponsored_trials')
+        self.n_cosponsored_trials = attributes[:'n_cosponsored_trials']
+      end
     end
 
     # Show invalid properties with the reasons. Usually used together with valid?
@@ -345,6 +375,8 @@ module PharmaObservatory
           competitor_company_name == o.competitor_company_name &&
           competitor_group_id == o.competitor_group_id &&
           competitor_group_name == o.competitor_group_name &&
+          competitor_class == o.competitor_class &&
+          n_class_candidates == o.n_class_candidates &&
           competitor_rank == o.competitor_rank &&
           competitor_score == o.competitor_score &&
           target_sim == o.target_sim &&
@@ -361,7 +393,8 @@ module PharmaObservatory
           n_competitor_indications == o.n_competitor_indications &&
           top_shared_targets == o.top_shared_targets &&
           top_shared_indications == o.top_shared_indications &&
-          top_shared_mechanisms == o.top_shared_mechanisms
+          top_shared_mechanisms == o.top_shared_mechanisms &&
+          n_cosponsored_trials == o.n_cosponsored_trials
     end
 
     # @see the `==` method
@@ -373,7 +406,7 @@ module PharmaObservatory
     # Calculates hash code according to all attributes.
     # @return [Integer] Hash code
     def hash
-      [company_id, company_name, group_id, group_name, competitor_company_id, competitor_company_name, competitor_group_id, competitor_group_name, competitor_rank, competitor_score, target_sim, mechanism_sim, indication_sim, phase_sim, n_shared_targets, n_shared_mechanisms, n_shared_indications, n_phase_overlap_targets, n_company_targets, n_competitor_targets, n_company_indications, n_competitor_indications, top_shared_targets, top_shared_indications, top_shared_mechanisms].hash
+      [company_id, company_name, group_id, group_name, competitor_company_id, competitor_company_name, competitor_group_id, competitor_group_name, competitor_class, n_class_candidates, competitor_rank, competitor_score, target_sim, mechanism_sim, indication_sim, phase_sim, n_shared_targets, n_shared_mechanisms, n_shared_indications, n_phase_overlap_targets, n_company_targets, n_competitor_targets, n_company_indications, n_competitor_indications, top_shared_targets, top_shared_indications, top_shared_mechanisms, n_cosponsored_trials].hash
     end
 
     # Builds the object from hash

data/lib/pharmaobservatory/models/company_cosponsors_response.rb

@@ -0,0 +1,478 @@
+=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
+  class CompanyCosponsorsResponse
+    attr_accessor :dataset
+
+    attr_accessor :grain
+
+    attr_accessor :object_type
+
+    attr_accessor :id
+
+    attr_accessor :scope
+
+    attr_accessor :columns
+
+    attr_accessor :rows
+
+    # The exact count of the filtered rows on an ungrouped read, carried by the cursor; null when grouped.
+    attr_accessor :total
+
+    attr_accessor :next_cursor
+
+    attr_accessor :sort
+
+    attr_accessor :filters
+
+    attr_accessor :group_by
+
+    attr_accessor :measures
+
+    attr_accessor :attribution
+
+    attr_accessor :source_credit
+
+    attr_accessor :withheld_tiers
+
+    attr_accessor :withheld_columns
+
+    attr_accessor :freshness
+
+    attr_accessor :build
+
+    attr_accessor :build_state
+
+    attr_accessor :restriction
+
+    # Attribute mapping from ruby-style variable name to JSON key.
+    def self.attribute_map
+      {
+        :'dataset' => :'dataset',
+        :'grain' => :'grain',
+        :'object_type' => :'object_type',
+        :'id' => :'id',
+        :'scope' => :'scope',
+        :'columns' => :'columns',
+        :'rows' => :'rows',
+        :'total' => :'total',
+        :'next_cursor' => :'next_cursor',
+        :'sort' => :'sort',
+        :'filters' => :'filters',
+        :'group_by' => :'group_by',
+        :'measures' => :'measures',
+        :'attribution' => :'attribution',
+        :'source_credit' => :'source_credit',
+        :'withheld_tiers' => :'withheld_tiers',
+        :'withheld_columns' => :'withheld_columns',
+        :'freshness' => :'freshness',
+        :'build' => :'build',
+        :'build_state' => :'build_state',
+        :'restriction' => :'restriction'
+      }
+    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
+      {
+        :'dataset' => :'String',
+        :'grain' => :'String',
+        :'object_type' => :'String',
+        :'id' => :'String',
+        :'scope' => :'AnimalWelfareAssurancesResponseScope',
+        :'columns' => :'Array<DatasetColumn>',
+        :'rows' => :'Array<CompanyCosponsorsRow>',
+        :'total' => :'Integer',
+        :'next_cursor' => :'String',
+        :'sort' => :'Array<String>',
+        :'filters' => :'Array<Hash<String, Object>>',
+        :'group_by' => :'Array<String>',
+        :'measures' => :'Array<String>',
+        :'attribution' => :'Array<DatasetAttribution>',
+        :'source_credit' => :'String',
+        :'withheld_tiers' => :'Array<String>',
+        :'withheld_columns' => :'Array<String>',
+        :'freshness' => :'AnimalWelfareAssurancesResponseFreshness',
+        :'build' => :'AnimalWelfareAssurancesResponseBuild',
+        :'build_state' => :'DatasetBuildState',
+        :'restriction' => :'Hash<String, Object>'
+      }
+    end
+
+    # List of attributes with nullable: true
+    def self.openapi_nullable
+      Set.new([
+        :'object_type',
+        :'id',
+        :'scope',
+        :'total',
+        :'next_cursor',
+        :'restriction'
+      ])
+    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::CompanyCosponsorsResponse` 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::CompanyCosponsorsResponse`. 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?(:'dataset')
+        self.dataset = attributes[:'dataset']
+      else
+        self.dataset = nil
+      end
+
+      if attributes.key?(:'grain')
+        self.grain = attributes[:'grain']
+      end
+
+      if attributes.key?(:'object_type')
+        self.object_type = attributes[:'object_type']
+      end
+
+      if attributes.key?(:'id')
+        self.id = attributes[:'id']
+      end
+
+      if attributes.key?(:'scope')
+        self.scope = attributes[:'scope']
+      end
+
+      if attributes.key?(:'columns')
+        if (value = attributes[:'columns']).is_a?(Array)
+          self.columns = value
+        end
+      else
+        self.columns = nil
+      end
+
+      if attributes.key?(:'rows')
+        if (value = attributes[:'rows']).is_a?(Array)
+          self.rows = value
+        end
+      else
+        self.rows = nil
+      end
+
+      if attributes.key?(:'total')
+        self.total = attributes[:'total']
+      end
+
+      if attributes.key?(:'next_cursor')
+        self.next_cursor = attributes[:'next_cursor']
+      end
+
+      if attributes.key?(:'sort')
+        if (value = attributes[:'sort']).is_a?(Array)
+          self.sort = value
+        end
+      end
+
+      if attributes.key?(:'filters')
+        if (value = attributes[:'filters']).is_a?(Array)
+          self.filters = value
+        end
+      end
+
+      if attributes.key?(:'group_by')
+        if (value = attributes[:'group_by']).is_a?(Array)
+          self.group_by = value
+        end
+      end
+
+      if attributes.key?(:'measures')
+        if (value = attributes[:'measures']).is_a?(Array)
+          self.measures = value
+        end
+      end
+
+      if attributes.key?(:'attribution')
+        if (value = attributes[:'attribution']).is_a?(Array)
+          self.attribution = value
+        end
+      end
+
+      if attributes.key?(:'source_credit')
+        self.source_credit = attributes[:'source_credit']
+      end
+
+      if attributes.key?(:'withheld_tiers')
+        if (value = attributes[:'withheld_tiers']).is_a?(Array)
+          self.withheld_tiers = value
+        end
+      end
+
+      if attributes.key?(:'withheld_columns')
+        if (value = attributes[:'withheld_columns']).is_a?(Array)
+          self.withheld_columns = value
+        end
+      end
+
+      if attributes.key?(:'freshness')
+        self.freshness = attributes[:'freshness']
+      end
+
+      if attributes.key?(:'build')
+        self.build = attributes[:'build']
+      end
+
+      if attributes.key?(:'build_state')
+        self.build_state = attributes[:'build_state']
+      end
+
+      if attributes.key?(:'restriction')
+        if (value = attributes[:'restriction']).is_a?(Hash)
+          self.restriction = value
+        end
+      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
+      if @dataset.nil?
+        invalid_properties.push('invalid value for "dataset", dataset cannot be nil.')
+      end
+
+      if @columns.nil?
+        invalid_properties.push('invalid value for "columns", columns cannot be nil.')
+      end
+
+      if @rows.nil?
+        invalid_properties.push('invalid value for "rows", rows cannot be nil.')
+      end
+
+      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'
+      return false if @dataset.nil?
+      return false if @columns.nil?
+      return false if @rows.nil?
+      true
+    end
+
+    # Custom attribute writer method with validation
+    # @param [Object] dataset Value to be assigned
+    def dataset=(dataset)
+      if dataset.nil?
+        fail ArgumentError, 'dataset cannot be nil'
+      end
+
+      @dataset = dataset
+    end
+
+    # Custom attribute writer method with validation
+    # @param [Object] columns Value to be assigned
+    def columns=(columns)
+      if columns.nil?
+        fail ArgumentError, 'columns cannot be nil'
+      end
+
+      @columns = columns
+    end
+
+    # Custom attribute writer method with validation
+    # @param [Object] rows Value to be assigned
+    def rows=(rows)
+      if rows.nil?
+        fail ArgumentError, 'rows cannot be nil'
+      end
+
+      @rows = rows
+    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 &&
+          dataset == o.dataset &&
+          grain == o.grain &&
+          object_type == o.object_type &&
+          id == o.id &&
+          scope == o.scope &&
+          columns == o.columns &&
+          rows == o.rows &&
+          total == o.total &&
+          next_cursor == o.next_cursor &&
+          sort == o.sort &&
+          filters == o.filters &&
+          group_by == o.group_by &&
+          measures == o.measures &&
+          attribution == o.attribution &&
+          source_credit == o.source_credit &&
+          withheld_tiers == o.withheld_tiers &&
+          withheld_columns == o.withheld_columns &&
+          freshness == o.freshness &&
+          build == o.build &&
+          build_state == o.build_state &&
+          restriction == o.restriction
+    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
+      [dataset, grain, object_type, id, scope, columns, rows, total, next_cursor, sort, filters, group_by, measures, attribution, source_credit, withheld_tiers, withheld_columns, freshness, build, build_state, restriction].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