pharmaobservatory 0.1.2 → 0.1.3

data/lib/pharmaobservatory/models/{biomarkers_publishing_org200_response_rows_inner.rb → biomarker_publishing_companies_row.rb}

@@ -14,37 +14,67 @@ require 'date'
 require 'time'
 
 module PharmaObservatory
-  class BiomarkersPublishingOrg200ResponseRowsInner
-    attr_accessor :resolved_parent_id
+  # One row of the biomarker_publishing_companies dataset: one row per biomarker gene and company. A grouped request returns the group columns and the measures instead, as additional properties.
+  class BiomarkerPublishingCompaniesRow
+    # The biomarker route key of the gene the papers name (the gene symbol); the entry key for the biomarkers object type.
+    attr_accessor :route_key
 
-    attr_accessor :org_name
+    # The gene symbol.
+    attr_accessor :gene_symbol
 
-    attr_accessor :org_type
+    # Company level: the publisher's company.
+    attr_accessor :publisher_company_id
 
-    attr_accessor :best_match_tier
+    # Display name of the publisher's company.
+    attr_accessor :publisher_company_name
+
+    # Group level: the publisher's current ultimate parent company; a root company's group is itself.
+    attr_accessor :publisher_group_id
+
+    # Display name of the publisher's group.
+    attr_accessor :publisher_group_name
 
+    # Papers that name the gene from the company's organizations (a consortium paper is excluded).
     attr_accessor :n_publications
 
-    attr_accessor :n_papers_excluded_as_consortium
+    # The company's organizations the papers reach.
+    attr_accessor :n_member_orgs
+
+    # Strongest affiliation match tier.
+    attr_accessor :best_match_tier
 
+    # Earliest publication year.
     attr_accessor :first_pub_year
 
+    # Latest publication year.
     attr_accessor :last_pub_year
 
+    # A sample of the supporting PubMed ids.
     attr_accessor :supporting_pmids
 
+    # True when the sample is shorter than the paper count.
+    attr_accessor :supporting_pmids_truncated
+
+    # Papers left out because they name too many organizations.
+    attr_accessor :n_papers_excluded_as_consortium
+
     # Attribute mapping from ruby-style variable name to JSON key.
     def self.attribute_map
       {
-        :'resolved_parent_id' => :'resolved_parent_id',
-        :'org_name' => :'org_name',
-        :'org_type' => :'org_type',
-        :'best_match_tier' => :'best_match_tier',
+        :'route_key' => :'route_key',
+        :'gene_symbol' => :'gene_symbol',
+        :'publisher_company_id' => :'publisher_company_id',
+        :'publisher_company_name' => :'publisher_company_name',
+        :'publisher_group_id' => :'publisher_group_id',
+        :'publisher_group_name' => :'publisher_group_name',
         :'n_publications' => :'n_publications',
-        :'n_papers_excluded_as_consortium' => :'n_papers_excluded_as_consortium',
+        :'n_member_orgs' => :'n_member_orgs',
+        :'best_match_tier' => :'best_match_tier',
         :'first_pub_year' => :'first_pub_year',
         :'last_pub_year' => :'last_pub_year',
-        :'supporting_pmids' => :'supporting_pmids'
+        :'supporting_pmids' => :'supporting_pmids',
+        :'supporting_pmids_truncated' => :'supporting_pmids_truncated',
+        :'n_papers_excluded_as_consortium' => :'n_papers_excluded_as_consortium'
       }
     end
 
@@ -61,23 +91,40 @@ module PharmaObservatory
     # Attribute type mapping.
     def self.openapi_types
       {
-        :'resolved_parent_id' => :'String',
-        :'org_name' => :'String',
-        :'org_type' => :'String',
-        :'best_match_tier' => :'String',
+        :'route_key' => :'String',
+        :'gene_symbol' => :'String',
+        :'publisher_company_id' => :'String',
+        :'publisher_company_name' => :'String',
+        :'publisher_group_id' => :'String',
+        :'publisher_group_name' => :'String',
         :'n_publications' => :'Integer',
-        :'n_papers_excluded_as_consortium' => :'Integer',
-        :'first_pub_year' => :'Object',
-        :'last_pub_year' => :'Object',
-        :'supporting_pmids' => :'Array<Object>'
+        :'n_member_orgs' => :'Integer',
+        :'best_match_tier' => :'String',
+        :'first_pub_year' => :'Integer',
+        :'last_pub_year' => :'Integer',
+        :'supporting_pmids' => :'Array<String>',
+        :'supporting_pmids_truncated' => :'Boolean',
+        :'n_papers_excluded_as_consortium' => :'Integer'
       }
     end
 
     # List of attributes with nullable: true
     def self.openapi_nullable
       Set.new([
+        :'route_key',
+        :'gene_symbol',
+        :'publisher_company_id',
+        :'publisher_company_name',
+        :'publisher_group_id',
+        :'publisher_group_name',
+        :'n_publications',
+        :'n_member_orgs',
+        :'best_match_tier',
         :'first_pub_year',
         :'last_pub_year',
+        :'supporting_pmids',
+        :'supporting_pmids_truncated',
+        :'n_papers_excluded_as_consortium'
       ])
     end
 
@@ -85,72 +132,74 @@ module PharmaObservatory
     # @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::BiomarkersPublishingOrg200ResponseRowsInner` initialize method"
+        fail ArgumentError, "The input argument (attributes) must be a hash in `PharmaObservatory::BiomarkerPublishingCompaniesRow` 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::BiomarkersPublishingOrg200ResponseRowsInner`. Please check the name to make sure it's valid. List of attributes: " + acceptable_attribute_map.keys.inspect
+          fail ArgumentError, "`#{k}` is not a valid attribute in `PharmaObservatory::BiomarkerPublishingCompaniesRow`. 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?(:'resolved_parent_id')
-        self.resolved_parent_id = attributes[:'resolved_parent_id']
-      else
-        self.resolved_parent_id = nil
+      if attributes.key?(:'route_key')
+        self.route_key = attributes[:'route_key']
       end
 
-      if attributes.key?(:'org_name')
-        self.org_name = attributes[:'org_name']
-      else
-        self.org_name = nil
+      if attributes.key?(:'gene_symbol')
+        self.gene_symbol = attributes[:'gene_symbol']
       end
 
-      if attributes.key?(:'org_type')
-        self.org_type = attributes[:'org_type']
-      else
-        self.org_type = nil
+      if attributes.key?(:'publisher_company_id')
+        self.publisher_company_id = attributes[:'publisher_company_id']
       end
 
-      if attributes.key?(:'best_match_tier')
-        self.best_match_tier = attributes[:'best_match_tier']
-      else
-        self.best_match_tier = nil
+      if attributes.key?(:'publisher_company_name')
+        self.publisher_company_name = attributes[:'publisher_company_name']
+      end
+
+      if attributes.key?(:'publisher_group_id')
+        self.publisher_group_id = attributes[:'publisher_group_id']
+      end
+
+      if attributes.key?(:'publisher_group_name')
+        self.publisher_group_name = attributes[:'publisher_group_name']
       end
 
       if attributes.key?(:'n_publications')
         self.n_publications = attributes[:'n_publications']
-      else
-        self.n_publications = nil
       end
 
-      if attributes.key?(:'n_papers_excluded_as_consortium')
-        self.n_papers_excluded_as_consortium = attributes[:'n_papers_excluded_as_consortium']
-      else
-        self.n_papers_excluded_as_consortium = nil
+      if attributes.key?(:'n_member_orgs')
+        self.n_member_orgs = attributes[:'n_member_orgs']
+      end
+
+      if attributes.key?(:'best_match_tier')
+        self.best_match_tier = attributes[:'best_match_tier']
       end
 
       if attributes.key?(:'first_pub_year')
         self.first_pub_year = attributes[:'first_pub_year']
-      else
-        self.first_pub_year = nil
       end
 
       if attributes.key?(:'last_pub_year')
         self.last_pub_year = attributes[:'last_pub_year']
-      else
-        self.last_pub_year = nil
       end
 
       if attributes.key?(:'supporting_pmids')
         if (value = attributes[:'supporting_pmids']).is_a?(Array)
           self.supporting_pmids = value
         end
-      else
-        self.supporting_pmids = nil
+      end
+
+      if attributes.key?(:'supporting_pmids_truncated')
+        self.supporting_pmids_truncated = attributes[:'supporting_pmids_truncated']
+      end
+
+      if attributes.key?(:'n_papers_excluded_as_consortium')
+        self.n_papers_excluded_as_consortium = attributes[:'n_papers_excluded_as_consortium']
       end
     end
 
@@ -159,34 +208,6 @@ module PharmaObservatory
     def list_invalid_properties
       warn '[DEPRECATED] the `list_invalid_properties` method is obsolete'
       invalid_properties = Array.new
-      if @resolved_parent_id.nil?
-        invalid_properties.push('invalid value for "resolved_parent_id", resolved_parent_id cannot be nil.')
-      end
-
-      if @org_name.nil?
-        invalid_properties.push('invalid value for "org_name", org_name cannot be nil.')
-      end
-
-      if @org_type.nil?
-        invalid_properties.push('invalid value for "org_type", org_type cannot be nil.')
-      end
-
-      if @best_match_tier.nil?
-        invalid_properties.push('invalid value for "best_match_tier", best_match_tier cannot be nil.')
-      end
-
-      if @n_publications.nil?
-        invalid_properties.push('invalid value for "n_publications", n_publications cannot be nil.')
-      end
-
-      if @n_papers_excluded_as_consortium.nil?
-        invalid_properties.push('invalid value for "n_papers_excluded_as_consortium", n_papers_excluded_as_consortium cannot be nil.')
-      end
-
-      if @supporting_pmids.nil?
-        invalid_properties.push('invalid value for "supporting_pmids", supporting_pmids cannot be nil.')
-      end
-
       invalid_properties
     end
 
@@ -194,100 +215,28 @@ module PharmaObservatory
     # @return true if the model is valid
     def valid?
       warn '[DEPRECATED] the `valid?` method is obsolete'
-      return false if @resolved_parent_id.nil?
-      return false if @org_name.nil?
-      return false if @org_type.nil?
-      return false if @best_match_tier.nil?
-      return false if @n_publications.nil?
-      return false if @n_papers_excluded_as_consortium.nil?
-      return false if @supporting_pmids.nil?
       true
     end
 
-    # Custom attribute writer method with validation
-    # @param [Object] resolved_parent_id Value to be assigned
-    def resolved_parent_id=(resolved_parent_id)
-      if resolved_parent_id.nil?
-        fail ArgumentError, 'resolved_parent_id cannot be nil'
-      end
-
-      @resolved_parent_id = resolved_parent_id
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] org_name Value to be assigned
-    def org_name=(org_name)
-      if org_name.nil?
-        fail ArgumentError, 'org_name cannot be nil'
-      end
-
-      @org_name = org_name
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] org_type Value to be assigned
-    def org_type=(org_type)
-      if org_type.nil?
-        fail ArgumentError, 'org_type cannot be nil'
-      end
-
-      @org_type = org_type
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] best_match_tier Value to be assigned
-    def best_match_tier=(best_match_tier)
-      if best_match_tier.nil?
-        fail ArgumentError, 'best_match_tier cannot be nil'
-      end
-
-      @best_match_tier = best_match_tier
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] n_publications Value to be assigned
-    def n_publications=(n_publications)
-      if n_publications.nil?
-        fail ArgumentError, 'n_publications cannot be nil'
-      end
-
-      @n_publications = n_publications
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] n_papers_excluded_as_consortium Value to be assigned
-    def n_papers_excluded_as_consortium=(n_papers_excluded_as_consortium)
-      if n_papers_excluded_as_consortium.nil?
-        fail ArgumentError, 'n_papers_excluded_as_consortium cannot be nil'
-      end
-
-      @n_papers_excluded_as_consortium = n_papers_excluded_as_consortium
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] supporting_pmids Value to be assigned
-    def supporting_pmids=(supporting_pmids)
-      if supporting_pmids.nil?
-        fail ArgumentError, 'supporting_pmids cannot be nil'
-      end
-
-      @supporting_pmids = supporting_pmids
-    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 &&
-          resolved_parent_id == o.resolved_parent_id &&
-          org_name == o.org_name &&
-          org_type == o.org_type &&
-          best_match_tier == o.best_match_tier &&
+          route_key == o.route_key &&
+          gene_symbol == o.gene_symbol &&
+          publisher_company_id == o.publisher_company_id &&
+          publisher_company_name == o.publisher_company_name &&
+          publisher_group_id == o.publisher_group_id &&
+          publisher_group_name == o.publisher_group_name &&
           n_publications == o.n_publications &&
-          n_papers_excluded_as_consortium == o.n_papers_excluded_as_consortium &&
+          n_member_orgs == o.n_member_orgs &&
+          best_match_tier == o.best_match_tier &&
           first_pub_year == o.first_pub_year &&
           last_pub_year == o.last_pub_year &&
-          supporting_pmids == o.supporting_pmids
+          supporting_pmids == o.supporting_pmids &&
+          supporting_pmids_truncated == o.supporting_pmids_truncated &&
+          n_papers_excluded_as_consortium == o.n_papers_excluded_as_consortium
     end
 
     # @see the `==` method
@@ -299,7 +248,7 @@ module PharmaObservatory
     # Calculates hash code according to all attributes.
     # @return [Integer] Hash code
     def hash
-      [resolved_parent_id, org_name, org_type, best_match_tier, n_publications, n_papers_excluded_as_consortium, first_pub_year, last_pub_year, supporting_pmids].hash
+      [route_key, gene_symbol, publisher_company_id, publisher_company_name, publisher_group_id, publisher_group_name, n_publications, n_member_orgs, best_match_tier, first_pub_year, last_pub_year, supporting_pmids, supporting_pmids_truncated, n_papers_excluded_as_consortium].hash
     end
 
     # Builds the object from hash