pharmaobservatory 0.1.2 → 0.1.3

data/lib/pharmaobservatory/models/{biomarkers_cgi200_response_rows_inner.rb → biomarker_evidence_row.rb}

@@ -14,37 +14,87 @@ require 'date'
 require 'time'
 
 module PharmaObservatory
-  class BiomarkersCgi200ResponseRowsInner
-    attr_accessor :biomarker
+  # One row of the biomarker_evidence dataset: one row per evidence assertion. A grouped request returns the group columns and the measures instead, as additional properties.
+  class BiomarkerEvidenceRow
+    # The evidence assertion id.
+    attr_accessor :biomarker_evidence_id
 
-    attr_accessor :variant_count
+    # The biomarker route key of the gene this evidence is about (the gene symbol); the entry key for the biomarkers object type.
+    attr_accessor :route_key
 
-    attr_accessor :drug
+    # The gene symbol the evidence is about.
+    attr_accessor :gene_symbol
 
-    attr_accessor :canonical_drug_id
+    # The target's Ensembl gene id.
+    attr_accessor :target_id
 
-    attr_accessor :response
+    # The UniProt accession.
+    attr_accessor :uniprot_accession
 
-    attr_accessor :disease
+    # The biomarker as the source names it (the gene or the variant).
+    attr_accessor :biomarker
 
+    # cancer_actionable_cgi, ot_association or trial_mention.
+    attr_accessor :evidence_type
+
+    # The source the assertion comes from.
     attr_accessor :source
 
-    attr_accessor :source_label
+    # The condition key.
+    attr_accessor :condition_id
+
+    # The condition as the source names it.
+    attr_accessor :condition_name
+
+    # The therapeutic area.
+    attr_accessor :therapeutic_area
 
+    # The drug as filed.
+    attr_accessor :drug_name
+
+    # The drug key.
+    attr_accessor :drug_id
+
+    # The molecule key. Null today: the evidence mart carries no molecule column.
+    attr_accessor :molecule_id
+
+    # The reported response (for example Responsive, Resistant).
+    attr_accessor :response
+
+    # The association score, for an Open Targets row.
     attr_accessor :score
 
+    # Variants the assertion covers.
+    attr_accessor :variant_count
+
+    # The trial registry id, for a trial-mention row.
+    attr_accessor :trial_id
+
+    # The sample type, for a trial-mention row.
+    attr_accessor :sample_type
+
     # Attribute mapping from ruby-style variable name to JSON key.
     def self.attribute_map
       {
+        :'biomarker_evidence_id' => :'biomarker_evidence_id',
+        :'route_key' => :'route_key',
+        :'gene_symbol' => :'gene_symbol',
+        :'target_id' => :'target_id',
+        :'uniprot_accession' => :'uniprot_accession',
         :'biomarker' => :'biomarker',
-        :'variant_count' => :'variant_count',
-        :'drug' => :'drug',
-        :'canonical_drug_id' => :'canonical_drug_id',
-        :'response' => :'response',
-        :'disease' => :'disease',
+        :'evidence_type' => :'evidence_type',
         :'source' => :'source',
-        :'source_label' => :'source_label',
-        :'score' => :'score'
+        :'condition_id' => :'condition_id',
+        :'condition_name' => :'condition_name',
+        :'therapeutic_area' => :'therapeutic_area',
+        :'drug_name' => :'drug_name',
+        :'drug_id' => :'drug_id',
+        :'molecule_id' => :'molecule_id',
+        :'response' => :'response',
+        :'score' => :'score',
+        :'variant_count' => :'variant_count',
+        :'trial_id' => :'trial_id',
+        :'sample_type' => :'sample_type'
       }
     end
 
@@ -61,22 +111,50 @@ module PharmaObservatory
     # Attribute type mapping.
     def self.openapi_types
       {
+        :'biomarker_evidence_id' => :'String',
+        :'route_key' => :'String',
+        :'gene_symbol' => :'String',
+        :'target_id' => :'String',
+        :'uniprot_accession' => :'String',
         :'biomarker' => :'String',
-        :'variant_count' => :'Integer',
-        :'drug' => :'String',
-        :'canonical_drug_id' => :'String',
-        :'response' => :'String',
-        :'disease' => :'String',
+        :'evidence_type' => :'String',
         :'source' => :'String',
-        :'source_label' => :'String',
-        :'score' => :'Float'
+        :'condition_id' => :'String',
+        :'condition_name' => :'String',
+        :'therapeutic_area' => :'String',
+        :'drug_name' => :'String',
+        :'drug_id' => :'String',
+        :'molecule_id' => :'String',
+        :'response' => :'String',
+        :'score' => :'Float',
+        :'variant_count' => :'Integer',
+        :'trial_id' => :'String',
+        :'sample_type' => :'String'
       }
     end
 
     # List of attributes with nullable: true
     def self.openapi_nullable
       Set.new([
-        :'canonical_drug_id',
+        :'biomarker_evidence_id',
+        :'route_key',
+        :'gene_symbol',
+        :'target_id',
+        :'uniprot_accession',
+        :'biomarker',
+        :'evidence_type',
+        :'source',
+        :'condition_id',
+        :'condition_name',
+        :'therapeutic_area',
+        :'drug_name',
+        :'drug_id',
+        :'molecule_id',
+        :'response',
+        :'score',
+        :'variant_count',
+        :'trial_id',
+        :'sample_type'
       ])
     end
 
@@ -84,110 +162,100 @@ 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::BiomarkersCgi200ResponseRowsInner` initialize method"
+        fail ArgumentError, "The input argument (attributes) must be a hash in `PharmaObservatory::BiomarkerEvidenceRow` 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::BiomarkersCgi200ResponseRowsInner`. 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::BiomarkerEvidenceRow`. 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')
-        self.biomarker = attributes[:'biomarker']
-      else
-        self.biomarker = nil
+      if attributes.key?(:'biomarker_evidence_id')
+        self.biomarker_evidence_id = attributes[:'biomarker_evidence_id']
       end
 
-      if attributes.key?(:'variant_count')
-        self.variant_count = attributes[:'variant_count']
-      else
-        self.variant_count = nil
+      if attributes.key?(:'route_key')
+        self.route_key = attributes[:'route_key']
       end
 
-      if attributes.key?(:'drug')
-        self.drug = attributes[:'drug']
-      else
-        self.drug = nil
+      if attributes.key?(:'gene_symbol')
+        self.gene_symbol = attributes[:'gene_symbol']
       end
 
-      if attributes.key?(:'canonical_drug_id')
-        self.canonical_drug_id = attributes[:'canonical_drug_id']
-      else
-        self.canonical_drug_id = nil
+      if attributes.key?(:'target_id')
+        self.target_id = attributes[:'target_id']
       end
 
-      if attributes.key?(:'response')
-        self.response = attributes[:'response']
-      else
-        self.response = nil
+      if attributes.key?(:'uniprot_accession')
+        self.uniprot_accession = attributes[:'uniprot_accession']
       end
 
-      if attributes.key?(:'disease')
-        self.disease = attributes[:'disease']
-      else
-        self.disease = nil
+      if attributes.key?(:'biomarker')
+        self.biomarker = attributes[:'biomarker']
+      end
+
+      if attributes.key?(:'evidence_type')
+        self.evidence_type = attributes[:'evidence_type']
       end
 
       if attributes.key?(:'source')
         self.source = attributes[:'source']
-      else
-        self.source = nil
       end
 
-      if attributes.key?(:'source_label')
-        self.source_label = attributes[:'source_label']
-      else
-        self.source_label = nil
+      if attributes.key?(:'condition_id')
+        self.condition_id = attributes[:'condition_id']
       end
 
-      if attributes.key?(:'score')
-        self.score = attributes[:'score']
-      else
-        self.score = nil
+      if attributes.key?(:'condition_name')
+        self.condition_name = attributes[:'condition_name']
       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 @biomarker.nil?
-        invalid_properties.push('invalid value for "biomarker", biomarker cannot be nil.')
+      if attributes.key?(:'therapeutic_area')
+        self.therapeutic_area = attributes[:'therapeutic_area']
       end
 
-      if @variant_count.nil?
-        invalid_properties.push('invalid value for "variant_count", variant_count cannot be nil.')
+      if attributes.key?(:'drug_name')
+        self.drug_name = attributes[:'drug_name']
       end
 
-      if @drug.nil?
-        invalid_properties.push('invalid value for "drug", drug cannot be nil.')
+      if attributes.key?(:'drug_id')
+        self.drug_id = attributes[:'drug_id']
       end
 
-      if @response.nil?
-        invalid_properties.push('invalid value for "response", response cannot be nil.')
+      if attributes.key?(:'molecule_id')
+        self.molecule_id = attributes[:'molecule_id']
       end
 
-      if @disease.nil?
-        invalid_properties.push('invalid value for "disease", disease cannot be nil.')
+      if attributes.key?(:'response')
+        self.response = attributes[:'response']
       end
 
-      if @source.nil?
-        invalid_properties.push('invalid value for "source", source cannot be nil.')
+      if attributes.key?(:'score')
+        self.score = attributes[:'score']
       end
 
-      if @source_label.nil?
-        invalid_properties.push('invalid value for "source_label", source_label cannot be nil.')
+      if attributes.key?(:'variant_count')
+        self.variant_count = attributes[:'variant_count']
       end
 
-      if @score.nil?
-        invalid_properties.push('invalid value for "score", score cannot be nil.')
+      if attributes.key?(:'trial_id')
+        self.trial_id = attributes[:'trial_id']
       end
 
+      if attributes.key?(:'sample_type')
+        self.sample_type = attributes[:'sample_type']
+      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
 
@@ -195,111 +263,33 @@ module PharmaObservatory
     # @return true if the model is valid
     def valid?
       warn '[DEPRECATED] the `valid?` method is obsolete'
-      return false if @biomarker.nil?
-      return false if @variant_count.nil?
-      return false if @drug.nil?
-      return false if @response.nil?
-      return false if @disease.nil?
-      return false if @source.nil?
-      return false if @source_label.nil?
-      return false if @score.nil?
       true
     end
 
-    # Custom attribute writer method with validation
-    # @param [Object] biomarker Value to be assigned
-    def biomarker=(biomarker)
-      if biomarker.nil?
-        fail ArgumentError, 'biomarker cannot be nil'
-      end
-
-      @biomarker = biomarker
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] variant_count Value to be assigned
-    def variant_count=(variant_count)
-      if variant_count.nil?
-        fail ArgumentError, 'variant_count cannot be nil'
-      end
-
-      @variant_count = variant_count
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] drug Value to be assigned
-    def drug=(drug)
-      if drug.nil?
-        fail ArgumentError, 'drug cannot be nil'
-      end
-
-      @drug = drug
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] response Value to be assigned
-    def response=(response)
-      if response.nil?
-        fail ArgumentError, 'response cannot be nil'
-      end
-
-      @response = response
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] disease Value to be assigned
-    def disease=(disease)
-      if disease.nil?
-        fail ArgumentError, 'disease cannot be nil'
-      end
-
-      @disease = disease
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] source Value to be assigned
-    def source=(source)
-      if source.nil?
-        fail ArgumentError, 'source cannot be nil'
-      end
-
-      @source = source
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] source_label Value to be assigned
-    def source_label=(source_label)
-      if source_label.nil?
-        fail ArgumentError, 'source_label cannot be nil'
-      end
-
-      @source_label = source_label
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] score Value to be assigned
-    def score=(score)
-      if score.nil?
-        fail ArgumentError, 'score cannot be nil'
-      end
-
-      @score = score
-    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_evidence_id == o.biomarker_evidence_id &&
+          route_key == o.route_key &&
+          gene_symbol == o.gene_symbol &&
+          target_id == o.target_id &&
+          uniprot_accession == o.uniprot_accession &&
           biomarker == o.biomarker &&
-          variant_count == o.variant_count &&
-          drug == o.drug &&
-          canonical_drug_id == o.canonical_drug_id &&
-          response == o.response &&
-          disease == o.disease &&
+          evidence_type == o.evidence_type &&
           source == o.source &&
-          source_label == o.source_label &&
-          score == o.score
+          condition_id == o.condition_id &&
+          condition_name == o.condition_name &&
+          therapeutic_area == o.therapeutic_area &&
+          drug_name == o.drug_name &&
+          drug_id == o.drug_id &&
+          molecule_id == o.molecule_id &&
+          response == o.response &&
+          score == o.score &&
+          variant_count == o.variant_count &&
+          trial_id == o.trial_id &&
+          sample_type == o.sample_type
     end
 
     # @see the `==` method
@@ -311,7 +301,7 @@ module PharmaObservatory
     # Calculates hash code according to all attributes.
     # @return [Integer] Hash code
     def hash
-      [biomarker, variant_count, drug, canonical_drug_id, response, disease, source, source_label, score].hash
+      [biomarker_evidence_id, route_key, gene_symbol, target_id, uniprot_accession, biomarker, evidence_type, source, condition_id, condition_name, therapeutic_area, drug_name, drug_id, molecule_id, response, score, variant_count, trial_id, sample_type].hash
     end
 
     # Builds the object from hash