pharmaobservatory 0.1.2 → 0.1.3

data/lib/pharmaobservatory/models/{biomarkers_list200_response_rows_inner.rb → biomarkers_row.rb}

@@ -14,65 +14,110 @@ require 'date'
 require 'time'
 
 module PharmaObservatory
-  class BiomarkersList200ResponseRowsInner
-    attr_accessor :route_key
+  # One row of the biomarkers dataset: one row per biomarker (a gene, protein variant or other feature). A grouped request returns the group columns and the measures instead, as additional properties.
+  class BiomarkersRow
+    # The biomarker key.
+    attr_accessor :biomarker_id
 
-    attr_accessor :display_name
+    # The biomarker's route key, the id the web page uses and the one entry key every biomarker dataset takes (the gene symbol for a gene biomarker).
+    attr_accessor :route_key
 
+    # gene, protein_variant or another feature kind.
     attr_accessor :biomarker_kind
 
+    # Whether the biomarker's identity is confirmed.
     attr_accessor :identity_status
 
+    # The biomarker's display name.
+    attr_accessor :display_name
+
+    # The parent biomarker (a variant's gene).
+    attr_accessor :parent_biomarker_id
+
+    # The gene symbol.
     attr_accessor :gene_symbol
 
+    # The amino-acid change, for a variant.
     attr_accessor :amino_acid_change
 
+    # The target's Ensembl gene id.
+    attr_accessor :target_id
+
+    # The HGNC gene id.
+    attr_accessor :hgnc_id
+
+    # The UniProt accession.
+    attr_accessor :uniprot_accession
+
+    # Feature code for a non-gene feature.
+    attr_accessor :feature_code
+
+    # Feature type for a non-gene feature.
+    attr_accessor :feature_type
+
+    # Strongest evidence tier: 1 FDA companion diagnostic through 6 no evidence.
+    attr_accessor :evidence_tier
+
+    # The tier's name.
+    attr_accessor :evidence_tier_label
+
+    # FDA companion diagnostic assertions.
     attr_accessor :n_fda_cdx_assertions
 
+    # FDA biomarker qualification project assertions.
     attr_accessor :n_fda_bqp_assertions
 
+    # Cancer Genome Interpreter actionable rows.
     attr_accessor :n_cancer_actionable_cgi
 
+    # Open Targets target-disease associations.
     attr_accessor :n_ot_association
 
+    # Trials that name the biomarker.
     attr_accessor :n_trial_mention
 
+    # Publication variant mentions.
     attr_accessor :n_publication_variant_mentions
 
-    attr_accessor :kind_label
-
-    attr_accessor :evidence_tier
-
-    attr_accessor :evidence_tier_label
-
+    # Whether clinical validation evidence exists.
     attr_accessor :has_clinical_validation_evidence
 
+    # Whether analytical validation evidence exists.
     attr_accessor :has_analytical_validation_evidence
 
+    # Papers naming an assay provider for the biomarker.
     attr_accessor :n_assay_provider_papers
 
+    # Assay-provider suppliers named.
     attr_accessor :n_assay_provider_suppliers
 
+    # Of those, diagnostic providers.
     attr_accessor :n_diagnostic_provider_suppliers
 
     # Attribute mapping from ruby-style variable name to JSON key.
     def self.attribute_map
       {
+        :'biomarker_id' => :'biomarker_id',
         :'route_key' => :'route_key',
-        :'display_name' => :'display_name',
         :'biomarker_kind' => :'biomarker_kind',
         :'identity_status' => :'identity_status',
+        :'display_name' => :'display_name',
+        :'parent_biomarker_id' => :'parent_biomarker_id',
         :'gene_symbol' => :'gene_symbol',
         :'amino_acid_change' => :'amino_acid_change',
+        :'target_id' => :'target_id',
+        :'hgnc_id' => :'hgnc_id',
+        :'uniprot_accession' => :'uniprot_accession',
+        :'feature_code' => :'feature_code',
+        :'feature_type' => :'feature_type',
+        :'evidence_tier' => :'evidence_tier',
+        :'evidence_tier_label' => :'evidence_tier_label',
         :'n_fda_cdx_assertions' => :'n_fda_cdx_assertions',
         :'n_fda_bqp_assertions' => :'n_fda_bqp_assertions',
         :'n_cancer_actionable_cgi' => :'n_cancer_actionable_cgi',
         :'n_ot_association' => :'n_ot_association',
         :'n_trial_mention' => :'n_trial_mention',
         :'n_publication_variant_mentions' => :'n_publication_variant_mentions',
-        :'kind_label' => :'kind_label',
-        :'evidence_tier' => :'evidence_tier',
-        :'evidence_tier_label' => :'evidence_tier_label',
         :'has_clinical_validation_evidence' => :'has_clinical_validation_evidence',
         :'has_analytical_validation_evidence' => :'has_analytical_validation_evidence',
         :'n_assay_provider_papers' => :'n_assay_provider_papers',
@@ -94,21 +139,27 @@ module PharmaObservatory
     # Attribute type mapping.
     def self.openapi_types
       {
+        :'biomarker_id' => :'String',
         :'route_key' => :'String',
-        :'display_name' => :'String',
         :'biomarker_kind' => :'String',
         :'identity_status' => :'String',
+        :'display_name' => :'String',
+        :'parent_biomarker_id' => :'String',
         :'gene_symbol' => :'String',
-        :'amino_acid_change' => :'Object',
+        :'amino_acid_change' => :'String',
+        :'target_id' => :'String',
+        :'hgnc_id' => :'String',
+        :'uniprot_accession' => :'String',
+        :'feature_code' => :'String',
+        :'feature_type' => :'String',
+        :'evidence_tier' => :'Integer',
+        :'evidence_tier_label' => :'String',
         :'n_fda_cdx_assertions' => :'Integer',
         :'n_fda_bqp_assertions' => :'Integer',
         :'n_cancer_actionable_cgi' => :'Integer',
         :'n_ot_association' => :'Integer',
         :'n_trial_mention' => :'Integer',
         :'n_publication_variant_mentions' => :'Integer',
-        :'kind_label' => :'String',
-        :'evidence_tier' => :'Integer',
-        :'evidence_tier_label' => :'String',
         :'has_clinical_validation_evidence' => :'Boolean',
         :'has_analytical_validation_evidence' => :'Boolean',
         :'n_assay_provider_papers' => :'Integer',
@@ -120,8 +171,27 @@ module PharmaObservatory
     # List of attributes with nullable: true
     def self.openapi_nullable
       Set.new([
+        :'biomarker_id',
+        :'route_key',
+        :'biomarker_kind',
+        :'identity_status',
+        :'display_name',
+        :'parent_biomarker_id',
         :'gene_symbol',
         :'amino_acid_change',
+        :'target_id',
+        :'hgnc_id',
+        :'uniprot_accession',
+        :'feature_code',
+        :'feature_type',
+        :'evidence_tier',
+        :'evidence_tier_label',
+        :'n_fda_cdx_assertions',
+        :'n_fda_bqp_assertions',
+        :'n_cancer_actionable_cgi',
+        :'n_ot_association',
+        :'n_trial_mention',
+        :'n_publication_variant_mentions',
         :'has_clinical_validation_evidence',
         :'has_analytical_validation_evidence',
         :'n_assay_provider_papers',
@@ -134,136 +204,120 @@ 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::BiomarkersList200ResponseRowsInner` initialize method"
+        fail ArgumentError, "The input argument (attributes) must be a hash in `PharmaObservatory::BiomarkersRow` 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::BiomarkersList200ResponseRowsInner`. 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::BiomarkersRow`. 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']
-      else
-        self.route_key = nil
+      if attributes.key?(:'biomarker_id')
+        self.biomarker_id = attributes[:'biomarker_id']
       end
 
-      if attributes.key?(:'display_name')
-        self.display_name = attributes[:'display_name']
-      else
-        self.display_name = nil
+      if attributes.key?(:'route_key')
+        self.route_key = attributes[:'route_key']
       end
 
       if attributes.key?(:'biomarker_kind')
         self.biomarker_kind = attributes[:'biomarker_kind']
-      else
-        self.biomarker_kind = nil
       end
 
       if attributes.key?(:'identity_status')
         self.identity_status = attributes[:'identity_status']
-      else
-        self.identity_status = nil
+      end
+
+      if attributes.key?(:'display_name')
+        self.display_name = attributes[:'display_name']
+      end
+
+      if attributes.key?(:'parent_biomarker_id')
+        self.parent_biomarker_id = attributes[:'parent_biomarker_id']
       end
 
       if attributes.key?(:'gene_symbol')
         self.gene_symbol = attributes[:'gene_symbol']
-      else
-        self.gene_symbol = nil
       end
 
       if attributes.key?(:'amino_acid_change')
         self.amino_acid_change = attributes[:'amino_acid_change']
-      else
-        self.amino_acid_change = nil
+      end
+
+      if attributes.key?(:'target_id')
+        self.target_id = attributes[:'target_id']
+      end
+
+      if attributes.key?(:'hgnc_id')
+        self.hgnc_id = attributes[:'hgnc_id']
+      end
+
+      if attributes.key?(:'uniprot_accession')
+        self.uniprot_accession = attributes[:'uniprot_accession']
+      end
+
+      if attributes.key?(:'feature_code')
+        self.feature_code = attributes[:'feature_code']
+      end
+
+      if attributes.key?(:'feature_type')
+        self.feature_type = attributes[:'feature_type']
+      end
+
+      if attributes.key?(:'evidence_tier')
+        self.evidence_tier = attributes[:'evidence_tier']
+      end
+
+      if attributes.key?(:'evidence_tier_label')
+        self.evidence_tier_label = attributes[:'evidence_tier_label']
       end
 
       if attributes.key?(:'n_fda_cdx_assertions')
         self.n_fda_cdx_assertions = attributes[:'n_fda_cdx_assertions']
-      else
-        self.n_fda_cdx_assertions = nil
       end
 
       if attributes.key?(:'n_fda_bqp_assertions')
         self.n_fda_bqp_assertions = attributes[:'n_fda_bqp_assertions']
-      else
-        self.n_fda_bqp_assertions = nil
       end
 
       if attributes.key?(:'n_cancer_actionable_cgi')
         self.n_cancer_actionable_cgi = attributes[:'n_cancer_actionable_cgi']
-      else
-        self.n_cancer_actionable_cgi = nil
       end
 
       if attributes.key?(:'n_ot_association')
         self.n_ot_association = attributes[:'n_ot_association']
-      else
-        self.n_ot_association = nil
       end
 
       if attributes.key?(:'n_trial_mention')
         self.n_trial_mention = attributes[:'n_trial_mention']
-      else
-        self.n_trial_mention = nil
       end
 
       if attributes.key?(:'n_publication_variant_mentions')
         self.n_publication_variant_mentions = attributes[:'n_publication_variant_mentions']
-      else
-        self.n_publication_variant_mentions = nil
-      end
-
-      if attributes.key?(:'kind_label')
-        self.kind_label = attributes[:'kind_label']
-      else
-        self.kind_label = nil
-      end
-
-      if attributes.key?(:'evidence_tier')
-        self.evidence_tier = attributes[:'evidence_tier']
-      else
-        self.evidence_tier = nil
-      end
-
-      if attributes.key?(:'evidence_tier_label')
-        self.evidence_tier_label = attributes[:'evidence_tier_label']
-      else
-        self.evidence_tier_label = nil
       end
 
       if attributes.key?(:'has_clinical_validation_evidence')
         self.has_clinical_validation_evidence = attributes[:'has_clinical_validation_evidence']
-      else
-        self.has_clinical_validation_evidence = nil
       end
 
       if attributes.key?(:'has_analytical_validation_evidence')
         self.has_analytical_validation_evidence = attributes[:'has_analytical_validation_evidence']
-      else
-        self.has_analytical_validation_evidence = nil
       end
 
       if attributes.key?(:'n_assay_provider_papers')
         self.n_assay_provider_papers = attributes[:'n_assay_provider_papers']
-      else
-        self.n_assay_provider_papers = nil
       end
 
       if attributes.key?(:'n_assay_provider_suppliers')
         self.n_assay_provider_suppliers = attributes[:'n_assay_provider_suppliers']
-      else
-        self.n_assay_provider_suppliers = nil
       end
 
       if attributes.key?(:'n_diagnostic_provider_suppliers')
         self.n_diagnostic_provider_suppliers = attributes[:'n_diagnostic_provider_suppliers']
-      else
-        self.n_diagnostic_provider_suppliers = nil
       end
     end
 
@@ -272,58 +326,6 @@ module PharmaObservatory
     def list_invalid_properties
       warn '[DEPRECATED] the `list_invalid_properties` method is obsolete'
       invalid_properties = Array.new
-      if @route_key.nil?
-        invalid_properties.push('invalid value for "route_key", route_key cannot be nil.')
-      end
-
-      if @display_name.nil?
-        invalid_properties.push('invalid value for "display_name", display_name cannot be nil.')
-      end
-
-      if @biomarker_kind.nil?
-        invalid_properties.push('invalid value for "biomarker_kind", biomarker_kind cannot be nil.')
-      end
-
-      if @identity_status.nil?
-        invalid_properties.push('invalid value for "identity_status", identity_status cannot be nil.')
-      end
-
-      if @n_fda_cdx_assertions.nil?
-        invalid_properties.push('invalid value for "n_fda_cdx_assertions", n_fda_cdx_assertions cannot be nil.')
-      end
-
-      if @n_fda_bqp_assertions.nil?
-        invalid_properties.push('invalid value for "n_fda_bqp_assertions", n_fda_bqp_assertions cannot be nil.')
-      end
-
-      if @n_cancer_actionable_cgi.nil?
-        invalid_properties.push('invalid value for "n_cancer_actionable_cgi", n_cancer_actionable_cgi cannot be nil.')
-      end
-
-      if @n_ot_association.nil?
-        invalid_properties.push('invalid value for "n_ot_association", n_ot_association cannot be nil.')
-      end
-
-      if @n_trial_mention.nil?
-        invalid_properties.push('invalid value for "n_trial_mention", n_trial_mention cannot be nil.')
-      end
-
-      if @n_publication_variant_mentions.nil?
-        invalid_properties.push('invalid value for "n_publication_variant_mentions", n_publication_variant_mentions cannot be nil.')
-      end
-
-      if @kind_label.nil?
-        invalid_properties.push('invalid value for "kind_label", kind_label cannot be nil.')
-      end
-
-      if @evidence_tier.nil?
-        invalid_properties.push('invalid value for "evidence_tier", evidence_tier cannot be nil.')
-      end
-
-      if @evidence_tier_label.nil?
-        invalid_properties.push('invalid value for "evidence_tier_label", evidence_tier_label cannot be nil.')
-      end
-
       invalid_properties
     end
 
@@ -331,172 +333,35 @@ module PharmaObservatory
     # @return true if the model is valid
     def valid?
       warn '[DEPRECATED] the `valid?` method is obsolete'
-      return false if @route_key.nil?
-      return false if @display_name.nil?
-      return false if @biomarker_kind.nil?
-      return false if @identity_status.nil?
-      return false if @n_fda_cdx_assertions.nil?
-      return false if @n_fda_bqp_assertions.nil?
-      return false if @n_cancer_actionable_cgi.nil?
-      return false if @n_ot_association.nil?
-      return false if @n_trial_mention.nil?
-      return false if @n_publication_variant_mentions.nil?
-      return false if @kind_label.nil?
-      return false if @evidence_tier.nil?
-      return false if @evidence_tier_label.nil?
       true
     end
 
-    # Custom attribute writer method with validation
-    # @param [Object] route_key Value to be assigned
-    def route_key=(route_key)
-      if route_key.nil?
-        fail ArgumentError, 'route_key cannot be nil'
-      end
-
-      @route_key = route_key
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] display_name Value to be assigned
-    def display_name=(display_name)
-      if display_name.nil?
-        fail ArgumentError, 'display_name cannot be nil'
-      end
-
-      @display_name = display_name
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] biomarker_kind Value to be assigned
-    def biomarker_kind=(biomarker_kind)
-      if biomarker_kind.nil?
-        fail ArgumentError, 'biomarker_kind cannot be nil'
-      end
-
-      @biomarker_kind = biomarker_kind
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] identity_status Value to be assigned
-    def identity_status=(identity_status)
-      if identity_status.nil?
-        fail ArgumentError, 'identity_status cannot be nil'
-      end
-
-      @identity_status = identity_status
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] n_fda_cdx_assertions Value to be assigned
-    def n_fda_cdx_assertions=(n_fda_cdx_assertions)
-      if n_fda_cdx_assertions.nil?
-        fail ArgumentError, 'n_fda_cdx_assertions cannot be nil'
-      end
-
-      @n_fda_cdx_assertions = n_fda_cdx_assertions
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] n_fda_bqp_assertions Value to be assigned
-    def n_fda_bqp_assertions=(n_fda_bqp_assertions)
-      if n_fda_bqp_assertions.nil?
-        fail ArgumentError, 'n_fda_bqp_assertions cannot be nil'
-      end
-
-      @n_fda_bqp_assertions = n_fda_bqp_assertions
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] n_cancer_actionable_cgi Value to be assigned
-    def n_cancer_actionable_cgi=(n_cancer_actionable_cgi)
-      if n_cancer_actionable_cgi.nil?
-        fail ArgumentError, 'n_cancer_actionable_cgi cannot be nil'
-      end
-
-      @n_cancer_actionable_cgi = n_cancer_actionable_cgi
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] n_ot_association Value to be assigned
-    def n_ot_association=(n_ot_association)
-      if n_ot_association.nil?
-        fail ArgumentError, 'n_ot_association cannot be nil'
-      end
-
-      @n_ot_association = n_ot_association
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] n_trial_mention Value to be assigned
-    def n_trial_mention=(n_trial_mention)
-      if n_trial_mention.nil?
-        fail ArgumentError, 'n_trial_mention cannot be nil'
-      end
-
-      @n_trial_mention = n_trial_mention
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] n_publication_variant_mentions Value to be assigned
-    def n_publication_variant_mentions=(n_publication_variant_mentions)
-      if n_publication_variant_mentions.nil?
-        fail ArgumentError, 'n_publication_variant_mentions cannot be nil'
-      end
-
-      @n_publication_variant_mentions = n_publication_variant_mentions
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] kind_label Value to be assigned
-    def kind_label=(kind_label)
-      if kind_label.nil?
-        fail ArgumentError, 'kind_label cannot be nil'
-      end
-
-      @kind_label = kind_label
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] evidence_tier Value to be assigned
-    def evidence_tier=(evidence_tier)
-      if evidence_tier.nil?
-        fail ArgumentError, 'evidence_tier cannot be nil'
-      end
-
-      @evidence_tier = evidence_tier
-    end
-
-    # Custom attribute writer method with validation
-    # @param [Object] evidence_tier_label Value to be assigned
-    def evidence_tier_label=(evidence_tier_label)
-      if evidence_tier_label.nil?
-        fail ArgumentError, 'evidence_tier_label cannot be nil'
-      end
-
-      @evidence_tier_label = evidence_tier_label
-    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_id == o.biomarker_id &&
           route_key == o.route_key &&
-          display_name == o.display_name &&
           biomarker_kind == o.biomarker_kind &&
           identity_status == o.identity_status &&
+          display_name == o.display_name &&
+          parent_biomarker_id == o.parent_biomarker_id &&
           gene_symbol == o.gene_symbol &&
           amino_acid_change == o.amino_acid_change &&
+          target_id == o.target_id &&
+          hgnc_id == o.hgnc_id &&
+          uniprot_accession == o.uniprot_accession &&
+          feature_code == o.feature_code &&
+          feature_type == o.feature_type &&
+          evidence_tier == o.evidence_tier &&
+          evidence_tier_label == o.evidence_tier_label &&
           n_fda_cdx_assertions == o.n_fda_cdx_assertions &&
           n_fda_bqp_assertions == o.n_fda_bqp_assertions &&
           n_cancer_actionable_cgi == o.n_cancer_actionable_cgi &&
           n_ot_association == o.n_ot_association &&
           n_trial_mention == o.n_trial_mention &&
           n_publication_variant_mentions == o.n_publication_variant_mentions &&
-          kind_label == o.kind_label &&
-          evidence_tier == o.evidence_tier &&
-          evidence_tier_label == o.evidence_tier_label &&
           has_clinical_validation_evidence == o.has_clinical_validation_evidence &&
           has_analytical_validation_evidence == o.has_analytical_validation_evidence &&
           n_assay_provider_papers == o.n_assay_provider_papers &&
@@ -513,7 +378,7 @@ module PharmaObservatory
     # Calculates hash code according to all attributes.
     # @return [Integer] Hash code
     def hash
-      [route_key, display_name, biomarker_kind, identity_status, gene_symbol, amino_acid_change, n_fda_cdx_assertions, n_fda_bqp_assertions, n_cancer_actionable_cgi, n_ot_association, n_trial_mention, n_publication_variant_mentions, kind_label, evidence_tier, evidence_tier_label, has_clinical_validation_evidence, has_analytical_validation_evidence, n_assay_provider_papers, n_assay_provider_suppliers, n_diagnostic_provider_suppliers].hash
+      [biomarker_id, route_key, biomarker_kind, identity_status, display_name, parent_biomarker_id, gene_symbol, amino_acid_change, target_id, hgnc_id, uniprot_accession, feature_code, feature_type, evidence_tier, evidence_tier_label, n_fda_cdx_assertions, n_fda_bqp_assertions, n_cancer_actionable_cgi, n_ot_association, n_trial_mention, n_publication_variant_mentions, has_clinical_validation_evidence, has_analytical_validation_evidence, n_assay_provider_papers, n_assay_provider_suppliers, n_diagnostic_provider_suppliers].hash
     end
 
     # Builds the object from hash