pharmaobservatory 0.1.3 → 0.1.4

data/lib/pharmaobservatory/models/biomarker_validation_row.rb

@@ -0,0 +1,509 @@
+=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_validation dataset: one row per evidence assertion on a gene. A grouped request returns the group columns and the measures instead, as additional properties.
+  class BiomarkerValidationRow
+    # The evidence assertion id.
+    attr_accessor :biomarker_validation_id
+
+    # The biomarker's route key, the entry key for the biomarkers object type; for a gene it is the gene symbol.
+    attr_accessor :route_key
+
+    # The gene symbol (HGNC, the HUGO Gene Nomenclature Committee).
+    attr_accessor :gene_symbol
+
+    # The biomarker key.
+    attr_accessor :biomarker_id
+
+    # The biomarker's display name.
+    attr_accessor :biomarker_display_name
+
+    # The kind of biomarker the evidence is filed against.
+    attr_accessor :biomarker_kind
+
+    # The organization that can supply the evidence, as the source names it (null when the source names none that resolved).
+    attr_accessor :organization_name
+
+    # Legal-entity level: the organization record (null when unresolved).
+    attr_accessor :organization_org_id
+
+    # Company level: the organization's company (null when unresolved).
+    attr_accessor :organization_company_id
+
+    # Display name of the organization's company.
+    attr_accessor :organization_company_name
+
+    # Group level: the organization's current ultimate parent; a root's group is itself.
+    attr_accessor :organization_group_id
+
+    # Display name of the organization's group.
+    attr_accessor :organization_group_name
+
+    # What the organization is to the evidence: lead_sponsor, collaborator, contract_vendor, assay_manufacturer, qualification_submitter, testing_lab or publishing_org.
+    attr_accessor :organization_role
+
+    # How the organization name matched an organization record.
+    attr_accessor :organization_match_tier
+
+    # The rung on the validation ladder, 1 to 4. A rung is a kind of evidence, never a score: rows are not ranked across organizations or evidence types.
+    attr_accessor :tier
+
+    # The rung's name, for example fda_authorized_companion_diagnostic or named_in_inclusion_criteria.
+    attr_accessor :tier_label
+
+    # The evidence lane: fda_bqp_qualification, fda_cdx_authorization, aact_endpoint_role, aact_eligibility_section, aact_biospecimen, trial_mention or clinvar_clinical_testing.
+    attr_accessor :evidence_type
+
+    # Sibling rows sharing this biomarker, organization and role. Not the number of source records behind a ClinVar row (clinvar_scv_count).
+    attr_accessor :evidence_count
+
+    # The source reference the row cites.
+    attr_accessor :evidence_ref
+
+    # What kind of reference evidence_ref is.
+    attr_accessor :evidence_ref_kind
+
+    # The trial key (an NCT id) when the evidence is a trial; null otherwise.
+    attr_accessor :trial_id
+
+    # A link to the cited record.
+    attr_accessor :citation_url
+
+    # False for the FDA Biomarker Qualification Program arm, whose captured links are known to go stale; true otherwise. A link marked false may not resolve.
+    attr_accessor :citation_verified
+
+    # The text span the evidence rests on, where the source gives one.
+    attr_accessor :evidence_snippet
+
+    # The biomarker's role in the evidence, where the source states it.
+    attr_accessor :biomarker_role
+
+    # True when the evidence is a claim that the biomarker is a surrogate endpoint.
+    attr_accessor :is_surrogate_endpoint_claim
+
+    # For a ClinVar row, the number of ClinVar submission records the row collapses; null otherwise.
+    attr_accessor :clinvar_scv_count
+
+    # Attribute mapping from ruby-style variable name to JSON key.
+    def self.attribute_map
+      {
+        :'biomarker_validation_id' => :'biomarker_validation_id',
+        :'route_key' => :'route_key',
+        :'gene_symbol' => :'gene_symbol',
+        :'biomarker_id' => :'biomarker_id',
+        :'biomarker_display_name' => :'biomarker_display_name',
+        :'biomarker_kind' => :'biomarker_kind',
+        :'organization_name' => :'organization_name',
+        :'organization_org_id' => :'organization_org_id',
+        :'organization_company_id' => :'organization_company_id',
+        :'organization_company_name' => :'organization_company_name',
+        :'organization_group_id' => :'organization_group_id',
+        :'organization_group_name' => :'organization_group_name',
+        :'organization_role' => :'organization_role',
+        :'organization_match_tier' => :'organization_match_tier',
+        :'tier' => :'tier',
+        :'tier_label' => :'tier_label',
+        :'evidence_type' => :'evidence_type',
+        :'evidence_count' => :'evidence_count',
+        :'evidence_ref' => :'evidence_ref',
+        :'evidence_ref_kind' => :'evidence_ref_kind',
+        :'trial_id' => :'trial_id',
+        :'citation_url' => :'citation_url',
+        :'citation_verified' => :'citation_verified',
+        :'evidence_snippet' => :'evidence_snippet',
+        :'biomarker_role' => :'biomarker_role',
+        :'is_surrogate_endpoint_claim' => :'is_surrogate_endpoint_claim',
+        :'clinvar_scv_count' => :'clinvar_scv_count'
+      }
+    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
+      {
+        :'biomarker_validation_id' => :'String',
+        :'route_key' => :'String',
+        :'gene_symbol' => :'String',
+        :'biomarker_id' => :'String',
+        :'biomarker_display_name' => :'String',
+        :'biomarker_kind' => :'String',
+        :'organization_name' => :'String',
+        :'organization_org_id' => :'String',
+        :'organization_company_id' => :'String',
+        :'organization_company_name' => :'String',
+        :'organization_group_id' => :'String',
+        :'organization_group_name' => :'String',
+        :'organization_role' => :'String',
+        :'organization_match_tier' => :'String',
+        :'tier' => :'Integer',
+        :'tier_label' => :'String',
+        :'evidence_type' => :'String',
+        :'evidence_count' => :'Integer',
+        :'evidence_ref' => :'String',
+        :'evidence_ref_kind' => :'String',
+        :'trial_id' => :'String',
+        :'citation_url' => :'String',
+        :'citation_verified' => :'Boolean',
+        :'evidence_snippet' => :'String',
+        :'biomarker_role' => :'String',
+        :'is_surrogate_endpoint_claim' => :'Boolean',
+        :'clinvar_scv_count' => :'Integer'
+      }
+    end
+
+    # List of attributes with nullable: true
+    def self.openapi_nullable
+      Set.new([
+        :'biomarker_validation_id',
+        :'route_key',
+        :'gene_symbol',
+        :'biomarker_id',
+        :'biomarker_display_name',
+        :'biomarker_kind',
+        :'organization_name',
+        :'organization_org_id',
+        :'organization_company_id',
+        :'organization_company_name',
+        :'organization_group_id',
+        :'organization_group_name',
+        :'organization_role',
+        :'organization_match_tier',
+        :'tier',
+        :'tier_label',
+        :'evidence_type',
+        :'evidence_count',
+        :'evidence_ref',
+        :'evidence_ref_kind',
+        :'trial_id',
+        :'citation_url',
+        :'citation_verified',
+        :'evidence_snippet',
+        :'biomarker_role',
+        :'is_surrogate_endpoint_claim',
+        :'clinvar_scv_count'
+      ])
+    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::BiomarkerValidationRow` 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::BiomarkerValidationRow`. 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_validation_id')
+        self.biomarker_validation_id = attributes[:'biomarker_validation_id']
+      end
+
+      if attributes.key?(:'route_key')
+        self.route_key = attributes[:'route_key']
+      end
+
+      if attributes.key?(:'gene_symbol')
+        self.gene_symbol = attributes[:'gene_symbol']
+      end
+
+      if attributes.key?(:'biomarker_id')
+        self.biomarker_id = attributes[:'biomarker_id']
+      end
+
+      if attributes.key?(:'biomarker_display_name')
+        self.biomarker_display_name = attributes[:'biomarker_display_name']
+      end
+
+      if attributes.key?(:'biomarker_kind')
+        self.biomarker_kind = attributes[:'biomarker_kind']
+      end
+
+      if attributes.key?(:'organization_name')
+        self.organization_name = attributes[:'organization_name']
+      end
+
+      if attributes.key?(:'organization_org_id')
+        self.organization_org_id = attributes[:'organization_org_id']
+      end
+
+      if attributes.key?(:'organization_company_id')
+        self.organization_company_id = attributes[:'organization_company_id']
+      end
+
+      if attributes.key?(:'organization_company_name')
+        self.organization_company_name = attributes[:'organization_company_name']
+      end
+
+      if attributes.key?(:'organization_group_id')
+        self.organization_group_id = attributes[:'organization_group_id']
+      end
+
+      if attributes.key?(:'organization_group_name')
+        self.organization_group_name = attributes[:'organization_group_name']
+      end
+
+      if attributes.key?(:'organization_role')
+        self.organization_role = attributes[:'organization_role']
+      end
+
+      if attributes.key?(:'organization_match_tier')
+        self.organization_match_tier = attributes[:'organization_match_tier']
+      end
+
+      if attributes.key?(:'tier')
+        self.tier = attributes[:'tier']
+      end
+
+      if attributes.key?(:'tier_label')
+        self.tier_label = attributes[:'tier_label']
+      end
+
+      if attributes.key?(:'evidence_type')
+        self.evidence_type = attributes[:'evidence_type']
+      end
+
+      if attributes.key?(:'evidence_count')
+        self.evidence_count = attributes[:'evidence_count']
+      end
+
+      if attributes.key?(:'evidence_ref')
+        self.evidence_ref = attributes[:'evidence_ref']
+      end
+
+      if attributes.key?(:'evidence_ref_kind')
+        self.evidence_ref_kind = attributes[:'evidence_ref_kind']
+      end
+
+      if attributes.key?(:'trial_id')
+        self.trial_id = attributes[:'trial_id']
+      end
+
+      if attributes.key?(:'citation_url')
+        self.citation_url = attributes[:'citation_url']
+      end
+
+      if attributes.key?(:'citation_verified')
+        self.citation_verified = attributes[:'citation_verified']
+      end
+
+      if attributes.key?(:'evidence_snippet')
+        self.evidence_snippet = attributes[:'evidence_snippet']
+      end
+
+      if attributes.key?(:'biomarker_role')
+        self.biomarker_role = attributes[:'biomarker_role']
+      end
+
+      if attributes.key?(:'is_surrogate_endpoint_claim')
+        self.is_surrogate_endpoint_claim = attributes[:'is_surrogate_endpoint_claim']
+      end
+
+      if attributes.key?(:'clinvar_scv_count')
+        self.clinvar_scv_count = attributes[:'clinvar_scv_count']
+      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 &&
+          biomarker_validation_id == o.biomarker_validation_id &&
+          route_key == o.route_key &&
+          gene_symbol == o.gene_symbol &&
+          biomarker_id == o.biomarker_id &&
+          biomarker_display_name == o.biomarker_display_name &&
+          biomarker_kind == o.biomarker_kind &&
+          organization_name == o.organization_name &&
+          organization_org_id == o.organization_org_id &&
+          organization_company_id == o.organization_company_id &&
+          organization_company_name == o.organization_company_name &&
+          organization_group_id == o.organization_group_id &&
+          organization_group_name == o.organization_group_name &&
+          organization_role == o.organization_role &&
+          organization_match_tier == o.organization_match_tier &&
+          tier == o.tier &&
+          tier_label == o.tier_label &&
+          evidence_type == o.evidence_type &&
+          evidence_count == o.evidence_count &&
+          evidence_ref == o.evidence_ref &&
+          evidence_ref_kind == o.evidence_ref_kind &&
+          trial_id == o.trial_id &&
+          citation_url == o.citation_url &&
+          citation_verified == o.citation_verified &&
+          evidence_snippet == o.evidence_snippet &&
+          biomarker_role == o.biomarker_role &&
+          is_surrogate_endpoint_claim == o.is_surrogate_endpoint_claim &&
+          clinvar_scv_count == o.clinvar_scv_count
+    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
+      [biomarker_validation_id, route_key, gene_symbol, biomarker_id, biomarker_display_name, biomarker_kind, organization_name, organization_org_id, organization_company_id, organization_company_name, organization_group_id, organization_group_name, organization_role, organization_match_tier, tier, tier_label, evidence_type, evidence_count, evidence_ref, evidence_ref_kind, trial_id, citation_url, citation_verified, evidence_snippet, biomarker_role, is_surrogate_endpoint_claim, clinvar_scv_count].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/biomarkers_row.rb

@@ -43,7 +43,7 @@ module PharmaObservatory
     # The target's Ensembl gene id.
     attr_accessor :target_id
 
-    # The HGNC gene id.
+    # The HUGO Gene Nomenclature Committee (HGNC) gene id.
     attr_accessor :hgnc_id
 
     # The UniProt accession.
@@ -55,7 +55,7 @@ module PharmaObservatory
     # Feature type for a non-gene feature.
     attr_accessor :feature_type
 
-    # Strongest evidence tier: 1 FDA companion diagnostic through 6 no evidence.
+    # Strongest evidence tier: 1 companion diagnostic of the US Food and Drug Administration (FDA) through 6 no evidence.
     attr_accessor :evidence_tier
 
     # The tier's name.

data/lib/pharmaobservatory/models/cell_lines_row.rb

@@ -67,7 +67,7 @@ module PharmaObservatory
     # The Cellosaurus comment, for a problematic line.
     attr_accessor :problematic_comment
 
-    # ICLAC registration ids.
+    # International Cell Line Authentication Committee (ICLAC) registration ids.
     attr_accessor :iclac_registration_ids
 
     # The Cellosaurus release the check ran against.

data/lib/pharmaobservatory/models/companies_record.rb

@@ -70,7 +70,7 @@ module PharmaObservatory
         :'object_type' => :'String',
         :'id' => :'String',
         :'record' => :'CompaniesRow',
-        :'attributes' => :'Object',
+        :'attributes' => :'CompaniesRecordAttributes',
         :'datasets' => :'Array<DatasetListing>',
         :'attribution' => :'Array<DatasetAttribution>',
         :'source_credit' => :'String',