pharmaobservatory 0.1.7 → 0.1.9

data/lib/pharmaobservatory/models/biomarker_assay_providers_row.rb

@@ -0,0 +1,520 @@
+=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_assay_providers dataset: one row per biomarker key and assay-provider company name key. A grouped request returns the group columns and the measures instead, as additional properties.
+  class BiomarkerAssayProvidersRow
+    # The route key of the gene the biomarker resolved to, the entry key for the biomarkers object type. Null when the extraction did not resolve a gene.
+    attr_accessor :route_key
+
+    # The grouping key of the biomarker. The biomarker's key when its gene resolved, otherwise raw: followed by the lower-cased name as written, so two spellings of one unresolved biomarker are two keys.
+    attr_accessor :biomarker_key
+
+    # The biomarker's own key; null for a pair whose gene did not resolve.
+    attr_accessor :biomarker_id
+
+    # The biomarker's name, as resolved or else as extracted.
+    attr_accessor :biomarker_display_name
+
+    # resolved: the gene resolved. unresolved: a gene symbol was extracted and matched nothing. not_applicable: no gene symbol was extracted.
+    attr_accessor :gene_resolution_status
+
+    # The normalised company name the provider rows are grouped on.
+    attr_accessor :company_name_key
+
+    # The provider company name as it appears in the papers.
+    attr_accessor :provider_name
+
+    # The provider's legal entity key, where the marketplace match resolves one.
+    attr_accessor :provider_org_id
+
+    # The provider's company key.
+    attr_accessor :provider_company_id
+
+    # The provider's company name.
+    attr_accessor :provider_company_name
+
+    # The provider's current ultimate parent group key.
+    attr_accessor :provider_group_id
+
+    # The provider's group name.
+    attr_accessor :provider_group_name
+
+    # Whether the provider name matches a supplier in the Scientist.com marketplace.
+    attr_accessor :rx_matched
+
+    # The matched marketplace supplier's id; join to the suppliers dataset.
+    attr_accessor :rx_provider_id
+
+    # The matched marketplace supplier's name.
+    attr_accessor :rx_provider_name
+
+    # The matched supplier's marketplace profile slug.
+    attr_accessor :rx_provider_slug
+
+    # Whether any paper for the pair mentions clinical validation of the assay.
+    attr_accessor :has_clinical_validation
+
+    # Whether any paper for the pair mentions analytical validation of the assay.
+    attr_accessor :has_analytical_validation
+
+    # Papers naming the biomarker and the provider, dated or not.
+    attr_accessor :n_papers
+
+    # Papers with a recoverable publication date.
+    attr_accessor :n_dated_papers
+
+    # Papers with no recoverable publication date. n_dated_papers plus n_undated_papers is n_papers.
+    attr_accessor :n_undated_papers
+
+    # The latest publication date among the dated papers, in UTC. Null when no paper is dated, which is not a statement that none was published recently.
+    attr_accessor :most_recent_published_at
+
+    # The PubMed id of the most recent dated paper.
+    attr_accessor :most_recent_pmid
+
+    # The title of that paper.
+    attr_accessor :most_recent_title
+
+    # True when the provider matches a marketplace supplier or at least two papers name the pair.
+    attr_accessor :meets_curated_threshold
+
+    # The company-level class. diagnostic_provider makes or supplies the diagnostic assay; reagent_supplier is the vendor whose kit appears in a methods section; context_dependent, pharma_or_other and not_a_company are the other decisions; unclassified means no decision yet.
+    attr_accessor :assay_provider_class
+
+    # Where the class decision came from; null when unclassified.
+    attr_accessor :assay_provider_class_source
+
+    # When the class was decided, in UTC; null when unclassified.
+    attr_accessor :assay_provider_class_decided_at
+
+    # Attribute mapping from ruby-style variable name to JSON key.
+    def self.attribute_map
+      {
+        :'route_key' => :'route_key',
+        :'biomarker_key' => :'biomarker_key',
+        :'biomarker_id' => :'biomarker_id',
+        :'biomarker_display_name' => :'biomarker_display_name',
+        :'gene_resolution_status' => :'gene_resolution_status',
+        :'company_name_key' => :'company_name_key',
+        :'provider_name' => :'provider_name',
+        :'provider_org_id' => :'provider_org_id',
+        :'provider_company_id' => :'provider_company_id',
+        :'provider_company_name' => :'provider_company_name',
+        :'provider_group_id' => :'provider_group_id',
+        :'provider_group_name' => :'provider_group_name',
+        :'rx_matched' => :'rx_matched',
+        :'rx_provider_id' => :'rx_provider_id',
+        :'rx_provider_name' => :'rx_provider_name',
+        :'rx_provider_slug' => :'rx_provider_slug',
+        :'has_clinical_validation' => :'has_clinical_validation',
+        :'has_analytical_validation' => :'has_analytical_validation',
+        :'n_papers' => :'n_papers',
+        :'n_dated_papers' => :'n_dated_papers',
+        :'n_undated_papers' => :'n_undated_papers',
+        :'most_recent_published_at' => :'most_recent_published_at',
+        :'most_recent_pmid' => :'most_recent_pmid',
+        :'most_recent_title' => :'most_recent_title',
+        :'meets_curated_threshold' => :'meets_curated_threshold',
+        :'assay_provider_class' => :'assay_provider_class',
+        :'assay_provider_class_source' => :'assay_provider_class_source',
+        :'assay_provider_class_decided_at' => :'assay_provider_class_decided_at'
+      }
+    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
+      {
+        :'route_key' => :'String',
+        :'biomarker_key' => :'String',
+        :'biomarker_id' => :'String',
+        :'biomarker_display_name' => :'String',
+        :'gene_resolution_status' => :'String',
+        :'company_name_key' => :'String',
+        :'provider_name' => :'String',
+        :'provider_org_id' => :'String',
+        :'provider_company_id' => :'String',
+        :'provider_company_name' => :'String',
+        :'provider_group_id' => :'String',
+        :'provider_group_name' => :'String',
+        :'rx_matched' => :'Boolean',
+        :'rx_provider_id' => :'String',
+        :'rx_provider_name' => :'String',
+        :'rx_provider_slug' => :'String',
+        :'has_clinical_validation' => :'Boolean',
+        :'has_analytical_validation' => :'Boolean',
+        :'n_papers' => :'Integer',
+        :'n_dated_papers' => :'Integer',
+        :'n_undated_papers' => :'Integer',
+        :'most_recent_published_at' => :'Time',
+        :'most_recent_pmid' => :'String',
+        :'most_recent_title' => :'String',
+        :'meets_curated_threshold' => :'Boolean',
+        :'assay_provider_class' => :'String',
+        :'assay_provider_class_source' => :'String',
+        :'assay_provider_class_decided_at' => :'Time'
+      }
+    end
+
+    # List of attributes with nullable: true
+    def self.openapi_nullable
+      Set.new([
+        :'route_key',
+        :'biomarker_key',
+        :'biomarker_id',
+        :'biomarker_display_name',
+        :'gene_resolution_status',
+        :'company_name_key',
+        :'provider_name',
+        :'provider_org_id',
+        :'provider_company_id',
+        :'provider_company_name',
+        :'provider_group_id',
+        :'provider_group_name',
+        :'rx_matched',
+        :'rx_provider_id',
+        :'rx_provider_name',
+        :'rx_provider_slug',
+        :'has_clinical_validation',
+        :'has_analytical_validation',
+        :'n_papers',
+        :'n_dated_papers',
+        :'n_undated_papers',
+        :'most_recent_published_at',
+        :'most_recent_pmid',
+        :'most_recent_title',
+        :'meets_curated_threshold',
+        :'assay_provider_class',
+        :'assay_provider_class_source',
+        :'assay_provider_class_decided_at'
+      ])
+    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::BiomarkerAssayProvidersRow` 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::BiomarkerAssayProvidersRow`. 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']
+      end
+
+      if attributes.key?(:'biomarker_key')
+        self.biomarker_key = attributes[:'biomarker_key']
+      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?(:'gene_resolution_status')
+        self.gene_resolution_status = attributes[:'gene_resolution_status']
+      end
+
+      if attributes.key?(:'company_name_key')
+        self.company_name_key = attributes[:'company_name_key']
+      end
+
+      if attributes.key?(:'provider_name')
+        self.provider_name = attributes[:'provider_name']
+      end
+
+      if attributes.key?(:'provider_org_id')
+        self.provider_org_id = attributes[:'provider_org_id']
+      end
+
+      if attributes.key?(:'provider_company_id')
+        self.provider_company_id = attributes[:'provider_company_id']
+      end
+
+      if attributes.key?(:'provider_company_name')
+        self.provider_company_name = attributes[:'provider_company_name']
+      end
+
+      if attributes.key?(:'provider_group_id')
+        self.provider_group_id = attributes[:'provider_group_id']
+      end
+
+      if attributes.key?(:'provider_group_name')
+        self.provider_group_name = attributes[:'provider_group_name']
+      end
+
+      if attributes.key?(:'rx_matched')
+        self.rx_matched = attributes[:'rx_matched']
+      end
+
+      if attributes.key?(:'rx_provider_id')
+        self.rx_provider_id = attributes[:'rx_provider_id']
+      end
+
+      if attributes.key?(:'rx_provider_name')
+        self.rx_provider_name = attributes[:'rx_provider_name']
+      end
+
+      if attributes.key?(:'rx_provider_slug')
+        self.rx_provider_slug = attributes[:'rx_provider_slug']
+      end
+
+      if attributes.key?(:'has_clinical_validation')
+        self.has_clinical_validation = attributes[:'has_clinical_validation']
+      end
+
+      if attributes.key?(:'has_analytical_validation')
+        self.has_analytical_validation = attributes[:'has_analytical_validation']
+      end
+
+      if attributes.key?(:'n_papers')
+        self.n_papers = attributes[:'n_papers']
+      end
+
+      if attributes.key?(:'n_dated_papers')
+        self.n_dated_papers = attributes[:'n_dated_papers']
+      end
+
+      if attributes.key?(:'n_undated_papers')
+        self.n_undated_papers = attributes[:'n_undated_papers']
+      end
+
+      if attributes.key?(:'most_recent_published_at')
+        self.most_recent_published_at = attributes[:'most_recent_published_at']
+      end
+
+      if attributes.key?(:'most_recent_pmid')
+        self.most_recent_pmid = attributes[:'most_recent_pmid']
+      end
+
+      if attributes.key?(:'most_recent_title')
+        self.most_recent_title = attributes[:'most_recent_title']
+      end
+
+      if attributes.key?(:'meets_curated_threshold')
+        self.meets_curated_threshold = attributes[:'meets_curated_threshold']
+      end
+
+      if attributes.key?(:'assay_provider_class')
+        self.assay_provider_class = attributes[:'assay_provider_class']
+      end
+
+      if attributes.key?(:'assay_provider_class_source')
+        self.assay_provider_class_source = attributes[:'assay_provider_class_source']
+      end
+
+      if attributes.key?(:'assay_provider_class_decided_at')
+        self.assay_provider_class_decided_at = attributes[:'assay_provider_class_decided_at']
+      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 &&
+          route_key == o.route_key &&
+          biomarker_key == o.biomarker_key &&
+          biomarker_id == o.biomarker_id &&
+          biomarker_display_name == o.biomarker_display_name &&
+          gene_resolution_status == o.gene_resolution_status &&
+          company_name_key == o.company_name_key &&
+          provider_name == o.provider_name &&
+          provider_org_id == o.provider_org_id &&
+          provider_company_id == o.provider_company_id &&
+          provider_company_name == o.provider_company_name &&
+          provider_group_id == o.provider_group_id &&
+          provider_group_name == o.provider_group_name &&
+          rx_matched == o.rx_matched &&
+          rx_provider_id == o.rx_provider_id &&
+          rx_provider_name == o.rx_provider_name &&
+          rx_provider_slug == o.rx_provider_slug &&
+          has_clinical_validation == o.has_clinical_validation &&
+          has_analytical_validation == o.has_analytical_validation &&
+          n_papers == o.n_papers &&
+          n_dated_papers == o.n_dated_papers &&
+          n_undated_papers == o.n_undated_papers &&
+          most_recent_published_at == o.most_recent_published_at &&
+          most_recent_pmid == o.most_recent_pmid &&
+          most_recent_title == o.most_recent_title &&
+          meets_curated_threshold == o.meets_curated_threshold &&
+          assay_provider_class == o.assay_provider_class &&
+          assay_provider_class_source == o.assay_provider_class_source &&
+          assay_provider_class_decided_at == o.assay_provider_class_decided_at
+    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
+      [route_key, biomarker_key, biomarker_id, biomarker_display_name, gene_resolution_status, company_name_key, provider_name, provider_org_id, provider_company_id, provider_company_name, provider_group_id, provider_group_name, rx_matched, rx_provider_id, rx_provider_name, rx_provider_slug, has_clinical_validation, has_analytical_validation, n_papers, n_dated_papers, n_undated_papers, most_recent_published_at, most_recent_pmid, most_recent_title, meets_curated_threshold, assay_provider_class, assay_provider_class_source, assay_provider_class_decided_at].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/biomarker_assay_whitespace_response.rb

@@ -102,7 +102,7 @@ module PharmaObservatory
         :'grain' => :'String',
         :'object_type' => :'String',
         :'id' => :'String',
-        :'scope' => :'BiomarkerAssayEvidenceResponseScope',
+        :'scope' => :'AnimalWelfareAssurancesResponseScope',
         :'columns' => :'Array<DatasetColumn>',
         :'rows' => :'Array<BiomarkerAssayWhitespaceRow>',
         :'total' => :'Integer',
@@ -115,8 +115,8 @@ module PharmaObservatory
         :'source_credit' => :'String',
         :'withheld_tiers' => :'Array<String>',
         :'withheld_columns' => :'Array<String>',
-        :'freshness' => :'BiomarkerAssayEvidenceResponseFreshness',
-        :'build' => :'BiomarkerAssayEvidenceResponseBuild',
+        :'freshness' => :'AnimalWelfareAssurancesResponseFreshness',
+        :'build' => :'AnimalWelfareAssurancesResponseBuild',
         :'build_state' => :'DatasetBuildState',
         :'restriction' => :'Hash<String, Object>'
       }

data/lib/pharmaobservatory/models/biomarker_bqp_assertions_response.rb

@@ -102,7 +102,7 @@ module PharmaObservatory
         :'grain' => :'String',
         :'object_type' => :'String',
         :'id' => :'String',
-        :'scope' => :'BiomarkerAssayEvidenceResponseScope',
+        :'scope' => :'AnimalWelfareAssurancesResponseScope',
         :'columns' => :'Array<DatasetColumn>',
         :'rows' => :'Array<BiomarkerBqpAssertionsRow>',
         :'total' => :'Integer',
@@ -115,8 +115,8 @@ module PharmaObservatory
         :'source_credit' => :'String',
         :'withheld_tiers' => :'Array<String>',
         :'withheld_columns' => :'Array<String>',
-        :'freshness' => :'BiomarkerAssayEvidenceResponseFreshness',
-        :'build' => :'BiomarkerAssayEvidenceResponseBuild',
+        :'freshness' => :'AnimalWelfareAssurancesResponseFreshness',
+        :'build' => :'AnimalWelfareAssurancesResponseBuild',
         :'build_state' => :'DatasetBuildState',
         :'restriction' => :'Hash<String, Object>'
       }

data/lib/pharmaobservatory/models/biomarker_cdx_assertions_response.rb

@@ -102,7 +102,7 @@ module PharmaObservatory
         :'grain' => :'String',
         :'object_type' => :'String',
         :'id' => :'String',
-        :'scope' => :'BiomarkerAssayEvidenceResponseScope',
+        :'scope' => :'AnimalWelfareAssurancesResponseScope',
         :'columns' => :'Array<DatasetColumn>',
         :'rows' => :'Array<BiomarkerCdxAssertionsRow>',
         :'total' => :'Integer',
@@ -115,8 +115,8 @@ module PharmaObservatory
         :'source_credit' => :'String',
         :'withheld_tiers' => :'Array<String>',
         :'withheld_columns' => :'Array<String>',
-        :'freshness' => :'BiomarkerAssayEvidenceResponseFreshness',
-        :'build' => :'BiomarkerAssayEvidenceResponseBuild',
+        :'freshness' => :'AnimalWelfareAssurancesResponseFreshness',
+        :'build' => :'AnimalWelfareAssurancesResponseBuild',
         :'build_state' => :'DatasetBuildState',
         :'restriction' => :'Hash<String, Object>'
       }