pharmaobservatory 0.1.4 → 0.1.6

data/lib/pharmaobservatory/models/biomarker_assay_evidence_row.rb

@@ -0,0 +1,506 @@
+=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_evidence dataset: one row per extracted biomarker mention in a PubMed paper. A grouped request returns the group columns and the measures instead, as additional properties.
+  class BiomarkerAssayEvidenceRow
+    # The extracted mention's id.
+    attr_accessor :biomarker_assay_evidence_id
+
+    # The route key of the gene the mention resolved to, the entry key for the biomarkers object type. Null when the gene did not resolve.
+    attr_accessor :route_key
+
+    # The resolved gene's biomarker key. Null when the gene did not resolve.
+    attr_accessor :biomarker_id
+
+    # The id of the source document the facts were extracted from.
+    attr_accessor :document_id
+
+    # The PubMed id of the paper.
+    attr_accessor :pmid
+
+    # The position of the mention in the paper's extracted biomarker list, from 1.
+    attr_accessor :biomarker_ordinal
+
+    # The biomarker name as extracted.
+    attr_accessor :biomarker_name_as_extracted
+
+    # The gene symbol as extracted, before resolution. Null when the mention names no gene.
+    attr_accessor :gene_symbol_as_extracted
+
+    # The synonyms the paper gives, a document-level list repeated on each of its rows.
+    attr_accessor :biomarker_synonyms
+
+    # How the mention resolved to a gene. resolved_direct: exact symbol match. resolved_alias: an unambiguous dictionary alias. unresolved: a symbol was extracted that matches nothing or an ambiguous alias; not guessed. not_applicable: no gene symbol was extracted.
+    attr_accessor :gene_resolution_status
+
+    # exact_gene_symbol or dictionary_alias; null when the gene did not resolve.
+    attr_accessor :gene_resolution_method
+
+    # The assay, trade name or platform the paper names. A document-level value.
+    attr_accessor :assay_name
+
+    # The specimen type (blood, plasma, tissue). A document-level value.
+    attr_accessor :specimen_type
+
+    # The reference method the performance was measured against, when reported.
+    attr_accessor :comparator_method
+
+    # The performance as the paper states it (sensitivity, specificity, area under the curve), as text and not computed.
+    attr_accessor :reported_performance
+
+    # What the paper claims about the validation type: a fact about the text, not a tier.
+    attr_accessor :validation_type_mentioned
+
+    # Organization names as extracted that run or provide the assay. Not resolved to a company.
+    attr_accessor :assay_provider_company
+
+    # Organization names as extracted that funded the study. Never merged with the assay provider.
+    attr_accessor :funding_organizations
+
+    # Always literature_assay_validation, which tells these rows from the other evidence types.
+    attr_accessor :evidence_type
+
+    # The sentences of the paper the facts were read from. Null when the extraction gave none.
+    attr_accessor :evidence_quote
+
+    # The extraction model's self-reported confidence. Not a reliability signal: it does not track whether the extraction is correct; never use it as a quality gate.
+    attr_accessor :confidence
+
+    # The paper's title.
+    attr_accessor :title
+
+    # The paper's publication timestamp, in UTC. Null for about one paper in seven, whose source gives a bare year.
+    attr_accessor :published_at
+
+    # The model that extracted the facts.
+    attr_accessor :extraction_model
+
+    # When the facts were extracted, in UTC.
+    attr_accessor :extracted_at
+
+    # The address of the paper the facts were extracted from.
+    attr_accessor :source_url
+
+    # Attribute mapping from ruby-style variable name to JSON key.
+    def self.attribute_map
+      {
+        :'biomarker_assay_evidence_id' => :'biomarker_assay_evidence_id',
+        :'route_key' => :'route_key',
+        :'biomarker_id' => :'biomarker_id',
+        :'document_id' => :'document_id',
+        :'pmid' => :'pmid',
+        :'biomarker_ordinal' => :'biomarker_ordinal',
+        :'biomarker_name_as_extracted' => :'biomarker_name_as_extracted',
+        :'gene_symbol_as_extracted' => :'gene_symbol_as_extracted',
+        :'biomarker_synonyms' => :'biomarker_synonyms',
+        :'gene_resolution_status' => :'gene_resolution_status',
+        :'gene_resolution_method' => :'gene_resolution_method',
+        :'assay_name' => :'assay_name',
+        :'specimen_type' => :'specimen_type',
+        :'comparator_method' => :'comparator_method',
+        :'reported_performance' => :'reported_performance',
+        :'validation_type_mentioned' => :'validation_type_mentioned',
+        :'assay_provider_company' => :'assay_provider_company',
+        :'funding_organizations' => :'funding_organizations',
+        :'evidence_type' => :'evidence_type',
+        :'evidence_quote' => :'evidence_quote',
+        :'confidence' => :'confidence',
+        :'title' => :'title',
+        :'published_at' => :'published_at',
+        :'extraction_model' => :'extraction_model',
+        :'extracted_at' => :'extracted_at',
+        :'source_url' => :'source_url'
+      }
+    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_assay_evidence_id' => :'String',
+        :'route_key' => :'String',
+        :'biomarker_id' => :'String',
+        :'document_id' => :'String',
+        :'pmid' => :'String',
+        :'biomarker_ordinal' => :'Integer',
+        :'biomarker_name_as_extracted' => :'String',
+        :'gene_symbol_as_extracted' => :'String',
+        :'biomarker_synonyms' => :'Array<String>',
+        :'gene_resolution_status' => :'String',
+        :'gene_resolution_method' => :'String',
+        :'assay_name' => :'String',
+        :'specimen_type' => :'String',
+        :'comparator_method' => :'String',
+        :'reported_performance' => :'String',
+        :'validation_type_mentioned' => :'String',
+        :'assay_provider_company' => :'Array<String>',
+        :'funding_organizations' => :'Array<String>',
+        :'evidence_type' => :'String',
+        :'evidence_quote' => :'Array<String>',
+        :'confidence' => :'String',
+        :'title' => :'String',
+        :'published_at' => :'Time',
+        :'extraction_model' => :'String',
+        :'extracted_at' => :'Time',
+        :'source_url' => :'String'
+      }
+    end
+
+    # List of attributes with nullable: true
+    def self.openapi_nullable
+      Set.new([
+        :'biomarker_assay_evidence_id',
+        :'route_key',
+        :'biomarker_id',
+        :'document_id',
+        :'pmid',
+        :'biomarker_ordinal',
+        :'biomarker_name_as_extracted',
+        :'gene_symbol_as_extracted',
+        :'biomarker_synonyms',
+        :'gene_resolution_status',
+        :'gene_resolution_method',
+        :'assay_name',
+        :'specimen_type',
+        :'comparator_method',
+        :'reported_performance',
+        :'validation_type_mentioned',
+        :'assay_provider_company',
+        :'funding_organizations',
+        :'evidence_type',
+        :'evidence_quote',
+        :'confidence',
+        :'title',
+        :'published_at',
+        :'extraction_model',
+        :'extracted_at',
+        :'source_url'
+      ])
+    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::BiomarkerAssayEvidenceRow` 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::BiomarkerAssayEvidenceRow`. 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_assay_evidence_id')
+        self.biomarker_assay_evidence_id = attributes[:'biomarker_assay_evidence_id']
+      end
+
+      if attributes.key?(:'route_key')
+        self.route_key = attributes[:'route_key']
+      end
+
+      if attributes.key?(:'biomarker_id')
+        self.biomarker_id = attributes[:'biomarker_id']
+      end
+
+      if attributes.key?(:'document_id')
+        self.document_id = attributes[:'document_id']
+      end
+
+      if attributes.key?(:'pmid')
+        self.pmid = attributes[:'pmid']
+      end
+
+      if attributes.key?(:'biomarker_ordinal')
+        self.biomarker_ordinal = attributes[:'biomarker_ordinal']
+      end
+
+      if attributes.key?(:'biomarker_name_as_extracted')
+        self.biomarker_name_as_extracted = attributes[:'biomarker_name_as_extracted']
+      end
+
+      if attributes.key?(:'gene_symbol_as_extracted')
+        self.gene_symbol_as_extracted = attributes[:'gene_symbol_as_extracted']
+      end
+
+      if attributes.key?(:'biomarker_synonyms')
+        if (value = attributes[:'biomarker_synonyms']).is_a?(Array)
+          self.biomarker_synonyms = value
+        end
+      end
+
+      if attributes.key?(:'gene_resolution_status')
+        self.gene_resolution_status = attributes[:'gene_resolution_status']
+      end
+
+      if attributes.key?(:'gene_resolution_method')
+        self.gene_resolution_method = attributes[:'gene_resolution_method']
+      end
+
+      if attributes.key?(:'assay_name')
+        self.assay_name = attributes[:'assay_name']
+      end
+
+      if attributes.key?(:'specimen_type')
+        self.specimen_type = attributes[:'specimen_type']
+      end
+
+      if attributes.key?(:'comparator_method')
+        self.comparator_method = attributes[:'comparator_method']
+      end
+
+      if attributes.key?(:'reported_performance')
+        self.reported_performance = attributes[:'reported_performance']
+      end
+
+      if attributes.key?(:'validation_type_mentioned')
+        self.validation_type_mentioned = attributes[:'validation_type_mentioned']
+      end
+
+      if attributes.key?(:'assay_provider_company')
+        if (value = attributes[:'assay_provider_company']).is_a?(Array)
+          self.assay_provider_company = value
+        end
+      end
+
+      if attributes.key?(:'funding_organizations')
+        if (value = attributes[:'funding_organizations']).is_a?(Array)
+          self.funding_organizations = value
+        end
+      end
+
+      if attributes.key?(:'evidence_type')
+        self.evidence_type = attributes[:'evidence_type']
+      end
+
+      if attributes.key?(:'evidence_quote')
+        if (value = attributes[:'evidence_quote']).is_a?(Array)
+          self.evidence_quote = value
+        end
+      end
+
+      if attributes.key?(:'confidence')
+        self.confidence = attributes[:'confidence']
+      end
+
+      if attributes.key?(:'title')
+        self.title = attributes[:'title']
+      end
+
+      if attributes.key?(:'published_at')
+        self.published_at = attributes[:'published_at']
+      end
+
+      if attributes.key?(:'extraction_model')
+        self.extraction_model = attributes[:'extraction_model']
+      end
+
+      if attributes.key?(:'extracted_at')
+        self.extracted_at = attributes[:'extracted_at']
+      end
+
+      if attributes.key?(:'source_url')
+        self.source_url = attributes[:'source_url']
+      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_assay_evidence_id == o.biomarker_assay_evidence_id &&
+          route_key == o.route_key &&
+          biomarker_id == o.biomarker_id &&
+          document_id == o.document_id &&
+          pmid == o.pmid &&
+          biomarker_ordinal == o.biomarker_ordinal &&
+          biomarker_name_as_extracted == o.biomarker_name_as_extracted &&
+          gene_symbol_as_extracted == o.gene_symbol_as_extracted &&
+          biomarker_synonyms == o.biomarker_synonyms &&
+          gene_resolution_status == o.gene_resolution_status &&
+          gene_resolution_method == o.gene_resolution_method &&
+          assay_name == o.assay_name &&
+          specimen_type == o.specimen_type &&
+          comparator_method == o.comparator_method &&
+          reported_performance == o.reported_performance &&
+          validation_type_mentioned == o.validation_type_mentioned &&
+          assay_provider_company == o.assay_provider_company &&
+          funding_organizations == o.funding_organizations &&
+          evidence_type == o.evidence_type &&
+          evidence_quote == o.evidence_quote &&
+          confidence == o.confidence &&
+          title == o.title &&
+          published_at == o.published_at &&
+          extraction_model == o.extraction_model &&
+          extracted_at == o.extracted_at &&
+          source_url == o.source_url
+    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_assay_evidence_id, route_key, biomarker_id, document_id, pmid, biomarker_ordinal, biomarker_name_as_extracted, gene_symbol_as_extracted, biomarker_synonyms, gene_resolution_status, gene_resolution_method, assay_name, specimen_type, comparator_method, reported_performance, validation_type_mentioned, assay_provider_company, funding_organizations, evidence_type, evidence_quote, confidence, title, published_at, extraction_model, extracted_at, source_url].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