pharmaobservatory 0.1.4 → 0.1.6

data/lib/pharmaobservatory/models/condition_recruitment_duration_row.rb

@@ -0,0 +1,597 @@
+=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 condition_recruitment_duration dataset: one row per condition with at least one trial. A grouped request returns the group columns and the measures instead, as additional properties.
+  class ConditionRecruitmentDurationRow
+    # The condition key, a MeSH (Medical Subject Headings) descriptor id (D followed by six to nine digits).
+    attr_accessor :condition_id
+
+    # The condition's MeSH heading.
+    attr_accessor :condition_name
+
+    # Trials in the condition series (the rows of condition_trials).
+    attr_accessor :n_trials_in_series
+
+    # Of those, trials with a row in the per-trial predictions at the cutoff.
+    attr_accessor :n_evaluated
+
+    # n_trials_in_series - n_evaluated: registered after the cutoff or a coverage gap; the data cannot tell which.
+    attr_accessor :n_not_evaluated
+
+    # Evaluated trials with prediction_status out_of_population.
+    attr_accessor :n_out_of_population
+
+    # Evaluated trials with prediction_status completed.
+    attr_accessor :n_completed
+
+    # Evaluated trials with prediction_status stopped.
+    attr_accessor :n_stopped
+
+    # Evaluated trials with prediction_status no_registration_record.
+    attr_accessor :n_no_registration_record
+
+    # Evaluated trials with prediction_status retrospective_registration.
+    attr_accessor :n_retrospective_registration
+
+    # Evaluated trials with prediction_status start_not_actual.
+    attr_accessor :n_start_not_actual
+
+    # Evaluated trials with prediction_status fit_failed.
+    attr_accessor :n_fit_failed
+
+    # Evaluated trials with prediction_status predicted, superseded or not.
+    attr_accessor :n_predicted
+
+    # Predicted trials whose CURRENT record shows the outcome (COMPLETED, TERMINATED, WITHDRAWN or an ACTUAL primary completion); kept out of every predicted figure.
+    attr_accessor :n_predicted_superseded
+
+    # n_predicted - n_predicted_superseded; the denominator of every predicted figure.
+    attr_accessor :n_predicted_open
+
+    # Open predicted trials whose figure sits at the horizon cap (an at-cap row contributes the cap to the median).
+    attr_accessor :n_predicted_at_cap
+
+    # Open predicted trials running past their predicted end at the cutoff.
+    attr_accessor :n_predicted_overdue
+
+    # Open predicted trials in a phase bucket the backtest measured (error_phase_mae_months not null).
+    attr_accessor :n_predicted_error_measured
+
+    # Median of the carried predicted months over open predicted trials (capped at horizon_cap_months). NULL under min_n.
+    attr_accessor :predicted_months_median
+
+    # 25th percentile, same rows and floor.
+    attr_accessor :predicted_months_p25
+
+    # 75th percentile, same rows and floor.
+    attr_accessor :predicted_months_p75
+
+    # Median of the carried baseline months over the same open predicted trials. NULL under min_n.
+    attr_accessor :baseline_months_median
+
+    # Trials with a registered span (primary completion typed ACTUAL today, plausible start and completion), from the realized-duration input.
+    attr_accessor :n_realized
+
+    # Median registered start to primary completion in months over n_realized trials. NULL under min_n.
+    attr_accessor :realized_months_median
+
+    # 25th percentile, same rows and floor.
+    attr_accessor :realized_months_p25
+
+    # 75th percentile, same rows and floor.
+    attr_accessor :realized_months_p75
+
+    # Realized spans above horizon_cap_months, so a reader sees how many would have hit the cap.
+    attr_accessor :n_realized_over_cap
+
+    # The floor applied: a median is withheld below this many trials, carried so a reader sees the floor used.
+    attr_accessor :min_n
+
+    # rolled_up (open predicted >= min_n), below_floor (1 <= open < min_n, counts only), none_predicted (evaluated, no open prediction), none_evaluated.
+    attr_accessor :rollup_status
+
+    # rolled_up (n_realized >= min_n), below_floor, or none.
+    attr_accessor :realized_status
+
+    # The date the model's training data ends.
+    attr_accessor :training_cutoff
+
+    # The recruitment-duration model.
+    attr_accessor :model_name
+
+    # The model version.
+    attr_accessor :model_version
+
+    # The cap on predicted months (36 today), from the prediction rows.
+    attr_accessor :horizon_cap_months
+
+    # The run's method sentence from the run provenance, never re-authored.
+    attr_accessor :method
+
+    # Attribute mapping from ruby-style variable name to JSON key.
+    def self.attribute_map
+      {
+        :'condition_id' => :'condition_id',
+        :'condition_name' => :'condition_name',
+        :'n_trials_in_series' => :'n_trials_in_series',
+        :'n_evaluated' => :'n_evaluated',
+        :'n_not_evaluated' => :'n_not_evaluated',
+        :'n_out_of_population' => :'n_out_of_population',
+        :'n_completed' => :'n_completed',
+        :'n_stopped' => :'n_stopped',
+        :'n_no_registration_record' => :'n_no_registration_record',
+        :'n_retrospective_registration' => :'n_retrospective_registration',
+        :'n_start_not_actual' => :'n_start_not_actual',
+        :'n_fit_failed' => :'n_fit_failed',
+        :'n_predicted' => :'n_predicted',
+        :'n_predicted_superseded' => :'n_predicted_superseded',
+        :'n_predicted_open' => :'n_predicted_open',
+        :'n_predicted_at_cap' => :'n_predicted_at_cap',
+        :'n_predicted_overdue' => :'n_predicted_overdue',
+        :'n_predicted_error_measured' => :'n_predicted_error_measured',
+        :'predicted_months_median' => :'predicted_months_median',
+        :'predicted_months_p25' => :'predicted_months_p25',
+        :'predicted_months_p75' => :'predicted_months_p75',
+        :'baseline_months_median' => :'baseline_months_median',
+        :'n_realized' => :'n_realized',
+        :'realized_months_median' => :'realized_months_median',
+        :'realized_months_p25' => :'realized_months_p25',
+        :'realized_months_p75' => :'realized_months_p75',
+        :'n_realized_over_cap' => :'n_realized_over_cap',
+        :'min_n' => :'min_n',
+        :'rollup_status' => :'rollup_status',
+        :'realized_status' => :'realized_status',
+        :'training_cutoff' => :'training_cutoff',
+        :'model_name' => :'model_name',
+        :'model_version' => :'model_version',
+        :'horizon_cap_months' => :'horizon_cap_months',
+        :'method' => :'method'
+      }
+    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
+      {
+        :'condition_id' => :'String',
+        :'condition_name' => :'String',
+        :'n_trials_in_series' => :'Integer',
+        :'n_evaluated' => :'Integer',
+        :'n_not_evaluated' => :'Integer',
+        :'n_out_of_population' => :'Integer',
+        :'n_completed' => :'Integer',
+        :'n_stopped' => :'Integer',
+        :'n_no_registration_record' => :'Integer',
+        :'n_retrospective_registration' => :'Integer',
+        :'n_start_not_actual' => :'Integer',
+        :'n_fit_failed' => :'Integer',
+        :'n_predicted' => :'Integer',
+        :'n_predicted_superseded' => :'Integer',
+        :'n_predicted_open' => :'Integer',
+        :'n_predicted_at_cap' => :'Integer',
+        :'n_predicted_overdue' => :'Integer',
+        :'n_predicted_error_measured' => :'Integer',
+        :'predicted_months_median' => :'Float',
+        :'predicted_months_p25' => :'Float',
+        :'predicted_months_p75' => :'Float',
+        :'baseline_months_median' => :'Float',
+        :'n_realized' => :'Integer',
+        :'realized_months_median' => :'Float',
+        :'realized_months_p25' => :'Float',
+        :'realized_months_p75' => :'Float',
+        :'n_realized_over_cap' => :'Integer',
+        :'min_n' => :'Integer',
+        :'rollup_status' => :'String',
+        :'realized_status' => :'String',
+        :'training_cutoff' => :'Date',
+        :'model_name' => :'String',
+        :'model_version' => :'String',
+        :'horizon_cap_months' => :'Integer',
+        :'method' => :'String'
+      }
+    end
+
+    # List of attributes with nullable: true
+    def self.openapi_nullable
+      Set.new([
+        :'condition_id',
+        :'condition_name',
+        :'n_trials_in_series',
+        :'n_evaluated',
+        :'n_not_evaluated',
+        :'n_out_of_population',
+        :'n_completed',
+        :'n_stopped',
+        :'n_no_registration_record',
+        :'n_retrospective_registration',
+        :'n_start_not_actual',
+        :'n_fit_failed',
+        :'n_predicted',
+        :'n_predicted_superseded',
+        :'n_predicted_open',
+        :'n_predicted_at_cap',
+        :'n_predicted_overdue',
+        :'n_predicted_error_measured',
+        :'predicted_months_median',
+        :'predicted_months_p25',
+        :'predicted_months_p75',
+        :'baseline_months_median',
+        :'n_realized',
+        :'realized_months_median',
+        :'realized_months_p25',
+        :'realized_months_p75',
+        :'n_realized_over_cap',
+        :'min_n',
+        :'rollup_status',
+        :'realized_status',
+        :'training_cutoff',
+        :'model_name',
+        :'model_version',
+        :'horizon_cap_months',
+        :'method'
+      ])
+    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::ConditionRecruitmentDurationRow` 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::ConditionRecruitmentDurationRow`. 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?(:'condition_id')
+        self.condition_id = attributes[:'condition_id']
+      end
+
+      if attributes.key?(:'condition_name')
+        self.condition_name = attributes[:'condition_name']
+      end
+
+      if attributes.key?(:'n_trials_in_series')
+        self.n_trials_in_series = attributes[:'n_trials_in_series']
+      end
+
+      if attributes.key?(:'n_evaluated')
+        self.n_evaluated = attributes[:'n_evaluated']
+      end
+
+      if attributes.key?(:'n_not_evaluated')
+        self.n_not_evaluated = attributes[:'n_not_evaluated']
+      end
+
+      if attributes.key?(:'n_out_of_population')
+        self.n_out_of_population = attributes[:'n_out_of_population']
+      end
+
+      if attributes.key?(:'n_completed')
+        self.n_completed = attributes[:'n_completed']
+      end
+
+      if attributes.key?(:'n_stopped')
+        self.n_stopped = attributes[:'n_stopped']
+      end
+
+      if attributes.key?(:'n_no_registration_record')
+        self.n_no_registration_record = attributes[:'n_no_registration_record']
+      end
+
+      if attributes.key?(:'n_retrospective_registration')
+        self.n_retrospective_registration = attributes[:'n_retrospective_registration']
+      end
+
+      if attributes.key?(:'n_start_not_actual')
+        self.n_start_not_actual = attributes[:'n_start_not_actual']
+      end
+
+      if attributes.key?(:'n_fit_failed')
+        self.n_fit_failed = attributes[:'n_fit_failed']
+      end
+
+      if attributes.key?(:'n_predicted')
+        self.n_predicted = attributes[:'n_predicted']
+      end
+
+      if attributes.key?(:'n_predicted_superseded')
+        self.n_predicted_superseded = attributes[:'n_predicted_superseded']
+      end
+
+      if attributes.key?(:'n_predicted_open')
+        self.n_predicted_open = attributes[:'n_predicted_open']
+      end
+
+      if attributes.key?(:'n_predicted_at_cap')
+        self.n_predicted_at_cap = attributes[:'n_predicted_at_cap']
+      end
+
+      if attributes.key?(:'n_predicted_overdue')
+        self.n_predicted_overdue = attributes[:'n_predicted_overdue']
+      end
+
+      if attributes.key?(:'n_predicted_error_measured')
+        self.n_predicted_error_measured = attributes[:'n_predicted_error_measured']
+      end
+
+      if attributes.key?(:'predicted_months_median')
+        self.predicted_months_median = attributes[:'predicted_months_median']
+      end
+
+      if attributes.key?(:'predicted_months_p25')
+        self.predicted_months_p25 = attributes[:'predicted_months_p25']
+      end
+
+      if attributes.key?(:'predicted_months_p75')
+        self.predicted_months_p75 = attributes[:'predicted_months_p75']
+      end
+
+      if attributes.key?(:'baseline_months_median')
+        self.baseline_months_median = attributes[:'baseline_months_median']
+      end
+
+      if attributes.key?(:'n_realized')
+        self.n_realized = attributes[:'n_realized']
+      end
+
+      if attributes.key?(:'realized_months_median')
+        self.realized_months_median = attributes[:'realized_months_median']
+      end
+
+      if attributes.key?(:'realized_months_p25')
+        self.realized_months_p25 = attributes[:'realized_months_p25']
+      end
+
+      if attributes.key?(:'realized_months_p75')
+        self.realized_months_p75 = attributes[:'realized_months_p75']
+      end
+
+      if attributes.key?(:'n_realized_over_cap')
+        self.n_realized_over_cap = attributes[:'n_realized_over_cap']
+      end
+
+      if attributes.key?(:'min_n')
+        self.min_n = attributes[:'min_n']
+      end
+
+      if attributes.key?(:'rollup_status')
+        self.rollup_status = attributes[:'rollup_status']
+      end
+
+      if attributes.key?(:'realized_status')
+        self.realized_status = attributes[:'realized_status']
+      end
+
+      if attributes.key?(:'training_cutoff')
+        self.training_cutoff = attributes[:'training_cutoff']
+      end
+
+      if attributes.key?(:'model_name')
+        self.model_name = attributes[:'model_name']
+      end
+
+      if attributes.key?(:'model_version')
+        self.model_version = attributes[:'model_version']
+      end
+
+      if attributes.key?(:'horizon_cap_months')
+        self.horizon_cap_months = attributes[:'horizon_cap_months']
+      end
+
+      if attributes.key?(:'method')
+        self.method = attributes[:'method']
+      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 &&
+          condition_id == o.condition_id &&
+          condition_name == o.condition_name &&
+          n_trials_in_series == o.n_trials_in_series &&
+          n_evaluated == o.n_evaluated &&
+          n_not_evaluated == o.n_not_evaluated &&
+          n_out_of_population == o.n_out_of_population &&
+          n_completed == o.n_completed &&
+          n_stopped == o.n_stopped &&
+          n_no_registration_record == o.n_no_registration_record &&
+          n_retrospective_registration == o.n_retrospective_registration &&
+          n_start_not_actual == o.n_start_not_actual &&
+          n_fit_failed == o.n_fit_failed &&
+          n_predicted == o.n_predicted &&
+          n_predicted_superseded == o.n_predicted_superseded &&
+          n_predicted_open == o.n_predicted_open &&
+          n_predicted_at_cap == o.n_predicted_at_cap &&
+          n_predicted_overdue == o.n_predicted_overdue &&
+          n_predicted_error_measured == o.n_predicted_error_measured &&
+          predicted_months_median == o.predicted_months_median &&
+          predicted_months_p25 == o.predicted_months_p25 &&
+          predicted_months_p75 == o.predicted_months_p75 &&
+          baseline_months_median == o.baseline_months_median &&
+          n_realized == o.n_realized &&
+          realized_months_median == o.realized_months_median &&
+          realized_months_p25 == o.realized_months_p25 &&
+          realized_months_p75 == o.realized_months_p75 &&
+          n_realized_over_cap == o.n_realized_over_cap &&
+          min_n == o.min_n &&
+          rollup_status == o.rollup_status &&
+          realized_status == o.realized_status &&
+          training_cutoff == o.training_cutoff &&
+          model_name == o.model_name &&
+          model_version == o.model_version &&
+          horizon_cap_months == o.horizon_cap_months &&
+          method == o.method
+    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
+      [condition_id, condition_name, n_trials_in_series, n_evaluated, n_not_evaluated, n_out_of_population, n_completed, n_stopped, n_no_registration_record, n_retrospective_registration, n_start_not_actual, n_fit_failed, n_predicted, n_predicted_superseded, n_predicted_open, n_predicted_at_cap, n_predicted_overdue, n_predicted_error_measured, predicted_months_median, predicted_months_p25, predicted_months_p75, baseline_months_median, n_realized, realized_months_median, realized_months_p25, realized_months_p75, n_realized_over_cap, min_n, rollup_status, realized_status, training_cutoff, model_name, model_version, horizon_cap_months, method].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/condition_sites_response.rb

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