pharmaobservatory 0.1.5 → 0.1.7

data/lib/pharmaobservatory/models/condition_trial_start_forecast_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 condition_trial_start_forecast dataset: one row per condition and target year. A grouped request returns the group columns and the measures instead, as additional properties.
+  class ConditionTrialStartForecastRow
+    # 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
+
+    # The calendar year forecast.
+    attr_accessor :target_year
+
+    # Years ahead of the build year (0 is the current year).
+    attr_accessor :horizon_offset
+
+    # Months of the target year already observed.
+    attr_accessor :months_observed
+
+    # Months of the target year forecast.
+    attr_accessor :months_forecast
+
+    # Trials started in the target year up to the training cutoff.
+    attr_accessor :input_observed_through_cutoff
+
+    # Trials registered as planned to start in the rest of the target year.
+    attr_accessor :input_planned_remaining
+
+    # The forecast trial starts for the whole target year. A forecast of the eventual count, never an actual count, and it carries no interval.
+    attr_accessor :forecast_point
+
+    # The series' forecast status.
+    attr_accessor :forecast_status
+
+    # Trials of the condition (as in condition_trials) with a start date in the 60 calendar months ending with the cutoff month.
+    attr_accessor :input_trials_window_60m
+
+    # Average trial starts per year over the last 60 months.
+    attr_accessor :input_starts_per_year_60m
+
+    # The series size bucket the backtest error is measured in.
+    attr_accessor :size_bucket
+
+    # The horizon the backtest error was measured at.
+    attr_accessor :backtest_horizon
+
+    # Backtest symmetric mean absolute percentage error.
+    attr_accessor :backtest_smape_pct
+
+    # Backtest relative bias.
+    attr_accessor :backtest_rel_bias
+
+    # Backtest mean absolute error relative to the seasonal naive baseline.
+    attr_accessor :backtest_relmae_vs_snaive
+
+    # Series the backtest covered.
+    attr_accessor :backtest_n_series
+
+    # The kind of series the backtest error was measured on.
+    attr_accessor :backtest_series_kind
+
+    # The backtest run reference.
+    attr_accessor :backtest_ref
+
+    # The multiple of input_planned_remaining the planned-start method adds to the months after the training cutoff; null on a row built with the flat mean alone.
+    attr_accessor :planned_start_coefficient
+
+    # On a planned-start row, whether the stricter re-check (trained only on target years at least two before the cutoff year) adopted the same cell; null on a flat-mean row.
+    attr_accessor :planned_start_stricter_check_agrees
+
+    # On a planned-start row, the relative bias (forecast minus actual over actual) of the stricter re-check; null on a flat-mean row.
+    attr_accessor :planned_start_stricter_check_rel_bias
+
+    # The forecasting model.
+    attr_accessor :model_name
+
+    # The model version.
+    attr_accessor :model_version
+
+    # The date the model's training data ends.
+    attr_accessor :training_cutoff
+
+    # How the forecast was produced.
+    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',
+        :'target_year' => :'target_year',
+        :'horizon_offset' => :'horizon_offset',
+        :'months_observed' => :'months_observed',
+        :'months_forecast' => :'months_forecast',
+        :'input_observed_through_cutoff' => :'input_observed_through_cutoff',
+        :'input_planned_remaining' => :'input_planned_remaining',
+        :'forecast_point' => :'forecast_point',
+        :'forecast_status' => :'forecast_status',
+        :'input_trials_window_60m' => :'input_trials_window_60m',
+        :'input_starts_per_year_60m' => :'input_starts_per_year_60m',
+        :'size_bucket' => :'size_bucket',
+        :'backtest_horizon' => :'backtest_horizon',
+        :'backtest_smape_pct' => :'backtest_smape_pct',
+        :'backtest_rel_bias' => :'backtest_rel_bias',
+        :'backtest_relmae_vs_snaive' => :'backtest_relmae_vs_snaive',
+        :'backtest_n_series' => :'backtest_n_series',
+        :'backtest_series_kind' => :'backtest_series_kind',
+        :'backtest_ref' => :'backtest_ref',
+        :'planned_start_coefficient' => :'planned_start_coefficient',
+        :'planned_start_stricter_check_agrees' => :'planned_start_stricter_check_agrees',
+        :'planned_start_stricter_check_rel_bias' => :'planned_start_stricter_check_rel_bias',
+        :'model_name' => :'model_name',
+        :'model_version' => :'model_version',
+        :'training_cutoff' => :'training_cutoff',
+        :'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',
+        :'target_year' => :'Integer',
+        :'horizon_offset' => :'Integer',
+        :'months_observed' => :'Integer',
+        :'months_forecast' => :'Integer',
+        :'input_observed_through_cutoff' => :'Integer',
+        :'input_planned_remaining' => :'Integer',
+        :'forecast_point' => :'Float',
+        :'forecast_status' => :'String',
+        :'input_trials_window_60m' => :'Integer',
+        :'input_starts_per_year_60m' => :'Float',
+        :'size_bucket' => :'String',
+        :'backtest_horizon' => :'String',
+        :'backtest_smape_pct' => :'Float',
+        :'backtest_rel_bias' => :'Float',
+        :'backtest_relmae_vs_snaive' => :'Float',
+        :'backtest_n_series' => :'Integer',
+        :'backtest_series_kind' => :'String',
+        :'backtest_ref' => :'String',
+        :'planned_start_coefficient' => :'Float',
+        :'planned_start_stricter_check_agrees' => :'Boolean',
+        :'planned_start_stricter_check_rel_bias' => :'Float',
+        :'model_name' => :'String',
+        :'model_version' => :'String',
+        :'training_cutoff' => :'Date',
+        :'method' => :'String'
+      }
+    end
+
+    # List of attributes with nullable: true
+    def self.openapi_nullable
+      Set.new([
+        :'condition_id',
+        :'condition_name',
+        :'target_year',
+        :'horizon_offset',
+        :'months_observed',
+        :'months_forecast',
+        :'input_observed_through_cutoff',
+        :'input_planned_remaining',
+        :'forecast_point',
+        :'forecast_status',
+        :'input_trials_window_60m',
+        :'input_starts_per_year_60m',
+        :'size_bucket',
+        :'backtest_horizon',
+        :'backtest_smape_pct',
+        :'backtest_rel_bias',
+        :'backtest_relmae_vs_snaive',
+        :'backtest_n_series',
+        :'backtest_series_kind',
+        :'backtest_ref',
+        :'planned_start_coefficient',
+        :'planned_start_stricter_check_agrees',
+        :'planned_start_stricter_check_rel_bias',
+        :'model_name',
+        :'model_version',
+        :'training_cutoff',
+        :'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::ConditionTrialStartForecastRow` 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::ConditionTrialStartForecastRow`. 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?(:'target_year')
+        self.target_year = attributes[:'target_year']
+      end
+
+      if attributes.key?(:'horizon_offset')
+        self.horizon_offset = attributes[:'horizon_offset']
+      end
+
+      if attributes.key?(:'months_observed')
+        self.months_observed = attributes[:'months_observed']
+      end
+
+      if attributes.key?(:'months_forecast')
+        self.months_forecast = attributes[:'months_forecast']
+      end
+
+      if attributes.key?(:'input_observed_through_cutoff')
+        self.input_observed_through_cutoff = attributes[:'input_observed_through_cutoff']
+      end
+
+      if attributes.key?(:'input_planned_remaining')
+        self.input_planned_remaining = attributes[:'input_planned_remaining']
+      end
+
+      if attributes.key?(:'forecast_point')
+        self.forecast_point = attributes[:'forecast_point']
+      end
+
+      if attributes.key?(:'forecast_status')
+        self.forecast_status = attributes[:'forecast_status']
+      end
+
+      if attributes.key?(:'input_trials_window_60m')
+        self.input_trials_window_60m = attributes[:'input_trials_window_60m']
+      end
+
+      if attributes.key?(:'input_starts_per_year_60m')
+        self.input_starts_per_year_60m = attributes[:'input_starts_per_year_60m']
+      end
+
+      if attributes.key?(:'size_bucket')
+        self.size_bucket = attributes[:'size_bucket']
+      end
+
+      if attributes.key?(:'backtest_horizon')
+        self.backtest_horizon = attributes[:'backtest_horizon']
+      end
+
+      if attributes.key?(:'backtest_smape_pct')
+        self.backtest_smape_pct = attributes[:'backtest_smape_pct']
+      end
+
+      if attributes.key?(:'backtest_rel_bias')
+        self.backtest_rel_bias = attributes[:'backtest_rel_bias']
+      end
+
+      if attributes.key?(:'backtest_relmae_vs_snaive')
+        self.backtest_relmae_vs_snaive = attributes[:'backtest_relmae_vs_snaive']
+      end
+
+      if attributes.key?(:'backtest_n_series')
+        self.backtest_n_series = attributes[:'backtest_n_series']
+      end
+
+      if attributes.key?(:'backtest_series_kind')
+        self.backtest_series_kind = attributes[:'backtest_series_kind']
+      end
+
+      if attributes.key?(:'backtest_ref')
+        self.backtest_ref = attributes[:'backtest_ref']
+      end
+
+      if attributes.key?(:'planned_start_coefficient')
+        self.planned_start_coefficient = attributes[:'planned_start_coefficient']
+      end
+
+      if attributes.key?(:'planned_start_stricter_check_agrees')
+        self.planned_start_stricter_check_agrees = attributes[:'planned_start_stricter_check_agrees']
+      end
+
+      if attributes.key?(:'planned_start_stricter_check_rel_bias')
+        self.planned_start_stricter_check_rel_bias = attributes[:'planned_start_stricter_check_rel_bias']
+      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?(:'training_cutoff')
+        self.training_cutoff = attributes[:'training_cutoff']
+      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 &&
+          target_year == o.target_year &&
+          horizon_offset == o.horizon_offset &&
+          months_observed == o.months_observed &&
+          months_forecast == o.months_forecast &&
+          input_observed_through_cutoff == o.input_observed_through_cutoff &&
+          input_planned_remaining == o.input_planned_remaining &&
+          forecast_point == o.forecast_point &&
+          forecast_status == o.forecast_status &&
+          input_trials_window_60m == o.input_trials_window_60m &&
+          input_starts_per_year_60m == o.input_starts_per_year_60m &&
+          size_bucket == o.size_bucket &&
+          backtest_horizon == o.backtest_horizon &&
+          backtest_smape_pct == o.backtest_smape_pct &&
+          backtest_rel_bias == o.backtest_rel_bias &&
+          backtest_relmae_vs_snaive == o.backtest_relmae_vs_snaive &&
+          backtest_n_series == o.backtest_n_series &&
+          backtest_series_kind == o.backtest_series_kind &&
+          backtest_ref == o.backtest_ref &&
+          planned_start_coefficient == o.planned_start_coefficient &&
+          planned_start_stricter_check_agrees == o.planned_start_stricter_check_agrees &&
+          planned_start_stricter_check_rel_bias == o.planned_start_stricter_check_rel_bias &&
+          model_name == o.model_name &&
+          model_version == o.model_version &&
+          training_cutoff == o.training_cutoff &&
+          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, target_year, horizon_offset, months_observed, months_forecast, input_observed_through_cutoff, input_planned_remaining, forecast_point, forecast_status, input_trials_window_60m, input_starts_per_year_60m, size_bucket, backtest_horizon, backtest_smape_pct, backtest_rel_bias, backtest_relmae_vs_snaive, backtest_n_series, backtest_series_kind, backtest_ref, planned_start_coefficient, planned_start_stricter_check_agrees, planned_start_stricter_check_rel_bias, model_name, model_version, training_cutoff, 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_trials_response.rb

@@ -102,7 +102,7 @@ module PharmaObservatory
         :'grain' => :'String',
         :'object_type' => :'String',
         :'id' => :'String',
-        :'scope' => :'BiomarkerCdxAssertionsResponseScope',
+        :'scope' => :'BiomarkerAssayEvidenceResponseScope',
         :'columns' => :'Array<DatasetColumn>',
         :'rows' => :'Array<ConditionTrialsRow>',
         :'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>'
       }

data/lib/pharmaobservatory/models/condition_trials_row.rb

@@ -79,7 +79,7 @@ module PharmaObservatory
     # Display name of the lead sponsor's group.
     attr_accessor :sponsor_group_name
 
-    # The funder class the registry declared for the sponsor (INDUSTRY, NIH, FED, OTHER_GOV, NETWORK, OTHER, INDIV, AMBIG, UNKNOWN). UNKNOWN is the registry's own code for a class it does not state. Null when the trial has no lead sponsor row.
+    # The funder class the registry declared for the sponsor (INDUSTRY, NIH for the US National Institutes of Health, FED, OTHER_GOV, NETWORK, OTHER, INDIV, AMBIG, UNKNOWN). UNKNOWN is the registry's own code for a class it does not state. Null when the trial has no lead sponsor row.
     attr_accessor :sponsor_agency_class
 
     # Attribute mapping from ruby-style variable name to JSON key.

data/lib/pharmaobservatory/models/conditions_record.rb

@@ -74,8 +74,8 @@ module PharmaObservatory
         :'datasets' => :'Array<DatasetListing>',
         :'attribution' => :'Array<DatasetAttribution>',
         :'source_credit' => :'String',
-        :'freshness' => :'BiomarkerCdxAssertionsResponseFreshness',
-        :'build' => :'BiomarkerCdxAssertionsResponseBuild',
+        :'freshness' => :'BiomarkerAssayEvidenceResponseFreshness',
+        :'build' => :'BiomarkerAssayEvidenceResponseBuild',
         :'build_state' => :'DatasetBuildState',
         :'restriction' => :'Hash<String, Object>'
       }

data/lib/pharmaobservatory/models/conditions_record_attributes.rb

@@ -19,11 +19,14 @@ module PharmaObservatory
 
     attr_accessor :condition_delivery
 
+    attr_accessor :condition_recruitment_duration
+
     # Attribute mapping from ruby-style variable name to JSON key.
     def self.attribute_map
       {
         :'condition_burden' => :'condition_burden',
-        :'condition_delivery' => :'condition_delivery'
+        :'condition_delivery' => :'condition_delivery',
+        :'condition_recruitment_duration' => :'condition_recruitment_duration'
       }
     end
 
@@ -41,7 +44,8 @@ module PharmaObservatory
     def self.openapi_types
       {
         :'condition_burden' => :'ConditionBurdenRow',
-        :'condition_delivery' => :'ConditionDeliveryRow'
+        :'condition_delivery' => :'ConditionDeliveryRow',
+        :'condition_recruitment_duration' => :'ConditionRecruitmentDurationRow'
       }
     end
 
@@ -74,6 +78,10 @@ module PharmaObservatory
       if attributes.key?(:'condition_delivery')
         self.condition_delivery = attributes[:'condition_delivery']
       end
+
+      if attributes.key?(:'condition_recruitment_duration')
+        self.condition_recruitment_duration = attributes[:'condition_recruitment_duration']
+      end
     end
 
     # Show invalid properties with the reasons. Usually used together with valid?
@@ -97,7 +105,8 @@ module PharmaObservatory
       return true if self.equal?(o)
       self.class == o.class &&
           condition_burden == o.condition_burden &&
-          condition_delivery == o.condition_delivery
+          condition_delivery == o.condition_delivery &&
+          condition_recruitment_duration == o.condition_recruitment_duration
     end
 
     # @see the `==` method
@@ -109,7 +118,7 @@ module PharmaObservatory
     # Calculates hash code according to all attributes.
     # @return [Integer] Hash code
     def hash
-      [condition_burden, condition_delivery].hash
+      [condition_burden, condition_delivery, condition_recruitment_duration].hash
     end
 
     # Builds the object from hash

data/lib/pharmaobservatory/models/conditions_response.rb

@@ -102,7 +102,7 @@ module PharmaObservatory
         :'grain' => :'String',
         :'object_type' => :'String',
         :'id' => :'String',
-        :'scope' => :'BiomarkerCdxAssertionsResponseScope',
+        :'scope' => :'BiomarkerAssayEvidenceResponseScope',
         :'columns' => :'Array<DatasetColumn>',
         :'rows' => :'Array<ConditionsRow>',
         :'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>'
       }