pharmaobservatory 0.1.4 → 0.1.6

data/lib/pharmaobservatory/models/trial_delivery_row.rb

@@ -28,9 +28,12 @@ module PharmaObservatory
     # INTERVENTIONAL, OBSERVATIONAL or EXPANDED_ACCESS.
     attr_accessor :study_type
 
-    # The registry's phase code.
+    # The registry's phase code (PHASE1, PHASE2, PHASE2/PHASE3, NA and so on). Null when the registry gives no phase (observational and expanded-access trials); phase_label carries the display label for those.
     attr_accessor :phase
 
+    # The trial phase as a display label (Phase 2, Phase 3, Observational, Not applicable, Expanded access, Unknown). The same trial's phase column holds the registry code.
+    attr_accessor :phase_label
+
     # Planned enrollment from the earliest snapshot typed ESTIMATED.
     attr_accessor :planned_enrollment
 
@@ -50,7 +53,7 @@ module PharmaObservatory
     attr_accessor :enrollment_met
 
     # Whether a planned and an actual enrollment are both recorded.
-    attr_accessor :has_enrollment_delta
+    attr_accessor :enrollment_delta_known
 
     # Where the planned enrollment came from: history_earliest_estimated, type_estimated_current or none.
     attr_accessor :planned_basis
@@ -70,10 +73,10 @@ module PharmaObservatory
     # Completion date once typed ACTUAL.
     attr_accessor :actual_completion_date
 
-    # Type of the current primary completion date (ACTUAL or ESTIMATED).
+    # ACTUAL (a date that has occurred) or ESTIMATED (a planned date). The registry's older ANTICIPATED is published as ESTIMATED.
     attr_accessor :primary_completion_date_type
 
-    # Type of the current completion date (ACTUAL or ESTIMATED).
+    # ACTUAL (a date that has occurred) or ESTIMATED (a planned date). The registry's older ANTICIPATED is published as ESTIMATED.
     attr_accessor :completion_date_type
 
     # Actual minus planned primary completion date; positive is later than planned (null without both).
@@ -96,13 +99,14 @@ module PharmaObservatory
         :'overall_status_summary' => :'overall_status_summary',
         :'study_type' => :'study_type',
         :'phase' => :'phase',
+        :'phase_label' => :'phase_label',
         :'planned_enrollment' => :'planned_enrollment',
         :'actual_enrollment' => :'actual_enrollment',
         :'enrollment_type' => :'enrollment_type',
         :'enrollment_delta' => :'enrollment_delta',
         :'enrollment_attainment_pct' => :'enrollment_attainment_pct',
         :'enrollment_met' => :'enrollment_met',
-        :'has_enrollment_delta' => :'has_enrollment_delta',
+        :'enrollment_delta_known' => :'enrollment_delta_known',
         :'planned_basis' => :'planned_basis',
         :'actual_basis' => :'actual_basis',
         :'planned_primary_completion_date' => :'planned_primary_completion_date',
@@ -136,13 +140,14 @@ module PharmaObservatory
         :'overall_status_summary' => :'String',
         :'study_type' => :'String',
         :'phase' => :'String',
+        :'phase_label' => :'String',
         :'planned_enrollment' => :'Integer',
         :'actual_enrollment' => :'Integer',
         :'enrollment_type' => :'String',
         :'enrollment_delta' => :'Integer',
         :'enrollment_attainment_pct' => :'Float',
         :'enrollment_met' => :'Boolean',
-        :'has_enrollment_delta' => :'Boolean',
+        :'enrollment_delta_known' => :'Boolean',
         :'planned_basis' => :'String',
         :'actual_basis' => :'String',
         :'planned_primary_completion_date' => :'Date',
@@ -166,13 +171,14 @@ module PharmaObservatory
         :'overall_status_summary',
         :'study_type',
         :'phase',
+        :'phase_label',
         :'planned_enrollment',
         :'actual_enrollment',
         :'enrollment_type',
         :'enrollment_delta',
         :'enrollment_attainment_pct',
         :'enrollment_met',
-        :'has_enrollment_delta',
+        :'enrollment_delta_known',
         :'planned_basis',
         :'actual_basis',
         :'planned_primary_completion_date',
@@ -224,6 +230,10 @@ module PharmaObservatory
         self.phase = attributes[:'phase']
       end
 
+      if attributes.key?(:'phase_label')
+        self.phase_label = attributes[:'phase_label']
+      end
+
       if attributes.key?(:'planned_enrollment')
         self.planned_enrollment = attributes[:'planned_enrollment']
       end
@@ -248,8 +258,8 @@ module PharmaObservatory
         self.enrollment_met = attributes[:'enrollment_met']
       end
 
-      if attributes.key?(:'has_enrollment_delta')
-        self.has_enrollment_delta = attributes[:'has_enrollment_delta']
+      if attributes.key?(:'enrollment_delta_known')
+        self.enrollment_delta_known = attributes[:'enrollment_delta_known']
       end
 
       if attributes.key?(:'planned_basis')
@@ -326,13 +336,14 @@ module PharmaObservatory
           overall_status_summary == o.overall_status_summary &&
           study_type == o.study_type &&
           phase == o.phase &&
+          phase_label == o.phase_label &&
           planned_enrollment == o.planned_enrollment &&
           actual_enrollment == o.actual_enrollment &&
           enrollment_type == o.enrollment_type &&
           enrollment_delta == o.enrollment_delta &&
           enrollment_attainment_pct == o.enrollment_attainment_pct &&
           enrollment_met == o.enrollment_met &&
-          has_enrollment_delta == o.has_enrollment_delta &&
+          enrollment_delta_known == o.enrollment_delta_known &&
           planned_basis == o.planned_basis &&
           actual_basis == o.actual_basis &&
           planned_primary_completion_date == o.planned_primary_completion_date &&
@@ -356,7 +367,7 @@ module PharmaObservatory
     # Calculates hash code according to all attributes.
     # @return [Integer] Hash code
     def hash
-      [trial_id, lead_sponsor_name, overall_status_summary, study_type, phase, planned_enrollment, actual_enrollment, enrollment_type, enrollment_delta, enrollment_attainment_pct, enrollment_met, has_enrollment_delta, planned_basis, actual_basis, planned_primary_completion_date, actual_primary_completion_date, planned_completion_date, actual_completion_date, primary_completion_date_type, completion_date_type, primary_completion_slip_days, completion_slip_days, completion_slipped, has_completion_delta].hash
+      [trial_id, lead_sponsor_name, overall_status_summary, study_type, phase, phase_label, planned_enrollment, actual_enrollment, enrollment_type, enrollment_delta, enrollment_attainment_pct, enrollment_met, enrollment_delta_known, planned_basis, actual_basis, planned_primary_completion_date, actual_primary_completion_date, planned_completion_date, actual_completion_date, primary_completion_date_type, completion_date_type, primary_completion_slip_days, completion_slip_days, completion_slipped, has_completion_delta].hash
     end
 
     # Builds the object from hash

data/lib/pharmaobservatory/models/trial_demographics_response.rb

@@ -102,7 +102,7 @@ module PharmaObservatory
         :'grain' => :'String',
         :'object_type' => :'String',
         :'id' => :'String',
-        :'scope' => :'BiomarkerCdxAssertionsResponseScope',
+        :'scope' => :'BiomarkerAssayEvidenceResponseScope',
         :'columns' => :'Array<DatasetColumn>',
         :'rows' => :'Array<TrialDemographicsRow>',
         :'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/trial_drug_classes_response.rb

@@ -0,0 +1,478 @@
+=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
+  class TrialDrugClassesResponse
+    attr_accessor :dataset
+
+    attr_accessor :grain
+
+    attr_accessor :object_type
+
+    attr_accessor :id
+
+    attr_accessor :scope
+
+    attr_accessor :columns
+
+    attr_accessor :rows
+
+    # The exact count of the filtered rows on an ungrouped read, carried by the cursor; null when grouped.
+    attr_accessor :total
+
+    attr_accessor :next_cursor
+
+    attr_accessor :sort
+
+    attr_accessor :filters
+
+    attr_accessor :group_by
+
+    attr_accessor :measures
+
+    attr_accessor :attribution
+
+    attr_accessor :source_credit
+
+    attr_accessor :withheld_tiers
+
+    attr_accessor :withheld_columns
+
+    attr_accessor :freshness
+
+    attr_accessor :build
+
+    attr_accessor :build_state
+
+    attr_accessor :restriction
+
+    # Attribute mapping from ruby-style variable name to JSON key.
+    def self.attribute_map
+      {
+        :'dataset' => :'dataset',
+        :'grain' => :'grain',
+        :'object_type' => :'object_type',
+        :'id' => :'id',
+        :'scope' => :'scope',
+        :'columns' => :'columns',
+        :'rows' => :'rows',
+        :'total' => :'total',
+        :'next_cursor' => :'next_cursor',
+        :'sort' => :'sort',
+        :'filters' => :'filters',
+        :'group_by' => :'group_by',
+        :'measures' => :'measures',
+        :'attribution' => :'attribution',
+        :'source_credit' => :'source_credit',
+        :'withheld_tiers' => :'withheld_tiers',
+        :'withheld_columns' => :'withheld_columns',
+        :'freshness' => :'freshness',
+        :'build' => :'build',
+        :'build_state' => :'build_state',
+        :'restriction' => :'restriction'
+      }
+    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
+      {
+        :'dataset' => :'String',
+        :'grain' => :'String',
+        :'object_type' => :'String',
+        :'id' => :'String',
+        :'scope' => :'BiomarkerAssayEvidenceResponseScope',
+        :'columns' => :'Array<DatasetColumn>',
+        :'rows' => :'Array<TrialDrugClassesRow>',
+        :'total' => :'Integer',
+        :'next_cursor' => :'String',
+        :'sort' => :'Array<String>',
+        :'filters' => :'Array<Hash<String, Object>>',
+        :'group_by' => :'Array<String>',
+        :'measures' => :'Array<String>',
+        :'attribution' => :'Array<DatasetAttribution>',
+        :'source_credit' => :'String',
+        :'withheld_tiers' => :'Array<String>',
+        :'withheld_columns' => :'Array<String>',
+        :'freshness' => :'BiomarkerAssayEvidenceResponseFreshness',
+        :'build' => :'BiomarkerAssayEvidenceResponseBuild',
+        :'build_state' => :'DatasetBuildState',
+        :'restriction' => :'Hash<String, Object>'
+      }
+    end
+
+    # List of attributes with nullable: true
+    def self.openapi_nullable
+      Set.new([
+        :'object_type',
+        :'id',
+        :'scope',
+        :'total',
+        :'next_cursor',
+        :'restriction'
+      ])
+    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::TrialDrugClassesResponse` 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::TrialDrugClassesResponse`. 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?(:'dataset')
+        self.dataset = attributes[:'dataset']
+      else
+        self.dataset = nil
+      end
+
+      if attributes.key?(:'grain')
+        self.grain = attributes[:'grain']
+      end
+
+      if attributes.key?(:'object_type')
+        self.object_type = attributes[:'object_type']
+      end
+
+      if attributes.key?(:'id')
+        self.id = attributes[:'id']
+      end
+
+      if attributes.key?(:'scope')
+        self.scope = attributes[:'scope']
+      end
+
+      if attributes.key?(:'columns')
+        if (value = attributes[:'columns']).is_a?(Array)
+          self.columns = value
+        end
+      else
+        self.columns = nil
+      end
+
+      if attributes.key?(:'rows')
+        if (value = attributes[:'rows']).is_a?(Array)
+          self.rows = value
+        end
+      else
+        self.rows = nil
+      end
+
+      if attributes.key?(:'total')
+        self.total = attributes[:'total']
+      end
+
+      if attributes.key?(:'next_cursor')
+        self.next_cursor = attributes[:'next_cursor']
+      end
+
+      if attributes.key?(:'sort')
+        if (value = attributes[:'sort']).is_a?(Array)
+          self.sort = value
+        end
+      end
+
+      if attributes.key?(:'filters')
+        if (value = attributes[:'filters']).is_a?(Array)
+          self.filters = value
+        end
+      end
+
+      if attributes.key?(:'group_by')
+        if (value = attributes[:'group_by']).is_a?(Array)
+          self.group_by = value
+        end
+      end
+
+      if attributes.key?(:'measures')
+        if (value = attributes[:'measures']).is_a?(Array)
+          self.measures = value
+        end
+      end
+
+      if attributes.key?(:'attribution')
+        if (value = attributes[:'attribution']).is_a?(Array)
+          self.attribution = value
+        end
+      end
+
+      if attributes.key?(:'source_credit')
+        self.source_credit = attributes[:'source_credit']
+      end
+
+      if attributes.key?(:'withheld_tiers')
+        if (value = attributes[:'withheld_tiers']).is_a?(Array)
+          self.withheld_tiers = value
+        end
+      end
+
+      if attributes.key?(:'withheld_columns')
+        if (value = attributes[:'withheld_columns']).is_a?(Array)
+          self.withheld_columns = value
+        end
+      end
+
+      if attributes.key?(:'freshness')
+        self.freshness = attributes[:'freshness']
+      end
+
+      if attributes.key?(:'build')
+        self.build = attributes[:'build']
+      end
+
+      if attributes.key?(:'build_state')
+        self.build_state = attributes[:'build_state']
+      end
+
+      if attributes.key?(:'restriction')
+        if (value = attributes[:'restriction']).is_a?(Hash)
+          self.restriction = value
+        end
+      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
+      if @dataset.nil?
+        invalid_properties.push('invalid value for "dataset", dataset cannot be nil.')
+      end
+
+      if @columns.nil?
+        invalid_properties.push('invalid value for "columns", columns cannot be nil.')
+      end
+
+      if @rows.nil?
+        invalid_properties.push('invalid value for "rows", rows cannot be nil.')
+      end
+
+      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'
+      return false if @dataset.nil?
+      return false if @columns.nil?
+      return false if @rows.nil?
+      true
+    end
+
+    # Custom attribute writer method with validation
+    # @param [Object] dataset Value to be assigned
+    def dataset=(dataset)
+      if dataset.nil?
+        fail ArgumentError, 'dataset cannot be nil'
+      end
+
+      @dataset = dataset
+    end
+
+    # Custom attribute writer method with validation
+    # @param [Object] columns Value to be assigned
+    def columns=(columns)
+      if columns.nil?
+        fail ArgumentError, 'columns cannot be nil'
+      end
+
+      @columns = columns
+    end
+
+    # Custom attribute writer method with validation
+    # @param [Object] rows Value to be assigned
+    def rows=(rows)
+      if rows.nil?
+        fail ArgumentError, 'rows cannot be nil'
+      end
+
+      @rows = rows
+    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 &&
+          dataset == o.dataset &&
+          grain == o.grain &&
+          object_type == o.object_type &&
+          id == o.id &&
+          scope == o.scope &&
+          columns == o.columns &&
+          rows == o.rows &&
+          total == o.total &&
+          next_cursor == o.next_cursor &&
+          sort == o.sort &&
+          filters == o.filters &&
+          group_by == o.group_by &&
+          measures == o.measures &&
+          attribution == o.attribution &&
+          source_credit == o.source_credit &&
+          withheld_tiers == o.withheld_tiers &&
+          withheld_columns == o.withheld_columns &&
+          freshness == o.freshness &&
+          build == o.build &&
+          build_state == o.build_state &&
+          restriction == o.restriction
+    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
+      [dataset, grain, object_type, id, scope, columns, rows, total, next_cursor, sort, filters, group_by, measures, attribution, source_credit, withheld_tiers, withheld_columns, freshness, build, build_state, restriction].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