pharmaobservatory 0.1.4 → 0.1.6

data/lib/pharmaobservatory/models/trial_drug_classes_row.rb

@@ -0,0 +1,278 @@
+=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 trial_drug_classes dataset: one row per trial and canonical drug. A grouped request returns the group columns and the measures instead, as additional properties.
+  class TrialDrugClassesRow
+    # The trial's ClinicalTrials.gov registry id (NCT, National Clinical Trial, number).
+    attr_accessor :trial_id
+
+    # The canonical drug key the trial's intervention names matched.
+    attr_accessor :drug_id
+
+    # The drug's display name.
+    attr_accessor :drug_name
+
+    # The drug key after same-substance drug records are merged.
+    attr_accessor :resolved_drug_id
+
+    # True when the drug is marked approved by any regulator (false means investigational or unknown).
+    attr_accessor :approved_anywhere
+
+    # The ATC first-level class of the drug (null when it has none).
+    attr_accessor :atc_class
+
+    # Attribute mapping from ruby-style variable name to JSON key.
+    def self.attribute_map
+      {
+        :'trial_id' => :'trial_id',
+        :'drug_id' => :'drug_id',
+        :'drug_name' => :'drug_name',
+        :'resolved_drug_id' => :'resolved_drug_id',
+        :'approved_anywhere' => :'approved_anywhere',
+        :'atc_class' => :'atc_class'
+      }
+    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
+      {
+        :'trial_id' => :'String',
+        :'drug_id' => :'String',
+        :'drug_name' => :'String',
+        :'resolved_drug_id' => :'String',
+        :'approved_anywhere' => :'Boolean',
+        :'atc_class' => :'String'
+      }
+    end
+
+    # List of attributes with nullable: true
+    def self.openapi_nullable
+      Set.new([
+        :'trial_id',
+        :'drug_id',
+        :'drug_name',
+        :'resolved_drug_id',
+        :'approved_anywhere',
+        :'atc_class'
+      ])
+    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::TrialDrugClassesRow` 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::TrialDrugClassesRow`. 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?(:'trial_id')
+        self.trial_id = attributes[:'trial_id']
+      end
+
+      if attributes.key?(:'drug_id')
+        self.drug_id = attributes[:'drug_id']
+      end
+
+      if attributes.key?(:'drug_name')
+        self.drug_name = attributes[:'drug_name']
+      end
+
+      if attributes.key?(:'resolved_drug_id')
+        self.resolved_drug_id = attributes[:'resolved_drug_id']
+      end
+
+      if attributes.key?(:'approved_anywhere')
+        self.approved_anywhere = attributes[:'approved_anywhere']
+      end
+
+      if attributes.key?(:'atc_class')
+        self.atc_class = attributes[:'atc_class']
+      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 &&
+          trial_id == o.trial_id &&
+          drug_id == o.drug_id &&
+          drug_name == o.drug_name &&
+          resolved_drug_id == o.resolved_drug_id &&
+          approved_anywhere == o.approved_anywhere &&
+          atc_class == o.atc_class
+    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
+      [trial_id, drug_id, drug_name, resolved_drug_id, approved_anywhere, atc_class].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/trial_drugs_response.rb

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

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

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

@@ -19,9 +19,12 @@ module PharmaObservatory
     # The trial's ClinicalTrials.gov registry id (NCT, National Clinical Trial, number).
     attr_accessor :trial_id
 
-    # 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
+
     # The lead sponsor name as filed.
     attr_accessor :lead_sponsor_name
 
@@ -55,10 +58,10 @@ module PharmaObservatory
     # Completion date.
     attr_accessor :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
 
-    # 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
 
     # Whether the inputs support a rate.
@@ -84,6 +87,7 @@ module PharmaObservatory
       {
         :'trial_id' => :'trial_id',
         :'phase' => :'phase',
+        :'phase_label' => :'phase_label',
         :'lead_sponsor_name' => :'lead_sponsor_name',
         :'overall_status_summary' => :'overall_status_summary',
         :'actual_enrollment' => :'actual_enrollment',
@@ -121,6 +125,7 @@ module PharmaObservatory
       {
         :'trial_id' => :'String',
         :'phase' => :'String',
+        :'phase_label' => :'String',
         :'lead_sponsor_name' => :'String',
         :'overall_status_summary' => :'String',
         :'actual_enrollment' => :'Integer',
@@ -148,6 +153,7 @@ module PharmaObservatory
       Set.new([
         :'trial_id',
         :'phase',
+        :'phase_label',
         :'lead_sponsor_name',
         :'overall_status_summary',
         :'actual_enrollment',
@@ -194,6 +200,10 @@ module PharmaObservatory
         self.phase = attributes[:'phase']
       end
 
+      if attributes.key?(:'phase_label')
+        self.phase_label = attributes[:'phase_label']
+      end
+
       if attributes.key?(:'lead_sponsor_name')
         self.lead_sponsor_name = attributes[:'lead_sponsor_name']
       end
@@ -293,6 +303,7 @@ module PharmaObservatory
       self.class == o.class &&
           trial_id == o.trial_id &&
           phase == o.phase &&
+          phase_label == o.phase_label &&
           lead_sponsor_name == o.lead_sponsor_name &&
           overall_status_summary == o.overall_status_summary &&
           actual_enrollment == o.actual_enrollment &&
@@ -323,7 +334,7 @@ module PharmaObservatory
     # Calculates hash code according to all attributes.
     # @return [Integer] Hash code
     def hash
-      [trial_id, phase, lead_sponsor_name, overall_status_summary, actual_enrollment, enrollment_type, enrollment_is_plausible, active_sites, facility_country_count, has_us_facility, start_date, primary_completion_date, completion_date, primary_completion_date_type, completion_date_type, is_rate_computable, rate_flag_reason, duration_months, duration_months_overall, pts_per_month, pts_per_site_month].hash
+      [trial_id, phase, phase_label, lead_sponsor_name, overall_status_summary, actual_enrollment, enrollment_type, enrollment_is_plausible, active_sites, facility_country_count, has_us_facility, start_date, primary_completion_date, completion_date, primary_completion_date_type, completion_date_type, is_rate_computable, rate_flag_reason, duration_months, duration_months_overall, pts_per_month, pts_per_site_month].hash
     end
 
     # Builds the object from hash

data/lib/pharmaobservatory/models/trial_extracted_endpoints_response.rb

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