pharmaobservatory 0.1.1 → 0.1.3

data/lib/pharmaobservatory/models/cell_lines_row.rb

@@ -0,0 +1,423 @@
+=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 cell_lines dataset: one row per cell line in the Scientist.com catalog. A grouped request returns the group columns and the measures instead, as additional properties.
+  class CellLinesRow
+    # The catalog listing's model id (scientist_model_id).
+    attr_accessor :cell_line_id
+
+    # Other catalog model ids for the same line.
+    attr_accessor :alternate_cell_line_ids
+
+    # The lot id.
+    attr_accessor :model_lot_id
+
+    # The cell line's name.
+    attr_accessor :cell_type
+
+    # The supplier's catalog id.
+    attr_accessor :provider_id
+
+    # The supplier as listed.
+    attr_accessor :supplier
+
+    # The species.
+    attr_accessor :sample_species
+
+    # Whether the listing is enabled in the storefront.
+    attr_accessor :storefront_enable
+
+    # Mutation data as listed.
+    attr_accessor :mutation_data
+
+    # The listing status.
+    attr_accessor :status
+
+    # confirmed_problematic, review_candidate, no_problematic_match or missing_cell_type.
+    attr_accessor :safety_status
+
+    # resolved, unresolved_review, no_match or missing_input.
+    attr_accessor :resolution_status
+
+    # Whether the line is confirmed problematic in Cellosaurus.
+    attr_accessor :confirmed_problematic
+
+    # The displayed Cellosaurus accession.
+    attr_accessor :cellosaurus_accession
+
+    # Link to the Cellosaurus entry.
+    attr_accessor :cellosaurus_url
+
+    # The problem category, for a problematic line.
+    attr_accessor :problem_category
+
+    # The Cellosaurus comment, for a problematic line.
+    attr_accessor :problematic_comment
+
+    # ICLAC registration ids.
+    attr_accessor :iclac_registration_ids
+
+    # The Cellosaurus release the check ran against.
+    attr_accessor :release_version
+
+    # Attribute mapping from ruby-style variable name to JSON key.
+    def self.attribute_map
+      {
+        :'cell_line_id' => :'cell_line_id',
+        :'alternate_cell_line_ids' => :'alternate_cell_line_ids',
+        :'model_lot_id' => :'model_lot_id',
+        :'cell_type' => :'cell_type',
+        :'provider_id' => :'provider_id',
+        :'supplier' => :'supplier',
+        :'sample_species' => :'sample_species',
+        :'storefront_enable' => :'storefront_enable',
+        :'mutation_data' => :'mutation_data',
+        :'status' => :'status',
+        :'safety_status' => :'safety_status',
+        :'resolution_status' => :'resolution_status',
+        :'confirmed_problematic' => :'confirmed_problematic',
+        :'cellosaurus_accession' => :'cellosaurus_accession',
+        :'cellosaurus_url' => :'cellosaurus_url',
+        :'problem_category' => :'problem_category',
+        :'problematic_comment' => :'problematic_comment',
+        :'iclac_registration_ids' => :'iclac_registration_ids',
+        :'release_version' => :'release_version'
+      }
+    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
+      {
+        :'cell_line_id' => :'String',
+        :'alternate_cell_line_ids' => :'String',
+        :'model_lot_id' => :'String',
+        :'cell_type' => :'String',
+        :'provider_id' => :'String',
+        :'supplier' => :'String',
+        :'sample_species' => :'String',
+        :'storefront_enable' => :'Boolean',
+        :'mutation_data' => :'String',
+        :'status' => :'String',
+        :'safety_status' => :'String',
+        :'resolution_status' => :'String',
+        :'confirmed_problematic' => :'Boolean',
+        :'cellosaurus_accession' => :'String',
+        :'cellosaurus_url' => :'String',
+        :'problem_category' => :'String',
+        :'problematic_comment' => :'String',
+        :'iclac_registration_ids' => :'Array<String>',
+        :'release_version' => :'String'
+      }
+    end
+
+    # List of attributes with nullable: true
+    def self.openapi_nullable
+      Set.new([
+        :'cell_line_id',
+        :'alternate_cell_line_ids',
+        :'model_lot_id',
+        :'cell_type',
+        :'provider_id',
+        :'supplier',
+        :'sample_species',
+        :'storefront_enable',
+        :'mutation_data',
+        :'status',
+        :'safety_status',
+        :'resolution_status',
+        :'confirmed_problematic',
+        :'cellosaurus_accession',
+        :'cellosaurus_url',
+        :'problem_category',
+        :'problematic_comment',
+        :'iclac_registration_ids',
+        :'release_version'
+      ])
+    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::CellLinesRow` 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::CellLinesRow`. 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?(:'cell_line_id')
+        self.cell_line_id = attributes[:'cell_line_id']
+      end
+
+      if attributes.key?(:'alternate_cell_line_ids')
+        self.alternate_cell_line_ids = attributes[:'alternate_cell_line_ids']
+      end
+
+      if attributes.key?(:'model_lot_id')
+        self.model_lot_id = attributes[:'model_lot_id']
+      end
+
+      if attributes.key?(:'cell_type')
+        self.cell_type = attributes[:'cell_type']
+      end
+
+      if attributes.key?(:'provider_id')
+        self.provider_id = attributes[:'provider_id']
+      end
+
+      if attributes.key?(:'supplier')
+        self.supplier = attributes[:'supplier']
+      end
+
+      if attributes.key?(:'sample_species')
+        self.sample_species = attributes[:'sample_species']
+      end
+
+      if attributes.key?(:'storefront_enable')
+        self.storefront_enable = attributes[:'storefront_enable']
+      end
+
+      if attributes.key?(:'mutation_data')
+        self.mutation_data = attributes[:'mutation_data']
+      end
+
+      if attributes.key?(:'status')
+        self.status = attributes[:'status']
+      end
+
+      if attributes.key?(:'safety_status')
+        self.safety_status = attributes[:'safety_status']
+      end
+
+      if attributes.key?(:'resolution_status')
+        self.resolution_status = attributes[:'resolution_status']
+      end
+
+      if attributes.key?(:'confirmed_problematic')
+        self.confirmed_problematic = attributes[:'confirmed_problematic']
+      end
+
+      if attributes.key?(:'cellosaurus_accession')
+        self.cellosaurus_accession = attributes[:'cellosaurus_accession']
+      end
+
+      if attributes.key?(:'cellosaurus_url')
+        self.cellosaurus_url = attributes[:'cellosaurus_url']
+      end
+
+      if attributes.key?(:'problem_category')
+        self.problem_category = attributes[:'problem_category']
+      end
+
+      if attributes.key?(:'problematic_comment')
+        self.problematic_comment = attributes[:'problematic_comment']
+      end
+
+      if attributes.key?(:'iclac_registration_ids')
+        if (value = attributes[:'iclac_registration_ids']).is_a?(Array)
+          self.iclac_registration_ids = value
+        end
+      end
+
+      if attributes.key?(:'release_version')
+        self.release_version = attributes[:'release_version']
+      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 &&
+          cell_line_id == o.cell_line_id &&
+          alternate_cell_line_ids == o.alternate_cell_line_ids &&
+          model_lot_id == o.model_lot_id &&
+          cell_type == o.cell_type &&
+          provider_id == o.provider_id &&
+          supplier == o.supplier &&
+          sample_species == o.sample_species &&
+          storefront_enable == o.storefront_enable &&
+          mutation_data == o.mutation_data &&
+          status == o.status &&
+          safety_status == o.safety_status &&
+          resolution_status == o.resolution_status &&
+          confirmed_problematic == o.confirmed_problematic &&
+          cellosaurus_accession == o.cellosaurus_accession &&
+          cellosaurus_url == o.cellosaurus_url &&
+          problem_category == o.problem_category &&
+          problematic_comment == o.problematic_comment &&
+          iclac_registration_ids == o.iclac_registration_ids &&
+          release_version == o.release_version
+    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
+      [cell_line_id, alternate_cell_line_ids, model_lot_id, cell_type, provider_id, supplier, sample_species, storefront_enable, mutation_data, status, safety_status, resolution_status, confirmed_problematic, cellosaurus_accession, cellosaurus_url, problem_category, problematic_comment, iclac_registration_ids, release_version].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/{api_v1_resolve_entity_get200_response_candidates_inner.rb → companies_record.rb}

@@ -14,25 +14,43 @@ require 'date'
 require 'time'
 
 module PharmaObservatory
-  class ApiV1ResolveEntityGet200ResponseCandidatesInner
+  class CompaniesRecord
+    attr_accessor :object_type
+
     attr_accessor :id
 
-    attr_accessor :display_name
+    attr_accessor :record
 
-    attr_accessor :subtitle
+    attr_accessor :attributes
 
-    attr_accessor :restriction
+    attr_accessor :datasets
+
+    attr_accessor :attribution
+
+    attr_accessor :source_credit
+
+    attr_accessor :freshness
+
+    attr_accessor :build
 
-    attr_accessor :name_withheld_note
+    attr_accessor :build_state
+
+    attr_accessor :restriction
 
     # Attribute mapping from ruby-style variable name to JSON key.
     def self.attribute_map
       {
+        :'object_type' => :'object_type',
         :'id' => :'id',
-        :'display_name' => :'display_name',
-        :'subtitle' => :'subtitle',
-        :'restriction' => :'restriction',
-        :'name_withheld_note' => :'name_withheld_note'
+        :'record' => :'record',
+        :'attributes' => :'attributes',
+        :'datasets' => :'datasets',
+        :'attribution' => :'attribution',
+        :'source_credit' => :'source_credit',
+        :'freshness' => :'freshness',
+        :'build' => :'build',
+        :'build_state' => :'build_state',
+        :'restriction' => :'restriction'
       }
     end
 
@@ -49,21 +67,24 @@ module PharmaObservatory
     # Attribute type mapping.
     def self.openapi_types
       {
+        :'object_type' => :'String',
         :'id' => :'String',
-        :'display_name' => :'String',
-        :'subtitle' => :'String',
-        :'restriction' => :'ApiV1ResolveEntityGet200ResponseCandidatesInnerRestriction',
-        :'name_withheld_note' => :'String'
+        :'record' => :'CompaniesRow',
+        :'attributes' => :'Object',
+        :'datasets' => :'Array<DatasetListing>',
+        :'attribution' => :'Array<DatasetAttribution>',
+        :'source_credit' => :'String',
+        :'freshness' => :'BiomarkerCdxAssertionsResponseFreshness',
+        :'build' => :'BiomarkerCdxAssertionsResponseBuild',
+        :'build_state' => :'DatasetBuildState',
+        :'restriction' => :'Hash<String, Object>'
       }
     end
 
     # List of attributes with nullable: true
     def self.openapi_nullable
       Set.new([
-        :'display_name',
-        :'subtitle',
-        :'restriction',
-        :'name_withheld_note'
+        :'restriction'
       ])
     end
 
@@ -71,44 +92,74 @@ module PharmaObservatory
     # @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::ApiV1ResolveEntityGet200ResponseCandidatesInner` initialize method"
+        fail ArgumentError, "The input argument (attributes) must be a hash in `PharmaObservatory::CompaniesRecord` 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::ApiV1ResolveEntityGet200ResponseCandidatesInner`. Please check the name to make sure it's valid. List of attributes: " + acceptable_attribute_map.keys.inspect
+          fail ArgumentError, "`#{k}` is not a valid attribute in `PharmaObservatory::CompaniesRecord`. 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?(:'object_type')
+        self.object_type = attributes[:'object_type']
+      else
+        self.object_type = nil
+      end
+
       if attributes.key?(:'id')
         self.id = attributes[:'id']
       else
         self.id = nil
       end
 
-      if attributes.key?(:'display_name')
-        self.display_name = attributes[:'display_name']
+      if attributes.key?(:'record')
+        self.record = attributes[:'record']
       else
-        self.display_name = nil
+        self.record = nil
       end
 
-      if attributes.key?(:'subtitle')
-        self.subtitle = attributes[:'subtitle']
-      else
-        self.subtitle = nil
+      if attributes.key?(:'attributes')
+        self.attributes = attributes[:'attributes']
       end
 
-      if attributes.key?(:'restriction')
-        self.restriction = attributes[:'restriction']
+      if attributes.key?(:'datasets')
+        if (value = attributes[:'datasets']).is_a?(Array)
+          self.datasets = value
+        end
       else
-        self.restriction = nil
+        self.datasets = nil
+      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?(:'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?(:'name_withheld_note')
-        self.name_withheld_note = attributes[:'name_withheld_note']
+      if attributes.key?(:'restriction')
+        if (value = attributes[:'restriction']).is_a?(Hash)
+          self.restriction = value
+        end
       end
     end
 
@@ -117,10 +168,22 @@ module PharmaObservatory
     def list_invalid_properties
       warn '[DEPRECATED] the `list_invalid_properties` method is obsolete'
       invalid_properties = Array.new
+      if @object_type.nil?
+        invalid_properties.push('invalid value for "object_type", object_type cannot be nil.')
+      end
+
       if @id.nil?
         invalid_properties.push('invalid value for "id", id cannot be nil.')
       end
 
+      if @record.nil?
+        invalid_properties.push('invalid value for "record", record cannot be nil.')
+      end
+
+      if @datasets.nil?
+        invalid_properties.push('invalid value for "datasets", datasets cannot be nil.')
+      end
+
       invalid_properties
     end
 
@@ -128,10 +191,23 @@ module PharmaObservatory
     # @return true if the model is valid
     def valid?
       warn '[DEPRECATED] the `valid?` method is obsolete'
+      return false if @object_type.nil?
       return false if @id.nil?
+      return false if @record.nil?
+      return false if @datasets.nil?
       true
     end
 
+    # Custom attribute writer method with validation
+    # @param [Object] object_type Value to be assigned
+    def object_type=(object_type)
+      if object_type.nil?
+        fail ArgumentError, 'object_type cannot be nil'
+      end
+
+      @object_type = object_type
+    end
+
     # Custom attribute writer method with validation
     # @param [Object] id Value to be assigned
     def id=(id)
@@ -142,16 +218,42 @@ module PharmaObservatory
       @id = id
     end
 
+    # Custom attribute writer method with validation
+    # @param [Object] record Value to be assigned
+    def record=(record)
+      if record.nil?
+        fail ArgumentError, 'record cannot be nil'
+      end
+
+      @record = record
+    end
+
+    # Custom attribute writer method with validation
+    # @param [Object] datasets Value to be assigned
+    def datasets=(datasets)
+      if datasets.nil?
+        fail ArgumentError, 'datasets cannot be nil'
+      end
+
+      @datasets = datasets
+    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 &&
+          object_type == o.object_type &&
           id == o.id &&
-          display_name == o.display_name &&
-          subtitle == o.subtitle &&
-          restriction == o.restriction &&
-          name_withheld_note == o.name_withheld_note
+          record == o.record &&
+          attributes == o.attributes &&
+          datasets == o.datasets &&
+          attribution == o.attribution &&
+          source_credit == o.source_credit &&
+          freshness == o.freshness &&
+          build == o.build &&
+          build_state == o.build_state &&
+          restriction == o.restriction
     end
 
     # @see the `==` method
@@ -163,7 +265,7 @@ module PharmaObservatory
     # Calculates hash code according to all attributes.
     # @return [Integer] Hash code
     def hash
-      [id, display_name, subtitle, restriction, name_withheld_note].hash
+      [object_type, id, record, attributes, datasets, attribution, source_credit, freshness, build, build_state, restriction].hash
     end
 
     # Builds the object from hash