pharmaobservatory 0.1.4 → 0.1.6

data/lib/pharmaobservatory/models/targets_row.rb

@@ -0,0 +1,498 @@
+=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 targets dataset: one row per target (an Ensembl gene in the Open Targets roster). A grouped request returns the group columns and the measures instead, as additional properties.
+  class TargetsRow
+    # The target's Ensembl gene id (ENSG followed by eleven digits): the entry key for the targets object type. A gene symbol is not a value here; it is a separate column.
+    attr_accessor :target_id
+
+    # The target's HGNC gene symbol; the target page address accepts it.
+    attr_accessor :symbol
+
+    # The gene's name.
+    attr_accessor :name
+
+    # Open Targets biotype of the gene (protein_coding and so on); null where the source gives none.
+    attr_accessor :biotype
+
+    # The UniProt accession of the gene's canonical protein; null where there is none.
+    attr_accessor :uniprot_accession
+
+    # The protein's recommended name from UniProt; null where the gene has no protein record.
+    attr_accessor :protein_name
+
+    # The HGNC gene id (HGNC:nnnn) from UniProt; null where the gene has no protein record.
+    attr_accessor :hgnc_id
+
+    # The NCBI Gene id from UniProt; null where the gene has no protein record.
+    attr_accessor :ncbi_gene_id
+
+    # Whether the gene has a biomarker record; the biomarkers datasets enter on the gene symbol.
+    attr_accessor :has_biomarker
+
+    # Distinct drugs that act on the target, any evidence tier.
+    attr_accessor :n_drugs
+
+    # Of n_drugs, those with a curated Open Targets mechanism edge (the floor).
+    attr_accessor :n_drugs_curated
+
+    # Of n_drugs, those found only through ChEMBL or the curated investigational assets.
+    attr_accessor :n_drugs_investigational
+
+    # True when no drug beyond the curated floor is known for the target.
+    attr_accessor :moa_floor_only
+
+    # Distinct trials whose drug interventions act on the target.
+    attr_accessor :n_trials
+
+    # Of n_trials, those reached through a curated mechanism edge.
+    attr_accessor :n_trials_curated
+
+    # Of n_trials, those reached only through ChEMBL or curated investigational assets.
+    attr_accessor :n_trials_investigational
+
+    # Distinct drug and indication programs against the target (a specific indication with at least two trials); the crowding headline.
+    attr_accessor :n_programs
+
+    # Of n_programs, those with no terminated, withdrawn or suspended trial.
+    attr_accessor :n_active_programs
+
+    # The furthest phase band (0 to 4) that carries any program; 0 when the target has none.
+    attr_accessor :lead_phase
+
+    # Rank of n_programs among targets that have programs (1 is the most crowded); null when the target has none.
+    attr_accessor :programs_rank
+
+    # Share of programmed targets with fewer programs than this one, 0 to 1; null when the target has none.
+    attr_accessor :programs_pctile
+
+    # Distinct approved drugs with a curated mechanism edge to the target.
+    attr_accessor :n_approved_drugs
+
+    # Distinct papers with a gene mention in the trial-cited PubMed corpus.
+    attr_accessor :n_publication_mention_papers
+
+    # True when any Open Targets datasource has a target-disease association for the gene.
+    attr_accessor :has_ot_association
+
+    # Protein Data Bank structures mapped to the gene's protein.
+    attr_accessor :n_pdb
+
+    # True when at least one Protein Data Bank structure maps to the gene's protein.
+    attr_accessor :has_pdb
+
+    # Attribute mapping from ruby-style variable name to JSON key.
+    def self.attribute_map
+      {
+        :'target_id' => :'target_id',
+        :'symbol' => :'symbol',
+        :'name' => :'name',
+        :'biotype' => :'biotype',
+        :'uniprot_accession' => :'uniprot_accession',
+        :'protein_name' => :'protein_name',
+        :'hgnc_id' => :'hgnc_id',
+        :'ncbi_gene_id' => :'ncbi_gene_id',
+        :'has_biomarker' => :'has_biomarker',
+        :'n_drugs' => :'n_drugs',
+        :'n_drugs_curated' => :'n_drugs_curated',
+        :'n_drugs_investigational' => :'n_drugs_investigational',
+        :'moa_floor_only' => :'moa_floor_only',
+        :'n_trials' => :'n_trials',
+        :'n_trials_curated' => :'n_trials_curated',
+        :'n_trials_investigational' => :'n_trials_investigational',
+        :'n_programs' => :'n_programs',
+        :'n_active_programs' => :'n_active_programs',
+        :'lead_phase' => :'lead_phase',
+        :'programs_rank' => :'programs_rank',
+        :'programs_pctile' => :'programs_pctile',
+        :'n_approved_drugs' => :'n_approved_drugs',
+        :'n_publication_mention_papers' => :'n_publication_mention_papers',
+        :'has_ot_association' => :'has_ot_association',
+        :'n_pdb' => :'n_pdb',
+        :'has_pdb' => :'has_pdb'
+      }
+    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
+      {
+        :'target_id' => :'String',
+        :'symbol' => :'String',
+        :'name' => :'String',
+        :'biotype' => :'String',
+        :'uniprot_accession' => :'String',
+        :'protein_name' => :'String',
+        :'hgnc_id' => :'String',
+        :'ncbi_gene_id' => :'String',
+        :'has_biomarker' => :'Boolean',
+        :'n_drugs' => :'Integer',
+        :'n_drugs_curated' => :'Integer',
+        :'n_drugs_investigational' => :'Integer',
+        :'moa_floor_only' => :'Boolean',
+        :'n_trials' => :'Integer',
+        :'n_trials_curated' => :'Integer',
+        :'n_trials_investigational' => :'Integer',
+        :'n_programs' => :'Float',
+        :'n_active_programs' => :'Float',
+        :'lead_phase' => :'Integer',
+        :'programs_rank' => :'Integer',
+        :'programs_pctile' => :'Float',
+        :'n_approved_drugs' => :'Integer',
+        :'n_publication_mention_papers' => :'Integer',
+        :'has_ot_association' => :'Boolean',
+        :'n_pdb' => :'Integer',
+        :'has_pdb' => :'Boolean'
+      }
+    end
+
+    # List of attributes with nullable: true
+    def self.openapi_nullable
+      Set.new([
+        :'target_id',
+        :'symbol',
+        :'name',
+        :'biotype',
+        :'uniprot_accession',
+        :'protein_name',
+        :'hgnc_id',
+        :'ncbi_gene_id',
+        :'has_biomarker',
+        :'n_drugs',
+        :'n_drugs_curated',
+        :'n_drugs_investigational',
+        :'moa_floor_only',
+        :'n_trials',
+        :'n_trials_curated',
+        :'n_trials_investigational',
+        :'n_programs',
+        :'n_active_programs',
+        :'lead_phase',
+        :'programs_rank',
+        :'programs_pctile',
+        :'n_approved_drugs',
+        :'n_publication_mention_papers',
+        :'has_ot_association',
+        :'n_pdb',
+        :'has_pdb'
+      ])
+    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::TargetsRow` 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::TargetsRow`. 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?(:'target_id')
+        self.target_id = attributes[:'target_id']
+      end
+
+      if attributes.key?(:'symbol')
+        self.symbol = attributes[:'symbol']
+      end
+
+      if attributes.key?(:'name')
+        self.name = attributes[:'name']
+      end
+
+      if attributes.key?(:'biotype')
+        self.biotype = attributes[:'biotype']
+      end
+
+      if attributes.key?(:'uniprot_accession')
+        self.uniprot_accession = attributes[:'uniprot_accession']
+      end
+
+      if attributes.key?(:'protein_name')
+        self.protein_name = attributes[:'protein_name']
+      end
+
+      if attributes.key?(:'hgnc_id')
+        self.hgnc_id = attributes[:'hgnc_id']
+      end
+
+      if attributes.key?(:'ncbi_gene_id')
+        self.ncbi_gene_id = attributes[:'ncbi_gene_id']
+      end
+
+      if attributes.key?(:'has_biomarker')
+        self.has_biomarker = attributes[:'has_biomarker']
+      end
+
+      if attributes.key?(:'n_drugs')
+        self.n_drugs = attributes[:'n_drugs']
+      end
+
+      if attributes.key?(:'n_drugs_curated')
+        self.n_drugs_curated = attributes[:'n_drugs_curated']
+      end
+
+      if attributes.key?(:'n_drugs_investigational')
+        self.n_drugs_investigational = attributes[:'n_drugs_investigational']
+      end
+
+      if attributes.key?(:'moa_floor_only')
+        self.moa_floor_only = attributes[:'moa_floor_only']
+      end
+
+      if attributes.key?(:'n_trials')
+        self.n_trials = attributes[:'n_trials']
+      end
+
+      if attributes.key?(:'n_trials_curated')
+        self.n_trials_curated = attributes[:'n_trials_curated']
+      end
+
+      if attributes.key?(:'n_trials_investigational')
+        self.n_trials_investigational = attributes[:'n_trials_investigational']
+      end
+
+      if attributes.key?(:'n_programs')
+        self.n_programs = attributes[:'n_programs']
+      end
+
+      if attributes.key?(:'n_active_programs')
+        self.n_active_programs = attributes[:'n_active_programs']
+      end
+
+      if attributes.key?(:'lead_phase')
+        self.lead_phase = attributes[:'lead_phase']
+      end
+
+      if attributes.key?(:'programs_rank')
+        self.programs_rank = attributes[:'programs_rank']
+      end
+
+      if attributes.key?(:'programs_pctile')
+        self.programs_pctile = attributes[:'programs_pctile']
+      end
+
+      if attributes.key?(:'n_approved_drugs')
+        self.n_approved_drugs = attributes[:'n_approved_drugs']
+      end
+
+      if attributes.key?(:'n_publication_mention_papers')
+        self.n_publication_mention_papers = attributes[:'n_publication_mention_papers']
+      end
+
+      if attributes.key?(:'has_ot_association')
+        self.has_ot_association = attributes[:'has_ot_association']
+      end
+
+      if attributes.key?(:'n_pdb')
+        self.n_pdb = attributes[:'n_pdb']
+      end
+
+      if attributes.key?(:'has_pdb')
+        self.has_pdb = attributes[:'has_pdb']
+      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 &&
+          target_id == o.target_id &&
+          symbol == o.symbol &&
+          name == o.name &&
+          biotype == o.biotype &&
+          uniprot_accession == o.uniprot_accession &&
+          protein_name == o.protein_name &&
+          hgnc_id == o.hgnc_id &&
+          ncbi_gene_id == o.ncbi_gene_id &&
+          has_biomarker == o.has_biomarker &&
+          n_drugs == o.n_drugs &&
+          n_drugs_curated == o.n_drugs_curated &&
+          n_drugs_investigational == o.n_drugs_investigational &&
+          moa_floor_only == o.moa_floor_only &&
+          n_trials == o.n_trials &&
+          n_trials_curated == o.n_trials_curated &&
+          n_trials_investigational == o.n_trials_investigational &&
+          n_programs == o.n_programs &&
+          n_active_programs == o.n_active_programs &&
+          lead_phase == o.lead_phase &&
+          programs_rank == o.programs_rank &&
+          programs_pctile == o.programs_pctile &&
+          n_approved_drugs == o.n_approved_drugs &&
+          n_publication_mention_papers == o.n_publication_mention_papers &&
+          has_ot_association == o.has_ot_association &&
+          n_pdb == o.n_pdb &&
+          has_pdb == o.has_pdb
+    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
+      [target_id, symbol, name, biotype, uniprot_accession, protein_name, hgnc_id, ncbi_gene_id, has_biomarker, n_drugs, n_drugs_curated, n_drugs_investigational, moa_floor_only, n_trials, n_trials_curated, n_trials_investigational, n_programs, n_active_programs, lead_phase, programs_rank, programs_pctile, n_approved_drugs, n_publication_mention_papers, has_ot_association, n_pdb, has_pdb].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_adverse_events_response.rb

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

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

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