openphar 0.1.0

data/lib/openphar/models/ph_int/test_method.rb

@@ -0,0 +1,50 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    module PhInt
+      # Test Method
+      #
+      # Represents analytical test methods from Ph.Int. Section 7.
+      #
+      # Test methods define procedures for quality control testing
+      # of pharmaceutical substances and products.
+      #
+      # @example
+      #   method = PhInt::TestMethod.new(
+      #     id: 'phint-method-hplc',
+      #     method_id: '2.2.29',
+      #     method_type: 'Chromatography',
+      #     description: { 'en' => 'Liquid chromatography...' }
+      #   )
+      class TestMethod < BaseEntity
+        attribute :method_id, :string
+        attribute :pref_label, :hash, default: {}
+        attribute :method_type, :string
+        attribute :description, :hash, default: {}
+        attribute :publisher, :string
+        attribute :belongs_to_edition, :string
+
+        json do
+          map '@id', to: :id
+          map 'methodId', to: :method_id
+          map 'prefLabel', to: :pref_label
+          map 'methodType', to: :method_type
+          map 'description', to: :description
+          map 'publisher', to: :publisher
+          map 'belongsToEdition', to: :belongs_to_edition
+        end
+
+        class << self
+          def neo4j_labels
+            ['TestMethod']
+          end
+
+          def jsonld_type
+            'TestMethod'
+          end
+        end
+      end
+    end
+  end
+end

data/lib/openphar/models/ph_int/test_solution.rb

@@ -0,0 +1,39 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    module PhInt
+      # Test Solution
+      #
+      # A solution used in pharmacopoeial tests.
+      # Test solutions have a specific concentration and may have
+      # specific storage requirements.
+      #
+      # @example
+      #   solution = PhInt::TestSolution.new(
+      #     id: 'phint-ts-ferric-chloride',
+      #     concentration: '5% w/v',
+      #     storage_conditions: { 'temperature' => '2-8°C' }
+      #   )
+      class TestSolution < Reagent
+        attribute :concentration, :string
+        attribute :storage_conditions, :hash, default: {}
+
+        json do
+          map 'concentration', to: :concentration
+          map 'storageConditions', to: :storage_conditions
+        end
+
+        class << self
+          def neo4j_labels
+            %w[Reagent TestSolution]
+          end
+
+          def jsonld_type
+            'TestSolution'
+          end
+        end
+      end
+    end
+  end
+end

data/lib/openphar/models/ph_int/volumetric_solution.rb

@@ -0,0 +1,38 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    module PhInt
+      # Volumetric Solution
+      #
+      # A solution of known concentration used for titrations.
+      # Volumetric solutions must be standardized against a primary standard.
+      #
+      # @example
+      #   solution = PhInt::VolumetricSolution.new(
+      #     id: 'phint-vs-hcl-01m',
+      #     molarity: '0.1 mol/L',
+      #     standardization: { 'primaryStandard' => 'Sodium carbonate' }
+      #   )
+      class VolumetricSolution < Reagent
+        attribute :molarity, :string
+        attribute :standardization, :hash, default: {}
+
+        json do
+          map 'molarity', to: :molarity
+          map 'standardization', to: :standardization
+        end
+
+        class << self
+          def neo4j_labels
+            %w[Reagent VolumetricSolution]
+          end
+
+          def jsonld_type
+            'VolumetricSolution'
+          end
+        end
+      end
+    end
+  end
+end

data/lib/openphar/models/ph_int.rb

@@ -0,0 +1,37 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    # International Pharmacopoeia (Ph.Int.) specific models.
+    #
+    # Contains models unique to the WHO International Pharmacopoeia:
+    # - Radiopharmaceuticals (radioactive drugs)
+    # - Dosage form monographs
+    # - Test methods and reagents
+    # - Reference substances
+    #
+    # @example
+    #   # Access Ph.Int. models
+    #   Openphar::Models::PhInt::RadiopharmaceuticalMonograph
+    #   Openphar::Models::PhInt::TestMethod
+    #
+    # @see https://www.who.int/teams/health-product-and-policy-standards/inn-and-pharmacopoeia
+    module PhInt
+      # Monograph types
+      autoload :RadiopharmaceuticalMonograph,
+               'openphar/models/ph_int/radiopharmaceutical_monograph'
+      autoload :DosageFormMonograph,
+               'openphar/models/ph_int/dosage_form_monograph'
+
+      # Test methods and reagents
+      autoload :TestMethod, 'openphar/models/ph_int/test_method'
+      autoload :Reagent, 'openphar/models/ph_int/reagent'
+      autoload :TestSolution, 'openphar/models/ph_int/test_solution'
+      autoload :VolumetricSolution, 'openphar/models/ph_int/volumetric_solution'
+      autoload :BufferSolution, 'openphar/models/ph_int/buffer_solution'
+
+      # Reference substances
+      autoload :ReferenceSubstance, 'openphar/models/ph_int/reference_substance'
+    end
+  end
+end

data/lib/openphar/models/physical_specification.rb

@@ -0,0 +1,17 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    # Represents a physical specification
+    #
+    # Physical specifications define limits for physical properties
+    # such as melting point, optical rotation, density, etc.
+    class PhysicalSpecification < TestSpecification
+      attribute :physical_property, :hash, default: {}
+
+      json do
+        map 'physicalProperty', to: :physical_property
+      end
+    end
+  end
+end

data/lib/openphar/models/publisher.rb

@@ -0,0 +1,98 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    # Represents a pharmacopoeia publisher
+    class Publisher < Lutaml::Model::Serializable
+      attribute :id, :string
+      attribute :code, :string
+      attribute :name, :hash, default: {}
+      attribute :country, :string
+      attribute :url, :string
+
+      # Publisher registry
+      PUBLISHERS = {
+        'JP' => {
+          code: 'JP',
+          name: { 'en' => 'Japanese Pharmacopoeia', 'ja' => '日本薬局方' },
+          country: 'JP',
+          url: 'https://www.mhlw.go.jp/topics/bukyoku/iyaku/yakkyoku/'
+        },
+        'PhInt' => {
+          code: 'PhInt',
+          name: { 'en' => 'International Pharmacopoeia', 'fr' => 'Pharmacopée Internationale' },
+          country: 'INT',
+          url: 'https://www.who.int/teams/health-product-and-policy-standards/inn-and-pharmacopoeia'
+        },
+        'API' => {
+          code: 'API',
+          name: { 'en' => 'Ayurvedic Pharmacopoeia of India' },
+          country: 'IN',
+          url: 'https://main.ayush.gov.in/'
+        },
+        'HKCMMS' => {
+          code: 'HKCMMS',
+          name: { 'en' => 'Hong Kong Chinese Materia Medica Standards', 'zh-Hant' => '香港中藥材標準' },
+          country: 'HK',
+          url: 'https://www.cmms.org.hk/'
+        },
+        'THP' => {
+          code: 'THP',
+          name: { 'en' => 'Thai Herbal Pharmacopoeia', 'th' => 'ตำรายาจารีกสมุนไพร' },
+          country: 'TH',
+          url: 'https://www.fda.moph.go.th/'
+        },
+        'AHP' => {
+          code: 'AHP',
+          name: { 'en' => 'American Herbal Pharmacopoeia' },
+          country: 'US',
+          url: 'https://www.herbal-ahp.org/'
+        },
+        'WHO' => {
+          code: 'WHO',
+          name: { 'en' => 'WHO Monographs on Selected Medicinal Plants' },
+          country: 'INT',
+          url: 'https://www.who.int/'
+        }
+      }.freeze
+
+      json do
+        map '@id', to: :id
+        map 'code', to: :code
+        map 'name', to: :name
+        map 'country', to: :country
+        map 'url', to: :url
+      end
+
+      class << self
+        # Find a publisher by code
+        def find(code)
+          return nil unless PUBLISHERS.key?(code)
+
+          data = PUBLISHERS[code]
+          new(
+            id: code,
+            code: data[:code],
+            name: data[:name],
+            country: data[:country],
+            url: data[:url]
+          )
+        end
+
+        # Returns all publishers
+        def all
+          PUBLISHERS.keys.map { |code| find(code) }
+        end
+
+        # Returns the IRI for a publisher
+        def iri(code)
+          "#{Openphar.base_iri}/ontology/core/#{code}"
+        end
+      end
+
+      def iri
+        self.class.iri(code)
+      end
+    end
+  end
+end

data/lib/openphar/models/purity_specification.rb

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+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    # Represents a purity specification
+    #
+    # Purity specifications define limits for impurities in a substance.
+    class PuritySpecification < TestSpecification
+      attribute :impurity_type, :hash, default: {}
+
+      json do
+        map 'impurityType', to: :impurity_type
+      end
+    end
+  end
+end

data/lib/openphar/models/supplement.rb

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    # Represents a supplement to a pharmacopoeia edition
+    #
+    # Supplements are updates issued between main editions,
+    # containing additions, deletions, and revisions.
+    class Supplement < Lutaml::Model::Serializable
+      attribute :id, :string
+      attribute :supplement_number, :string
+      attribute :supplement_to, :string
+      attribute :publication_date, :date
+      attribute :effective_date, :date
+      attribute :pref_label, :hash, default: {}
+
+      json do
+        map 'id', to: :id
+        map 'supplementNumber', to: :supplement_number
+        map 'supplementTo', to: :supplement_to
+        map 'supplementPublicationDate', to: :publication_date
+        map 'supplementEffectiveDate', to: :effective_date
+        map 'prefLabel', to: :pref_label
+      end
+
+      def iri
+        "#{Openphar.base_iri}/data/edition/#{id}"
+      end
+    end
+  end
+end

data/lib/openphar/models/test_specification.rb

@@ -0,0 +1,29 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    # Represents a test specification within a monograph
+    #
+    # Base class for all test specification types. Each test specification
+    # defines acceptance criteria for a specific quality test.
+    class TestSpecification < Lutaml::Model::Serializable
+      attribute :id, :string
+      attribute :test_name, :hash, default: {}
+      attribute :test_type, :string
+      attribute :harmonized_method, :string
+      attribute :publisher_method, :string
+      attribute :test_conditions, :hash, default: {}
+      attribute :limit, Limit
+
+      json do
+        map '@id', to: :id
+        map 'testName', to: :test_name
+        map 'testType', to: :test_type
+        map 'harmonizedMethod', to: :harmonized_method
+        map 'publisherMethod', to: :publisher_method
+        map 'testConditions', to: :test_conditions
+        map 'limit', to: :limit
+      end
+    end
+  end
+end

data/lib/openphar/models/thp.rb

@@ -0,0 +1,24 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    # Thai Herbal Pharmacopoeia (THP) specific models.
+    #
+    # Contains models unique to the Thai Herbal Pharmacopoeia:
+    # - Thai traditional medicine monographs
+    # - Bilingual (Thai/English) content
+    # - Cannabis monographs (legal in Thailand)
+    #
+    # @example
+    #   # Access THP models
+    #   Openphar::Models::THP::ThaiHerbalMonograph
+    #
+    # @see http://www.fda.moph.go.th/
+    module THP
+      # Placeholder for THP-specific models
+      # Will include:
+      # - ThaiHerbalMonograph
+      # - CannabisMonograph (THP-specific)
+    end
+  end
+end

data/lib/openphar/models/vitamin_monograph.rb

@@ -0,0 +1,28 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    # Represents a vitamin monograph
+    #
+    # Vitamins are essential organic compounds required in small amounts.
+    class VitaminMonograph < ChemicalDrugMonograph
+      attribute :vitamin_type, :string
+      attribute :biological_activity, :string
+
+      json do
+        map 'vitaminType', to: :vitamin_type
+        map 'biologicalActivity', to: :biological_activity
+      end
+
+      class << self
+        def neo4j_labels
+          %w[Monograph ChemicalDrug Vitamin]
+        end
+
+        def jsonld_type
+          'VitaminMonograph'
+        end
+      end
+    end
+  end
+end

data/lib/openphar/models.rb

@@ -0,0 +1,58 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    # Data models for pharmacopoeia entities.
+    #
+    # All models inherit from BaseEntity and define their attributes,
+    # JSON mappings, and serialization methods.
+    #
+    # == Namespace Structure
+    #
+    # Core models are defined directly in Openphar::Models:
+    # - Monograph and its subclasses (CrudeDrugMonograph, ChemicalDrugMonograph, etc.)
+    # - Limit, TestSpecification and subclasses
+    # - Edition, Supplement, Publisher
+    #
+    # Publisher-specific models are in sub-modules:
+    # - Openphar::Models::PhInt (International Pharmacopoeia)
+    # - Openphar::Models::JP (Japan Pharmacopoeia)
+
+    # Base class with common serialization
+    autoload :BaseEntity, 'openphar/models/base_entity'
+
+    # Quantitative limits
+    autoload :Limit, 'openphar/models/limit'
+
+    # Test specifications (one class per file)
+    autoload :TestSpecification, 'openphar/models/test_specification'
+    autoload :AssaySpecification, 'openphar/models/assay_specification'
+    autoload :PuritySpecification, 'openphar/models/purity_specification'
+    autoload :PhysicalSpecification, 'openphar/models/physical_specification'
+    autoload :IdentificationSpecification, 'openphar/models/identification_specification'
+
+    # Bibliographic entities (one class per file)
+    autoload :Edition, 'openphar/models/edition'
+    autoload :Supplement, 'openphar/models/supplement'
+    autoload :Publisher, 'openphar/models/publisher'
+
+    # Monograph types (one class per file)
+    autoload :Monograph, 'openphar/models/monograph'
+    autoload :CrudeDrugMonograph, 'openphar/models/crude_drug_monograph'
+    autoload :ChemicalDrugMonograph, 'openphar/models/chemical_drug_monograph'
+    autoload :FormulationMonograph, 'openphar/models/formulation_monograph'
+    autoload :VitaminMonograph, 'openphar/models/vitamin_monograph'
+    autoload :AminoAcidMonograph, 'openphar/models/amino_acid_monograph'
+    autoload :MineralSubstanceMonograph, 'openphar/models/mineral_substance_monograph'
+    autoload :BiologicalSubstanceMonograph, 'openphar/models/biological_substance_monograph'
+
+    # Publisher-specific model modules
+    autoload :PhInt, 'openphar/models/ph_int'
+    autoload :JP, 'openphar/models/jp'
+    autoload :Chp, 'openphar/models/chp'
+    autoload :AHP, 'openphar/models/ahp'
+    autoload :API, 'openphar/models/api'
+    autoload :HKCMMS, 'openphar/models/hkcmms'
+    autoload :THP, 'openphar/models/thp'
+  end
+end