nuva 0.1.5

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA256:
+  metadata.gz: 1e148630bce72f2f69b968c056be4d444aace8d18315310357a05f6f4caff9c6
+  data.tar.gz: '07290eea14dcd22ba6fd882d5b76bca612cb31c8a7d323561bd694d61179742b'
+SHA512:
+  metadata.gz: edb17bf2804b877d575416e27c59bc2833e5f78a13b3521815a3b4de2f6112d741ea45f58578b35955bb09c51dfc3a745578ace6fb245b870fd4dc1bd8b7f02e
+  data.tar.gz: be3a3e224cc7900e34d9add113e7989058e22db563fc81645707d101fde200baffb8ba40e491d1ac0fb73148af0bcd1e27d42750044f7a59fd283f40476454cf

data/lib/Code_pb.rb

@@ -0,0 +1,17 @@
+# Generated by the protocol buffer compiler.  DO NOT EDIT!
+# source: Code.proto
+
+require 'google/protobuf'
+
+Google::Protobuf::DescriptorPool.generated_pool.build do
+  add_file("Code.proto", :syntax => :proto2) do
+    add_message "nuva.Code" do
+      required :nomenclature, :string, 1
+      required :value, :string, 2
+    end
+  end
+end
+
+module Nuva
+  Code = ::Google::Protobuf::DescriptorPool.generated_pool.lookup("nuva.Code").msgclass
+end

data/lib/Disease_pb.rb

@@ -0,0 +1,27 @@
+# Generated by the protocol buffer compiler.  DO NOT EDIT!
+# source: Disease.proto
+
+require 'google/protobuf'
+
+require 'google/protobuf/timestamp_pb'
+require_relative 'Code_pb'
+
+Google::Protobuf::DescriptorPool.generated_pool.build do
+  add_file("Disease.proto", :syntax => :proto2) do
+    add_message "nuva.Disease" do
+      required :id, :string, 1
+      required :name, :string, 2
+      required :code, :uint32, 3
+      repeated :codes, :message, 4, "nuva.Code"
+      required :vaccinable, :bool, 5
+      required :screenable, :bool, 6
+      repeated :valence_ids, :string, 7
+      optional :created_at, :message, 16, "google.protobuf.Timestamp"
+      optional :updated_at, :message, 17, "google.protobuf.Timestamp"
+    end
+  end
+end
+
+module Nuva
+  Disease = ::Google::Protobuf::DescriptorPool.generated_pool.lookup("nuva.Disease").msgclass
+end

data/lib/InjectionMethod_pb.rb

@@ -0,0 +1,21 @@
+# Generated by the protocol buffer compiler.  DO NOT EDIT!
+# source: InjectionMethod.proto
+
+require 'google/protobuf'
+
+Google::Protobuf::DescriptorPool.generated_pool.build do
+  add_file("InjectionMethod.proto", :syntax => :proto2) do
+    add_enum "nuva.InjectionMethod" do
+      value :UnspecifiedInjectionMethod, 0
+      value :Intramuscular, 1
+      value :Subcutaneous, 2
+      value :Oral, 3
+      value :Intranasal, 4
+      value :Intradermal, 5
+    end
+  end
+end
+
+module Nuva
+  InjectionMethod = ::Google::Protobuf::DescriptorPool.generated_pool.lookup("nuva.InjectionMethod").enummodule
+end

data/lib/NuvaDatabase_pb.rb

@@ -0,0 +1,27 @@
+# Generated by the protocol buffer compiler.  DO NOT EDIT!
+# source: NuvaDatabase.proto
+
+require 'google/protobuf'
+
+require 'google/protobuf/timestamp_pb'
+require_relative 'VersionInfo_pb'
+require_relative 'Vaccine_pb'
+require_relative 'Disease_pb'
+require_relative 'Valence_pb'
+
+Google::Protobuf::DescriptorPool.generated_pool.build do
+  add_file("NuvaDatabase.proto", :syntax => :proto2) do
+    add_message "nuva.NuvaDatabase" do
+      required :version, :message, 1, "nuva.VersionInfo"
+      required :generated_at, :message, 2, "google.protobuf.Timestamp"
+      required :locale, :string, 3
+      repeated :vaccines, :message, 4, "nuva.Vaccine"
+      repeated :diseases, :message, 5, "nuva.Disease"
+      repeated :valences, :message, 6, "nuva.Valence"
+    end
+  end
+end
+
+module Nuva
+  NuvaDatabase = ::Google::Protobuf::DescriptorPool.generated_pool.lookup("nuva.NuvaDatabase").msgclass
+end

data/lib/Vaccine_pb.rb

@@ -0,0 +1,32 @@
+# Generated by the protocol buffer compiler.  DO NOT EDIT!
+# source: Vaccine.proto
+
+require 'google/protobuf'
+
+require 'google/protobuf/timestamp_pb'
+require_relative 'InjectionMethod_pb'
+require_relative 'Code_pb'
+
+Google::Protobuf::DescriptorPool.generated_pool.build do
+  add_file("Vaccine.proto", :syntax => :proto2) do
+    add_message "nuva.Vaccine" do
+      required :id, :string, 1
+      required :name, :string, 2
+      required :short_description, :string, 3
+      required :description, :string, 4
+      repeated :injection_methods, :enum, 5, "nuva.InjectionMethod"
+      required :code, :uint32, 6
+      repeated :codes, :message, 7, "nuva.Code"
+      repeated :valence_ids, :string, 8
+      repeated :other_names, :string, 9
+      required :generic, :bool, 10
+      optional :replaced_by_id, :string, 11
+      required :created_at, :message, 16, "google.protobuf.Timestamp"
+      required :updated_at, :message, 17, "google.protobuf.Timestamp"
+    end
+  end
+end
+
+module Nuva
+  Vaccine = ::Google::Protobuf::DescriptorPool.generated_pool.lookup("nuva.Vaccine").msgclass
+end

data/lib/Valence_pb.rb

@@ -0,0 +1,28 @@
+# Generated by the protocol buffer compiler.  DO NOT EDIT!
+# source: Valence.proto
+
+require 'google/protobuf'
+
+require 'google/protobuf/timestamp_pb'
+
+Google::Protobuf::DescriptorPool.generated_pool.build do
+  add_file("Valence.proto", :syntax => :proto2) do
+    add_message "nuva.Valence" do
+      required :id, :string, 1
+      required :parent_id, :string, 2
+      required :code, :uint32, 3
+      required :name, :string, 4
+      required :abbreviation, :string, 5
+      optional :translated_abbreviation, :string, 6
+      repeated :disease_ids, :string, 7
+      repeated :vaccine_ids, :string, 8
+      optional :antigene_type, :string, 9
+      required :created_at, :message, 16, "google.protobuf.Timestamp"
+      required :updated_at, :message, 17, "google.protobuf.Timestamp"
+    end
+  end
+end
+
+module Nuva
+  Valence = ::Google::Protobuf::DescriptorPool.generated_pool.lookup("nuva.Valence").msgclass
+end

data/lib/VersionInfo_pb.rb

@@ -0,0 +1,18 @@
+# Generated by the protocol buffer compiler.  DO NOT EDIT!
+# source: VersionInfo.proto
+
+require 'google/protobuf'
+
+Google::Protobuf::DescriptorPool.generated_pool.build do
+  add_file("VersionInfo.proto", :syntax => :proto2) do
+    add_message "nuva.VersionInfo" do
+      required :major, :uint32, 1
+      required :minor, :uint32, 2
+      required :patch, :uint32, 3
+    end
+  end
+end
+
+module Nuva
+  VersionInfo = ::Google::Protobuf::DescriptorPool.generated_pool.lookup("nuva.VersionInfo").msgclass
+end

data/lib/nuva.rb

@@ -0,0 +1,75 @@
+require_relative './version'
+require_relative './NuvaDatabase_pb'
+require_relative './repository'
+require_relative './queries'
+require 'net/http'
+require 'json'
+require 'ostruct'
+
+module Nuva
+    class Nuva
+        attr_reader :repositories
+        attr_reader :queries
+
+        def initialize(db)
+            @db = db
+            
+            @repositories = OpenStruct.new
+            @repositories.vaccines = VaccineRepository.new db.vaccines
+            @repositories.valences = ValenceRepository.new db.valences
+            @repositories.diseases = DiseaseRepository.new db.diseases
+            @repositories.freeze
+
+            @queries = OpenStruct.new
+            @queries.valences_by_vaccine = ::Nuva::Queries::ValencesByVaccine.new @repositories
+            @queries.vaccines_by_valence = ::Nuva::Queries::VaccinesByValence.new @repositories
+            @queries.vaccines_by_disease = ::Nuva::Queries::VaccinesByDisease.new @repositories
+            @queries.valences_by_disease = ::Nuva::Queries::ValencesByDisease.new @repositories
+            @queries.diseases_by_vaccine = ::Nuva::Queries::DiseasesByVaccine.new @repositories
+            @queries.diseases_by_valence = ::Nuva::Queries::DiseasesByValence.new @repositories
+            @queries.vaccine_fuzzy_search = ::Nuva::Queries::VaccineFuzzySearch.new @repositories
+            @queries.lookup_vaccine_by_code = ::Nuva::Queries::LookupVaccineByCode.new @repositories
+            @queries.lookup_equivalent_vaccines = ::Nuva::Queries::LookupEquivalentVaccines.new @repositories
+            @queries.lookup_specialized_vaccines = ::Nuva::Queries::LookupSpecializedVaccines.new @repositories, @queries.valences_by_vaccine
+            @queries.lookup_generalized_vaccines = ::Nuva::Queries::LookupGeneralizedVaccines.new @repositories, @queries.valences_by_vaccine
+            @queries.all_nomenclatures = ::Nuva::Queries::AllNomenclatures.new @repositories
+            @queries.all_code_by_nomenclature = ::Nuva::Queries::AllCodeByNomenclature.new @repositories
+            @queries.freeze
+        end
+
+        def self.load(lang = "en")
+            latest_version_uri = URI "https://nuva.fra1.cdn.digitaloceanspaces.com/versions/last.json"
+
+            ::Net::HTTP.start(latest_version_uri.host, latest_version_uri.port,
+                :use_ssl => latest_version_uri.scheme == 'https') do |http|
+                
+                # Fetch version manifest
+                req = ::Net::HTTP::Get.new latest_version_uri
+
+                res = http.request req
+                res.value
+
+                manifest = JSON::parse(res.body)
+
+                dump_hash = manifest['dump_hash']
+
+                # Fetch latest database
+                dump_uri = latest_version_uri.dup
+                dump_uri.path = "/proto/#{dump_hash}_#{lang}.db"
+
+                req = ::Net::HTTP::Get.new dump_uri
+
+                res = http.request req
+                res.value
+
+                # The return value of the block is returned by the start method
+                ::Nuva::Nuva.new(::Nuva::NuvaDatabase.decode(res.body))
+            end
+
+        end
+
+        def self.load_from_file(path)
+            Nuva.new(NuvaDatabase.decode(File.read(path)))
+        end
+    end
+end

data/lib/queries.rb

@@ -0,0 +1,247 @@
+require 'fuzzy_match'
+
+module Nuva
+  module Queries
+    class ValencesByVaccine
+      def initialize(repositories)
+        h = Hash.new { |h, k| h[k] = [] }
+        @valences_by_vaccine_id = repositories[:valences].all.reduce(h) do |acc, valence|
+          valence.vaccine_ids.each do |vaccine_id|
+            acc[vaccine_id] << valence
+          end
+          acc
+        end
+      end
+
+      def call(vaccine)
+        @valences_by_vaccine_id[vaccine.id]
+      end
+    end
+
+    class VaccinesByValence
+      def initialize(repositories)
+        h = Hash.new { |h, k| h[k] = [] }
+        @vaccines_by_valence_id = repositories[:vaccines].all.reduce(h) do |acc, vaccine|
+          vaccine.valence_ids.each do |valence_id|
+            acc[valence_id] << vaccine
+          end
+          acc
+        end
+      end
+
+      def call(valence)
+        @vaccines_by_valence_id[valence.id]
+      end
+    end
+
+    class VaccinesByDisease
+      def initialize(repositories)
+        h = Hash.new { |h, k| h[k] = [] }
+        @vaccines_by_disease_id = repositories[:valences].all.reduce(h) do |acc, valence|
+          valence.disease_ids.each do |disease_id|
+            valence.vaccine_ids.each do |vaccine_id|
+              acc[disease_id] << repositories[:vaccines].find(vaccine_id)
+            end
+          end
+          acc
+        end
+      end
+
+      def call(disease)
+        @vaccines_by_disease_id[disease.id]
+      end
+    end
+
+    class ValencesByDisease
+      def initialize(repositories)
+        h = Hash.new { |h, k| h[k] = [] }
+        @valences_by_disease_id = repositories[:valences].all.reduce(h) do |acc, valence|
+          valence.disease_ids.each do |disease_id|
+            acc[disease_id] << valence
+          end
+          acc
+        end
+      end
+
+      def call(disease)
+        @valences_by_disease_id[disease.id]
+      end
+    end
+
+    class DiseasesByVaccine
+      def initialize(repositories)
+        h = Hash.new { |h, k| h[k] = [] }
+        @diseases_by_vaccine_id = repositories[:valences].all.reduce(h) do |acc, valence|
+          valence.vaccine_ids.each do |vaccine_id|
+            valence.disease_ids.each do |disease_id|
+              acc[vaccine_id] << repositories[:diseases].find(disease_id)
+            end
+          end
+          acc
+        end
+      end
+
+      def call(vaccine)
+        @diseases_by_vaccine_id[vaccine.id]
+      end
+    end
+
+    class DiseasesByValence
+      def initialize(repositories)
+        h = Hash.new { |h, k| h[k] = [] }
+        @diseases_by_valence_id = repositories[:diseases].all.reduce(h) do |acc, disease|
+          disease.valence_ids.each do |valence_id|
+            acc[valence_id] << disease
+          end
+          acc
+        end
+      end
+
+      def call(valence)
+        @diseases_by_valence_id[valence.id]
+      end
+    end
+
+    class VaccineFuzzySearch
+      def initialize(repositories)
+        @engine = FuzzyMatch.new(repositories.vaccines.all, :read => ->(v) {
+          return v.name
+        })
+      end
+
+      def call(pattern)
+        @engine.find_all(pattern)
+      end
+    end
+
+    # lookupVaccineByCode(code: string): Vaccine | undefined;
+    # lookupEquivalentVaccines(vaccine: Vaccine): Vaccine[];
+    # lookupSpecializedVaccines(vaccine: Vaccine): Vaccine[];
+    # lookupGeneralizedVaccines(vaccine: Vaccine): Vaccine[];
+    # allNomenclatures(): string[];
+    # allCodeByNomenclature(): {
+    #   [nomenclature: string]: Code[];
+    # };
+
+    class LookupVaccineByCode
+      def initialize(repositories)
+        @vaccines = repositories.vaccines
+      end
+
+      def call(code)
+        @vaccines.all.find do |vac|
+          "NUVA-#{vac.code}" == code || vac.codes.any? do |x| x.value == code end
+        end
+      end
+    end
+
+    class LookupEquivalentVaccines
+      def initialize(repositories)
+        @vaccines = repositories.vaccines
+      end
+
+      def call(vaccine)
+        vids = vaccine.valence_ids.sort
+        @vaccines.all.filter do |v|
+          v.valence_ids.length == vids.length && v.id != vaccine.id && vids == v.valence_ids.sort
+        end
+      end
+    end
+
+    class LookupSpecializedVaccines
+      def initialize(repositories, valencesByVaccine)
+        @vaccines = repositories.vaccines
+        @valences = repositories.valences
+        @valencesByVaccine = valencesByVaccine
+      end
+
+      def call(vaccine)
+        targetValences = @valencesByVaccine.(vaccine)
+        list = @vaccines.all.filter do |candidate|
+          candidate.id != vaccine.id && targetValences.all? do |targetValence|
+            @valencesByVaccine.(candidate).any? do |candidateValence|
+              child_of? candidateValence, targetValence
+            end
+          end
+        end
+        list.sort_by do |v| @valencesByVaccine.(v).length end
+      end
+
+      private def child_of?(valence, parent)
+        unless valence.nil?
+          return true if valence.id == parent.id
+          valence = @valences.find valence.parent_id
+        end
+        
+        false
+      end
+    end
+
+
+    class LookupGeneralizedVaccines
+      def initialize(repositories, valencesByVaccine)
+        @vaccines = repositories.vaccines
+        @valences = repositories.valences
+        @valencesByVaccine = valencesByVaccine
+      end
+
+      def call(vaccine)
+        targetValences = @valencesByVaccine.(vaccine)
+        list = @vaccines.all.filter do |candidate|
+          candidate.id != vaccine.id && targetValences.all? do |targetValence|
+            @valencesByVaccine.(candidate).any? do |candidateValence|
+              child_of? candidateValence, targetValence
+            end
+          end
+        end
+        list.sort_by do |v| @valencesByVaccine.(v).length end
+      end
+
+      private def parent_of?(valence, parent)
+        child_of? parent, valence
+      end
+
+      private def child_of?(valence, parent)
+        unless valence.nil?
+          return true if valence.id == parent.id
+          valence = @valences.find valence.parent_id
+        end
+        
+        false
+      end
+    end
+
+    class AllNomenclatures
+      def initialize(repositories)
+        @vaccines = repositories.vaccines
+      end
+
+      def call
+        (@vaccines.all.flat_map do |v|
+          v.codes.map(&:nomenclature)
+        end).uniq
+      end
+    end
+
+    class AllCodeByNomenclature
+      def initialize(repositories)
+        @vaccines = repositories.vaccines
+      end
+
+      def call()
+        @vaccines
+          .all
+          .flat_map(&:codes)
+          .reduce(Hash.new { |hash, key| hash[key] = [] }) {
+            |hash, code|
+            
+            hash[code.nomenclature] << code.value
+            hash
+          }
+          .map { |key, value| [key, value.uniq] }
+          .to_h
+      end
+    end
+
+  end
+end

data/lib/repositories/disease_repository.rb

@@ -0,0 +1,4 @@
+module Nuva
+  class DiseaseRepository < Repository
+  end
+end

data/lib/repositories/vaccine_repository.rb

@@ -0,0 +1,4 @@
+module Nuva
+  class VaccineRepository < Repository
+  end
+end

data/lib/repositories/valence_repository.rb

@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+module Nuva
+  class ValenceRepository < Repository
+    def initialize(data)
+      super data
+      @ancestor_ids_by_id = {}
+      @data.each_value do |valence|
+        # Build hash of ancestor IDs for valence
+        @ancestor_ids_by_id[valence.id] = lookup_ancestors(valence).uniq
+      end
+      @ancestor_ids_by_id.freeze
+    end
+
+    def get_ancestor_ids(valence_id)
+      @ancestor_ids_by_id[valence_id]
+    end
+
+    private
+
+    def lookup_ancestors(valence)
+      return [] if valence.nil?
+
+      lookup_ancestors(find(valence.parent_id)) << valence.parent_id
+    end
+  end
+end

data/lib/repository.rb

@@ -0,0 +1,35 @@
+module Nuva
+  class Repository
+    attr_reader :data
+
+    def initialize(data)
+      @data = index_array_by_id(data)
+    end
+
+    def find(id)
+      @data[id]
+    end
+
+    def all
+      @data.values
+    end
+
+    def by_ids(ids)
+      ids.map { |x| find x }.compact
+    end
+
+    # def by_ids(ids)
+      # @data.select { |k, _v| ids.include?(k) }.values
+    # end
+
+    private
+
+    def index_array_by_id(array)
+      array.each_with_object({}) { |item, acc| acc[item.id] = item }
+    end
+  end
+end
+
+require_relative 'repositories/disease_repository'
+require_relative 'repositories/vaccine_repository'
+require_relative 'repositories/valence_repository'

data/lib/version.rb

@@ -0,0 +1,3 @@
+module Nuva
+  VERSION = '0.1.5'
+end

data/nuva.gemspec

@@ -0,0 +1,16 @@
+require_relative "lib/version"
+
+Gem::Specification.new do |s|
+  s.name        = 'nuva'
+  s.version     = Nuva::VERSION
+  s.licenses    = ['MIT']
+  s.summary     = "NUVA"
+  s.description = "nuva library aims to simplify working and interacting with the NUVA nomenclature through queries and repositories"
+  s.authors     = ["Syadem"]
+  s.email       = ''
+  s.files       = Dir.chdir(File.expand_path(__dir__)) {
+    `find . -type f -name '*.rb' -print0`.split("\0").concat %w[nuva.gemspec]
+  }
+  s.add_dependency 'google-protobuf', '~> 3.25', '>= 3.25.3'
+  s.add_dependency 'fuzzy_match', '~> 2.1'
+end

metadata

@@ -0,0 +1,92 @@
+--- !ruby/object:Gem::Specification
+name: nuva
+version: !ruby/object:Gem::Version
+  version: 0.1.5
+platform: ruby
+authors:
+- Syadem
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2024-03-25 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: google-protobuf
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.25'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.25.3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.25'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.25.3
+- !ruby/object:Gem::Dependency
+  name: fuzzy_match
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.1'
+description: nuva library aims to simplify working and interacting with the NUVA nomenclature
+  through queries and repositories
+email: ''
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- "./lib/Code_pb.rb"
+- "./lib/Disease_pb.rb"
+- "./lib/InjectionMethod_pb.rb"
+- "./lib/NuvaDatabase_pb.rb"
+- "./lib/Vaccine_pb.rb"
+- "./lib/Valence_pb.rb"
+- "./lib/VersionInfo_pb.rb"
+- "./lib/nuva.rb"
+- "./lib/queries.rb"
+- "./lib/repositories/disease_repository.rb"
+- "./lib/repositories/vaccine_repository.rb"
+- "./lib/repositories/valence_repository.rb"
+- "./lib/repository.rb"
+- "./lib/version.rb"
+- nuva.gemspec
+homepage:
+licenses:
+- MIT
+metadata: {}
+post_install_message:
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.5.3
+signing_key:
+specification_version: 4
+summary: NUVA
+test_files: []