gnfinder 0.9.0.1 → 0.15.4

checksums.yaml

@@ -1,7 +1,7 @@
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data/.rubocop.yml

@@ -1,10 +1,14 @@
 AllCops:
-  TargetRubyVersion: 2.6
+  NewCops: disable
+  TargetRubyVersion: 3.0
   Exclude:
     - 'lib/protob_pb.rb'
     - 'lib/protob_services_pb.rb'
 Style/StringLiterals:
   EnforcedStyle: single_quotes
+Metrics/AbcSize:
+  Exclude:
+    - '**/*'
 Metrics/BlockLength:
   Exclude:
     - 'spec/**/*'

data/CHANGELOG.md

@@ -2,6 +2,10 @@
 
 ## Unreleased
 
+## [v0.15.4]
+
+- Add [#14]: Compatibility with gnfider v0.15.4, switching to REST API.
+
 ## [v0.2.0]
 
 - Compatibility with gnfinder v0.7.0
@@ -29,10 +33,28 @@
 
 This document follows [changelog guidelines]
 
+[v0.15.4]: https://github.com/GlobalNamesArchitecture/gnfinder/compare/v0.1.0...v0.15.4
+[v0.2.0]: https://github.com/GlobalNamesArchitecture/gnfinder/compare/v0.1.3...v0.2.0
+[v0.1.3]: https://github.com/GlobalNamesArchitecture/gnfinder/compare/v0.1.2...v0.1.3
+[v0.1.2]: https://github.com/GlobalNamesArchitecture/gnfinder/compare/v0.1.1...v0.1.2
 [v0.1.1]: https://github.com/GlobalNamesArchitecture/gnfinder/compare/v0.1.0...v0.1.1
 [v0.1.0]: https://github.com/GlobalNamesArchitecture/gnfinder/tree/v0.1.0
 
-[#6]: https://github.com/GlobalNamesArchitecture/gnfinder/issues/5
+[#20]: https://github.com/GlobalNamesArchitecture/gnfinder/issues/20
+[#19]: https://github.com/GlobalNamesArchitecture/gnfinder/issues/19
+[#18]: https://github.com/GlobalNamesArchitecture/gnfinder/issues/18
+[#17]: https://github.com/GlobalNamesArchitecture/gnfinder/issues/17
+[#16]: https://github.com/GlobalNamesArchitecture/gnfinder/issues/16
+[#15]: https://github.com/GlobalNamesArchitecture/gnfinder/issues/15
+[#14]: https://github.com/GlobalNamesArchitecture/gnfinder/issues/14
+[#13]: https://github.com/GlobalNamesArchitecture/gnfinder/issues/13
+[#12]: https://github.com/GlobalNamesArchitecture/gnfinder/issues/12
+[#11]: https://github.com/GlobalNamesArchitecture/gnfinder/issues/11
+[#10]: https://github.com/GlobalNamesArchitecture/gnfinder/issues/10
+[#9]: https://github.com/GlobalNamesArchitecture/gnfinder/issues/9
+[#8]: https://github.com/GlobalNamesArchitecture/gnfinder/issues/8
+[#7]: https://github.com/GlobalNamesArchitecture/gnfinder/issues/7
+[#6]: https://github.com/GlobalNamesArchitecture/gnfinder/issues/6
 [#5]: https://github.com/GlobalNamesArchitecture/gnfinder/issues/5
 [#4]: https://github.com/GlobalNamesArchitecture/gnfinder/issues/4
 [#3]: https://github.com/GlobalNamesArchitecture/gnfinder/issues/3

data/README.md

@@ -159,16 +159,16 @@ res = gf.find_names(txt, verification: true, sources: [1, 4, 179])
 ### Combination of parameters.
 
 It is possible to combine parameters. However if a parameter makes no sense in
-a particular context. It is silently ignored.
+a particular context it is silently ignored.
 
 ```ruby
 # Runs Bayes' algorithms using English training set, runs verification and
 # returns matched results for 3 data-sources if they are available.
-res = gf.find_names(txt, language: eng, verification: true,
+res = gf.find_names(txt, language: 'eng', verification: true,
                            sources: [1, 4, 179])
 
 # Ignores `sources:` settings, because `with_verification` is not set to `true`
-res = gf.find_names(txt, language: eng, sources: [1, 4, 179])
+res = gf.find_names(txt, language: 'eng', sources: [1, 4, 179])
 ```
 
 ## Development
@@ -214,4 +214,4 @@ bundle exec rspec
 [client]: https://github.com/GlobalNamesArchitecture/gnfinder/blob/master/lib/gnfinder/client.rb
 [data-source list]: http://index.globalnames.org/datasource
 [proto file]: https://github.com/GlobalNamesArchitecture/gnfinder/blob/master/lib/protob_pb.rb
-[tests]: https://github.com/GlobalNamesArchitecture/gnfinder/blob/master/spec/lib/client_spec.rb
+[tests]: https://github.com/GlobalNamesArchitecture/gnfinder/blob/master/spec/lib/client_spec.rb

data/gnfinder.gemspec

@@ -20,12 +20,12 @@ Gem::Specification.new do |gem|
                       .reject { |f| f.match(%r{^(test|spec|features)/}) }
 
   gem.require_paths = ['lib']
-  gem.required_ruby_version = '~> 2.6'
-  gem.add_development_dependency 'bundler', '~> 2.0'
-  gem.add_development_dependency 'byebug', '~> 10.0'
-  gem.add_development_dependency 'grpc', '~> 1.15'
-  gem.add_development_dependency 'grpc-tools', '~> 1.15'
-  gem.add_development_dependency 'rake', '~> 12.3'
-  gem.add_development_dependency 'rspec', '~> 3.8'
-  gem.add_development_dependency 'rubocop', '~> 0.59'
+  gem.required_ruby_version = '~> 3.0'
+  gem.add_dependency 'rest-client', '~> 2.1'
+  gem.add_development_dependency 'bundler', '~> 2.2'
+  gem.add_development_dependency 'byebug', '~> 11.1'
+  gem.add_development_dependency 'rake', '~> 13.0'
+  gem.add_development_dependency 'rspec', '~> 3.10'
+  gem.add_development_dependency 'rubocop', '~> 1.20'
+  gem.add_development_dependency 'solargraph', '~> 0.43'
 end

data/lib/gnfinder/client.rb

@@ -1,47 +1,70 @@
 # frozen_string_literal: true
 
 module Gnfinder
-  GNFINDER_MIN_VERSION = 'v0.9.0'
-
   # Gnfinder::Client connects to gnfinder server
   class Client
-    def initialize(host = '0.0.0.0', port = '8778')
-      @stub = Protob::GNFinder::Stub.new("#{host}:#{port}",
-                                         :this_channel_is_insecure)
-      return if gnfinder_version.version >= GNFINDER_MIN_VERSION
-
-      raise 'gRPC server of gnfinder should be at least ' \
-            ' #{GNFINDER_MIN_VERSION}.\n Download latest version from ' \
-            'https://github.com/gnames/gnfinder/releases/latest.'
+    def initialize(host = 'https://gnfinder.globalnames.org', port = '')
+      api_path = '/api/v1'
+      url = host + api_path
+      url = "#{host}:#{port}#{api_path}" if port.to_s != ''
+      @site = RestClient::Resource.new(url, read_timeout: 60)
+      @port = port
     end
 
     def gnfinder_version
-      @stub.ver(Protob::Void.new)
+      resp = @site['/version'].get
+      ver = JSON.parse(resp.body, symbolize_names: true)
+      OpenStruct.new(ver)
     end
 
     def ping
-      @stub.ping(Protob::Void.new).value
+      @site['/ping'].get.body
     end
 
     # rubocop:disable all
     def find_names(text, opts = {})
       if text.to_s.strip == ''
-        return Protob::Output.new
+        return to_open_struct({ "names": [] })
       end
 
       params = { text: text }
-      params[:no_bayes] = true if opts[:no_bayes]
+      params[:noBayes] = true if opts[:no_bayes]
+      params[:oddsDetails] = true if opts[:odds_details]
       params[:language] = opts[:language] if opts[:language].to_s.strip != ''
-      if opts[:detect_language]
-        params[:detect_language] = opts[:detect_language]
+
+      if opts[:words_around] && opts[:words_around] > 0
+        params[:wordsAround] = opts[:words_around]
       end
+
       params[:verification] = true if opts[:verification]
+
       if opts[:sources] && !opts[:sources].empty?
         params[:sources] = opts[:sources]
       end
 
-      @stub.find_names(Protob::Params.new(params))
+      res = @site['find'].post params.to_json, {content_type: :json, accept: :json}
+      output = JSON.parse(res.body)
+      res = output["metadata"]
+      res["names"] = output["names"] || []
+      res = res.deep_transform_keys(&:underscore)
+      if res["names"].nil?
+        res["names"] = []
+      end
+      to_open_struct(res)
     end
     # rubocop:enable all
+
+    private
+
+    def to_open_struct(obj)
+      case obj
+      when Hash
+        OpenStruct.new(obj.transform_values { |val| to_open_struct(val) })
+      when Array
+        obj.map { |o| to_open_struct(o) }
+      else # Assumed to be a primitive value
+        obj
+      end
+    end
   end
 end

data/lib/gnfinder/version.rb

@@ -3,7 +3,7 @@
 # Gnfinder is a namespace module for gndinfer gem.
 module Gnfinder
   # Version corresponds to the minimal supported version of Go gnfinder
-  VERSION = '0.9.0.1'
+  VERSION = '0.15.4'
 
   def self.version
     VERSION

data/lib/gnfinder.rb

@@ -1,8 +1,9 @@
 # frozen_string_literal: true
 
+require 'rest-client'
+require 'json'
+require_relative 'hash'
 require_relative 'gnfinder/version'
-require_relative 'protob_pb.rb'
-require_relative 'protob_services_pb.rb'
 require_relative 'gnfinder/client'
 
 # Gnfinder is a namespace module for gndinfer gem.

data/lib/hash.rb

@@ -0,0 +1,170 @@
+# frozen_string_literal: true
+
+# Monkey patch for underscores.
+class String
+  def underscore
+    gsub(/::/, '/')
+      .gsub(/([a-z\d])([A-Z])/) do
+      "#{Regexp.last_match(1)}_#{Regexp.last_match(2)}"
+    end
+      .downcase
+  end
+end
+
+# Hash monkey patches from ActiveSupport
+class Hash
+  # Returns a new hash with all keys converted to strings.
+  #
+  #   hash = { name: 'Rob', age: '28' }
+  #
+  #   hash.stringify_keys
+  #   # => {"name"=>"Rob", "age"=>"28"}
+  def stringify_keys
+    transform_keys(&:to_s)
+  end
+
+  # Destructively converts all keys to strings. Same as
+  # +stringify_keys+, but modifies +self+.
+  def stringify_keys!
+    transform_keys!(&:to_s)
+  end
+
+  # Returns a new hash with all keys converted to symbols, as long as
+  # they respond to +to_sym+.
+  #
+  #   hash = { 'name' => 'Rob', 'age' => '28' }
+  #
+  #   hash.symbolize_keys
+  #   # => {:name=>"Rob", :age=>"28"}
+  def symbolize_keys
+    transform_keys do |key|
+      key.to_sym
+    rescue StandardError
+      key
+    end
+  end
+  alias to_options symbolize_keys
+
+  # Destructively converts all keys to symbols, as long as they respond
+  # to +to_sym+. Same as +symbolize_keys+, but modifies +self+.
+  def symbolize_keys!
+    transform_keys! do |key|
+      key.to_sym
+    rescue StandardError
+      key
+    end
+  end
+  alias to_options! symbolize_keys!
+
+  # Validates all keys in a hash match <tt>*valid_keys</tt>, raising
+  # +ArgumentError+ on a mismatch.
+  #
+  # Note that keys are treated differently than HashWithIndifferentAccess,
+  # meaning that string and symbol keys will not match.
+  def assert_valid_keys(*valid_keys)
+    valid_keys.flatten!
+    each_key do |k|
+      unless valid_keys.include?(k)
+        raise ArgumentError, "Unknown key: #{k.inspect}. Valid keys are: #{valid_keys.map(&:inspect).join(', ')}"
+      end
+    end
+  end
+
+  # Returns a new hash with all keys converted by the block operation.
+  # This includes the keys from the root hash and from all
+  # nested hashes and arrays.
+  #
+  #  hash = { person: { name: 'Rob', age: '28' } }
+  #
+  #  hash.deep_transform_keys{ |key| key.to_s.upcase }
+  #  # => {"PERSON"=>{"NAME"=>"Rob", "AGE"=>"28"}}
+  def deep_transform_keys(&block)
+    _deep_transform_keys_in_object(self, &block)
+  end
+
+  # Destructively converts all keys by using the block operation.
+  # This includes the keys from the root hash and from all
+  # nested hashes and arrays.
+  def deep_transform_keys!(&block)
+    _deep_transform_keys_in_object!(self, &block)
+  end
+
+  # Returns a new hash with all keys converted to strings.
+  # This includes the keys from the root hash and from all
+  # nested hashes and arrays.
+  #
+  #   hash = { person: { name: 'Rob', age: '28' } }
+  #
+  #   hash.deep_stringify_keys
+  #   # => {"person"=>{"name"=>"Rob", "age"=>"28"}}
+  def deep_stringify_keys
+    deep_transform_keys(&:to_s)
+  end
+
+  # Destructively converts all keys to strings.
+  # This includes the keys from the root hash and from all
+  # nested hashes and arrays.
+  def deep_stringify_keys!
+    deep_transform_keys!(&:to_s)
+  end
+
+  # Returns a new hash with all keys converted to symbols, as long as
+  # they respond to +to_sym+. This includes the keys from the root hash
+  # and from all nested hashes and arrays.
+  #
+  #   hash = { 'person' => { 'name' => 'Rob', 'age' => '28' } }
+  #
+  #   hash.deep_symbolize_keys
+  #   # => {:person=>{:name=>"Rob", :age=>"28"}}
+  def deep_symbolize_keys
+    deep_transform_keys do |key|
+      key.to_sym
+    rescue StandardError
+      key
+    end
+  end
+
+  # Destructively converts all keys to symbols, as long as they respond
+  # to +to_sym+. This includes the keys from the root hash and from all
+  # nested hashes and arrays.
+  def deep_symbolize_keys!
+    deep_transform_keys! do |key|
+      key.to_sym
+    rescue StandardError
+      key
+    end
+  end
+
+  private
+
+  # Support methods for deep transforming nested hashes and arrays.
+  def _deep_transform_keys_in_object(object, &block)
+    case object
+    when Hash
+      object.each_with_object(self.class.new) do |(key, value), result|
+        result[yield(key)] = _deep_transform_keys_in_object(value, &block)
+      end
+    when Array
+      object.map { |e| _deep_transform_keys_in_object(e, &block) }
+    else
+      object
+    end
+  end
+
+  # rubocop:disable all
+  def _deep_transform_keys_in_object!(object, &block)
+    case object
+    when Hash
+      object.each_key do |key|
+        value = object.delete(key)
+        object[yield(key)] = _deep_transform_keys_in_object!(value, &block)
+      end
+      object
+    when Array
+      object.map! { |e| _deep_transform_keys_in_object!(e, &block) }
+    else
+      object
+    end
+  end
+  # rubocop:enable all
+end

metadata

@@ -1,113 +1,113 @@
 --- !ruby/object:Gem::Specification
 name: gnfinder
 version: !ruby/object:Gem::Version
-  version: 0.9.0.1
+  version: 0.15.4
 platform: ruby
 authors:
 - Dmitry Mozzherin
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2019-12-03 00:00:00.000000000 Z
+date: 2021-09-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: bundler
+  name: rest-client
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.0'
-  type: :development
+        version: '2.1'
+  type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.0'
+        version: '2.1'
 - !ruby/object:Gem::Dependency
-  name: byebug
+  name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: '2.2'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: '2.2'
 - !ruby/object:Gem::Dependency
-  name: grpc
+  name: byebug
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.15'
+        version: '11.1'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.15'
+        version: '11.1'
 - !ruby/object:Gem::Dependency
-  name: grpc-tools
+  name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.15'
+        version: '13.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.15'
+        version: '13.0'
 - !ruby/object:Gem::Dependency
-  name: rake
+  name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '12.3'
+        version: '3.10'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '12.3'
+        version: '3.10'
 - !ruby/object:Gem::Dependency
-  name: rspec
+  name: rubocop
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.8'
+        version: '1.20'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.8'
+        version: '1.20'
 - !ruby/object:Gem::Dependency
-  name: rubocop
+  name: solargraph
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.59'
+        version: '0.43'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.59'
+        version: '0.43'
 description: |-
   The gem searches for scientific names in texts using
                        gRPC server running gnfinder app written in Go language
@@ -128,13 +128,12 @@ files:
 - lib/gnfinder.rb
 - lib/gnfinder/client.rb
 - lib/gnfinder/version.rb
-- lib/protob_pb.rb
-- lib/protob_services_pb.rb
+- lib/hash.rb
 homepage: http://github.com/GlobalNamesArchitecture/gnfinder
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -142,15 +141,15 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - "~>"
     - !ruby/object:Gem::Version
-      version: '2.6'
+      version: '3.0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
-signing_key: 
+rubygems_version: 3.2.22
+signing_key:
 specification_version: 4
 summary: Scientific names finder
 test_files: []

data/lib/protob_pb.rb

@@ -1,88 +0,0 @@
-# Generated by the protocol buffer compiler.  DO NOT EDIT!
-# source: protob.proto
-
-require 'google/protobuf'
-
-Google::Protobuf::DescriptorPool.generated_pool.build do
-  add_file("protob.proto", :syntax => :proto3) do
-    add_message "protob.Void" do
-    end
-    add_message "protob.Pong" do
-      optional :value, :string, 1
-    end
-    add_message "protob.Version" do
-      optional :version, :string, 1
-      optional :build, :string, 2
-    end
-    add_message "protob.Params" do
-      optional :text, :string, 1
-      optional :no_bayes, :bool, 3
-      optional :language, :string, 4
-      optional :detect_language, :bool, 5
-      optional :verification, :bool, 6
-      repeated :sources, :int32, 7
-    end
-    add_message "protob.Output" do
-      optional :date, :string, 1
-      optional :finder_version, :string, 2
-      optional :language, :string, 3
-      optional :language_detected, :string, 4
-      optional :detect_language, :bool, 5
-      optional :total_tokens, :int32, 6
-      optional :total_candidates, :int32, 7
-      optional :total_names, :int32, 8
-      repeated :names, :message, 9, "protob.NameString"
-    end
-    add_message "protob.NameString" do
-      optional :type, :string, 1
-      optional :verbatim, :string, 2
-      optional :name, :string, 3
-      optional :odds, :float, 4
-      optional :offset_start, :int32, 5
-      optional :offset_end, :int32, 6
-      optional :verification, :message, 7, "protob.Verification"
-    end
-    add_message "protob.Verification" do
-      optional :best_result, :message, 1, "protob.ResultData"
-      repeated :preferred_results, :message, 2, "protob.ResultData"
-      optional :data_sources_num, :int32, 3
-      optional :data_source_quality, :string, 4
-      optional :retries, :int32, 5
-      optional :error, :string, 6
-    end
-    add_message "protob.ResultData" do
-      optional :data_source_id, :int32, 1
-      optional :data_source_title, :string, 2
-      optional :taxon_id, :string, 3
-      optional :matched_name, :string, 4
-      optional :matched_canonical, :string, 5
-      optional :current_name, :string, 6
-      optional :synonym, :bool, 7
-      optional :classification_path, :string, 8
-      optional :classification_rank, :string, 9
-      optional :classification_ids, :string, 10
-      optional :edit_distance, :int32, 11
-      optional :stem_edit_distance, :int32, 12
-      optional :match_type, :enum, 13, "protob.MatchType"
-    end
-    add_enum "protob.MatchType" do
-      value :NONE, 0
-      value :EXACT, 1
-      value :FUZZY, 2
-      value :PARTIAL_EXACT, 3
-      value :PARTIAL_FUZZY, 4
-    end
-  end
-end
-
-module Protob
-  Void = Google::Protobuf::DescriptorPool.generated_pool.lookup("protob.Void").msgclass
-  Pong = Google::Protobuf::DescriptorPool.generated_pool.lookup("protob.Pong").msgclass
-  Version = Google::Protobuf::DescriptorPool.generated_pool.lookup("protob.Version").msgclass
-  Params = Google::Protobuf::DescriptorPool.generated_pool.lookup("protob.Params").msgclass
-  Output = Google::Protobuf::DescriptorPool.generated_pool.lookup("protob.Output").msgclass
-  NameString = Google::Protobuf::DescriptorPool.generated_pool.lookup("protob.NameString").msgclass
-  Verification = Google::Protobuf::DescriptorPool.generated_pool.lookup("protob.Verification").msgclass
-  ResultData = Google::Protobuf::DescriptorPool.generated_pool.lookup("protob.ResultData").msgclass
-  MatchType = Google::Protobuf::DescriptorPool.generated_pool.lookup("protob.MatchType").enummodule
-end

data/lib/protob_services_pb.rb

@@ -1,24 +0,0 @@
-# Generated by the protocol buffer compiler.  DO NOT EDIT!
-# Source: protob.proto for package 'protob'
-
-require 'grpc'
-require 'protob_pb'
-
-module Protob
-  module GNFinder
-    class Service
-
-      include GRPC::GenericService
-
-      self.marshal_class_method = :encode
-      self.unmarshal_class_method = :decode
-      self.service_name = 'protob.GNFinder'
-
-      rpc :Ping, Void, Pong
-      rpc :Ver, Void, Version
-      rpc :FindNames, Params, Output
-    end
-
-    Stub = Service.rpc_stub_class
-  end
-end