gnparser 0.2.0 → 0.4.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/.gitignore

@@ -1,7 +1,9 @@
 *.sw?
 .DS_Store
 coverage
+.gem
 rdoc
+*.gem
 pkg
 *.swp
 *.swo
@@ -16,3 +18,4 @@ bin
 .bundle
 bundle_bin
 Gemfile.lock
+.byebug.history

data/README.md

@@ -53,93 +53,58 @@ puts ver.value
 puts ver.build_time.size
 ```
 
-### Output formats
+### Parsing name-strings
 
-gem supports the following formats:
+Refer to [gnparser.proto] file to learn available fields.
 
-**compact**
-: JSON output in one line. This is the default format.
+All parsing methods take the following options:
 
-**pretty**
-: ``Pretty`` JSON output.
+``skip_cleaning:``
+: if `true` names-strings get stripped from HTML tags, if there are any. For example `<i>Homo sapiens</i> <b>L.</b>` becomes `Homo sapiens L.`. It is `false` by default.
 
-**simple**
-: Pipe-separated string where the fields are, id, verbatim name, canonical form,
-extended canonical form, authorship, year, quality of parsing.
+``jobs_number:`` allows to control how many jobs will run in parallel by gnparser. Note that gnparser gRPC server also has a max jobs number option. So if ``jobs_number`` is higher than gRPC MaxJobsNumber, it is ignored.
 
-**debug**
-: Abtract Syntax Tree of the parsed result.
-
-### Option preserve_order
-
-To speed parsing up parser normally executes several jobs in parallel, and
-as a result the order the jobs go back may be different from input. It means
-the user has to match output's ``verbatim`` field with the list of its names.
-
-If speed of parsing is sufficient you can use one-threaded parsing that
-guarantees that the order of output will be exactly the same as the order of
-the input. For this purpose use ``preserve_order: true`` option.
-
-### Parse one name
+#### Parse one name
 
 ```ruby
 res = gnp.parse('Puma concolor L.')
-puts res.value
-puts res.error
+puts res.canonical.simple
+puts res.authorship.value
+puts res.name_type
+puts res.species
 ```
 
-For non-default format:
+Skipping cleaning from HTML tags:
 
 ```ruby
-res = gnp.parse('Puma concolor (Linn.)', format: :pretty)
-...
-res = gnp.parse('Puma concolor (Linn.)', format: 'pretty')
-...
-res = gnp.parse('Puma concolor (Linn.)', format: 'simple')
-...
-res = gnp.parse('Puma concolor (Linn.)', format: :simple)
+res = gnp.parse('<i>Puma concolor</i> (Linn.)', skip_cleaning: true)
+#parsed will be false
+res.parsed
 ...
+res = gnp.parse('<i>Puma concolor</i> (Linn.)')
+#parsed will be true
+res.parsed
+res.normalized
 ```
 
-### Parse an array of names
+#### Parse an array of names
+
+There is a limit of 10,000 name strings per batch. Results are always returned in the same order as input.
 
 ```ruby
 names = ['Plantago major L.', 'Homo sapiens Linn. 1758', 'Bubo bubo']
 
-# fast, might get output in different order from input
-res = gnp.parse_ary(names, format: :pretty)
+# run using 3 jobs
+res = gnp.parse_ary(names, jobs_number: 3)
 res.each do |r|
-  puts r.value
-  puts r.error
+  puts r.canonical.full
 end
 
-# slower, returns the same order for output as it was for input
-results = []
-res = gnp.parse_ary(names, format: :pretty, preserve_order: true)
-res.each_with_index |r, i|
-  results << { input: names[i], output:  r }
-end
-```
-
-### Parse names from a file
-
-File should have one name string per line.
-
-```ruby
-path = File.join(__dir__, "path", "to", "names.txt")
-res = gnp.parse_file(path, format: :compact)
-res.each do |r|
-  puts r.value
-  puts r.error
-end
 
-# preserving order of items in output
-results = []
-res = gnp.parse_file(path, format: :compact, preserve_order: true)
-res.each_with_index |r, i|
-  results << { input: names[i], output:  r }
-end
+# do not strip HTML tags (in this case there are none in the input)
+res = gnp.parse_ary(names, skip_cleaning: true)
 ```
 
 [gnparser]: https://gitlab.com/gogna/gnparser
 [releases]: https://gitlab.com/gogna/gnparser/releases
+[gnparser.proto]: https://gitlab.com/gogna/gnparser/blob/master/pb/gnparser.proto

data/Rakefile

@@ -26,9 +26,9 @@ end
 
 task :grpc do
   cmd = 'grpc_tools_ruby_protoc ' \
-    '-I $GOPATH/src/gitlab.com/gogna/gnparser/grpc ' \
+    '-I $GOPATH/src/gitlab.com/gogna/gnparser/pb ' \
         '--ruby_out=lib --grpc_out=lib ' \
-        '$GOPATH/src/gitlab.com/gogna/gnparser/grpc/gnparser.proto'
+        '$GOPATH/src/gitlab.com/gogna/gnparser/pb/gnparser.proto'
   puts cmd
   `#{cmd}`
 end

data/gnparser.gemspec

@@ -23,7 +23,7 @@ Gem::Specification.new do |gem|
   gem.required_ruby_version = '~> 2.5'
   gem.add_dependency 'grpc', '~> 1.15'
   gem.add_dependency 'grpc-tools', '~> 1.15'
-  gem.add_development_dependency 'bundler', '~> 1.16'
+  gem.add_development_dependency 'bundler', '~> 2.0'
   gem.add_development_dependency 'byebug', '~> 10.0'
   gem.add_development_dependency 'rake', '~> 12.3'
   gem.add_development_dependency 'rspec', '~> 3.8'

data/lib/gnparser/client.rb

@@ -1,19 +1,13 @@
 # frozen_string_literal: true
 
 module GNparser
-  FORMATS = {
-    compact: Grpc::Format::Compact,
-    pretty: Grpc::Format::Pretty,
-    simple: Grpc::Format::Simple,
-    debug: Grpc::Format::Debug
-  }.freeze
   # Gnfinder::Client connects to gnfinder server
   class Client
-    PARSER_MIN_VERSION = 'v0.6.0'
+    PARSER_MIN_VERSION = 'v0.9.0'
 
     def initialize(host = '0.0.0.0', port = '8778')
-      @stub = Grpc::GNparser::Stub.new("#{host}:#{port}",
-                                       :this_channel_is_insecure)
+      @stub = Pb::GNparser::Stub.new("#{host}:#{port}",
+                                     :this_channel_is_insecure)
       return if parser_version.value >= PARSER_MIN_VERSION
 
       raise 'gRPC server of gnparser should be at least ' \
@@ -21,73 +15,30 @@ module GNparser
             'https://gitlab/gogna/gnparser/releases.'
     end
 
+    # parser_version retrieves the version of gnparser used by gRPC service.
     def parser_version
-      @stub.ver(Grpc::Void.new)
+      @stub.ver(Pb::Void.new)
     end
 
+    # parse parses one name at a time and returns protocol buffer object with
+    # the results. If the name-string contains HTML tags they will be stripped
+    # by gRPC method.
     def parse(name, opts = {})
-      parse_iter([name], opts).next
-    end
-
-    def parse_ary(ary, opts = {})
-      parse_iter(ary, opts)
-    end
-
-    def parse_file(path, opts = {})
-      f = File.open(path)
-      parse_iter(f, opts)
-    end
-
-    private
-
-    def parse_iter(iter, opts)
-      format = opts[:format] || :compact
-      preserve_order = opts[:preserve_order]
-      enum = InputEnum.new(iter, format)
-      if preserve_order
-        @stub.parse_in_order(enum.each_item)
-      else
-        @stub.parse(enum.each_item)
-      end
-    end
-  end
-
-  # InputEnum yields names one after another
-  class InputEnum
-    def initialize(iter, format = nil)
-      @iter = iter
-      @format = format
-    end
-
-    def each_item
-      return enum_for(:each_item) unless block_given?
-
-      yield input_format if @format
-
-      @iter.each do |l|
-        input = Grpc::Input.new
-        input.name = l.strip
-        yield input
-      end
-    end
-
-    private
-
-    def input_format
-      frm = find_format
-      @format = nil
-      input = Grpc::Input.new
-      input.format = frm
-      input
-    end
-
-    def find_format
-      format = @format.to_sym
-      if FORMATS.key?(format)
-        FORMATS[format]
-      else
-        FORMATS[:compact]
-      end
+      parse_ary([name], opts)[0]
+    end
+
+    # parse_ary parses an array of name-strings and returns an array of
+    # protocol buffer objects with the results. The array preserves the same
+    # order of elements. If the name-string contains HTML tags they will be
+    # stripped internally by the gnparser.
+    def parse_ary(names, opts = {})
+      input = Pb::InputArray.new
+      input.names += names
+      input.skip_cleaning = true if opts[:skip_cleaning]
+      jobs = opts[:jobs_number].to_i
+      input.jobs_number = jobs if jobs.positive?
+      res = @stub.parse_array(input)
+      res.output
     end
   end
 end

data/lib/gnparser/version.rb

@@ -2,7 +2,7 @@
 
 # GNparser is a namespace module for gnparser gem.
 module GNparser
-  VERSION = '0.2.0'
+  VERSION = '0.4.0'
 
   def self.version
     VERSION

data/lib/gnparser_pb.rb

@@ -4,34 +4,144 @@
 require 'google/protobuf'
 
 Google::Protobuf::DescriptorPool.generated_pool.build do
-  add_message "grpc.Version" do
+  add_message "pb.Version" do
     optional :value, :string, 1
     optional :build_time, :string, 2
   end
-  add_message "grpc.Void" do
+  add_message "pb.Void" do
   end
-  add_message "grpc.Input" do
-    oneof :content do
-      optional :format, :enum, 1, "grpc.Format"
-      optional :name, :string, 2
+  add_message "pb.InputArray" do
+    optional :jobs_number, :int32, 1
+    optional :skip_cleaning, :bool, 2
+    repeated :names, :string, 3
+  end
+  add_message "pb.OutputArray" do
+    repeated :output, :message, 1, "pb.Parsed"
+  end
+  add_message "pb.Parsed" do
+    optional :parsed, :bool, 1
+    optional :quality, :int32, 2
+    repeated :quality_warning, :message, 3, "pb.QualityWarning"
+    optional :verbatim, :string, 4
+    optional :normalized, :string, 5
+    optional :canonical, :message, 6, "pb.Canonical"
+    optional :authorship, :message, 7, "pb.Authorship"
+    repeated :positions, :message, 8, "pb.Position"
+    optional :hybrid, :bool, 9
+    optional :bacteria, :bool, 10
+    optional :tail, :string, 11
+    optional :id, :string, 12
+    optional :parser_version, :string, 13
+    optional :cardinality, :int32, 14
+    optional :name_type, :enum, 15, "pb.NameType"
+    repeated :details_hybrid_formula, :message, 20, "pb.HybridFormula"
+    oneof :details do
+      optional :uninomial, :message, 16, "pb.Uninomial"
+      optional :species, :message, 17, "pb.Species"
+      optional :comparison, :message, 18, "pb.Comparison"
+      optional :approximation, :message, 19, "pb.Approximation"
     end
   end
-  add_message "grpc.Output" do
-    optional :value, :string, 2
-    optional :error, :string, 3
+  add_message "pb.HybridFormula" do
+    oneof :element do
+      optional :uninomial, :message, 1, "pb.Uninomial"
+      optional :species, :message, 2, "pb.Species"
+      optional :comparison, :message, 3, "pb.Comparison"
+      optional :approximation, :message, 4, "pb.Approximation"
+    end
+  end
+  add_message "pb.Canonical" do
+    optional :simple, :string, 1
+    optional :full, :string, 2
+  end
+  add_message "pb.Position" do
+    optional :type, :string, 1
+    optional :start, :int32, 2
+    optional :end, :int32, 3
+  end
+  add_message "pb.QualityWarning" do
+    optional :quality, :int32, 1
+    optional :message, :string, 2
+  end
+  add_message "pb.Uninomial" do
+    optional :value, :string, 1
+    optional :rank, :string, 2
+    optional :parent, :string, 3
+    optional :authorship, :message, 4, "pb.Authorship"
+  end
+  add_message "pb.Species" do
+    optional :genus, :string, 1
+    optional :sub_genus, :string, 2
+    optional :species, :string, 3
+    optional :species_authorship, :message, 4, "pb.Authorship"
+    repeated :infra_species, :message, 5, "pb.InfraSpecies"
+  end
+  add_message "pb.InfraSpecies" do
+    optional :value, :string, 1
+    optional :rank, :string, 2
+    optional :authorship, :message, 3, "pb.Authorship"
+  end
+  add_message "pb.Comparison" do
+    optional :genus, :string, 1
+    optional :species, :string, 2
+    optional :species_authorship, :message, 3, "pb.Authorship"
+    optional :comparison, :string, 4
+  end
+  add_message "pb.Approximation" do
+    optional :genus, :string, 1
+    optional :species, :string, 2
+    optional :species_authorship, :message, 3, "pb.Authorship"
+    optional :approximation, :string, 4
+    optional :ignored, :string, 5
+  end
+  add_message "pb.Authorship" do
+    optional :value, :string, 1
+    repeated :all_authors, :string, 2
+    optional :original, :message, 3, "pb.AuthGroup"
+    optional :combination, :message, 4, "pb.AuthGroup"
+  end
+  add_message "pb.AuthGroup" do
+    repeated :authors, :string, 1
+    optional :year, :string, 2
+    optional :approximate_year, :bool, 3
+    optional :ex_authors, :message, 4, "pb.Authors"
+    optional :emend_authors, :message, 5, "pb.Authors"
+  end
+  add_message "pb.Authors" do
+    repeated :authors, :string, 1
+    optional :year, :string, 2
+    optional :approximate_year, :bool, 3
   end
-  add_enum "grpc.Format" do
-    value :Compact, 0
-    value :Pretty, 1
-    value :Simple, 2
-    value :Debug, 3
+  add_enum "pb.NameType" do
+    value :NONE, 0
+    value :UNINOMIAL, 1
+    value :SPECIES, 2
+    value :COMPARISON, 3
+    value :APPROX_SURROGATE, 4
+    value :SURROGATE, 5
+    value :NAMED_HYBRID, 6
+    value :HYBRID_FORMULA, 7
+    value :VIRUS, 8
   end
 end
 
-module Grpc
-  Version = Google::Protobuf::DescriptorPool.generated_pool.lookup("grpc.Version").msgclass
-  Void = Google::Protobuf::DescriptorPool.generated_pool.lookup("grpc.Void").msgclass
-  Input = Google::Protobuf::DescriptorPool.generated_pool.lookup("grpc.Input").msgclass
-  Output = Google::Protobuf::DescriptorPool.generated_pool.lookup("grpc.Output").msgclass
-  Format = Google::Protobuf::DescriptorPool.generated_pool.lookup("grpc.Format").enummodule
+module Pb
+  Version = Google::Protobuf::DescriptorPool.generated_pool.lookup("pb.Version").msgclass
+  Void = Google::Protobuf::DescriptorPool.generated_pool.lookup("pb.Void").msgclass
+  InputArray = Google::Protobuf::DescriptorPool.generated_pool.lookup("pb.InputArray").msgclass
+  OutputArray = Google::Protobuf::DescriptorPool.generated_pool.lookup("pb.OutputArray").msgclass
+  Parsed = Google::Protobuf::DescriptorPool.generated_pool.lookup("pb.Parsed").msgclass
+  HybridFormula = Google::Protobuf::DescriptorPool.generated_pool.lookup("pb.HybridFormula").msgclass
+  Canonical = Google::Protobuf::DescriptorPool.generated_pool.lookup("pb.Canonical").msgclass
+  Position = Google::Protobuf::DescriptorPool.generated_pool.lookup("pb.Position").msgclass
+  QualityWarning = Google::Protobuf::DescriptorPool.generated_pool.lookup("pb.QualityWarning").msgclass
+  Uninomial = Google::Protobuf::DescriptorPool.generated_pool.lookup("pb.Uninomial").msgclass
+  Species = Google::Protobuf::DescriptorPool.generated_pool.lookup("pb.Species").msgclass
+  InfraSpecies = Google::Protobuf::DescriptorPool.generated_pool.lookup("pb.InfraSpecies").msgclass
+  Comparison = Google::Protobuf::DescriptorPool.generated_pool.lookup("pb.Comparison").msgclass
+  Approximation = Google::Protobuf::DescriptorPool.generated_pool.lookup("pb.Approximation").msgclass
+  Authorship = Google::Protobuf::DescriptorPool.generated_pool.lookup("pb.Authorship").msgclass
+  AuthGroup = Google::Protobuf::DescriptorPool.generated_pool.lookup("pb.AuthGroup").msgclass
+  Authors = Google::Protobuf::DescriptorPool.generated_pool.lookup("pb.Authors").msgclass
+  NameType = Google::Protobuf::DescriptorPool.generated_pool.lookup("pb.NameType").enummodule
 end

data/lib/gnparser_services_pb.rb

@@ -1,10 +1,10 @@
 # Generated by the protocol buffer compiler.  DO NOT EDIT!
-# Source: gnparser.proto for package 'grpc'
+# Source: gnparser.proto for package 'pb'
 
 require 'grpc'
 require 'gnparser_pb'
 
-module Grpc
+module Pb
   module GNparser
     class Service
 
@@ -12,11 +12,14 @@ module Grpc
 
       self.marshal_class_method = :encode
       self.unmarshal_class_method = :decode
-      self.service_name = 'grpc.GNparser'
+      self.service_name = 'pb.GNparser'
 
+      # Ver takes an empty argument (Void) and returns description of the gnparser
+      # version and build date and time.
       rpc :Ver, Void, Version
-      rpc :Parse, stream(Input), stream(Output)
-      rpc :ParseInOrder, stream(Input), stream(Output)
+      # ParseArray takes a list of name-strings (up to 10000), and retuns back
+      # a list of parsed results, preserving the order of input.
+      rpc :ParseArray, InputArray, OutputArray
     end
 
     Stub = Service.rpc_stub_class

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: gnparser
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.4.0
 platform: ruby
 authors:
 - Dmitry Mozzherin
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-01-17 00:00:00.000000000 Z
+date: 2019-08-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: grpc
@@ -44,14 +44,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.16'
+        version: '2.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.16'
+        version: '2.0'
 - !ruby/object:Gem::Dependency
   name: byebug
   requirement: !ruby/object:Gem::Requirement
@@ -116,14 +116,12 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
-- ".byebug_history"
 - ".gitignore"
 - ".rspec"
 - ".rubocop.yml"
 - ".vscode/settings.json"
 - CHANGELOG.md
 - Gemfile
-- Gemfile.lock
 - LICENSE
 - README.md
 - Rakefile

data/.byebug_history

@@ -1,16 +0,0 @@
-q
-res.next
-q
-res.next
-res
-q
-res.each {|r| puts r}
-res.next
-p res
-q
-res.next
-res
-c
-q
-puts res.next
-res