dwc-archive 1.0.1 → 1.1.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 8e61e692fe24c4b6bd56e38a7b19a357ba0acdd3180999e606bd6fc8e55dae29
-  data.tar.gz: 1bf6ee067e24d6cb75d415eaa1f10bcf37a96d7daee7a1935248a6a58a0cb5ed
+  metadata.gz: 6e4de59525e7e4a3f212dac828b97ff489f5ec40f764758a5b81b7fef09cc166
+  data.tar.gz: 2f408d2a04bac402c395928a6d048d2d28daed3235119c149684026b233e2126
 SHA512:
-  metadata.gz: a162b05026795e2e4ea8e92683682fab820fb0cfcea68a8c166eb9dc012246ba01a16af4e17af39a2ae28bf2b6a3b85f877ac53b71e27915f8529cb4d973d67a
-  data.tar.gz: 10a59bee9c60103c91fd5403c4c765903521e640dab3c6ef7ff78eaceb04938aa0bd554e9941bdd90260a2f0a2e4927be3d0ada830b2a4310be405f2ead1184f
+  metadata.gz: 145cd2d7d2f9e1c87c76ddca220fd56f1e44cca70ceb6995edfeba73d985e166709cf4254b6b2e19f143ffd02d879700587d61c6b9da239bdaff4288fde17cf9
+  data.tar.gz: e92697139838d7d720bfd9aca87ddf4537a8e272b6fabb04a05f92bfde047c9a45867e46e9b27b39d738c822ba6a843a73b3670b45da16ad9c2aca5df0523913

data/.github/workflows/build.yml

@@ -0,0 +1,35 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+# This workflow will download a prebuilt Ruby version, install dependencies and run tests with Rake
+# For more information see: https://github.com/marketplace/actions/setup-ruby-jruby-and-truffleruby
+
+name: build
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        ruby-version: ['2.6', '2.7', '3.0']
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Ruby
+    # To automatically get bug fixes and new Ruby versions for ruby/setup-ruby,
+    # change this to (see https://github.com/ruby/setup-ruby#versioning):
+    # uses: ruby/setup-ruby@v1
+      uses: ruby/setup-ruby@473e4d8fe5dd94ee328fdfca9f8c9c7afc9dae5e
+      with:
+        ruby-version: ${{ matrix.ruby-version }}
+        bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+    - name: Run tests
+      run: bundle exec rake

data/.gitignore

@@ -26,5 +26,6 @@ bin
 .bundle
 bundle_bin
 Gemfile.lock
+.byebug_history
 
 

data/.rubocop.yml

@@ -1,5 +1,5 @@
 AllCops:
-  TargetRubyVersion: 2.4
+  TargetRubyVersion: 2.6
   Exclude:
     - features/**/*
     - .bundle/**/*

data/.ruby-version

@@ -1 +1 @@
-2.5.1
+3.0.0

data/CHANGELOG

@@ -1,3 +1,5 @@
+1.1.0  Update name parser to go-based biodiversity
+
 1.0.1  Cleanup and gems update
 
 0.9.11 Removed VERSION duplicate

data/LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2010-2012 Marine Biological Laboratory
+Copyright (c) 2010-2020 Dmitry Mozzherin
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

data/README.md

@@ -27,7 +27,7 @@ Usage
 
 ```ruby
 require 'rubygems'
-require 'dwc-archive'
+require 'dwc_archive'
 
 dwc = DarwinCore.new('/path_to_file/archive_file.tar.gz')
 dwc.archive.files      # the archive file list
@@ -179,11 +179,11 @@ Note on Patches/Pull Requests
 Copyright
 ---------
 
-Author -- [Dmitry Mozzherin][13]
+Author -- [@dimus][13]
 
-Contributors -- [Matt Yoder][14]
+Contributors -- [@mjy][14], [@LocoDelAssembly][16]
 
-Copyright (c) 2010-2014 [Marine Biological Laboratory][15]. See LICENSE for details.
+Copyright (c) 2010-2020 [@dimus][15]. See LICENSE for details.
 
 [1]: https://badge.fury.io/rb/dwc-archive.png
 [2]: http://badge.fury.io/rb/dwc-archive
@@ -200,3 +200,4 @@ Copyright (c) 2010-2014 [Marine Biological Laboratory][15]. See LICENSE for deta
 [13]: https://github.com/dimus
 [14]: https://github.com/mjy
 [15]: http://mbl.edu
+[16]: https://github.com/LocoDelAssembly

data/dwc-archive.gemspec

@@ -15,24 +15,23 @@ Gem::Specification.new do |gem|
   gem.homepage      = "http://github.com/GlobalNamesArchitecture/dwc-archive"
   gem.license       = "MIT"
 
-  gem.required_ruby_version = ">= 2.4.1"
+  gem.required_ruby_version = ">= 2.6.0"
   gem.files         = `git ls-files`.split("\n").map(&:strip)
   gem.executables   = gem.files.grep(%r{^bin/}) { |f| File.basename(f) }
   gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
   gem.require_paths = ["lib"]
 
   # gem.add_runtime_dependency "minitar", "~> 0.6"
-  gem.add_runtime_dependency "nokogiri", "~> 1.8"
-  gem.add_runtime_dependency "parsley-store", "~> 0.3"
+  gem.add_runtime_dependency "biodiversity", "~> 5.2.0"
+  gem.add_runtime_dependency "nokogiri", "~> 1.11"
 
-  # gem.add_development_dependency "byebug", "~> 3.4"
-  gem.add_development_dependency "bundler", "~> 1.16"
-  gem.add_development_dependency "coveralls", "~> 0.8"
-  gem.add_development_dependency "cucumber", "~> 3.1"
-  gem.add_development_dependency "git", "~> 1.4"
-  gem.add_development_dependency "rake", "~> 12.3"
-  gem.add_development_dependency "rspec", "~> 3.7"
-  gem.add_development_dependency "rubocop", "~> 0.58"
-  gem.add_development_dependency "solargraph", "~> 0.23"
-  gem.add_development_dependency "travis", "~> 1.8"
+  gem.add_development_dependency "bundler", "~> 2.2"
+  gem.add_development_dependency "byebug", "~> 11.1"
+  gem.add_development_dependency "cucumber", "~> 5"
+  gem.add_development_dependency "git", "~> 1.8"
+  gem.add_development_dependency "rake", "~> 13"
+  gem.add_development_dependency "rspec", "~> 3.10"
+  gem.add_development_dependency "rubocop", "~> 1.8"
+  gem.add_development_dependency "solargraph", "~> 0.40"
+  gem.add_development_dependency "travis", "~> 1.10"
 end

data/lib/dwc_archive.rb

@@ -6,7 +6,7 @@ require "digest"
 require "csv"
 require "logger"
 require "nokogiri"
-require "parsley-store"
+require "biodiversity"
 require_relative "dwc_archive/xml_reader"
 require_relative "dwc_archive/ingester"
 require_relative "dwc_archive/errors"
@@ -39,11 +39,12 @@ class DarwinCore
 
     def files(path)
       return nil unless path && FileTest.exists?(path)
-      Dir.entries(path).reject { |e| e.match(/[\.]{1,2}$/) }.sort
+
+      Dir.entries(path).reject { |e| e.match(/[.]{1,2}$/) }.sort
     end
 
     def random_path(tmp_dir)
-      File.join(tmp_dir, "dwc_" + rand(10_000_000_000).to_s)
+      File.join(tmp_dir, "dwc_#{rand(10_000_000_000)}")
     end
   end
 
@@ -52,15 +53,14 @@ class DarwinCore
 
   def self.nil_field?(field)
     return true if [nil, "", "/N"].include?(field)
+
     false
   end
 
   def self.clean_all(tmp_dir = DEFAULT_TMP_DIR)
     Dir.entries(tmp_dir).each do |entry|
       path = File.join(tmp_dir, entry)
-      if FileTest.directory?(path) && entry.match(/^dwc_[\d]+$/)
-        FileUtils.rm_rf(path)
-      end
+      FileUtils.rm_rf(path) if FileTest.directory?(path) && entry.match(/^dwc_\d+$/)
     end
   end
 
@@ -96,6 +96,7 @@ class DarwinCore
   # list of synonyms and vernacular names.
   def normalize_classification
     return nil unless parent_id?
+
     @classification_normalizer ||=
       DarwinCore::ClassificationNormalizer.new(self)
     @classification_normalizer.normalize
@@ -112,9 +113,11 @@ class DarwinCore
 
   def extensions
     return @extensions if @extensions
+
     root_key = @archive.meta.keys[0]
     ext = @archive.meta[root_key][:extension]
     return @extensions = [] unless ext
+
     ext = [ext] if ext.class != Array
     @extensions = ext.map { |e| DarwinCore::Extension.new(self, e) }
   end

data/lib/dwc_archive/archive.rb

@@ -52,6 +52,7 @@ class DarwinCore
     def prepare_eml_file
       @eml = nil
       return unless files.include?("eml.xml")
+
       eml_file = File.open(File.join(@expander.path, "eml.xml"))
       @eml = DarwinCore::XmlReader.from_xml(eml_file)
     end

data/lib/dwc_archive/classification_normalizer.rb

@@ -1,10 +1,11 @@
-# encoding: utf-8
+# frozen_string_literal: true
+
 class DarwinCore
   # Returns tree representation of Darwin Core file with vernacular and
   # and synonyms attached to the taxon nodes
   class ClassificationNormalizer
     attr_reader :error_names, :tree, :normalized_data, :dwc
-    alias_method :darwin_core, :dwc
+    alias darwin_core dwc
 
     def initialize(dwc_instance)
       @dwc = dwc_instance
@@ -12,7 +13,6 @@ class DarwinCore
       @extensions = @dwc.extensions.map { |e| [e, find_fields(e)] }
       @normalized_data = {}
       @synonyms = {}
-      @parser = ParsleyStore.new(1, 2)
       @name_strings = {}
       @vernacular_name_strings = {}
       @error_names = []
@@ -25,6 +25,7 @@ class DarwinCore
 
     def add_vernacular_name_string(name_string)
       return if @vernacular_name_strings[name_string]
+
       @vernacular_name_strings[name_string] = 1
     end
 
@@ -70,7 +71,9 @@ class DarwinCore
 
     def get_canonical_name(a_scientific_name)
       return nil unless @with_canonical_names
-      canonical_name = @parser.parse(a_scientific_name, canonical_only: true)
+
+      canonical_name = Biodiversity::Parser.parse(a_scientific_name).
+                       dig(:canonical, :simple)
       canonical_name.to_s.empty? ? a_scientific_name : canonical_name
     end
 
@@ -85,15 +88,13 @@ class DarwinCore
     end
 
     def status_synonym?(status)
-      status && status.match(/^syn/)
+      status&.match(/^syn/)
     end
 
     def add_synonym_from_core(taxon_id, row)
       cf = @core_fields
       @synonyms[row[cf[:id]]] = taxon_id
-      unless @normalized_data[row[taxon_id]]
-        @normalized_data[row[taxon_id]] = DarwinCore::TaxonNormalized.new
-      end
+      @normalized_data[row[taxon_id]] = DarwinCore::TaxonNormalized.new unless @normalized_data[row[taxon_id]]
 
       taxon = @normalized_data[row[taxon_id]]
       synonym = SynonymNormalized.new(
@@ -105,7 +106,7 @@ class DarwinCore
         cf[:localid] ? row[cf[:localid]] : nil,
         cf[:globalid] ? row[cf[:globalid]] : nil
       )
-      taxon.synonyms <<  synonym
+      taxon.synonyms << synonym
       add_name_string(synonym.name)
       add_name_string(synonym.canonical_name)
     end
@@ -115,14 +116,10 @@ class DarwinCore
       canonical_name = nil
       scientific_name = row[fields[:scientificname]].strip
       if separate_canonical_and_authorship?(row, fields)
-        if @with_canonical_names
-          canonical_name = row[fields[:scientificname]].strip
-        end
+        canonical_name = row[fields[:scientificname]].strip if @with_canonical_names
         scientific_name += " #{row[fields[:scientificnameauthorship]].strip}"
       else
-        if @with_canonical_names
-          canonical_name = get_canonical_name(row[fields[:scientificname]])
-        end
+        canonical_name = get_canonical_name(row[fields[:scientificname]]) if @with_canonical_names
       end
       fields[:canonicalname] = row.size
       row << canonical_name
@@ -131,18 +128,17 @@ class DarwinCore
 
     def separate_canonical_and_authorship?(row, fields)
       authorship = ""
-      if fields[:scientificnameauthorship]
-        authorship = row[fields[:scientificnameauthorship]].to_s.strip
-      end
+      authorship = row[fields[:scientificnameauthorship]].to_s.strip if fields[:scientificnameauthorship]
       !(authorship.empty? || row[fields[:scientificname]].index(authorship))
     end
 
     def ingest_core
       @normalized_data = {}
       has_name_and_id = @core_fields[:id] && @core_fields[:scientificname]
-      fail(DarwinCore::CoreFileError,
-           "Darwin Core core fields must contain taxon id and scientific name"
-      ) unless has_name_and_id
+      unless has_name_and_id
+        raise(DarwinCore::CoreFileError,
+              "Darwin Core core fields must contain taxon id and scientific name")
+      end
       @dwc.core.read do |rows|
         rows[1].each do |error|
           @error_names << { data: error,
@@ -161,32 +157,28 @@ class DarwinCore
             add_synonym_from_core(parent_id, r) if parent_id?
           else
             unless @normalized_data[r[@core_fields[:id]]]
-              if gnub_archive?
-                new_taxon = DarwinCore::GnubTaxon.new
-              else
-                new_taxon = DarwinCore::TaxonNormalized.new
-              end
+              new_taxon = if gnub_archive?
+                            DarwinCore::GnubTaxon.new
+                          else
+                            DarwinCore::TaxonNormalized.new
+                          end
               @normalized_data[r[@core_fields[:id]]] = new_taxon
             end
             taxon = @normalized_data[r[@core_fields[:id]]]
             if gnub_archive?
               taxon.uuid = r[@core_fields[:originalnameusageid]]
               taxon.uuid_path = r[@core_fields[:originalnameusageidpath]].
-                split("|")
+                                split("|")
             end
             taxon.id = r[@core_fields[:id]]
             taxon.current_name = r[@core_fields[:scientificname]]
             taxon.current_name_canonical = r[@core_fields[:canonicalname]]
             taxon.parent_id = parent_id? ? r[parent_id] : nil
             taxon.rank = r[@core_fields[:taxonrank]] if @core_fields[:taxonrank]
-            if @core_fields[:taxonomicstatus]
-              taxon.status = r[@core_fields[:taxonomicstatus]]
-            end
+            taxon.status = r[@core_fields[:taxonomicstatus]] if @core_fields[:taxonomicstatus]
             taxon.source = r[@core_fields[:source]] if @core_fields[:source]
             taxon.local_id = r[@core_fields[:localid]] if @core_fields[:localid]
-            if @core_fields[:globalid]
-              taxon.global_id = r[@core_fields[:globalid]]
-            end
+            taxon.global_id = r[@core_fields[:globalid]] if @core_fields[:globalid]
             taxon.linnean_classification_path =
               get_linnean_classification_path(r, taxon)
             add_name_string(taxon.current_name)
@@ -211,6 +203,7 @@ class DarwinCore
       @paths_num = 0
       @normalized_data.each do |_taxon_id, taxon|
         next unless taxon.classification_path_id.empty?
+
         res = get_classification_path(taxon)
         next if res == "error"
       end
@@ -218,6 +211,7 @@ class DarwinCore
 
     def get_classification_path(taxon)
       return unless taxon.classification_path_id.empty?
+
       @paths_num += 1
       if @paths_num % 10_000 == 0
         DarwinCore.logger_write(@dwc.object_id,
@@ -225,17 +219,13 @@ class DarwinCore
       end
       current_node = { taxon.id => {} }
       if DarwinCore.nil_field?(taxon.parent_id)
-        if @with_canonical_names
-          taxon.classification_path << taxon.current_name_canonical
-        end
+        taxon.classification_path << taxon.current_name_canonical if @with_canonical_names
         taxon.classification_path_id << taxon.id
         @tree.merge!(current_node)
       else
         parent_cp = parent_cpid = nil
         if @normalized_data[taxon.parent_id]
-          if @with_canonical_names
-            parent_cp = @normalized_data[taxon.parent_id].classification_path
-          end
+          parent_cp = @normalized_data[taxon.parent_id].classification_path if @with_canonical_names
           parent_cpid = @normalized_data[taxon.parent_id].
                         classification_path_id
         else
@@ -245,9 +235,7 @@ class DarwinCore
                               error: :deprecated_parent,
                               current_parent: current_parent }
 
-            if @with_canonical_names
-              parent_cp = current_parent.classification_path
-            end
+            parent_cp = current_parent.classification_path if @with_canonical_names
             parent_cpid = current_parent.classification_path_id
           else
             @error_names << { data: taxon,
@@ -256,6 +244,7 @@ class DarwinCore
           end
         end
         return "error" unless parent_cpid
+
         if parent_cpid.empty?
           res = "error"
           begin
@@ -266,6 +255,7 @@ class DarwinCore
                               current_parent: nil }
           end
           return res if res == "error"
+
           if @with_canonical_names
             taxon.classification_path += @normalized_data[taxon.parent_id].
                                          classification_path +
@@ -293,7 +283,7 @@ class DarwinCore
           rescue NoMethodError => e
             DarwinCore.logger_write(@dwc.object_id,
                                     "Error '#{e.message}' taxon #{taxon.id}")
-            return "error"
+            "error"
           end
         end
       end
@@ -379,8 +369,8 @@ class DarwinCore
 
     # Collect linnean classification path only on species level
     def get_linnean_classification_path(row, _taxon)
-      [:kingdom, :phylum, :class, :order, :family, :genus,
-       :subgenus].each_with_object([]) do |clade, res|
+      %i[kingdom phylum class order family genus
+         subgenus].each_with_object([]) do |clade, res|
         res << [row[@core_fields[clade]], clade] if @core_fields[clade]
       end
     end

data/lib/dwc_archive/errors.rb

@@ -2,12 +2,20 @@
 
 class DarwinCore
   class Error < RuntimeError; end
+
   class FileNotFoundError < Error; end
+
   class UnpackingError < Error; end
+
   class InvalidArchiveError < Error; end
+
   class CoreFileError < Error; end
+
   class ExtensionFileError < Error; end
+
   class GeneratorError < Error; end
+
   class ParentNotCurrentError < Error; end
+
   class EncodingError < Error; end
 end

data/lib/dwc_archive/expander.rb

@@ -13,6 +13,7 @@ class DarwinCore
     def unpack
       clean
       raise DarwinCore::FileNotFoundError unless File.exist?(@archive_path)
+
       success = @unpacker.call(@dir_path, @archive_path) if @unpacker
       if @unpacker && success && $CHILD_STATUS.exitstatus.zero?
         success
@@ -37,11 +38,9 @@ class DarwinCore
     private
 
     def init_unpacker
-      file_command = IO.popen("file -z " + esc(@archive_path))
-      file_type    = file_command.read
-      file_command.close
-      return tar_unpacker if file_type =~ /tar.*gzip/i
-      return zip_unpacker if file_type =~ /Zip/
+      return tar_unpacker if @archive_path =~ /tar.gz$/i
+      return zip_unpacker if @archive_path =~ /zip$/i
+
       nil
     end
 
@@ -61,11 +60,11 @@ class DarwinCore
     end
 
     def esc(a_str)
-      "'" + a_str.gsub(92.chr, '\\\\\\').gsub("'", "\\\\'") + "'"
+      "'#{a_str.gsub(92.chr, '\\\\\\').gsub("'", "\\\\'")}'"
     end
 
     def path_entries(dir)
-      Dir.entries(dir).reject { |e| e.match(/[\.]{1,2}$/) }.sort
+      Dir.entries(dir).reject { |e| e.match(/\.{1,2}$/) }.sort
     end
 
     def files_path
@@ -79,6 +78,7 @@ class DarwinCore
         check_path = File.join(@dir_path, e)
         next unless FileTest.directory?(check_path) &&
                     path_entries(check_path).include?("meta.xml")
+
         res = check_path
         break
       end

data/lib/dwc_archive/generator.rb

@@ -12,7 +12,7 @@ class DarwinCore
       @meta_xml_data = { extensions: [] }
       @eml_xml_data = { id: nil, title: nil, authors: [], abstrac: nil,
                         citation: nil, url: nil }
-      @write = "w:utf-8"
+      @write = 'w:utf-8'
     end
 
     def clean
@@ -20,14 +20,14 @@ class DarwinCore
     end
 
     def add_core(data, file_name, keep_headers = true)
-      opts = { type: "core", data: data, file_name: file_name,
+      opts = { type: 'core', data: data, file_name: file_name,
                keep_headers: keep_headers }
       prepare_csv_file(opts)
     end
 
     def add_extension(data, file_name, keep_headers = true,
-                      row_type = "http://rs.tdwg.org/dwc/terms/Taxon")
-      opts = { type: "extension", data: data, file_name: file_name,
+                      row_type = 'http://rs.tdwg.org/dwc/terms/Taxon')
+      opts = { type: 'extension', data: data, file_name: file_name,
                keep_headers: keep_headers, row_type: row_type }
       prepare_csv_file(opts)
     end
@@ -57,7 +57,7 @@ class DarwinCore
     def prepare_csv_file(opts)
       c = CSV.open(File.join(@path, opts[:file_name]), @write)
       attributes = prepare_attributes(opts)
-      if opts[:type] == "core"
+      if opts[:type] == 'core'
         @meta_xml_data[:core] = attributes
       else
         @meta_xml_data[:extensions] << attributes
@@ -83,7 +83,8 @@ class DarwinCore
         f = f.strip
         err = "No header in #{file_type} data, or header fields are not urls"
         raise DarwinCore::GeneratorError, err unless f =~ %r{^http://}
-        f.split("/")[-1]
+
+        f.split('/')[-1]
       end
     end
   end

data/lib/dwc_archive/ingester.rb

@@ -1,11 +1,9 @@
-# encoding: utf-8
 class DarwinCore
   # This module abstracts information for reading csv file to be used
   # in several classes which need such functionality
   module Ingester
-    attr_reader :data, :properties, :encoding, :fields_separator, :size
-    attr_reader :file_path, :fields, :line_separator, :quote_character,
-                :ignore_headers
+    attr_reader :data, :properties, :encoding, :fields_separator, :size, :file_path, :fields, :line_separator,
+                :quote_character, :ignore_headers
 
     def size
       @size ||= init_size
@@ -16,16 +14,19 @@ class DarwinCore
       res = []
       errors = []
       args = define_csv_args
-      min_size = @fields.map { |f| f[:index].to_i || 0 }.sort[-1] + 1
-      csv = CSV.new(open(@file_path), args)
+      min_size = @fields.map { |f| f[:index].to_i || 0 }.max + 1
+      csv = CSV.new(open(@file_path), **args)
       csv.each_with_index do |r, i|
         next if @ignore_headers && i == 0
+
         min_size > r.size ? errors << r : process_csv_row(res, errors, r)
         next if i == 0 || i % batch_size != 0
+
         DarwinCore.logger_write(@dwc.object_id,
                                 format("Ingested %s records from %s",
                                        i, name))
         next unless block_given?
+
         yield [res, errors]
         res = []
         errors = []
@@ -70,12 +71,14 @@ class DarwinCore
 
     def init_encoding
       @encoding = @properties[:encoding] || "UTF-8"
-      accepted_encoding = ["utf-8", "utf8", "utf-16", "utf16"].
+      accepted_encoding = %w[utf-8 utf8 utf-16 utf16].
                           include?(@encoding.downcase)
-      fail(
-        DarwinCore::EncodingError,
-        "No support for encodings other than utf-8 or utf-16 at the moment"
-      ) unless accepted_encoding
+      unless accepted_encoding
+        raise(
+          DarwinCore::EncodingError,
+          "No support for encodings other than utf-8 or utf-16 at the moment"
+        )
+      end
     end
 
     def init_file_path
@@ -83,14 +86,16 @@ class DarwinCore
              @data[:attributes][:location] ||
              @data[:files][:location]
       @file_path = File.join(@path, file)
-      fail DarwinCore::FileNotFoundError, "No file data" unless @file_path
+      raise DarwinCore::FileNotFoundError, "No file data" unless @file_path
     end
 
     def init_fields
       @data[:field] = [data[:field]] if data[:field].class != Array
       @fields = @data[:field].map { |f| f[:attributes] }
-      fail DarwinCore::InvalidArchiveError,
-           "No data fields are found" if @fields.empty?
+      if @fields.empty?
+        raise DarwinCore::InvalidArchiveError,
+              "No data fields are found"
+      end
     end
 
     def init_field_separator
@@ -100,7 +105,7 @@ class DarwinCore
     end
 
     def init_size
-      `wc -l #{@file_path}`.match(/^\s*([\d]+)\s/)[1].to_i
+      `wc -l #{@file_path}`.match(/^\s*(\d+)\s/)[1].to_i
     end
   end
 end

data/lib/dwc_archive/metadata.rb

@@ -25,6 +25,7 @@ class DarwinCore
 
     def authors
       return nil unless defined?(@metadata[:eml][:dataset][:creator])
+
       authors = [@metadata[:eml][:dataset][:creator]].flatten
       authors.map do |au|
         { first_name: au[:individualName][:givenName],

data/lib/dwc_archive/version.rb

@@ -2,5 +2,5 @@
 
 # Version constant of the class
 class DarwinCore
-  VERSION = "1.0.1"
+  VERSION = "1.1.4"
 end

data/lib/dwc_archive/xml_reader.rb

@@ -35,13 +35,14 @@ class DarwinCore
       end
 
       def prepare(data)
-        data.class == String && data.to_i.to_s == data ? data.to_i : data
+        data.instance_of?(String) && data.to_i.to_s == data ? data.to_i : data
       end
 
       def add_attributes
         return if @node.attributes.empty?
+
         @val[:attributes] = {}
-        @node.attributes.keys.each do |key|
+        @node.attributes.each_key do |key|
           add_attribute(@val[:attributes], @node.attributes[key])
         end
       end

data/spec/lib/darwin_core_spec.rb

@@ -1,18 +1,11 @@
 # frozen_string_literal: true
 
+require "set"
+
 describe DarwinCore do
   subject { DarwinCore }
   let(:file_dir) { File.expand_path("../files", __dir__) }
 
-  describe "redis connection" do
-    it "redis is running" do
-      expect do
-        socket = TCPSocket.open("localhost", 6379)
-        socket.close
-      end.to_not raise_error
-    end
-  end
-
   it "has version" do
     expect(DarwinCore::VERSION).to match(/\d+\.\d+\.\d/)
   end
@@ -37,10 +30,10 @@ describe DarwinCore do
     it "cleans dwca directories" do
       Dir.chdir(tmp_dir)
       FileUtils.mkdir("dwc_123") unless File.exist?("dwc_123")
-      dwca_dirs = Dir.entries(tmp_dir).select { |d| d.match(/^dwc_[\d]+$/) }
+      dwca_dirs = Dir.entries(tmp_dir).select { |d| d.match(/^dwc_\d+$/) }
       expect(dwca_dirs.size).to be > 0
       subject.clean_all
-      dwca_dirs = Dir.entries(tmp_dir).select { |d| d.match(/^dwc_[\d]+$/) }
+      dwca_dirs = Dir.entries(tmp_dir).select { |d| d.match(/^dwc_\d+$/) }
       expect(dwca_dirs.size).to be 0
     end
 
@@ -48,7 +41,7 @@ describe DarwinCore do
       it "does nothing" do
         subject.clean_all
         subject.clean_all
-        dwca_dirs = Dir.entries(tmp_dir).select { |d| d.match(/^dwc_[\d]+$/) }
+        dwca_dirs = Dir.entries(tmp_dir).select { |d| d.match(/^dwc_\d+$/) }
         expect(dwca_dirs.size).to be 0
       end
     end
@@ -121,7 +114,7 @@ describe DarwinCore do
     end
 
     context "filename with spaces and non-alphanumeric chars" do
-      let(:file_path) { File.join(file_dir, "file with characters(3).gz") }
+      let(:file_path) { File.join(file_dir, "file with characters(3).tar.gz") }
 
       it "creates archive" do
         expect(dwca.archive.valid?).to be true
@@ -237,7 +230,8 @@ describe DarwinCore do
     let(:file_path) { File.join(file_dir, "data.tar.gz") }
     let(:normalized) { dwca.normalize_classification }
     let(:encodings) do
-      normalized.each_with_object(Set.new) do |taxon, e|
+      set = Set.new
+      normalized.each_with_object(set) do |taxon, e|
         taxon[1].classification_path.each { |p| e << p.encoding }
       end
     end

data/spec/lib/gnub_taxon_spec.rb

@@ -13,10 +13,10 @@ describe DarwinCore::GnubTaxon do
     expect(tn).to be_kind_of DarwinCore::GnubTaxon
     expect(tn).to be_kind_of DarwinCore::TaxonNormalized
     expect(tn.uuid).to eq "8faa91f6-663f-4cfe-b785-0ab4e9415a51"
-    expect(tn.uuid_path).to eq [
-      "9a9f9eeb-d5f9-4ff6-b6cb-a5ad345e33c3",
-      "bf4c91c0-3d1f-44c7-9d3b-249382182a26",
-      "8faa91f6-663f-4cfe-b785-0ab4e9415a51"
+    expect(tn.uuid_path).to eq %w[
+      9a9f9eeb-d5f9-4ff6-b6cb-a5ad345e33c3
+      bf4c91c0-3d1f-44c7-9d3b-249382182a26
+      8faa91f6-663f-4cfe-b785-0ab4e9415a51
     ]
   end
 

data/spec/spec_helper.rb

@@ -1,8 +1,5 @@
 # frozen_string_literal: true
 
-require "coveralls"
-Coveralls.wear!
-
 require "dwc_archive"
 require "rspec"
 require "rspec/mocks"

metadata

@@ -1,169 +1,169 @@
 --- !ruby/object:Gem::Specification
 name: dwc-archive
 version: !ruby/object:Gem::Version
-  version: 1.0.1
+  version: 1.1.4
 platform: ruby
 authors:
 - Dmitry Mozzherin
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2018-07-17 00:00:00.000000000 Z
+date: 2021-03-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: nokogiri
+  name: biodiversity
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.8'
+        version: 5.2.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.8'
+        version: 5.2.0
 - !ruby/object:Gem::Dependency
-  name: parsley-store
+  name: nokogiri
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.3'
+        version: '1.11'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.3'
+        version: '1.11'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.16'
+        version: '2.2'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.16'
+        version: '2.2'
 - !ruby/object:Gem::Dependency
-  name: coveralls
+  name: byebug
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.8'
+        version: '11.1'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.8'
+        version: '11.1'
 - !ruby/object:Gem::Dependency
   name: cucumber
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.1'
+        version: '5'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.1'
+        version: '5'
 - !ruby/object:Gem::Dependency
   name: git
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.4'
+        version: '1.8'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.4'
+        version: '1.8'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '12.3'
+        version: '13'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '12.3'
+        version: '13'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.7'
+        version: '3.10'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.7'
+        version: '3.10'
 - !ruby/object:Gem::Dependency
   name: rubocop
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.58'
+        version: '1.8'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.58'
+        version: '1.8'
 - !ruby/object:Gem::Dependency
   name: solargraph
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.23'
+        version: '0.40'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.23'
+        version: '0.40'
 - !ruby/object:Gem::Dependency
   name: travis
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.8'
+        version: '1.10'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.8'
+        version: '1.10'
 description: Darwin Core Archive is the current standard exchange format for GLobal
   Names Architecture modules. This gem makes it easy to incorporate files in Darwin
   Core Archive format into a ruby project.
@@ -174,11 +174,11 @@ extensions: []
 extra_rdoc_files: []
 files:
 - ".document"
+- ".github/workflows/build.yml"
 - ".gitignore"
 - ".rspec"
 - ".rubocop.yml"
 - ".ruby-version"
-- ".travis.yml"
 - CHANGELOG
 - Gemfile
 - LICENSE
@@ -212,7 +212,7 @@ files:
 - spec/files/data_with_quotes.tar.gz
 - spec/files/eml.xml
 - spec/files/empty_coreid.tar.gz
-- spec/files/file with characters(3).gz
+- spec/files/file with characters(3).tar.gz
 - spec/files/flat_list.tar.gz
 - spec/files/generator_eml.xml
 - spec/files/generator_meta.xml
@@ -245,7 +245,7 @@ homepage: http://github.com/GlobalNamesArchitecture/dwc-archive
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -253,16 +253,15 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: 2.4.1
+      version: 2.6.0
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.7.6
-signing_key: 
+rubygems_version: 3.2.15
+signing_key:
 specification_version: 4
 summary: Handler of Darwin Core Archive files
 test_files:
@@ -277,7 +276,7 @@ test_files:
 - spec/files/data_with_quotes.tar.gz
 - spec/files/eml.xml
 - spec/files/empty_coreid.tar.gz
-- spec/files/file with characters(3).gz
+- spec/files/file with characters(3).tar.gz
 - spec/files/flat_list.tar.gz
 - spec/files/generator_eml.xml
 - spec/files/generator_meta.xml

data/.travis.yml

@@ -1,15 +0,0 @@
-rvm:
-  - 2.4
-  - 2.5
-before_install:
-  - sudo apt-get update
-# bundler_args: --without development
-services:
-  - redis-server
-script:
-  - bundle exec cucumber
-  - bundle exec rake
-branches:
-  only:
-      - master
-