dwc-archive 1.1.1 → 1.1.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: a5d4e174cb4ec6df2328fe99abb52b13587c74f22f01efb2a9017db4d9f1d7ba
-  data.tar.gz: e341038db2a23282173cf2e4671750739464dca6076f7560694cc40251bdd036
+  metadata.gz: f91a9aa06150210f94bd69bb408dc21340feb21294c958f1fe0b03eeda4dab57
+  data.tar.gz: eb6c0d368729f09aa91ddc7a131545b1fa1cdfcab5c09a9326e05bcd6e55cdea
 SHA512:
-  metadata.gz: 8b51b82724e21acab76e1763dc2375658080a16dc440c9913fd632aff195a45c34e7bf9446cf5d4afc9fc397c8ee562763ab36532ab5992421e5ed3f2df64273
-  data.tar.gz: 04cbcc92c8b565b2c5f8e8bf082d284b65c55520d91f19c16bc63789519ea374f5ed0466c176ce69907a83566caa8efd2f834399f7b57a26801603455cf2b118
+  metadata.gz: 99a1903bd90f161180c59934a5533c55c3c838aeecd0a37476b7b240004c798ea9149a1511eac8ac3a434df1c2e5d5940bb0b6f125f0f7949decf62bcd78900a
+  data.tar.gz: 5922fca1a5e0a26ede79e9b3ee4d4a3255c9f1403b7ec71a9f5ce1b929f1dfc71abde50c82541a76a09899be9710e557f1850003f5ec04aa6c81e53f55933fd1

data/dwc-archive.gemspec

@@ -15,23 +15,23 @@ Gem::Specification.new do |gem|
   gem.homepage      = "http://github.com/GlobalNamesArchitecture/dwc-archive"
   gem.license       = "MIT"
 
-  gem.required_ruby_version = ">= 2.5.0"
+  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", "~> 1.10"
-  gem.add_runtime_dependency "biodiversity", "~> 4"
+  gem.add_runtime_dependency "biodiversity", "~> 5"
+  gem.add_runtime_dependency "nokogiri", "~> 1.11"
 
+  gem.add_development_dependency "bundler", "~> 2.2"
   gem.add_development_dependency "byebug", "~> 11.1"
-  gem.add_development_dependency "bundler", "~> 2.1"
-  gem.add_development_dependency "cucumber", "~> 4"
-  gem.add_development_dependency "git", "~> 1.7"
+  gem.add_development_dependency "cucumber", "~> 5"
+  gem.add_development_dependency "git", "~> 1.8"
   gem.add_development_dependency "rake", "~> 13"
-  gem.add_development_dependency "rspec", "~> 3.9"
-  gem.add_development_dependency "rubocop", "~> 0.85"
-  gem.add_development_dependency "solargraph", "~> 0.39"
-  gem.add_development_dependency "travis", "~> 1.9"
+  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

@@ -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

@@ -73,7 +73,7 @@ class DarwinCore
       return nil unless @with_canonical_names
 
       canonical_name = Biodiversity::Parser.parse(a_scientific_name).
-                       dig(:canonicalName, :simple)
+                       dig(:canonical, :simple)
       canonical_name.to_s.empty? ? a_scientific_name : canonical_name
     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 && $CHILD_STATUS.exitstatus.zero?
         success
@@ -39,6 +40,7 @@ class DarwinCore
     def init_unpacker
       return tar_unpacker if @archive_path =~ /tar.gz$/i
       return zip_unpacker if @archive_path =~ /zip$/i
+
       nil
     end
 
@@ -58,11 +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
@@ -76,6 +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/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 = "1.1.1"
+  VERSION = "1.1.2"
 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

@@ -28,10 +28,10 @@ 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
 
@@ -39,7 +39,7 @@ 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

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
 

metadata

@@ -1,99 +1,99 @@
 --- !ruby/object:Gem::Specification
 name: dwc-archive
 version: !ruby/object:Gem::Version
-  version: 1.1.1
+  version: 1.1.2
 platform: ruby
 authors:
 - Dmitry Mozzherin
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-06-04 00:00:00.000000000 Z
+date: 2021-01-19 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: '1.10'
+        version: '5'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.10'
+        version: '5'
 - !ruby/object:Gem::Dependency
-  name: biodiversity
+  name: nokogiri
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '4'
+        version: '1.11'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '4'
+        version: '1.11'
 - !ruby/object:Gem::Dependency
-  name: byebug
+  name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '11.1'
+        version: '2.2'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '11.1'
+        version: '2.2'
 - !ruby/object:Gem::Dependency
-  name: bundler
+  name: byebug
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.1'
+        version: '11.1'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.1'
+        version: '11.1'
 - !ruby/object:Gem::Dependency
   name: cucumber
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '4'
+        version: '5'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '4'
+        version: '5'
 - !ruby/object:Gem::Dependency
   name: git
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.7'
+        version: '1.8'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.7'
+        version: '1.8'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
@@ -114,56 +114,56 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.9'
+        version: '3.10'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.9'
+        version: '3.10'
 - !ruby/object:Gem::Dependency
   name: rubocop
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.85'
+        version: '1.8'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.85'
+        version: '1.8'
 - !ruby/object:Gem::Dependency
   name: solargraph
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.39'
+        version: '0.40'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.39'
+        version: '0.40'
 - !ruby/object:Gem::Dependency
   name: travis
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.9'
+        version: '1.10'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.9'
+        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.
@@ -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
@@ -253,15 +253,15 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: 2.5.0
+      version: 2.6.0
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.2
-signing_key: 
+rubygems_version: 3.2.6
+signing_key:
 specification_version: 4
 summary: Handler of Darwin Core Archive files
 test_files: