dwc-archive 1.1.2 → 1.1.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: f91a9aa06150210f94bd69bb408dc21340feb21294c958f1fe0b03eeda4dab57
-  data.tar.gz: eb6c0d368729f09aa91ddc7a131545b1fa1cdfcab5c09a9326e05bcd6e55cdea
+  metadata.gz: 024cdcbe976462942f15dee141a48d4dc0595ccfb1b4013ace4b88fd742ec6a6
+  data.tar.gz: 29aff6c8699d82f74513874a90cbfe796b2db8f1c94134500cbc154bf3dd61d8
 SHA512:
-  metadata.gz: 99a1903bd90f161180c59934a5533c55c3c838aeecd0a37476b7b240004c798ea9149a1511eac8ac3a434df1c2e5d5940bb0b6f125f0f7949decf62bcd78900a
-  data.tar.gz: 5922fca1a5e0a26ede79e9b3ee4d4a3255c9f1403b7ec71a9f5ce1b929f1dfc71abde50c82541a76a09899be9710e557f1850003f5ec04aa6c81e53f55933fd1
+  metadata.gz: 794cb8f3092f0005970421f68fba890553f825f9ef77902f3460fe16240a5438ec8fd277aa95eccae9335072dad5c42a25df87a326d5abd7f53f6271b411271c
+  data.tar.gz: fe2491aabacc15866880c54767f7b874b0c7c01c894947a671c3f0a7b10a1785a806731067100c426b39f80ec1d300e7298c7d0a4b8d30e7d2cab73847859622

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/.ruby-version

@@ -1 +1 @@
-2.7.1
+3.0.2

data/dwc-archive.gemspec

@@ -22,7 +22,7 @@ Gem::Specification.new do |gem|
   gem.require_paths = ["lib"]
 
   # gem.add_runtime_dependency "minitar", "~> 0.6"
-  gem.add_runtime_dependency "biodiversity", "~> 5"
+  gem.add_runtime_dependency "biodiversity", "~> 5.5.2"
   gem.add_runtime_dependency "nokogiri", "~> 1.11"
 
   gem.add_development_dependency "bundler", "~> 2.2"

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/version.rb

@@ -2,5 +2,5 @@
 
 # Version constant of the class
 class DarwinCore
-  VERSION = "1.1.2"
+  VERSION = "1.1.6"
 end

data/spec/lib/darwin_core_spec.rb

@@ -1,5 +1,7 @@
 # frozen_string_literal: true
 
+require "set"
+
 describe DarwinCore do
   subject { DarwinCore }
   let(:file_dir) { File.expand_path("../files", __dir__) }
@@ -228,7 +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

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: dwc-archive
 version: !ruby/object:Gem::Version
-  version: 1.1.2
+  version: 1.1.6
 platform: ruby
 authors:
 - Dmitry Mozzherin
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-01-19 00:00:00.000000000 Z
+date: 2021-11-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: biodiversity
@@ -16,14 +16,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '5'
+        version: 5.5.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '5'
+        version: 5.5.2
 - !ruby/object:Gem::Dependency
   name: nokogiri
   requirement: !ruby/object:Gem::Requirement
@@ -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
@@ -260,7 +260,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.6
+rubygems_version: 3.2.22
 signing_key:
 specification_version: 4
 summary: Handler of Darwin Core Archive files

data/.travis.yml

@@ -1,13 +0,0 @@
-rvm:
-  - 2.5
-  - 2.6
-  - 2.7
-before_install:
-  - sudo apt-get update
-  - gem install bundler
-script:
-  - bundle exec cucumber
-  - bundle exec rake
-branches:
-  only:
-      - master