dwc-archive 0.9.5 → 1.1.0
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- checksums.yaml +7 -0
- data/.gitignore +31 -0
- data/.rspec +3 -0
- data/.rubocop.yml +23 -0
- data/.ruby-version +1 -0
- data/.travis.yml +5 -4
- data/CHANGELOG +17 -5
- data/Gemfile +3 -15
- data/LICENSE +1 -1
- data/README.md +143 -111
- data/Rakefile +13 -49
- data/dwc-archive.gemspec +37 -0
- data/features/step_definitions/dwc-creator_steps.rb +5 -5
- data/features/step_definitions/dwc-reader_steps.rb +47 -28
- data/features/support/env.rb +1 -1
- data/lib/dwc_archive.rb +121 -0
- data/lib/dwc_archive/archive.rb +59 -0
- data/lib/dwc_archive/classification_normalizer.rb +394 -0
- data/lib/dwc_archive/core.rb +25 -0
- data/lib/{dwc-archive → dwc_archive}/errors.rb +2 -0
- data/lib/dwc_archive/expander.rb +85 -0
- data/lib/{dwc-archive → dwc_archive}/extension.rb +5 -3
- data/lib/dwc_archive/generator.rb +90 -0
- data/lib/dwc_archive/generator_eml_xml.rb +116 -0
- data/lib/dwc_archive/generator_meta_xml.rb +72 -0
- data/lib/dwc_archive/gnub_taxon.rb +14 -0
- data/lib/dwc_archive/ingester.rb +106 -0
- data/lib/dwc_archive/metadata.rb +56 -0
- data/lib/dwc_archive/taxon_normalized.rb +23 -0
- data/lib/dwc_archive/version.rb +6 -0
- data/lib/dwc_archive/xml_reader.rb +89 -0
- data/spec/files/file with characters(3).gz b/data/spec/files/file with → characters(3).tar.gz +0 -0
- data/spec/files/generator_eml.xml +47 -0
- data/spec/files/generator_meta.xml +19 -0
- data/spec/files/gnub.tar.gz +0 -0
- data/spec/lib/classification_normalizer_spec.rb +214 -0
- data/spec/lib/core_spec.rb +100 -0
- data/spec/lib/darwin_core_spec.rb +249 -0
- data/spec/lib/generator_eml_xml_spec.rb +22 -0
- data/spec/lib/generator_meta_xml_spec.rb +22 -0
- data/spec/lib/generator_spec.rb +124 -0
- data/spec/lib/gnub_taxon_spec.rb +32 -0
- data/spec/lib/metadata_spec.rb +89 -0
- data/spec/lib/taxon_normalized_spec.rb +142 -0
- data/spec/lib/xml_reader_spec.rb +11 -11
- data/spec/spec_helper.rb +78 -7
- metadata +181 -92
- data/.rvmrc +0 -1
- data/Gemfile.lock +0 -155
- data/VERSION +0 -1
- data/lib/dwc-archive.rb +0 -95
- data/lib/dwc-archive/.expander.rb.swo +0 -0
- data/lib/dwc-archive/archive.rb +0 -37
- data/lib/dwc-archive/classification_normalizer.rb +0 -332
- data/lib/dwc-archive/core.rb +0 -17
- data/lib/dwc-archive/expander.rb +0 -80
- data/lib/dwc-archive/generator.rb +0 -75
- data/lib/dwc-archive/generator_eml_xml.rb +0 -84
- data/lib/dwc-archive/generator_meta_xml.rb +0 -50
- data/lib/dwc-archive/ingester.rb +0 -101
- data/lib/dwc-archive/metadata.rb +0 -42
- data/lib/dwc-archive/utf_regex_ruby18.rb +0 -10
- data/lib/dwc-archive/xml_reader.rb +0 -64
- data/spec/lib/dwc-archive_spec.rb +0 -236
- data/spec/spec.opts +0 -1
@@ -0,0 +1,100 @@
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# frozen_string_literal: true
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require_relative "../spec_helper"
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describe DarwinCore::Core do
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subject(:dwca) { DarwinCore.new(file_path) }
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subject(:core) { DarwinCore::Core.new(dwca) }
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let(:file_path) do
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File.join(File.expand_path("../files", __dir__), file_name)
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end
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let(:file_name) { "data.tar.gz" }
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describe ".new" do
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it "creates new core" do
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expect(core).to be_kind_of DarwinCore::Core
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end
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end
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describe "#id" do
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it "returns core id" do
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expect(core.id[:index]).to eq 0
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expect(core.id[:term]).to eq "http://rs.tdwg.org/dwc/terms/TaxonID"
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end
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context "no coreid" do
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let(:file_name) { "empty_coreid.tar.gz" }
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it "does not return coreid" do
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expect(core.id[:index]).to eq 0
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expect(core.id[:term]).to be_nil
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end
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end
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end
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describe "#data" do
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it "gers core data" do
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expect(core.data).to be_kind_of Hash
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end
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end
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describe "#properties" do
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it "gers core properties" do
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expect(core.properties).to be_kind_of Hash
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expect(core.properties.keys).to match_array %i[
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encoding fieldsTerminatedBy linesTerminatedBy fieldsEnclosedBy
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ignoreHeaderLines rowType
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]
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end
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end
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describe "#encoding" do
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it "returns encoding of the data" do
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expect(core.encoding).to eq "UTF-8"
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end
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end
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describe "#fields_separator" do
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it "returns separator of fields for csv files" do
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expect(core.fields_separator).to be_nil
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end
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end
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describe "#size" do
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it "returns number of lines in the core" do
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expect(core.size).to eq 588
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end
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end
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describe "#file_path" do
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it "returns file path of core file" do
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expect(core.file_path).to match "DarwinCore.txt"
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end
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end
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describe "#fields" do
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it "returns fields of the core file" do
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expect(core.fields.size).to eq 7
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expect(core.fields).to be_kind_of Array
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expect(core.fields[0]).to be_kind_of Hash
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end
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end
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describe "#line_separator" do
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it "returns characters separating lines in csv file" do
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expect(core.line_separator).to eq "\\n"
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end
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end
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describe "#quote_character" do
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it "returns quote character for the csv file" do
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expect(core.quote_character).to eq ""
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end
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end
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describe "#ignore headers" do
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it "returns true if headers should not be included into data" do
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expect(core.ignore_headers).to eq true
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end
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end
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end
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# frozen_string_literal: true
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describe DarwinCore do
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subject { DarwinCore }
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let(:file_dir) { File.expand_path("../files", __dir__) }
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it "has version" do
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expect(DarwinCore::VERSION).to match(/\d+\.\d+\.\d/)
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end
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describe ".nil_field?" do
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it "is true for nil fields" do
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[nil, "/N", ""].each do |i|
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expect(DarwinCore.nil_field?(i)).to be true
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end
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end
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it "is false for non-nil fields" do
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[0, "0", "123", 123, "dsdfs434343/N"].each do |i|
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expect(subject.nil_field?(i)).to be false
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end
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end
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end
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describe ".clean_all" do
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let(:tmp_dir) { DarwinCore::DEFAULT_TMP_DIR }
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it "cleans dwca directories" do
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Dir.chdir(tmp_dir)
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FileUtils.mkdir("dwc_123") unless File.exist?("dwc_123")
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dwca_dirs = Dir.entries(tmp_dir).select { |d| d.match(/^dwc_[\d]+$/) }
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expect(dwca_dirs.size).to be > 0
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subject.clean_all
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dwca_dirs = Dir.entries(tmp_dir).select { |d| d.match(/^dwc_[\d]+$/) }
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expect(dwca_dirs.size).to be 0
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end
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context "no dwc files exist" do
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it "does nothing" do
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subject.clean_all
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subject.clean_all
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dwca_dirs = Dir.entries(tmp_dir).select { |d| d.match(/^dwc_[\d]+$/) }
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expect(dwca_dirs.size).to be 0
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end
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end
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end
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describe ".logger" do
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it { expect(subject.logger).to be_kind_of Logger }
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end
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describe ".logger=" do
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it "sets logger" do
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expect(subject.logger = "fake logger").to eq "fake logger"
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expect(subject.logger).to eq "fake logger"
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end
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end
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describe ".logger_reset" do
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it "resets logger" do
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subject.logger = "fake logger"
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expect(subject.logger).to eq "fake logger"
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subject.logger_reset
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expect(subject.logger).to be_kind_of Logger
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end
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end
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describe ".new" do
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subject(:dwca) { DarwinCore.new(file_path) }
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context "tar.gz and zip files supplied" do
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files = %w[data.zip data.tar.gz minimal.tar.gz junk_dir_inside.zip]
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files.each do |file|
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let(:file_path) { File.join(file_dir, file) }
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it "creates archive from #{file}" do
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expect(dwca.archive.valid?).to be true
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end
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end
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end
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context "when file does not exist" do
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let(:file_path) { File.join(file_dir, "no_file.gz") }
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it "raises not found" do
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expect { dwca }.to raise_error DarwinCore::FileNotFoundError
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end
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end
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context "archive cannot unpack" do
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let(:file_path) { File.join(file_dir, "broken.tar.gz") }
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it "raises unpacking error" do
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expect { dwca }.to raise_error DarwinCore::UnpackingError
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end
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end
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context "archive is broken" do
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let(:file_path) { File.join(file_dir, "invalid.tar.gz") }
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it "raises error of invalid archive" do
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expect { dwca }.to raise_error DarwinCore::InvalidArchiveError
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end
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end
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context "archive is not in utf-8 encoding" do
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let(:file_path) { File.join(file_dir, "latin1.tar.gz") }
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it "raises wrong encoding error" do
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expect { dwca }.to raise_error DarwinCore::EncodingError
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end
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end
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context "filename with spaces and non-alphanumeric chars" do
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let(:file_path) { File.join(file_dir, "file with characters(3).tar.gz") }
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it "creates archive" do
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expect(dwca.archive.valid?).to be true
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end
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end
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end
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describe "file_name" do
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subject(:dwca) { DarwinCore.new(file_path) }
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let(:file_path) { File.join(file_dir, "data.tar.gz") }
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it "returns file name" do
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expect(dwca.file_name).to eq "data.tar.gz"
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end
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end
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describe "path" do
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subject(:dwca) { DarwinCore.new(file_path) }
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let(:file_path) { File.join(file_dir, "data.tar.gz") }
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it "returns path of the archive" do
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expect(dwca.path).to match(/spec.files.data\.tar\.gz/)
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end
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end
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describe "#archive" do
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subject(:dwca) { DarwinCore.new(file_path) }
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let(:file_path) { File.join(file_dir, "data.tar.gz") }
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it "returns archive" do
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expect(dwca.archive).to be_kind_of DarwinCore::Archive
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end
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end
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describe "#core" do
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subject(:dwca) { DarwinCore.new(file_path) }
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let(:file_path) { File.join(file_dir, "data.tar.gz") }
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it "returns core" do
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expect(dwca.core).to be_kind_of DarwinCore::Core
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end
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end
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describe "#metadata" do
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subject(:dwca) { DarwinCore.new(file_path) }
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let(:file_path) { File.join(file_dir, "data.tar.gz") }
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it "returns eml" do
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expect(dwca.eml).to be_kind_of DarwinCore::Metadata
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expect(dwca.metadata).to be_kind_of DarwinCore::Metadata
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end
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end
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describe "#extensions" do
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subject(:dwca) { DarwinCore.new(file_path) }
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let(:file_path) { File.join(file_dir, "data.tar.gz") }
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it "returns extensions" do
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extensions = dwca.extensions
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expect(extensions).to be_kind_of Array
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expect(extensions[0]).to be_kind_of DarwinCore::Extension
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end
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end
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describe "#checksum" do
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subject(:dwca) { DarwinCore.new(file_path) }
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let(:file_path) { File.join(file_dir, "data.tar.gz") }
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it "creates checksum hash" do
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expect(dwca.checksum).to eq "7d94fc28ffaf434b66fbc790aa5ef00d834057bf"
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end
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end
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describe "#parent_id?" do
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subject(:dwca) { DarwinCore.new(file_path) }
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context "has classification" do
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let(:file_path) { File.join(file_dir, "data.tar.gz") }
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it "returns true" do
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expect(dwca.parent_id?).to be true
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end
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end
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context "does not have classification" do
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let(:file_path) { File.join(file_dir, "gnub.tar.gz") }
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it "returns false" do
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expect(dwca.parent_id?).to be false
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end
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end
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end
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describe "#classification_normalizer" do
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subject(:dwca) { DarwinCore.new(file_path) }
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let(:file_path) { File.join(file_dir, "data.tar.gz") }
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context "not initialized" do
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it "is nil" do
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expect(dwca.classification_normalizer).to be_nil
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end
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end
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context "initialized" do
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it "is DarwinCore::ClassificationNormalizer" do
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dwca.normalize_classification
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expect(dwca.classification_normalizer).
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to be_kind_of DarwinCore::ClassificationNormalizer
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end
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end
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end
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describe "#normalize_classification" do
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subject(:dwca) { DarwinCore.new(file_path) }
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let(:file_path) { File.join(file_dir, "data.tar.gz") }
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let(:normalized) { dwca.normalize_classification }
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let(:encodings) do
|
231
|
+
normalized.each_with_object(Set.new) do |taxon, e|
|
232
|
+
taxon[1].classification_path.each { |p| e << p.encoding }
|
233
|
+
end
|
234
|
+
end
|
235
|
+
|
236
|
+
it "returns hash" do
|
237
|
+
expect(normalized).to be_kind_of Hash
|
238
|
+
end
|
239
|
+
|
240
|
+
it "uses utf-8 encoding for classification paths" do
|
241
|
+
expect(encodings.map(&:to_s).to_a).to eq ["UTF-8"]
|
242
|
+
end
|
243
|
+
|
244
|
+
it "has elements of DarwinCore::TaxonNormalized type" do
|
245
|
+
expect(normalized["leptogastrinae:tid:2857"]).
|
246
|
+
to be_kind_of DarwinCore::TaxonNormalized
|
247
|
+
end
|
248
|
+
end
|
249
|
+
end
|
@@ -0,0 +1,22 @@
|
|
1
|
+
# frozen_string_literal: true
|
2
|
+
|
3
|
+
describe DarwinCore::Generator::EmlXml do
|
4
|
+
subject { DarwinCore::Generator::EmlXml.new(data, path) }
|
5
|
+
let(:data) { EML_DATA }
|
6
|
+
let(:path) { DarwinCore::DEFAULT_TMP_DIR }
|
7
|
+
|
8
|
+
describe ".new" do
|
9
|
+
it { is_expected.to be_kind_of DarwinCore::Generator::EmlXml }
|
10
|
+
end
|
11
|
+
|
12
|
+
describe "#create" do
|
13
|
+
let(:content) do
|
14
|
+
subject.create
|
15
|
+
File.read(File.join(path, "eml.xml"))
|
16
|
+
end
|
17
|
+
|
18
|
+
it "should create eml xml" do
|
19
|
+
expect(content).to match(/Test Classification/)
|
20
|
+
end
|
21
|
+
end
|
22
|
+
end
|
@@ -0,0 +1,22 @@
|
|
1
|
+
# frozen_string_literal: true
|
2
|
+
|
3
|
+
describe DarwinCore::Generator::MetaXml do
|
4
|
+
subject { DarwinCore::Generator::MetaXml.new(data, path) }
|
5
|
+
let(:data) { META_DATA }
|
6
|
+
let(:path) { DarwinCore::DEFAULT_TMP_DIR }
|
7
|
+
|
8
|
+
describe ".new" do
|
9
|
+
it { is_expected.to be_kind_of DarwinCore::Generator::MetaXml }
|
10
|
+
end
|
11
|
+
|
12
|
+
describe "#create" do
|
13
|
+
let(:content) do
|
14
|
+
subject.create
|
15
|
+
File.read(File.join(path, "meta.xml"))
|
16
|
+
end
|
17
|
+
|
18
|
+
it "creates metadata file" do
|
19
|
+
expect(content).to match(%r{<location>core.csv</location>})
|
20
|
+
end
|
21
|
+
end
|
22
|
+
end
|
@@ -0,0 +1,124 @@
|
|
1
|
+
# frozen_string_literal: true
|
2
|
+
|
3
|
+
describe DarwinCore::Generator do
|
4
|
+
subject(:gen) { DarwinCore::Generator.new(dwc_path, tmp_dir) }
|
5
|
+
let(:tmp_dir) { DarwinCore::DEFAULT_TMP_DIR }
|
6
|
+
let(:dwc_path) { File.join(tmp_dir, "spec_dwca.tar.gz") }
|
7
|
+
|
8
|
+
def generate_dwca(gen)
|
9
|
+
gen.add_core(CORE_DATA.dup, "core.csv", true)
|
10
|
+
gen.add_extension(EXTENSION_DATA.dup, "vern.csv", true,
|
11
|
+
"http://rs.gbif.org/terms/1.0/VernacularName")
|
12
|
+
gen.add_meta_xml
|
13
|
+
gen.add_eml_xml(EML_DATA)
|
14
|
+
end
|
15
|
+
|
16
|
+
describe ".new" do
|
17
|
+
it "initializes empty DwCA" do
|
18
|
+
expect(gen).to be_kind_of DarwinCore::Generator
|
19
|
+
end
|
20
|
+
end
|
21
|
+
|
22
|
+
describe "#add_core" do
|
23
|
+
it "adds core to DwCA instance" do
|
24
|
+
gen.add_core(CORE_DATA.dup, "core.csv", true)
|
25
|
+
core = File.read(File.join(gen.path, "core.csv"))
|
26
|
+
expect(core).to match(/taxonID,parentNameUsageID,scientificName/)
|
27
|
+
end
|
28
|
+
|
29
|
+
context "urls are not given in header" do
|
30
|
+
it "raises error" do
|
31
|
+
data = CORE_DATA.dup
|
32
|
+
data[0] = data[0].map { |f| f.split("/")[-1] }
|
33
|
+
expect { gen.add_core(data, "core.csv", true) }.
|
34
|
+
to raise_error DarwinCore::GeneratorError
|
35
|
+
end
|
36
|
+
end
|
37
|
+
end
|
38
|
+
|
39
|
+
describe "#add_extension" do
|
40
|
+
it "adds extension to DwCA instance" do
|
41
|
+
gen.add_extension(EXTENSION_DATA.dup,
|
42
|
+
"vern.csv",
|
43
|
+
true,
|
44
|
+
"http://rs.gbif.org/terms/1.0/VernacularName")
|
45
|
+
extension = File.read(File.join(gen.path, "vern.csv"))
|
46
|
+
|
47
|
+
expect(extension).to match(/Береза/)
|
48
|
+
end
|
49
|
+
end
|
50
|
+
|
51
|
+
describe "#add_meta_xml" do
|
52
|
+
it "creates metadata for DwCA" do
|
53
|
+
gen.add_core(CORE_DATA.dup, "core.csv", true)
|
54
|
+
gen.add_extension(EXTENSION_DATA.dup,
|
55
|
+
"vern.csv",
|
56
|
+
true,
|
57
|
+
"http://rs.gbif.org/terms/1.0/VernacularName")
|
58
|
+
|
59
|
+
gen.add_meta_xml
|
60
|
+
meta = File.read(File.join(gen.path, "meta.xml")).strip
|
61
|
+
meta_from_file = File.read(
|
62
|
+
File.expand_path("../files/generator_meta.xml", __dir__)
|
63
|
+
).strip
|
64
|
+
expect(meta).to eq meta_from_file
|
65
|
+
end
|
66
|
+
end
|
67
|
+
|
68
|
+
describe "#add_eml_data" do
|
69
|
+
it "adds eml data" do
|
70
|
+
gen.add_eml_xml(EML_DATA)
|
71
|
+
eml = File.read(File.join(gen.path, "eml.xml")).strip
|
72
|
+
eml.gsub!(%r{(<pubDate>).*?(</pubDate>)}, '\12013-12-30 14:45:33 -0500\2')
|
73
|
+
eml.gsub!(/(packageId=").*?"/, '\11234/2013-12-30::19:45:33"')
|
74
|
+
|
75
|
+
eml_from_file = File.read(
|
76
|
+
File.expand_path("../files/generator_eml.xml", __dir__)
|
77
|
+
).strip
|
78
|
+
expect(eml.strip).to eq eml_from_file.strip
|
79
|
+
end
|
80
|
+
end
|
81
|
+
|
82
|
+
describe "#path" do
|
83
|
+
it "returns temporary path for assembling DwCA" do
|
84
|
+
expect(gen.path).to match(/dwc_\d+$/)
|
85
|
+
end
|
86
|
+
end
|
87
|
+
|
88
|
+
describe "#files" do
|
89
|
+
before(:example) { generate_dwca(gen) }
|
90
|
+
|
91
|
+
it "returns created files" do
|
92
|
+
expect(gen.files).
|
93
|
+
to match_array ["core.csv", "eml.xml", "meta.xml", "vern.csv"]
|
94
|
+
end
|
95
|
+
end
|
96
|
+
|
97
|
+
describe "#pack" do
|
98
|
+
before(:example) do
|
99
|
+
FileUtils.rm dwc_path if File.exist?(dwc_path)
|
100
|
+
generate_dwca(gen)
|
101
|
+
end
|
102
|
+
|
103
|
+
it "creates final DwCA file" do
|
104
|
+
gen.pack
|
105
|
+
expect(File.exist?(dwc_path)).to be true
|
106
|
+
end
|
107
|
+
end
|
108
|
+
|
109
|
+
describe "#clean" do
|
110
|
+
before(:example) { gen.add_eml_xml(EML_DATA) }
|
111
|
+
|
112
|
+
it "removes temporary directory for DwCA" do
|
113
|
+
expect(File.exist?(gen.path)).to be true
|
114
|
+
gen.clean
|
115
|
+
expect(File.exist?(gen.path)).to be false
|
116
|
+
end
|
117
|
+
end
|
118
|
+
|
119
|
+
describe "#eml_xml_data" do
|
120
|
+
it "returns current eml data" do
|
121
|
+
expect(gen.eml_xml_data).to be_kind_of Hash
|
122
|
+
end
|
123
|
+
end
|
124
|
+
end
|