dwc-archive 0.9.6 → 1.1.1

data/spec/lib/core_spec.rb

@@ -0,0 +1,100 @@
+# frozen_string_literal: true
+
+require_relative "../spec_helper"
+
+describe DarwinCore::Core do
+  subject(:dwca) { DarwinCore.new(file_path) }
+  subject(:core) { DarwinCore::Core.new(dwca) }
+  let(:file_path) do
+    File.join(File.expand_path("../files", __dir__), file_name)
+  end
+  let(:file_name) { "data.tar.gz" }
+
+  describe ".new" do
+    it "creates new core" do
+      expect(core).to be_kind_of DarwinCore::Core
+    end
+  end
+
+  describe "#id" do
+    it "returns core id" do
+      expect(core.id[:index]).to eq 0
+      expect(core.id[:term]).to eq "http://rs.tdwg.org/dwc/terms/TaxonID"
+    end
+
+    context "no coreid" do
+      let(:file_name) { "empty_coreid.tar.gz" }
+
+      it "does not return coreid" do
+        expect(core.id[:index]).to eq 0
+        expect(core.id[:term]).to be_nil
+      end
+    end
+  end
+
+  describe "#data" do
+    it "gers core data" do
+      expect(core.data).to be_kind_of Hash
+    end
+  end
+
+  describe "#properties" do
+    it "gers core properties" do
+      expect(core.properties).to be_kind_of Hash
+      expect(core.properties.keys).to match_array %i[
+        encoding fieldsTerminatedBy linesTerminatedBy fieldsEnclosedBy
+        ignoreHeaderLines rowType
+      ]
+    end
+  end
+
+  describe "#encoding" do
+    it "returns encoding of the data" do
+      expect(core.encoding).to eq "UTF-8"
+    end
+  end
+
+  describe "#fields_separator" do
+    it "returns separator of fields for csv files" do
+      expect(core.fields_separator).to be_nil
+    end
+  end
+
+  describe "#size" do
+    it "returns number of lines in the core" do
+      expect(core.size).to eq 588
+    end
+  end
+
+  describe "#file_path" do
+    it "returns file path of core file" do
+      expect(core.file_path).to match "DarwinCore.txt"
+    end
+  end
+
+  describe "#fields" do
+    it "returns fields of the core file" do
+      expect(core.fields.size).to eq 7
+      expect(core.fields).to be_kind_of Array
+      expect(core.fields[0]).to be_kind_of Hash
+    end
+  end
+
+  describe "#line_separator" do
+    it "returns characters separating lines in csv file" do
+      expect(core.line_separator).to eq "\\n"
+    end
+  end
+
+  describe "#quote_character" do
+    it "returns quote character for the csv file" do
+      expect(core.quote_character).to eq ""
+    end
+  end
+
+  describe "#ignore headers" do
+    it "returns true if headers should not be included into data" do
+      expect(core.ignore_headers).to eq true
+    end
+  end
+end

data/spec/lib/darwin_core_spec.rb

@@ -0,0 +1,249 @@
+# frozen_string_literal: true
+
+describe DarwinCore do
+  subject { DarwinCore }
+  let(:file_dir) { File.expand_path("../files", __dir__) }
+
+  it "has version" do
+    expect(DarwinCore::VERSION).to match(/\d+\.\d+\.\d/)
+  end
+
+  describe ".nil_field?" do
+    it "is true for nil fields" do
+      [nil, "/N", ""].each do |i|
+        expect(DarwinCore.nil_field?(i)).to be true
+      end
+    end
+
+    it "is false for non-nil  fields" do
+      [0, "0", "123", 123, "dsdfs434343/N"].each do |i|
+        expect(subject.nil_field?(i)).to be false
+      end
+    end
+  end
+
+  describe ".clean_all" do
+    let(:tmp_dir) { DarwinCore::DEFAULT_TMP_DIR }
+
+    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]+$/) }
+      expect(dwca_dirs.size).to be > 0
+      subject.clean_all
+      dwca_dirs = Dir.entries(tmp_dir).select { |d| d.match(/^dwc_[\d]+$/) }
+      expect(dwca_dirs.size).to be 0
+    end
+
+    context "no dwc files exist" do
+      it "does nothing" do
+        subject.clean_all
+        subject.clean_all
+        dwca_dirs = Dir.entries(tmp_dir).select { |d| d.match(/^dwc_[\d]+$/) }
+        expect(dwca_dirs.size).to be 0
+      end
+    end
+  end
+
+  describe ".logger" do
+    it { expect(subject.logger).to be_kind_of Logger }
+  end
+
+  describe ".logger=" do
+    it "sets logger" do
+      expect(subject.logger = "fake logger").to eq "fake logger"
+      expect(subject.logger).to eq "fake logger"
+    end
+  end
+
+  describe ".logger_reset" do
+    it "resets logger" do
+      subject.logger = "fake logger"
+      expect(subject.logger).to eq "fake logger"
+      subject.logger_reset
+      expect(subject.logger).to be_kind_of Logger
+    end
+  end
+
+  describe ".new" do
+    subject(:dwca) { DarwinCore.new(file_path) }
+
+    context "tar.gz and zip files supplied" do
+      files = %w[data.zip data.tar.gz minimal.tar.gz junk_dir_inside.zip]
+      files.each do |file|
+        let(:file_path) { File.join(file_dir, file) }
+
+        it "creates archive from  #{file}" do
+          expect(dwca.archive.valid?).to be true
+        end
+      end
+    end
+
+    context "when file does not exist" do
+      let(:file_path) { File.join(file_dir, "no_file.gz") }
+
+      it "raises not found" do
+        expect { dwca }.to raise_error DarwinCore::FileNotFoundError
+      end
+    end
+
+    context "archive cannot unpack" do
+      let(:file_path) { File.join(file_dir, "broken.tar.gz") }
+
+      it "raises unpacking error" do
+        expect { dwca }.to raise_error DarwinCore::UnpackingError
+      end
+    end
+
+    context "archive is broken" do
+      let(:file_path) { File.join(file_dir, "invalid.tar.gz") }
+
+      it "raises error of invalid archive" do
+        expect { dwca }.to raise_error DarwinCore::InvalidArchiveError
+      end
+    end
+
+    context "archive is not in utf-8 encoding" do
+      let(:file_path) { File.join(file_dir, "latin1.tar.gz") }
+
+      it "raises wrong encoding error" do
+        expect { dwca }.to raise_error DarwinCore::EncodingError
+      end
+    end
+
+    context "filename with spaces and non-alphanumeric chars" do
+      let(:file_path) { File.join(file_dir, "file with characters(3).tar.gz") }
+
+      it "creates archive" do
+        expect(dwca.archive.valid?).to be true
+      end
+    end
+  end
+
+  describe "file_name" do
+    subject(:dwca) { DarwinCore.new(file_path) }
+    let(:file_path) { File.join(file_dir, "data.tar.gz") }
+
+    it "returns file name" do
+      expect(dwca.file_name).to eq "data.tar.gz"
+    end
+  end
+
+  describe "path" do
+    subject(:dwca) { DarwinCore.new(file_path) }
+    let(:file_path) { File.join(file_dir, "data.tar.gz") }
+
+    it "returns path of the archive" do
+      expect(dwca.path).to match(/spec.files.data\.tar\.gz/)
+    end
+  end
+
+  describe "#archive" do
+    subject(:dwca) { DarwinCore.new(file_path) }
+    let(:file_path) { File.join(file_dir, "data.tar.gz") }
+
+    it "returns archive" do
+      expect(dwca.archive).to be_kind_of DarwinCore::Archive
+    end
+  end
+
+  describe "#core" do
+    subject(:dwca) { DarwinCore.new(file_path) }
+    let(:file_path) { File.join(file_dir, "data.tar.gz") }
+
+    it "returns core" do
+      expect(dwca.core).to be_kind_of DarwinCore::Core
+    end
+  end
+
+  describe "#metadata" do
+    subject(:dwca) { DarwinCore.new(file_path) }
+    let(:file_path) { File.join(file_dir, "data.tar.gz") }
+
+    it "returns eml" do
+      expect(dwca.eml).to be_kind_of DarwinCore::Metadata
+      expect(dwca.metadata).to be_kind_of DarwinCore::Metadata
+    end
+  end
+
+  describe "#extensions" do
+    subject(:dwca) { DarwinCore.new(file_path) }
+    let(:file_path) { File.join(file_dir, "data.tar.gz") }
+
+    it "returns extensions" do
+      extensions = dwca.extensions
+      expect(extensions).to be_kind_of Array
+      expect(extensions[0]).to be_kind_of DarwinCore::Extension
+    end
+  end
+
+  describe "#checksum" do
+    subject(:dwca) { DarwinCore.new(file_path) }
+    let(:file_path) { File.join(file_dir, "data.tar.gz") }
+
+    it "creates checksum hash" do
+      expect(dwca.checksum).to eq "7d94fc28ffaf434b66fbc790aa5ef00d834057bf"
+    end
+  end
+
+  describe "#parent_id?" do
+    subject(:dwca) { DarwinCore.new(file_path) }
+
+    context "has classification" do
+      let(:file_path) { File.join(file_dir, "data.tar.gz") }
+      it "returns true" do
+        expect(dwca.parent_id?).to be true
+      end
+    end
+
+    context "does not have classification" do
+      let(:file_path) { File.join(file_dir, "gnub.tar.gz") }
+      it "returns false" do
+        expect(dwca.parent_id?).to be false
+      end
+    end
+  end
+
+  describe "#classification_normalizer" do
+    subject(:dwca) { DarwinCore.new(file_path) }
+    let(:file_path) { File.join(file_dir, "data.tar.gz") }
+
+    context "not initialized" do
+      it "is nil" do
+        expect(dwca.classification_normalizer).to be_nil
+      end
+    end
+
+    context "initialized" do
+      it "is DarwinCore::ClassificationNormalizer" do
+        dwca.normalize_classification
+        expect(dwca.classification_normalizer).
+          to be_kind_of DarwinCore::ClassificationNormalizer
+      end
+    end
+  end
+
+  describe "#normalize_classification" do
+    subject(:dwca) { DarwinCore.new(file_path) }
+    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|
+        taxon[1].classification_path.each { |p| e << p.encoding }
+      end
+    end
+
+    it "returns hash" do
+      expect(normalized).to be_kind_of Hash
+    end
+
+    it "uses utf-8 encoding for classification paths" do
+      expect(encodings.map(&:to_s).to_a).to eq ["UTF-8"]
+    end
+
+    it "has elements of DarwinCore::TaxonNormalized type" do
+      expect(normalized["leptogastrinae:tid:2857"]).
+        to be_kind_of DarwinCore::TaxonNormalized
+    end
+  end
+end

data/spec/lib/generator_eml_xml_spec.rb

@@ -0,0 +1,22 @@
+# frozen_string_literal: true
+
+describe DarwinCore::Generator::EmlXml do
+  subject { DarwinCore::Generator::EmlXml.new(data, path) }
+  let(:data) { EML_DATA }
+  let(:path) { DarwinCore::DEFAULT_TMP_DIR }
+
+  describe ".new" do
+    it { is_expected.to be_kind_of DarwinCore::Generator::EmlXml }
+  end
+
+  describe "#create" do
+    let(:content) do
+      subject.create
+      File.read(File.join(path, "eml.xml"))
+    end
+
+    it "should create eml xml" do
+      expect(content).to match(/Test Classification/)
+    end
+  end
+end

data/spec/lib/generator_meta_xml_spec.rb

@@ -0,0 +1,22 @@
+# frozen_string_literal: true
+
+describe DarwinCore::Generator::MetaXml do
+  subject { DarwinCore::Generator::MetaXml.new(data, path) }
+  let(:data) { META_DATA }
+  let(:path) { DarwinCore::DEFAULT_TMP_DIR }
+
+  describe ".new" do
+    it { is_expected.to be_kind_of DarwinCore::Generator::MetaXml }
+  end
+
+  describe "#create" do
+    let(:content) do
+      subject.create
+      File.read(File.join(path, "meta.xml"))
+    end
+
+    it "creates metadata file" do
+      expect(content).to match(%r{<location>core.csv</location>})
+    end
+  end
+end

data/spec/lib/generator_spec.rb

@@ -0,0 +1,124 @@
+# frozen_string_literal: true
+
+describe DarwinCore::Generator do
+  subject(:gen) { DarwinCore::Generator.new(dwc_path, tmp_dir) }
+  let(:tmp_dir) { DarwinCore::DEFAULT_TMP_DIR }
+  let(:dwc_path) { File.join(tmp_dir, "spec_dwca.tar.gz") }
+
+  def generate_dwca(gen)
+    gen.add_core(CORE_DATA.dup, "core.csv", true)
+    gen.add_extension(EXTENSION_DATA.dup, "vern.csv", true,
+                      "http://rs.gbif.org/terms/1.0/VernacularName")
+    gen.add_meta_xml
+    gen.add_eml_xml(EML_DATA)
+  end
+
+  describe ".new" do
+    it "initializes empty DwCA" do
+      expect(gen).to be_kind_of DarwinCore::Generator
+    end
+  end
+
+  describe "#add_core" do
+    it "adds core to DwCA instance" do
+      gen.add_core(CORE_DATA.dup, "core.csv", true)
+      core = File.read(File.join(gen.path, "core.csv"))
+      expect(core).to match(/taxonID,parentNameUsageID,scientificName/)
+    end
+
+    context "urls are not given in header" do
+      it "raises error" do
+        data = CORE_DATA.dup
+        data[0] = data[0].map { |f| f.split("/")[-1] }
+        expect { gen.add_core(data, "core.csv", true) }.
+          to raise_error DarwinCore::GeneratorError
+      end
+    end
+  end
+
+  describe "#add_extension" do
+    it "adds extension to DwCA instance" do
+      gen.add_extension(EXTENSION_DATA.dup,
+                        "vern.csv",
+                        true,
+                        "http://rs.gbif.org/terms/1.0/VernacularName")
+      extension = File.read(File.join(gen.path, "vern.csv"))
+
+      expect(extension).to match(/Береза/)
+    end
+  end
+
+  describe "#add_meta_xml" do
+    it "creates metadata for DwCA" do
+      gen.add_core(CORE_DATA.dup, "core.csv", true)
+      gen.add_extension(EXTENSION_DATA.dup,
+                        "vern.csv",
+                        true,
+                        "http://rs.gbif.org/terms/1.0/VernacularName")
+
+      gen.add_meta_xml
+      meta = File.read(File.join(gen.path, "meta.xml")).strip
+      meta_from_file = File.read(
+        File.expand_path("../files/generator_meta.xml", __dir__)
+      ).strip
+      expect(meta).to eq meta_from_file
+    end
+  end
+
+  describe "#add_eml_data" do
+    it "adds eml data" do
+      gen.add_eml_xml(EML_DATA)
+      eml = File.read(File.join(gen.path, "eml.xml")).strip
+      eml.gsub!(%r{(<pubDate>).*?(</pubDate>)}, '\12013-12-30 14:45:33 -0500\2')
+      eml.gsub!(/(packageId=").*?"/, '\11234/2013-12-30::19:45:33"')
+
+      eml_from_file = File.read(
+        File.expand_path("../files/generator_eml.xml", __dir__)
+      ).strip
+      expect(eml.strip).to eq eml_from_file.strip
+    end
+  end
+
+  describe "#path" do
+    it "returns temporary path for assembling DwCA" do
+      expect(gen.path).to match(/dwc_\d+$/)
+    end
+  end
+
+  describe "#files" do
+    before(:example) { generate_dwca(gen) }
+
+    it "returns created files" do
+      expect(gen.files).
+        to match_array ["core.csv", "eml.xml", "meta.xml", "vern.csv"]
+    end
+  end
+
+  describe "#pack" do
+    before(:example) do
+      FileUtils.rm dwc_path if File.exist?(dwc_path)
+      generate_dwca(gen)
+    end
+
+    it "creates final DwCA file" do
+      gen.pack
+      expect(File.exist?(dwc_path)).to be true
+    end
+  end
+
+  describe "#clean" do
+    before(:example) { gen.add_eml_xml(EML_DATA) }
+
+    it "removes temporary directory for DwCA" do
+      expect(File.exist?(gen.path)).to be true
+      gen.clean
+      expect(File.exist?(gen.path)).to be false
+    end
+  end
+
+  describe "#eml_xml_data" do
+    it "returns current eml data" do
+      expect(gen.eml_xml_data).to be_kind_of Hash
+    end
+  end
+end