ro-crate 0.4.10 → 0.4.14

data/test/reader_test.rb

@@ -4,12 +4,13 @@ class ReaderTest < Test::Unit::TestCase
   test 'reading from directory' do
     crate = ROCrate::Reader.read(fixture_file('workflow-0.2.0').path)
 
-    refute crate.dereference('.ssh/id_rsa')
+    refute crate.dereference('~/.ssh/id_rsa')
 
     entity = crate.dereference('workflow/workflow.knime')
     assert_not_nil entity
     assert entity.is_a?(ROCrate::File)
-    assert_equal 'SoftwareSourceCode', entity.type
+    assert entity.has_type?('SoftwareSourceCode')
+    assert entity.has_type?('File')
 
     entity = crate.dereference('workflow/')
     assert_not_nil entity
@@ -19,22 +20,26 @@ class ReaderTest < Test::Unit::TestCase
     entity = crate.dereference('tools/RetroPath2.cwl')
     assert_not_nil entity
     assert entity.is_a?(ROCrate::File)
-    assert_equal 'SoftwareSourceCode', entity.type
+    assert entity.has_type?('SoftwareSourceCode')
+    assert entity.has_type?('File')
 
     entity = crate.dereference('workflow/workflow.svg')
     assert_not_nil entity
     assert entity.is_a?(ROCrate::File)
-    assert_equal 'ImageObject', entity.type
+    assert entity.has_type?('ImageObject')
+    assert entity.has_type?('File')
 
     entity = crate.dereference('Dockerfile')
     assert_not_nil entity
     assert entity.is_a?(ROCrate::File)
-    assert_equal 'SoftwareSourceCode', entity.type
+    assert entity.has_type?('SoftwareSourceCode')
+    assert entity.has_type?('File')
 
     entity = crate.dereference('test/test.sh')
     assert_not_nil entity
     assert entity.is_a?(ROCrate::File)
-    assert_equal 'SoftwareSourceCode', entity.type
+    assert entity.has_type?('SoftwareSourceCode')
+    assert entity.has_type?('File')
 
     # Example is broken
     # entity = crate.dereference('README.md')
@@ -46,12 +51,13 @@ class ReaderTest < Test::Unit::TestCase
   test 'reading from zip' do
     crate = ROCrate::Reader.read(fixture_file('workflow-0.2.0.zip'))
 
-    refute crate.dereference('.ssh/id_rsa')
+    refute crate.dereference('~/.ssh/id_rsa')
 
     entity = crate.dereference('workflow/workflow.knime')
     assert_not_nil entity
     assert entity.is_a?(ROCrate::File)
-    assert_equal 'SoftwareSourceCode', entity.type
+    assert entity.has_type?('SoftwareSourceCode')
+    assert entity.has_type?('File')
 
     entity = crate.dereference('workflow/')
     assert_not_nil entity
@@ -61,22 +67,26 @@ class ReaderTest < Test::Unit::TestCase
     entity = crate.dereference('tools/RetroPath2.cwl')
     assert_not_nil entity
     assert entity.is_a?(ROCrate::File)
-    assert_equal 'SoftwareSourceCode', entity.type
+    assert entity.has_type?('SoftwareSourceCode')
+    assert entity.has_type?('File')
 
     entity = crate.dereference('workflow/workflow.svg')
     assert_not_nil entity
     assert entity.is_a?(ROCrate::File)
-    assert_equal 'ImageObject', entity.type
+    assert entity.has_type?('ImageObject')
+    assert entity.has_type?('File')
 
     entity = crate.dereference('Dockerfile')
     assert_not_nil entity
     assert entity.is_a?(ROCrate::File)
-    assert_equal 'SoftwareSourceCode', entity.type
+    assert entity.has_type?('SoftwareSourceCode')
+    assert entity.has_type?('File')
 
     entity = crate.dereference('test/test.sh')
     assert_not_nil entity
     assert entity.is_a?(ROCrate::File)
-    assert_equal 'SoftwareSourceCode', entity.type
+    assert entity.has_type?('SoftwareSourceCode')
+    assert entity.has_type?('File')
 
     # Example is broken
     # entity = crate.dereference('README.md')
@@ -88,12 +98,12 @@ class ReaderTest < Test::Unit::TestCase
   test 'reading from zip with directories' do
     crate = ROCrate::Reader.read_zip(fixture_file('directory.zip'))
 
-    assert crate.entries['fish/info.txt']
-    assert_equal '1234', crate.entries['fish/info.txt'].source.read.chomp
-    assert crate.entries['fish/root.txt']
-    assert crate.entries['fish/data/info.txt']
-    assert crate.entries['fish/data/nested.txt']
-    assert crate.entries['fish/data/binary.jpg']
+    assert crate.payload['fish/info.txt']
+    assert_equal '1234', crate.payload['fish/info.txt'].source.read.chomp
+    assert crate.payload['fish/root.txt']
+    assert crate.payload['fish/data/info.txt']
+    assert crate.payload['fish/data/nested.txt']
+    assert crate.payload['fish/data/binary.jpg']
     assert_equal ['./', 'fish/', 'ro-crate-metadata.jsonld', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
   end
 
@@ -101,22 +111,22 @@ class ReaderTest < Test::Unit::TestCase
     Dir.mktmpdir('test-1234-banana') do |dir|
       crate = ROCrate::Reader.read_zip(fixture_file('directory.zip'), target_dir: dir)
 
-      assert crate.entries['fish/info.txt']
-      assert crate.entries['fish/info.txt'].source.to_s.include?('/test-1234-banana')
+      assert crate.payload['fish/info.txt']
+      assert crate.payload['fish/info.txt'].source.to_s.include?('/test-1234-banana')
     end
   end
 
   test 'reading from directory with directories' do
     crate = ROCrate::Reader.read_directory(fixture_file('directory_crate').path)
 
-    assert crate.entries.values.all? { |e| e.is_a?(ROCrate::Entry) }
-    assert crate.entries['fish/info.txt']
-    assert_equal '1234', crate.entries['fish/info.txt'].source.read.chomp
-    refute crate.entries['fish/root.txt'].directory?
-    assert crate.entries['fish/data'].directory?
-    assert crate.entries['fish/data/info.txt']
-    refute crate.entries['fish/data/nested.txt'].remote?
-    assert crate.entries['fish/data/binary.jpg']
+    assert crate.payload.values.all? { |e| e.is_a?(ROCrate::Entry) }
+    assert crate.payload['fish/info.txt']
+    assert_equal '1234', crate.payload['fish/info.txt'].source.read.chomp
+    refute crate.payload['fish/root.txt'].directory?
+    assert crate.payload['fish/data'].directory?
+    assert crate.payload['fish/data/info.txt']
+    refute crate.payload['fish/data/nested.txt'].remote?
+    assert crate.payload['fish/data/binary.jpg']
     assert_equal ['./', 'fish/', 'ro-crate-metadata.jsonld', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
   end
 
@@ -162,37 +172,38 @@ class ReaderTest < Test::Unit::TestCase
     assert ext_file.source.is_a?(ROCrate::RemoteEntry)
     assert_equal 'http://example.com/external_ref.txt', ext_file.id
     assert_equal 'file contents', ext_file.source.read
+    assert crate.preview.source.source.is_a?(ROCrate::PreviewGenerator)
   end
 
   test 'reading from directory with unlisted files' do
     crate = ROCrate::Reader.read_directory(fixture_file('sparse_directory_crate').path)
 
-    assert_equal 11, crate.entries.count
-    assert crate.entries['listed_file.txt']
-    assert crate.entries['unlisted_file.txt']
-    assert crate.entries['fish']
-    assert_equal '1234', crate.entries['fish/info.txt'].source.read.chomp
-    refute crate.entries['fish/root.txt'].directory?
-    assert crate.entries['fish/data'].directory?
-    assert crate.entries['fish/data/info.txt']
-    refute crate.entries['fish/data/nested.txt'].remote?
-    assert crate.entries['fish/data/binary.jpg']
+    assert_equal 11, crate.payload.count
+    assert crate.payload['listed_file.txt']
+    assert crate.payload['unlisted_file.txt']
+    assert crate.payload['fish']
+    assert_equal '1234', crate.payload['fish/info.txt'].source.read.chomp
+    refute crate.payload['fish/root.txt'].directory?
+    assert crate.payload['fish/data'].directory?
+    assert crate.payload['fish/data/info.txt']
+    refute crate.payload['fish/data/nested.txt'].remote?
+    assert crate.payload['fish/data/binary.jpg']
     assert_equal ['./', 'listed_file.txt', 'ro-crate-metadata.jsonld', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
   end
 
   test 'reading from a zip with unlisted files' do
     crate = ROCrate::Reader.read_zip(fixture_file('sparse_directory_crate.zip').path)
 
-    assert_equal 11, crate.entries.count
-    assert crate.entries['listed_file.txt']
-    assert crate.entries['unlisted_file.txt']
-    assert crate.entries['fish']
-    assert_equal '1234', crate.entries['fish/info.txt'].source.read.chomp
-    refute crate.entries['fish/root.txt'].directory?
-    assert crate.entries['fish/data'].directory?
-    assert crate.entries['fish/data/info.txt']
-    refute crate.entries['fish/data/nested.txt'].remote?
-    assert crate.entries['fish/data/binary.jpg']
+    assert_equal 11, crate.payload.count
+    assert crate.payload['listed_file.txt']
+    assert crate.payload['unlisted_file.txt']
+    assert crate.payload['fish']
+    assert_equal '1234', crate.payload['fish/info.txt'].source.read.chomp
+    refute crate.payload['fish/root.txt'].directory?
+    assert crate.payload['fish/data'].directory?
+    assert crate.payload['fish/data/info.txt']
+    refute crate.payload['fish/data/nested.txt'].remote?
+    assert crate.payload['fish/data/binary.jpg']
     assert_equal ['./', 'listed_file.txt', 'ro-crate-metadata.jsonld', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
   end
 
@@ -201,30 +212,71 @@ class ReaderTest < Test::Unit::TestCase
     string_io.write(::File.read(fixture_file('sparse_directory_crate.zip').path))
     string_io.rewind
     assert string_io.is_a?(StringIO)
-    assert_equal 11, ROCrate::Reader.read_zip(string_io).entries.count
+    assert_equal 11, ROCrate::Reader.read_zip(string_io).payload.count
 
     path = Pathname.new(fixture_file('sparse_directory_crate.zip').path)
     assert path.is_a?(Pathname)
-    assert_equal 11, ROCrate::Reader.read_zip(path).entries.count
+    assert_equal 11, ROCrate::Reader.read_zip(path).payload.count
 
     file = ::File.open(fixture_file('sparse_directory_crate.zip').path)
     assert file.is_a?(::File)
-    assert_equal 11, ROCrate::Reader.read_zip(file).entries.count
+    assert_equal 11, ROCrate::Reader.read_zip(file).payload.count
 
     string = fixture_file('sparse_directory_crate.zip').path
     assert string.is_a?(String)
-    assert_equal 11, ROCrate::Reader.read_zip(string).entries.count
+    assert_equal 11, ROCrate::Reader.read_zip(string).payload.count
   end
 
   test 'reading from zip where the crate root is nested somewhere within' do
     crate = ROCrate::Reader.read_zip(fixture_file('nested_directory.zip'))
 
-    assert crate.entries['fish/info.txt']
-    assert_equal '1234', crate.entries['fish/info.txt'].source.read.chomp
-    assert crate.entries['fish/root.txt']
-    assert crate.entries['fish/data/info.txt']
-    assert crate.entries['fish/data/nested.txt']
-    assert crate.entries['fish/data/binary.jpg']
+    assert crate.payload['fish/info.txt']
+    assert_equal '1234', crate.payload['fish/info.txt'].source.read.chomp
+    assert crate.payload['fish/root.txt']
+    assert crate.payload['fish/data/info.txt']
+    assert crate.payload['fish/data/nested.txt']
+    assert crate.payload['fish/data/binary.jpg']
     assert_equal ['./', 'fish/', 'ro-crate-metadata.json', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
   end
+
+  test 'reading preserves any additions to @context' do
+    crate = ROCrate::Reader.read_directory(fixture_file('ro-crate-galaxy-sortchangecase').path)
+
+    context = crate.metadata.context
+    assert_equal [
+                     'https://w3id.org/ro/crate/1.1/context',
+                     {
+                         'TestSuite' => 'https://w3id.org/ro/terms/test#TestSuite',
+                         'TestInstance' => 'https://w3id.org/ro/terms/test#TestInstance',
+                         'TestService' => 'https://w3id.org/ro/terms/test#TestService',
+                         'TestDefinition' => 'https://w3id.org/ro/terms/test#TestDefinition',
+                         'PlanemoEngine' => 'https://w3id.org/ro/terms/test#PlanemoEngine',
+                         'JenkinsService' => 'https://w3id.org/ro/terms/test#JenkinsService',
+                         'TravisService' => 'https://w3id.org/ro/terms/test#TravisService',
+                         'GithubService' => 'https://w3id.org/ro/terms/test#GithubService',
+                         'instance' => 'https://w3id.org/ro/terms/test#instance',
+                         'runsOn' => 'https://w3id.org/ro/terms/test#runsOn',
+                         'resource' => 'https://w3id.org/ro/terms/test#resource',
+                         'definition' => 'https://w3id.org/ro/terms/test#definition',
+                         'engineVersion' => 'https://w3id.org/ro/terms/test#engineVersion'
+                     }
+                 ], context
+  end
+
+  test 'existing preview is used even if not mentioned in metadata' do
+    crate = ROCrate::Reader.read_zip(fixture_file('biobb_hpc_workflows-condapack.zip').path)
+    assert crate.preview.source.source.is_a?(Pathname)
+    assert_equal 80526, crate.preview.source.read.length
+  end
+
+  test 'read crate with data entity that is neither file or directory' do
+    crate = ROCrate::Reader.read_directory(fixture_file('misc_data_entity_crate').path)
+
+    entity = crate.get('#collection')
+    assert entity.is_a?(ROCrate::DataEntity)
+    refute entity.is_a?(ROCrate::File)
+    refute entity.is_a?(ROCrate::Directory)
+    assert entity.has_type?('RepositoryCollection')
+    assert entity.payload.empty?
+  end
 end

data/test/test_helper.rb

@@ -6,5 +6,9 @@ require 'ro_crate'
 require 'webmock/test_unit'
 
 def fixture_file(name, *args)
-  ::File.open(::File.join(::File.dirname(__FILE__), 'fixtures', name), *args)
+  ::File.open(::File.join(fixture_dir, name), *args)
+end
+
+def fixture_dir
+  ::File.join(::File.dirname(__FILE__), 'fixtures')
 end

data/test/writer_test.rb

@@ -47,8 +47,12 @@ class WriterTest < Test::Unit::TestCase
   end
 
   test 'writing to zip' do
+    # Remote entries should not be written, so this 500 error should not affect anything.
+    stub_request(:get, 'http://example.com/external_ref.txt').to_return(status: 500)
+
     crate = ROCrate::Crate.new
     crate.add_file(fixture_file('info.txt'))
+    crate.add_file('http://example.com/external_ref.txt')
     crate.add_file(fixture_file('data.csv'), 'directory/data.csv')
 
     Tempfile.create do |file|
@@ -57,6 +61,7 @@ class WriterTest < Test::Unit::TestCase
       Zip::File.open(file) do |zipfile|
         assert zipfile.file.exist?(ROCrate::Metadata::IDENTIFIER)
         assert zipfile.file.exist?(ROCrate::Preview::IDENTIFIER)
+        refute zipfile.file.exist?('external_ref.txt')
         assert_equal 6, zipfile.file.size('info.txt')
         assert_equal 20, zipfile.file.size('directory/data.csv')
       end
@@ -124,12 +129,75 @@ class WriterTest < Test::Unit::TestCase
       actual_files =  Dir.chdir(dir) { Dir.glob('**/*') }
       assert_equal expected_files, actual_files
       expected_files.each do |file|
-        next if file == 'ro-crate-metadata.jsonld' # Expected context gets updated.
-        next if file == 'ro-crate-preview.html' # RO-Crate preview format changed
         abs_file_path = ::File.join(fixture, file)
         next if ::File.directory?(abs_file_path)
         assert_equal ::File.read(abs_file_path), ::File.read(::File.join(dir, file)), "#{file} didn't match"
       end
     end
   end
+
+  test 'reading/writing multiple times does not change the crate' do
+    input_dir = fixture_file('sparse_directory_crate').path
+    Dir.mktmpdir do |dir|
+      3.times do |i|
+        output_dir = ::File.join(dir, "new_directory_#{i}")
+        crate = ROCrate::Reader.read(input_dir)
+
+        ROCrate::Writer.new(crate).write(output_dir)
+        expected_files = Dir.chdir(input_dir) { Dir.glob('**/*') }
+        actual_files =  Dir.chdir(output_dir) { Dir.glob('**/*') }
+        assert_equal expected_files, actual_files
+        expected_files.each do |file|
+          abs_file_path = ::File.join(input_dir, file)
+          next if ::File.directory?(abs_file_path)
+          assert_equal ::File.read(abs_file_path), ::File.read(::File.join(output_dir, file)), "#{file} didn't match"
+        end
+
+        input_dir = output_dir
+      end
+    end
+  end
+
+  test 'writing with conflicting paths in payload obeys specificity rules' do
+    crate = ROCrate::Crate.new
+
+    # Payload from crate
+    crate.add_all(fixture_file('directory').path, false)
+    Dir.mktmpdir do |dir|
+      ROCrate::Writer.new(crate).write(dir)
+
+      assert_equal "5678\n", ::File.read(::File.join(dir, 'data', 'info.txt'))
+    end
+
+    # Payload from crate + directory
+    crate.add_directory(fixture_file('conflicting_data_directory').path.to_s, 'data')
+    Dir.mktmpdir do |dir|
+      ROCrate::Writer.new(crate).write(dir)
+
+      assert_equal 'abcd', ::File.read(::File.join(dir, 'data', 'info.txt')), 'Directory payload should take priority over Crate.'
+      assert_equal "No, I am nested!\n", ::File.read(::File.join(dir, 'data', 'nested.txt')), 'Directory payload should take priority over Crate.'
+      assert ::File.exist?(::File.join(dir, 'data', 'binary.jpg'))
+    end
+
+    # Payload from crate + directory + file
+    crate.add_file(StringIO.new('xyz'), 'data/info.txt')
+    Dir.mktmpdir do |dir|
+      ROCrate::Writer.new(crate).write(dir)
+
+      assert_equal 'xyz', ::File.read(::File.join(dir, 'data', 'info.txt')), 'File payload should take priority over Crate and Directory.'
+      assert_equal "No, I am nested!\n", ::File.read(::File.join(dir, 'data', 'nested.txt')), 'Directory payload should take priority over Crate.'
+      assert ::File.exist?(::File.join(dir, 'data', 'binary.jpg'))
+    end
+  end
+
+  test 'write crate with data entity that is neither file or directory' do
+    crate = ROCrate::Reader.read_directory(fixture_file('misc_data_entity_crate').path)
+    Dir.mktmpdir do |dir|
+      ROCrate::Writer.new(crate).write(dir)
+      Dir.chdir(dir) do
+      file_list = Dir.glob('*').sort
+      assert_equal ["ro-crate-metadata.json", "ro-crate-preview.html"], file_list
+    end
+    end
+  end
 end

metadata

@@ -1,29 +1,35 @@
 --- !ruby/object:Gem::Specification
 name: ro-crate
 version: !ruby/object:Gem::Version
-  version: 0.4.10
+  version: 0.4.14
 platform: ruby
 authors:
 - Finn Bacall
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-03-09 00:00:00.000000000 Z
+date: 2021-11-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: addressable
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '2.7'
+    - - "<"
       - !ruby/object:Gem::Version
-        version: 2.7.0
+        version: '2.9'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '2.7'
+    - - "<"
       - !ruby/object:Gem::Version
-        version: 2.7.0
+        version: '2.9'
 - !ruby/object:Gem::Dependency
   name: rubyzip
   requirement: !ruby/object:Gem::Requirement
@@ -72,14 +78,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.16.1
+        version: 0.21.2
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.16.1
+        version: 0.21.2
 - !ruby/object:Gem::Dependency
   name: yard
   requirement: !ruby/object:Gem::Requirement
@@ -137,6 +143,7 @@ files:
 - lib/ro_crate/model/organization.rb
 - lib/ro_crate/model/person.rb
 - lib/ro_crate/model/preview.rb
+- lib/ro_crate/model/preview_generator.rb
 - lib/ro_crate/model/remote_entry.rb
 - lib/ro_crate/reader.rb
 - lib/ro_crate/ro-crate-preview.html.erb
@@ -145,6 +152,9 @@ files:
 - test/crate_test.rb
 - test/directory_test.rb
 - test/entity_test.rb
+- test/fixtures/biobb_hpc_workflows-condapack.zip
+- test/fixtures/conflicting_data_directory/info.txt
+- test/fixtures/conflicting_data_directory/nested.txt
 - test/fixtures/crate-spec1.1/file with spaces.txt
 - test/fixtures/crate-spec1.1/ro-crate-metadata.json
 - test/fixtures/data.csv
@@ -165,7 +175,15 @@ files:
 - test/fixtures/directory_crate/ro-crate-preview.html
 - test/fixtures/file with spaces.txt
 - test/fixtures/info.txt
+- test/fixtures/misc_data_entity_crate/ro-crate-metadata.json
 - test/fixtures/nested_directory.zip
+- test/fixtures/ro-crate-galaxy-sortchangecase/LICENSE
+- test/fixtures/ro-crate-galaxy-sortchangecase/README.md
+- test/fixtures/ro-crate-galaxy-sortchangecase/ro-crate-metadata.json
+- test/fixtures/ro-crate-galaxy-sortchangecase/sort-and-change-case.ga
+- test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/input.bed
+- test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/output_exp.bed
+- test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/sort-and-change-case-test.yml
 - test/fixtures/spaces/file with spaces.txt
 - test/fixtures/spaces/ro-crate-metadata.jsonld
 - test/fixtures/sparse_directory_crate.zip