ro-crate 0.4.3 → 0.4.8

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: f62e7c90a54f26aa6b18cf98310c998ada8c6836975c997f551b2b1ab7d85e29
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+  data.tar.gz: 16616f82e91760e9a6ff3eff1199c327143401086b0f9c577908e28d023e27828b7e36eeffc65333ec3aa440697b8f18cddd9406185f116ccc59ff238c98b1e9

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    ro-crate (0.4.3)
+    ro-crate (0.4.8)
       addressable (~> 2.7.0)
       rubyzip (~> 2.0.0)
 

data/lib/ro_crate/model/crate.rb

@@ -68,22 +68,23 @@ module ROCrate
     #
     # @param source_directory [String, Pathname, ::File,] The source directory that will be included in the crate.
     # @param create_entities [Boolean] Whether to create data entities for the added content, or just include them anonymously.
+    # @param include_hidden [Boolean] Whether to include hidden files, i.e. those prefixed by a `.` (period).
     #
     # @return [Array<DataEntity>] Any entities that were created from the directory contents. Will be empty if `create_entities` was false.
-    def add_all(source_directory, create_entities = true)
+    def add_all(source_directory, create_entities = true, include_hidden: false)
       added = []
 
-      Dir.chdir(source_directory) { Dir.glob('**/*') }.each do |rel_path|
-        source_path = Pathname.new(::File.join(source_directory, rel_path)).expand_path
-        if create_entities
+      if create_entities
+        list_all_files(source_directory, include_hidden: include_hidden).each do |rel_path|
+          source_path = Pathname.new(::File.join(source_directory, rel_path)).expand_path
           if source_path.directory?
             added << add_directory(source_path, rel_path)
           else
             added << add_file(source_path, rel_path)
           end
-        else
-          populate_entries(Pathname.new(::File.expand_path(source_directory)))
         end
+      else
+        populate_entries(Pathname.new(::File.expand_path(source_directory)), include_hidden: include_hidden)
       end
 
       added
@@ -216,16 +217,20 @@ module ROCrate
 
     alias_method :own_entries, :entries
     ##
-    # A map of all the files/directories contained in the RO-Crate, where the key is the destination path within the crate
-    # and the value is an Entry where the source data can be read.
+    # # The RO-Crate's "payload" of the crate - a map of all the files/directories contained in the RO-Crate, where the
+    # key is the destination path within the crate and the value is an Entry where the source data can be read.
     #
     # @return [Hash{String => Entry}>]
     def entries
-      entries = {}
-
-      (default_entities | data_entities).each do |entity|
-        (entity == self ? own_entries : entity.entries).each do |path, io|
-          entries[path] = io
+      # Gather a map of entries, starting from the crate itself, then any directory data entities, then finally any
+      # file data entities. This ensures in the case of a conflict, the more "specific" data entities take priority.
+      entries = own_entries
+      non_self_entities = default_entities.reject { |e| e == self }
+      sorted_entities = (non_self_entities | data_entities).sort_by { |e| e.is_a?(ROCrate::Directory) ? 0 : 1 }
+
+      sorted_entities.each do |entity|
+        entity.entries.each do |path, entry|
+          entries[path] = entry
         end
       end
 

data/lib/ro_crate/model/directory.rb

@@ -21,7 +21,7 @@ module ROCrate
 
       if source_directory
         source_directory = Pathname.new(::File.expand_path(source_directory))
-        @entry = source_directory
+        @entry = Entry.new(source_directory)
         populate_entries(source_directory)
         crate_path = source_directory.basename.to_s if crate_path.nil?
       end
@@ -30,8 +30,8 @@ module ROCrate
     end
 
     ##
-    # A map of all the files/directories under this directory, where the key is the destination path within the crate
-    # and the value is an Entry where the source data can be read.
+    # The "payload" of this directory - a map of all the files/directories, where the key is the destination path
+    # within the crate and the value is an Entry where the source data can be read.
     #
     # @return [Hash{String => Entry}>]
     def entries
@@ -51,13 +51,14 @@ module ROCrate
     # Populate this directory with files/directories from a given source directory on disk.
     #
     # @param source_directory [Pathname] The source directory to populate from.
+    # @param include_hidden [Boolean] Whether to include hidden files, i.e. those prefixed by a `.` (period).
     #
     # @return [Hash{String => Entry}>] The files/directories that were populated.
     #   The key is the relative path of the file/directory, and the value is an Entry object where data can be read etc.
-    def populate_entries(source_directory)
+    def populate_entries(source_directory, include_hidden: false)
       raise 'Not a directory' unless ::File.directory?(source_directory)
       @directory_entries = {}
-      Dir.chdir(source_directory) { Dir.glob('**/*') }.each do |rel_path|
+      list_all_files(source_directory, include_hidden: include_hidden).each do |rel_path|
         source_path = Pathname.new(::File.join(source_directory, rel_path)).expand_path
         @directory_entries[rel_path] = Entry.new(source_path)
       end
@@ -69,6 +70,14 @@ module ROCrate
       ::File.join(filepath, relative_path)
     end
 
+    def list_all_files(source_directory, include_hidden: false)
+      args = ['**/*']
+      args << ::File::FNM_DOTMATCH if include_hidden
+      Dir.chdir(source_directory) { Dir.glob(*args) }.reject do |path|
+        path == '.' || path == '..' || path.end_with?('/.')
+      end
+    end
+
     def default_properties
       super.merge(
         '@id' => "#{SecureRandom.uuid}/",

data/lib/ro_crate/model/file.rb

@@ -52,7 +52,9 @@ module ROCrate
     end
 
     ##
-    # A map of all the files/directories associated with this File. Should only be a single key and value.
+    # The "payload". A map with a single key and value, of the relative filepath within the crate, to the source on disk
+    # where the actual bytes of the file can be read. Blank if remote.
+    #
     # (for compatibility with Directory#entries)
     #
     # @return [Hash{String => Entry}>] The key is the location within the crate, and the value is an Entry.

data/lib/ro_crate/reader.rb

@@ -3,29 +3,67 @@ module ROCrate
   # A class to handle reading of RO-Crates from Zip files or directories.
   class Reader
     ##
-    # Reads an RO-Crate from a directory of zip file.
+    # Reads an RO-Crate from a directory or zip file.
     #
-    # @param source [String, ::File, Pathname] The source location for the crate.
+    # @param source [String, ::File, Pathname, #read] The location of the zip or directory, or an IO-like object containing a zip.
     # @param target_dir [String, ::File, Pathname] The target directory where the crate should be unzipped (if its a Zip file).
     # @return [Crate] The RO-Crate.
     def self.read(source, target_dir: Dir.mktmpdir)
       raise "Not a directory!" unless ::File.directory?(target_dir)
-      if ::File.directory?(source)
+      begin
+        is_dir = ::File.directory?(source)
+      rescue TypeError
+        is_dir = false
+      end
+
+      if is_dir
         read_directory(source)
       else
         read_zip(source, target_dir: target_dir)
       end
     end
 
+    ##
+    # Extract the contents of the given Zip file/data to the given directory.
+    #
+    # @param source [String, ::File, Pathname, #read] The location of the zip file, or an IO-like object.
+    # @param target [String, ::File, Pathname] The target directory where the file should be unzipped.
+    def self.unzip_to(source, target)
+      source = Pathname.new(::File.expand_path(source)) if source.is_a?(String)
+
+      if source.is_a?(Pathname) || source.is_a?(::File)
+        unzip_file_to(source, target)
+      else
+        unzip_io_to(source, target)
+      end
+    end
+
+    ##
+    # Extract the given Zip file data to the given directory.
+    #
+    # @param source [#read] An IO-like object containing a Zip file.
+    # @param target [String, ::File, Pathname] The target directory where the file should be unzipped.
+    def self.unzip_io_to(io, target)
+      Dir.chdir(target) do
+        Zip::InputStream.open(io) do |input|
+          while (entry = input.get_next_entry)
+            unless ::File.exist?(entry.name) || entry.name_is_directory?
+              FileUtils::mkdir_p(::File.dirname(entry.name))
+              ::File.binwrite(entry.name, input.read)
+            end
+          end
+        end
+      end
+    end
+
     ##
     # Extract the contents of the given Zip file to the given directory.
     #
     # @param source [String, ::File, Pathname] The location of the zip file.
     # @param target [String, ::File, Pathname] The target directory where the file should be unzipped.
-    def self.unzip_to(source, target)
-      source = ::File.expand_path(source)
+    def self.unzip_file_to(file_or_path, target)
       Dir.chdir(target) do
-        Zip::File.open(source) do |zipfile|
+        Zip::File.open(file_or_path) do |zipfile|
           zipfile.each do |entry|
             unless ::File.exist?(entry.name)
               FileUtils::mkdir_p(::File.dirname(entry.name))
@@ -40,7 +78,7 @@ module ROCrate
     # Reads an RO-Crate from a zip file. It first extracts the Zip file to a temporary directory, and then calls
     # #read_directory.
     #
-    # @param source [String, ::File, Pathname] The location of the zip file.
+    # @param source [String, ::File, Pathname, #read] The location of the zip file, or an IO-like object.
     # @param target_dir [String, ::File, Pathname] The target directory where the crate should be unzipped.
     # @return [Crate] The RO-Crate.
     def self.read_zip(source, target_dir: Dir.mktmpdir)
@@ -55,6 +93,8 @@ module ROCrate
     # @param source [String, ::File, Pathname] The location of the directory.
     # @return [Crate] The RO-Crate.
     def self.read_directory(source)
+      raise "Not a directory!" unless ::File.directory?(source)
+
       source = ::File.expand_path(source)
       metadata_file = Dir.entries(source).detect { |entry| entry == ROCrate::Metadata::IDENTIFIER ||
           entry == ROCrate::Metadata::IDENTIFIER_1_0 }
@@ -107,6 +147,7 @@ module ROCrate
         crate.metadata.properties = entity_hash.delete(ROCrate::Metadata::IDENTIFIER)
         preview_properties = entity_hash.delete(ROCrate::Preview::IDENTIFIER)
         crate.preview.properties = preview_properties if preview_properties
+        crate.add_all(source, false)
         extract_data_entities(crate, source, entity_hash).each do |entity|
           crate.add_data_entity(entity)
         end

data/ro_crate.gemspec

@@ -1,6 +1,6 @@
 Gem::Specification.new do |s|
   s.name        = 'ro-crate'
-  s.version     = '0.4.3'
+  s.version     = '0.4.8'
   s.summary     = 'Create, manipulate, read RO-Crates.'
   s.authors     = ['Finn Bacall']
   s.email       = 'finn.bacall@manchester.ac.uk'

data/test/crate_test.rb

@@ -201,44 +201,54 @@ class CrateTest < Test::Unit::TestCase
 
   test 'can add an entire directory tree as data entities' do
     crate = ROCrate::Crate.new
-    entities = crate.add_all(fixture_file('directory').path)
+    entities = crate.add_all(fixture_file('directory').path, include_hidden: true)
 
     paths = crate.entries.keys
-    assert_equal 8, paths.length
+    assert_equal 11, paths.length
     assert_includes paths, 'data'
     assert_includes paths, 'root.txt'
     assert_includes paths, 'info.txt'
     assert_includes paths, 'data/binary.jpg'
     assert_includes paths, 'data/info.txt'
     assert_includes paths, 'data/nested.txt'
+    assert_includes paths, '.dotfile'
+    assert_includes paths, '.dir'
+    assert_includes paths, '.dir/test.txt'
     assert_includes paths, 'ro-crate-metadata.json'
     assert_includes paths, 'ro-crate-preview.html'
 
-    assert_equal 6, entities.length
+    assert_equal 9, entities.length
     assert_equal 'ROCrate::Directory', crate.dereference('data/').class.name
     assert_equal 'ROCrate::File', crate.dereference('root.txt').class.name
     assert_equal 'ROCrate::File', crate.dereference('info.txt').class.name
     assert_equal 'ROCrate::File', crate.dereference('data/binary.jpg').class.name
     assert_equal 'ROCrate::File', crate.dereference('data/info.txt').class.name
     assert_equal 'ROCrate::File', crate.dereference('data/nested.txt').class.name
+    assert_equal 'ROCrate::File', crate.dereference('.dotfile').class.name
+    assert_equal 'ROCrate::Directory', crate.dereference('.dir/').class.name
+    assert_equal 'ROCrate::File', crate.dereference('.dir/test.txt').class.name
 
     assert_equal "5678\n", crate.dereference('data/info.txt').source.read
+    assert_equal "Am I included?\n", crate.dereference('.dotfile').source.read
   end
 
   test 'can create an RO-Crate using content from a given directory' do
     crate = ROCrate::Crate.new
-    entities = crate.add_all(fixture_file('directory').path, false)
+    entities = crate.add_all(fixture_file('directory').path, false, include_hidden: true)
 
     assert_empty entities
 
     paths = crate.entries.keys
-    assert_equal 8, paths.length
+    assert_equal 11, paths.length
     assert_includes paths, 'data'
     assert_includes paths, 'root.txt'
     assert_includes paths, 'info.txt'
     assert_includes paths, 'data/binary.jpg'
     assert_includes paths, 'data/info.txt'
     assert_includes paths, 'data/nested.txt'
+    assert_includes paths, '.dotfile'
+    assert_includes paths, '.dir'
+    assert_includes paths, '.dir/test.txt'
     assert_includes paths, 'ro-crate-metadata.json'
     assert_includes paths, 'ro-crate-preview.html'
 
@@ -249,5 +259,38 @@ class CrateTest < Test::Unit::TestCase
     assert_nil crate.dereference('data/binary.jpg')
     assert_nil crate.dereference('data/info.txt')
     assert_nil crate.dereference('data/nested.txt')
+    assert_nil crate.dereference('.dotfile')
+  end
+
+  test 'can create an RO-Crate using content from a given directory, excluding hidden files' do
+    crate = ROCrate::Crate.new
+    entities = crate.add_all(fixture_file('directory').path)
+
+    paths = crate.entries.keys
+    assert_equal 8, paths.length
+    assert_includes paths, 'data'
+    assert_includes paths, 'root.txt'
+    assert_includes paths, 'info.txt'
+    assert_includes paths, 'data/binary.jpg'
+    assert_includes paths, 'data/info.txt'
+    assert_includes paths, 'data/nested.txt'
+    assert_not_includes paths, '.dotfile'
+    assert_not_includes paths, '.dir'
+    assert_not_includes paths, '.dir/test.txt'
+    assert_includes paths, 'ro-crate-metadata.json'
+    assert_includes paths, 'ro-crate-preview.html'
+
+    assert_equal 6, entities.length
+    assert_equal 'ROCrate::Directory', crate.dereference('data/').class.name
+    assert_equal 'ROCrate::File', crate.dereference('root.txt').class.name
+    assert_equal 'ROCrate::File', crate.dereference('info.txt').class.name
+    assert_equal 'ROCrate::File', crate.dereference('data/binary.jpg').class.name
+    assert_equal 'ROCrate::File', crate.dereference('data/info.txt').class.name
+    assert_equal 'ROCrate::File', crate.dereference('data/nested.txt').class.name
+    assert_nil crate.dereference('.dotfile')
+    assert_nil crate.dereference('.dir/')
+    assert_nil crate.dereference('.dir/test.txt')
+
+    assert_equal "5678\n", crate.dereference('data/info.txt').source.read
   end
 end

data/test/fixtures/directory/.dir/test.txt

@@ -0,0 +1 @@
+123

data/test/fixtures/directory/.dotfile

@@ -0,0 +1 @@
+Am I included?

data/test/fixtures/sparse_directory_crate/fish/data/info.txt

@@ -0,0 +1 @@
+5678

data/test/fixtures/sparse_directory_crate/fish/data/nested.txt

@@ -0,0 +1 @@
+I'm nested

data/test/fixtures/sparse_directory_crate/fish/info.txt

@@ -0,0 +1 @@
+1234

data/test/fixtures/sparse_directory_crate/fish/root.txt

@@ -0,0 +1 @@
+I'm at the root

data/test/fixtures/sparse_directory_crate/listed_file.txt

@@ -0,0 +1 @@
+123

data/test/fixtures/sparse_directory_crate/ro-crate-metadata.jsonld

@@ -0,0 +1,32 @@
+{
+  "@context": "https://w3id.org/ro/crate/1.0/context",
+  "@graph": [
+    {
+      "@id": "ro-crate-metadata.jsonld",
+      "@type": "CreativeWork",
+      "about": {
+        "@id": "./"
+      }
+    },
+    {
+      "@id": "ro-crate-preview.html",
+      "@type": "CreativeWork",
+      "about": {
+        "@id": "./"
+      }
+    },
+    {
+      "@id": "./",
+      "@type": "Dataset",
+      "hasPart": [
+        {
+          "@id": "listed_file.txt"
+        }
+      ]
+    },
+    {
+      "@id": "listed_file.txt",
+      "@type": "File"
+    }
+  ]
+}

data/test/fixtures/sparse_directory_crate/ro-crate-preview.html

@@ -0,0 +1,66 @@
+<!DOCTYPE html>
+<html>
+<head>
+  <title>New RO-Crate</title>
+  <script type="application/ld+json">{
+  "@context": "https://w3id.org/ro/crate/1.1/context",
+  "@graph": [
+    {
+      "@id": "ro-crate-metadata.jsonld",
+      "@type": "CreativeWork",
+      "about": {
+        "@id": "./"
+      }
+    },
+    {
+      "@id": "ro-crate-preview.html",
+      "@type": "CreativeWork",
+      "about": {
+        "@id": "./"
+      }
+    },
+    {
+      "@id": "./",
+      "@type": "Dataset",
+      "hasPart": [
+        {
+          "@id": "fish/"
+        }
+      ]
+    },
+    {
+      "@id": "fish/",
+      "@type": "Dataset"
+    }
+  ]
+}</script>
+  <meta name="generator" content="https://github.com/fbacall/ro-crate-ruby">
+  <meta name="keywords" content="RO-Crate">
+</head>
+<body>
+  <h1>New RO-Crate</h1>
+  
+  <p>
+    
+  </p>
+  <dl>
+    
+    
+    
+    
+  </dl>
+
+  <h2>Contents</h2>
+  <ul>
+    
+      <li id="__data_entity_fish/">
+        
+          <strong>fish/</strong>
+        
+        
+        
+      </li>
+    
+  </ul>
+</body>
+</html>

data/test/fixtures/sparse_directory_crate/unlisted_file.txt

@@ -0,0 +1 @@
+456

data/test/reader_test.rb

@@ -109,11 +109,13 @@ class ReaderTest < Test::Unit::TestCase
   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
-    assert crate.entries['fish/root.txt']
+    refute crate.entries['fish/root.txt'].directory?
+    assert crate.entries['fish/data'].directory?
     assert crate.entries['fish/data/info.txt']
-    assert crate.entries['fish/data/nested.txt']
+    refute crate.entries['fish/data/nested.txt'].remote?
     assert crate.entries['fish/data/binary.jpg']
     assert_equal ['./', 'fish/', 'ro-crate-metadata.jsonld', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
   end
@@ -161,4 +163,56 @@ class ReaderTest < Test::Unit::TestCase
     assert_equal 'http://example.com/external_ref.txt', ext_file.id
     assert_equal 'file contents', ext_file.source.read
   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 ['./', '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 ['./', 'listed_file.txt', 'ro-crate-metadata.jsonld', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
+  end
+
+  test 'reading a zip from various object types' do
+    string_io = StringIO.new
+    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
+
+    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
+
+    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
+
+    string = fixture_file('sparse_directory_crate.zip').path
+    assert string.is_a?(String)
+    assert_equal 11, ROCrate::Reader.read_zip(string).entries.count
+  end
 end

data/test/writer_test.rb

@@ -112,4 +112,24 @@ class WriterTest < Test::Unit::TestCase
       assert_equal 2529, ::File.size(::File.join(dir, 'data', 'binary.jpg'))
     end
   end
+
+  test 'reading and writing out a directory crate produces an identical crate' do
+    fixture = fixture_file('sparse_directory_crate').path
+    Dir.mktmpdir do |dir|
+      dir = ::File.join(dir, 'new_directory')
+      crate = ROCrate::Reader.read(fixture)
+
+      ROCrate::Writer.new(crate).write(dir)
+      expected_files = Dir.chdir(fixture) { Dir.glob('**/*') }
+      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
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: ro-crate
 version: !ruby/object:Gem::Version
-  version: 0.4.3
+  version: 0.4.8
 platform: ruby
 authors:
 - Finn Bacall
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-02-24 00:00:00.000000000 Z
+date: 2021-02-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: addressable
@@ -149,6 +149,8 @@ files:
 - test/fixtures/crate-spec1.1/ro-crate-metadata.json
 - test/fixtures/data.csv
 - test/fixtures/directory.zip
+- test/fixtures/directory/.dir/test.txt
+- test/fixtures/directory/.dotfile
 - test/fixtures/directory/data/binary.jpg
 - test/fixtures/directory/data/info.txt
 - test/fixtures/directory/data/nested.txt
@@ -165,6 +167,16 @@ files:
 - test/fixtures/info.txt
 - test/fixtures/spaces/file with spaces.txt
 - test/fixtures/spaces/ro-crate-metadata.jsonld
+- test/fixtures/sparse_directory_crate.zip
+- test/fixtures/sparse_directory_crate/fish/data/binary.jpg
+- test/fixtures/sparse_directory_crate/fish/data/info.txt
+- test/fixtures/sparse_directory_crate/fish/data/nested.txt
+- test/fixtures/sparse_directory_crate/fish/info.txt
+- test/fixtures/sparse_directory_crate/fish/root.txt
+- test/fixtures/sparse_directory_crate/listed_file.txt
+- test/fixtures/sparse_directory_crate/ro-crate-metadata.jsonld
+- test/fixtures/sparse_directory_crate/ro-crate-preview.html
+- test/fixtures/sparse_directory_crate/unlisted_file.txt
 - test/fixtures/workflow-0.2.0.zip
 - test/fixtures/workflow-0.2.0/Dockerfile
 - test/fixtures/workflow-0.2.0/README.md