ro-crate 0.4.11 → 0.4.15

data/test/fixtures/unlinked_entity_crate/sort-and-change-case.ga

@@ -0,0 +1,118 @@
+{
+    "uuid": "e2a8566c-c025-4181-9e90-7ed29d4e4df1",
+    "tags": [],
+    "format-version": "0.1",
+    "name": "sort-and-change-case",
+    "version": 0,
+    "steps": {
+        "0": {
+            "tool_id": null,
+            "tool_version": null,
+            "outputs": [],
+            "workflow_outputs": [],
+            "input_connections": {},
+            "tool_state": "{}",
+            "id": 0,
+            "uuid": "5a36fad2-66c7-4b9e-8759-0fbcae9b8541",
+            "errors": null,
+            "name": "Input dataset",
+            "label": "bed_input",
+            "inputs": [],
+            "position": {
+                "top": 200,
+                "left": 200
+            },
+            "annotation": "",
+            "content_id": null,
+            "type": "data_input"
+        },
+        "1": {
+            "tool_id": "sort1",
+            "tool_version": "1.1.0",
+            "outputs": [
+                {
+                    "type": "input",
+                    "name": "out_file1"
+                }
+            ],
+            "workflow_outputs": [
+                {
+                    "output_name": "out_file1",
+                    "uuid": "8237f71a-bc2a-494e-a63c-09c1e65ef7c8",
+                    "label": "sorted_bed"
+                }
+            ],
+            "input_connections": {
+                "input": {
+                    "output_name": "output",
+                    "id": 0
+                }
+            },
+            "tool_state": "{\"__page__\": null, \"style\": \"\\\"alpha\\\"\", \"column\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"column_set\": \"[]\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"header_lines\": \"\\\"0\\\"\", \"order\": \"\\\"ASC\\\"\"}",
+            "id": 1,
+            "uuid": "0b6b3cda-c75f-452b-85b1-8ae4f3302ba4",
+            "errors": null,
+            "name": "Sort",
+            "post_job_actions": {},
+            "label": "sort",
+            "inputs": [
+                {
+                    "name": "input",
+                    "description": "runtime parameter for tool Sort"
+                }
+            ],
+            "position": {
+                "top": 200,
+                "left": 420
+            },
+            "annotation": "",
+            "content_id": "sort1",
+            "type": "tool"
+        },
+        "2": {
+            "tool_id": "ChangeCase",
+            "tool_version": "1.0.0",
+            "outputs": [
+                {
+                    "type": "tabular",
+                    "name": "out_file1"
+                }
+            ],
+            "workflow_outputs": [
+                {
+                    "output_name": "out_file1",
+                    "uuid": "c31cd733-dab6-4d50-9fec-b644d162397b",
+                    "label": "uppercase_bed"
+                }
+            ],
+            "input_connections": {
+                "input": {
+                    "output_name": "out_file1",
+                    "id": 1
+                }
+            },
+            "tool_state": "{\"__page__\": null, \"casing\": \"\\\"up\\\"\", \"__rerun_remap_job_id__\": null, \"cols\": \"\\\"c1\\\"\", \"delimiter\": \"\\\"TAB\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+            "id": 2,
+            "uuid": "9698bcde-0729-48fe-b88d-ccfb6f6153b4",
+            "errors": null,
+            "name": "Change Case",
+            "post_job_actions": {},
+            "label": "change_case",
+            "inputs": [
+                {
+                    "name": "input",
+                    "description": "runtime parameter for tool Change Case"
+                }
+            ],
+            "position": {
+                "top": 200,
+                "left": 640
+            },
+            "annotation": "",
+            "content_id": "ChangeCase",
+            "type": "tool"
+        }
+    },
+    "annotation": "",
+    "a_galaxy_workflow": "true"
+}

data/test/fixtures/unlinked_entity_crate/test/test1/input.bed

@@ -0,0 +1,3 @@
+chr1	66999824	67210768
+chr7	48998526	50489626
+chr1	66874821	66010368

data/test/fixtures/unlinked_entity_crate/test/test1/output_exp.bed

@@ -0,0 +1,3 @@
+CHR1	66874821	66010368
+CHR1	66999824	67210768
+CHR7	48998526	50489626

data/test/fixtures/unlinked_entity_crate/test/test1/sort-and-change-case-test.yml

@@ -0,0 +1,8 @@
+- doc: test with a small input
+  job:
+    bed_input:
+      class: File
+      path: input.bed
+  outputs:
+    uppercase_bed:
+      path: output_exp.bed

data/test/fixtures/workflow-0.2.0/ro-crate-metadata.jsonld

@@ -123,7 +123,7 @@
         },
         {
             "@id": "workflow/workflow.knime",
-            "@type": "SoftwareSourceCode",
+            "@type": ["File", "SoftwareSourceCode"],
             "additionalType": {
                 "@id": "wfdesc:Workflow"
             },
@@ -161,7 +161,7 @@
         },
         {
             "@id": "tools/RetroPath2.cwl",
-            "@type": "SoftwareSourceCode",
+            "@type": ["File", "SoftwareSourceCode"],
             "additionalType": {
                 "@id": "wfdesc:Workflow"
             },
@@ -188,7 +188,7 @@
         },
         {
             "@id": "workflow/workflow.svg",
-            "@type": "ImageObject",
+            "@type": ["File", "ImageObject"],
             "additionalType": {"@id": "roterms:Sketch"},
             "encodingFormat": "image/svg+xml",
             "description": "Diagram of RetroPath2.0 workflow",
@@ -201,7 +201,7 @@
         },
         {
             "@id": "Dockerfile",
-            "@type": "SoftwareSourceCode",
+            "@type": ["File", "SoftwareSourceCode"],
             "url": {
                 "@id": "https://hub.docker.com/r/ibisba/retropath2/"
             },
@@ -220,7 +220,7 @@
         },
         {
             "@id": "test/test.sh",
-            "@type": "SoftwareSourceCode",
+            "@type": ["File", "SoftwareSourceCode"],
             "additionalType": {
                 "@id": "wf4ever:Script"
             },

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 +212,30 @@ 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
 
@@ -251,4 +262,21 @@ class ReaderTest < Test::Unit::TestCase
                      }
                  ], 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
@@ -152,4 +157,47 @@ class WriterTest < Test::Unit::TestCase
       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: 0.4.11
+  version: 0.4.15
 platform: ruby
 authors:
 - Finn Bacall
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-04-30 00:00:00.000000000 Z
+date: 2022-02-15 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
@@ -146,6 +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
@@ -166,6 +175,7 @@ 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
@@ -186,6 +196,13 @@ files:
 - 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/unlinked_entity_crate/LICENSE
+- test/fixtures/unlinked_entity_crate/README.md
+- test/fixtures/unlinked_entity_crate/ro-crate-metadata.json
+- test/fixtures/unlinked_entity_crate/sort-and-change-case.ga
+- test/fixtures/unlinked_entity_crate/test/test1/input.bed
+- test/fixtures/unlinked_entity_crate/test/test1/output_exp.bed
+- test/fixtures/unlinked_entity_crate/test/test1/sort-and-change-case-test.yml
 - test/fixtures/workflow-0.2.0.zip
 - test/fixtures/workflow-0.2.0/Dockerfile
 - test/fixtures/workflow-0.2.0/README.md
@@ -2433,7 +2450,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.8
+rubygems_version: 3.1.6
 signing_key: 
 specification_version: 4
 summary: Create, manipulate, read RO-Crates.