ro-crate 0.4.9 → 0.4.13

data/lib/ro_crate/writer.rb

@@ -16,14 +16,14 @@ module ROCrate
     # @param overwrite [Boolean] Whether or not to overwrite existing files.
     def write(dir, overwrite: true)
       FileUtils.mkdir_p(dir) # Make any parent directories
-      @crate.entries.each do |path, entry|
+      @crate.payload.each do |path, entry|
         fullpath = ::File.join(dir, path)
         next if !overwrite && ::File.exist?(fullpath)
         next if entry.directory?
         FileUtils.mkdir_p(::File.dirname(fullpath))
         temp = Tempfile.new('ro-crate-temp')
         begin
-          entry.write(temp)
+          entry.write_to(temp)
           temp.close
           FileUtils.mv(temp, fullpath)
         ensure
@@ -38,9 +38,9 @@ module ROCrate
     # @param destination [String, ::File] The destination where to write the RO-Crate zip.
     def write_zip(destination)
       Zip::File.open(destination, Zip::File::CREATE) do |zip|
-        @crate.entries.each do |path, entry|
+        @crate.payload.each do |path, entry|
           next if entry.directory?
-          zip.get_output_stream(path) { |s| entry.write(s) }
+          zip.get_output_stream(path) { |s| entry.write_to(s) }
         end
       end
     end

data/lib/ro_crate.rb

@@ -10,10 +10,11 @@ require 'ro_crate/json_ld_hash'
 require 'ro_crate/model/entity'
 require 'ro_crate/model/data_entity'
 require 'ro_crate/model/file'
-require 'ro_crate/model/remote_entry'
 require 'ro_crate/model/entry'
+require 'ro_crate/model/remote_entry'
 require 'ro_crate/model/directory'
 require 'ro_crate/model/metadata'
+require 'ro_crate/model/preview_generator'
 require 'ro_crate/model/preview'
 require 'ro_crate/model/crate'
 require 'ro_crate/model/contextual_entity'

data/ro_crate.gemspec

@@ -1,6 +1,6 @@
 Gem::Specification.new do |s|
   s.name        = 'ro-crate'
-  s.version     = '0.4.9'
+  s.version     = '0.4.13'
   s.summary     = 'Create, manipulate, read RO-Crates.'
   s.authors     = ['Finn Bacall']
   s.email       = 'finn.bacall@manchester.ac.uk'
@@ -8,11 +8,11 @@ Gem::Specification.new do |s|
   s.homepage    = 'https://github.com/ResearchObject/ro-crate-ruby'
   s.require_paths = ['lib']
   s.licenses    = ['MIT']
-  s.add_runtime_dependency 'addressable', '~> 2.7.0'
+  s.add_runtime_dependency 'addressable', '>= 2.7', '< 2.9'
   s.add_runtime_dependency 'rubyzip', '~> 2.0.0'
   s.add_development_dependency 'rake', '~> 13.0.0'
   s.add_development_dependency 'test-unit', '~> 3.2.3'
-  s.add_development_dependency 'simplecov', '~> 0.16.1'
+  s.add_development_dependency 'simplecov', '~> 0.21.2'
   s.add_development_dependency 'yard', '~> 0.9.25'
   s.add_development_dependency 'webmock', '~> 3.8.3'
 end

data/test/crate_test.rb

@@ -164,6 +164,18 @@ class CrateTest < Test::Unit::TestCase
     assert_equal 2, crate1.contextual_entities.first.properties['cats']
   end
 
+  test 'sharing entities' do
+    crate = ROCrate::Crate.new
+    info = crate.add_file(fixture_file('info.txt'),'the_info.txt')
+    bob = crate.add_person('bob', name: 'Bob Jones')
+    crate.author = bob
+    info.author = bob
+
+    assert_equal [bob], crate.contextual_entities
+    assert_equal bob, info.author
+    assert_equal bob, crate.author
+  end
+
   test 'external files' do
     crate = ROCrate::Crate.new
     local = crate.add_file(fixture_file('info.txt'))
@@ -203,7 +215,7 @@ class CrateTest < Test::Unit::TestCase
     crate = ROCrate::Crate.new
     entities = crate.add_all(fixture_file('directory').path, include_hidden: true)
 
-    paths = crate.entries.keys
+    paths = crate.payload.keys
     assert_equal 11, paths.length
     assert_includes paths, 'data'
     assert_includes paths, 'root.txt'
@@ -238,7 +250,7 @@ class CrateTest < Test::Unit::TestCase
 
     assert_empty entities
 
-    paths = crate.entries.keys
+    paths = crate.payload.keys
     assert_equal 11, paths.length
     assert_includes paths, 'data'
     assert_includes paths, 'root.txt'
@@ -266,7 +278,7 @@ class CrateTest < Test::Unit::TestCase
     crate = ROCrate::Crate.new
     entities = crate.add_all(fixture_file('directory').path)
 
-    paths = crate.entries.keys
+    paths = crate.payload.keys
     assert_equal 8, paths.length
     assert_includes paths, 'data'
     assert_includes paths, 'root.txt'
@@ -293,4 +305,47 @@ class CrateTest < Test::Unit::TestCase
 
     assert_equal "5678\n", crate.dereference('data/info.txt').source.read
   end
+
+  test 'can delete entities' do
+    crate = ROCrate::Crate.new
+    file = crate.add_file(StringIO.new(''), 'file')
+    person = crate.add_person('#bob', { name: 'Bob' })
+    file.author = person
+
+    assert crate.delete(file)
+    assert_not_include crate.entities, file
+    assert_not_include crate.entities, person
+  end
+
+  test 'can delete entities by id' do
+    crate = ROCrate::Crate.new
+    file = crate.add_file(StringIO.new(''), 'file')
+    person = crate.add_person('#bob', { name: 'Bob' })
+    file.author = person
+
+    assert crate.delete('file')
+    assert_not_include crate.entities, file
+    assert_not_include crate.entities, person
+  end
+
+  test 'legacy entries method still returns same result as payload' do
+    crate = ROCrate::Crate.new
+    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 crate.payload.keys, crate.entries.keys
+  end
 end

data/test/directory_test.rb

@@ -5,41 +5,41 @@ class DirectoryTest < Test::Unit::TestCase
     crate = ROCrate::Crate.new
     crate.add_directory(fixture_file('directory'))
 
-    entries = crate.entries
+    payload = crate.payload
     base_path = ::File.dirname(fixture_file('directory'))
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/info.txt')), entries['directory/info.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/root.txt')), entries['directory/root.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data')), entries['directory/data'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/info.txt')), entries['directory/data/info.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/nested.txt')), entries['directory/data/nested.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/binary.jpg')), entries['directory/data/binary.jpg'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/info.txt')), payload['directory/info.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/root.txt')), payload['directory/root.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data')), payload['directory/data'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/info.txt')), payload['directory/data/info.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/nested.txt')), payload['directory/data/nested.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/binary.jpg')), payload['directory/data/binary.jpg'].path
   end
 
   test 'adding directory via path' do
     crate = ROCrate::Crate.new
     crate.add_directory(fixture_file('directory').path.to_s)
 
-    entries = crate.entries
+    payload = crate.payload
     base_path = ::File.dirname(fixture_file('directory'))
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/info.txt')), entries['directory/info.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/root.txt')), entries['directory/root.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data')), entries['directory/data'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/info.txt')), entries['directory/data/info.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/nested.txt')), entries['directory/data/nested.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/binary.jpg')), entries['directory/data/binary.jpg'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/info.txt')), payload['directory/info.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/root.txt')), payload['directory/root.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data')), payload['directory/data'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/info.txt')), payload['directory/data/info.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/nested.txt')), payload['directory/data/nested.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/binary.jpg')), payload['directory/data/binary.jpg'].path
   end
 
   test 'adding to given path' do
     crate = ROCrate::Crate.new
     crate.add_directory(fixture_file('directory').path.to_s, 'fish')
 
-    entries = crate.entries
+    payload = crate.payload
     base_path = ::File.dirname(fixture_file('directory'))
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/info.txt')), entries['fish/info.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/root.txt')), entries['fish/root.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data')), entries['fish/data'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/info.txt')), entries['fish/data/info.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/nested.txt')), entries['fish/data/nested.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/binary.jpg')), entries['fish/data/binary.jpg'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/info.txt')), payload['fish/info.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/root.txt')), payload['fish/root.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data')), payload['fish/data'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/info.txt')), payload['fish/data/info.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/nested.txt')), payload['fish/data/nested.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/binary.jpg')), payload['fish/data/binary.jpg'].path
   end
 end

data/test/entity_test.rb

@@ -91,4 +91,118 @@ class EntityTest < Test::Unit::TestCase
     assert_equal "http://www.data.com/my%20crate/", ROCrate::Crate.format_id('http://www.data.com/my%20crate'), 'Crate ID should end with /'
     assert_equal "http://www.data.com/my%20crate/", ROCrate::Crate.format_id('http://www.data.com/my%20crate/')
   end
+
+  test 'linked entities' do
+    crate = ROCrate::Crate.new
+    file = crate.add_file(StringIO.new(''), 'file')
+    person = crate.add_person('#bob', { name: 'Bob' })
+    file.author = person
+
+    linked = file.linked_entities
+    assert_include linked, person
+    assert_equal 1, linked.length
+
+    linked = crate.linked_entities
+    assert_include linked, file
+    assert_equal 1, linked.length
+
+    linked = crate.linked_entities(deep: true)
+    assert_include linked, file
+    assert_include linked, person
+    assert_equal 2, linked.length
+  end
+
+  test 'deleting entities removes linked entities' do
+    crate = ROCrate::Crate.new
+    file = crate.add_file(StringIO.new(''), 'file')
+    person = crate.add_person('#bob', { name: 'Bob' })
+    file.author = person
+
+    assert file.delete
+    assert_not_include crate.entities, file
+    assert_not_include crate.entities, person
+  end
+
+  test 'deleting entities does not remove dangling entities if option set' do
+    crate = ROCrate::Crate.new
+    file = crate.add_file(StringIO.new(''), 'file')
+    person = crate.add_person('#bob', { name: 'Bob' })
+    file.author = person
+
+    assert file.delete(remove_orphaned: false)
+    assert_not_include crate.entities, file
+    assert_include crate.entities, person
+  end
+
+  test 'creating files in various ways' do
+    stub_request(:get, 'http://example.com/external_ref.txt').to_return(status: 200, body: 'file contents')
+
+    crate = ROCrate::Crate.new
+
+    f1 = nil
+    Dir.chdir(fixture_dir) { f1 = ROCrate::File.new(crate, 'data.csv') }
+    refute f1.source.remote?
+    refute f1.source.directory?
+    assert_equal 20, f1.source.read.length
+    t = Tempfile.new('tf1')
+    f1.source.write_to(t)
+    t.rewind
+    assert_equal 20, t.read.length
+
+    f2 = ROCrate::File.new(crate, fixture_file('info.txt'), { author: crate.add_person('bob', name: 'Bob').reference })
+    refute f2.source.remote?
+    refute f2.source.directory?
+    assert f2.source.read
+    assert_equal 6, f2.source.read.length
+    t = Tempfile.new('tf2')
+    f2.source.write_to(t)
+    t.rewind
+    assert_equal 6, t.read.length
+
+    f3 = ROCrate::File.new(crate, 'http://example.com/external_ref.txt')
+    assert f3.source.remote?
+    refute f3.source.directory?
+    assert f3.source.read
+    assert_equal 13, f3.source.read.length
+    t = Tempfile.new('tf3')
+    f3.source.write_to(t)
+    t.rewind
+    assert_equal 13, t.read.length
+
+    f3 = ROCrate::File.new(crate, 'http://example.com/external_ref.txt')
+    assert f3.source.remote?
+    refute f3.source.directory?
+    assert f3.source.read
+    assert_equal 13, f3.source.read.length
+    t = Tempfile.new('tf3')
+    f3.source.write_to(t)
+    t.rewind
+    assert_equal 13, t.read.length
+  end
+
+  test 'assigning and checking type' do
+    crate = ROCrate::Crate.new
+    file = ROCrate::File.new(crate, 'data.csv')
+
+    assert file.has_type?('File')
+
+    file.type = ['File', 'Workflow']
+
+    assert file.has_type?('Workflow')
+    assert file.has_type?('File')
+    refute file.has_type?('Banana')
+  end
+
+  test 'inspecting object truncates very long property list' do
+    crate = ROCrate::Crate.new
+    entity = ROCrate::ContextualEntity.new(crate, 'hello')
+
+    assert entity.inspect.start_with?("<#ROCrate::ContextualEntity arcp://uuid,")
+
+    entity['veryLong'] = ('123456789a' * 100)
+
+    ins = entity.inspect
+    assert ins.length < 1000
+    assert ins.end_with?('...>')
+  end
 end

data/test/fixtures/conflicting_data_directory/info.txt

@@ -0,0 +1 @@
+abcd

data/test/fixtures/conflicting_data_directory/nested.txt

@@ -0,0 +1 @@
+No, I am nested!

data/test/fixtures/ro-crate-galaxy-sortchangecase/LICENSE

@@ -0,0 +1,176 @@
+
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+
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+      of your accepting any such warranty or additional liability.
+

data/test/fixtures/ro-crate-galaxy-sortchangecase/README.md

@@ -0,0 +1,6 @@
+# Galaxy mini workflow
+
+A tiny Galaxy workflow that sorts tabular lines according to the first column
+and changes the text to upper case.
+
+This RO-Crate is based on an [example from the Life Monitor repository](https://github.com/crs4/life_monitor/tree/8437be177822d0e2b3fed30db094b91c2fc14391/interaction_experiments/data/crates/ro-crate-galaxy-sortchangecase).