ro-crate 0.4.9 → 0.4.13

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 +129,64 @@ 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
 end

metadata

@@ -1,29 +1,35 @@
 --- !ruby/object:Gem::Specification
 name: ro-crate
 version: !ruby/object:Gem::Version
-  version: 0.4.9
+  version: 0.4.13
 platform: ruby
 authors:
 - Finn Bacall
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-03-01 00:00:00.000000000 Z
+date: 2021-09-29 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
@@ -165,6 +175,14 @@ files:
 - test/fixtures/directory_crate/ro-crate-preview.html
 - test/fixtures/file with spaces.txt
 - test/fixtures/info.txt
+- 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