ro-crate 0.4.6 → 0.4.11

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Files changed (30) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile.lock +8 -8
  3. data/README.md +37 -0
  4. data/lib/ro_crate.rb +1 -0
  5. data/lib/ro_crate/model/contextual_entity.rb +2 -14
  6. data/lib/ro_crate/model/crate.rb +14 -0
  7. data/lib/ro_crate/model/data_entity.rb +3 -3
  8. data/lib/ro_crate/model/directory.rb +1 -3
  9. data/lib/ro_crate/model/entity.rb +24 -2
  10. data/lib/ro_crate/model/file.rb +1 -3
  11. data/lib/ro_crate/model/metadata.rb +9 -1
  12. data/lib/ro_crate/model/organization.rb +1 -1
  13. data/lib/ro_crate/model/preview.rb +3 -15
  14. data/lib/ro_crate/model/preview_generator.rb +40 -0
  15. data/lib/ro_crate/reader.rb +122 -26
  16. data/ro_crate.gemspec +2 -2
  17. data/test/crate_test.rb +12 -0
  18. data/test/entity_test.rb +21 -0
  19. data/test/fixtures/nested_directory.zip +0 -0
  20. data/test/fixtures/ro-crate-galaxy-sortchangecase/LICENSE +176 -0
  21. data/test/fixtures/ro-crate-galaxy-sortchangecase/README.md +6 -0
  22. data/test/fixtures/ro-crate-galaxy-sortchangecase/ro-crate-metadata.json +133 -0
  23. data/test/fixtures/ro-crate-galaxy-sortchangecase/sort-and-change-case.ga +118 -0
  24. data/test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/input.bed +3 -0
  25. data/test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/output_exp.bed +3 -0
  26. data/test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/sort-and-change-case-test.yml +8 -0
  27. data/test/fixtures/sparse_directory_crate/ro-crate-preview.html +60 -59
  28. data/test/reader_test.rb +56 -0
  29. data/test/writer_test.rb +22 -2
  30. metadata +13 -4
data/test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/input.bed ADDED
@@ -0,0 +1,3 @@
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+ chr1 66999824 67210768
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+ chr7 48998526 50489626
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+ chr1 66874821 66010368
data/test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/output_exp.bed ADDED
@@ -0,0 +1,3 @@
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+ CHR1 66874821 66010368
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+ CHR1 66999824 67210768
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+ CHR7 48998526 50489626
data/test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/sort-and-change-case-test.yml ADDED
@@ -0,0 +1,8 @@
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+ - doc: test with a small input
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+ job:
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+ bed_input:
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+ class: File
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+ path: input.bed
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+ outputs:
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+ uppercase_bed:
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+ path: output_exp.bed
data/test/fixtures/sparse_directory_crate/ro-crate-preview.html CHANGED
@@ -1,66 +1,67 @@
1
1
  <!DOCTYPE html>
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  <html>
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  <head>
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- <title>New RO-Crate</title>
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- <script type="application/ld+json">{
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- "@context": "https://w3id.org/ro/crate/1.1/context",
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- "@graph": [
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- {
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- "@id": "ro-crate-metadata.jsonld",
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- "@type": "CreativeWork",
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- "about": {
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- "@id": "./"
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- }
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- },
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- {
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- "@id": "ro-crate-preview.html",
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- "@type": "CreativeWork",
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- "about": {
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- "@id": "./"
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- }
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- },
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- {
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- "@id": "./",
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- "@type": "Dataset",
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- "hasPart": [
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- {
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- "@id": "fish/"
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- }
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- ]
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- },
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- {
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- "@id": "fish/",
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- "@type": "Dataset"
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- }
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- ]
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- }</script>
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- <meta name="generator" content="https://github.com/fbacall/ro-crate-ruby">
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- <meta name="keywords" content="RO-Crate">
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+ <title>New RO-Crate</title>
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+ <script type="application/ld+json">{
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+ "@context": "https://w3id.org/ro/crate/1.0/context",
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+ "@graph": [
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+ {
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+ "@id": "ro-crate-metadata.jsonld",
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+ "@type": "CreativeWork",
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+ "about": {
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+ "@id": "./"
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+ }
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+ },
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+ {
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+ "@id": "ro-crate-preview.html",
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+ "@type": "CreativeWork",
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+ "about": {
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+ "@id": "./"
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+ }
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+ },
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+ {
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+ "@id": "./",
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+ "@type": "Dataset",
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+ "hasPart": [
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+ {
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+ "@id": "listed_file.txt"
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+ }
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+ ]
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+ },
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+ {
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+ "@id": "listed_file.txt",
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+ "@type": "File"
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+ }
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+ ]
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+ }</script>
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+ <meta name="generator" content="https://github.com/fbacall/ro-crate-ruby">
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+ <meta name="keywords" content="RO-Crate">
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  </head>
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  <body>
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- <h1>New RO-Crate</h1>
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-
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- <p>
44
-
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- </p>
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- <dl>
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-
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-
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-
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-
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- </dl>
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+ <h1>New RO-Crate</h1>
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+ Some stuff has been added here blablabla
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43
 
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- <h2>Contents</h2>
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- <ul>
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-
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- <li id="__data_entity_fish/">
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-
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- <strong>fish/</strong>
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-
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-
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-
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- </li>
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-
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- </ul>
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+ <p>
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+
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+ </p>
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+ <dl>
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+
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+
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+
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+
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+ </dl>
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+
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+ <h2>Contents</h2>
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+ <ul>
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+
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+ <li id="__data_entity_listed_file.txt">
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+
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+ <strong>listed_file.txt</strong>
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+
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+
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+
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+ </li>
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+
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+ </ul>
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  </body>
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- </html>
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+ </html>
data/test/reader_test.rb CHANGED
@@ -195,4 +195,60 @@ class ReaderTest < Test::Unit::TestCase
195
195
  assert crate.entries['fish/data/binary.jpg']
196
196
  assert_equal ['./', 'listed_file.txt', 'ro-crate-metadata.jsonld', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
197
197
  end
198
+
199
+ test 'reading a zip from various object types' do
200
+ string_io = StringIO.new
201
+ string_io.write(::File.read(fixture_file('sparse_directory_crate.zip').path))
202
+ string_io.rewind
203
+ assert string_io.is_a?(StringIO)
204
+ assert_equal 11, ROCrate::Reader.read_zip(string_io).entries.count
205
+
206
+ path = Pathname.new(fixture_file('sparse_directory_crate.zip').path)
207
+ assert path.is_a?(Pathname)
208
+ assert_equal 11, ROCrate::Reader.read_zip(path).entries.count
209
+
210
+ file = ::File.open(fixture_file('sparse_directory_crate.zip').path)
211
+ assert file.is_a?(::File)
212
+ assert_equal 11, ROCrate::Reader.read_zip(file).entries.count
213
+
214
+ string = fixture_file('sparse_directory_crate.zip').path
215
+ assert string.is_a?(String)
216
+ assert_equal 11, ROCrate::Reader.read_zip(string).entries.count
217
+ end
218
+
219
+ test 'reading from zip where the crate root is nested somewhere within' do
220
+ crate = ROCrate::Reader.read_zip(fixture_file('nested_directory.zip'))
221
+
222
+ assert crate.entries['fish/info.txt']
223
+ assert_equal '1234', crate.entries['fish/info.txt'].source.read.chomp
224
+ assert crate.entries['fish/root.txt']
225
+ assert crate.entries['fish/data/info.txt']
226
+ assert crate.entries['fish/data/nested.txt']
227
+ assert crate.entries['fish/data/binary.jpg']
228
+ assert_equal ['./', 'fish/', 'ro-crate-metadata.json', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
229
+ end
230
+
231
+ test 'reading preserves any additions to @context' do
232
+ crate = ROCrate::Reader.read_directory(fixture_file('ro-crate-galaxy-sortchangecase').path)
233
+
234
+ context = crate.metadata.context
235
+ assert_equal [
236
+ 'https://w3id.org/ro/crate/1.1/context',
237
+ {
238
+ 'TestSuite' => 'https://w3id.org/ro/terms/test#TestSuite',
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+ 'TestInstance' => 'https://w3id.org/ro/terms/test#TestInstance',
240
+ 'TestService' => 'https://w3id.org/ro/terms/test#TestService',
241
+ 'TestDefinition' => 'https://w3id.org/ro/terms/test#TestDefinition',
242
+ 'PlanemoEngine' => 'https://w3id.org/ro/terms/test#PlanemoEngine',
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+ 'JenkinsService' => 'https://w3id.org/ro/terms/test#JenkinsService',
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+ 'TravisService' => 'https://w3id.org/ro/terms/test#TravisService',
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+ 'GithubService' => 'https://w3id.org/ro/terms/test#GithubService',
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+ 'instance' => 'https://w3id.org/ro/terms/test#instance',
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+ 'runsOn' => 'https://w3id.org/ro/terms/test#runsOn',
248
+ 'resource' => 'https://w3id.org/ro/terms/test#resource',
249
+ 'definition' => 'https://w3id.org/ro/terms/test#definition',
250
+ 'engineVersion' => 'https://w3id.org/ro/terms/test#engineVersion'
251
+ }
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+ ], context
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+ end
198
254
  end
data/test/writer_test.rb CHANGED
@@ -124,12 +124,32 @@ class WriterTest < Test::Unit::TestCase
124
124
  actual_files = Dir.chdir(dir) { Dir.glob('**/*') }
125
125
  assert_equal expected_files, actual_files
126
126
  expected_files.each do |file|
127
- next if file == 'ro-crate-metadata.jsonld' # Expected context gets updated.
128
- next if file == 'ro-crate-preview.html' # RO-Crate preview format changed
129
127
  abs_file_path = ::File.join(fixture, file)
130
128
  next if ::File.directory?(abs_file_path)
131
129
  assert_equal ::File.read(abs_file_path), ::File.read(::File.join(dir, file)), "#{file} didn't match"
132
130
  end
133
131
  end
134
132
  end
133
+
134
+ test 'reading/writing multiple times does not change the crate' do
135
+ input_dir = fixture_file('sparse_directory_crate').path
136
+ Dir.mktmpdir do |dir|
137
+ 3.times do |i|
138
+ output_dir = ::File.join(dir, "new_directory_#{i}")
139
+ crate = ROCrate::Reader.read(input_dir)
140
+
141
+ ROCrate::Writer.new(crate).write(output_dir)
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+ expected_files = Dir.chdir(input_dir) { Dir.glob('**/*') }
143
+ actual_files = Dir.chdir(output_dir) { Dir.glob('**/*') }
144
+ assert_equal expected_files, actual_files
145
+ expected_files.each do |file|
146
+ abs_file_path = ::File.join(input_dir, file)
147
+ next if ::File.directory?(abs_file_path)
148
+ assert_equal ::File.read(abs_file_path), ::File.read(::File.join(output_dir, file)), "#{file} didn't match"
149
+ end
150
+
151
+ input_dir = output_dir
152
+ end
153
+ end
154
+ end
135
155
  end
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: ro-crate
3
3
  version: !ruby/object:Gem::Version
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- version: 0.4.6
4
+ version: 0.4.11
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5
  platform: ruby
6
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  authors:
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7
  - Finn Bacall
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8
  autorequire:
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  bindir: bin
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  cert_chain: []
11
- date: 2021-02-25 00:00:00.000000000 Z
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+ date: 2021-04-30 00:00:00.000000000 Z
12
12
  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: addressable
@@ -72,14 +72,14 @@ dependencies:
72
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
75
- version: 0.16.1
75
+ version: 0.21.2
76
76
  type: :development
77
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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80
  - - "~>"
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  - !ruby/object:Gem::Version
82
- version: 0.16.1
82
+ version: 0.21.2
83
83
  - !ruby/object:Gem::Dependency
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  name: yard
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  requirement: !ruby/object:Gem::Requirement
@@ -137,6 +137,7 @@ files:
137
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  - lib/ro_crate/model/organization.rb
138
138
  - lib/ro_crate/model/person.rb
139
139
  - lib/ro_crate/model/preview.rb
140
+ - lib/ro_crate/model/preview_generator.rb
140
141
  - lib/ro_crate/model/remote_entry.rb
141
142
  - lib/ro_crate/reader.rb
142
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  - lib/ro_crate/ro-crate-preview.html.erb
@@ -165,6 +166,14 @@ files:
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  - test/fixtures/directory_crate/ro-crate-preview.html
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  - test/fixtures/file with spaces.txt
167
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  - test/fixtures/info.txt
169
+ - test/fixtures/nested_directory.zip
170
+ - test/fixtures/ro-crate-galaxy-sortchangecase/LICENSE
171
+ - test/fixtures/ro-crate-galaxy-sortchangecase/README.md
172
+ - test/fixtures/ro-crate-galaxy-sortchangecase/ro-crate-metadata.json
173
+ - test/fixtures/ro-crate-galaxy-sortchangecase/sort-and-change-case.ga
174
+ - test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/input.bed
175
+ - test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/output_exp.bed
176
+ - test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/sort-and-change-case-test.yml
168
177
  - test/fixtures/spaces/file with spaces.txt
169
178
  - test/fixtures/spaces/ro-crate-metadata.jsonld
170
179
  - test/fixtures/sparse_directory_crate.zip