ro-crate 0.4.9 → 0.4.13
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/Gemfile.lock +13 -13
- data/README.md +39 -0
- data/lib/ro_crate/model/crate.rb +48 -6
- data/lib/ro_crate/model/data_entity.rb +5 -4
- data/lib/ro_crate/model/directory.rb +2 -4
- data/lib/ro_crate/model/entity.rb +41 -4
- data/lib/ro_crate/model/entry.rb +2 -2
- data/lib/ro_crate/model/file.rb +2 -4
- data/lib/ro_crate/model/metadata.rb +9 -1
- data/lib/ro_crate/model/organization.rb +1 -1
- data/lib/ro_crate/model/preview.rb +3 -15
- data/lib/ro_crate/model/preview_generator.rb +40 -0
- data/lib/ro_crate/model/remote_entry.rb +1 -12
- data/lib/ro_crate/reader.rb +76 -19
- data/lib/ro_crate/writer.rb +4 -4
- data/lib/ro_crate.rb +2 -1
- data/ro_crate.gemspec +3 -3
- data/test/crate_test.rb +58 -3
- data/test/directory_test.rb +21 -21
- data/test/entity_test.rb +114 -0
- data/test/fixtures/biobb_hpc_workflows-condapack.zip +0 -0
- data/test/fixtures/conflicting_data_directory/info.txt +1 -0
- data/test/fixtures/conflicting_data_directory/nested.txt +1 -0
- data/test/fixtures/nested_directory.zip +0 -0
- data/test/fixtures/ro-crate-galaxy-sortchangecase/LICENSE +176 -0
- data/test/fixtures/ro-crate-galaxy-sortchangecase/README.md +6 -0
- data/test/fixtures/ro-crate-galaxy-sortchangecase/ro-crate-metadata.json +133 -0
- data/test/fixtures/ro-crate-galaxy-sortchangecase/sort-and-change-case.ga +118 -0
- data/test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/input.bed +3 -0
- data/test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/output_exp.bed +3 -0
- data/test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/sort-and-change-case-test.yml +8 -0
- data/test/fixtures/sparse_directory_crate/ro-crate-preview.html +60 -59
- data/test/reader_test.rb +83 -40
- data/test/test_helper.rb +5 -1
- data/test/writer_test.rb +59 -2
- metadata +26 -8
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+
}
|
|
21
|
+
},
|
|
22
|
+
{
|
|
23
|
+
"@id": "./",
|
|
24
|
+
"@type": "Dataset",
|
|
25
|
+
"hasPart": [
|
|
26
|
+
{
|
|
27
|
+
"@id": "listed_file.txt"
|
|
28
|
+
}
|
|
29
|
+
]
|
|
30
|
+
},
|
|
31
|
+
{
|
|
32
|
+
"@id": "listed_file.txt",
|
|
33
|
+
"@type": "File"
|
|
34
|
+
}
|
|
35
|
+
]
|
|
36
|
+
}</script>
|
|
37
|
+
<meta name="generator" content="https://github.com/fbacall/ro-crate-ruby">
|
|
38
|
+
<meta name="keywords" content="RO-Crate">
|
|
39
39
|
</head>
|
|
40
40
|
<body>
|
|
41
|
-
|
|
42
|
-
|
|
43
|
-
<p>
|
|
44
|
-
|
|
45
|
-
</p>
|
|
46
|
-
<dl>
|
|
47
|
-
|
|
48
|
-
|
|
49
|
-
|
|
50
|
-
|
|
51
|
-
</dl>
|
|
41
|
+
<h1>New RO-Crate</h1>
|
|
42
|
+
Some stuff has been added here blablabla
|
|
52
43
|
|
|
53
|
-
|
|
54
|
-
|
|
55
|
-
|
|
56
|
-
|
|
57
|
-
|
|
58
|
-
|
|
59
|
-
|
|
60
|
-
|
|
61
|
-
|
|
62
|
-
|
|
63
|
-
|
|
64
|
-
|
|
44
|
+
<p>
|
|
45
|
+
|
|
46
|
+
</p>
|
|
47
|
+
<dl>
|
|
48
|
+
|
|
49
|
+
|
|
50
|
+
|
|
51
|
+
|
|
52
|
+
</dl>
|
|
53
|
+
|
|
54
|
+
<h2>Contents</h2>
|
|
55
|
+
<ul>
|
|
56
|
+
|
|
57
|
+
<li id="__data_entity_listed_file.txt">
|
|
58
|
+
|
|
59
|
+
<strong>listed_file.txt</strong>
|
|
60
|
+
|
|
61
|
+
|
|
62
|
+
|
|
63
|
+
</li>
|
|
64
|
+
|
|
65
|
+
</ul>
|
|
65
66
|
</body>
|
|
66
|
-
</html>
|
|
67
|
+
</html>
|
data/test/reader_test.rb
CHANGED
|
@@ -88,12 +88,12 @@ class ReaderTest < Test::Unit::TestCase
|
|
|
88
88
|
test 'reading from zip with directories' do
|
|
89
89
|
crate = ROCrate::Reader.read_zip(fixture_file('directory.zip'))
|
|
90
90
|
|
|
91
|
-
assert crate.
|
|
92
|
-
assert_equal '1234', crate.
|
|
93
|
-
assert crate.
|
|
94
|
-
assert crate.
|
|
95
|
-
assert crate.
|
|
96
|
-
assert crate.
|
|
91
|
+
assert crate.payload['fish/info.txt']
|
|
92
|
+
assert_equal '1234', crate.payload['fish/info.txt'].source.read.chomp
|
|
93
|
+
assert crate.payload['fish/root.txt']
|
|
94
|
+
assert crate.payload['fish/data/info.txt']
|
|
95
|
+
assert crate.payload['fish/data/nested.txt']
|
|
96
|
+
assert crate.payload['fish/data/binary.jpg']
|
|
97
97
|
assert_equal ['./', 'fish/', 'ro-crate-metadata.jsonld', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
|
|
98
98
|
end
|
|
99
99
|
|
|
@@ -101,22 +101,22 @@ class ReaderTest < Test::Unit::TestCase
|
|
|
101
101
|
Dir.mktmpdir('test-1234-banana') do |dir|
|
|
102
102
|
crate = ROCrate::Reader.read_zip(fixture_file('directory.zip'), target_dir: dir)
|
|
103
103
|
|
|
104
|
-
assert crate.
|
|
105
|
-
assert crate.
|
|
104
|
+
assert crate.payload['fish/info.txt']
|
|
105
|
+
assert crate.payload['fish/info.txt'].source.to_s.include?('/test-1234-banana')
|
|
106
106
|
end
|
|
107
107
|
end
|
|
108
108
|
|
|
109
109
|
test 'reading from directory with directories' do
|
|
110
110
|
crate = ROCrate::Reader.read_directory(fixture_file('directory_crate').path)
|
|
111
111
|
|
|
112
|
-
assert crate.
|
|
113
|
-
assert crate.
|
|
114
|
-
assert_equal '1234', crate.
|
|
115
|
-
refute crate.
|
|
116
|
-
assert crate.
|
|
117
|
-
assert crate.
|
|
118
|
-
refute crate.
|
|
119
|
-
assert crate.
|
|
112
|
+
assert crate.payload.values.all? { |e| e.is_a?(ROCrate::Entry) }
|
|
113
|
+
assert crate.payload['fish/info.txt']
|
|
114
|
+
assert_equal '1234', crate.payload['fish/info.txt'].source.read.chomp
|
|
115
|
+
refute crate.payload['fish/root.txt'].directory?
|
|
116
|
+
assert crate.payload['fish/data'].directory?
|
|
117
|
+
assert crate.payload['fish/data/info.txt']
|
|
118
|
+
refute crate.payload['fish/data/nested.txt'].remote?
|
|
119
|
+
assert crate.payload['fish/data/binary.jpg']
|
|
120
120
|
assert_equal ['./', 'fish/', 'ro-crate-metadata.jsonld', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
|
|
121
121
|
end
|
|
122
122
|
|
|
@@ -162,37 +162,38 @@ class ReaderTest < Test::Unit::TestCase
|
|
|
162
162
|
assert ext_file.source.is_a?(ROCrate::RemoteEntry)
|
|
163
163
|
assert_equal 'http://example.com/external_ref.txt', ext_file.id
|
|
164
164
|
assert_equal 'file contents', ext_file.source.read
|
|
165
|
+
assert crate.preview.source.source.is_a?(ROCrate::PreviewGenerator)
|
|
165
166
|
end
|
|
166
167
|
|
|
167
168
|
test 'reading from directory with unlisted files' do
|
|
168
169
|
crate = ROCrate::Reader.read_directory(fixture_file('sparse_directory_crate').path)
|
|
169
170
|
|
|
170
|
-
assert_equal 11, crate.
|
|
171
|
-
assert crate.
|
|
172
|
-
assert crate.
|
|
173
|
-
assert crate.
|
|
174
|
-
assert_equal '1234', crate.
|
|
175
|
-
refute crate.
|
|
176
|
-
assert crate.
|
|
177
|
-
assert crate.
|
|
178
|
-
refute crate.
|
|
179
|
-
assert crate.
|
|
171
|
+
assert_equal 11, crate.payload.count
|
|
172
|
+
assert crate.payload['listed_file.txt']
|
|
173
|
+
assert crate.payload['unlisted_file.txt']
|
|
174
|
+
assert crate.payload['fish']
|
|
175
|
+
assert_equal '1234', crate.payload['fish/info.txt'].source.read.chomp
|
|
176
|
+
refute crate.payload['fish/root.txt'].directory?
|
|
177
|
+
assert crate.payload['fish/data'].directory?
|
|
178
|
+
assert crate.payload['fish/data/info.txt']
|
|
179
|
+
refute crate.payload['fish/data/nested.txt'].remote?
|
|
180
|
+
assert crate.payload['fish/data/binary.jpg']
|
|
180
181
|
assert_equal ['./', 'listed_file.txt', 'ro-crate-metadata.jsonld', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
|
|
181
182
|
end
|
|
182
183
|
|
|
183
184
|
test 'reading from a zip with unlisted files' do
|
|
184
185
|
crate = ROCrate::Reader.read_zip(fixture_file('sparse_directory_crate.zip').path)
|
|
185
186
|
|
|
186
|
-
assert_equal 11, crate.
|
|
187
|
-
assert crate.
|
|
188
|
-
assert crate.
|
|
189
|
-
assert crate.
|
|
190
|
-
assert_equal '1234', crate.
|
|
191
|
-
refute crate.
|
|
192
|
-
assert crate.
|
|
193
|
-
assert crate.
|
|
194
|
-
refute crate.
|
|
195
|
-
assert crate.
|
|
187
|
+
assert_equal 11, crate.payload.count
|
|
188
|
+
assert crate.payload['listed_file.txt']
|
|
189
|
+
assert crate.payload['unlisted_file.txt']
|
|
190
|
+
assert crate.payload['fish']
|
|
191
|
+
assert_equal '1234', crate.payload['fish/info.txt'].source.read.chomp
|
|
192
|
+
refute crate.payload['fish/root.txt'].directory?
|
|
193
|
+
assert crate.payload['fish/data'].directory?
|
|
194
|
+
assert crate.payload['fish/data/info.txt']
|
|
195
|
+
refute crate.payload['fish/data/nested.txt'].remote?
|
|
196
|
+
assert crate.payload['fish/data/binary.jpg']
|
|
196
197
|
assert_equal ['./', 'listed_file.txt', 'ro-crate-metadata.jsonld', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
|
|
197
198
|
end
|
|
198
199
|
|
|
@@ -201,18 +202,60 @@ class ReaderTest < Test::Unit::TestCase
|
|
|
201
202
|
string_io.write(::File.read(fixture_file('sparse_directory_crate.zip').path))
|
|
202
203
|
string_io.rewind
|
|
203
204
|
assert string_io.is_a?(StringIO)
|
|
204
|
-
assert_equal 11, ROCrate::Reader.read_zip(string_io).
|
|
205
|
+
assert_equal 11, ROCrate::Reader.read_zip(string_io).payload.count
|
|
205
206
|
|
|
206
207
|
path = Pathname.new(fixture_file('sparse_directory_crate.zip').path)
|
|
207
208
|
assert path.is_a?(Pathname)
|
|
208
|
-
assert_equal 11, ROCrate::Reader.read_zip(path).
|
|
209
|
+
assert_equal 11, ROCrate::Reader.read_zip(path).payload.count
|
|
209
210
|
|
|
210
211
|
file = ::File.open(fixture_file('sparse_directory_crate.zip').path)
|
|
211
212
|
assert file.is_a?(::File)
|
|
212
|
-
assert_equal 11, ROCrate::Reader.read_zip(file).
|
|
213
|
+
assert_equal 11, ROCrate::Reader.read_zip(file).payload.count
|
|
213
214
|
|
|
214
215
|
string = fixture_file('sparse_directory_crate.zip').path
|
|
215
216
|
assert string.is_a?(String)
|
|
216
|
-
assert_equal 11, ROCrate::Reader.read_zip(string).
|
|
217
|
+
assert_equal 11, ROCrate::Reader.read_zip(string).payload.count
|
|
218
|
+
end
|
|
219
|
+
|
|
220
|
+
test 'reading from zip where the crate root is nested somewhere within' do
|
|
221
|
+
crate = ROCrate::Reader.read_zip(fixture_file('nested_directory.zip'))
|
|
222
|
+
|
|
223
|
+
assert crate.payload['fish/info.txt']
|
|
224
|
+
assert_equal '1234', crate.payload['fish/info.txt'].source.read.chomp
|
|
225
|
+
assert crate.payload['fish/root.txt']
|
|
226
|
+
assert crate.payload['fish/data/info.txt']
|
|
227
|
+
assert crate.payload['fish/data/nested.txt']
|
|
228
|
+
assert crate.payload['fish/data/binary.jpg']
|
|
229
|
+
assert_equal ['./', 'fish/', 'ro-crate-metadata.json', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
|
|
230
|
+
end
|
|
231
|
+
|
|
232
|
+
test 'reading preserves any additions to @context' do
|
|
233
|
+
crate = ROCrate::Reader.read_directory(fixture_file('ro-crate-galaxy-sortchangecase').path)
|
|
234
|
+
|
|
235
|
+
context = crate.metadata.context
|
|
236
|
+
assert_equal [
|
|
237
|
+
'https://w3id.org/ro/crate/1.1/context',
|
|
238
|
+
{
|
|
239
|
+
'TestSuite' => 'https://w3id.org/ro/terms/test#TestSuite',
|
|
240
|
+
'TestInstance' => 'https://w3id.org/ro/terms/test#TestInstance',
|
|
241
|
+
'TestService' => 'https://w3id.org/ro/terms/test#TestService',
|
|
242
|
+
'TestDefinition' => 'https://w3id.org/ro/terms/test#TestDefinition',
|
|
243
|
+
'PlanemoEngine' => 'https://w3id.org/ro/terms/test#PlanemoEngine',
|
|
244
|
+
'JenkinsService' => 'https://w3id.org/ro/terms/test#JenkinsService',
|
|
245
|
+
'TravisService' => 'https://w3id.org/ro/terms/test#TravisService',
|
|
246
|
+
'GithubService' => 'https://w3id.org/ro/terms/test#GithubService',
|
|
247
|
+
'instance' => 'https://w3id.org/ro/terms/test#instance',
|
|
248
|
+
'runsOn' => 'https://w3id.org/ro/terms/test#runsOn',
|
|
249
|
+
'resource' => 'https://w3id.org/ro/terms/test#resource',
|
|
250
|
+
'definition' => 'https://w3id.org/ro/terms/test#definition',
|
|
251
|
+
'engineVersion' => 'https://w3id.org/ro/terms/test#engineVersion'
|
|
252
|
+
}
|
|
253
|
+
], context
|
|
254
|
+
end
|
|
255
|
+
|
|
256
|
+
test 'existing preview is used even if not mentioned in metadata' do
|
|
257
|
+
crate = ROCrate::Reader.read_zip(fixture_file('biobb_hpc_workflows-condapack.zip').path)
|
|
258
|
+
assert crate.preview.source.source.is_a?(Pathname)
|
|
259
|
+
assert_equal 80526, crate.preview.source.read.length
|
|
217
260
|
end
|
|
218
261
|
end
|
data/test/test_helper.rb
CHANGED
|
@@ -6,5 +6,9 @@ require 'ro_crate'
|
|
|
6
6
|
require 'webmock/test_unit'
|
|
7
7
|
|
|
8
8
|
def fixture_file(name, *args)
|
|
9
|
-
::File.open(::File.join(
|
|
9
|
+
::File.open(::File.join(fixture_dir, name), *args)
|
|
10
|
+
end
|
|
11
|
+
|
|
12
|
+
def fixture_dir
|
|
13
|
+
::File.join(::File.dirname(__FILE__), 'fixtures')
|
|
10
14
|
end
|