ro-crate 0.4.9 → 0.4.13
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- 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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<title>New RO-Crate</title>
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|
+
{
|
|
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
|