ro-crate 0.4.8 → 0.4.12
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- checksums.yaml +4 -4
- data/Gemfile.lock +13 -13
- data/README.md +39 -0
- data/lib/ro_crate/model/contextual_entity.rb +2 -14
- data/lib/ro_crate/model/crate.rb +52 -6
- data/lib/ro_crate/model/data_entity.rb +6 -5
- data/lib/ro_crate/model/directory.rb +3 -5
- data/lib/ro_crate/model/entity.rb +65 -6
- 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 +77 -20
- 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 +37 -3
- data/test/directory_test.rb +21 -21
- data/test/entity_test.rb +135 -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
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
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|
104
|
-
assert crate.
|
105
|
-
assert crate.
|
104
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+
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
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|
109
109
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test 'reading from directory with directories' do
|
110
110
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crate = ROCrate::Reader.read_directory(fixture_file('directory_crate').path)
|
111
111
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|
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
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|
@@ -162,37 +162,38 @@ class ReaderTest < Test::Unit::TestCase
|
|
162
162
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assert ext_file.source.is_a?(ROCrate::RemoteEntry)
|
163
163
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assert_equal 'http://example.com/external_ref.txt', ext_file.id
|
164
164
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assert_equal 'file contents', ext_file.source.read
|
165
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+
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
|
data/test/writer_test.rb
CHANGED
@@ -47,8 +47,12 @@ class WriterTest < Test::Unit::TestCase
|
|
47
47
|
end
|
48
48
|
|
49
49
|
test 'writing to zip' do
|
50
|
+
# Remote entries should not be written, so this 500 error should not affect anything.
|
51
|
+
stub_request(:get, 'http://example.com/external_ref.txt').to_return(status: 500)
|
52
|
+
|
50
53
|
crate = ROCrate::Crate.new
|
51
54
|
crate.add_file(fixture_file('info.txt'))
|
55
|
+
crate.add_file('http://example.com/external_ref.txt')
|
52
56
|
crate.add_file(fixture_file('data.csv'), 'directory/data.csv')
|
53
57
|
|
54
58
|
Tempfile.create do |file|
|
@@ -57,6 +61,7 @@ class WriterTest < Test::Unit::TestCase
|
|
57
61
|
Zip::File.open(file) do |zipfile|
|
58
62
|
assert zipfile.file.exist?(ROCrate::Metadata::IDENTIFIER)
|
59
63
|
assert zipfile.file.exist?(ROCrate::Preview::IDENTIFIER)
|
64
|
+
refute zipfile.file.exist?('external_ref.txt')
|
60
65
|
assert_equal 6, zipfile.file.size('info.txt')
|
61
66
|
assert_equal 20, zipfile.file.size('directory/data.csv')
|
62
67
|
end
|
@@ -124,12 +129,64 @@ class WriterTest < Test::Unit::TestCase
|
|
124
129
|
actual_files = Dir.chdir(dir) { Dir.glob('**/*') }
|
125
130
|
assert_equal expected_files, actual_files
|
126
131
|
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
132
|
abs_file_path = ::File.join(fixture, file)
|
130
133
|
next if ::File.directory?(abs_file_path)
|
131
134
|
assert_equal ::File.read(abs_file_path), ::File.read(::File.join(dir, file)), "#{file} didn't match"
|
132
135
|
end
|
133
136
|
end
|
134
137
|
end
|
138
|
+
|
139
|
+
test 'reading/writing multiple times does not change the crate' do
|
140
|
+
input_dir = fixture_file('sparse_directory_crate').path
|
141
|
+
Dir.mktmpdir do |dir|
|
142
|
+
3.times do |i|
|
143
|
+
output_dir = ::File.join(dir, "new_directory_#{i}")
|
144
|
+
crate = ROCrate::Reader.read(input_dir)
|
145
|
+
|
146
|
+
ROCrate::Writer.new(crate).write(output_dir)
|
147
|
+
expected_files = Dir.chdir(input_dir) { Dir.glob('**/*') }
|
148
|
+
actual_files = Dir.chdir(output_dir) { Dir.glob('**/*') }
|
149
|
+
assert_equal expected_files, actual_files
|
150
|
+
expected_files.each do |file|
|
151
|
+
abs_file_path = ::File.join(input_dir, file)
|
152
|
+
next if ::File.directory?(abs_file_path)
|
153
|
+
assert_equal ::File.read(abs_file_path), ::File.read(::File.join(output_dir, file)), "#{file} didn't match"
|
154
|
+
end
|
155
|
+
|
156
|
+
input_dir = output_dir
|
157
|
+
end
|
158
|
+
end
|
159
|
+
end
|
160
|
+
|
161
|
+
test 'writing with conflicting paths in payload obeys specificity rules' do
|
162
|
+
crate = ROCrate::Crate.new
|
163
|
+
|
164
|
+
# Payload from crate
|
165
|
+
crate.add_all(fixture_file('directory').path, false)
|
166
|
+
Dir.mktmpdir do |dir|
|
167
|
+
ROCrate::Writer.new(crate).write(dir)
|
168
|
+
|
169
|
+
assert_equal "5678\n", ::File.read(::File.join(dir, 'data', 'info.txt'))
|
170
|
+
end
|
171
|
+
|
172
|
+
# Payload from crate + directory
|
173
|
+
crate.add_directory(fixture_file('conflicting_data_directory').path.to_s, 'data')
|
174
|
+
Dir.mktmpdir do |dir|
|
175
|
+
ROCrate::Writer.new(crate).write(dir)
|
176
|
+
|
177
|
+
assert_equal 'abcd', ::File.read(::File.join(dir, 'data', 'info.txt')), 'Directory payload should take priority over Crate.'
|
178
|
+
assert_equal "No, I am nested!\n", ::File.read(::File.join(dir, 'data', 'nested.txt')), 'Directory payload should take priority over Crate.'
|
179
|
+
assert ::File.exist?(::File.join(dir, 'data', 'binary.jpg'))
|
180
|
+
end
|
181
|
+
|
182
|
+
# Payload from crate + directory + file
|
183
|
+
crate.add_file(StringIO.new('xyz'), 'data/info.txt')
|
184
|
+
Dir.mktmpdir do |dir|
|
185
|
+
ROCrate::Writer.new(crate).write(dir)
|
186
|
+
|
187
|
+
assert_equal 'xyz', ::File.read(::File.join(dir, 'data', 'info.txt')), 'File payload should take priority over Crate and Directory.'
|
188
|
+
assert_equal "No, I am nested!\n", ::File.read(::File.join(dir, 'data', 'nested.txt')), 'Directory payload should take priority over Crate.'
|
189
|
+
assert ::File.exist?(::File.join(dir, 'data', 'binary.jpg'))
|
190
|
+
end
|
191
|
+
end
|
135
192
|
end
|
metadata
CHANGED
@@ -1,29 +1,35 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: ro-crate
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.4.
|
4
|
+
version: 0.4.12
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Finn Bacall
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2021-
|
11
|
+
date: 2021-09-29 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: addressable
|
15
15
|
requirement: !ruby/object:Gem::Requirement
|
16
16
|
requirements:
|
17
|
-
- - "
|
17
|
+
- - ">="
|
18
|
+
- !ruby/object:Gem::Version
|
19
|
+
version: '2.7'
|
20
|
+
- - "<"
|
18
21
|
- !ruby/object:Gem::Version
|
19
|
-
version: 2.
|
22
|
+
version: '2.9'
|
20
23
|
type: :runtime
|
21
24
|
prerelease: false
|
22
25
|
version_requirements: !ruby/object:Gem::Requirement
|
23
26
|
requirements:
|
24
|
-
- - "
|
27
|
+
- - ">="
|
28
|
+
- !ruby/object:Gem::Version
|
29
|
+
version: '2.7'
|
30
|
+
- - "<"
|
25
31
|
- !ruby/object:Gem::Version
|
26
|
-
version: 2.
|
32
|
+
version: '2.9'
|
27
33
|
- !ruby/object:Gem::Dependency
|
28
34
|
name: rubyzip
|
29
35
|
requirement: !ruby/object:Gem::Requirement
|
@@ -72,14 +78,14 @@ dependencies:
|
|
72
78
|
requirements:
|
73
79
|
- - "~>"
|
74
80
|
- !ruby/object:Gem::Version
|
75
|
-
version: 0.
|
81
|
+
version: 0.21.2
|
76
82
|
type: :development
|
77
83
|
prerelease: false
|
78
84
|
version_requirements: !ruby/object:Gem::Requirement
|
79
85
|
requirements:
|
80
86
|
- - "~>"
|
81
87
|
- !ruby/object:Gem::Version
|
82
|
-
version: 0.
|
88
|
+
version: 0.21.2
|
83
89
|
- !ruby/object:Gem::Dependency
|
84
90
|
name: yard
|
85
91
|
requirement: !ruby/object:Gem::Requirement
|
@@ -137,6 +143,7 @@ files:
|
|
137
143
|
- lib/ro_crate/model/organization.rb
|
138
144
|
- lib/ro_crate/model/person.rb
|
139
145
|
- lib/ro_crate/model/preview.rb
|
146
|
+
- lib/ro_crate/model/preview_generator.rb
|
140
147
|
- lib/ro_crate/model/remote_entry.rb
|
141
148
|
- lib/ro_crate/reader.rb
|
142
149
|
- lib/ro_crate/ro-crate-preview.html.erb
|
@@ -145,6 +152,9 @@ files:
|
|
145
152
|
- test/crate_test.rb
|
146
153
|
- test/directory_test.rb
|
147
154
|
- test/entity_test.rb
|
155
|
+
- test/fixtures/biobb_hpc_workflows-condapack.zip
|
156
|
+
- test/fixtures/conflicting_data_directory/info.txt
|
157
|
+
- test/fixtures/conflicting_data_directory/nested.txt
|
148
158
|
- test/fixtures/crate-spec1.1/file with spaces.txt
|
149
159
|
- test/fixtures/crate-spec1.1/ro-crate-metadata.json
|
150
160
|
- test/fixtures/data.csv
|
@@ -165,6 +175,14 @@ files:
|
|
165
175
|
- test/fixtures/directory_crate/ro-crate-preview.html
|
166
176
|
- test/fixtures/file with spaces.txt
|
167
177
|
- test/fixtures/info.txt
|
178
|
+
- test/fixtures/nested_directory.zip
|
179
|
+
- test/fixtures/ro-crate-galaxy-sortchangecase/LICENSE
|
180
|
+
- test/fixtures/ro-crate-galaxy-sortchangecase/README.md
|
181
|
+
- test/fixtures/ro-crate-galaxy-sortchangecase/ro-crate-metadata.json
|
182
|
+
- test/fixtures/ro-crate-galaxy-sortchangecase/sort-and-change-case.ga
|
183
|
+
- test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/input.bed
|
184
|
+
- test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/output_exp.bed
|
185
|
+
- test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/sort-and-change-case-test.yml
|
168
186
|
- test/fixtures/spaces/file with spaces.txt
|
169
187
|
- test/fixtures/spaces/ro-crate-metadata.jsonld
|
170
188
|
- test/fixtures/sparse_directory_crate.zip
|