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
data/test/writer_test.rb
CHANGED
@@ -47,8 +47,12 @@ class WriterTest < Test::Unit::TestCase
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|
47
47
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end
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48
48
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|
49
49
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test 'writing to zip' do
|
50
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+
# Remote entries should not be written, so this 500 error should not affect anything.
|
51
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+
stub_request(:get, 'http://example.com/external_ref.txt').to_return(status: 500)
|
52
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+
|
50
53
|
crate = ROCrate::Crate.new
|
51
54
|
crate.add_file(fixture_file('info.txt'))
|
55
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+
crate.add_file('http://example.com/external_ref.txt')
|
52
56
|
crate.add_file(fixture_file('data.csv'), 'directory/data.csv')
|
53
57
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|
54
58
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Tempfile.create do |file|
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@@ -57,6 +61,7 @@ class WriterTest < Test::Unit::TestCase
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|
57
61
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Zip::File.open(file) do |zipfile|
|
58
62
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assert zipfile.file.exist?(ROCrate::Metadata::IDENTIFIER)
|
59
63
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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
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|
124
129
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actual_files = Dir.chdir(dir) { Dir.glob('**/*') }
|
125
130
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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
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-
next if file == 'ro-crate-preview.html' # RO-Crate preview format changed
|
129
132
|
abs_file_path = ::File.join(fixture, file)
|
130
133
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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
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end
|
133
136
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end
|
134
137
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end
|
138
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+
|
139
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+
test 'reading/writing multiple times does not change the crate' do
|
140
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+
input_dir = fixture_file('sparse_directory_crate').path
|
141
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+
Dir.mktmpdir do |dir|
|
142
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+
3.times do |i|
|
143
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+
output_dir = ::File.join(dir, "new_directory_#{i}")
|
144
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+
crate = ROCrate::Reader.read(input_dir)
|
145
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+
|
146
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+
ROCrate::Writer.new(crate).write(output_dir)
|
147
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+
expected_files = Dir.chdir(input_dir) { Dir.glob('**/*') }
|
148
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+
actual_files = Dir.chdir(output_dir) { Dir.glob('**/*') }
|
149
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+
assert_equal expected_files, actual_files
|
150
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+
expected_files.each do |file|
|
151
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+
abs_file_path = ::File.join(input_dir, file)
|
152
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+
next if ::File.directory?(abs_file_path)
|
153
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+
assert_equal ::File.read(abs_file_path), ::File.read(::File.join(output_dir, file)), "#{file} didn't match"
|
154
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+
end
|
155
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+
|
156
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+
input_dir = output_dir
|
157
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+
end
|
158
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+
end
|
159
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+
end
|
160
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+
|
161
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+
test 'writing with conflicting paths in payload obeys specificity rules' do
|
162
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+
crate = ROCrate::Crate.new
|
163
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+
|
164
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+
# Payload from crate
|
165
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+
crate.add_all(fixture_file('directory').path, false)
|
166
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+
Dir.mktmpdir do |dir|
|
167
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+
ROCrate::Writer.new(crate).write(dir)
|
168
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+
|
169
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+
assert_equal "5678\n", ::File.read(::File.join(dir, 'data', 'info.txt'))
|
170
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+
end
|
171
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+
|
172
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+
# Payload from crate + directory
|
173
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+
crate.add_directory(fixture_file('conflicting_data_directory').path.to_s, 'data')
|
174
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+
Dir.mktmpdir do |dir|
|
175
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+
ROCrate::Writer.new(crate).write(dir)
|
176
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+
|
177
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+
assert_equal 'abcd', ::File.read(::File.join(dir, 'data', 'info.txt')), 'Directory payload should take priority over Crate.'
|
178
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+
assert_equal "No, I am nested!\n", ::File.read(::File.join(dir, 'data', 'nested.txt')), 'Directory payload should take priority over Crate.'
|
179
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+
assert ::File.exist?(::File.join(dir, 'data', 'binary.jpg'))
|
180
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+
end
|
181
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+
|
182
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+
# Payload from crate + directory + file
|
183
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+
crate.add_file(StringIO.new('xyz'), 'data/info.txt')
|
184
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+
Dir.mktmpdir do |dir|
|
185
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+
ROCrate::Writer.new(crate).write(dir)
|
186
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+
|
187
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+
assert_equal 'xyz', ::File.read(::File.join(dir, 'data', 'info.txt')), 'File payload should take priority over Crate and Directory.'
|
188
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+
assert_equal "No, I am nested!\n", ::File.read(::File.join(dir, 'data', 'nested.txt')), 'Directory payload should take priority over Crate.'
|
189
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+
assert ::File.exist?(::File.join(dir, 'data', 'binary.jpg'))
|
190
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+
end
|
191
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+
end
|
135
192
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end
|
metadata
CHANGED
@@ -1,29 +1,35 @@
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1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: ro-crate
|
3
3
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version: !ruby/object:Gem::Version
|
4
|
-
version: 0.4.
|
4
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+
version: 0.4.13
|
5
5
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platform: ruby
|
6
6
|
authors:
|
7
7
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- Finn Bacall
|
8
8
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autorequire:
|
9
9
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bindir: bin
|
10
10
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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
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+
- - ">="
|
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
|