ro-crate 0.4.13 → 0.4.14
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- checksums.yaml +4 -4
- data/Gemfile.lock +1 -1
- data/lib/ro_crate/model/data_entity.rb +17 -5
- data/lib/ro_crate/model/directory.rb +3 -3
- data/lib/ro_crate/model/file.rb +5 -1
- data/lib/ro_crate/reader.rb +7 -5
- data/ro_crate.gemspec +1 -1
- data/test/entity_test.rb +3 -3
- data/test/fixtures/misc_data_entity_crate/ro-crate-metadata.json +33 -0
- data/test/fixtures/ro-crate-galaxy-sortchangecase/ro-crate-metadata.json +10 -3
- data/test/fixtures/workflow-0.2.0/ro-crate-metadata.jsonld +5 -5
- data/test/fixtures/workflow-0.2.0.zip +0 -0
- data/test/reader_test.rb +33 -12
- data/test/writer_test.rb +11 -0
- metadata +3 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 5d94d65b4375c3923a828f763c749e9958d975c2f3fd3ee55b996f718cd9317c
|
4
|
+
data.tar.gz: 3ce5e362db42e5a790991bef4fe252d507a35e83eff00a58b1fe99ce4f5808e6
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: dd26c3d0fc2783f7424ba022ae03d5cc14c0e4aa7f96e2c6b682f82be3af9cee5cacb1480b414b5ab2f37d08e19b38b377455afd1ec74017901788a4a6500bab
|
7
|
+
data.tar.gz: eb6f983303b2b50fafaec3a03c4c3f855b4c12a4fcd80611d20916ec1f64c078973e842d1425c3101a1609b16db3bdfbe56eccde2a703de0efc360df0a48550f
|
data/Gemfile.lock
CHANGED
@@ -5,10 +5,6 @@ module ROCrate
|
|
5
5
|
class DataEntity < Entity
|
6
6
|
properties(%w[name contentSize dateModified encodingFormat identifier sameAs author])
|
7
7
|
|
8
|
-
def self.format_local_id(id)
|
9
|
-
super.chomp('/')
|
10
|
-
end
|
11
|
-
|
12
8
|
##
|
13
9
|
# Return an appropriate specialization of DataEntity for the given properties.
|
14
10
|
# @param props [Hash] Set of properties to try and infer the type from.
|
@@ -18,11 +14,27 @@ module ROCrate
|
|
18
14
|
type = [type] unless type.is_a?(Array)
|
19
15
|
if type.include?('Dataset')
|
20
16
|
ROCrate::Directory
|
21
|
-
|
17
|
+
elsif type.include?('File')
|
22
18
|
ROCrate::File
|
19
|
+
else
|
20
|
+
self
|
23
21
|
end
|
24
22
|
end
|
25
23
|
|
24
|
+
##
|
25
|
+
# Create a new ROCrate::DataEntity. This entity represents something that is neither a file or directory, but
|
26
|
+
# still constitutes part of the crate.
|
27
|
+
# PLEASE NOTE, the new data entity will not be added to the crate. To do this, call Crate#add_data_entity.
|
28
|
+
#
|
29
|
+
# @param crate [Crate] The RO-Crate that owns this directory.
|
30
|
+
# @param source [nil] Ignored. For compatibility with the File and Directory constructor signatures.
|
31
|
+
# @param id [String, nil] An ID to identify this DataEntity, or nil to auto-generate an appropriate one,
|
32
|
+
# (or determine via the properties param)
|
33
|
+
# @param properties [Hash{String => Object}] A hash of JSON-LD properties to associate with this DataEntity.
|
34
|
+
def initialize(crate, source = nil, id = nil, properties = {})
|
35
|
+
super(crate, id, properties)
|
36
|
+
end
|
37
|
+
|
26
38
|
##
|
27
39
|
# The payload of all the files/directories associated with this DataEntity, mapped by their relative file path.
|
28
40
|
#
|
@@ -3,11 +3,11 @@ module ROCrate
|
|
3
3
|
# A data entity that represents a directory of potentially many files and subdirectories (or none).
|
4
4
|
class Directory < DataEntity
|
5
5
|
def self.format_local_id(id)
|
6
|
-
super + '/'
|
6
|
+
super.chomp('/') + '/'
|
7
7
|
end
|
8
8
|
|
9
9
|
##
|
10
|
-
# Create a new Directory. PLEASE NOTE, the new directory will not be added to the crate. To do this, call
|
10
|
+
# Create a new ROCrate::Directory. PLEASE NOTE, the new directory will not be added to the crate. To do this, call
|
11
11
|
# Crate#add_data_entity, or just use Crate#add_directory.
|
12
12
|
#
|
13
13
|
# @param crate [Crate] The RO-Crate that owns this directory.
|
@@ -24,7 +24,7 @@ module ROCrate
|
|
24
24
|
crate_path = source_directory.basename.to_s if crate_path.nil?
|
25
25
|
end
|
26
26
|
|
27
|
-
super(crate, crate_path, properties)
|
27
|
+
super(crate, nil, crate_path, properties)
|
28
28
|
end
|
29
29
|
|
30
30
|
##
|
data/lib/ro_crate/model/file.rb
CHANGED
@@ -2,6 +2,10 @@ module ROCrate
|
|
2
2
|
##
|
3
3
|
# A data entity that represents a single file.
|
4
4
|
class File < DataEntity
|
5
|
+
def self.format_local_id(id)
|
6
|
+
super.chomp('/')
|
7
|
+
end
|
8
|
+
|
5
9
|
##
|
6
10
|
# Create a new ROCrate::File. PLEASE NOTE, the new file will not be added to the crate. To do this, call
|
7
11
|
# Crate#add_data_entity, or just use Crate#add_file.
|
@@ -32,7 +36,7 @@ module ROCrate
|
|
32
36
|
crate_path = source.to_s if source.is_a?(URI) && source.absolute?
|
33
37
|
end
|
34
38
|
|
35
|
-
super(crate, crate_path, properties)
|
39
|
+
super(crate, nil, crate_path, properties)
|
36
40
|
|
37
41
|
if source.is_a?(URI) && source.absolute?
|
38
42
|
@entry = RemoteEntry.new(source)
|
data/lib/ro_crate/reader.rb
CHANGED
@@ -245,10 +245,10 @@ module ROCrate
|
|
245
245
|
fullpath = ::File.join(source, i)
|
246
246
|
path = Pathname.new(fullpath) if ::File.exist?(fullpath)
|
247
247
|
end
|
248
|
-
unless path
|
249
|
-
|
250
|
-
|
251
|
-
end
|
248
|
+
# unless path
|
249
|
+
# warn "Missing file/directory: #{id}, skipping..."
|
250
|
+
# return nil
|
251
|
+
# end
|
252
252
|
end
|
253
253
|
|
254
254
|
entity_class.new(crate, path, decoded_id, entity_props)
|
@@ -262,7 +262,9 @@ module ROCrate
|
|
262
262
|
# mapped by its @id, or nil if nothing is found.
|
263
263
|
def self.extract_metadata_entity(entities)
|
264
264
|
key = entities.detect do |_, props|
|
265
|
-
props
|
265
|
+
conforms = props['conformsTo']
|
266
|
+
conforms = [conforms] unless conforms.is_a?(Array)
|
267
|
+
conforms.compact.any? { |c| c['@id']&.start_with?(ROCrate::Metadata::RO_CRATE_BASE) }
|
266
268
|
end&.first
|
267
269
|
|
268
270
|
return entities.delete(key) if key
|
data/ro_crate.gemspec
CHANGED
data/test/entity_test.rb
CHANGED
@@ -38,11 +38,11 @@ class EntityTest < Test::Unit::TestCase
|
|
38
38
|
test 'fetch appropriate class for type' do
|
39
39
|
assert_equal ROCrate::File, ROCrate::DataEntity.specialize({ '@type' => 'File' })
|
40
40
|
assert_equal ROCrate::File, ROCrate::DataEntity.specialize({ '@type' => ['File', 'Image'] })
|
41
|
-
assert_equal ROCrate::
|
42
|
-
assert_equal ROCrate::
|
41
|
+
assert_equal ROCrate::DataEntity, ROCrate::DataEntity.specialize({ '@type' => 'SoftwareSourceCode' })
|
42
|
+
assert_equal ROCrate::DataEntity, ROCrate::DataEntity.specialize({ '@type' => 'anything that isnt a directory' })
|
43
43
|
assert_equal ROCrate::Directory, ROCrate::DataEntity.specialize({ '@type' => 'Dataset' })
|
44
44
|
assert_equal ROCrate::Directory, ROCrate::DataEntity.specialize({ '@type' => ['Dataset', 'Image'] })
|
45
|
-
assert_equal ROCrate::
|
45
|
+
assert_equal ROCrate::DataEntity, ROCrate::DataEntity.specialize({ '@type' => 'Person' })
|
46
46
|
assert_equal ROCrate::File, ROCrate::DataEntity.specialize({ '@type' => ['File', 'Image'], '@id' => 'http://www.external.com' })
|
47
47
|
|
48
48
|
assert_equal ROCrate::Person, ROCrate::ContextualEntity.specialize({ '@type' => 'Person' })
|
@@ -0,0 +1,33 @@
|
|
1
|
+
{
|
2
|
+
"@context": [
|
3
|
+
"https://w3id.org/ro/crate/1.1/context",
|
4
|
+
{
|
5
|
+
"@vocab": "http://schema.org/"
|
6
|
+
},
|
7
|
+
{
|
8
|
+
"@base": null
|
9
|
+
}
|
10
|
+
],
|
11
|
+
"@graph": [
|
12
|
+
{
|
13
|
+
"@id": "#collection",
|
14
|
+
"@type": "RepositoryCollection",
|
15
|
+
"name": "Test collection"
|
16
|
+
},
|
17
|
+
{
|
18
|
+
"@id": "./",
|
19
|
+
"@type": "Dataset",
|
20
|
+
"hasFile": [],
|
21
|
+
"hasPart": [{"@id": "#collection"}],
|
22
|
+
"name": "testing hasPart"
|
23
|
+
},
|
24
|
+
{
|
25
|
+
"@id": "ro-crate-metadata.json",
|
26
|
+
"@type": "CreativeWork",
|
27
|
+
"about": {
|
28
|
+
"@id": "./"
|
29
|
+
},
|
30
|
+
"identifier": "ro-crate-metadata.json"
|
31
|
+
}
|
32
|
+
]
|
33
|
+
}
|
@@ -24,9 +24,10 @@
|
|
24
24
|
"about": {
|
25
25
|
"@id": "./"
|
26
26
|
},
|
27
|
-
"conformsTo":
|
28
|
-
"@id": "https://w3id.org/ro/crate/1.1"
|
29
|
-
|
27
|
+
"conformsTo": [
|
28
|
+
{ "@id": "https://w3id.org/ro/crate/1.1" },
|
29
|
+
{ "@id": "https://about.workflowhub.eu/Workflow-RO-Crate/" }
|
30
|
+
]
|
30
31
|
},
|
31
32
|
{
|
32
33
|
"@id": "./",
|
@@ -128,6 +129,12 @@
|
|
128
129
|
"@type": "SoftwareApplication",
|
129
130
|
"name": "Planemo",
|
130
131
|
"url": {"@id": "https://github.com/galaxyproject/planemo"}
|
132
|
+
},
|
133
|
+
{
|
134
|
+
"@id": "https://about.workflowhub.eu/Workflow-RO-Crate/",
|
135
|
+
"@type": "CreativeWork",
|
136
|
+
"name": "Workflow RO-Crate Profile",
|
137
|
+
"version": "0.2.0"
|
131
138
|
}
|
132
139
|
]
|
133
140
|
}
|
@@ -123,7 +123,7 @@
|
|
123
123
|
},
|
124
124
|
{
|
125
125
|
"@id": "workflow/workflow.knime",
|
126
|
-
"@type": "SoftwareSourceCode",
|
126
|
+
"@type": ["File", "SoftwareSourceCode"],
|
127
127
|
"additionalType": {
|
128
128
|
"@id": "wfdesc:Workflow"
|
129
129
|
},
|
@@ -161,7 +161,7 @@
|
|
161
161
|
},
|
162
162
|
{
|
163
163
|
"@id": "tools/RetroPath2.cwl",
|
164
|
-
"@type": "SoftwareSourceCode",
|
164
|
+
"@type": ["File", "SoftwareSourceCode"],
|
165
165
|
"additionalType": {
|
166
166
|
"@id": "wfdesc:Workflow"
|
167
167
|
},
|
@@ -188,7 +188,7 @@
|
|
188
188
|
},
|
189
189
|
{
|
190
190
|
"@id": "workflow/workflow.svg",
|
191
|
-
"@type": "ImageObject",
|
191
|
+
"@type": ["File", "ImageObject"],
|
192
192
|
"additionalType": {"@id": "roterms:Sketch"},
|
193
193
|
"encodingFormat": "image/svg+xml",
|
194
194
|
"description": "Diagram of RetroPath2.0 workflow",
|
@@ -201,7 +201,7 @@
|
|
201
201
|
},
|
202
202
|
{
|
203
203
|
"@id": "Dockerfile",
|
204
|
-
"@type": "SoftwareSourceCode",
|
204
|
+
"@type": ["File", "SoftwareSourceCode"],
|
205
205
|
"url": {
|
206
206
|
"@id": "https://hub.docker.com/r/ibisba/retropath2/"
|
207
207
|
},
|
@@ -220,7 +220,7 @@
|
|
220
220
|
},
|
221
221
|
{
|
222
222
|
"@id": "test/test.sh",
|
223
|
-
"@type": "SoftwareSourceCode",
|
223
|
+
"@type": ["File", "SoftwareSourceCode"],
|
224
224
|
"additionalType": {
|
225
225
|
"@id": "wf4ever:Script"
|
226
226
|
},
|
Binary file
|
data/test/reader_test.rb
CHANGED
@@ -4,12 +4,13 @@ class ReaderTest < Test::Unit::TestCase
|
|
4
4
|
test 'reading from directory' do
|
5
5
|
crate = ROCrate::Reader.read(fixture_file('workflow-0.2.0').path)
|
6
6
|
|
7
|
-
refute crate.dereference('
|
7
|
+
refute crate.dereference('~/.ssh/id_rsa')
|
8
8
|
|
9
9
|
entity = crate.dereference('workflow/workflow.knime')
|
10
10
|
assert_not_nil entity
|
11
11
|
assert entity.is_a?(ROCrate::File)
|
12
|
-
|
12
|
+
assert entity.has_type?('SoftwareSourceCode')
|
13
|
+
assert entity.has_type?('File')
|
13
14
|
|
14
15
|
entity = crate.dereference('workflow/')
|
15
16
|
assert_not_nil entity
|
@@ -19,22 +20,26 @@ class ReaderTest < Test::Unit::TestCase
|
|
19
20
|
entity = crate.dereference('tools/RetroPath2.cwl')
|
20
21
|
assert_not_nil entity
|
21
22
|
assert entity.is_a?(ROCrate::File)
|
22
|
-
|
23
|
+
assert entity.has_type?('SoftwareSourceCode')
|
24
|
+
assert entity.has_type?('File')
|
23
25
|
|
24
26
|
entity = crate.dereference('workflow/workflow.svg')
|
25
27
|
assert_not_nil entity
|
26
28
|
assert entity.is_a?(ROCrate::File)
|
27
|
-
|
29
|
+
assert entity.has_type?('ImageObject')
|
30
|
+
assert entity.has_type?('File')
|
28
31
|
|
29
32
|
entity = crate.dereference('Dockerfile')
|
30
33
|
assert_not_nil entity
|
31
34
|
assert entity.is_a?(ROCrate::File)
|
32
|
-
|
35
|
+
assert entity.has_type?('SoftwareSourceCode')
|
36
|
+
assert entity.has_type?('File')
|
33
37
|
|
34
38
|
entity = crate.dereference('test/test.sh')
|
35
39
|
assert_not_nil entity
|
36
40
|
assert entity.is_a?(ROCrate::File)
|
37
|
-
|
41
|
+
assert entity.has_type?('SoftwareSourceCode')
|
42
|
+
assert entity.has_type?('File')
|
38
43
|
|
39
44
|
# Example is broken
|
40
45
|
# entity = crate.dereference('README.md')
|
@@ -46,12 +51,13 @@ class ReaderTest < Test::Unit::TestCase
|
|
46
51
|
test 'reading from zip' do
|
47
52
|
crate = ROCrate::Reader.read(fixture_file('workflow-0.2.0.zip'))
|
48
53
|
|
49
|
-
refute crate.dereference('
|
54
|
+
refute crate.dereference('~/.ssh/id_rsa')
|
50
55
|
|
51
56
|
entity = crate.dereference('workflow/workflow.knime')
|
52
57
|
assert_not_nil entity
|
53
58
|
assert entity.is_a?(ROCrate::File)
|
54
|
-
|
59
|
+
assert entity.has_type?('SoftwareSourceCode')
|
60
|
+
assert entity.has_type?('File')
|
55
61
|
|
56
62
|
entity = crate.dereference('workflow/')
|
57
63
|
assert_not_nil entity
|
@@ -61,22 +67,26 @@ class ReaderTest < Test::Unit::TestCase
|
|
61
67
|
entity = crate.dereference('tools/RetroPath2.cwl')
|
62
68
|
assert_not_nil entity
|
63
69
|
assert entity.is_a?(ROCrate::File)
|
64
|
-
|
70
|
+
assert entity.has_type?('SoftwareSourceCode')
|
71
|
+
assert entity.has_type?('File')
|
65
72
|
|
66
73
|
entity = crate.dereference('workflow/workflow.svg')
|
67
74
|
assert_not_nil entity
|
68
75
|
assert entity.is_a?(ROCrate::File)
|
69
|
-
|
76
|
+
assert entity.has_type?('ImageObject')
|
77
|
+
assert entity.has_type?('File')
|
70
78
|
|
71
79
|
entity = crate.dereference('Dockerfile')
|
72
80
|
assert_not_nil entity
|
73
81
|
assert entity.is_a?(ROCrate::File)
|
74
|
-
|
82
|
+
assert entity.has_type?('SoftwareSourceCode')
|
83
|
+
assert entity.has_type?('File')
|
75
84
|
|
76
85
|
entity = crate.dereference('test/test.sh')
|
77
86
|
assert_not_nil entity
|
78
87
|
assert entity.is_a?(ROCrate::File)
|
79
|
-
|
88
|
+
assert entity.has_type?('SoftwareSourceCode')
|
89
|
+
assert entity.has_type?('File')
|
80
90
|
|
81
91
|
# Example is broken
|
82
92
|
# entity = crate.dereference('README.md')
|
@@ -258,4 +268,15 @@ class ReaderTest < Test::Unit::TestCase
|
|
258
268
|
assert crate.preview.source.source.is_a?(Pathname)
|
259
269
|
assert_equal 80526, crate.preview.source.read.length
|
260
270
|
end
|
271
|
+
|
272
|
+
test 'read crate with data entity that is neither file or directory' do
|
273
|
+
crate = ROCrate::Reader.read_directory(fixture_file('misc_data_entity_crate').path)
|
274
|
+
|
275
|
+
entity = crate.get('#collection')
|
276
|
+
assert entity.is_a?(ROCrate::DataEntity)
|
277
|
+
refute entity.is_a?(ROCrate::File)
|
278
|
+
refute entity.is_a?(ROCrate::Directory)
|
279
|
+
assert entity.has_type?('RepositoryCollection')
|
280
|
+
assert entity.payload.empty?
|
281
|
+
end
|
261
282
|
end
|
data/test/writer_test.rb
CHANGED
@@ -189,4 +189,15 @@ class WriterTest < Test::Unit::TestCase
|
|
189
189
|
assert ::File.exist?(::File.join(dir, 'data', 'binary.jpg'))
|
190
190
|
end
|
191
191
|
end
|
192
|
+
|
193
|
+
test 'write crate with data entity that is neither file or directory' do
|
194
|
+
crate = ROCrate::Reader.read_directory(fixture_file('misc_data_entity_crate').path)
|
195
|
+
Dir.mktmpdir do |dir|
|
196
|
+
ROCrate::Writer.new(crate).write(dir)
|
197
|
+
Dir.chdir(dir) do
|
198
|
+
file_list = Dir.glob('*').sort
|
199
|
+
assert_equal ["ro-crate-metadata.json", "ro-crate-preview.html"], file_list
|
200
|
+
end
|
201
|
+
end
|
202
|
+
end
|
192
203
|
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
|
4
|
-
version: 0.4.
|
4
|
+
version: 0.4.14
|
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: 2021-11-02 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: addressable
|
@@ -175,6 +175,7 @@ files:
|
|
175
175
|
- test/fixtures/directory_crate/ro-crate-preview.html
|
176
176
|
- test/fixtures/file with spaces.txt
|
177
177
|
- test/fixtures/info.txt
|
178
|
+
- test/fixtures/misc_data_entity_crate/ro-crate-metadata.json
|
178
179
|
- test/fixtures/nested_directory.zip
|
179
180
|
- test/fixtures/ro-crate-galaxy-sortchangecase/LICENSE
|
180
181
|
- test/fixtures/ro-crate-galaxy-sortchangecase/README.md
|