ro-crate 0.4.13 → 0.4.16
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- checksums.yaml +4 -4
- data/.github/workflows/tests.yml +5 -0
- data/.ruby-version +1 -1
- data/Gemfile.lock +2 -2
- data/lib/ro_crate/json_ld_hash.rb +5 -0
- data/lib/ro_crate/model/contextual_entity.rb +1 -2
- data/lib/ro_crate/model/crate.rb +14 -0
- data/lib/ro_crate/model/data_entity.rb +17 -5
- data/lib/ro_crate/model/directory.rb +3 -3
- data/lib/ro_crate/model/entity.rb +10 -3
- data/lib/ro_crate/model/file.rb +5 -1
- data/lib/ro_crate/model/remote_entry.rb +1 -1
- data/lib/ro_crate/reader.rb +7 -5
- data/ro_crate.gemspec +1 -1
- data/test/crate_test.rb +28 -0
- data/test/entity_test.rb +5 -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/unlinked_entity_crate/LICENSE +176 -0
- data/test/fixtures/unlinked_entity_crate/README.md +2 -0
- data/test/fixtures/unlinked_entity_crate/ro-crate-metadata.json +150 -0
- data/test/fixtures/unlinked_entity_crate/sort-and-change-case.ga +118 -0
- data/test/fixtures/unlinked_entity_crate/test/test1/input.bed +3 -0
- data/test/fixtures/unlinked_entity_crate/test/test1/output_exp.bed +3 -0
- data/test/fixtures/unlinked_entity_crate/test/test1/sort-and-change-case-test.yml +8 -0
- 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 +11 -3
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: b489bc85ce753f46035d1f5843ac9539de35e1403b92a9139c19061901d6b2d6
|
4
|
+
data.tar.gz: 6aab0b3d9f9323d7470554d82a887376fc00db95f68d0fae011416c66eb38937
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 55769c5b1a9b22ec5ad19e762ce9651e47407dbd01673c790c59753c6ac617cfa2ea81ecdcc6004313775069344845147c765e6396303491c94091e006c98b5b
|
7
|
+
data.tar.gz: 1798256fa994b7851da4b0adf0d78514aeaadc2e48935820d3c1f5dc546a8a633d5da11db19adeec7bd8763093a133744551e37f702d943a376c1b082e12d388
|
data/.github/workflows/tests.yml
CHANGED
@@ -3,6 +3,10 @@ on: [push, pull_request]
|
|
3
3
|
jobs:
|
4
4
|
run-tests:
|
5
5
|
runs-on: ubuntu-latest
|
6
|
+
strategy:
|
7
|
+
matrix:
|
8
|
+
ruby: ['2.6', '2.7']
|
9
|
+
fail-fast: false
|
6
10
|
steps:
|
7
11
|
- name: Checkout
|
8
12
|
uses: actions/checkout@v2.3.1 # If you're using actions/checkout@v2 you must set persist-credentials to false in most cases for the deployment to work correctly.
|
@@ -11,6 +15,7 @@ jobs:
|
|
11
15
|
- name: Setup Ruby
|
12
16
|
uses: ruby/setup-ruby@v1
|
13
17
|
with:
|
18
|
+
ruby-version: ${{ matrix.ruby }}
|
14
19
|
bundler-cache: true # runs 'bundle install' and caches installed gems automatically
|
15
20
|
- name: Run tests
|
16
21
|
run: bundle exec rake test
|
data/.ruby-version
CHANGED
@@ -1 +1 @@
|
|
1
|
-
ruby-2.
|
1
|
+
ruby-2.7.5
|
data/Gemfile.lock
CHANGED
@@ -2,6 +2,11 @@ module ROCrate
|
|
2
2
|
##
|
3
3
|
# A wrapper class for Hash that adds methods to dereference Entities within an RO-Crate.
|
4
4
|
class JSONLDHash < ::Hash
|
5
|
+
def self.[](graph, content = {})
|
6
|
+
@graph = graph
|
7
|
+
super(stringified(content))
|
8
|
+
end
|
9
|
+
|
5
10
|
def initialize(graph, content = {})
|
6
11
|
@graph = graph
|
7
12
|
super()
|
@@ -4,8 +4,7 @@ module ROCrate
|
|
4
4
|
# Contextual Entities are used to describe and provide context to the Data Entities within the crate.
|
5
5
|
class ContextualEntity < Entity
|
6
6
|
def self.format_local_id(id)
|
7
|
-
|
8
|
-
i.start_with?('#') ? i : "##{i}"
|
7
|
+
super(id.start_with?('#') ? id : "##{id}")
|
9
8
|
end
|
10
9
|
|
11
10
|
##
|
data/lib/ro_crate/model/crate.rb
CHANGED
@@ -288,6 +288,20 @@ module ROCrate
|
|
288
288
|
deleted
|
289
289
|
end
|
290
290
|
|
291
|
+
##
|
292
|
+
# Remove any contextual entities that are not linked from any other entity.
|
293
|
+
# Optionally takes a block to decide whether the given entity should be removed or not, otherwise removes all
|
294
|
+
# unlinked entities.
|
295
|
+
# @yieldparam [ContextualEntity] entity An unlinked contextual entity.
|
296
|
+
# @yieldparam [Boolean] remove Should this entity be removed?
|
297
|
+
#
|
298
|
+
# @return [Array<ContextualEntity>] The entities that were removed.
|
299
|
+
def gc(&block)
|
300
|
+
unlinked_entities = contextual_entities - metadata.linked_entities(deep: true)
|
301
|
+
|
302
|
+
unlinked_entities.select(&block).each { |e| e.delete(remove_orphaned: false) }
|
303
|
+
end
|
304
|
+
|
291
305
|
private
|
292
306
|
|
293
307
|
def full_entry_path(relative_path)
|
@@ -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
|
##
|
@@ -57,7 +57,12 @@ module ROCrate
|
|
57
57
|
# @param id [String] The candidate local ID to be formatted.
|
58
58
|
# @return [String] The formatted local ID.
|
59
59
|
def self.format_local_id(id)
|
60
|
-
|
60
|
+
if id.start_with?('#')
|
61
|
+
'#' + Addressable::URI.encode_component(id[1..-1], Addressable::URI::CharacterClasses::QUERY)
|
62
|
+
else
|
63
|
+
# Remove initial ./ if present
|
64
|
+
Addressable::URI.encode_component(id.sub(/\A\.\//, ''), Addressable::URI::CharacterClasses::PATH)
|
65
|
+
end
|
61
66
|
end
|
62
67
|
|
63
68
|
##
|
@@ -242,14 +247,16 @@ module ROCrate
|
|
242
247
|
# @param linked [Hash{String => Entity}] Discovered entities, mapped by their ID, to avoid loops when recursing.
|
243
248
|
# @return [Array<Entity>]
|
244
249
|
def linked_entities(deep: false, linked: {})
|
245
|
-
properties.
|
250
|
+
properties.each_key do |key|
|
251
|
+
value = properties[key] # We're doing this to call the JSONLDHash#[] method which wraps
|
246
252
|
value = [value] if value.is_a?(JSONLDHash)
|
247
253
|
|
248
254
|
if value.is_a?(Array)
|
249
255
|
value.each do |v|
|
250
256
|
if v.is_a?(JSONLDHash) && !linked.key?(v['@id'])
|
251
257
|
entity = v.dereference
|
252
|
-
|
258
|
+
next unless entity
|
259
|
+
linked[entity.id] = entity
|
253
260
|
if deep
|
254
261
|
entity.linked_entities(deep: true, linked: linked).each do |e|
|
255
262
|
linked[e.id] = e
|
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/crate_test.rb
CHANGED
@@ -348,4 +348,32 @@ class CrateTest < Test::Unit::TestCase
|
|
348
348
|
|
349
349
|
assert_equal crate.payload.keys, crate.entries.keys
|
350
350
|
end
|
351
|
+
|
352
|
+
test 'can garbage collect unlinked entities' do
|
353
|
+
crate = ROCrate::Reader.read(fixture_file('unlinked_entity_crate').path)
|
354
|
+
|
355
|
+
unlinked = crate.gc
|
356
|
+
assert_equal 2, unlinked.length
|
357
|
+
ids = unlinked.map(&:id)
|
358
|
+
assert_includes ids, '#joe'
|
359
|
+
assert_includes ids, '#joehouse'
|
360
|
+
assert_not_includes crate.contextual_entities, unlinked.first
|
361
|
+
assert_not_includes crate.contextual_entities, unlinked.last
|
362
|
+
assert_nil crate.get('#joe')
|
363
|
+
assert_nil crate.get('#joehouse')
|
364
|
+
end
|
365
|
+
|
366
|
+
test 'can conditionally garbage collect unlinked entities using a block' do
|
367
|
+
crate = ROCrate::Reader.read(fixture_file('unlinked_entity_crate').path)
|
368
|
+
|
369
|
+
unlinked = crate.gc do |entity|
|
370
|
+
entity.is_a?(ROCrate::Person)
|
371
|
+
end
|
372
|
+
assert_equal 1, unlinked.length
|
373
|
+
ids = unlinked.map(&:id)
|
374
|
+
assert_includes ids, '#joe'
|
375
|
+
assert_not_includes crate.contextual_entities, unlinked.first
|
376
|
+
assert_nil crate.get('#joe')
|
377
|
+
assert crate.get('#joehouse')
|
378
|
+
end
|
351
379
|
end
|
data/test/entity_test.rb
CHANGED
@@ -1,3 +1,4 @@
|
|
1
|
+
# encoding: utf-8
|
1
2
|
require 'test_helper'
|
2
3
|
|
3
4
|
class EntityTest < Test::Unit::TestCase
|
@@ -38,11 +39,11 @@ class EntityTest < Test::Unit::TestCase
|
|
38
39
|
test 'fetch appropriate class for type' do
|
39
40
|
assert_equal ROCrate::File, ROCrate::DataEntity.specialize({ '@type' => 'File' })
|
40
41
|
assert_equal ROCrate::File, ROCrate::DataEntity.specialize({ '@type' => ['File', 'Image'] })
|
41
|
-
assert_equal ROCrate::
|
42
|
-
assert_equal ROCrate::
|
42
|
+
assert_equal ROCrate::DataEntity, ROCrate::DataEntity.specialize({ '@type' => 'SoftwareSourceCode' })
|
43
|
+
assert_equal ROCrate::DataEntity, ROCrate::DataEntity.specialize({ '@type' => 'anything that isnt a directory' })
|
43
44
|
assert_equal ROCrate::Directory, ROCrate::DataEntity.specialize({ '@type' => 'Dataset' })
|
44
45
|
assert_equal ROCrate::Directory, ROCrate::DataEntity.specialize({ '@type' => ['Dataset', 'Image'] })
|
45
|
-
assert_equal ROCrate::
|
46
|
+
assert_equal ROCrate::DataEntity, ROCrate::DataEntity.specialize({ '@type' => 'Person' })
|
46
47
|
assert_equal ROCrate::File, ROCrate::DataEntity.specialize({ '@type' => ['File', 'Image'], '@id' => 'http://www.external.com' })
|
47
48
|
|
48
49
|
assert_equal ROCrate::Person, ROCrate::ContextualEntity.specialize({ '@type' => 'Person' })
|
@@ -75,6 +76,7 @@ class EntityTest < Test::Unit::TestCase
|
|
75
76
|
assert_equal "#Hello%20World/Goodbye%20World", ROCrate::ContextualEntity.format_id('#Hello World/Goodbye World')
|
76
77
|
assert_equal "#Hello%20World/Goodbye%20World", ROCrate::ContextualEntity.format_id('Hello World/Goodbye World')
|
77
78
|
assert_equal "#%F0%9F%98%8A", ROCrate::ContextualEntity.format_id("😊")
|
79
|
+
assert_equal "https://orcid.org/0000-0002-0048-3300", ROCrate::ContextualEntity.format_id("https://orcid.org/0000-0002-0048-3300")
|
78
80
|
|
79
81
|
assert_equal "test123/hello.txt", ROCrate::File.format_id('./test123/hello.txt')
|
80
82
|
assert_equal "test123/hello.txt", ROCrate::File.format_id('./test123/hello.txt/')
|
@@ -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"
|
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{
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{
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"TestService": "https://w3id.org/ro/terms/test#TestService",
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"TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition",
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"PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine",
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"JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",
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"TravisService": "https://w3id.org/ro/terms/test#TravisService",
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"GithubService": "https://w3id.org/ro/terms/test#GithubService",
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"instance": "https://w3id.org/ro/terms/test#instance",
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],
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"@graph": [
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"about": {
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{ "@id": "https://about.workflowhub.eu/Workflow-RO-Crate/" }
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"name": "sort-and-change-case",
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"description": "sort lines and change text to upper case",
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"license": "Apache-2.0",
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"mentions": [
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"File",
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"SoftwareSourceCode",
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"ComputationalWorkflow"
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],
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"programmingLanguage": {
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"@id": "#galaxy"
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"name": "sort-and-change-case"
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{
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"@type": "ComputerLanguage",
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"name": "Galaxy",
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"identifier": {
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"@id": "https://galaxyproject.org/"
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"engineVersion": ">=0.70"
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"name": "Jenkins",
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"url": {"@id": "https://www.jenkins.io"}
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{
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"@id": "https://w3id.org/ro/terms/test#PlanemoEngine",
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"@type": "SoftwareApplication",
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"name": "Planemo",
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"url": {"@id": "https://github.com/galaxyproject/planemo"}
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},
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{
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"@id": "https://about.workflowhub.eu/Workflow-RO-Crate/",
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"@type": "CreativeWork",
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"name": "Workflow RO-Crate Profile",
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"version": "0.2.0"
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},
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{
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"@id": "#joe",
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"name": "Joe Jones"
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},
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{
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"@id": "#joehouse",
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"@type": "Organization",
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"name": "Joe's House"
|
148
|
+
}
|
149
|
+
]
|
150
|
+
}
|
@@ -0,0 +1,118 @@
|
|
1
|
+
{
|
2
|
+
"uuid": "e2a8566c-c025-4181-9e90-7ed29d4e4df1",
|
3
|
+
"tags": [],
|
4
|
+
"format-version": "0.1",
|
5
|
+
"name": "sort-and-change-case",
|
6
|
+
"version": 0,
|
7
|
+
"steps": {
|
8
|
+
"0": {
|
9
|
+
"tool_id": null,
|
10
|
+
"tool_version": null,
|
11
|
+
"outputs": [],
|
12
|
+
"workflow_outputs": [],
|
13
|
+
"input_connections": {},
|
14
|
+
"tool_state": "{}",
|
15
|
+
"id": 0,
|
16
|
+
"uuid": "5a36fad2-66c7-4b9e-8759-0fbcae9b8541",
|
17
|
+
"errors": null,
|
18
|
+
"name": "Input dataset",
|
19
|
+
"label": "bed_input",
|
20
|
+
"inputs": [],
|
21
|
+
"position": {
|
22
|
+
"top": 200,
|
23
|
+
"left": 200
|
24
|
+
},
|
25
|
+
"annotation": "",
|
26
|
+
"content_id": null,
|
27
|
+
"type": "data_input"
|
28
|
+
},
|
29
|
+
"1": {
|
30
|
+
"tool_id": "sort1",
|
31
|
+
"tool_version": "1.1.0",
|
32
|
+
"outputs": [
|
33
|
+
{
|
34
|
+
"type": "input",
|
35
|
+
"name": "out_file1"
|
36
|
+
}
|
37
|
+
],
|
38
|
+
"workflow_outputs": [
|
39
|
+
{
|
40
|
+
"output_name": "out_file1",
|
41
|
+
"uuid": "8237f71a-bc2a-494e-a63c-09c1e65ef7c8",
|
42
|
+
"label": "sorted_bed"
|
43
|
+
}
|
44
|
+
],
|
45
|
+
"input_connections": {
|
46
|
+
"input": {
|
47
|
+
"output_name": "output",
|
48
|
+
"id": 0
|
49
|
+
}
|
50
|
+
},
|
51
|
+
"tool_state": "{\"__page__\": null, \"style\": \"\\\"alpha\\\"\", \"column\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"column_set\": \"[]\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"header_lines\": \"\\\"0\\\"\", \"order\": \"\\\"ASC\\\"\"}",
|
52
|
+
"id": 1,
|
53
|
+
"uuid": "0b6b3cda-c75f-452b-85b1-8ae4f3302ba4",
|
54
|
+
"errors": null,
|
55
|
+
"name": "Sort",
|
56
|
+
"post_job_actions": {},
|
57
|
+
"label": "sort",
|
58
|
+
"inputs": [
|
59
|
+
{
|
60
|
+
"name": "input",
|
61
|
+
"description": "runtime parameter for tool Sort"
|
62
|
+
}
|
63
|
+
],
|
64
|
+
"position": {
|
65
|
+
"top": 200,
|
66
|
+
"left": 420
|
67
|
+
},
|
68
|
+
"annotation": "",
|
69
|
+
"content_id": "sort1",
|
70
|
+
"type": "tool"
|
71
|
+
},
|
72
|
+
"2": {
|
73
|
+
"tool_id": "ChangeCase",
|
74
|
+
"tool_version": "1.0.0",
|
75
|
+
"outputs": [
|
76
|
+
{
|
77
|
+
"type": "tabular",
|
78
|
+
"name": "out_file1"
|
79
|
+
}
|
80
|
+
],
|
81
|
+
"workflow_outputs": [
|
82
|
+
{
|
83
|
+
"output_name": "out_file1",
|
84
|
+
"uuid": "c31cd733-dab6-4d50-9fec-b644d162397b",
|
85
|
+
"label": "uppercase_bed"
|
86
|
+
}
|
87
|
+
],
|
88
|
+
"input_connections": {
|
89
|
+
"input": {
|
90
|
+
"output_name": "out_file1",
|
91
|
+
"id": 1
|
92
|
+
}
|
93
|
+
},
|
94
|
+
"tool_state": "{\"__page__\": null, \"casing\": \"\\\"up\\\"\", \"__rerun_remap_job_id__\": null, \"cols\": \"\\\"c1\\\"\", \"delimiter\": \"\\\"TAB\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
|
95
|
+
"id": 2,
|
96
|
+
"uuid": "9698bcde-0729-48fe-b88d-ccfb6f6153b4",
|
97
|
+
"errors": null,
|
98
|
+
"name": "Change Case",
|
99
|
+
"post_job_actions": {},
|
100
|
+
"label": "change_case",
|
101
|
+
"inputs": [
|
102
|
+
{
|
103
|
+
"name": "input",
|
104
|
+
"description": "runtime parameter for tool Change Case"
|
105
|
+
}
|
106
|
+
],
|
107
|
+
"position": {
|
108
|
+
"top": 200,
|
109
|
+
"left": 640
|
110
|
+
},
|
111
|
+
"annotation": "",
|
112
|
+
"content_id": "ChangeCase",
|
113
|
+
"type": "tool"
|
114
|
+
}
|
115
|
+
},
|
116
|
+
"annotation": "",
|
117
|
+
"a_galaxy_workflow": "true"
|
118
|
+
}
|
@@ -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: 0.4.16
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Finn Bacall
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date:
|
11
|
+
date: 2022-03-09 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
|
@@ -195,6 +196,13 @@ files:
|
|
195
196
|
- test/fixtures/sparse_directory_crate/ro-crate-metadata.jsonld
|
196
197
|
- test/fixtures/sparse_directory_crate/ro-crate-preview.html
|
197
198
|
- test/fixtures/sparse_directory_crate/unlisted_file.txt
|
199
|
+
- test/fixtures/unlinked_entity_crate/LICENSE
|
200
|
+
- test/fixtures/unlinked_entity_crate/README.md
|
201
|
+
- test/fixtures/unlinked_entity_crate/ro-crate-metadata.json
|
202
|
+
- test/fixtures/unlinked_entity_crate/sort-and-change-case.ga
|
203
|
+
- test/fixtures/unlinked_entity_crate/test/test1/input.bed
|
204
|
+
- test/fixtures/unlinked_entity_crate/test/test1/output_exp.bed
|
205
|
+
- test/fixtures/unlinked_entity_crate/test/test1/sort-and-change-case-test.yml
|
198
206
|
- test/fixtures/workflow-0.2.0.zip
|
199
207
|
- test/fixtures/workflow-0.2.0/Dockerfile
|
200
208
|
- test/fixtures/workflow-0.2.0/README.md
|
@@ -2442,7 +2450,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
2442
2450
|
- !ruby/object:Gem::Version
|
2443
2451
|
version: '0'
|
2444
2452
|
requirements: []
|
2445
|
-
rubygems_version: 3.
|
2453
|
+
rubygems_version: 3.1.6
|
2446
2454
|
signing_key:
|
2447
2455
|
specification_version: 4
|
2448
2456
|
summary: Create, manipulate, read RO-Crates.
|