ro-crate 0.4.10 → 0.4.11
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/Gemfile.lock +8 -8
- data/README.md +37 -0
- data/lib/ro_crate.rb +1 -0
- data/lib/ro_crate/model/crate.rb +9 -0
- data/lib/ro_crate/model/data_entity.rb +2 -2
- data/lib/ro_crate/model/directory.rb +0 -2
- data/lib/ro_crate/model/file.rb +1 -3
- 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/reader.rb +53 -18
- data/ro_crate.gemspec +2 -2
- data/test/crate_test.rb +12 -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 +24 -0
- data/test/writer_test.rb +22 -2
- metadata +12 -4
checksums.yaml
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 62f3979b325743d31720f803dbf75690ad6b7b9bcf9f2cbf63d8200a2bb204ba
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data.tar.gz: 3a229e06492a3f9a90721799f43929d6a5ca01fc0a0ff34d917eeebff037d9d4
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 242b8e326756d51ab583726db7fb94763286f2764bdf1f0523cd9dab5fa560fe4da3016a4a4b84b0cc6bcef4ec096aeae7dc2fd344ef6cb5ee045cf99a954ef9
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data.tar.gz: 4abaece91d997ac398ee627f639fc98c924768c255bac1bb6c9ce7f43fc03f5b018a2fc657008863c65537592261e85f697ef2c7e200c20621ba41ff0a933541
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data/Gemfile.lock
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PATH
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remote: .
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specs:
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ro-crate (0.4.
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ro-crate (0.4.11)
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addressable (~> 2.7.0)
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rubyzip (~> 2.0.0)
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public_suffix (>= 2.0.2, < 5.0)
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crack (0.4.3)
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safe_yaml (~> 1.0.0)
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docile (1.3.
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docile (1.3.5)
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hashdiff (1.0.1)
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json (2.3.1)
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power_assert (0.4.1)
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public_suffix (4.0.3)
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rake (13.0.0)
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rubyzip (2.0.0)
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safe_yaml (1.0.5)
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simplecov (0.
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simplecov (0.21.2)
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docile (~> 1.1)
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simplecov-html (0.
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simplecov-html (~> 0.11)
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simplecov_json_formatter (~> 0.1)
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simplecov-html (0.12.3)
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simplecov_json_formatter (0.1.2)
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test-unit (3.2.3)
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power_assert
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webmock (3.8.3)
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DEPENDENCIES
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rake (~> 13.0.0)
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ro-crate!
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simplecov (~> 0.
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simplecov (~> 0.21.2)
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test-unit (~> 3.2.3)
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webmock (~> 3.8.3)
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yard (~> 0.9.25)
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data/README.md
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## Usage
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This gem consists a hierarchy of classes to model RO-Crate "entities": the crate itself, data entities
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(files and directory) and contextual entities (with a limited set of specializations, such as `ROCrate::Person`).
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They are all descendents of the `ROCrate::Entity` class, with the `ROCrate::Crate` class representing the crate itself.
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The `ROCrate::Reader` class handles reading of RO-Crates into the above model, from a Zip file or directory.
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The `ROCrate::Writer` class can write out an `ROCrate::Crate` instance into a Zip file or directory.
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**Note:** for performance reasons, the gem is currently not linked-data aware and will allow you to set properties that
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are not semantically valid.
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### Entities
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Entities correspond to entries in the `@graph` of the RO-Crate's metadata JSON-LD file. Each entity class is
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basically a wrapper around a set of JSON properties, with some convenience methods for getting/setting some
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commonly used properties (`crate.name = "My first crate"`).
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These convenience getter/setter methods will automatically handle turning objects into references and adding them to the
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`@graph` if necessary.
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##### Getting/Setting Arbitrary Properties of Entities
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As well as using the pre-defined getter/setter methods, you can get/set arbitrary properties like so.
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To set the "creativeWorkStatus" property of the RO-Crate itself to a string literal:
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```ruby
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crate['creativeWorkStatus'] = 'work-in-progress'
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```
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If you want to reference other entities in the crate, you can get a JSON-LD reference from an entity object by using the `reference` method:
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```ruby
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joe = crate.add_person('joe', { name: 'Joe Bloggs' }) # Add the entity to the @graph
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crate['copyrightHolder'] = joe.reference # Reference the entity from the "copyrightHolder" property
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```
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and to resolve those references back to the object, use the `dereference` method:
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```ruby
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joe = crate['copyrightHolder'].dereference
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```
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### Documentation
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[Click here for API documentation](https://www.researchobject.org/ro-crate-ruby/).
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data/lib/ro_crate.rb
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@@ -14,6 +14,7 @@ require 'ro_crate/model/remote_entry'
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require 'ro_crate/model/entry'
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require 'ro_crate/model/directory'
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require 'ro_crate/model/metadata'
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require 'ro_crate/model/preview_generator'
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require 'ro_crate/model/preview'
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require 'ro_crate/model/crate'
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require 'ro_crate/model/contextual_entity'
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data/lib/ro_crate/model/crate.rb
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@preview ||= ROCrate::Preview.new(self)
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end
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##
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# Set the RO-Crate preview file
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# @param preview [Preview] the preview to set.
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#
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# @return [Preview]
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def preview=(preview)
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@preview = claim(preview)
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end
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##
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# All the entities within the crate. Includes contextual entities, data entities, the crate itself and its metadata file.
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#
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# A class to represent a "Data Entity" within an RO-Crate.
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# Data Entities are the actual physical files and directories within the Crate.
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class DataEntity < Entity
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properties(%w[name contentSize dateModified encodingFormat identifier sameAs author])
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def self.format_local_id(id)
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super.chomp('/')
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end
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# @return [Class]
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def self.specialize(props)
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type = props['@type']
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id = props['@id']
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abs = URI(id)&.absolute? rescue false
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type = [type] unless type.is_a?(Array)
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if type.include?('Dataset')
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ROCrate::Directory
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##
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# A data entity that represents a directory of potentially many files and subdirectories (or none).
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class Directory < DataEntity
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properties(%w[name contentSize dateModified encodingFormat identifier sameAs])
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def self.format_local_id(id)
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super + '/'
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end
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data/lib/ro_crate/model/file.rb
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##
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# A data entity that represents a single file.
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class File < DataEntity
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properties(%w[name contentSize dateModified encodingFormat identifier sameAs])
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##
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# Create a new ROCrate::File. PLEASE NOTE, the new file will not be added to the crate. To do this, call
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# Crate#add_data_entity, or just use Crate#add_file.
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#
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# @param crate [Crate] The RO-Crate that owns this file.
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# @param source [String, Pathname, ::File,
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# @param source [String, Pathname, ::File, URI, nil, #read] The source on the disk (or on the internet if a URI) where this file will be read.
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# @param crate_path [String] The relative path within the RO-Crate where this file will be written.
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# @param properties [Hash{String => Object}] A hash of JSON-LD properties to associate with this file.
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def initialize(crate, source, crate_path = nil, properties = {})
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# @return [String] The rendered JSON-LD as a "prettified" string.
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def generate
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graph = crate.entities.map(&:properties).reject(&:empty?)
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JSON.pretty_generate('@context' =>
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JSON.pretty_generate('@context' => context, '@graph' => graph)
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end
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def context
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@context || CONTEXT
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end
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def context= c
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@context = c
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end
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private
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# @return [String]
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attr_accessor :template
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def initialize(crate, properties = {})
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def initialize(crate, source = nil, properties = {})
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source ||= PreviewGenerator.new(self)
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@template = nil
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super(crate,
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end
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##
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# Generate the crate's `ro-crate-preview.html`.
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# @return [String] The rendered HTML as a string.
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def generate
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b = crate.get_binding
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renderer = ERB.new(template || ::File.read(DEFAULT_TEMPLATE))
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renderer.result(b)
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super(crate, source, IDENTIFIER, properties)
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end
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private
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def source
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Entry.new(StringIO.new(generate))
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end
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def default_properties
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{
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'@id' => IDENTIFIER,
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require 'erb'
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module ROCrate
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##
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# A class to handle generation of an RO-Crate's preview HTML in an IO-like way (to fit into an Entry).
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class PreviewGenerator
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##
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# @param preview [Preview] The RO-Crate preview object.
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def initialize(preview)
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@preview = preview
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end
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def read(*args)
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io.read(*args)
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end
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##
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# Generate the crate's `ro-crate-preview.html`.
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# @return [String] The rendered HTML as a string.
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def generate
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b = crate.get_binding
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renderer = ERB.new(template)
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renderer.result(b)
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end
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def template
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@preview.template || ::File.read(Preview::DEFAULT_TEMPLATE)
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end
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def crate
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@preview.crate
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end
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private
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def io
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@io ||= StringIO.new(generate)
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end
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end
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end
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data/lib/ro_crate/reader.rb
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entry == ROCrate::Metadata::IDENTIFIER_1_0 }
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if metadata_file
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-
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metadata_json = ::File.read(::File.join(source, metadata_file))
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metadata = JSON.parse(metadata_json)
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entities = entities_from_metadata(metadata)
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context = metadata['@context']
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build_crate(entities, source, context: context)
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else
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raise 'No metadata found!'
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end
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##
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# Extracts all the entities from the @graph of the RO-Crate Metadata.
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#
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# @param
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# @param metadata [Hash] A Hash containing the parsed metadata JSON.
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# @return [Hash{String => Hash}] A Hash of all the entities, mapped by their @id.
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def self.entities_from_metadata(
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metadata = JSON.parse(metadata_json)
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def self.entities_from_metadata(metadata)
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graph = metadata['@graph']
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if graph
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# Do some normalization...
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entities[ROCrate::Metadata::IDENTIFIER] = extract_metadata_entity(entities)
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raise "No metadata entity found in @graph!" unless entities[ROCrate::Metadata::IDENTIFIER]
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entities[ROCrate::Preview::IDENTIFIER] = extract_preview_entity(entities)
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entities[ROCrate::Crate::IDENTIFIER] = extract_root_entity(entities)
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raise "No root entity (with @id: #{entities[ROCrate::Metadata::IDENTIFIER].dig('about', '@id')}) found in @graph!" unless entities[ROCrate::Crate::IDENTIFIER]
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end
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##
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# Create
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# Create and populate crate from the given set of entities.
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#
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# @param entity_hash [Hash{String => Hash}] A Hash containing all the entities in the @graph, mapped by their @id.
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# @param source [String, ::File, Pathname] The location of the RO-Crate being read.
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# @param crate_class [Class] The class to use to instantiate the crate,
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# useful if you have created a subclass of ROCrate::Crate that you want to use. (defaults to ROCrate::Crate).
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# @param context [nil, String, Array, Hash] A custom JSON-LD @context (parsed), or nil to use default.
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# @return [Crate] The RO-Crate.
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def self.build_crate(entity_hash, source, crate_class: ROCrate::Crate, context:)
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crate = initialize_crate(entity_hash, source, crate_class: crate_class, context: context)
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extract_data_entities(crate, source, entity_hash).each do |entity|
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crate.add_data_entity(entity)
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end
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# The remaining entities in the hash must be contextual.
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extract_contextual_entities(crate, entity_hash).each do |entity|
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crate.add_contextual_entity(entity)
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end
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crate
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end
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##
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# Initialize a crate from the given set of entities.
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#
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# @param entity_hash [Hash{String => Hash}] A Hash containing all the entities in the @graph, mapped by their @id.
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# @param source [String, ::File, Pathname] The location of the RO-Crate being read.
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# @param crate_class [Class] The class to use to instantiate the crate,
|
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|
+
# useful if you have created a subclass of ROCrate::Crate that you want to use. (defaults to ROCrate::Crate).
|
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|
+
# @param context [nil, String, Array, Hash] A custom JSON-LD @context (parsed), or nil to use default.
|
146
177
|
# @return [Crate] The RO-Crate.
|
147
|
-
def self.
|
148
|
-
|
178
|
+
def self.initialize_crate(entity_hash, source, crate_class: ROCrate::Crate, context:)
|
179
|
+
crate_class.new.tap do |crate|
|
149
180
|
crate.properties = entity_hash.delete(ROCrate::Crate::IDENTIFIER)
|
150
181
|
crate.metadata.properties = entity_hash.delete(ROCrate::Metadata::IDENTIFIER)
|
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|
+
crate.metadata.context = context
|
151
183
|
preview_properties = entity_hash.delete(ROCrate::Preview::IDENTIFIER)
|
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|
-
|
153
|
-
|
154
|
-
|
155
|
-
crate.add_data_entity(entity)
|
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|
-
end
|
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|
-
# The remaining entities in the hash must be contextual.
|
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|
-
extract_contextual_entities(crate, entity_hash).each do |entity|
|
159
|
-
crate.add_contextual_entity(entity)
|
184
|
+
if preview_properties
|
185
|
+
preview_path = ::File.join(source, ROCrate::Preview::IDENTIFIER)
|
186
|
+
crate.preview = ROCrate::Preview.new(crate, ::File.exists?(preview_path) ? Pathname.new(preview_path) : nil, preview_properties)
|
160
187
|
end
|
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|
+
crate.add_all(source, false)
|
161
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|
end
|
162
190
|
end
|
163
191
|
|
@@ -229,8 +257,8 @@ module ROCrate
|
|
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|
##
|
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|
# Extract the metadata entity from the entity hash, according to the rules defined here:
|
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|
# https://www.researchobject.org/ro-crate/1.1/root-data-entity.html#finding-the-root-data-entity
|
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|
-
# @return [Hash{String => Hash}] A Hash containing (hopefully) one value, the metadata entity's properties
|
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|
-
# mapped by its @id.
|
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|
+
# @return [nil, Hash{String => Hash}] A Hash containing (hopefully) one value, the metadata entity's properties
|
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|
+
# mapped by its @id, or nil if nothing is found.
|
234
262
|
def self.extract_metadata_entity(entities)
|
235
263
|
key = entities.detect do |_, props|
|
236
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|
props.dig('conformsTo', '@id')&.start_with?(ROCrate::Metadata::RO_CRATE_BASE)
|
@@ -245,6 +273,13 @@ module ROCrate
|
|
245
273
|
entities.delete(ROCrate::Metadata::IDENTIFIER_1_0))
|
246
274
|
end
|
247
275
|
|
276
|
+
##
|
277
|
+
# Extract the ro-crate-preview entity from the entity hash.
|
278
|
+
# @return [Hash{String => Hash}] A Hash containing the preview entity's properties mapped by its @id, or nil if nothing is found.
|
279
|
+
def self.extract_preview_entity(entities)
|
280
|
+
entities.delete("./#{ROCrate::Preview::IDENTIFIER}") || entities.delete(ROCrate::Preview::IDENTIFIER)
|
281
|
+
end
|
282
|
+
|
248
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|
##
|
249
284
|
# Extract the root entity from the entity hash, according to the rules defined here:
|
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|
# https://www.researchobject.org/ro-crate/1.1/root-data-entity.html#finding-the-root-data-entity
|
data/ro_crate.gemspec
CHANGED
@@ -1,6 +1,6 @@
|
|
1
1
|
Gem::Specification.new do |s|
|
2
2
|
s.name = 'ro-crate'
|
3
|
-
s.version = '0.4.
|
3
|
+
s.version = '0.4.11'
|
4
4
|
s.summary = 'Create, manipulate, read RO-Crates.'
|
5
5
|
s.authors = ['Finn Bacall']
|
6
6
|
s.email = 'finn.bacall@manchester.ac.uk'
|
@@ -12,7 +12,7 @@ Gem::Specification.new do |s|
|
|
12
12
|
s.add_runtime_dependency 'rubyzip', '~> 2.0.0'
|
13
13
|
s.add_development_dependency 'rake', '~> 13.0.0'
|
14
14
|
s.add_development_dependency 'test-unit', '~> 3.2.3'
|
15
|
-
s.add_development_dependency 'simplecov', '~> 0.
|
15
|
+
s.add_development_dependency 'simplecov', '~> 0.21.2'
|
16
16
|
s.add_development_dependency 'yard', '~> 0.9.25'
|
17
17
|
s.add_development_dependency 'webmock', '~> 3.8.3'
|
18
18
|
end
|
data/test/crate_test.rb
CHANGED
@@ -164,6 +164,18 @@ class CrateTest < Test::Unit::TestCase
|
|
164
164
|
assert_equal 2, crate1.contextual_entities.first.properties['cats']
|
165
165
|
end
|
166
166
|
|
167
|
+
test 'sharing entities' do
|
168
|
+
crate = ROCrate::Crate.new
|
169
|
+
info = crate.add_file(fixture_file('info.txt'),'the_info.txt')
|
170
|
+
bob = crate.add_person('bob', name: 'Bob Jones')
|
171
|
+
crate.author = bob
|
172
|
+
info.author = bob
|
173
|
+
|
174
|
+
assert_equal [bob], crate.contextual_entities
|
175
|
+
assert_equal bob, info.author
|
176
|
+
assert_equal bob, crate.author
|
177
|
+
end
|
178
|
+
|
167
179
|
test 'external files' do
|
168
180
|
crate = ROCrate::Crate.new
|
169
181
|
local = crate.add_file(fixture_file('info.txt'))
|
@@ -0,0 +1,176 @@
|
|
1
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+
|
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|
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|
3
|
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@@ -0,0 +1,6 @@
|
|
1
|
+
# Galaxy mini workflow
|
2
|
+
|
3
|
+
A tiny Galaxy workflow that sorts tabular lines according to the first column
|
4
|
+
and changes the text to upper case.
|
5
|
+
|
6
|
+
This RO-Crate is based on an [example from the Life Monitor repository](https://github.com/crs4/life_monitor/tree/8437be177822d0e2b3fed30db094b91c2fc14391/interaction_experiments/data/crates/ro-crate-galaxy-sortchangecase).
|
@@ -0,0 +1,133 @@
|
|
1
|
+
{
|
2
|
+
"@context": [
|
3
|
+
"https://w3id.org/ro/crate/1.1/context",
|
4
|
+
{
|
5
|
+
"TestSuite": "https://w3id.org/ro/terms/test#TestSuite",
|
6
|
+
"TestInstance": "https://w3id.org/ro/terms/test#TestInstance",
|
7
|
+
"TestService": "https://w3id.org/ro/terms/test#TestService",
|
8
|
+
"TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition",
|
9
|
+
"PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine",
|
10
|
+
"JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",
|
11
|
+
"TravisService": "https://w3id.org/ro/terms/test#TravisService",
|
12
|
+
"GithubService": "https://w3id.org/ro/terms/test#GithubService",
|
13
|
+
"instance": "https://w3id.org/ro/terms/test#instance",
|
14
|
+
"runsOn": "https://w3id.org/ro/terms/test#runsOn",
|
15
|
+
"resource": "https://w3id.org/ro/terms/test#resource",
|
16
|
+
"definition": "https://w3id.org/ro/terms/test#definition",
|
17
|
+
"engineVersion": "https://w3id.org/ro/terms/test#engineVersion"
|
18
|
+
}
|
19
|
+
],
|
20
|
+
"@graph": [
|
21
|
+
{
|
22
|
+
"@id": "ro-crate-metadata.json",
|
23
|
+
"@type": "CreativeWork",
|
24
|
+
"about": {
|
25
|
+
"@id": "./"
|
26
|
+
},
|
27
|
+
"conformsTo": {
|
28
|
+
"@id": "https://w3id.org/ro/crate/1.1"
|
29
|
+
}
|
30
|
+
},
|
31
|
+
{
|
32
|
+
"@id": "./",
|
33
|
+
"@type": "Dataset",
|
34
|
+
"name": "sort-and-change-case",
|
35
|
+
"description": "sort lines and change text to upper case",
|
36
|
+
"license": "Apache-2.0",
|
37
|
+
"mainEntity": {
|
38
|
+
"@id": "sort-and-change-case.ga"
|
39
|
+
},
|
40
|
+
"hasPart": [
|
41
|
+
{
|
42
|
+
"@id": "sort-and-change-case.ga"
|
43
|
+
},
|
44
|
+
{
|
45
|
+
"@id": "LICENSE"
|
46
|
+
},
|
47
|
+
{
|
48
|
+
"@id": "README.md"
|
49
|
+
},
|
50
|
+
{
|
51
|
+
"@id": "test/test1/sort-and-change-case-test.yml"
|
52
|
+
}
|
53
|
+
],
|
54
|
+
"mentions": [
|
55
|
+
{
|
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|
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"identifier": {
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"runsOn": {"@id": "https://w3id.org/ro/terms/test#JenkinsService"},
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{
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],
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"conformsTo": {"@id": "https://w3id.org/ro/terms/test#PlanemoEngine"},
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"engineVersion": ">=0.70"
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},
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{
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"name": "Jenkins",
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"url": {"@id": "https://www.jenkins.io"}
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},
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{
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"@id": "https://w3id.org/ro/terms/test#PlanemoEngine",
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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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}
|
@@ -0,0 +1,118 @@
|
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{
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"uuid": "e2a8566c-c025-4181-9e90-7ed29d4e4df1",
|
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"tags": [],
|
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"format-version": "0.1",
|
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"name": "sort-and-change-case",
|
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"version": 0,
|
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"steps": {
|
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"0": {
|
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"tool_id": null,
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|
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"tool_state": "{}",
|
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"id": 0,
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"uuid": "5a36fad2-66c7-4b9e-8759-0fbcae9b8541",
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"errors": null,
|
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"name": "Input dataset",
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"label": "bed_input",
|
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"inputs": [],
|
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"position": {
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|
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|
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|
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},
|
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"1": {
|
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|
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|
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"outputs": [
|
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|
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|
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|
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],
|
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"workflow_outputs": [
|
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{
|
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"output_name": "out_file1",
|
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"uuid": "8237f71a-bc2a-494e-a63c-09c1e65ef7c8",
|
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"label": "sorted_bed"
|
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|
+
}
|
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+
],
|
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|
+
"input_connections": {
|
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|
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"input": {
|
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"output_name": "output",
|
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"id": 0
|
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}
|
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},
|
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|
+
"tool_state": "{\"__page__\": null, \"style\": \"\\\"alpha\\\"\", \"column\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"column_set\": \"[]\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"header_lines\": \"\\\"0\\\"\", \"order\": \"\\\"ASC\\\"\"}",
|
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|
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"id": 1,
|
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|
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"uuid": "0b6b3cda-c75f-452b-85b1-8ae4f3302ba4",
|
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|
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"errors": null,
|
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|
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"name": "Sort",
|
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|
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"post_job_actions": {},
|
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|
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"label": "sort",
|
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"inputs": [
|
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{
|
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"name": "input",
|
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"description": "runtime parameter for tool Sort"
|
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|
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}
|
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|
+
],
|
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"position": {
|
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"top": 200,
|
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"left": 420
|
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},
|
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"annotation": "",
|
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"content_id": "sort1",
|
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|
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"type": "tool"
|
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|
+
},
|
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|
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"2": {
|
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|
+
"tool_id": "ChangeCase",
|
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|
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"tool_version": "1.0.0",
|
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|
+
"outputs": [
|
76
|
+
{
|
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|
+
"type": "tabular",
|
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|
+
"name": "out_file1"
|
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|
+
}
|
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|
+
],
|
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|
+
"workflow_outputs": [
|
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|
+
{
|
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|
+
"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",
|
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|
+
"id": 1
|
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|
+
}
|
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|
+
},
|
94
|
+
"tool_state": "{\"__page__\": null, \"casing\": \"\\\"up\\\"\", \"__rerun_remap_job_id__\": null, \"cols\": \"\\\"c1\\\"\", \"delimiter\": \"\\\"TAB\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
|
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|
+
"id": 2,
|
96
|
+
"uuid": "9698bcde-0729-48fe-b88d-ccfb6f6153b4",
|
97
|
+
"errors": null,
|
98
|
+
"name": "Change Case",
|
99
|
+
"post_job_actions": {},
|
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|
+
"label": "change_case",
|
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|
+
"inputs": [
|
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|
+
{
|
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|
+
"name": "input",
|
104
|
+
"description": "runtime parameter for tool Change Case"
|
105
|
+
}
|
106
|
+
],
|
107
|
+
"position": {
|
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|
+
"top": 200,
|
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|
+
"left": 640
|
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|
+
},
|
111
|
+
"annotation": "",
|
112
|
+
"content_id": "ChangeCase",
|
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|
+
"type": "tool"
|
114
|
+
}
|
115
|
+
},
|
116
|
+
"annotation": "",
|
117
|
+
"a_galaxy_workflow": "true"
|
118
|
+
}
|
@@ -1,66 +1,67 @@
|
|
1
1
|
<!DOCTYPE html>
|
2
2
|
<html>
|
3
3
|
<head>
|
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|
-
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-
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|
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|
-
|
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|
-
}</script>
|
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|
-
|
38
|
-
|
4
|
+
<title>New RO-Crate</title>
|
5
|
+
<script type="application/ld+json">{
|
6
|
+
"@context": "https://w3id.org/ro/crate/1.0/context",
|
7
|
+
"@graph": [
|
8
|
+
{
|
9
|
+
"@id": "ro-crate-metadata.jsonld",
|
10
|
+
"@type": "CreativeWork",
|
11
|
+
"about": {
|
12
|
+
"@id": "./"
|
13
|
+
}
|
14
|
+
},
|
15
|
+
{
|
16
|
+
"@id": "ro-crate-preview.html",
|
17
|
+
"@type": "CreativeWork",
|
18
|
+
"about": {
|
19
|
+
"@id": "./"
|
20
|
+
}
|
21
|
+
},
|
22
|
+
{
|
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>
|
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|
-
|
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
|
-
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
-
|
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
@@ -227,4 +227,28 @@ class ReaderTest < Test::Unit::TestCase
|
|
227
227
|
assert crate.entries['fish/data/binary.jpg']
|
228
228
|
assert_equal ['./', 'fish/', 'ro-crate-metadata.json', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
|
229
229
|
end
|
230
|
+
|
231
|
+
test 'reading preserves any additions to @context' do
|
232
|
+
crate = ROCrate::Reader.read_directory(fixture_file('ro-crate-galaxy-sortchangecase').path)
|
233
|
+
|
234
|
+
context = crate.metadata.context
|
235
|
+
assert_equal [
|
236
|
+
'https://w3id.org/ro/crate/1.1/context',
|
237
|
+
{
|
238
|
+
'TestSuite' => 'https://w3id.org/ro/terms/test#TestSuite',
|
239
|
+
'TestInstance' => 'https://w3id.org/ro/terms/test#TestInstance',
|
240
|
+
'TestService' => 'https://w3id.org/ro/terms/test#TestService',
|
241
|
+
'TestDefinition' => 'https://w3id.org/ro/terms/test#TestDefinition',
|
242
|
+
'PlanemoEngine' => 'https://w3id.org/ro/terms/test#PlanemoEngine',
|
243
|
+
'JenkinsService' => 'https://w3id.org/ro/terms/test#JenkinsService',
|
244
|
+
'TravisService' => 'https://w3id.org/ro/terms/test#TravisService',
|
245
|
+
'GithubService' => 'https://w3id.org/ro/terms/test#GithubService',
|
246
|
+
'instance' => 'https://w3id.org/ro/terms/test#instance',
|
247
|
+
'runsOn' => 'https://w3id.org/ro/terms/test#runsOn',
|
248
|
+
'resource' => 'https://w3id.org/ro/terms/test#resource',
|
249
|
+
'definition' => 'https://w3id.org/ro/terms/test#definition',
|
250
|
+
'engineVersion' => 'https://w3id.org/ro/terms/test#engineVersion'
|
251
|
+
}
|
252
|
+
], context
|
253
|
+
end
|
230
254
|
end
|
data/test/writer_test.rb
CHANGED
@@ -124,12 +124,32 @@ class WriterTest < Test::Unit::TestCase
|
|
124
124
|
actual_files = Dir.chdir(dir) { Dir.glob('**/*') }
|
125
125
|
assert_equal expected_files, actual_files
|
126
126
|
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
127
|
abs_file_path = ::File.join(fixture, file)
|
130
128
|
next if ::File.directory?(abs_file_path)
|
131
129
|
assert_equal ::File.read(abs_file_path), ::File.read(::File.join(dir, file)), "#{file} didn't match"
|
132
130
|
end
|
133
131
|
end
|
134
132
|
end
|
133
|
+
|
134
|
+
test 'reading/writing multiple times does not change the crate' do
|
135
|
+
input_dir = fixture_file('sparse_directory_crate').path
|
136
|
+
Dir.mktmpdir do |dir|
|
137
|
+
3.times do |i|
|
138
|
+
output_dir = ::File.join(dir, "new_directory_#{i}")
|
139
|
+
crate = ROCrate::Reader.read(input_dir)
|
140
|
+
|
141
|
+
ROCrate::Writer.new(crate).write(output_dir)
|
142
|
+
expected_files = Dir.chdir(input_dir) { Dir.glob('**/*') }
|
143
|
+
actual_files = Dir.chdir(output_dir) { Dir.glob('**/*') }
|
144
|
+
assert_equal expected_files, actual_files
|
145
|
+
expected_files.each do |file|
|
146
|
+
abs_file_path = ::File.join(input_dir, file)
|
147
|
+
next if ::File.directory?(abs_file_path)
|
148
|
+
assert_equal ::File.read(abs_file_path), ::File.read(::File.join(output_dir, file)), "#{file} didn't match"
|
149
|
+
end
|
150
|
+
|
151
|
+
input_dir = output_dir
|
152
|
+
end
|
153
|
+
end
|
154
|
+
end
|
135
155
|
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: 0.4.11
|
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: 2021-04-30 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: addressable
|
@@ -72,14 +72,14 @@ dependencies:
|
|
72
72
|
requirements:
|
73
73
|
- - "~>"
|
74
74
|
- !ruby/object:Gem::Version
|
75
|
-
version: 0.
|
75
|
+
version: 0.21.2
|
76
76
|
type: :development
|
77
77
|
prerelease: false
|
78
78
|
version_requirements: !ruby/object:Gem::Requirement
|
79
79
|
requirements:
|
80
80
|
- - "~>"
|
81
81
|
- !ruby/object:Gem::Version
|
82
|
-
version: 0.
|
82
|
+
version: 0.21.2
|
83
83
|
- !ruby/object:Gem::Dependency
|
84
84
|
name: yard
|
85
85
|
requirement: !ruby/object:Gem::Requirement
|
@@ -137,6 +137,7 @@ files:
|
|
137
137
|
- lib/ro_crate/model/organization.rb
|
138
138
|
- lib/ro_crate/model/person.rb
|
139
139
|
- lib/ro_crate/model/preview.rb
|
140
|
+
- lib/ro_crate/model/preview_generator.rb
|
140
141
|
- lib/ro_crate/model/remote_entry.rb
|
141
142
|
- lib/ro_crate/reader.rb
|
142
143
|
- lib/ro_crate/ro-crate-preview.html.erb
|
@@ -166,6 +167,13 @@ files:
|
|
166
167
|
- test/fixtures/file with spaces.txt
|
167
168
|
- test/fixtures/info.txt
|
168
169
|
- test/fixtures/nested_directory.zip
|
170
|
+
- test/fixtures/ro-crate-galaxy-sortchangecase/LICENSE
|
171
|
+
- test/fixtures/ro-crate-galaxy-sortchangecase/README.md
|
172
|
+
- test/fixtures/ro-crate-galaxy-sortchangecase/ro-crate-metadata.json
|
173
|
+
- test/fixtures/ro-crate-galaxy-sortchangecase/sort-and-change-case.ga
|
174
|
+
- test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/input.bed
|
175
|
+
- test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/output_exp.bed
|
176
|
+
- test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/sort-and-change-case-test.yml
|
169
177
|
- test/fixtures/spaces/file with spaces.txt
|
170
178
|
- test/fixtures/spaces/ro-crate-metadata.jsonld
|
171
179
|
- test/fixtures/sparse_directory_crate.zip
|