ro-crate 0.4.1 → 0.4.6
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- checksums.yaml +4 -4
- data/.ruby-version +1 -1
- data/Gemfile.lock +1 -1
- data/README.md +11 -7
- data/lib/ro_crate/json_ld_hash.rb +1 -1
- data/lib/ro_crate/model/contextual_entity.rb +1 -1
- data/lib/ro_crate/model/crate.rb +54 -15
- data/lib/ro_crate/model/data_entity.rb +1 -1
- data/lib/ro_crate/model/directory.rb +39 -11
- data/lib/ro_crate/model/entity.rb +3 -3
- data/lib/ro_crate/model/entry.rb +1 -1
- data/lib/ro_crate/model/file.rb +5 -3
- data/lib/ro_crate/model/remote_entry.rb +1 -1
- data/lib/ro_crate/reader.rb +18 -15
- data/lib/ro_crate/ro-crate-preview.html.erb +3 -3
- data/lib/ro_crate/writer.rb +3 -3
- data/ro_crate.gemspec +2 -2
- data/test/crate_test.rb +95 -0
- data/test/fixtures/directory.zip +0 -0
- data/test/fixtures/directory/.dir/test.txt +1 -0
- data/test/fixtures/directory/.dotfile +1 -0
- data/test/fixtures/directory_crate/ro-crate-metadata.jsonld +7 -0
- data/test/fixtures/directory_crate/ro-crate-preview.html +66 -0
- data/test/fixtures/sparse_directory_crate.zip +0 -0
- data/test/fixtures/sparse_directory_crate/fish/data/binary.jpg +0 -0
- data/test/fixtures/sparse_directory_crate/fish/data/info.txt +1 -0
- data/test/fixtures/sparse_directory_crate/fish/data/nested.txt +1 -0
- data/test/fixtures/sparse_directory_crate/fish/info.txt +1 -0
- data/test/fixtures/sparse_directory_crate/fish/root.txt +1 -0
- data/test/fixtures/sparse_directory_crate/listed_file.txt +1 -0
- data/test/fixtures/sparse_directory_crate/ro-crate-metadata.jsonld +32 -0
- data/test/fixtures/sparse_directory_crate/ro-crate-preview.html +66 -0
- data/test/fixtures/sparse_directory_crate/unlisted_file.txt +1 -0
- data/test/reader_test.rb +36 -2
- data/test/writer_test.rb +33 -0
- metadata +16 -3
checksums.yaml
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metadata.gz:
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data.tar.gz: 77a17a0436f2dea14254a3501f9db349eed5460851d94ab4e87adb7be83e1b38
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metadata.gz: 711a45d7aaa63f8a5a7bba78e433d82875311472d6f4abfd6d388dd8565a7707036152c81de4059fd92da5b7851925caf9d808f39d115752e68eaddbdc85bac1
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data.tar.gz: ce14efaf63e7224adc79cdb11d27bdec933be290ccf60196014cb7ce9380136451265a8f814e1ca7b70286fc32852024d429334bbaab18208d31095cd619dc9e
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data/.ruby-version
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ruby-2.
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ruby-2.6.6
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data/Gemfile.lock
CHANGED
data/README.md
CHANGED
@@ -1,9 +1,9 @@
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# ro-crate-ruby
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This is a WIP gem for creating, manipulating and reading RO
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This is a WIP gem for creating, manipulating and reading RO-Crates (conforming to version 1.1 of the specification).
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* RO
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* RO
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* RO-Crate - https://researchobject.github.io/ro-crate/
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* RO-Crate spec (1.1) - https://researchobject.github.io/ro-crate/1.1/
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## Installation
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@@ -31,13 +31,17 @@ crate = ROCrate::Crate.new
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crate.add_file(File.open('Gemfile')) # Using IO-like objects
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crate.add_file('README.md') # or paths
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# Quickly add everything from a directory into the crate
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crate = ROCrate::Crate.new
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crate.add_all('workspace/secret_project/dataset123')
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# Write to a zip file
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ROCrate::Writer.new(crate).write_zip(File.new('ro_crate.zip', 'w'))
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# Write to a directory
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ROCrate::Writer.new(crate).write('./ro_crate_stuff')
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# Read an RO
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# Read an RO-Crate
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crate = ROCrate::Reader.read('./an_ro_crate_directory')
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# Make some changes
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@@ -55,9 +59,9 @@ ext_file = crate.add_external_file('https://example.com/my_file.txt')
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ROCrate::Writer.new(crate).write('./an_ro_crate_directory')
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```
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### RO
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A simple HTML preview page is generated when an RO
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metadata. This preview is written to `ro-crate-preview.html` at the root of the RO
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### RO-Crate Preview
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A simple HTML preview page is generated when an RO-Crate is written, containing a list of the crate's contents and some
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metadata. This preview is written to `ro-crate-preview.html` at the root of the RO-Crate.
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The default template can be seen here [here](lib/ro_crate/ro-crate-preview.html.erb).
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module ROCrate
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##
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# A wrapper class for Hash that adds methods to dereference Entities within an RO
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# A wrapper class for Hash that adds methods to dereference Entities within an RO-Crate.
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class JSONLDHash < ::Hash
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def initialize(graph, content = {})
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@graph = graph
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module ROCrate
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##
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# A class to represent a "Contextual Entity" within an RO
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# A class to represent a "Contextual Entity" within an RO-Crate.
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# Contextual Entities are used to describe and provide context to the Data Entities within the crate.
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class ContextualEntity < Entity
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def self.format_id(id)
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data/lib/ro_crate/model/crate.rb
CHANGED
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module ROCrate
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##
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# A Ruby abstraction of an RO
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# A Ruby abstraction of an RO-Crate.
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class Crate < Directory
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IDENTIFIER = './'.freeze
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attr_reader :data_entities
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end
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##
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# Initialize an empty RO
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# Initialize an empty RO-Crate.
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def initialize(id = IDENTIFIER, properties = {})
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@data_entities = []
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@contextual_entities = []
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@@ -24,7 +24,7 @@ module ROCrate
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# Create a new file and add it to the crate.
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#
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# @param source [String, Pathname, ::File, #read, nil] The source on the disk where this file will be read.
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# @param crate_path [String] The relative path within the RO
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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 entity_class [Class] The class to use to instantiate the Entity,
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# useful if you have created a subclass of ROCrate::File that you want to use. (defaults to ROCrate::File).
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# @param properties [Hash{String => Object}] A hash of JSON-LD properties to associate with this file.
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@@ -51,7 +51,7 @@ module ROCrate
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# Create a new directory and add it to the crate.
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#
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# @param source_directory [String, Pathname, ::File, #read, nil] The source directory that will be included in the crate.
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# @param crate_path [String] The relative path within the RO
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# @param crate_path [String] The relative path within the RO-Crate where this directory will be written.
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# @param entity_class [Class] The class to use to instantiate the Entity,
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# useful if you have created a subclass of ROCrate::Directory that you want to use. (defaults to ROCrate::Directory).
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# @param properties [Hash{String => Object}] A hash of JSON-LD properties to associate with this directory.
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@@ -61,6 +61,35 @@ module ROCrate
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entity_class.new(self, source_directory, crate_path, properties).tap { |e| add_data_entity(e) }
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end
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##
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# Recursively add the contents of the given source directory at the root of the crate.
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# Useful for quickly RO-Crate-ifying a directory.
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# Creates data entities for each file/directory discovered (excluding the top level directory itself) if `create_entities` is true.
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#
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# @param source_directory [String, Pathname, ::File,] The source directory that will be included in the crate.
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# @param create_entities [Boolean] Whether to create data entities for the added content, or just include them anonymously.
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# @param include_hidden [Boolean] Whether to include hidden files, i.e. those prefixed by a `.` (period).
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#
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# @return [Array<DataEntity>] Any entities that were created from the directory contents. Will be empty if `create_entities` was false.
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def add_all(source_directory, create_entities = true, include_hidden: false)
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added = []
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if create_entities
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list_all_files(source_directory, include_hidden: include_hidden).each do |rel_path|
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source_path = Pathname.new(::File.join(source_directory, rel_path)).expand_path
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if source_path.directory?
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added << add_directory(source_path, rel_path)
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else
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added << add_file(source_path, rel_path)
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end
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end
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else
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populate_entries(Pathname.new(::File.expand_path(source_directory)), include_hidden: include_hidden)
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end
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added
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end
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##
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# Create a new ROCrate::Person and add it to the crate
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#
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end
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##
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# The RO
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# The RO-Crate metadata file
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#
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# @return [Metadata]
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def metadata
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end
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##
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# The RO
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# The RO-Crate preview file
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#
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# @return [Preview]
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def preview
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@@ -143,7 +172,7 @@ module ROCrate
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end
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##
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# Entities for the metadata file and crate itself, which should be present in all RO
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# Entities for the metadata file and crate itself, which should be present in all RO-Crates.
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#
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# @return [Array<Entity>]
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def default_entities
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entity.class.new(crate, entity.id, entity.raw_properties)
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end
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alias_method :own_entries, :entries
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##
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#
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# and the value is an Entry where the source data can be read.
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# # The RO-Crate's "payload" of the crate - a map of all the files/directories contained in the RO-Crate, where the
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# key is the destination path within the crate and the value is an Entry where the source data can be read.
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#
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# @return [Hash{String => Entry}>]
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def entries
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entries
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-
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-
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-
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# Gather a map of entries, starting from the crate itself, then any directory data entities, then finally any
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# file data entities. This ensures in the case of a conflict, the more "specific" data entities take priority.
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entries = own_entries
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non_self_entities = default_entities.reject { |e| e == self }
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sorted_entities = (non_self_entities | data_entities).sort_by { |e| e.is_a?(ROCrate::Directory) ? 0 : 1 }
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sorted_entities.each do |entity|
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entity.entries.each do |path, entry|
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entries[path] = entry
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end
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end
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@@ -207,5 +240,11 @@ module ROCrate
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def get_binding
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binding
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end
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private
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def full_entry_path(relative_path)
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relative_path
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end
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end
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end
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module ROCrate
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##
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# A class to represent a "Data Entity" within an RO
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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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def self.format_id(id)
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# Create a new Directory. PLEASE NOTE, the new directory will not be added to the crate. To do this, call
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# Crate#add_data_entity, or just use Crate#add_directory.
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#
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# @param crate [Crate] The RO
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# @param crate [Crate] The RO-Crate that owns this directory.
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# @param source_directory [String, Pathname, ::File, nil] The source directory that will be included in the crate.
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# @param crate_path [String] The relative path within the RO
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# @param crate_path [String] The relative path within the RO-Crate where this directory will be written.
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# @param properties [Hash{String => Object}] A hash of JSON-LD properties to associate with this directory.
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def initialize(crate, source_directory = nil, crate_path = nil, properties = {})
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@directory_entries = {}
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if source_directory
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raise 'Not a directory' unless ::File.directory?(source_directory)
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source_directory = Pathname.new(::File.expand_path(source_directory))
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@entry = Entry.new(source_directory)
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populate_entries(source_directory)
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crate_path = source_directory.basename.to_s if crate_path.nil?
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-
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Dir.chdir(source_directory) { Dir.glob('**/*') }.each do |rel_path|
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source_path = Pathname.new(::File.join(source_directory, rel_path)).expand_path
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@directory_entries[rel_path] = Entry.new(source_path)
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-
end
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end
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super(crate, crate_path, properties)
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end
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##
|
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-
#
|
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# and the value is an Entry where the source data can be read.
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# The "payload" of this directory - a map of all the files/directories, where the key is the destination path
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# within the crate and the value is an Entry where the source data can be read.
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#
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# @return [Hash{String => Entry}>]
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def entries
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entries = {}
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entries[filepath.chomp('/')] = @entry if @entry
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@directory_entries.each do |rel_path, entry|
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-
entries[
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entries[full_entry_path(rel_path)] = entry
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end
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entries
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@@ -50,6 +47,37 @@ module ROCrate
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private
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##
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# Populate this directory with files/directories from a given source directory on disk.
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#
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# @param source_directory [Pathname] The source directory to populate from.
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# @param include_hidden [Boolean] Whether to include hidden files, i.e. those prefixed by a `.` (period).
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#
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# @return [Hash{String => Entry}>] The files/directories that were populated.
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# The key is the relative path of the file/directory, and the value is an Entry object where data can be read etc.
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def populate_entries(source_directory, include_hidden: false)
|
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raise 'Not a directory' unless ::File.directory?(source_directory)
|
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@directory_entries = {}
|
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list_all_files(source_directory, include_hidden: include_hidden).each do |rel_path|
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source_path = Pathname.new(::File.join(source_directory, rel_path)).expand_path
|
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@directory_entries[rel_path] = Entry.new(source_path)
|
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end
|
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+
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@directory_entries
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end
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def full_entry_path(relative_path)
|
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::File.join(filepath, relative_path)
|
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end
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def list_all_files(source_directory, include_hidden: false)
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args = ['**/*']
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args << ::File::FNM_DOTMATCH if include_hidden
|
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Dir.chdir(source_directory) { Dir.glob(*args) }.reject do |path|
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path == '.' || path == '..' || path.end_with?('/.')
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end
|
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end
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def default_properties
|
54
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|
super.merge(
|
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'@id' => "#{SecureRandom.uuid}/",
|
@@ -1,7 +1,7 @@
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1
1
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module ROCrate
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2
2
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##
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3
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-
# A generic "Entity" within an RO
|
4
|
-
# RO
|
3
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+
# A generic "Entity" within an RO-Crate. It has an identifier and a set of properties, and will be referenced in the
|
4
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+
# RO-Crate Metadata's @graph.
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5
5
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class Entity
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6
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attr_reader :crate
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attr_reader :properties
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@@ -60,7 +60,7 @@ module ROCrate
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##
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# Automatically replace an Entity or Array of Entities with a reference or Array of references. Also associates
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# the Entity/Entities with the current crate. This is useful for maintaining the flat @graph of entities that the
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-
# RO
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63
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+
# RO-Crate metadata file requires.
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#
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# @param value [Entity, Array<Entity>, Object] A value that may be reference or array of references.
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# @return [Hash, Array<Hash>, Object] Return a reference, Array of references, or just the object itself if
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data/lib/ro_crate/model/entry.rb
CHANGED
data/lib/ro_crate/model/file.rb
CHANGED
@@ -8,9 +8,9 @@ module ROCrate
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8
8
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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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9
9
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# Crate#add_data_entity, or just use Crate#add_file.
|
10
10
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#
|
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-
# @param crate [Crate] The RO
|
11
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+
# @param crate [Crate] The RO-Crate that owns this file.
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12
12
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# @param source [String, Pathname, ::File, #read, URI, nil] The source on the disk (or on the internet if a URI) where this file will be read.
|
13
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-
# @param crate_path [String] The relative path within the RO
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13
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+
# @param crate_path [String] The relative path within the RO-Crate where this file will be written.
|
14
14
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# @param properties [Hash{String => Object}] A hash of JSON-LD properties to associate with this file.
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15
15
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def initialize(crate, source, crate_path = nil, properties = {})
|
16
16
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if crate_path.is_a?(Hash) && properties.empty?
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@@ -52,7 +52,9 @@ module ROCrate
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52
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end
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53
53
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##
|
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-
# A map
|
55
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+
# The "payload". A map with a single key and value, of the relative filepath within the crate, to the source on disk
|
56
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+
# where the actual bytes of the file can be read. Blank if remote.
|
57
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+
#
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# (for compatibility with Directory#entries)
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57
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#
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# @return [Hash{String => Entry}>] The key is the location within the crate, and the value is an Entry.
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@@ -1,6 +1,6 @@
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1
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module ROCrate
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2
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##
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-
# A class to represent a reference within an RO
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# A class to represent a reference within an RO-Crate, to a remote file held on the internet somewhere.
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# It handles the actual reading/writing of bytes.
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class RemoteEntry
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attr_reader :uri
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data/lib/ro_crate/reader.rb
CHANGED
@@ -1,13 +1,13 @@
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1
1
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module ROCrate
|
2
2
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##
|
3
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-
# A class to handle reading of RO
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# A class to handle reading of RO-Crates from Zip files or directories.
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4
4
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class Reader
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5
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##
|
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-
# Reads an RO
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+
# Reads an RO-Crate from a directory of zip file.
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7
7
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#
|
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8
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# @param source [String, ::File, Pathname] The source location for the crate.
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9
9
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# @param target_dir [String, ::File, Pathname] The target directory where the crate should be unzipped (if its a Zip file).
|
10
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-
# @return [Crate] The RO
|
10
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+
# @return [Crate] The RO-Crate.
|
11
11
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def self.read(source, target_dir: Dir.mktmpdir)
|
12
12
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raise "Not a directory!" unless ::File.directory?(target_dir)
|
13
13
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if ::File.directory?(source)
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@@ -37,12 +37,12 @@ module ROCrate
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|
37
37
|
end
|
38
38
|
|
39
39
|
##
|
40
|
-
# Reads an RO
|
40
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+
# Reads an RO-Crate from a zip file. It first extracts the Zip file to a temporary directory, and then calls
|
41
41
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# #read_directory.
|
42
42
|
#
|
43
43
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# @param source [String, ::File, Pathname] The location of the zip file.
|
44
44
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# @param target_dir [String, ::File, Pathname] The target directory where the crate should be unzipped.
|
45
|
-
# @return [Crate] The RO
|
45
|
+
# @return [Crate] The RO-Crate.
|
46
46
|
def self.read_zip(source, target_dir: Dir.mktmpdir)
|
47
47
|
unzip_to(source, target_dir)
|
48
48
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|
@@ -50,10 +50,10 @@ module ROCrate
|
|
50
50
|
end
|
51
51
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|
52
52
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##
|
53
|
-
# Reads an RO
|
53
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+
# Reads an RO-Crate from a directory.
|
54
54
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#
|
55
55
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# @param source [String, ::File, Pathname] The location of the directory.
|
56
|
-
# @return [Crate] The RO
|
56
|
+
# @return [Crate] The RO-Crate.
|
57
57
|
def self.read_directory(source)
|
58
58
|
source = ::File.expand_path(source)
|
59
59
|
metadata_file = Dir.entries(source).detect { |entry| entry == ROCrate::Metadata::IDENTIFIER ||
|
@@ -68,7 +68,7 @@ module ROCrate
|
|
68
68
|
end
|
69
69
|
|
70
70
|
##
|
71
|
-
# Extracts all the entities from the @graph of the RO
|
71
|
+
# Extracts all the entities from the @graph of the RO-Crate Metadata.
|
72
72
|
#
|
73
73
|
# @param metadata_json [String] A string containing the metadata JSON.
|
74
74
|
# @return [Hash{String => Hash}] A Hash of all the entities, mapped by their @id.
|
@@ -99,12 +99,15 @@ module ROCrate
|
|
99
99
|
# Create a crate from the given set of entities.
|
100
100
|
#
|
101
101
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# @param entity_hash [Hash{String => Hash}] A Hash containing all the entities in the @graph, mapped by their @id.
|
102
|
-
# @param source [String, ::File, Pathname] The location of the RO
|
103
|
-
# @return [Crate] The RO
|
102
|
+
# @param source [String, ::File, Pathname] The location of the RO-Crate being read.
|
103
|
+
# @return [Crate] The RO-Crate.
|
104
104
|
def self.build_crate(entity_hash, source)
|
105
105
|
ROCrate::Crate.new.tap do |crate|
|
106
106
|
crate.properties = entity_hash.delete(ROCrate::Crate::IDENTIFIER)
|
107
107
|
crate.metadata.properties = entity_hash.delete(ROCrate::Metadata::IDENTIFIER)
|
108
|
+
preview_properties = entity_hash.delete(ROCrate::Preview::IDENTIFIER)
|
109
|
+
crate.preview.properties = preview_properties if preview_properties
|
110
|
+
crate.add_all(source, false)
|
108
111
|
extract_data_entities(crate, source, entity_hash).each do |entity|
|
109
112
|
crate.add_data_entity(entity)
|
110
113
|
end
|
@@ -118,8 +121,8 @@ module ROCrate
|
|
118
121
|
##
|
119
122
|
# Discover data entities from the `hasPart` property of a crate, and create DataEntity objects for them.
|
120
123
|
# Entities are looked up in the given `entity_hash` (and then removed from it).
|
121
|
-
# @param crate [Crate] The RO
|
122
|
-
# @param source [String, ::File, Pathname] The location of the RO
|
124
|
+
# @param crate [Crate] The RO-Crate being read.
|
125
|
+
# @param source [String, ::File, Pathname] The location of the RO-Crate being read.
|
123
126
|
# @param entity_hash [Hash] A Hash containing all the entities in the @graph, mapped by their @id.
|
124
127
|
# @return [Array<ROCrate::File, ROCrate::Directory>] The extracted DataEntity objects.
|
125
128
|
def self.extract_data_entities(crate, source, entity_hash)
|
@@ -135,7 +138,7 @@ module ROCrate
|
|
135
138
|
|
136
139
|
##
|
137
140
|
# Create appropriately specialized ContextualEntity objects from the given hash of entities and their properties.
|
138
|
-
# @param crate [Crate] The RO
|
141
|
+
# @param crate [Crate] The RO-Crate being read.
|
139
142
|
# @param entity_hash [Hash] A Hash containing all the entities in the @graph, mapped by their @id.
|
140
143
|
# @return [Array<ContextualEntity>] The extracted ContextualEntity objects.
|
141
144
|
def self.extract_contextual_entities(crate, entity_hash)
|
@@ -152,8 +155,8 @@ module ROCrate
|
|
152
155
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|
153
156
|
##
|
154
157
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# Create a DataEntity of the given class.
|
155
|
-
# @param crate [Crate] The RO
|
156
|
-
# @param source [String, ::File, Pathname] The location of the RO
|
158
|
+
# @param crate [Crate] The RO-Crate being read.
|
159
|
+
# @param source [String, ::File, Pathname] The location of the RO-Crate being read.
|
157
160
|
# @param entity_props [Hash] A Hash containing the entity's properties, including its @id.
|
158
161
|
# @return [ROCrate::File, ROCrate::Directory, nil] The DataEntity object,
|
159
162
|
# or nil if it referenced a local file that wasn't found.
|
@@ -1,13 +1,13 @@
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1
1
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<!DOCTYPE html>
|
2
2
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<html>
|
3
3
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<head>
|
4
|
-
<title><%= name || "New RO
|
4
|
+
<title><%= name || "New RO-Crate" %></title>
|
5
5
|
<script type="application/ld+json"><%= metadata.generate %></script>
|
6
6
|
<meta name="generator" content="https://github.com/fbacall/ro-crate-ruby">
|
7
|
-
<meta name="keywords" content="RO
|
7
|
+
<meta name="keywords" content="RO-Crate">
|
8
8
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</head>
|
9
9
|
<body>
|
10
|
-
<h1><%= name || "New RO
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10
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+
<h1><%= name || "New RO-Crate" %></h1>
|
11
11
|
<% if url %>
|
12
12
|
<a href="<%= url %>" target="_blank"><%= url %></a>
|
13
13
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<% end %>
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data/lib/ro_crate/writer.rb
CHANGED
@@ -1,10 +1,10 @@
|
|
1
1
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module ROCrate
|
2
2
|
##
|
3
|
-
# A class to handle writing of RO
|
3
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+
# A class to handle writing of RO-Crates to Zip files or directories.
|
4
4
|
class Writer
|
5
5
|
##
|
6
6
|
# Initialize a new Writer for the given Crate.
|
7
|
-
# @param crate [Crate] The RO
|
7
|
+
# @param crate [Crate] The RO-Crate to be written.
|
8
8
|
def initialize(crate)
|
9
9
|
@crate = crate
|
10
10
|
end
|
@@ -35,7 +35,7 @@ module ROCrate
|
|
35
35
|
##
|
36
36
|
# Write the crate to a zip file.
|
37
37
|
#
|
38
|
-
# @param destination [String, ::File] The destination where to write the RO
|
38
|
+
# @param destination [String, ::File] The destination where to write the RO-Crate zip.
|
39
39
|
def write_zip(destination)
|
40
40
|
Zip::File.open(destination, Zip::File::CREATE) do |zip|
|
41
41
|
@crate.entries.each do |path, entry|
|
data/ro_crate.gemspec
CHANGED
@@ -1,7 +1,7 @@
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|
1
1
|
Gem::Specification.new do |s|
|
2
2
|
s.name = 'ro-crate'
|
3
|
-
s.version = '0.4.
|
4
|
-
s.summary = 'Create, manipulate, read RO
|
3
|
+
s.version = '0.4.6'
|
4
|
+
s.summary = 'Create, manipulate, read RO-Crates.'
|
5
5
|
s.authors = ['Finn Bacall']
|
6
6
|
s.email = 'finn.bacall@manchester.ac.uk'
|
7
7
|
s.files = `git ls-files`.split("\n")
|
data/test/crate_test.rb
CHANGED
@@ -198,4 +198,99 @@ class CrateTest < Test::Unit::TestCase
|
|
198
198
|
assert_equal file, new_crate.get('some/file.txt')
|
199
199
|
assert_equal file, new_crate.get('http://mycoolwebsite.golf/ro_crate/some/file.txt')
|
200
200
|
end
|
201
|
+
|
202
|
+
test 'can add an entire directory tree as data entities' do
|
203
|
+
crate = ROCrate::Crate.new
|
204
|
+
entities = crate.add_all(fixture_file('directory').path, include_hidden: true)
|
205
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+
|
206
|
+
paths = crate.entries.keys
|
207
|
+
assert_equal 11, paths.length
|
208
|
+
assert_includes paths, 'data'
|
209
|
+
assert_includes paths, 'root.txt'
|
210
|
+
assert_includes paths, 'info.txt'
|
211
|
+
assert_includes paths, 'data/binary.jpg'
|
212
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+
assert_includes paths, 'data/info.txt'
|
213
|
+
assert_includes paths, 'data/nested.txt'
|
214
|
+
assert_includes paths, '.dotfile'
|
215
|
+
assert_includes paths, '.dir'
|
216
|
+
assert_includes paths, '.dir/test.txt'
|
217
|
+
assert_includes paths, 'ro-crate-metadata.json'
|
218
|
+
assert_includes paths, 'ro-crate-preview.html'
|
219
|
+
|
220
|
+
assert_equal 9, entities.length
|
221
|
+
assert_equal 'ROCrate::Directory', crate.dereference('data/').class.name
|
222
|
+
assert_equal 'ROCrate::File', crate.dereference('root.txt').class.name
|
223
|
+
assert_equal 'ROCrate::File', crate.dereference('info.txt').class.name
|
224
|
+
assert_equal 'ROCrate::File', crate.dereference('data/binary.jpg').class.name
|
225
|
+
assert_equal 'ROCrate::File', crate.dereference('data/info.txt').class.name
|
226
|
+
assert_equal 'ROCrate::File', crate.dereference('data/nested.txt').class.name
|
227
|
+
assert_equal 'ROCrate::File', crate.dereference('.dotfile').class.name
|
228
|
+
assert_equal 'ROCrate::Directory', crate.dereference('.dir/').class.name
|
229
|
+
assert_equal 'ROCrate::File', crate.dereference('.dir/test.txt').class.name
|
230
|
+
|
231
|
+
assert_equal "5678\n", crate.dereference('data/info.txt').source.read
|
232
|
+
assert_equal "Am I included?\n", crate.dereference('.dotfile').source.read
|
233
|
+
end
|
234
|
+
|
235
|
+
test 'can create an RO-Crate using content from a given directory' do
|
236
|
+
crate = ROCrate::Crate.new
|
237
|
+
entities = crate.add_all(fixture_file('directory').path, false, include_hidden: true)
|
238
|
+
|
239
|
+
assert_empty entities
|
240
|
+
|
241
|
+
paths = crate.entries.keys
|
242
|
+
assert_equal 11, paths.length
|
243
|
+
assert_includes paths, 'data'
|
244
|
+
assert_includes paths, 'root.txt'
|
245
|
+
assert_includes paths, 'info.txt'
|
246
|
+
assert_includes paths, 'data/binary.jpg'
|
247
|
+
assert_includes paths, 'data/info.txt'
|
248
|
+
assert_includes paths, 'data/nested.txt'
|
249
|
+
assert_includes paths, '.dotfile'
|
250
|
+
assert_includes paths, '.dir'
|
251
|
+
assert_includes paths, '.dir/test.txt'
|
252
|
+
assert_includes paths, 'ro-crate-metadata.json'
|
253
|
+
assert_includes paths, 'ro-crate-preview.html'
|
254
|
+
|
255
|
+
# Should not create any data entities
|
256
|
+
assert_nil crate.dereference('data/')
|
257
|
+
assert_nil crate.dereference('root.txt')
|
258
|
+
assert_nil crate.dereference('info.txt')
|
259
|
+
assert_nil crate.dereference('data/binary.jpg')
|
260
|
+
assert_nil crate.dereference('data/info.txt')
|
261
|
+
assert_nil crate.dereference('data/nested.txt')
|
262
|
+
assert_nil crate.dereference('.dotfile')
|
263
|
+
end
|
264
|
+
|
265
|
+
test 'can create an RO-Crate using content from a given directory, excluding hidden files' do
|
266
|
+
crate = ROCrate::Crate.new
|
267
|
+
entities = crate.add_all(fixture_file('directory').path)
|
268
|
+
|
269
|
+
paths = crate.entries.keys
|
270
|
+
assert_equal 8, paths.length
|
271
|
+
assert_includes paths, 'data'
|
272
|
+
assert_includes paths, 'root.txt'
|
273
|
+
assert_includes paths, 'info.txt'
|
274
|
+
assert_includes paths, 'data/binary.jpg'
|
275
|
+
assert_includes paths, 'data/info.txt'
|
276
|
+
assert_includes paths, 'data/nested.txt'
|
277
|
+
assert_not_includes paths, '.dotfile'
|
278
|
+
assert_not_includes paths, '.dir'
|
279
|
+
assert_not_includes paths, '.dir/test.txt'
|
280
|
+
assert_includes paths, 'ro-crate-metadata.json'
|
281
|
+
assert_includes paths, 'ro-crate-preview.html'
|
282
|
+
|
283
|
+
assert_equal 6, entities.length
|
284
|
+
assert_equal 'ROCrate::Directory', crate.dereference('data/').class.name
|
285
|
+
assert_equal 'ROCrate::File', crate.dereference('root.txt').class.name
|
286
|
+
assert_equal 'ROCrate::File', crate.dereference('info.txt').class.name
|
287
|
+
assert_equal 'ROCrate::File', crate.dereference('data/binary.jpg').class.name
|
288
|
+
assert_equal 'ROCrate::File', crate.dereference('data/info.txt').class.name
|
289
|
+
assert_equal 'ROCrate::File', crate.dereference('data/nested.txt').class.name
|
290
|
+
assert_nil crate.dereference('.dotfile')
|
291
|
+
assert_nil crate.dereference('.dir/')
|
292
|
+
assert_nil crate.dereference('.dir/test.txt')
|
293
|
+
|
294
|
+
assert_equal "5678\n", crate.dereference('data/info.txt').source.read
|
295
|
+
end
|
201
296
|
end
|
data/test/fixtures/directory.zip
CHANGED
Binary file
|
@@ -0,0 +1 @@
|
|
1
|
+
123
|
@@ -0,0 +1 @@
|
|
1
|
+
Am I included?
|
@@ -0,0 +1,66 @@
|
|
1
|
+
<!DOCTYPE html>
|
2
|
+
<html>
|
3
|
+
<head>
|
4
|
+
<title>New RO-Crate</title>
|
5
|
+
<script type="application/ld+json">{
|
6
|
+
"@context": "https://w3id.org/ro/crate/1.1/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": "fish/"
|
28
|
+
}
|
29
|
+
]
|
30
|
+
},
|
31
|
+
{
|
32
|
+
"@id": "fish/",
|
33
|
+
"@type": "Dataset"
|
34
|
+
}
|
35
|
+
]
|
36
|
+
}</script>
|
37
|
+
<meta name="generator" content="https://github.com/fbacall/ro-crate-ruby">
|
38
|
+
<meta name="keywords" content="RO-Crate">
|
39
|
+
</head>
|
40
|
+
<body>
|
41
|
+
<h1>New RO-Crate</h1>
|
42
|
+
|
43
|
+
<p>
|
44
|
+
|
45
|
+
</p>
|
46
|
+
<dl>
|
47
|
+
|
48
|
+
|
49
|
+
|
50
|
+
|
51
|
+
</dl>
|
52
|
+
|
53
|
+
<h2>Contents</h2>
|
54
|
+
<ul>
|
55
|
+
|
56
|
+
<li id="__data_entity_fish/">
|
57
|
+
|
58
|
+
<strong>fish/</strong>
|
59
|
+
|
60
|
+
|
61
|
+
|
62
|
+
</li>
|
63
|
+
|
64
|
+
</ul>
|
65
|
+
</body>
|
66
|
+
</html>
|
Binary file
|
Binary file
|
@@ -0,0 +1 @@
|
|
1
|
+
5678
|
@@ -0,0 +1 @@
|
|
1
|
+
I'm nested
|
@@ -0,0 +1 @@
|
|
1
|
+
1234
|
@@ -0,0 +1 @@
|
|
1
|
+
I'm at the root
|
@@ -0,0 +1 @@
|
|
1
|
+
123
|
@@ -0,0 +1,32 @@
|
|
1
|
+
{
|
2
|
+
"@context": "https://w3id.org/ro/crate/1.0/context",
|
3
|
+
"@graph": [
|
4
|
+
{
|
5
|
+
"@id": "ro-crate-metadata.jsonld",
|
6
|
+
"@type": "CreativeWork",
|
7
|
+
"about": {
|
8
|
+
"@id": "./"
|
9
|
+
}
|
10
|
+
},
|
11
|
+
{
|
12
|
+
"@id": "ro-crate-preview.html",
|
13
|
+
"@type": "CreativeWork",
|
14
|
+
"about": {
|
15
|
+
"@id": "./"
|
16
|
+
}
|
17
|
+
},
|
18
|
+
{
|
19
|
+
"@id": "./",
|
20
|
+
"@type": "Dataset",
|
21
|
+
"hasPart": [
|
22
|
+
{
|
23
|
+
"@id": "listed_file.txt"
|
24
|
+
}
|
25
|
+
]
|
26
|
+
},
|
27
|
+
{
|
28
|
+
"@id": "listed_file.txt",
|
29
|
+
"@type": "File"
|
30
|
+
}
|
31
|
+
]
|
32
|
+
}
|
@@ -0,0 +1,66 @@
|
|
1
|
+
<!DOCTYPE html>
|
2
|
+
<html>
|
3
|
+
<head>
|
4
|
+
<title>New RO-Crate</title>
|
5
|
+
<script type="application/ld+json">{
|
6
|
+
"@context": "https://w3id.org/ro/crate/1.1/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": "fish/"
|
28
|
+
}
|
29
|
+
]
|
30
|
+
},
|
31
|
+
{
|
32
|
+
"@id": "fish/",
|
33
|
+
"@type": "Dataset"
|
34
|
+
}
|
35
|
+
]
|
36
|
+
}</script>
|
37
|
+
<meta name="generator" content="https://github.com/fbacall/ro-crate-ruby">
|
38
|
+
<meta name="keywords" content="RO-Crate">
|
39
|
+
</head>
|
40
|
+
<body>
|
41
|
+
<h1>New RO-Crate</h1>
|
42
|
+
|
43
|
+
<p>
|
44
|
+
|
45
|
+
</p>
|
46
|
+
<dl>
|
47
|
+
|
48
|
+
|
49
|
+
|
50
|
+
|
51
|
+
</dl>
|
52
|
+
|
53
|
+
<h2>Contents</h2>
|
54
|
+
<ul>
|
55
|
+
|
56
|
+
<li id="__data_entity_fish/">
|
57
|
+
|
58
|
+
<strong>fish/</strong>
|
59
|
+
|
60
|
+
|
61
|
+
|
62
|
+
</li>
|
63
|
+
|
64
|
+
</ul>
|
65
|
+
</body>
|
66
|
+
</html>
|
@@ -0,0 +1 @@
|
|
1
|
+
456
|
data/test/reader_test.rb
CHANGED
@@ -109,11 +109,13 @@ class ReaderTest < Test::Unit::TestCase
|
|
109
109
|
test 'reading from directory with directories' do
|
110
110
|
crate = ROCrate::Reader.read_directory(fixture_file('directory_crate').path)
|
111
111
|
|
112
|
+
assert crate.entries.values.all? { |e| e.is_a?(ROCrate::Entry) }
|
112
113
|
assert crate.entries['fish/info.txt']
|
113
114
|
assert_equal '1234', crate.entries['fish/info.txt'].source.read.chomp
|
114
|
-
|
115
|
+
refute crate.entries['fish/root.txt'].directory?
|
116
|
+
assert crate.entries['fish/data'].directory?
|
115
117
|
assert crate.entries['fish/data/info.txt']
|
116
|
-
|
118
|
+
refute crate.entries['fish/data/nested.txt'].remote?
|
117
119
|
assert crate.entries['fish/data/binary.jpg']
|
118
120
|
assert_equal ['./', 'fish/', 'ro-crate-metadata.jsonld', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
|
119
121
|
end
|
@@ -161,4 +163,36 @@ class ReaderTest < Test::Unit::TestCase
|
|
161
163
|
assert_equal 'http://example.com/external_ref.txt', ext_file.id
|
162
164
|
assert_equal 'file contents', ext_file.source.read
|
163
165
|
end
|
166
|
+
|
167
|
+
test 'reading from directory with unlisted files' do
|
168
|
+
crate = ROCrate::Reader.read_directory(fixture_file('sparse_directory_crate').path)
|
169
|
+
|
170
|
+
assert_equal 11, crate.entries.count
|
171
|
+
assert crate.entries['listed_file.txt']
|
172
|
+
assert crate.entries['unlisted_file.txt']
|
173
|
+
assert crate.entries['fish']
|
174
|
+
assert_equal '1234', crate.entries['fish/info.txt'].source.read.chomp
|
175
|
+
refute crate.entries['fish/root.txt'].directory?
|
176
|
+
assert crate.entries['fish/data'].directory?
|
177
|
+
assert crate.entries['fish/data/info.txt']
|
178
|
+
refute crate.entries['fish/data/nested.txt'].remote?
|
179
|
+
assert crate.entries['fish/data/binary.jpg']
|
180
|
+
assert_equal ['./', 'listed_file.txt', 'ro-crate-metadata.jsonld', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
|
181
|
+
end
|
182
|
+
|
183
|
+
test 'reading from a zip with unlisted files' do
|
184
|
+
crate = ROCrate::Reader.read_zip(fixture_file('sparse_directory_crate.zip').path)
|
185
|
+
|
186
|
+
assert_equal 11, crate.entries.count
|
187
|
+
assert crate.entries['listed_file.txt']
|
188
|
+
assert crate.entries['unlisted_file.txt']
|
189
|
+
assert crate.entries['fish']
|
190
|
+
assert_equal '1234', crate.entries['fish/info.txt'].source.read.chomp
|
191
|
+
refute crate.entries['fish/root.txt'].directory?
|
192
|
+
assert crate.entries['fish/data'].directory?
|
193
|
+
assert crate.entries['fish/data/info.txt']
|
194
|
+
refute crate.entries['fish/data/nested.txt'].remote?
|
195
|
+
assert crate.entries['fish/data/binary.jpg']
|
196
|
+
assert_equal ['./', 'listed_file.txt', 'ro-crate-metadata.jsonld', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
|
197
|
+
end
|
164
198
|
end
|
data/test/writer_test.rb
CHANGED
@@ -99,4 +99,37 @@ class WriterTest < Test::Unit::TestCase
|
|
99
99
|
end
|
100
100
|
end
|
101
101
|
end
|
102
|
+
|
103
|
+
test 'should write out same contents that it was created with' do
|
104
|
+
crate = ROCrate::Crate.new
|
105
|
+
crate.add_all(fixture_file('directory').path, false)
|
106
|
+
|
107
|
+
Dir.mktmpdir do |dir|
|
108
|
+
ROCrate::Writer.new(crate).write(dir)
|
109
|
+
assert ::File.exist?(::File.join(dir, ROCrate::Metadata::IDENTIFIER))
|
110
|
+
assert ::File.exist?(::File.join(dir, ROCrate::Preview::IDENTIFIER))
|
111
|
+
assert_equal 5, ::File.size(::File.join(dir, 'info.txt'))
|
112
|
+
assert_equal 2529, ::File.size(::File.join(dir, 'data', 'binary.jpg'))
|
113
|
+
end
|
114
|
+
end
|
115
|
+
|
116
|
+
test 'reading and writing out a directory crate produces an identical crate' do
|
117
|
+
fixture = fixture_file('sparse_directory_crate').path
|
118
|
+
Dir.mktmpdir do |dir|
|
119
|
+
dir = ::File.join(dir, 'new_directory')
|
120
|
+
crate = ROCrate::Reader.read(fixture)
|
121
|
+
|
122
|
+
ROCrate::Writer.new(crate).write(dir)
|
123
|
+
expected_files = Dir.chdir(fixture) { Dir.glob('**/*') }
|
124
|
+
actual_files = Dir.chdir(dir) { Dir.glob('**/*') }
|
125
|
+
assert_equal expected_files, actual_files
|
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
|
+
abs_file_path = ::File.join(fixture, file)
|
130
|
+
next if ::File.directory?(abs_file_path)
|
131
|
+
assert_equal ::File.read(abs_file_path), ::File.read(::File.join(dir, file)), "#{file} didn't match"
|
132
|
+
end
|
133
|
+
end
|
134
|
+
end
|
102
135
|
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: 0.4.6
|
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: 2021-02-25 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: addressable
|
@@ -149,6 +149,8 @@ files:
|
|
149
149
|
- test/fixtures/crate-spec1.1/ro-crate-metadata.json
|
150
150
|
- test/fixtures/data.csv
|
151
151
|
- test/fixtures/directory.zip
|
152
|
+
- test/fixtures/directory/.dir/test.txt
|
153
|
+
- test/fixtures/directory/.dotfile
|
152
154
|
- test/fixtures/directory/data/binary.jpg
|
153
155
|
- test/fixtures/directory/data/info.txt
|
154
156
|
- test/fixtures/directory/data/nested.txt
|
@@ -160,10 +162,21 @@ files:
|
|
160
162
|
- test/fixtures/directory_crate/fish/info.txt
|
161
163
|
- test/fixtures/directory_crate/fish/root.txt
|
162
164
|
- test/fixtures/directory_crate/ro-crate-metadata.jsonld
|
165
|
+
- test/fixtures/directory_crate/ro-crate-preview.html
|
163
166
|
- test/fixtures/file with spaces.txt
|
164
167
|
- test/fixtures/info.txt
|
165
168
|
- test/fixtures/spaces/file with spaces.txt
|
166
169
|
- test/fixtures/spaces/ro-crate-metadata.jsonld
|
170
|
+
- test/fixtures/sparse_directory_crate.zip
|
171
|
+
- test/fixtures/sparse_directory_crate/fish/data/binary.jpg
|
172
|
+
- test/fixtures/sparse_directory_crate/fish/data/info.txt
|
173
|
+
- test/fixtures/sparse_directory_crate/fish/data/nested.txt
|
174
|
+
- test/fixtures/sparse_directory_crate/fish/info.txt
|
175
|
+
- test/fixtures/sparse_directory_crate/fish/root.txt
|
176
|
+
- test/fixtures/sparse_directory_crate/listed_file.txt
|
177
|
+
- test/fixtures/sparse_directory_crate/ro-crate-metadata.jsonld
|
178
|
+
- test/fixtures/sparse_directory_crate/ro-crate-preview.html
|
179
|
+
- test/fixtures/sparse_directory_crate/unlisted_file.txt
|
167
180
|
- test/fixtures/workflow-0.2.0.zip
|
168
181
|
- test/fixtures/workflow-0.2.0/Dockerfile
|
169
182
|
- test/fixtures/workflow-0.2.0/README.md
|
@@ -2414,5 +2427,5 @@ requirements: []
|
|
2414
2427
|
rubygems_version: 3.0.8
|
2415
2428
|
signing_key:
|
2416
2429
|
specification_version: 4
|
2417
|
-
summary: Create, manipulate, read RO
|
2430
|
+
summary: Create, manipulate, read RO-Crates.
|
2418
2431
|
test_files: []
|