ro-crate 0.4.10 → 0.4.11

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    ro-crate (0.4.10)
+    ro-crate (0.4.11)
       addressable (~> 2.7.0)
       rubyzip (~> 2.0.0)
 
@@ -12,19 +12,19 @@ GEM
       public_suffix (>= 2.0.2, < 5.0)
     crack (0.4.3)
       safe_yaml (~> 1.0.0)
-    docile (1.3.1)
+    docile (1.3.5)
     hashdiff (1.0.1)
-    json (2.3.1)
     power_assert (0.4.1)
     public_suffix (4.0.3)
     rake (13.0.0)
     rubyzip (2.0.0)
     safe_yaml (1.0.5)
-    simplecov (0.16.1)
+    simplecov (0.21.2)
       docile (~> 1.1)
-      json (>= 1.8, < 3)
-      simplecov-html (~> 0.10.0)
-    simplecov-html (0.10.2)
+      simplecov-html (~> 0.11)
+      simplecov_json_formatter (~> 0.1)
+    simplecov-html (0.12.3)
+    simplecov_json_formatter (0.1.2)
     test-unit (3.2.3)
       power_assert
     webmock (3.8.3)
@@ -39,7 +39,7 @@ PLATFORMS
 DEPENDENCIES
   rake (~> 13.0.0)
   ro-crate!
-  simplecov (~> 0.16.1)
+  simplecov (~> 0.21.2)
   test-unit (~> 3.2.3)
   webmock (~> 3.8.3)
   yard (~> 0.9.25)

data/README.md

@@ -17,6 +17,43 @@ and run `bundle install`.
 
 ## Usage
 
+This gem consists a hierarchy of classes to model RO-Crate "entities": the crate itself, data entities 
+(files and directory) and contextual entities (with a limited set of specializations, such as `ROCrate::Person`). 
+They are all descendents of the `ROCrate::Entity` class, with the `ROCrate::Crate` class representing the crate itself. 
+
+The `ROCrate::Reader` class handles reading of RO-Crates into the above model, from a Zip file or directory.
+
+The `ROCrate::Writer` class can write out an `ROCrate::Crate` instance into a Zip file or directory.
+
+**Note:** for performance reasons, the gem is currently not linked-data aware and will allow you to set properties that 
+are not semantically valid.
+
+### Entities
+Entities correspond to entries in the `@graph` of the RO-Crate's metadata JSON-LD file. Each entity class is 
+basically a wrapper around a set of JSON properties, with some convenience methods for getting/setting some 
+commonly used properties (`crate.name = "My first crate"`).
+ 
+These convenience getter/setter methods will automatically handle turning objects into references and adding them to the 
+`@graph` if necessary.
+
+##### Getting/Setting Arbitrary Properties of Entities
+As well as using the pre-defined getter/setter methods, you can get/set arbitrary properties like so.
+
+To set the "creativeWorkStatus" property of the RO-Crate itself to a string literal:
+```ruby
+crate['creativeWorkStatus'] = 'work-in-progress'
+```
+
+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:
+```ruby
+joe = crate.add_person('joe', { name: 'Joe Bloggs' }) # Add the entity to the @graph
+crate['copyrightHolder'] = joe.reference # Reference the entity from the "copyrightHolder" property
+```
+and to resolve those references back to the object, use the `dereference` method:
+```ruby
+joe = crate['copyrightHolder'].dereference
+```
+
 ### Documentation
 
 [Click here for API documentation](https://www.researchobject.org/ro-crate-ruby/).

data/lib/ro_crate.rb

@@ -14,6 +14,7 @@ require 'ro_crate/model/remote_entry'
 require 'ro_crate/model/entry'
 require 'ro_crate/model/directory'
 require 'ro_crate/model/metadata'
+require 'ro_crate/model/preview_generator'
 require 'ro_crate/model/preview'
 require 'ro_crate/model/crate'
 require 'ro_crate/model/contextual_entity'

data/lib/ro_crate/model/crate.rb

@@ -168,6 +168,15 @@ module ROCrate
       @preview ||= ROCrate::Preview.new(self)
     end
 
+    ##
+    # Set the RO-Crate preview file
+    # @param preview [Preview] the preview to set.
+    #
+    # @return [Preview]
+    def preview=(preview)
+      @preview = claim(preview)
+    end
+
     ##
     # All the entities within the crate. Includes contextual entities, data entities, the crate itself and its metadata file.
     #

data/lib/ro_crate/model/data_entity.rb

@@ -3,6 +3,8 @@ module ROCrate
   # A class to represent a "Data Entity" within an RO-Crate.
   # Data Entities are the actual physical files and directories within the Crate.
   class DataEntity < Entity
+    properties(%w[name contentSize dateModified encodingFormat identifier sameAs author])
+
     def self.format_local_id(id)
       super.chomp('/')
     end
@@ -13,8 +15,6 @@ module ROCrate
     # @return [Class]
     def self.specialize(props)
       type = props['@type']
-      id = props['@id']
-      abs = URI(id)&.absolute? rescue false
       type = [type] unless type.is_a?(Array)
       if type.include?('Dataset')
         ROCrate::Directory

data/lib/ro_crate/model/directory.rb

@@ -2,8 +2,6 @@ module ROCrate
   ##
   # A data entity that represents a directory of potentially many files and subdirectories (or none).
   class Directory < DataEntity
-    properties(%w[name contentSize dateModified encodingFormat identifier sameAs])
-
     def self.format_local_id(id)
       super + '/'
     end

data/lib/ro_crate/model/file.rb

@@ -2,14 +2,12 @@ module ROCrate
   ##
   # A data entity that represents a single file.
   class File < DataEntity
-    properties(%w[name contentSize dateModified encodingFormat identifier sameAs])
-
     ##
     # Create a new ROCrate::File. PLEASE NOTE, the new file will not be added to the crate. To do this, call
     # Crate#add_data_entity, or just use Crate#add_file.
     #
     # @param crate [Crate] The RO-Crate that owns this file.
-    # @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.
+    # @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.
     # @param crate_path [String] The relative path within the RO-Crate where this file will be written.
     # @param properties [Hash{String => Object}] A hash of JSON-LD properties to associate with this file.
     def initialize(crate, source, crate_path = nil, properties = {})

data/lib/ro_crate/model/metadata.rb

@@ -17,7 +17,15 @@ module ROCrate
     # @return [String] The rendered JSON-LD as a "prettified" string.
     def generate
       graph = crate.entities.map(&:properties).reject(&:empty?)
-      JSON.pretty_generate('@context' => CONTEXT, '@graph' => graph)
+      JSON.pretty_generate('@context' => context, '@graph' => graph)
+    end
+
+    def context
+      @context || CONTEXT
+    end
+
+    def context= c
+      @context = c
     end
 
     private

data/lib/ro_crate/model/organization.rb

@@ -2,7 +2,7 @@ module ROCrate
   ##
   # A contextual entity that represents an organization.
   class Organization < ContextualEntity
-    properties(['name'])
+    properties(%w[name])
 
     private
 

data/lib/ro_crate/model/preview.rb

@@ -12,26 +12,14 @@ module ROCrate
     # @return [String]
     attr_accessor :template
 
-    def initialize(crate, properties = {})
+    def initialize(crate, source = nil, properties = {})
+      source ||= PreviewGenerator.new(self)
       @template = nil
-      super(crate, nil, IDENTIFIER, properties)
-    end
-
-    ##
-    # Generate the crate's `ro-crate-preview.html`.
-    # @return [String] The rendered HTML as a string.
-    def generate
-      b = crate.get_binding
-      renderer = ERB.new(template || ::File.read(DEFAULT_TEMPLATE))
-      renderer.result(b)
+      super(crate, source, IDENTIFIER, properties)
     end
 
     private
 
-    def source
-      Entry.new(StringIO.new(generate))
-    end
-
     def default_properties
       {
         '@id' => IDENTIFIER,

data/lib/ro_crate/model/preview_generator.rb

@@ -0,0 +1,40 @@
+require 'erb'
+
+module ROCrate
+  ##
+  # A class to handle generation of an RO-Crate's preview HTML in an IO-like way (to fit into an Entry).
+  class PreviewGenerator
+    ##
+    # @param preview [Preview] The RO-Crate preview object.
+    def initialize(preview)
+      @preview = preview
+    end
+
+    def read(*args)
+      io.read(*args)
+    end
+
+    ##
+    # Generate the crate's `ro-crate-preview.html`.
+    # @return [String] The rendered HTML as a string.
+    def generate
+      b = crate.get_binding
+      renderer = ERB.new(template)
+      renderer.result(b)
+    end
+
+    def template
+      @preview.template || ::File.read(Preview::DEFAULT_TEMPLATE)
+    end
+
+    def crate
+      @preview.crate
+    end
+
+    private
+
+    def io
+      @io ||= StringIO.new(generate)
+    end
+  end
+end

data/lib/ro_crate/reader.rb

@@ -103,8 +103,12 @@ module ROCrate
           entry == ROCrate::Metadata::IDENTIFIER_1_0 }
 
       if metadata_file
-        entities = entities_from_metadata(::File.read(::File.join(source, metadata_file)))
-        build_crate(entities, source)
+        metadata_json = ::File.read(::File.join(source, metadata_file))
+        metadata = JSON.parse(metadata_json)
+        entities = entities_from_metadata(metadata)
+        context = metadata['@context']
+
+        build_crate(entities, source, context: context)
       else
         raise 'No metadata found!'
       end
@@ -113,10 +117,9 @@ module ROCrate
     ##
     # Extracts all the entities from the @graph of the RO-Crate Metadata.
     #
-    # @param metadata_json [String] A string containing the metadata JSON.
+    # @param metadata [Hash] A Hash containing the parsed metadata JSON.
     # @return [Hash{String => Hash}] A Hash of all the entities, mapped by their @id.
-    def self.entities_from_metadata(metadata_json)
-      metadata = JSON.parse(metadata_json)
+    def self.entities_from_metadata(metadata)
       graph = metadata['@graph']
 
       if graph
@@ -129,6 +132,7 @@ module ROCrate
         # Do some normalization...
         entities[ROCrate::Metadata::IDENTIFIER] = extract_metadata_entity(entities)
         raise "No metadata entity found in @graph!" unless entities[ROCrate::Metadata::IDENTIFIER]
+        entities[ROCrate::Preview::IDENTIFIER] = extract_preview_entity(entities)
         entities[ROCrate::Crate::IDENTIFIER] = extract_root_entity(entities)
         raise "No root entity (with @id: #{entities[ROCrate::Metadata::IDENTIFIER].dig('about', '@id')}) found in @graph!" unless entities[ROCrate::Crate::IDENTIFIER]
 
@@ -139,25 +143,49 @@ module ROCrate
     end
 
     ##
-    # Create a crate from the given set of entities.
+    # Create and populate crate from the given set of entities.
+    #
+    # @param entity_hash [Hash{String => Hash}] A Hash containing all the entities in the @graph, mapped by their @id.
+    # @param source [String, ::File, Pathname] The location of the RO-Crate being read.
+    # @param crate_class [Class] The class to use to instantiate the crate,
+    #   useful if you have created a subclass of ROCrate::Crate that you want to use. (defaults to ROCrate::Crate).
+    # @param context [nil, String, Array, Hash] A custom JSON-LD @context (parsed), or nil to use default.
+    # @return [Crate] The RO-Crate.
+    def self.build_crate(entity_hash, source, crate_class: ROCrate::Crate, context:)
+      crate = initialize_crate(entity_hash, source, crate_class: crate_class, context: context)
+
+      extract_data_entities(crate, source, entity_hash).each do |entity|
+        crate.add_data_entity(entity)
+      end
+
+      # The remaining entities in the hash must be contextual.
+      extract_contextual_entities(crate, entity_hash).each do |entity|
+        crate.add_contextual_entity(entity)
+      end
+
+      crate
+    end
+
+    ##
+    # Initialize a crate from the given set of entities.
     #
     # @param entity_hash [Hash{String => Hash}] A Hash containing all the entities in the @graph, mapped by their @id.
     # @param source [String, ::File, Pathname] The location of the RO-Crate being read.
+    # @param crate_class [Class] The class to use to instantiate the crate,
+    #   useful if you have created a subclass of ROCrate::Crate that you want to use. (defaults to ROCrate::Crate).
+    # @param context [nil, String, Array, Hash] A custom JSON-LD @context (parsed), or nil to use default.
     # @return [Crate] The RO-Crate.
-    def self.build_crate(entity_hash, source)
-      ROCrate::Crate.new.tap do |crate|
+    def self.initialize_crate(entity_hash, source, crate_class: ROCrate::Crate, context:)
+      crate_class.new.tap do |crate|
         crate.properties = entity_hash.delete(ROCrate::Crate::IDENTIFIER)
         crate.metadata.properties = entity_hash.delete(ROCrate::Metadata::IDENTIFIER)
+        crate.metadata.context = context
         preview_properties = entity_hash.delete(ROCrate::Preview::IDENTIFIER)
-        crate.preview.properties = preview_properties if preview_properties
-        crate.add_all(source, false)
-        extract_data_entities(crate, source, entity_hash).each do |entity|
-          crate.add_data_entity(entity)
-        end
-        # The remaining entities in the hash must be contextual.
-        extract_contextual_entities(crate, entity_hash).each do |entity|
-          crate.add_contextual_entity(entity)
+        if preview_properties
+          preview_path = ::File.join(source, ROCrate::Preview::IDENTIFIER)
+          crate.preview = ROCrate::Preview.new(crate, ::File.exists?(preview_path) ? Pathname.new(preview_path) : nil, preview_properties)
         end
+        crate.add_all(source, false)
       end
     end
 
@@ -229,8 +257,8 @@ module ROCrate
     ##
     # Extract the metadata entity from the entity hash, according to the rules defined here:
     # https://www.researchobject.org/ro-crate/1.1/root-data-entity.html#finding-the-root-data-entity
-    # @return [Hash{String => Hash}] A Hash containing (hopefully) one value, the metadata entity's properties,
-    # mapped by its @id.
+    # @return [nil, Hash{String => Hash}] A Hash containing (hopefully) one value, the metadata entity's properties
+    # mapped by its @id, or nil if nothing is found.
     def self.extract_metadata_entity(entities)
       key = entities.detect do |_, props|
         props.dig('conformsTo', '@id')&.start_with?(ROCrate::Metadata::RO_CRATE_BASE)
@@ -245,6 +273,13 @@ module ROCrate
           entities.delete(ROCrate::Metadata::IDENTIFIER_1_0))
     end
 
+    ##
+    # Extract the ro-crate-preview entity from the entity hash.
+    # @return [Hash{String => Hash}] A Hash containing the preview entity's properties mapped by its @id, or nil if nothing is found.
+    def self.extract_preview_entity(entities)
+      entities.delete("./#{ROCrate::Preview::IDENTIFIER}") || entities.delete(ROCrate::Preview::IDENTIFIER)
+    end
+
     ##
     # Extract the root entity from the entity hash, according to the rules defined here:
     # https://www.researchobject.org/ro-crate/1.1/root-data-entity.html#finding-the-root-data-entity

data/ro_crate.gemspec

@@ -1,6 +1,6 @@
 Gem::Specification.new do |s|
   s.name        = 'ro-crate'
-  s.version     = '0.4.10'
+  s.version     = '0.4.11'
   s.summary     = 'Create, manipulate, read RO-Crates.'
   s.authors     = ['Finn Bacall']
   s.email       = 'finn.bacall@manchester.ac.uk'
@@ -12,7 +12,7 @@ Gem::Specification.new do |s|
   s.add_runtime_dependency 'rubyzip', '~> 2.0.0'
   s.add_development_dependency 'rake', '~> 13.0.0'
   s.add_development_dependency 'test-unit', '~> 3.2.3'
-  s.add_development_dependency 'simplecov', '~> 0.16.1'
+  s.add_development_dependency 'simplecov', '~> 0.21.2'
   s.add_development_dependency 'yard', '~> 0.9.25'
   s.add_development_dependency 'webmock', '~> 3.8.3'
 end

data/test/crate_test.rb

@@ -164,6 +164,18 @@ class CrateTest < Test::Unit::TestCase
     assert_equal 2, crate1.contextual_entities.first.properties['cats']
   end
 
+  test 'sharing entities' do
+    crate = ROCrate::Crate.new
+    info = crate.add_file(fixture_file('info.txt'),'the_info.txt')
+    bob = crate.add_person('bob', name: 'Bob Jones')
+    crate.author = bob
+    info.author = bob
+
+    assert_equal [bob], crate.contextual_entities
+    assert_equal bob, info.author
+    assert_equal bob, crate.author
+  end
+
   test 'external files' do
     crate = ROCrate::Crate.new
     local = crate.add_file(fixture_file('info.txt'))

data/test/fixtures/ro-crate-galaxy-sortchangecase/LICENSE

@@ -0,0 +1,176 @@
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
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+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
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+      "Object" form shall mean any form resulting from mechanical
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+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+

data/test/fixtures/ro-crate-galaxy-sortchangecase/README.md

@@ -0,0 +1,6 @@
+# Galaxy mini workflow
+
+A tiny Galaxy workflow that sorts tabular lines according to the first column
+and changes the text to upper case.
+
+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).

data/test/fixtures/ro-crate-galaxy-sortchangecase/ro-crate-metadata.json

@@ -0,0 +1,133 @@
+{
+    "@context": [
+        "https://w3id.org/ro/crate/1.1/context",
+        {
+            "TestSuite": "https://w3id.org/ro/terms/test#TestSuite",
+            "TestInstance": "https://w3id.org/ro/terms/test#TestInstance",
+            "TestService": "https://w3id.org/ro/terms/test#TestService",
+            "TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition",
+            "PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine",
+            "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",
+            "TravisService": "https://w3id.org/ro/terms/test#TravisService",
+            "GithubService": "https://w3id.org/ro/terms/test#GithubService",
+            "instance": "https://w3id.org/ro/terms/test#instance",
+            "runsOn": "https://w3id.org/ro/terms/test#runsOn",
+            "resource": "https://w3id.org/ro/terms/test#resource",
+            "definition": "https://w3id.org/ro/terms/test#definition",
+            "engineVersion": "https://w3id.org/ro/terms/test#engineVersion"
+        }
+    ],
+    "@graph": [
+        {
+            "@id": "ro-crate-metadata.json",
+            "@type": "CreativeWork",
+            "about": {
+                "@id": "./"
+            },
+            "conformsTo": {
+                "@id": "https://w3id.org/ro/crate/1.1"
+            }
+        },
+        {
+            "@id": "./",
+            "@type": "Dataset",
+            "name": "sort-and-change-case",
+            "description": "sort lines and change text to upper case",
+            "license": "Apache-2.0",
+            "mainEntity": {
+                "@id": "sort-and-change-case.ga"
+            },
+            "hasPart": [
+                {
+                    "@id": "sort-and-change-case.ga"
+                },
+                {
+                    "@id": "LICENSE"
+                },
+                {
+                    "@id": "README.md"
+                },
+                {
+                    "@id": "test/test1/sort-and-change-case-test.yml"
+                }
+            ],
+            "mentions": [
+                {
+                    "@id": "#test1"
+                }
+            ]
+        },
+        {
+            "@id": "sort-and-change-case.ga",
+            "@type": [
+                "File",
+                "SoftwareSourceCode",
+                "ComputationalWorkflow"
+            ],
+            "programmingLanguage": {
+                "@id": "#galaxy"
+            },
+            "name": "sort-and-change-case"
+        },
+        {
+            "@id": "LICENSE",
+            "@type": "File"
+        },
+        {
+            "@id": "README.md",
+            "@type": "File"
+        },
+        {
+            "@id": "#galaxy",
+            "@type": "ComputerLanguage",
+            "name": "Galaxy",
+            "identifier": {
+                "@id": "https://galaxyproject.org/"
+            },
+            "url": {
+                "@id": "https://galaxyproject.org/"
+            }
+        },
+        {
+            "@id": "#test1",
+            "name": "test1",
+            "@type": "TestSuite",
+            "mainEntity": {
+                "@id": "sort-and-change-case.ga"
+            },
+            "instance": [
+                {"@id": "#test1_1"}
+            ],
+            "definition": {"@id": "test/test1/sort-and-change-case-test.yml"}
+        },
+        {
+            "@id": "#test1_1",
+            "name": "test1_1",
+            "@type": "TestInstance",
+            "runsOn": {"@id": "https://w3id.org/ro/terms/test#JenkinsService"},
+            "url": "http://example.org/jenkins",
+            "resource": "job/tests/"
+        },
+        {
+            "@id": "test/test1/sort-and-change-case-test.yml",
+            "@type": [
+                "File",
+                "TestDefinition"
+            ],
+            "conformsTo": {"@id": "https://w3id.org/ro/terms/test#PlanemoEngine"},
+            "engineVersion": ">=0.70"
+        },
+        {
+            "@id": "https://w3id.org/ro/terms/test#JenkinsService",
+            "@type": "TestService",
+            "name": "Jenkins",
+            "url": {"@id": "https://www.jenkins.io"}
+        },
+        {
+            "@id": "https://w3id.org/ro/terms/test#PlanemoEngine",
+            "@type": "SoftwareApplication",
+            "name": "Planemo",
+            "url": {"@id": "https://github.com/galaxyproject/planemo"}
+        }
+    ]
+}

data/test/fixtures/ro-crate-galaxy-sortchangecase/sort-and-change-case.ga

@@ -0,0 +1,118 @@
+{
+    "uuid": "e2a8566c-c025-4181-9e90-7ed29d4e4df1",
+    "tags": [],
+    "format-version": "0.1",
+    "name": "sort-and-change-case",
+    "version": 0,
+    "steps": {
+        "0": {
+            "tool_id": null,
+            "tool_version": null,
+            "outputs": [],
+            "workflow_outputs": [],
+            "input_connections": {},
+            "tool_state": "{}",
+            "id": 0,
+            "uuid": "5a36fad2-66c7-4b9e-8759-0fbcae9b8541",
+            "errors": null,
+            "name": "Input dataset",
+            "label": "bed_input",
+            "inputs": [],
+            "position": {
+                "top": 200,
+                "left": 200
+            },
+            "annotation": "",
+            "content_id": null,
+            "type": "data_input"
+        },
+        "1": {
+            "tool_id": "sort1",
+            "tool_version": "1.1.0",
+            "outputs": [
+                {
+                    "type": "input",
+                    "name": "out_file1"
+                }
+            ],
+            "workflow_outputs": [
+                {
+                    "output_name": "out_file1",
+                    "uuid": "8237f71a-bc2a-494e-a63c-09c1e65ef7c8",
+                    "label": "sorted_bed"
+                }
+            ],
+            "input_connections": {
+                "input": {
+                    "output_name": "output",
+                    "id": 0
+                }
+            },
+            "tool_state": "{\"__page__\": null, \"style\": \"\\\"alpha\\\"\", \"column\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"column_set\": \"[]\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"header_lines\": \"\\\"0\\\"\", \"order\": \"\\\"ASC\\\"\"}",
+            "id": 1,
+            "uuid": "0b6b3cda-c75f-452b-85b1-8ae4f3302ba4",
+            "errors": null,
+            "name": "Sort",
+            "post_job_actions": {},
+            "label": "sort",
+            "inputs": [
+                {
+                    "name": "input",
+                    "description": "runtime parameter for tool Sort"
+                }
+            ],
+            "position": {
+                "top": 200,
+                "left": 420
+            },
+            "annotation": "",
+            "content_id": "sort1",
+            "type": "tool"
+        },
+        "2": {
+            "tool_id": "ChangeCase",
+            "tool_version": "1.0.0",
+            "outputs": [
+                {
+                    "type": "tabular",
+                    "name": "out_file1"
+                }
+            ],
+            "workflow_outputs": [
+                {
+                    "output_name": "out_file1",
+                    "uuid": "c31cd733-dab6-4d50-9fec-b644d162397b",
+                    "label": "uppercase_bed"
+                }
+            ],
+            "input_connections": {
+                "input": {
+                    "output_name": "out_file1",
+                    "id": 1
+                }
+            },
+            "tool_state": "{\"__page__\": null, \"casing\": \"\\\"up\\\"\", \"__rerun_remap_job_id__\": null, \"cols\": \"\\\"c1\\\"\", \"delimiter\": \"\\\"TAB\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+            "id": 2,
+            "uuid": "9698bcde-0729-48fe-b88d-ccfb6f6153b4",
+            "errors": null,
+            "name": "Change Case",
+            "post_job_actions": {},
+            "label": "change_case",
+            "inputs": [
+                {
+                    "name": "input",
+                    "description": "runtime parameter for tool Change Case"
+                }
+            ],
+            "position": {
+                "top": 200,
+                "left": 640
+            },
+            "annotation": "",
+            "content_id": "ChangeCase",
+            "type": "tool"
+        }
+    },
+    "annotation": "",
+    "a_galaxy_workflow": "true"
+}

data/test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/input.bed

@@ -0,0 +1,3 @@
+chr1	66999824	67210768
+chr7	48998526	50489626
+chr1	66874821	66010368

data/test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/output_exp.bed

@@ -0,0 +1,3 @@
+CHR1	66874821	66010368
+CHR1	66999824	67210768
+CHR7	48998526	50489626

data/test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/sort-and-change-case-test.yml

@@ -0,0 +1,8 @@
+- doc: test with a small input
+  job:
+    bed_input:
+      class: File
+      path: input.bed
+  outputs:
+    uppercase_bed:
+      path: output_exp.bed

data/test/fixtures/sparse_directory_crate/ro-crate-preview.html

@@ -1,66 +1,67 @@
 <!DOCTYPE html>
 <html>
 <head>
-  <title>New RO-Crate</title>
-  <script type="application/ld+json">{
-  "@context": "https://w3id.org/ro/crate/1.1/context",
-  "@graph": [
-    {
-      "@id": "ro-crate-metadata.jsonld",
-      "@type": "CreativeWork",
-      "about": {
-        "@id": "./"
-      }
-    },
-    {
-      "@id": "ro-crate-preview.html",
-      "@type": "CreativeWork",
-      "about": {
-        "@id": "./"
-      }
-    },
-    {
-      "@id": "./",
-      "@type": "Dataset",
-      "hasPart": [
-        {
-          "@id": "fish/"
-        }
-      ]
-    },
-    {
-      "@id": "fish/",
-      "@type": "Dataset"
-    }
-  ]
-}</script>
-  <meta name="generator" content="https://github.com/fbacall/ro-crate-ruby">
-  <meta name="keywords" content="RO-Crate">
+    <title>New RO-Crate</title>
+    <script type="application/ld+json">{
+        "@context": "https://w3id.org/ro/crate/1.0/context",
+        "@graph": [
+            {
+                "@id": "ro-crate-metadata.jsonld",
+                "@type": "CreativeWork",
+                "about": {
+                    "@id": "./"
+                }
+            },
+            {
+                "@id": "ro-crate-preview.html",
+                "@type": "CreativeWork",
+                "about": {
+                    "@id": "./"
+                }
+            },
+            {
+                "@id": "./",
+                "@type": "Dataset",
+                "hasPart": [
+                    {
+                        "@id": "listed_file.txt"
+                    }
+                ]
+            },
+            {
+                "@id": "listed_file.txt",
+                "@type": "File"
+            }
+        ]
+    }</script>
+    <meta name="generator" content="https://github.com/fbacall/ro-crate-ruby">
+    <meta name="keywords" content="RO-Crate">
 </head>
 <body>
-  <h1>New RO-Crate</h1>
-  
-  <p>
-    
-  </p>
-  <dl>
-    
-    
-    
-    
-  </dl>
+<h1>New RO-Crate</h1>
+Some stuff has been added here blablabla
 
-  <h2>Contents</h2>
-  <ul>
-    
-      <li id="__data_entity_fish/">
-        
-          <strong>fish/</strong>
-        
-        
-        
-      </li>
-    
-  </ul>
+<p>
+
+</p>
+<dl>
+
+
+
+
+</dl>
+
+<h2>Contents</h2>
+<ul>
+
+    <li id="__data_entity_listed_file.txt">
+
+        <strong>listed_file.txt</strong>
+
+
+
+    </li>
+
+</ul>
 </body>
-</html>
+</html>

data/test/reader_test.rb

@@ -227,4 +227,28 @@ class ReaderTest < Test::Unit::TestCase
     assert crate.entries['fish/data/binary.jpg']
     assert_equal ['./', 'fish/', 'ro-crate-metadata.json', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
   end
+
+  test 'reading preserves any additions to @context' do
+    crate = ROCrate::Reader.read_directory(fixture_file('ro-crate-galaxy-sortchangecase').path)
+
+    context = crate.metadata.context
+    assert_equal [
+                     'https://w3id.org/ro/crate/1.1/context',
+                     {
+                         'TestSuite' => 'https://w3id.org/ro/terms/test#TestSuite',
+                         'TestInstance' => 'https://w3id.org/ro/terms/test#TestInstance',
+                         'TestService' => 'https://w3id.org/ro/terms/test#TestService',
+                         'TestDefinition' => 'https://w3id.org/ro/terms/test#TestDefinition',
+                         'PlanemoEngine' => 'https://w3id.org/ro/terms/test#PlanemoEngine',
+                         'JenkinsService' => 'https://w3id.org/ro/terms/test#JenkinsService',
+                         'TravisService' => 'https://w3id.org/ro/terms/test#TravisService',
+                         'GithubService' => 'https://w3id.org/ro/terms/test#GithubService',
+                         'instance' => 'https://w3id.org/ro/terms/test#instance',
+                         'runsOn' => 'https://w3id.org/ro/terms/test#runsOn',
+                         'resource' => 'https://w3id.org/ro/terms/test#resource',
+                         'definition' => 'https://w3id.org/ro/terms/test#definition',
+                         'engineVersion' => 'https://w3id.org/ro/terms/test#engineVersion'
+                     }
+                 ], context
+  end
 end

data/test/writer_test.rb

@@ -124,12 +124,32 @@ class WriterTest < Test::Unit::TestCase
       actual_files =  Dir.chdir(dir) { Dir.glob('**/*') }
       assert_equal expected_files, actual_files
       expected_files.each do |file|
-        next if file == 'ro-crate-metadata.jsonld' # Expected context gets updated.
-        next if file == 'ro-crate-preview.html' # RO-Crate preview format changed
         abs_file_path = ::File.join(fixture, file)
         next if ::File.directory?(abs_file_path)
         assert_equal ::File.read(abs_file_path), ::File.read(::File.join(dir, file)), "#{file} didn't match"
       end
     end
   end
+
+  test 'reading/writing multiple times does not change the crate' do
+    input_dir = fixture_file('sparse_directory_crate').path
+    Dir.mktmpdir do |dir|
+      3.times do |i|
+        output_dir = ::File.join(dir, "new_directory_#{i}")
+        crate = ROCrate::Reader.read(input_dir)
+
+        ROCrate::Writer.new(crate).write(output_dir)
+        expected_files = Dir.chdir(input_dir) { Dir.glob('**/*') }
+        actual_files =  Dir.chdir(output_dir) { Dir.glob('**/*') }
+        assert_equal expected_files, actual_files
+        expected_files.each do |file|
+          abs_file_path = ::File.join(input_dir, file)
+          next if ::File.directory?(abs_file_path)
+          assert_equal ::File.read(abs_file_path), ::File.read(::File.join(output_dir, file)), "#{file} didn't match"
+        end
+
+        input_dir = output_dir
+      end
+    end
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: ro-crate
 version: !ruby/object:Gem::Version
-  version: 0.4.10
+  version: 0.4.11
 platform: ruby
 authors:
 - Finn Bacall
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-03-09 00:00:00.000000000 Z
+date: 2021-04-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: addressable
@@ -72,14 +72,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.16.1
+        version: 0.21.2
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.16.1
+        version: 0.21.2
 - !ruby/object:Gem::Dependency
   name: yard
   requirement: !ruby/object:Gem::Requirement
@@ -137,6 +137,7 @@ files:
 - lib/ro_crate/model/organization.rb
 - lib/ro_crate/model/person.rb
 - lib/ro_crate/model/preview.rb
+- lib/ro_crate/model/preview_generator.rb
 - lib/ro_crate/model/remote_entry.rb
 - lib/ro_crate/reader.rb
 - lib/ro_crate/ro-crate-preview.html.erb
@@ -166,6 +167,13 @@ files:
 - test/fixtures/file with spaces.txt
 - test/fixtures/info.txt
 - test/fixtures/nested_directory.zip
+- test/fixtures/ro-crate-galaxy-sortchangecase/LICENSE
+- test/fixtures/ro-crate-galaxy-sortchangecase/README.md
+- test/fixtures/ro-crate-galaxy-sortchangecase/ro-crate-metadata.json
+- test/fixtures/ro-crate-galaxy-sortchangecase/sort-and-change-case.ga
+- test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/input.bed
+- test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/output_exp.bed
+- test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/sort-and-change-case-test.yml
 - test/fixtures/spaces/file with spaces.txt
 - test/fixtures/spaces/ro-crate-metadata.jsonld
 - test/fixtures/sparse_directory_crate.zip