ro-crate 0.4.13 → 0.4.16

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 6b56ae58b682a4618dcb92ca78cbae720426316bc8ec50b9377fb9fda8ec9137
+  metadata.gz: b489bc85ce753f46035d1f5843ac9539de35e1403b92a9139c19061901d6b2d6
+  data.tar.gz: 6aab0b3d9f9323d7470554d82a887376fc00db95f68d0fae011416c66eb38937
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+  data.tar.gz: 1798256fa994b7851da4b0adf0d78514aeaadc2e48935820d3c1f5dc546a8a633d5da11db19adeec7bd8763093a133744551e37f702d943a376c1b082e12d388

data/.github/workflows/tests.yml

@@ -3,6 +3,10 @@ on: [push, pull_request]
 jobs:
   run-tests:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        ruby: ['2.6', '2.7']
+      fail-fast: false
     steps:
       - name: Checkout
         uses: actions/checkout@v2.3.1 # If you're using actions/checkout@v2 you must set persist-credentials to false in most cases for the deployment to work correctly.
@@ -11,6 +15,7 @@ jobs:
       - name: Setup Ruby
         uses: ruby/setup-ruby@v1
         with:
+          ruby-version: ${{ matrix.ruby }}
           bundler-cache: true # runs 'bundle install' and caches installed gems automatically
       - name: Run tests
         run: bundle exec rake test

data/.ruby-version

@@ -1 +1 @@
-ruby-2.6.6
+ruby-2.7.5

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    ro-crate (0.4.13)
+    ro-crate (0.4.16)
       addressable (>= 2.7, < 2.9)
       rubyzip (~> 2.0.0)
 
@@ -45,4 +45,4 @@ DEPENDENCIES
   yard (~> 0.9.25)
 
 BUNDLED WITH
-   1.17.3
+   2.3.6

data/lib/ro_crate/json_ld_hash.rb

@@ -2,6 +2,11 @@ module ROCrate
   ##
   # A wrapper class for Hash that adds methods to dereference Entities within an RO-Crate.
   class JSONLDHash < ::Hash
+    def self.[](graph, content = {})
+      @graph = graph
+      super(stringified(content))
+    end
+
     def initialize(graph, content = {})
       @graph = graph
       super()

data/lib/ro_crate/model/contextual_entity.rb

@@ -4,8 +4,7 @@ module ROCrate
   # Contextual Entities are used to describe and provide context to the Data Entities within the crate.
   class ContextualEntity < Entity
     def self.format_local_id(id)
-      i = super
-      i.start_with?('#') ? i : "##{i}"
+      super(id.start_with?('#') ? id : "##{id}")
     end
 
     ##

data/lib/ro_crate/model/crate.rb

@@ -288,6 +288,20 @@ module ROCrate
       deleted
     end
 
+    ##
+    # Remove any contextual entities that are not linked from any other entity.
+    # Optionally takes a block to decide whether the given entity should be removed or not, otherwise removes all
+    # unlinked entities.
+    # @yieldparam [ContextualEntity] entity An unlinked contextual entity.
+    # @yieldparam [Boolean] remove Should this entity be removed?
+    #
+    # @return [Array<ContextualEntity>] The entities that were removed.
+    def gc(&block)
+      unlinked_entities = contextual_entities - metadata.linked_entities(deep: true)
+
+      unlinked_entities.select(&block).each { |e| e.delete(remove_orphaned: false) }
+    end
+
     private
 
     def full_entry_path(relative_path)

data/lib/ro_crate/model/data_entity.rb

@@ -5,10 +5,6 @@ module ROCrate
   class DataEntity < Entity
     properties(%w[name contentSize dateModified encodingFormat identifier sameAs author])
 
-    def self.format_local_id(id)
-      super.chomp('/')
-    end
-
     ##
     # Return an appropriate specialization of DataEntity for the given properties.
     # @param props [Hash] Set of properties to try and infer the type from.
@@ -18,11 +14,27 @@ module ROCrate
       type = [type] unless type.is_a?(Array)
       if type.include?('Dataset')
         ROCrate::Directory
-      else
+      elsif type.include?('File')
         ROCrate::File
+      else
+        self
       end
     end
 
+    ##
+    # Create a new ROCrate::DataEntity. This entity represents something that is neither a file or directory, but
+    # still constitutes part of the crate.
+    # PLEASE NOTE, the new data entity will not be added to the crate. To do this, call Crate#add_data_entity.
+    #
+    # @param crate [Crate] The RO-Crate that owns this directory.
+    # @param source [nil] Ignored. For compatibility with the File and Directory constructor signatures.
+    # @param id [String, nil] An ID to identify this DataEntity, or nil to auto-generate an appropriate one,
+    #   (or determine via the properties param)
+    # @param properties [Hash{String => Object}] A hash of JSON-LD properties to associate with this DataEntity.
+    def initialize(crate, source = nil, id = nil, properties = {})
+      super(crate, id, properties)
+    end
+
     ##
     # The payload of all the files/directories associated with this DataEntity, mapped by their relative file path.
     #

data/lib/ro_crate/model/directory.rb

@@ -3,11 +3,11 @@ module ROCrate
   # A data entity that represents a directory of potentially many files and subdirectories (or none).
   class Directory < DataEntity
     def self.format_local_id(id)
-      super + '/'
+      super.chomp('/') + '/'
     end
 
     ##
-    # Create a new Directory. PLEASE NOTE, the new directory will not be added to the crate. To do this, call
+    # Create a new ROCrate::Directory. PLEASE NOTE, the new directory will not be added to the crate. To do this, call
     # Crate#add_data_entity, or just use Crate#add_directory.
     #
     # @param crate [Crate] The RO-Crate that owns this directory.
@@ -24,7 +24,7 @@ module ROCrate
         crate_path = source_directory.basename.to_s if crate_path.nil?
       end
 
-      super(crate, crate_path, properties)
+      super(crate, nil, crate_path, properties)
     end
 
     ##

data/lib/ro_crate/model/entity.rb

@@ -57,7 +57,12 @@ module ROCrate
     # @param id [String] The candidate local ID to be formatted.
     # @return [String] The formatted local ID.
     def self.format_local_id(id)
-      Addressable::URI.escape(id.sub(/\A\.\//, '')) # Remove initial ./ if present
+      if id.start_with?('#')
+        '#' + Addressable::URI.encode_component(id[1..-1], Addressable::URI::CharacterClasses::QUERY)
+      else
+        # Remove initial ./ if present
+        Addressable::URI.encode_component(id.sub(/\A\.\//, ''), Addressable::URI::CharacterClasses::PATH)
+      end
     end
 
     ##
@@ -242,14 +247,16 @@ module ROCrate
     # @param linked [Hash{String => Entity}] Discovered entities, mapped by their ID, to avoid loops when recursing.
     # @return [Array<Entity>]
     def linked_entities(deep: false, linked: {})
-      properties.each do |key, value|
+      properties.each_key do |key|
+        value = properties[key] # We're doing this to call the JSONLDHash#[] method which wraps
         value = [value] if value.is_a?(JSONLDHash)
 
         if value.is_a?(Array)
           value.each do |v|
             if v.is_a?(JSONLDHash) && !linked.key?(v['@id'])
               entity = v.dereference
-              linked[entity.id] = entity if entity
+              next unless entity
+              linked[entity.id] = entity
               if deep
                 entity.linked_entities(deep: true, linked: linked).each do |e|
                   linked[e.id] = e

data/lib/ro_crate/model/file.rb

@@ -2,6 +2,10 @@ module ROCrate
   ##
   # A data entity that represents a single file.
   class File < DataEntity
+    def self.format_local_id(id)
+      super.chomp('/')
+    end
+
     ##
     # 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.
@@ -32,7 +36,7 @@ module ROCrate
         crate_path = source.to_s if source.is_a?(URI) && source.absolute?
       end
 
-      super(crate, crate_path, properties)
+      super(crate, nil, crate_path, properties)
 
       if source.is_a?(URI) && source.absolute?
         @entry = RemoteEntry.new(source)

data/lib/ro_crate/model/remote_entry.rb

@@ -17,7 +17,7 @@ module ROCrate
     # @return [IO] An IO object for the remote resource.
     #
     def source
-      open(uri)
+      uri.open
     end
 
     ##

data/lib/ro_crate/reader.rb

@@ -245,10 +245,10 @@ module ROCrate
           fullpath = ::File.join(source, i)
           path = Pathname.new(fullpath) if ::File.exist?(fullpath)
         end
-        unless path
-          warn "Missing file/directory: #{id}, skipping..."
-          return nil
-        end
+        # unless path
+        #   warn "Missing file/directory: #{id}, skipping..."
+        #   return nil
+        # end
       end
 
       entity_class.new(crate, path, decoded_id, entity_props)
@@ -262,7 +262,9 @@ module ROCrate
     # 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)
+        conforms = props['conformsTo']
+        conforms = [conforms] unless conforms.is_a?(Array)
+        conforms.compact.any? { |c| c['@id']&.start_with?(ROCrate::Metadata::RO_CRATE_BASE) }
       end&.first
 
       return entities.delete(key) if key

data/ro_crate.gemspec

@@ -1,6 +1,6 @@
 Gem::Specification.new do |s|
   s.name        = 'ro-crate'
-  s.version     = '0.4.13'
+  s.version     = '0.4.16'
   s.summary     = 'Create, manipulate, read RO-Crates.'
   s.authors     = ['Finn Bacall']
   s.email       = 'finn.bacall@manchester.ac.uk'

data/test/crate_test.rb

@@ -348,4 +348,32 @@ class CrateTest < Test::Unit::TestCase
 
     assert_equal crate.payload.keys, crate.entries.keys
   end
+
+  test 'can garbage collect unlinked entities' do
+    crate = ROCrate::Reader.read(fixture_file('unlinked_entity_crate').path)
+
+    unlinked = crate.gc
+    assert_equal 2, unlinked.length
+    ids = unlinked.map(&:id)
+    assert_includes ids, '#joe'
+    assert_includes ids, '#joehouse'
+    assert_not_includes crate.contextual_entities, unlinked.first
+    assert_not_includes crate.contextual_entities, unlinked.last
+    assert_nil crate.get('#joe')
+    assert_nil crate.get('#joehouse')
+  end
+
+  test 'can conditionally garbage collect unlinked entities using a block' do
+    crate = ROCrate::Reader.read(fixture_file('unlinked_entity_crate').path)
+
+    unlinked = crate.gc do |entity|
+      entity.is_a?(ROCrate::Person)
+    end
+    assert_equal 1, unlinked.length
+    ids = unlinked.map(&:id)
+    assert_includes ids, '#joe'
+    assert_not_includes crate.contextual_entities, unlinked.first
+    assert_nil crate.get('#joe')
+    assert crate.get('#joehouse')
+  end
 end

data/test/entity_test.rb

@@ -1,3 +1,4 @@
+# encoding: utf-8
 require 'test_helper'
 
 class EntityTest < Test::Unit::TestCase
@@ -38,11 +39,11 @@ class EntityTest < Test::Unit::TestCase
   test 'fetch appropriate class for type' do
     assert_equal ROCrate::File, ROCrate::DataEntity.specialize({ '@type' => 'File' })
     assert_equal ROCrate::File, ROCrate::DataEntity.specialize({ '@type' => ['File', 'Image'] })
-    assert_equal ROCrate::File, ROCrate::DataEntity.specialize({ '@type' => 'SoftwareSourceCode' })
-    assert_equal ROCrate::File, ROCrate::DataEntity.specialize({ '@type' => 'anything that isnt a directory' })
+    assert_equal ROCrate::DataEntity, ROCrate::DataEntity.specialize({ '@type' => 'SoftwareSourceCode' })
+    assert_equal ROCrate::DataEntity, ROCrate::DataEntity.specialize({ '@type' => 'anything that isnt a directory' })
     assert_equal ROCrate::Directory, ROCrate::DataEntity.specialize({ '@type' => 'Dataset' })
     assert_equal ROCrate::Directory, ROCrate::DataEntity.specialize({ '@type' => ['Dataset', 'Image'] })
-    assert_equal ROCrate::File, ROCrate::DataEntity.specialize({ '@type' => 'Person' })
+    assert_equal ROCrate::DataEntity, ROCrate::DataEntity.specialize({ '@type' => 'Person' })
     assert_equal ROCrate::File, ROCrate::DataEntity.specialize({ '@type' => ['File', 'Image'], '@id' => 'http://www.external.com' })
 
     assert_equal ROCrate::Person, ROCrate::ContextualEntity.specialize({ '@type' => 'Person' })
@@ -75,6 +76,7 @@ class EntityTest < Test::Unit::TestCase
     assert_equal "#Hello%20World/Goodbye%20World", ROCrate::ContextualEntity.format_id('#Hello World/Goodbye World')
     assert_equal "#Hello%20World/Goodbye%20World", ROCrate::ContextualEntity.format_id('Hello World/Goodbye World')
     assert_equal "#%F0%9F%98%8A", ROCrate::ContextualEntity.format_id("😊")
+    assert_equal "https://orcid.org/0000-0002-0048-3300", ROCrate::ContextualEntity.format_id("https://orcid.org/0000-0002-0048-3300")
 
     assert_equal "test123/hello.txt", ROCrate::File.format_id('./test123/hello.txt')
     assert_equal "test123/hello.txt", ROCrate::File.format_id('./test123/hello.txt/')

data/test/fixtures/misc_data_entity_crate/ro-crate-metadata.json

@@ -0,0 +1,33 @@
+{
+  "@context": [
+    "https://w3id.org/ro/crate/1.1/context",
+    {
+      "@vocab": "http://schema.org/"
+    },
+    {
+      "@base": null
+    }
+  ],
+  "@graph": [
+    {
+      "@id": "#collection",
+      "@type": "RepositoryCollection",
+      "name": "Test collection"
+    },
+    {
+      "@id": "./",
+      "@type": "Dataset",
+      "hasFile": [],
+      "hasPart": [{"@id": "#collection"}],
+      "name": "testing hasPart"
+    },
+    {
+      "@id": "ro-crate-metadata.json",
+      "@type": "CreativeWork",
+      "about": {
+        "@id": "./"
+      },
+      "identifier": "ro-crate-metadata.json"
+    }
+  ]
+}

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

@@ -24,9 +24,10 @@
             "about": {
                 "@id": "./"
             },
-            "conformsTo": {
-                "@id": "https://w3id.org/ro/crate/1.1"
-            }
+            "conformsTo": [
+                { "@id": "https://w3id.org/ro/crate/1.1" },
+                { "@id": "https://about.workflowhub.eu/Workflow-RO-Crate/" }
+            ]
         },
         {
             "@id": "./",
@@ -128,6 +129,12 @@
             "@type": "SoftwareApplication",
             "name": "Planemo",
             "url": {"@id": "https://github.com/galaxyproject/planemo"}
+        },
+        {
+            "@id": "https://about.workflowhub.eu/Workflow-RO-Crate/",
+            "@type": "CreativeWork",
+            "name": "Workflow RO-Crate Profile",
+            "version": "0.2.0"
         }
     ]
 }

data/test/fixtures/unlinked_entity_crate/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.
+
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+      and distribution as defined by Sections 1 through 9 of this document.
+
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+
+      "Legal Entity" shall mean the union of the acting entity and all
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+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
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+
+      "Source" form shall mean the preferred form for making modifications,
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data/test/fixtures/unlinked_entity_crate/README.md

@@ -0,0 +1,2 @@
+# Unlinked Entity Crate
+Contains entities that are not linked from any other!

data/test/fixtures/unlinked_entity_crate/ro-crate-metadata.json

@@ -0,0 +1,150 @@
+{
+    "@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": "https://about.workflowhub.eu/Workflow-RO-Crate/" }
+            ]
+        },
+        {
+            "@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"}
+        },
+        {
+            "@id": "https://about.workflowhub.eu/Workflow-RO-Crate/",
+            "@type": "CreativeWork",
+            "name": "Workflow RO-Crate Profile",
+            "version": "0.2.0"
+        },
+        {
+            "@id": "#joe",
+            "@type": "Person",
+            "name": "Joe Jones"
+        },
+        {
+            "@id": "#joehouse",
+            "@type": "Organization",
+            "name": "Joe's House"
+        }
+    ]
+}

data/test/fixtures/unlinked_entity_crate/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/unlinked_entity_crate/test/test1/input.bed

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

data/test/fixtures/unlinked_entity_crate/test/test1/output_exp.bed

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

data/test/fixtures/unlinked_entity_crate/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/workflow-0.2.0/ro-crate-metadata.jsonld

@@ -123,7 +123,7 @@
         },
         {
             "@id": "workflow/workflow.knime",
-            "@type": "SoftwareSourceCode",
+            "@type": ["File", "SoftwareSourceCode"],
             "additionalType": {
                 "@id": "wfdesc:Workflow"
             },
@@ -161,7 +161,7 @@
         },
         {
             "@id": "tools/RetroPath2.cwl",
-            "@type": "SoftwareSourceCode",
+            "@type": ["File", "SoftwareSourceCode"],
             "additionalType": {
                 "@id": "wfdesc:Workflow"
             },
@@ -188,7 +188,7 @@
         },
         {
             "@id": "workflow/workflow.svg",
-            "@type": "ImageObject",
+            "@type": ["File", "ImageObject"],
             "additionalType": {"@id": "roterms:Sketch"},
             "encodingFormat": "image/svg+xml",
             "description": "Diagram of RetroPath2.0 workflow",
@@ -201,7 +201,7 @@
         },
         {
             "@id": "Dockerfile",
-            "@type": "SoftwareSourceCode",
+            "@type": ["File", "SoftwareSourceCode"],
             "url": {
                 "@id": "https://hub.docker.com/r/ibisba/retropath2/"
             },
@@ -220,7 +220,7 @@
         },
         {
             "@id": "test/test.sh",
-            "@type": "SoftwareSourceCode",
+            "@type": ["File", "SoftwareSourceCode"],
             "additionalType": {
                 "@id": "wf4ever:Script"
             },

data/test/reader_test.rb

@@ -4,12 +4,13 @@ class ReaderTest < Test::Unit::TestCase
   test 'reading from directory' do
     crate = ROCrate::Reader.read(fixture_file('workflow-0.2.0').path)
 
-    refute crate.dereference('.ssh/id_rsa')
+    refute crate.dereference('~/.ssh/id_rsa')
 
     entity = crate.dereference('workflow/workflow.knime')
     assert_not_nil entity
     assert entity.is_a?(ROCrate::File)
-    assert_equal 'SoftwareSourceCode', entity.type
+    assert entity.has_type?('SoftwareSourceCode')
+    assert entity.has_type?('File')
 
     entity = crate.dereference('workflow/')
     assert_not_nil entity
@@ -19,22 +20,26 @@ class ReaderTest < Test::Unit::TestCase
     entity = crate.dereference('tools/RetroPath2.cwl')
     assert_not_nil entity
     assert entity.is_a?(ROCrate::File)
-    assert_equal 'SoftwareSourceCode', entity.type
+    assert entity.has_type?('SoftwareSourceCode')
+    assert entity.has_type?('File')
 
     entity = crate.dereference('workflow/workflow.svg')
     assert_not_nil entity
     assert entity.is_a?(ROCrate::File)
-    assert_equal 'ImageObject', entity.type
+    assert entity.has_type?('ImageObject')
+    assert entity.has_type?('File')
 
     entity = crate.dereference('Dockerfile')
     assert_not_nil entity
     assert entity.is_a?(ROCrate::File)
-    assert_equal 'SoftwareSourceCode', entity.type
+    assert entity.has_type?('SoftwareSourceCode')
+    assert entity.has_type?('File')
 
     entity = crate.dereference('test/test.sh')
     assert_not_nil entity
     assert entity.is_a?(ROCrate::File)
-    assert_equal 'SoftwareSourceCode', entity.type
+    assert entity.has_type?('SoftwareSourceCode')
+    assert entity.has_type?('File')
 
     # Example is broken
     # entity = crate.dereference('README.md')
@@ -46,12 +51,13 @@ class ReaderTest < Test::Unit::TestCase
   test 'reading from zip' do
     crate = ROCrate::Reader.read(fixture_file('workflow-0.2.0.zip'))
 
-    refute crate.dereference('.ssh/id_rsa')
+    refute crate.dereference('~/.ssh/id_rsa')
 
     entity = crate.dereference('workflow/workflow.knime')
     assert_not_nil entity
     assert entity.is_a?(ROCrate::File)
-    assert_equal 'SoftwareSourceCode', entity.type
+    assert entity.has_type?('SoftwareSourceCode')
+    assert entity.has_type?('File')
 
     entity = crate.dereference('workflow/')
     assert_not_nil entity
@@ -61,22 +67,26 @@ class ReaderTest < Test::Unit::TestCase
     entity = crate.dereference('tools/RetroPath2.cwl')
     assert_not_nil entity
     assert entity.is_a?(ROCrate::File)
-    assert_equal 'SoftwareSourceCode', entity.type
+    assert entity.has_type?('SoftwareSourceCode')
+    assert entity.has_type?('File')
 
     entity = crate.dereference('workflow/workflow.svg')
     assert_not_nil entity
     assert entity.is_a?(ROCrate::File)
-    assert_equal 'ImageObject', entity.type
+    assert entity.has_type?('ImageObject')
+    assert entity.has_type?('File')
 
     entity = crate.dereference('Dockerfile')
     assert_not_nil entity
     assert entity.is_a?(ROCrate::File)
-    assert_equal 'SoftwareSourceCode', entity.type
+    assert entity.has_type?('SoftwareSourceCode')
+    assert entity.has_type?('File')
 
     entity = crate.dereference('test/test.sh')
     assert_not_nil entity
     assert entity.is_a?(ROCrate::File)
-    assert_equal 'SoftwareSourceCode', entity.type
+    assert entity.has_type?('SoftwareSourceCode')
+    assert entity.has_type?('File')
 
     # Example is broken
     # entity = crate.dereference('README.md')
@@ -258,4 +268,15 @@ class ReaderTest < Test::Unit::TestCase
     assert crate.preview.source.source.is_a?(Pathname)
     assert_equal 80526, crate.preview.source.read.length
   end
+
+  test 'read crate with data entity that is neither file or directory' do
+    crate = ROCrate::Reader.read_directory(fixture_file('misc_data_entity_crate').path)
+
+    entity = crate.get('#collection')
+    assert entity.is_a?(ROCrate::DataEntity)
+    refute entity.is_a?(ROCrate::File)
+    refute entity.is_a?(ROCrate::Directory)
+    assert entity.has_type?('RepositoryCollection')
+    assert entity.payload.empty?
+  end
 end

data/test/writer_test.rb

@@ -189,4 +189,15 @@ class WriterTest < Test::Unit::TestCase
       assert ::File.exist?(::File.join(dir, 'data', 'binary.jpg'))
     end
   end
+
+  test 'write crate with data entity that is neither file or directory' do
+    crate = ROCrate::Reader.read_directory(fixture_file('misc_data_entity_crate').path)
+    Dir.mktmpdir do |dir|
+      ROCrate::Writer.new(crate).write(dir)
+      Dir.chdir(dir) do
+      file_list = Dir.glob('*').sort
+      assert_equal ["ro-crate-metadata.json", "ro-crate-preview.html"], file_list
+    end
+    end
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: ro-crate
 version: !ruby/object:Gem::Version
-  version: 0.4.13
+  version: 0.4.16
 platform: ruby
 authors:
 - Finn Bacall
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-09-29 00:00:00.000000000 Z
+date: 2022-03-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: addressable
@@ -175,6 +175,7 @@ files:
 - test/fixtures/directory_crate/ro-crate-preview.html
 - test/fixtures/file with spaces.txt
 - test/fixtures/info.txt
+- test/fixtures/misc_data_entity_crate/ro-crate-metadata.json
 - test/fixtures/nested_directory.zip
 - test/fixtures/ro-crate-galaxy-sortchangecase/LICENSE
 - test/fixtures/ro-crate-galaxy-sortchangecase/README.md
@@ -195,6 +196,13 @@ files:
 - test/fixtures/sparse_directory_crate/ro-crate-metadata.jsonld
 - test/fixtures/sparse_directory_crate/ro-crate-preview.html
 - test/fixtures/sparse_directory_crate/unlisted_file.txt
+- test/fixtures/unlinked_entity_crate/LICENSE
+- test/fixtures/unlinked_entity_crate/README.md
+- test/fixtures/unlinked_entity_crate/ro-crate-metadata.json
+- test/fixtures/unlinked_entity_crate/sort-and-change-case.ga
+- test/fixtures/unlinked_entity_crate/test/test1/input.bed
+- test/fixtures/unlinked_entity_crate/test/test1/output_exp.bed
+- test/fixtures/unlinked_entity_crate/test/test1/sort-and-change-case-test.yml
 - test/fixtures/workflow-0.2.0.zip
 - test/fixtures/workflow-0.2.0/Dockerfile
 - test/fixtures/workflow-0.2.0/README.md
@@ -2442,7 +2450,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.8
+rubygems_version: 3.1.6
 signing_key: 
 specification_version: 4
 summary: Create, manipulate, read RO-Crates.