ro-crate 0.4.13 → 0.4.14

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 364757350da7d275b02def348bfd97782ad0ae31728c44f0691bc084e4d94ac9
-  data.tar.gz: 6b56ae58b682a4618dcb92ca78cbae720426316bc8ec50b9377fb9fda8ec9137
+  metadata.gz: 5d94d65b4375c3923a828f763c749e9958d975c2f3fd3ee55b996f718cd9317c
+  data.tar.gz: 3ce5e362db42e5a790991bef4fe252d507a35e83eff00a58b1fe99ce4f5808e6
 SHA512:
-  metadata.gz: a2b14f9c64528476a18f84d0292311484e975a3dc6085c00c94f5dac8d84fa144e91bb6138c876db4a4079aeec4222eb6a1f91458e2ef0260defa9d3a0a42d57
-  data.tar.gz: b56d257868b7cb94f341e844223d14988c280fff34bb54dd1a676d47681d96afc8193ebb60a22eecfef7e96dc0d2ce03ed1571190a1717fbe56d1b80ed579053
+  metadata.gz: dd26c3d0fc2783f7424ba022ae03d5cc14c0e4aa7f96e2c6b682f82be3af9cee5cacb1480b414b5ab2f37d08e19b38b377455afd1ec74017901788a4a6500bab
+  data.tar.gz: eb6f983303b2b50fafaec3a03c4c3f855b4c12a4fcd80611d20916ec1f64c078973e842d1425c3101a1609b16db3bdfbe56eccde2a703de0efc360df0a48550f

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    ro-crate (0.4.13)
+    ro-crate (0.4.14)
       addressable (>= 2.7, < 2.9)
       rubyzip (~> 2.0.0)
 

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/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/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     = '0.4.14'
   s.summary     = 'Create, manipulate, read RO-Crates.'
   s.authors     = ['Finn Bacall']
   s.email       = 'finn.bacall@manchester.ac.uk'

data/test/entity_test.rb

@@ -38,11 +38,11 @@ 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' })

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/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: 0.4.14
 platform: ruby
 authors:
 - Finn Bacall
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-09-29 00:00:00.000000000 Z
+date: 2021-11-02 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