ro-crate 0.4.5 → 0.4.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 78897fbce0fd01688c27516dceba600ed7cd984668fd16abde32a1713c0ba40f
-  data.tar.gz: 3194d882e4b7f6cd347d652d5da38cb2fe02cfb18e36d84f50e012193a538a69
+  metadata.gz: 4880110308b68d8bc35333b1fc8a8396ea30e36069f92e059b8c57ec3567d33e
+  data.tar.gz: 77a17a0436f2dea14254a3501f9db349eed5460851d94ab4e87adb7be83e1b38
 SHA512:
-  metadata.gz: ddc2f5ffe217717299f2e5d76313b2a124fabfbc7b1e1800db18ca36d2f79c716ef249c6fcb8a6a8bfd4e0c5bba3b8a30d6ae3498ef8fd0068d7df08985c72f5
-  data.tar.gz: 802bf935d2e911ce771e962d6faaf0821f682049424cf5ac893ec780b8fc89d22f844156a83dd38adbe045a31faa7e527b4d8406bcabe937bdf8a2e8afafcd93
+  metadata.gz: 711a45d7aaa63f8a5a7bba78e433d82875311472d6f4abfd6d388dd8565a7707036152c81de4059fd92da5b7851925caf9d808f39d115752e68eaddbdc85bac1
+  data.tar.gz: ce14efaf63e7224adc79cdb11d27bdec933be290ccf60196014cb7ce9380136451265a8f814e1ca7b70286fc32852024d429334bbaab18208d31095cd619dc9e

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    ro-crate (0.4.5)
+    ro-crate (0.4.6)
       addressable (~> 2.7.0)
       rubyzip (~> 2.0.0)
 

data/lib/ro_crate/model/crate.rb

@@ -217,15 +217,19 @@ module ROCrate
 
     alias_method :own_entries, :entries
     ##
-    # A map of all the files/directories contained in the RO-Crate, where the key is the destination path within the crate
-    # and the value is an Entry where the source data can be read.
+    # # The RO-Crate's "payload" of the crate - a map of all the files/directories contained in the RO-Crate, where the
+    # key is the destination path within the crate and the value is an Entry where the source data can be read.
     #
     # @return [Hash{String => Entry}>]
     def entries
-      entries = {}
-
-      (default_entities | data_entities).each do |entity|
-        (entity == self ? own_entries : entity.entries).each do |path, entry|
+      # Gather a map of entries, starting from the crate itself, then any directory data entities, then finally any
+      # file data entities. This ensures in the case of a conflict, the more "specific" data entities take priority.
+      entries = own_entries
+      non_self_entities = default_entities.reject { |e| e == self }
+      sorted_entities = (non_self_entities | data_entities).sort_by { |e| e.is_a?(ROCrate::Directory) ? 0 : 1 }
+
+      sorted_entities.each do |entity|
+        entity.entries.each do |path, entry|
           entries[path] = entry
         end
       end

data/lib/ro_crate/model/directory.rb

@@ -30,8 +30,8 @@ module ROCrate
     end
 
     ##
-    # A map of all the files/directories under this directory, where the key is the destination path within the crate
-    # and the value is an Entry where the source data can be read.
+    # The "payload" of this directory - a map of all the files/directories, where the key is the destination path
+    # within the crate and the value is an Entry where the source data can be read.
     #
     # @return [Hash{String => Entry}>]
     def entries

data/lib/ro_crate/model/file.rb

@@ -52,7 +52,9 @@ module ROCrate
     end
 
     ##
-    # A map of all the files/directories associated with this File. Should only be a single key and value.
+    # The "payload". A map with a single key and value, of the relative filepath within the crate, to the source on disk
+    # where the actual bytes of the file can be read. Blank if remote.
+    #
     # (for compatibility with Directory#entries)
     #
     # @return [Hash{String => Entry}>] The key is the location within the crate, and the value is an Entry.

data/lib/ro_crate/reader.rb

@@ -107,6 +107,7 @@ module ROCrate
         crate.metadata.properties = entity_hash.delete(ROCrate::Metadata::IDENTIFIER)
         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

data/ro_crate.gemspec

@@ -1,6 +1,6 @@
 Gem::Specification.new do |s|
   s.name        = 'ro-crate'
-  s.version     = '0.4.5'
+  s.version     = '0.4.6'
   s.summary     = 'Create, manipulate, read RO-Crates.'
   s.authors     = ['Finn Bacall']
   s.email       = 'finn.bacall@manchester.ac.uk'

data/test/fixtures/sparse_directory_crate/fish/data/info.txt

@@ -0,0 +1 @@
+5678

data/test/fixtures/sparse_directory_crate/fish/data/nested.txt

@@ -0,0 +1 @@
+I'm nested

data/test/fixtures/sparse_directory_crate/fish/info.txt

@@ -0,0 +1 @@
+1234

data/test/fixtures/sparse_directory_crate/fish/root.txt

@@ -0,0 +1 @@
+I'm at the root

data/test/fixtures/sparse_directory_crate/listed_file.txt

@@ -0,0 +1 @@
+123

data/test/fixtures/sparse_directory_crate/ro-crate-metadata.jsonld

@@ -0,0 +1,32 @@
+{
+  "@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"
+    }
+  ]
+}

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

@@ -0,0 +1,66 @@
+<!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">
+</head>
+<body>
+  <h1>New RO-Crate</h1>
+  
+  <p>
+    
+  </p>
+  <dl>
+    
+    
+    
+    
+  </dl>
+
+  <h2>Contents</h2>
+  <ul>
+    
+      <li id="__data_entity_fish/">
+        
+          <strong>fish/</strong>
+        
+        
+        
+      </li>
+    
+  </ul>
+</body>
+</html>

data/test/fixtures/sparse_directory_crate/unlisted_file.txt

@@ -0,0 +1 @@
+456

data/test/reader_test.rb

@@ -163,4 +163,36 @@ class ReaderTest < Test::Unit::TestCase
     assert_equal 'http://example.com/external_ref.txt', ext_file.id
     assert_equal 'file contents', ext_file.source.read
   end
+
+  test 'reading from directory with unlisted files' do
+    crate = ROCrate::Reader.read_directory(fixture_file('sparse_directory_crate').path)
+
+    assert_equal 11, crate.entries.count
+    assert crate.entries['listed_file.txt']
+    assert crate.entries['unlisted_file.txt']
+    assert crate.entries['fish']
+    assert_equal '1234', crate.entries['fish/info.txt'].source.read.chomp
+    refute crate.entries['fish/root.txt'].directory?
+    assert crate.entries['fish/data'].directory?
+    assert crate.entries['fish/data/info.txt']
+    refute crate.entries['fish/data/nested.txt'].remote?
+    assert crate.entries['fish/data/binary.jpg']
+    assert_equal ['./', 'listed_file.txt', 'ro-crate-metadata.jsonld', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
+  end
+
+  test 'reading from a zip with unlisted files' do
+    crate = ROCrate::Reader.read_zip(fixture_file('sparse_directory_crate.zip').path)
+
+    assert_equal 11, crate.entries.count
+    assert crate.entries['listed_file.txt']
+    assert crate.entries['unlisted_file.txt']
+    assert crate.entries['fish']
+    assert_equal '1234', crate.entries['fish/info.txt'].source.read.chomp
+    refute crate.entries['fish/root.txt'].directory?
+    assert crate.entries['fish/data'].directory?
+    assert crate.entries['fish/data/info.txt']
+    refute crate.entries['fish/data/nested.txt'].remote?
+    assert crate.entries['fish/data/binary.jpg']
+    assert_equal ['./', 'listed_file.txt', 'ro-crate-metadata.jsonld', 'ro-crate-preview.html'], crate.entities.map(&:id).sort
+  end
 end

data/test/writer_test.rb

@@ -112,4 +112,24 @@ class WriterTest < Test::Unit::TestCase
       assert_equal 2529, ::File.size(::File.join(dir, 'data', 'binary.jpg'))
     end
   end
+
+  test 'reading and writing out a directory crate produces an identical crate' do
+    fixture = fixture_file('sparse_directory_crate').path
+    Dir.mktmpdir do |dir|
+      dir = ::File.join(dir, 'new_directory')
+      crate = ROCrate::Reader.read(fixture)
+
+      ROCrate::Writer.new(crate).write(dir)
+      expected_files = Dir.chdir(fixture) { Dir.glob('**/*') }
+      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
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: ro-crate
 version: !ruby/object:Gem::Version
-  version: 0.4.5
+  version: 0.4.6
 platform: ruby
 authors:
 - Finn Bacall
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-02-24 00:00:00.000000000 Z
+date: 2021-02-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: addressable
@@ -167,6 +167,16 @@ files:
 - test/fixtures/info.txt
 - test/fixtures/spaces/file with spaces.txt
 - test/fixtures/spaces/ro-crate-metadata.jsonld
+- test/fixtures/sparse_directory_crate.zip
+- test/fixtures/sparse_directory_crate/fish/data/binary.jpg
+- test/fixtures/sparse_directory_crate/fish/data/info.txt
+- test/fixtures/sparse_directory_crate/fish/data/nested.txt
+- test/fixtures/sparse_directory_crate/fish/info.txt
+- test/fixtures/sparse_directory_crate/fish/root.txt
+- test/fixtures/sparse_directory_crate/listed_file.txt
+- 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/workflow-0.2.0.zip
 - test/fixtures/workflow-0.2.0/Dockerfile
 - test/fixtures/workflow-0.2.0/README.md