ro-crate 0.4.11 → 0.4.15

data/test/directory_test.rb

@@ -5,41 +5,41 @@ class DirectoryTest < Test::Unit::TestCase
     crate = ROCrate::Crate.new
     crate.add_directory(fixture_file('directory'))
 
-    entries = crate.entries
+    payload = crate.payload
     base_path = ::File.dirname(fixture_file('directory'))
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/info.txt')), entries['directory/info.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/root.txt')), entries['directory/root.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data')), entries['directory/data'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/info.txt')), entries['directory/data/info.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/nested.txt')), entries['directory/data/nested.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/binary.jpg')), entries['directory/data/binary.jpg'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/info.txt')), payload['directory/info.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/root.txt')), payload['directory/root.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data')), payload['directory/data'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/info.txt')), payload['directory/data/info.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/nested.txt')), payload['directory/data/nested.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/binary.jpg')), payload['directory/data/binary.jpg'].path
   end
 
   test 'adding directory via path' do
     crate = ROCrate::Crate.new
     crate.add_directory(fixture_file('directory').path.to_s)
 
-    entries = crate.entries
+    payload = crate.payload
     base_path = ::File.dirname(fixture_file('directory'))
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/info.txt')), entries['directory/info.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/root.txt')), entries['directory/root.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data')), entries['directory/data'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/info.txt')), entries['directory/data/info.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/nested.txt')), entries['directory/data/nested.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/binary.jpg')), entries['directory/data/binary.jpg'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/info.txt')), payload['directory/info.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/root.txt')), payload['directory/root.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data')), payload['directory/data'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/info.txt')), payload['directory/data/info.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/nested.txt')), payload['directory/data/nested.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/binary.jpg')), payload['directory/data/binary.jpg'].path
   end
 
   test 'adding to given path' do
     crate = ROCrate::Crate.new
     crate.add_directory(fixture_file('directory').path.to_s, 'fish')
 
-    entries = crate.entries
+    payload = crate.payload
     base_path = ::File.dirname(fixture_file('directory'))
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/info.txt')), entries['fish/info.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/root.txt')), entries['fish/root.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data')), entries['fish/data'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/info.txt')), entries['fish/data/info.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/nested.txt')), entries['fish/data/nested.txt'].path
-    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/binary.jpg')), entries['fish/data/binary.jpg'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/info.txt')), payload['fish/info.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/root.txt')), payload['fish/root.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data')), payload['fish/data'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/info.txt')), payload['fish/data/info.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/nested.txt')), payload['fish/data/nested.txt'].path
+    assert_equal ::File.expand_path(::File.join(base_path, 'directory/data/binary.jpg')), payload['fish/data/binary.jpg'].path
   end
 end

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' })
@@ -91,4 +91,118 @@ class EntityTest < Test::Unit::TestCase
     assert_equal "http://www.data.com/my%20crate/", ROCrate::Crate.format_id('http://www.data.com/my%20crate'), 'Crate ID should end with /'
     assert_equal "http://www.data.com/my%20crate/", ROCrate::Crate.format_id('http://www.data.com/my%20crate/')
   end
+
+  test 'linked entities' do
+    crate = ROCrate::Crate.new
+    file = crate.add_file(StringIO.new(''), 'file')
+    person = crate.add_person('#bob', { name: 'Bob' })
+    file.author = person
+
+    linked = file.linked_entities
+    assert_include linked, person
+    assert_equal 1, linked.length
+
+    linked = crate.linked_entities
+    assert_include linked, file
+    assert_equal 1, linked.length
+
+    linked = crate.linked_entities(deep: true)
+    assert_include linked, file
+    assert_include linked, person
+    assert_equal 2, linked.length
+  end
+
+  test 'deleting entities removes linked entities' do
+    crate = ROCrate::Crate.new
+    file = crate.add_file(StringIO.new(''), 'file')
+    person = crate.add_person('#bob', { name: 'Bob' })
+    file.author = person
+
+    assert file.delete
+    assert_not_include crate.entities, file
+    assert_not_include crate.entities, person
+  end
+
+  test 'deleting entities does not remove dangling entities if option set' do
+    crate = ROCrate::Crate.new
+    file = crate.add_file(StringIO.new(''), 'file')
+    person = crate.add_person('#bob', { name: 'Bob' })
+    file.author = person
+
+    assert file.delete(remove_orphaned: false)
+    assert_not_include crate.entities, file
+    assert_include crate.entities, person
+  end
+
+  test 'creating files in various ways' do
+    stub_request(:get, 'http://example.com/external_ref.txt').to_return(status: 200, body: 'file contents')
+
+    crate = ROCrate::Crate.new
+
+    f1 = nil
+    Dir.chdir(fixture_dir) { f1 = ROCrate::File.new(crate, 'data.csv') }
+    refute f1.source.remote?
+    refute f1.source.directory?
+    assert_equal 20, f1.source.read.length
+    t = Tempfile.new('tf1')
+    f1.source.write_to(t)
+    t.rewind
+    assert_equal 20, t.read.length
+
+    f2 = ROCrate::File.new(crate, fixture_file('info.txt'), { author: crate.add_person('bob', name: 'Bob').reference })
+    refute f2.source.remote?
+    refute f2.source.directory?
+    assert f2.source.read
+    assert_equal 6, f2.source.read.length
+    t = Tempfile.new('tf2')
+    f2.source.write_to(t)
+    t.rewind
+    assert_equal 6, t.read.length
+
+    f3 = ROCrate::File.new(crate, 'http://example.com/external_ref.txt')
+    assert f3.source.remote?
+    refute f3.source.directory?
+    assert f3.source.read
+    assert_equal 13, f3.source.read.length
+    t = Tempfile.new('tf3')
+    f3.source.write_to(t)
+    t.rewind
+    assert_equal 13, t.read.length
+
+    f3 = ROCrate::File.new(crate, 'http://example.com/external_ref.txt')
+    assert f3.source.remote?
+    refute f3.source.directory?
+    assert f3.source.read
+    assert_equal 13, f3.source.read.length
+    t = Tempfile.new('tf3')
+    f3.source.write_to(t)
+    t.rewind
+    assert_equal 13, t.read.length
+  end
+
+  test 'assigning and checking type' do
+    crate = ROCrate::Crate.new
+    file = ROCrate::File.new(crate, 'data.csv')
+
+    assert file.has_type?('File')
+
+    file.type = ['File', 'Workflow']
+
+    assert file.has_type?('Workflow')
+    assert file.has_type?('File')
+    refute file.has_type?('Banana')
+  end
+
+  test 'inspecting object truncates very long property list' do
+    crate = ROCrate::Crate.new
+    entity = ROCrate::ContextualEntity.new(crate, 'hello')
+
+    assert entity.inspect.start_with?("<#ROCrate::ContextualEntity arcp://uuid,")
+
+    entity['veryLong'] = ('123456789a' * 100)
+
+    ins = entity.inspect
+    assert ins.length < 1000
+    assert ins.end_with?('...>')
+  end
 end

data/test/fixtures/conflicting_data_directory/info.txt

@@ -0,0 +1 @@
+abcd

data/test/fixtures/conflicting_data_directory/nested.txt

@@ -0,0 +1 @@
+No, I am nested!

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/
+
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+
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+
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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"
+        }
+    ]
+}