ro-crate 0.4.6 → 0.4.11

data/ro_crate.gemspec

@@ -1,6 +1,6 @@
 Gem::Specification.new do |s|
   s.name        = 'ro-crate'
-  s.version     = '0.4.6'
+  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/entity_test.rb

@@ -70,4 +70,25 @@ class EntityTest < Test::Unit::TestCase
     assert_equal({ '@id' => '#fred' }, person.reference)
     assert_equal(person.canonical_id, crate.author.canonical_id)
   end
+
+  test 'format various IDs' do
+    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 "test123/hello.txt", ROCrate::File.format_id('./test123/hello.txt')
+    assert_equal "test123/hello.txt", ROCrate::File.format_id('./test123/hello.txt/')
+    assert_equal "http://www.data.com/my%20data.txt", ROCrate::File.format_id('http://www.data.com/my%20data.txt')
+    assert_equal "http://www.data.com/my%20data.txt/", ROCrate::File.format_id('http://www.data.com/my%20data.txt/'), 'Should not modify absolute URI for DataEntity'
+
+    assert_equal "my%20directory/", ROCrate::Directory.format_id('my directory')
+    assert_equal "my%20directory/", ROCrate::Directory.format_id('my directory/')
+    assert_equal 'http://www.data.com/my%20directory', ROCrate::Directory.format_id('http://www.data.com/my%20directory'), 'Should not modify absolute URI for DataEntity'
+    assert_equal 'http://www.data.com/my%20directory/', ROCrate::Directory.format_id('http://www.data.com/my%20directory/'), 'Should not modify absolute URI for DataEntity'
+
+    assert_equal "./", ROCrate::Crate.format_id('./')
+    assert_equal "cool%20crate/", ROCrate::Crate.format_id('./cool crate')
+    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
 end

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
+
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+      any Contribution intentionally submitted for inclusion in the Work
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+      the terms of any separate license agreement you may have executed
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+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
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+      whether in tort (including negligence), contract, or otherwise,
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+

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"
+}