ro-crate 0.4.14 → 0.4.15

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 3ce5e362db42e5a790991bef4fe252d507a35e83eff00a58b1fe99ce4f5808e6
+  metadata.gz: 92f4b8cd765215082edea1be4e3c065a29ddcdbbc43a79576a4782ba8d797f07
+  data.tar.gz: d8936210124988edd8fd942c978a93ea6ee6f17fa1bcbfd3b6528e7475143ca1
 SHA512:
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-  data.tar.gz: eb6f983303b2b50fafaec3a03c4c3f855b4c12a4fcd80611d20916ec1f64c078973e842d1425c3101a1609b16db3bdfbe56eccde2a703de0efc360df0a48550f
+  metadata.gz: cf88d846278c037fd4437db9f1cd5f3fd31d6901eeb161a38417a5919edaf9e013f28cfadea7a59bf77a687c5946f540ee6cfa28ccc001d473dac41eaf3c5f3e
+  data.tar.gz: ab8413b46ad23145ca6d68f2554cad6eacb9f2ecd349e890b6380295029da5426110e447c863170d997071a6dba3f76c72006ca6a90b9a456ac96858e114aa86

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 (0.4.14)
+    ro-crate (0.4.15)
       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/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/entity.rb

@@ -242,14 +242,16 @@ 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/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/ro_crate.gemspec

@@ -1,6 +1,6 @@
 Gem::Specification.new do |s|
   s.name        = 'ro-crate'
-  s.version     = '0.4.14'
+  s.version     = '0.4.15'
   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/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
+
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+      "You" (or "Your") shall mean an individual or Legal Entity
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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
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+      whether in tort (including negligence), contract, or otherwise,
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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

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: ro-crate
 version: !ruby/object:Gem::Version
-  version: 0.4.14
+  version: 0.4.15
 platform: ruby
 authors:
 - Finn Bacall
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-11-02 00:00:00.000000000 Z
+date: 2022-02-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: addressable
@@ -196,6 +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
@@ -2443,7 +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.