ro-crate 0.4.15 → 0.5.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 92f4b8cd765215082edea1be4e3c065a29ddcdbbc43a79576a4782ba8d797f07
-  data.tar.gz: d8936210124988edd8fd942c978a93ea6ee6f17fa1bcbfd3b6528e7475143ca1
+  metadata.gz: aa3bf8a8cdaa985143e1e2988d4fc24e14aad40bfd55763b4be17af23c8fa36a
+  data.tar.gz: 190326475ec90f7328e86252dd4f0c1150750ba8298fef7ba8337291ae988e21
 SHA512:
-  metadata.gz: cf88d846278c037fd4437db9f1cd5f3fd31d6901eeb161a38417a5919edaf9e013f28cfadea7a59bf77a687c5946f540ee6cfa28ccc001d473dac41eaf3c5f3e
-  data.tar.gz: ab8413b46ad23145ca6d68f2554cad6eacb9f2ecd349e890b6380295029da5426110e447c863170d997071a6dba3f76c72006ca6a90b9a456ac96858e114aa86
+  metadata.gz: 7cf568838eba39df6ff3770456a8f2133efe8797d1b916b0acf4523f1830623120e14e3a3e8d3e5bbbf09d7960fe5afc585389010ab674394cc80b3c944363d7
+  data.tar.gz: 151807e2411c7d7d09ef2930f75b1eca9f1274fce14ca28d084c7b609268defc70803832697d79b68b9efe282ed63b0af1b179fd1cb0de2dba641798b331afe9

data/.github/workflows/tests.yml

@@ -5,7 +5,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        ruby: ['2.6', '2.7']
+        ruby: ['2.6', '2.7', '3.0', '3.1']
       fail-fast: false
     steps:
       - name: Checkout

data/.ruby-version

@@ -1 +1 @@
-ruby-2.7.5
+ruby-3.0.4

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    ro-crate (0.4.15)
+    ro-crate (0.5.0)
       addressable (>= 2.7, < 2.9)
       rubyzip (~> 2.0.0)
 
@@ -14,9 +14,10 @@ GEM
       safe_yaml (~> 1.0.0)
     docile (1.3.5)
     hashdiff (1.0.1)
-    power_assert (1.1.3)
+    power_assert (2.0.1)
     public_suffix (4.0.6)
     rake (13.0.0)
+    rexml (3.2.5)
     rubyzip (2.0.0)
     safe_yaml (1.0.5)
     simplecov (0.21.2)
@@ -25,7 +26,7 @@ GEM
       simplecov_json_formatter (~> 0.1)
     simplecov-html (0.12.3)
     simplecov_json_formatter (0.1.2)
-    test-unit (3.2.9)
+    test-unit (3.5.3)
       power_assert
     webmock (3.8.3)
       addressable (>= 2.3.6)
@@ -38,9 +39,10 @@ PLATFORMS
 
 DEPENDENCIES
   rake (~> 13.0.0)
+  rexml (~> 3.2.5)
   ro-crate!
   simplecov (~> 0.21.2)
-  test-unit (~> 3.2.3)
+  test-unit (~> 3.5.3)
   webmock (~> 3.8.3)
   yard (~> 0.9.25)
 

data/lib/ro_crate/model/contextual_entity.rb

@@ -4,8 +4,7 @@ module ROCrate
   # Contextual Entities are used to describe and provide context to the Data Entities within the crate.
   class ContextualEntity < Entity
     def self.format_local_id(id)
-      i = super
-      i.start_with?('#') ? i : "##{i}"
+      super(id.start_with?('#') ? id : "##{id}")
     end
 
     ##

data/lib/ro_crate/model/crate.rb

@@ -1,3 +1,5 @@
+require 'set'
+
 module ROCrate
   ##
   # A Ruby abstraction of an RO-Crate.
@@ -20,8 +22,8 @@ module ROCrate
     ##
     # Initialize an empty RO-Crate.
     def initialize(id = IDENTIFIER, properties = {})
-      @data_entities = []
-      @contextual_entities = []
+      @data_entities = Set.new
+      @contextual_entities = Set.new
       super(self, nil, id, properties)
     end
 
@@ -144,8 +146,8 @@ module ROCrate
     # @return [Entity] the entity itself, or a clone of the entity "owned" by this crate.
     def add_contextual_entity(entity)
       entity = claim(entity)
-      contextual_entities.delete(entity) # Remove (then re-add) the entity if it exists
-      contextual_entities.push(entity)
+      contextual_entities.delete?(entity) # Remove (then re-add) the entity if it exists
+      contextual_entities.add(entity)
       entity
     end
 
@@ -156,8 +158,8 @@ module ROCrate
     # @return [Entity] the entity itself, or a clone of the entity "owned" by this crate.
     def add_data_entity(entity)
       entity = claim(entity)
-      data_entities.delete(entity) # Remove (then re-add) the entity if it exists
-      data_entities.push(entity)
+      data_entities.delete?(entity) # Remove (then re-add) the entity if it exists
+      data_entities.add(entity)
       entity
     end
 
@@ -189,7 +191,7 @@ module ROCrate
     ##
     # All the entities within the crate. Includes contextual entities, data entities, the crate itself and its metadata file.
     #
-    # @return [Array<Entity>]
+    # @return [Set<Entity>]
     def entities
       default_entities | data_entities | contextual_entities
     end
@@ -197,9 +199,9 @@ module ROCrate
     ##
     # Entities for the metadata file and crate itself, which should be present in all RO-Crates.
     #
-    # @return [Array<Entity>]
+    # @return [Set<Entity>]
     def default_entities
-      [metadata, preview, self]
+      Set.new([metadata, preview, self])
     end
 
     def properties
@@ -217,7 +219,7 @@ module ROCrate
     #
     # @return [Addressable::URI]
     def canonical_id
-      Addressable::URI.parse("arcp://uuid,#{uuid}").join(id)
+      @canonical_id ||= Addressable::URI.parse("arcp://uuid,#{uuid}").join(id)
     end
 
     ##
@@ -248,8 +250,7 @@ module ROCrate
       # 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_payload
-      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 = (default_entities.delete(self) | data_entities).sort_by { |e| e.is_a?(ROCrate::Directory) ? 0 : 1 }
 
       sorted_entities.each do |entity|
         entity.payload.each do |path, entry|
@@ -277,7 +278,7 @@ module ROCrate
       entity = dereference(entity) if entity.is_a?(String)
       return unless entity
 
-      deleted = data_entities.delete(entity) || contextual_entities.delete(entity)
+      deleted = data_entities.delete?(entity) || contextual_entities.delete?(entity)
 
       if deleted && remove_orphaned
         crate_entities = crate.linked_entities(deep: true)
@@ -293,7 +294,7 @@ module ROCrate
     # 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?
+    # @yieldreturn [Boolean] remove Should this entity be removed?
     #
     # @return [Array<ContextualEntity>] The entities that were removed.
     def gc(&block)

data/lib/ro_crate/model/entity.rb

@@ -57,7 +57,12 @@ module ROCrate
     # @param id [String] The candidate local ID to be formatted.
     # @return [String] The formatted local ID.
     def self.format_local_id(id)
-      Addressable::URI.escape(id.sub(/\A\.\//, '')) # Remove initial ./ if present
+      if id.start_with?('#')
+        '#' + Addressable::URI.encode_component(id[1..-1], Addressable::URI::CharacterClasses::QUERY)
+      else
+        # Remove initial ./ if present
+        Addressable::URI.encode_component(id.sub(/\A\.\//, ''), Addressable::URI::CharacterClasses::PATH)
+      end
     end
 
     ##
@@ -246,7 +251,7 @@ module ROCrate
         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)
+        if value.respond_to?(:each)
           value.each do |v|
             if v.is_a?(JSONLDHash) && !linked.key?(v['@id'])
               entity = v.dereference

data/lib/ro_crate/model/entry.rb

@@ -38,6 +38,12 @@ module ROCrate
       ::File.directory?(source) rescue false
     end
 
+    ##
+    # Does this Entry point to a symlink on the disk?
+    def symlink?
+      ::File.symlink?(source) rescue false
+    end
+
     ##
     # Does this Entry point to a remote resource?
     def remote?

data/lib/ro_crate/model/remote_entry.rb

@@ -21,11 +21,17 @@ module ROCrate
     end
 
     ##
-    # Does this RemoteEntry point to a directory on the disk?
+    # Does this RemoteEntry point to a directory
     def directory?
       false
     end
 
+    ##
+    # Does this RemoteEntry point to a symlink
+    def symlink?
+      false
+    end
+
     ##
     # Does this RemoteEntry point to a remote resource?
     def remote?

data/lib/ro_crate/reader.rb

@@ -182,7 +182,7 @@ module ROCrate
         crate.metadata.context = context
         preview_properties = entity_hash.delete(ROCrate::Preview::IDENTIFIER)
         preview_path = ::File.join(source, ROCrate::Preview::IDENTIFIER)
-        preview_path = ::File.exists?(preview_path) ? Pathname.new(preview_path) : nil
+        preview_path = ::File.exist?(preview_path) ? Pathname.new(preview_path) : nil
         if preview_properties || preview_path
           crate.preview = ROCrate::Preview.new(crate, preview_path, preview_properties || {})
         end

data/lib/ro_crate/writer.rb

@@ -21,13 +21,17 @@ module ROCrate
         next if !overwrite && ::File.exist?(fullpath)
         next if entry.directory?
         FileUtils.mkdir_p(::File.dirname(fullpath))
-        temp = Tempfile.new('ro-crate-temp')
-        begin
-          entry.write_to(temp)
-          temp.close
-          FileUtils.mv(temp, fullpath)
-        ensure
-          temp.unlink
+        if entry.symlink?
+          ::File.symlink(entry.source.readlink, fullpath)
+        else
+          temp = Tempfile.new('ro-crate-temp')
+          begin
+            entry.write_to(temp)
+            temp.close
+            FileUtils.mv(temp, fullpath)
+          ensure
+            temp.unlink
+          end
         end
       end
     end
@@ -40,7 +44,11 @@ module ROCrate
       Zip::File.open(destination, Zip::File::CREATE) do |zip|
         @crate.payload.each do |path, entry|
           next if entry.directory?
-          zip.get_output_stream(path) { |s| entry.write_to(s) }
+          if entry.symlink?
+            zip.add(path, entry.path) if entry.path
+          else
+            zip.get_output_stream(path) { |s| entry.write_to(s) }
+          end
         end
       end
     end

data/ro_crate.gemspec

@@ -1,6 +1,6 @@
 Gem::Specification.new do |s|
   s.name        = 'ro-crate'
-  s.version     = '0.4.15'
+  s.version     = '0.5.0'
   s.summary     = 'Create, manipulate, read RO-Crates.'
   s.authors     = ['Finn Bacall']
   s.email       = 'finn.bacall@manchester.ac.uk'
@@ -11,8 +11,9 @@ Gem::Specification.new do |s|
   s.add_runtime_dependency 'addressable', '>= 2.7', '< 2.9'
   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 'test-unit', '~> 3.5.3'
   s.add_development_dependency 'simplecov', '~> 0.21.2'
   s.add_development_dependency 'yard', '~> 0.9.25'
   s.add_development_dependency 'webmock', '~> 3.8.3'
+  s.add_development_dependency 'rexml', '~> 3.2.5'
 end

data/test/crate_test.rb

@@ -171,7 +171,8 @@ class CrateTest < Test::Unit::TestCase
     crate.author = bob
     info.author = bob
 
-    assert_equal [bob], crate.contextual_entities
+    assert_includes crate.contextual_entities, bob
+    assert_equal 1, crate.contextual_entities.length
     assert_equal bob, info.author
     assert_equal bob, crate.author
   end

data/test/entity_test.rb

@@ -1,3 +1,4 @@
+# encoding: utf-8
 require 'test_helper'
 
 class EntityTest < Test::Unit::TestCase
@@ -75,6 +76,7 @@ class EntityTest < Test::Unit::TestCase
     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 "https://orcid.org/0000-0002-0048-3300", ROCrate::ContextualEntity.format_id("https://orcid.org/0000-0002-0048-3300")
 
     assert_equal "test123/hello.txt", ROCrate::File.format_id('./test123/hello.txt')
     assert_equal "test123/hello.txt", ROCrate::File.format_id('./test123/hello.txt/')

data/test/fixtures/workflow-test-fixture-symlink/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 Finn Bacall
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

data/test/fixtures/workflow-test-fixture-symlink/README.md

@@ -0,0 +1,2 @@
+# workflow-test-fixture
+A workflow and associated files for use in SEEK's tests :)

data/test/fixtures/workflow-test-fixture-symlink/concat_two_files.ga

@@ -0,0 +1,151 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "",
+    "creator": [
+        {
+            "class": "Person",
+            "identifier": "",
+            "name": "Finn Bacall"
+        }
+    ],
+    "format-version": "0.1",
+    "license": "MIT",
+    "name": "Concat two files",
+    "steps": {
+        "0": {
+            "annotation": "",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "",
+                    "name": "input1"
+                }
+            ],
+            "label": "input1",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "bottom": 254.1999969482422,
+                "height": 61.19999694824219,
+                "left": 393,
+                "right": 593,
+                "top": 193,
+                "width": 200,
+                "x": 393,
+                "y": 193
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "7a90b91e-b143-4aa3-923d-fbcca5994d60",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "1a510a60-afcc-4491-911b-3519da79f22d"
+                }
+            ]
+        },
+        "1": {
+            "annotation": "",
+            "content_id": null,
+            "errors": null,
+            "id": 1,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "",
+                    "name": "input2"
+                }
+            ],
+            "label": "input2",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "bottom": 374.1999969482422,
+                "height": 61.19999694824219,
+                "left": 393,
+                "right": 593,
+                "top": 313,
+                "width": 200,
+                "x": 393,
+                "y": 313
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "baa13f22-7e0c-4533-b12c-7d31caf0c9b3",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "1ded3ee7-d176-4385-8d1e-09b74af213fe"
+                }
+            ]
+        },
+        "2": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
+            "errors": null,
+            "id": 2,
+            "input_connections": {
+                "inputs": {
+                    "id": 0,
+                    "output_name": "output"
+                },
+                "queries_0|inputs2": {
+                    "id": 1,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "Concatenate datasets",
+            "outputs": [
+                {
+                    "name": "out_file1",
+                    "type": "input"
+                }
+            ],
+            "position": {
+                "bottom": 336.1999969482422,
+                "height": 143.1999969482422,
+                "left": 613,
+                "right": 813,
+                "top": 193,
+                "width": 200,
+                "x": 613,
+                "y": 193
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
+            "tool_shed_repository": {
+                "changeset_revision": "ddf54b12c295",
+                "name": "text_processing",
+                "owner": "bgruening",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [{\"__index__\": 0, \"inputs2\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "0.1.0",
+            "type": "tool",
+            "uuid": "b2de7621-8ea3-4384-8f79-766ef38ebcfe",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "out_file1",
+                    "uuid": "cba40c62-d9bd-49e0-b636-48cfab67c107"
+                }
+            ]
+        }
+    },
+    "tags": [
+        "cat"
+    ],
+    "uuid": "94a9a580-75d1-434f-b2af-02017de43e23",
+    "version": 1
+}

data/test/fixtures/workflow-test-fixture-symlink/images/workflow-diagram.png

@@ -0,0 +1 @@
+../diagram.png

data/test/writer_test.rb

@@ -195,9 +195,36 @@ class WriterTest < Test::Unit::TestCase
     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
+        file_list = Dir.glob('*').sort
+        assert_equal ["ro-crate-metadata.json", "ro-crate-preview.html"], file_list
+      end
+    end
+  end
+
+  test 'write crate with data entity refers to a symlink as directory' do
+    crate = ROCrate::Crate.new
+    crate.add_all(fixture_file('workflow-test-fixture-symlink').path)
+    assert crate.payload['images/workflow-diagram.png'].source.symlink?
+
+    Dir.mktmpdir do |dir|
+      ROCrate::Writer.new(crate).write(dir)
+      Dir.chdir(dir) do
+        assert File.symlink?('images/workflow-diagram.png')
+      end
     end
+  end
+
+  test 'write crate with data entity refers to a symlink as zip' do
+    crate = ROCrate::Crate.new
+    crate.add_all(fixture_file('workflow-test-fixture-symlink').path)
+    assert crate.payload['images/workflow-diagram.png'].source.symlink?
+
+    Tempfile.create do |file|
+      ROCrate::Writer.new(crate).write_zip(file)
+
+      Zip::File.open(file) do |zipfile|
+        assert zipfile.find_entry('images/workflow-diagram.png').symlink?
+      end
     end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: ro-crate
 version: !ruby/object:Gem::Version
-  version: 0.4.15
+  version: 0.5.0
 platform: ruby
 authors:
 - Finn Bacall
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-02-15 00:00:00.000000000 Z
+date: 2022-09-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: addressable
@@ -64,14 +64,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 3.2.3
+        version: 3.5.3
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 3.2.3
+        version: 3.5.3
 - !ruby/object:Gem::Dependency
   name: simplecov
   requirement: !ruby/object:Gem::Requirement
@@ -114,6 +114,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 3.8.3
+- !ruby/object:Gem::Dependency
+  name: rexml
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.2.5
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.2.5
 description: 
 email: finn.bacall@manchester.ac.uk
 executables: []
@@ -2428,6 +2442,11 @@ files:
 - test/fixtures/workflow-0.2.0/workflow/workflow.knime
 - test/fixtures/workflow-0.2.0/workflow/workflow.svg
 - test/fixtures/workflow-0.2.0/workflow/workflowset.meta
+- test/fixtures/workflow-test-fixture-symlink/LICENSE
+- test/fixtures/workflow-test-fixture-symlink/README.md
+- test/fixtures/workflow-test-fixture-symlink/concat_two_files.ga
+- test/fixtures/workflow-test-fixture-symlink/diagram.png
+- test/fixtures/workflow-test-fixture-symlink/images/workflow-diagram.png
 - test/reader_test.rb
 - test/test_helper.rb
 - test/writer_test.rb
@@ -2450,7 +2469,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.6
+rubygems_version: 3.2.33
 signing_key: 
 specification_version: 4
 summary: Create, manipulate, read RO-Crates.