ro-crate 0.4.16 → 0.4.17

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: b489bc85ce753f46035d1f5843ac9539de35e1403b92a9139c19061901d6b2d6
-  data.tar.gz: 6aab0b3d9f9323d7470554d82a887376fc00db95f68d0fae011416c66eb38937
+  metadata.gz: ad52a377a6affc48a0923460f3db8ebc5209f520f918a57097d74863114d7e42
+  data.tar.gz: bef654ae3d00ebd302c62fda5b53789c63ecda1295964667133eef47692731dd
 SHA512:
-  metadata.gz: 55769c5b1a9b22ec5ad19e762ce9651e47407dbd01673c790c59753c6ac617cfa2ea81ecdcc6004313775069344845147c765e6396303491c94091e006c98b5b
-  data.tar.gz: 1798256fa994b7851da4b0adf0d78514aeaadc2e48935820d3c1f5dc546a8a633d5da11db19adeec7bd8763093a133744551e37f702d943a376c1b082e12d388
+  metadata.gz: 907b74cff05114843bac2710a54fe141587f55b577785075bdaca49c88aa4051b26dc66785c80a1cb9c4cdcfa66030509b0bf02cc1ff82b452f18e37d755ad2a
+  data.tar.gz: f2843ab1c44d290cee58f92ff302bf1a1cfb9f4f0a5275c400ff4fcca3b45d5a0470deb613730309eae6a9dead572433ebfc7d874749ab3311585077968d8b46

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    ro-crate (0.4.16)
+    ro-crate (0.4.17)
       addressable (>= 2.7, < 2.9)
       rubyzip (~> 2.0.0)
 

data/lib/ro_crate/model/crate.rb

@@ -293,7 +293,7 @@ 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/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/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     = '0.4.16'
+  s.version     = '0.4.17'
   s.summary     = 'Create, manipulate, read RO-Crates.'
   s.authors     = ['Finn Bacall']
   s.email       = 'finn.bacall@manchester.ac.uk'

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: 0.4.16
+  version: 0.4.17
 platform: ruby
 authors:
 - Finn Bacall
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-03-09 00:00:00.000000000 Z
+date: 2022-06-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: addressable
@@ -2428,6 +2428,11 @@ 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