Merge branch 'seek-1.16' into main

app/models/sample_type.rb

@@ -200,6 +200,19 @@ def can_see_hidden_item?(user)
     can_view?(user)
   end
 
+  def self.is_asset?
+    false
+  end
+
+  # although has a downloadable template, it doesn't have the full downloadable behaviour of an asset with data and it's own accessible permissions
+  def is_downloadable?
+    false
+  end
+
+  def self.supports_extended_metadata?
+    false
+  end
+
   private
 
   # whether the referring sample is valid and gives permission to view
@@ -292,9 +305,5 @@ def validate_title_is_not_type_of_seek_sample_multi
     end
   end
 
-  def self.supports_extended_metadata?
-    false
-  end
-
   class UnknownAttributeException < RuntimeError; end
 end

app/views/sample_types/_template.html.erb

@@ -1,3 +1,5 @@
+<% return unless @sample_type.can_download? %>
+<h2>Template</h2>
 <div id="template-details">
 
   <% if @sample_type.template %>

app/views/sample_types/show.html.erb

@@ -11,7 +11,7 @@
     <div class="col-md-9 col-sm-8 box_about_actor">
       <%= item_description h(@sample_type.description) -%>
 
-      <h2>Template</h2>
+
       <%= render :partial => "template" %>
 
       <h2>Attributes</h2>

config/help_links.yml

@@ -31,7 +31,7 @@ Document: https://docs.seek4science.org/help/user-guide/adding-assets.html
 Presentation: https://docs.seek4science.org/help/user-guide/adding-assets.html
 Event: https://docs.seek4science.org/help/user-guide/general-attributes.html#events
 clipboard_api_mozilla: https://developer.mozilla.org/en-US/docs/Web/API/Clipboard_API
-ExtendedMetadataType: https://docs.seek4science.org/tech/extended-metadata
-extended_metadata_technical_overview: https://github.com/seek4science/seek-documentation/blob/gh-pages-extended_metadata-type/tech/extended_metadata/extended-metadata-type.md
-extended_metadata_type_json_schema: https://github.com/seek4science/seek-documentation/blob/gh-pages-extended_metadata-type/tech/extended_metadata/extended_metadata_type_schema.json
-extended_metadata_type_example: https://github.com/seek4science/seek-documentation/blob/gh-pages-extended_metadata-type/tech/extended_metadata/a-complete-example.md
+ExtendedMetadataType: https://docs.seek4science.org/tech/extended-metadata/extended-metadata-type.html
+extended_metadata_technical_overview: https://docs.seek4science.org/tech/extended-metadata/extended-metadata-type.html
+extended_metadata_type_json_schema: https://docs.seek4science.org/tech/extended-metadata/extended-metadata-type-schema.json
+extended_metadata_type_example: https://docs.seek4science.org/tech/extended-metadata/a-complete-example.html

lib/tasks/seek_upgrades.rake

@@ -13,6 +13,7 @@ namespace :seek do
     update_observation_unit_policies
     fix_xlsx_marked_as_zip
     add_policies_to_existing_sample_types
+    fix_previous_sample_type_permissions
   ]
 
   # these are the tasks that are executes for each upgrade as standard, and rarely change
@@ -104,13 +105,13 @@ namespace :seek do
 
           # Visible if linked to public samples
           if st.samples.any? { |sample| sample.is_published? }
-            policy.access_type = Policy::VISIBLE
+            policy.access_type = Policy::ACCESSIBLE
           else
             policy.access_type = Policy::NO_ACCESS
           end
           # Visible to each project
           st.projects.map do |project|
-            policy.permissions << Permission.new(contributor_type: Permission::PROJECT, contributor_id: project.id, access_type: Policy::VISIBLE)
+            policy.permissions << Permission.new(contributor_type: Permission::PROJECT, contributor_id: project.id, access_type: Policy::ACCESSIBLE)
           end
           # Project admins can manage
           project_admins = st.projects.map(&:project_administrators).flatten
@@ -125,7 +126,23 @@ namespace :seek do
         counter += 1
       end
     end
-    puts "...Added policies to #{counter} sample types"
+    puts "... Added policies to #{counter} sample types"
+  end
+
+  task(fix_previous_sample_type_permissions: [:environment]) do
+    only_once('fix_previous_sample_type_permissions 1.16.0') do
+      puts '... Updating previous sample type permissions ...'
+      SampleType.includes(:policy).where.not(policy_id: nil).each do |sample_type|
+        policy = sample_type.policy
+        if policy.access_type == Policy::VISIBLE
+          policy.update_column(:access_type, Policy::ACCESSIBLE)
+        end
+        policy.permissions.where(access_type: Policy::VISIBLE).where(contributor_type: Permission::PROJECT).update_all(access_type: Policy::ACCESSIBLE)
+        putc('.')
+      end
+      AuthLookupUpdateQueue.enqueue(SampleType.all)
+      puts '... Finished updating previous sample type permissions'
+    end
   end
 
   private

test/functional/sample_types_controller_test.rb

@@ -255,6 +255,31 @@ class SampleTypesControllerTest < ActionController::TestCase
     assert_equal 'update', ActivityLog.last.action
   end
 
+  test 'template download link visibility' do
+    person = FactoryBot.create(:person)
+    sample_type = SampleType.new title: 'testing download',
+                                 uploaded_template: true,
+                                 project_ids: person.projects.collect(&:id),
+                                 contributor: person,
+                                 content_blob: FactoryBot.create(:sample_type_template_content_blob),
+                                 policy: FactoryBot.create(:downloadable_public_policy)
+    sample_type.build_attributes_from_template
+    disable_authorization_checks { sample_type.save! }
+    assert sample_type.can_view?
+    assert sample_type.can_download?
+    get :show, params: { id: sample_type }
+    assert_response :success
+    assert_select 'a[href=?]',download_sample_type_content_blob_path(sample_type,sample_type.template), text:'Download'
+
+    sample_type.policy = FactoryBot.create(:publicly_viewable_policy)
+    disable_authorization_checks { sample_type.save! }
+    assert sample_type.can_view?
+    refute sample_type.can_download?
+    get :show, params: { id: sample_type }
+    assert_response :success
+    assert_select 'a[href=?]',download_sample_type_content_blob_path(sample_type,sample_type.template), text:'Download', count:0
+  end
+
   test 'update changing from a CV attribute' do
     sample_type = FactoryBot.create(:apples_controlled_vocab_sample_type, project_ids: @project_ids,
                                                                           contributor: @person)

test/unit/sample_type_test.rb

@@ -114,6 +114,13 @@ def setup
     end
   end
 
+  test 'not an asset or downloadable' do
+    st = FactoryBot.create(:simple_sample_type)
+    refute st.is_asset?
+    refute st.is_downloadable?
+    refute st.is_downloadable_asset?
+  end
+
   test 'validate title and decription length' do
     long_desc = ('a' * 65536).freeze
     ok_desc = ('a' * 65535).freeze