Merge branch 'seek-1.16' into issue-2079

.github/workflows/tests.yml

@@ -86,6 +86,7 @@ jobs:
             ${{ runner.os }}-
       - name: Install Python dependencies
         run: |
+          python3.9 -m pip install --upgrade pip
           python3.9 -m pip install setuptools==58
           python3.9 -m pip install -r requirements.txt
       - name: Create test database

Dockerfile

@@ -46,6 +46,7 @@ RUN touch config/using-docker #allows us to see within SEEK we are running in a
 
 # Python dependencies from requirements.txt
 ENV PATH="/var/www/.local/bin:$PATH"
+RUN python3.9 -m pip install --upgrade pip
 RUN python3.9 -m pip install setuptools==58
 RUN python3.9 -m pip install -r requirements.txt
 

Gemfile.lock

@@ -460,7 +460,7 @@ GEM
       nokogiri (~> 1)
       rake
     mini_mime (1.1.5)
-    mini_portile2 (2.8.7)
+    mini_portile2 (2.8.8)
     minitest (5.25.1)
     minitest-reporters (1.5.0)
       ansi
@@ -492,7 +492,7 @@ GEM
       net-protocol
     netrc (0.11.0)
     nio4r (2.7.4)
-    nokogiri (1.16.7)
+    nokogiri (1.16.8)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     nori (1.1.5)
@@ -607,9 +607,9 @@ GEM
       activesupport (>= 5.0.0)
       minitest
       nokogiri (>= 1.6)
-    rails-html-sanitizer (1.6.0)
+    rails-html-sanitizer (1.6.1)
       loofah (~> 2.21)
-      nokogiri (~> 1.14)
+      nokogiri (>= 1.15.7, != 1.16.7, != 1.16.6, != 1.16.5, != 1.16.4, != 1.16.3, != 1.16.2, != 1.16.1, != 1.16.0.rc1, != 1.16.0)
     rails-observers (0.1.5)
       activemodel (>= 4.0)
     rails-perftest (0.0.7)

app/helpers/application_helper.rb

@@ -8,6 +8,9 @@ module ApplicationHelper
   include ImagesHelper
   include SessionsHelper
 
+  ALLOWED_HTML_WITH_TABLES = Rails::HTML::Concern::Scrubber::SafeList::DEFAULT_ALLOWED_TAGS.dup +
+    Set.new(%w(table thead tbody tfoot tr th td))
+
   def no_items_to_list_text
     content_tag :div, id: 'no-index-items-text' do
       "There are no #{resource_text_from_controller.pluralize} found that are visible to you."
@@ -224,7 +227,7 @@ def text_or_not_specified(text, options = {})
     else
       text.capitalize! if options[:capitalize]
       res = text.html_safe
-      res = sanitized_text(res)
+      res = sanitized_text(res, allow_tables: options[:markdown])
       res = truncate_without_splitting_words(res, options[:length]) if options[:length]
       if options[:markdown]
         # Convert `>` etc. back to `>` so markdown blockquotes can be used.
@@ -428,8 +431,10 @@ def using_docker?
     Seek::Docker.using_docker?
   end
 
-  def sanitized_text(text)
-    Rails::Html::SafeListSanitizer.new.sanitize(text)
+  def sanitized_text(text, allow_tables: false)
+    opts = {}
+    opts[:tags] = ALLOWED_HTML_WITH_TABLES if allow_tables
+    Rails::Html::SafeListSanitizer.new.sanitize(text, opts)
   end
 
   # whether manage attributes should be shown, dont show if editing (rather than new or managing)

app/helpers/filtering_helper.rb

@@ -2,6 +2,7 @@ module FilteringHelper
   def filter_link(key, filter, hidden: false, replace: false)
     link_to(page_and_sort_params.merge({ page: nil, filter: filter.active ? without_filter(key, filter.value) : with_filter(key, filter.value, replace: replace) }),
             title: filter.label,
+            rel: 'nofollow',
             class: "filter-option#{' filter-option-active' if filter.active}#{' filter-option-hidden' if hidden}") do
       content_tag(:span, filter.label, class: 'filter-option-label') +
           content_tag(:span, filter.count, class: 'filter-option-count')

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/projects/import_from_fairdata_station.html.erb

@@ -31,7 +31,7 @@
   <%= panel('Sharing permissions') do %>
     <div class="alert alert-info">
       <p>
-        The following sharing permissions will be applied to all the items created. It is possible to change them individually after they have been created. %>.
+        The following sharing permissions will be applied to all the items created. It is possible to change them individually after they have been created.
       </p>
       <p>
         Note that <strong>Download</strong> is shown but only applicable to some types. Where not applicable, then <strong>View</strong> will be applied.

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>

app/views/workflows/show.html.erb

@@ -29,11 +29,12 @@
 
         <% begin %>
           <% if @display_workflow.diagram_exists? || @display_workflow.can_render_diagram? %>
+            <% diagram_path = diagram_workflow_path(@workflow, version: @display_workflow.version) %>
+            <% is_svg = @display_workflow&.diagram&.extension == 'svg' %>
             <div class="row">
               <div class="col-md-12">
                 <div class="workflow-diagram">
-                  <% diagram_path = diagram_workflow_path(@workflow, version: @display_workflow.version) %>
-                  <% if @display_workflow&.diagram.extension == 'svg' %>
+                  <% if is_svg %>
                     <%= content_tag(:embed, '', type: 'image/svg+xml', src: diagram_path, class: 'svg-pan-zoom', width: 1000, height: 500)  %>
                     <p class="help-block">Click and drag the diagram to pan, double click or use the controls to zoom.</p>
                   <% else %>
@@ -44,7 +45,7 @@
             </div>
           <% end %>
         <% rescue StandardError => e %>
-          <% raise e if Rails.env.development? %>
+          <% raise e unless Rails.env.production? %>
           <% Rails.logger.error(e.inspect) %>
           <% Rails.logger.error(e.backtrace.join("\n")) %>
           <div class="alert alert-warning">Could not render the workflow diagram.</div>

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

config/version.yml

@@ -9,4 +9,4 @@
 
 major:        1
 minor:        16
-patch:        0-pre
+patch:        0

docker-compose-relative-root.yml

@@ -13,7 +13,7 @@ services:
   seek: # The SEEK application
     #build: .
 
-    image: fairdom/seek:1.16-dev
+    image: fairdom/seek:1.16
 
     container_name: seek
     command: docker/entrypoint.sh
@@ -42,7 +42,7 @@ services:
   seek_workers: # The SEEK delayed job workers
       #build: .
 
-      image: fairdom/seek:1.16-dev
+      image: fairdom/seek:1.16
       container_name: seek-workers
       command: docker/start_workers.sh
       restart: always

docker-compose-virtuoso.yml

@@ -11,7 +11,7 @@ services:
 
   seek: # The SEEK application
     #build: .
-    image: fairdom/seek:1.16-dev
+    image: fairdom/seek:1.16
     container_name: seek
     command: docker/entrypoint.sh
     restart: always
@@ -38,7 +38,7 @@ services:
 
   seek_workers: # The SEEK delayed job workers
     #build: .
-    image: fairdom/seek:1.16-dev
+    image: fairdom/seek:1.16
     container_name: seek-workers
     command: docker/start_workers.sh
     restart: always

docker-compose-with-email.yml

@@ -13,7 +13,7 @@ services:
   seek: # The SEEK application
     #build: .
 
-    image: fairdom/seek:1.16-dev
+    image: fairdom/seek:1.16
 
     container_name: seek
     command: docker/entrypoint.sh
@@ -42,7 +42,7 @@ services:
   seek_workers: # The SEEK delayed job workers
       #build: .
 
-      image: fairdom/seek:1.16-dev
+      image: fairdom/seek:1.16
       container_name: seek-workers
       command: docker/start_workers.sh
       restart: always

docker-compose.yml

@@ -13,7 +13,7 @@ services:
   seek: # The SEEK application
     #build: .
 
-    image: fairdom/seek:1.16-dev
+    image: fairdom/seek:1.16
 
     container_name: seek
     command: docker/entrypoint.sh
@@ -41,7 +41,7 @@ services:
   seek_workers: # The SEEK delayed job workers
       #build: .
 
-      image: fairdom/seek:1.16-dev
+      image: fairdom/seek:1.16
       container_name: seek-workers
       command: docker/start_workers.sh
       restart: always

lib/tasks/seek_dev.rake

@@ -413,7 +413,7 @@ namespace :seek_dev do
     pub_ids = Project.find(project_id).publications.map(&:id)
     pub_ids.each do |id|
       permission = Publication.find(id).policy.permissions.where(contributor_type: "Person", contributor_id: person_id).first_or_initialize
-      permission.update_attributes(access_type: Policy::MANAGING)
+      permission.update(access_type: Policy::MANAGING)
     end
 
   end

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

script/ansible/Deploy-SEEK.yml

@@ -192,6 +192,7 @@
     - name: Install SEEK's python requirements
       shell: bash -lc "{{ item }}"
       with_items:
+        - python3.9 -m pip install --upgrade pip
         - python3.9 -m pip install setuptools==58
         - python3.9 -m pip install -r requirements.txt
       args:

test/functional/documents_controller_test.rb

@@ -711,7 +711,7 @@ class DocumentsControllerTest < ActionController::TestCase
 
     assert_select '.filter-category[data-filter-category="project"]' do
       assert_select '.filter-category-title', text: 'Project'
-      assert_select '.filter-option', count: 2
+      assert_select ".filter-option[rel='nofollow']", count: 2
       assert_select '.filter-option.filter-option-active', count: 0
       assert_select ".filter-option[title='#{project.title}']" do
         assert_select '[href=?]', documents_path(filter: { project: project.id })
@@ -728,7 +728,7 @@ class DocumentsControllerTest < ActionController::TestCase
 
     assert_select '.filter-category[data-filter-category="contributor"]' do
       assert_select '.filter-category-title', text: 'Submitter'
-      assert_select '.filter-option', href: /documents\?filter\[contributor\]=\d+/, count: 8
+      assert_select ".filter-option[rel='nofollow']", href: /documents\?filter\[contributor\]=\d+/, count: 8
       assert_select '.filter-option.filter-option-active', count: 0
       # Should show 6 options and hide the rest
       assert_select '.filter-option.filter-option-hidden', count: 2
@@ -737,7 +737,7 @@ class DocumentsControllerTest < ActionController::TestCase
 
     assert_select '.filter-category[data-filter-category="tag"]' do
       assert_select '.filter-category-title', text: 'Tag'
-      assert_select '.filter-option', count: 1
+      assert_select ".filter-option[rel='nofollow']", count: 1
       assert_select '.filter-option.filter-option-active', count: 0
       assert_select ".filter-option[title='awkward&id=1unsafe[]tag !']" do
         assert_select '.filter-option-label', text: 'awkward&id=1unsafe[]tag !'
@@ -772,14 +772,14 @@ class DocumentsControllerTest < ActionController::TestCase
     # Should show other project in projects category
     assert_select '.filter-category[data-filter-category="project"]' do
       assert_select '.filter-category-title', text: 'Project'
-      assert_select '.filter-option.filter-option-active', count: 1
-      assert_select '.filter-option', count: 2
-      assert_select ".filter-option[title='#{project.title}']" do
+      assert_select ".filter-option[rel='nofollow'].filter-option-active", count: 1
+      assert_select ".filter-option[rel='nofollow']", count: 2
+      assert_select ".filter-option[title='#{project.title}'][rel='nofollow']" do
         assert_select '[href=?]', documents_path(filter: { programme: programme.id, project: [other_project.id, project.id] })
         assert_select '.filter-option-label', text: project.title
         assert_select '.filter-option-count', text: '7'
       end
-      assert_select ".filter-option[title='#{other_project.title}'].filter-option-active" do
+      assert_select ".filter-option[title='#{other_project.title}'][rel='nofollow'].filter-option-active" do
         assert_select '[href=?]', documents_path(filter: { programme: programme.id })
         assert_select '.filter-option-label', text: other_project.title
         assert_select '.filter-option-count', text: '1'
@@ -789,7 +789,7 @@ class DocumentsControllerTest < ActionController::TestCase
 
     assert_select '.filter-category[data-filter-category="contributor"]' do
       assert_select '.filter-category-title', text: 'Submitter'
-      assert_select '.filter-option', count: 1
+      assert_select ".filter-option[rel='nofollow']", count: 1
       assert_select '.filter-option.filter-option-active', count: 0
       assert_select '.filter-option.filter-option-hidden', count: 0
       assert_select ".filter-option[title='#{other_project_doc.contributor.name}']" do
@@ -808,11 +808,11 @@ class DocumentsControllerTest < ActionController::TestCase
 
     assert_select '.active-filters' do
       assert_select '.active-filter-category-title', count: 2
-      assert_select ".filter-option[title='#{programme.title}'].filter-option-active" do
+      assert_select ".filter-option[title='#{programme.title}'][rel='nofollow'].filter-option-active" do
         assert_select '[href=?]', documents_path(filter: { project: other_project.id })
         assert_select '.filter-option-label', text: programme.title
       end
-      assert_select ".filter-option[title='#{other_project.title}'].filter-option-active" do
+      assert_select ".filter-option[title='#{other_project.title}'][rel='nofollow'].filter-option-active" do
         assert_select '[href=?]', documents_path(filter: { programme: programme.id })
         assert_select '.filter-option-label', text: other_project.title
       end