From a6be662263c9267d89dbecc3b775169c3be0bcda Mon Sep 17 00:00:00 2001
From: Stuart Owen <stuart.owen@manchester.ac.uk>
Date: Mon, 2 Dec 2024 10:37:13 +0000
Subject: [PATCH 1/7] override some acts_as_asset and make a sample type
 neither an asset or downloadable? #2084

---
 app/models/sample_type.rb     | 17 +++++++++++++----
 test/unit/sample_type_test.rb |  7 +++++++
 2 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/app/models/sample_type.rb b/app/models/sample_type.rb
index d4b009245d..30c5f4a3cb 100644
--- a/app/models/sample_type.rb
+++ b/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
diff --git a/test/unit/sample_type_test.rb b/test/unit/sample_type_test.rb
index f5b7f93817..ab6d3b6979 100644
--- a/test/unit/sample_type_test.rb
+++ b/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

From 3aa4cb180e3743474dd7fef86d40ebf4f5400d3a Mon Sep 17 00:00:00 2001
From: Stuart Owen <stuart.owen@manchester.ac.uk>
Date: Mon, 2 Dec 2024 13:54:32 +0000
Subject: [PATCH 2/7] update upgrade task to set to accessible #2084

also a only once task to fix the previously updated permissions
---
 lib/tasks/seek_upgrades.rake | 22 +++++++++++++++++++---
 1 file changed, 19 insertions(+), 3 deletions(-)

diff --git a/lib/tasks/seek_upgrades.rake b/lib/tasks/seek_upgrades.rake
index d7b4717488..743be5d09d 100644
--- a/lib/tasks/seek_upgrades.rake
+++ b/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 +126,22 @@ 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
+      puts '... Finished updating previous sample type permissions'
+    end
   end
 
   private

From ad3eb186a7533beaff3a969da8f72e435f62f949 Mon Sep 17 00:00:00 2001
From: Stuart Owen <stuart.owen@manchester.ac.uk>
Date: Mon, 2 Dec 2024 15:05:25 +0000
Subject: [PATCH 3/7] ensure the template details and download link only shown
 if accessible #2084

---
 app/views/sample_types/_template.html.erb     |  2 ++
 app/views/sample_types/show.html.erb          |  2 +-
 .../sample_types_controller_test.rb           | 25 +++++++++++++++++++
 3 files changed, 28 insertions(+), 1 deletion(-)

diff --git a/app/views/sample_types/_template.html.erb b/app/views/sample_types/_template.html.erb
index 3fc87d9b24..4e85a2bcb4 100644
--- a/app/views/sample_types/_template.html.erb
+++ b/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 %>
diff --git a/app/views/sample_types/show.html.erb b/app/views/sample_types/show.html.erb
index 53c5740fe2..b3d622d902 100644
--- a/app/views/sample_types/show.html.erb
+++ b/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>
diff --git a/test/functional/sample_types_controller_test.rb b/test/functional/sample_types_controller_test.rb
index 2c7ca980c0..b90e5259b2 100644
--- a/test/functional/sample_types_controller_test.rb
+++ b/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)

From 8139c54960e75271e36cf7478102f962c7944565 Mon Sep 17 00:00:00 2001
From: Stuart Owen <stuart.owen@manchester.ac.uk>
Date: Tue, 3 Dec 2024 13:00:43 +0000
Subject: [PATCH 4/7] queue sample type authlookup jobs when fixing permissions
 #2084

---
 lib/tasks/seek_upgrades.rake | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/tasks/seek_upgrades.rake b/lib/tasks/seek_upgrades.rake
index 743be5d09d..c08bf5f80c 100644
--- a/lib/tasks/seek_upgrades.rake
+++ b/lib/tasks/seek_upgrades.rake
@@ -140,6 +140,7 @@ namespace :seek do
         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

From 51409e4e90c1c55a044818dc149c7ad93a3290c0 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 2 Dec 2024 22:19:16 +0000
Subject: [PATCH 5/7] Bump rails-html-sanitizer from 1.6.0 to 1.6.1

Bumps [rails-html-sanitizer](https://github.com/rails/rails-html-sanitizer) from 1.6.0 to 1.6.1.
- [Release notes](https://github.com/rails/rails-html-sanitizer/releases)
- [Changelog](https://github.com/rails/rails-html-sanitizer/blob/main/CHANGELOG.md)
- [Commits](https://github.com/rails/rails-html-sanitizer/compare/v1.6.0...v1.6.1)

---
updated-dependencies:
- dependency-name: rails-html-sanitizer
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 Gemfile.lock | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index a96deb5eee..d9f1c72416 100644
--- a/Gemfile.lock
+++ b/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)

From 3958ab5a073e6a84943ea994b3b850c631dda128 Mon Sep 17 00:00:00 2001
From: Stuart Owen <stuart.owen@manchester.ac.uk>
Date: Tue, 3 Dec 2024 13:45:29 +0000
Subject: [PATCH 6/7] updated help links for extended metadata to point to the
 website #2080

---
 config/help_links.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/config/help_links.yml b/config/help_links.yml
index a89de441cd..fa4529d68f 100644
--- a/config/help_links.yml
+++ b/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
\ No newline at end of file
+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
\ No newline at end of file

From 69035753616de84896cb6cc01b2cde707ccfe9a2 Mon Sep 17 00:00:00 2001
From: Stuart Owen <stuart.owen@manchester.ac.uk>
Date: Fri, 6 Dec 2024 09:39:34 +0000
Subject: [PATCH 7/7] update versions for 1.16.0

---
 config/version.yml               | 2 +-
 docker-compose-relative-root.yml | 4 ++--
 docker-compose-virtuoso.yml      | 4 ++--
 docker-compose-with-email.yml    | 4 ++--
 docker-compose.yml               | 4 ++--
 5 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/config/version.yml b/config/version.yml
index bf8dffd835..ed772484f9 100644
--- a/config/version.yml
+++ b/config/version.yml
@@ -9,4 +9,4 @@
 
 major:        1
 minor:        16
-patch:        0-pre
+patch:        0
diff --git a/docker-compose-relative-root.yml b/docker-compose-relative-root.yml
index 621085516c..48ebc41fab 100644
--- a/docker-compose-relative-root.yml
+++ b/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
diff --git a/docker-compose-virtuoso.yml b/docker-compose-virtuoso.yml
index 693f4f83d7..d30abc3fd5 100644
--- a/docker-compose-virtuoso.yml
+++ b/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
diff --git a/docker-compose-with-email.yml b/docker-compose-with-email.yml
index 43e9b3c771..5dd7d7f779 100644
--- a/docker-compose-with-email.yml
+++ b/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
diff --git a/docker-compose.yml b/docker-compose.yml
index dc96dd69cf..3ff795a728 100644
--- a/docker-compose.yml
+++ b/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