From 5a3b262fa459b5d30ab38def6e32eadbf3c966ae Mon Sep 17 00:00:00 2001
From: Alex Kriuchykhin <oleksii@scinote.net>
Date: Tue, 5 Dec 2023 13:27:20 +0100
Subject: [PATCH 1/4] Update Yomu gem, add reset protocols creator user
 assignments and extract missing asset texts rake tasks [SCI-9812] (#6761)

---
 Gemfile.lock        |  2 +-
 lib/tasks/data.rake | 38 +++++++++++++++++++++++++++++++++++++-
 2 files changed, 38 insertions(+), 2 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index e41c2e6b8..7191d38a8 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -50,7 +50,7 @@ GIT
 
 GIT
   remote: https://github.com/scinote-eln/yomu
-  revision: 020ab670b2919f3b436e926a890d1dad23d75676
+  revision: 09b7b4910f59453970aab03d7b3ddb60b41db89a
   branch: master
   specs:
     yomu (0.2.4)
diff --git a/lib/tasks/data.rake b/lib/tasks/data.rake
index 98d3a9450..8caefd19e 100644
--- a/lib/tasks/data.rake
+++ b/lib/tasks/data.rake
@@ -1,3 +1,7 @@
+# frozen_string_literal: true
+
+# rubocop:disable Metrics/BlockLength
+
 namespace :data do
   Rails.logger = Logger.new(STDOUT)
 
@@ -5,7 +9,6 @@ namespace :data do
   task clean_temp_files: :environment do
     Rails.logger.info "Cleaning temporary files older than 3 days"
     TempFile.where("created_at < ?", 3.days.ago).each do |tmp_file|
-
       TempFile.transaction do
         begin
           tmp_file.destroy!
@@ -194,4 +197,37 @@ namespace :data do
       end
     end
   end
+
+  desc 'Reset protocols creator user assignments'
+  task reset_protocols_creator_user_assignments: :environment do
+    ActiveRecord::Base.transaction do
+      owner_role = UserRole.find_predefined_owner_role
+      protocols =
+        Protocol.where(protocol_type: Protocol::REPOSITORY_TYPES)
+                .joins('LEFT OUTER JOIN "user_assignments" ON "user_assignments"."assignable_type" = \'Protocol\' ' \
+                       'AND "user_assignments"."assignable_id" = "protocols"."id" ' \
+                       'AND "user_assignments"."assigned" = 1 ' \
+                       'AND "user_assignments"."user_id" = "protocols"."added_by_id"')
+                .where('"user_assignments"."id" IS NULL')
+                .distinct
+      protocols.find_each do |protocol|
+        new_user_assignment = protocol.user_assignments
+                                      .find_or_initialize_by(user: protocol.added_by, team: protocol.team)
+        new_user_assignment.user_role = owner_role
+        new_user_assignment.assigned_by = protocol.added_by
+        new_user_assignment.assigned = :manually
+        new_user_assignment.save!
+      end
+    end
+  end
+
+  desc 'Extract missing asset texts'
+  task extract_missing_asset_texts: :environment do
+    Asset.joins(:file_blob)
+         .where.missing(:asset_text_datum)
+         .where(file_blob: { content_type: Constants::TEXT_EXTRACT_FILE_TYPES })
+         .find_each(&:extract_asset_text)
+  end
 end
+
+# rubocop:enable Metrics/BlockLength

From 5c852a1aa4f0f5952d404dbe055f653598a12ad9 Mon Sep 17 00:00:00 2001
From: Alex Kriuchykhin <oleksii@scinote.net>
Date: Fri, 8 Dec 2023 11:29:11 +0100
Subject: [PATCH 2/4] Trigger file text extraction on file update in an
 inventory [SCI-9842] (#6782)

---
 app/models/repository_asset_value.rb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/app/models/repository_asset_value.rb b/app/models/repository_asset_value.rb
index f619d5cd4..1d76ac298 100644
--- a/app/models/repository_asset_value.rb
+++ b/app/models/repository_asset_value.rb
@@ -70,6 +70,7 @@ class RepositoryAssetValue < ApplicationRecord
     asset.last_modified_by = user
     self.last_modified_by = user
     asset.save! && save!
+    asset.post_process_file(repository_cell.repository_column.repository.team)
   end
 
   def snapshot!(cell_snapshot)

From b089a85bc53829f72c467fc4cf916d3eb61c57aa Mon Sep 17 00:00:00 2001
From: Alex Kriuchykhin <oleksii@scinote.net>
Date: Fri, 8 Dec 2023 11:29:24 +0100
Subject: [PATCH 3/4] Update revision of Yomu gem [SCI-9824] (#6783)

---
 Gemfile.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 7191d38a8..16d9f6beb 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -50,7 +50,7 @@ GIT
 
 GIT
   remote: https://github.com/scinote-eln/yomu
-  revision: 09b7b4910f59453970aab03d7b3ddb60b41db89a
+  revision: fb518a5fbab82f692dea4ae1fdf30eae5df62590
   branch: master
   specs:
     yomu (0.2.4)

From 88543e792d93091a7462b3d769f39f63a0c47b6f Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <oleksii@scinote.net>
Date: Fri, 29 Dec 2023 11:36:55 +0100
Subject: [PATCH 4/4] Bump version to 1.28.0.7

---
 VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/VERSION b/VERSION
index b9acb1a38..1e6b3fcf0 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.28.0.6
+1.28.0.7