From 6a988e63325086aa89e7c2f509cf881e5a7a4164 Mon Sep 17 00:00:00 2001
From: Xiaoming Hu <xiaoming.hu@h-its.org>
Date: Thu, 8 May 2025 15:42:00 +0200
Subject: [PATCH 1/3] add rake task to update morpheus models

---
 lib/tasks/seek_upgrades.rake | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/lib/tasks/seek_upgrades.rake b/lib/tasks/seek_upgrades.rake
index 60f568af52..791eb05777 100644
--- a/lib/tasks/seek_upgrades.rake
+++ b/lib/tasks/seek_upgrades.rake
@@ -9,11 +9,14 @@ namespace :seek do
   task upgrade_version_tasks: %i[
     environment
     db:seed:007_sample_attribute_types
+    db:seed:003_model_formats
+    db:seed:004_model_recommended_environments
     update_rdf
     update_observation_unit_policies
     fix_xlsx_marked_as_zip
     add_policies_to_existing_sample_types
     fix_previous_sample_type_permissions
+    update_morpheus_model
   ]
 
   # these are the tasks that are executes for each upgrade as standard, and rarely change
@@ -91,6 +94,22 @@ namespace :seek do
     end
   end
 
+  task(update_morpheus_model: [:environment]) do
+    puts "... updating morpheus model"
+    Model.all.each do |model|
+      next unless model.is_morpheus_supported?
+      unless model.model_format
+        model.model_format = ModelFormat.find_by(title: 'Morpheus')
+      end
+      unless model.recommended_environment
+        model.recommended_environment = RecommendedModelEnvironment.find_by(title: 'Morpheus')
+      end
+      model.save
+      model.update_column(:model_format_id, model.model_format_id)
+      model.update_column(:recommended_environment_id, model.recommended_environment_id)
+    end
+  end
+
   task(add_policies_to_existing_sample_types: [:environment]) do
     puts '... Adding policies to existing sample types'
     counter = 0

From 01c426735b4feb6f8774d9c6e813174c0ae485aa Mon Sep 17 00:00:00 2001
From: Xiaoming Hu <xiaoming.hu@h-its.org>
Date: Wed, 4 Jun 2025 12:46:01 +0200
Subject: [PATCH 2/3] update PR according to Copilot review

---
 lib/tasks/seek_upgrades.rake | 22 +++++++++++++---------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/lib/tasks/seek_upgrades.rake b/lib/tasks/seek_upgrades.rake
index 791eb05777..a3a3220648 100644
--- a/lib/tasks/seek_upgrades.rake
+++ b/lib/tasks/seek_upgrades.rake
@@ -8,9 +8,9 @@ namespace :seek do
   # these are the tasks required for this version upgrade
   task upgrade_version_tasks: %i[
     environment
-    db:seed:007_sample_attribute_types
     db:seed:003_model_formats
     db:seed:004_model_recommended_environments
+    db:seed:007_sample_attribute_types
     update_rdf
     update_observation_unit_policies
     fix_xlsx_marked_as_zip
@@ -96,17 +96,21 @@ namespace :seek do
 
   task(update_morpheus_model: [:environment]) do
     puts "... updating morpheus model"
-    Model.all.each do |model|
+    Model.find_each do |model|
       next unless model.is_morpheus_supported?
-      unless model.model_format
-        model.model_format = ModelFormat.find_by(title: 'Morpheus')
-      end
-      unless model.recommended_environment
-        model.recommended_environment = RecommendedModelEnvironment.find_by(title: 'Morpheus')
+      begin
+        unless model.model_format
+          model.model_format = ModelFormat.find_by!(title: 'Morpheus')
+        end
+        unless model.recommended_environment
+          model.recommended_environment = RecommendedModelEnvironment.find_by!(title: 'Morpheus')
+        end
+      rescue ActiveRecord::RecordNotFound => e
+        puts "Error: #{e.message}. Ensure that the required 'Morpheus' records exist in the database."
+        abort("Aborting task due to missing 'Morpheus' records.")
       end
       model.save
-      model.update_column(:model_format_id, model.model_format_id)
-      model.update_column(:recommended_environment_id, model.recommended_environment_id)
+      model.update_columns(model_format_id: model.model_format_id, recommended_environment_id: model.recommended_environment_id)
     end
   end
 

From 95c9e92e33e27daff4e0fc36102f62e9cb988eaa Mon Sep 17 00:00:00 2001
From: Xiaoming Hu <xiaoming.hu@h-its.org>
Date: Wed, 4 Jun 2025 16:24:02 +0200
Subject: [PATCH 3/3] remove model.save to avoid timestamps being changed

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

diff --git a/lib/tasks/seek_upgrades.rake b/lib/tasks/seek_upgrades.rake
index a3a3220648..0588294723 100644
--- a/lib/tasks/seek_upgrades.rake
+++ b/lib/tasks/seek_upgrades.rake
@@ -109,7 +109,6 @@ namespace :seek do
         puts "Error: #{e.message}. Ensure that the required 'Morpheus' records exist in the database."
         abort("Aborting task due to missing 'Morpheus' records.")
       end
-      model.save
       model.update_columns(model_format_id: model.model_format_id, recommended_environment_id: model.recommended_environment_id)
     end
   end