From a562a73ad89aaf1870704bb8426586ad0225b099 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@vib.be>
Date: Wed, 10 Jan 2024 13:06:59 +0100
Subject: [PATCH] Add rake upgrade task for recognising ISA JSON compliant
 investigations

---
 lib/tasks/seek_upgrades.rake | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/lib/tasks/seek_upgrades.rake b/lib/tasks/seek_upgrades.rake
index 3b2dfccb81..672b0d1d2c 100644
--- a/lib/tasks/seek_upgrades.rake
+++ b/lib/tasks/seek_upgrades.rake
@@ -15,6 +15,7 @@ namespace :seek do
     rename_registered_sample_multiple_attribute_type
     remove_ontology_attribute_type
     db:seed:007_sample_attribute_types
+    recognise_isa_json_compliant_items
   ]
 
   # these are the tasks that are executes for each upgrade as standard, and rarely change
@@ -156,6 +157,21 @@ namespace :seek do
     puts " ... finished updating sample_resource_links of #{samples_updated.to_s} samples with data_file attributes"
   end
 
+  task(recognise_isa_json_compliant_items: [:environment]) do
+    puts '... searching for ISA compliant investigations'
+    investigations_updated = 0
+    disable_authorization_checks do
+      isa_json_compliant_studies = Study.all.select { |study| study.sample_types.any? }
+      isa_json_compliant_studies.each do |study|
+        inv = study.investigation
+        inv.update(is_isa_json_compliant: true)
+        inv.save
+        investigations_updated += 1
+      end
+    end
+    puts "...Updated #{investigations_updated} investigations"
+  end
+
   private
 
   ##