From 1ea11b2a8f59a7855cdd2fcc05f684d2dfc7ccde Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@vib.be>
Date: Thu, 20 Jun 2024 09:50:51 +0200
Subject: [PATCH] Use FileUtils instead of raw shell commands

---
 app/controllers/templates_controller.rb      | 8 ++++----
 lib/seek/isa_templates/template_extractor.rb | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/app/controllers/templates_controller.rb b/app/controllers/templates_controller.rb
index 908b9e0b27..b099d8bdda 100644
--- a/app/controllers/templates_controller.rb
+++ b/app/controllers/templates_controller.rb
@@ -94,7 +94,7 @@ def populate_template
     dir = Seek::Config.append_filestore_path('source_types')
 
     if Dir.exist?(dir)
-      `rm #{dir}/*`
+      FileUtils.delete(Dir.glob("#{dir}/*"))
     else
       FileUtils.mkdir_p(dir)
     end
@@ -172,7 +172,7 @@ def set_status
     elsif File.exist?(resultfile)
       res = File.read(resultfile)
       @status = res
-      `rm #{resultfile}`
+      FileUtils.delete(resultfile)
     else
       @status = 'not_started'
     end
@@ -187,12 +187,12 @@ def resultfile
   end
 
   def running!
-    `touch #{lockfile}`
+    FileUtils.touch(lockfile)
     set_status
   end
 
   def done!
-    `rm -f #{lockfile}`
+    FileUtils.delete(lockfile)
   end
 
   def running?
diff --git a/lib/seek/isa_templates/template_extractor.rb b/lib/seek/isa_templates/template_extractor.rb
index 18dbe5f1d6..4f11d633db 100644
--- a/lib/seek/isa_templates/template_extractor.rb
+++ b/lib/seek/isa_templates/template_extractor.rb
@@ -4,7 +4,7 @@ module Seek
   module IsaTemplates
     module TemplateExtractor
       def self.extract_templates
-        `touch #{resultfile}`
+        FileUtils.touch(resultfile)
         result = StringIO.new
         seed_isa_tags