Fix for_type function in AssayClass

ELIXIR-Belgium · Jan 17, 2024 · 60f9148 · 60f9148
1 parent 4415fe2
commit 60f9148
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Showing 8 changed files with 19 additions and 20 deletions.
diff --git a/app/controllers/isa_assays_controller.rb b/app/controllers/isa_assays_controller.rb
@@ -7,9 +7,9 @@ class IsaAssaysController < ApplicationController
 
   def new
     if params[:is_assay_stream]
-      @isa_assay = IsaAssay.new({ assay: { assay_class_id: AssayClass.find_by(key: 'ASS').id } })
+      @isa_assay = IsaAssay.new({ assay: { assay_class_id: AssayClass.for_type('assay_stream').id } })
     else
-      @isa_assay = IsaAssay.new({ assay: { assay_class_id: AssayClass.find_by(key: 'EXP').id } })
+      @isa_assay = IsaAssay.new({ assay: { assay_class_id: AssayClass.for_type('experimental').id } })
     end
   end
 
@@ -141,9 +141,9 @@ def set_up_instance_variable
 
   def find_requested_item
     if params[:is_assay_stream]
-      @isa_assay = IsaAssay.new({ assay: { assay_class_id: AssayClass.find_by(key: 'ASS').id } })
+      @isa_assay = IsaAssay.new({ assay: { assay_class_id: AssayClass.for_type('assay_stream').id } })
     else
-      @isa_assay = IsaAssay.new({ assay: { assay_class_id: AssayClass.find_by(key: 'EXP').id } })
+      @isa_assay = IsaAssay.new({ assay: { assay_class_id: AssayClass.for_type('experimental').id } })
     end
     @isa_assay.populate(params[:id])
 

diff --git a/app/models/assay_class.rb b/app/models/assay_class.rb
@@ -2,8 +2,8 @@ class AssayClass < ApplicationRecord
   # this returns an instance of AssayClass according to one of the types "experimental", "modelling" or "assay_stream"
   # if there is not a match nil is returned
   def self.for_type(type)
-    keys = { "experimental": 'EXP', "modelling": 'MODEL', 'assay_stream': 'ASS' }
-    AssayClass.find_by(key: keys[type])
+    keys = { "experimental": 'EXP', "modelling": 'MODEL', "assay_stream": 'ASS' }
+    AssayClass.find_by(key: keys[type.to_sym])
   end
 
   def self.experimental
@@ -15,7 +15,7 @@ def self.modelling
   end
 
   def self.assay_stream
-    for_type('assay_stream')
+    for_type('assaystream')
   end
 
   def is_modelling?

diff --git a/app/views/isa_assays/_form.html.erb b/app/views/isa_assays/_form.html.erb
@@ -7,11 +7,11 @@
   if @isa_assay.assay.new_record?
     if params[:is_assay_stream]
       assay_position = 0
-      assay_class_id = AssayClass.find_by(key: 'ASS')&.id
+      assay_class_id = AssayClass.for_type('assay_stream').id
       is_assay_stream = true
     else
       assay_position = params[:source_assay_id].nil? ? 1 : source_assay.position + 1
-      assay_class_id = AssayClass.find_by(key: 'EXP')&.id
+      assay_class_id = AssayClass.for_type('experimental').id
       is_assay_stream = false
     end
   else

diff --git a/config/default_data/assay_classes.yml b/config/default_data/assay_classes.yml
@@ -6,4 +6,9 @@ experimental_assay_class:
 modelling_assay_class:
   id: 2
   title: <%= I18n.t('assays.modelling_analysis') %>
-  key: MODEL
+  key: MODEL
+
+assay_stream_class:
+  id: 3
+  title: <%= I18n.t('assays.assay_stream') %>
+  key: ASS
diff --git a/config/locales/en.yml b/config/locales/en.yml
@@ -16,6 +16,7 @@ en:
     assay: "Assay"
     experimental_assay: "Experimental assay"
     modelling_analysis:  "Modelling analysis"
+    assay_stream:  "Assay Stream"
 
   isa_study: "ISA Study"
   study_design: "Study Design"

diff --git a/db/seeds/017_minimal_starter_isa_templates.seeds.rb b/db/seeds/017_minimal_starter_isa_templates.seeds.rb
@@ -200,10 +200,3 @@
 end
 
 puts 'Seeded minimal templates for organizing ISA JSON compliant experiments.'
-
-disable_authorization_checks do
-  AssayClass.find_or_create_by(title: 'Assay Stream', key: 'ASS',
-                               description: 'Special type of class that is user in Single Page, specifying this is a container for a stream of assays')
-end
-
-puts 'Seeded Extra Assay Class'
diff --git a/lib/tasks/seek_upgrades.rake b/lib/tasks/seek_upgrades.rake
@@ -15,7 +15,7 @@ namespace :seek do
     rename_registered_sample_multiple_attribute_type
     remove_ontology_attribute_type
     db:seed:007_sample_attribute_types
-    db:seed:017_minimal_starter_isa_templates
+    db:seed:001_create_controlled_vocabs
     recognise_isa_json_compliant_items
   ]
 

diff --git a/test/fixtures/assay_classes.yml b/test/fixtures/assay_classes.yml
@@ -7,5 +7,5 @@ modelling_assay_class:
   key: MODEL
 
 assay_stream_class:
-  title: 'Assay Stream'
-  key: 'ASS'
+  title: <%= I18n.t('assays.assay_stream') %>
+  key: ASS