Removed unused contig attributes.

app/controllers/contigs_controller.rb

@@ -429,8 +429,14 @@ def set_contig
   end
 
   # Never trust parameters from the scary internet, only allow the white list through.
+  #TODO mira and marker only used by fastq export
+  #TODO contig_names is only used by contig compare feature
+  #TODO filename and fastastring are only used by change via script action
+  #TODO: isolate_name used in form for contig, but cant that be done via id?
   def contig_params
-    params.require(:contig).permit(:mira, :marker, :overlap_length, :allowed_mismatch_percent, :imported, :contig_names, :filename, :fastastring, :comment, :assembled, :name, :consensus, :marker_id, :isolate_id, :marker_sequence_id, :chromatograms, :term,
-                                   :isolate_name, :verified, project_ids: [])
+    params.require(:contig).permit(:mira, :marker, :overlap_length, :allowed_mismatch_percent, :imported, :contig_names,
+                                   :filename, :fastastring, :comment, :assembled, :name, :consensus, :marker_id,
+                                   :isolate_id, :marker_sequence_id, :term, :isolate_name, :verified,
+                                   project_ids: [])
   end
 end

app/workers/compare_contigs.rb

@@ -1,6 +1,5 @@
 # frozen_string_literal: true
 
-# TODO: Marked for removal
 class CompareContigs
   include Sidekiq::Worker
 

db/migrate/20181018093520_remove_partial_cons_text_columns_from_contigs.rb

@@ -0,0 +1,6 @@
+class RemovePartialConsTextColumnsFromContigs < ActiveRecord::Migration[5.0]
+  def change
+    remove_column :contigs, :partial_cons1, :text
+    remove_column :contigs, :partial_cons2, :text
+  end
+end

db/migrate/20181018094614_remove_unused_columns_from_contigs.rb

@@ -0,0 +1,6 @@
+class RemoveUnusedColumnsFromContigs < ActiveRecord::Migration[5.0]
+  def change
+    remove_column :contigs, :aligned_cons, :string
+    remove_column :contigs, :overlaps, :integer
+  end
+end

db/schema.rb

@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 20181017085059) do
+ActiveRecord::Schema.define(version: 20181018094614) do
 
   # These are extensions that must be enabled in order to support this database
   enable_extension "plpgsql"
@@ -72,11 +72,7 @@
     t.integer  "isolate_id"
     t.integer  "marker_id"
     t.boolean  "assembled"
-    t.integer  "overlaps"
-    t.text     "partial_cons1"
-    t.text     "partial_cons2"
     t.boolean  "assembly_tried"
-    t.string   "aligned_cons",             limit: 255
     t.text     "fas"
     t.boolean  "verified",                             default: false
     t.integer  "verified_by"