Add Rails config to Rubocop linter

.rubocop.yml

@@ -1,3 +1,6 @@
+require:
+  - rubocop-rails
+
 AllCops:
   Exclude:
     - "Gemfile"

Gemfile

@@ -65,3 +65,5 @@ gem "capistrano", "~> 3.17"
 gem "capistrano-bundler", "~> 2.1"
 
 gem "capistrano-rvm", "~> 0.1.2"
+
+gem 'rubocop-rails', '~> 2.18'

Gemfile.lock

@@ -207,6 +207,10 @@ GEM
       unicode-display_width (>= 1.4.0, < 3.0)
     rubocop-ast (1.21.0)
       parser (>= 3.1.1.0)
+    rubocop-rails (2.18.0)
+      activesupport (>= 4.2.0)
+      rack (>= 1.1)
+      rubocop (>= 1.33.0, < 2.0)
     ruby-progressbar (1.11.0)
     ruby2_keywords (0.0.5)
     sawyer (0.9.2)
@@ -247,6 +251,7 @@ DEPENDENCIES
   rails-controller-testing (~> 1.0)
   responders (~> 3.0)
   rubocop (~> 1.36)
+  rubocop-rails (~> 2.18)
   stathat (~> 0.1.7)
   tzinfo-data
 

app/controllers/api/api_controller.rb

@@ -264,7 +264,7 @@ def taxa2tree
   # param[names]: "true" or "false", Include the lineage names
   def taxonomy
     @result = @query.where(id: @input)
-    @result = Hash[@result.map { |t| [t.id, t] }]
+    @result = @result.index_by(&:id)
     @input_order = @input.select { |i| @result.key? i.to_i }
     @result = @input_order.map { |i| @result[i.to_i] }
     respond_with(@result)

app/models/peptide.rb

@@ -13,7 +13,7 @@ class Peptide < ApplicationRecord
 
   belongs_to :uniprot_entry
   belongs_to :sequence
-  belongs_to :original_sequence, foreign_key: 'original_sequence_id', primary_key: 'id', class_name: 'Sequence'
+  belongs_to :original_sequence, primary_key: 'id', class_name: 'Sequence'
 
   # since this is a read-only model, these validations aren't used
   validates :sequence_id, presence: true

app/models/uniprot_entry.rb

@@ -26,9 +26,9 @@ class UniprotEntry < ApplicationRecord
   has_many :go_terms, through: :go_cross_references
   has_many :interpro_entries, through: :interpro_cross_references
 
-  belongs_to :taxon,            foreign_key: 'taxon_id',
-                                primary_key: 'id',
-                                class_name: 'Taxon'
+  belongs_to :taxon,
+             primary_key: 'id',
+             class_name: 'Taxon'
 
   belongs_to :lineage,          foreign_key: 'taxon_id',
                                 primary_key: 'taxon_id',
@@ -63,7 +63,7 @@ def self.summarize_fa(entries)
         GoCrossReference
           .where(uniprot_entry_id: id_batch)
           .all
-          .each do |cr|
+          .find_each do |cr|
             ups_with_go.add(cr.uniprot_entry_id)
             # Also count in how many proteins this GO term occurs
             data[cr.go_term_code] += 1
@@ -77,7 +77,7 @@ def self.summarize_fa(entries)
       EcCrossReference
         .where(uniprot_entry_id: id_batch)
         .all
-        .each do |cr|
+        .find_each do |cr|
         ups_with_ec.add(cr.uniprot_entry_id)
         # Also count in how many proteins this EC number occurs
         data["EC:#{cr.ec_number_code}"] += 1
@@ -91,7 +91,7 @@ def self.summarize_fa(entries)
       InterproCrossReference
         .where(uniprot_entry_id: id_batch)
         .all
-        .each do |cr|
+        .find_each do |cr|
         ups_with_ipr.add(cr.uniprot_entry_id)
         data["IPR:#{cr.interpro_entry_code}"] += 1
       end