Merge branch 'main' of https://github.com/seq-code/registry

Author: lmrodriguezr

Gemfile

@@ -33,6 +33,7 @@ gem 'pdf-reader'
 gem 'pg'
 gem 'puma', '~> 5.6'
 gem 'rails', '~> 6.1'
+gem 'rack-attack'
 gem 'redcarpet', '~> 3.5'
 gem 'redirect_safely', '~> 1.0'
 gem 'rexml'
@@ -43,6 +44,7 @@ gem 'serrano', '~> 1.0'
 # simple_form 5.3.0 introduced a bug that prevents custom inputs from being
 # loaded (see https://github.com/heartcombo/simple_form/issues/1824)
 gem 'simple_form', '~> 5.2.0'
+gem 'sitemap_generator'
 gem 'strain-code', '~> 0.3'
 # Turbolinks makes navigating your web application faster.
 # Read more: https://github.com/turbolinks/turbolinks

Gemfile.lock

@@ -61,7 +61,7 @@ GEM
       minitest (>= 5.1)
       tzinfo (~> 2.0)
       zeitwerk (~> 2.3)
-    addressable (2.8.9)
+    addressable (2.9.0)
       public_suffix (>= 2.0.2, < 8.0)
     afm (1.0.0)
     ast (2.4.3)
@@ -116,30 +116,30 @@ GEM
     drb (2.2.3)
     erb (6.0.2)
     erubi (1.13.1)
-    execjs (2.10.0)
+    execjs (2.10.1)
     faraday (2.14.1)
       faraday-net_http (>= 2.0, < 3.5)
       json
       logger
-    faraday-follow_redirects (0.3.0)
+    faraday-follow_redirects (0.5.0)
       faraday (>= 1, < 3)
     faraday-net_http (3.4.2)
       net-http (~> 0.5)
-    ffi (1.17.3)
-    ffi (1.17.3-x86_64-darwin)
-    ffi (1.17.3-x86_64-linux-gnu)
+    ffi (1.17.4)
+    ffi (1.17.4-x86_64-darwin)
+    ffi (1.17.4-x86_64-linux-gnu)
     font_awesome5_rails (1.5.0)
       nokogiri (>= 1.11.3)
       railties (>= 4.2)
     globalid (1.3.0)
       activesupport (>= 6.1)
-    google-protobuf (4.34.0)
+    google-protobuf (4.34.1)
       bigdecimal
       rake (~> 13.3)
-    google-protobuf (4.34.0-x86_64-darwin)
+    google-protobuf (4.34.1-x86_64-darwin)
       bigdecimal
       rake (~> 13.3)
-    google-protobuf (4.34.0-x86_64-linux-gnu)
+    google-protobuf (4.34.1-x86_64-linux-gnu)
       bigdecimal
       rake (~> 13.3)
     hashery (2.1.2)
@@ -168,10 +168,7 @@ GEM
       rails-dom-testing (>= 1, < 3)
       railties (>= 4.2.0)
       thor (>= 0.14, < 2.0)
-    json (2.19.2)
-    json-schema (6.2.0)
-      addressable (~> 2.8)
-      bigdecimal (>= 3.1, < 5)
+    json (2.19.3)
     language_server-protocol (3.17.0.5)
     lint_roller (1.1.0)
     listen (3.0.8)
@@ -188,8 +185,6 @@ GEM
       net-pop
       net-smtp
     marcel (1.1.0)
-    mcp (0.9.0)
-      json-schema (>= 4.1)
     method_source (1.1.0)
     miga-base (1.4.2.1)
       daemons (~> 1.3)
@@ -203,7 +198,7 @@ GEM
       logger
     mini_mime (1.1.5)
     mini_portile2 (2.8.9)
-    minitest (6.0.2)
+    minitest (6.0.3)
       drb (~> 2.0)
       prism (~> 1.5)
     multi_json (1.19.1)
@@ -235,8 +230,8 @@ GEM
     openssl (3.3.2)
     orm_adapter (0.5.0)
     ostruct (0.6.3)
-    parallel (1.27.0)
-    parser (3.3.10.2)
+    parallel (1.28.0)
+    parser (3.3.11.1)
       ast (~> 2.4.1)
       racc
     pdf-reader (2.15.1)
@@ -260,7 +255,9 @@ GEM
     puma (5.6.9)
       nio4r (~> 2.0)
     racc (1.8.1)
-    rack (2.2.22)
+    rack (2.2.23)
+    rack-attack (6.8.0)
+      rack (>= 1.0, < 4)
     rack-proxy (0.7.7)
       rack
     rack-test (2.2.0)
@@ -306,7 +303,7 @@ GEM
     redirect_safely (1.0.0)
       activemodel
     redis (4.8.1)
-    regexp_parser (2.11.3)
+    regexp_parser (2.12.0)
     reline (0.6.3)
       io-console (~> 0.5)
     responders (3.1.1)
@@ -316,11 +313,10 @@ GEM
     roo (2.9.0)
       nokogiri (~> 1)
       rubyzip (>= 1.3.0, < 3.0.0)
-    rubocop (1.85.1)
+    rubocop (1.86.0)
       json (~> 2.3)
       language_server-protocol (~> 3.17.0.2)
       lint_roller (~> 1.1.0)
-      mcp (~> 0.6)
       parallel (~> 1.10)
       parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
@@ -352,12 +348,12 @@ GEM
     rubyzip (2.4.1)
     sass (3.7.4)
       sass-listen (~> 4.0.0)
-    sass-embedded (1.98.0)
+    sass-embedded (1.99.0)
       google-protobuf (~> 4.31)
       rake (>= 13)
-    sass-embedded (1.98.0-x86_64-darwin)
+    sass-embedded (1.99.0-x86_64-darwin)
       google-protobuf (~> 4.31)
-    sass-embedded (1.98.0-x86_64-linux-gnu)
+    sass-embedded (1.99.0-x86_64-linux-gnu)
       google-protobuf (~> 4.31)
     sass-listen (4.0.0)
       rb-fsevent (~> 0.9, >= 0.9.4)
@@ -377,15 +373,17 @@ GEM
       rubyzip (>= 1.2.2, < 4.0)
       websocket (~> 1.0)
     semantic_range (3.1.1)
-    serrano (1.6)
-      faraday (~> 2.13, >= 2.13.1)
-      faraday-follow_redirects (>= 0.1, < 0.4)
-      multi_json (~> 1.15)
-      rexml (~> 3.2, >= 3.2.5)
-      thor (~> 1.2, >= 1.2.1)
+    serrano (1.7)
+      faraday (~> 2.14, >= 2.14.1)
+      faraday-follow_redirects (~> 0.5.0)
+      multi_json (~> 1.19, >= 1.19.1)
+      rexml (~> 3.4, >= 3.4.4)
+      thor (~> 1.5)
     simple_form (5.2.0)
       actionpack (>= 5.2)
       activemodel (>= 5.2)
+    sitemap_generator (6.3.0)
+      builder (~> 3.0)
     spring (2.1.1)
     spring-watcher-listen (2.0.1)
       listen (>= 2.7, < 4.0)
@@ -402,7 +400,7 @@ GEM
       mini_portile2 (~> 2.8.0)
     sqlite3 (2.9.2-x86_64-darwin)
     sqlite3 (2.9.2-x86_64-linux-gnu)
-    strain-code (0.4.0)
+    strain-code (0.4.2)
     stringio (3.2.0)
     thor (1.5.0)
     tilt (2.7.0)
@@ -486,6 +484,7 @@ DEPENDENCIES
   pdf-reader
   pg
   puma (~> 5.6)
+  rack-attack
   rails (~> 6.1)
   rdoc
   redcarpet (~> 3.5)
@@ -501,6 +500,7 @@ DEPENDENCIES
   selenium-webdriver
   serrano (~> 1.0)
   simple_form (~> 5.2.0)
+  sitemap_generator
   spring
   spring-watcher-listen (~> 2.0.0)
   strain-code (~> 0.3)

app/assets/javascripts/page.js

@@ -11,6 +11,10 @@ $(document).on("turbolinks:load", function() {
         $.get(container.data("async"), function(data) {
           container.find(".modal-body").html(data);
           t.data("loaded", true);
+        }).fail(function(data, err) {
+          container.find(".modal-body").html(
+            "Request failed with status " + data.status + " " + err
+          );
         });
     });
   });

app/controllers/application_controller.rb

@@ -42,7 +42,7 @@ def main
       names: Name.all_public.order(created_at: :desc),
       publications: Publication.all.order(journal_date: :desc),
       register_lists: Register.where(validated: true).order(updated_at: :desc),
-      genomes: Genome.all.order(created_at: :desc),
+      genomes: Genome.all_public.order(created_at: :desc),
       strains: Strain.all.order(created_at: :desc)
     }
     @display = {

app/controllers/genomes_controller.rb

@@ -16,7 +16,7 @@ class GenomesController < ApplicationController
 
   # GET /genomes or /genomes.json
   def index
-    @genomes = Genome.all.order(created_at: :desc)
+    @genomes = Genome.all_public.order(created_at: :desc)
                      .paginate(page: params[:page], per_page: 30)
     @crumbs = ['Genomes']
   end

app/controllers/journals_controller.rb

@@ -2,9 +2,8 @@ class JournalsController < ApplicationController
   # GET /journals
   # GET /journals.json
   def index
-    @journals = Publication.where.not(journal: ['', nil])
-          .select(:journal).reorder(:journal).distinct
-          .paginate(page: params[:page], per_page: 100)
+    @journals =
+      Publication.journals.paginate(page: params[:page], per_page: 100)
     @crumbs = ['Journals']
   end
 

app/controllers/names_controller.rb

@@ -1,16 +1,17 @@
 class NamesController < ApplicationController
   before_action(:set_tutorial)
+  before_action(:set_name_and_notifications, only: %i[show])
   before_action(
     :set_name,
     only: %i[
-      show edit update destroy network wiki
+      edit update destroy network wiki
       proposed_in not_validly_proposed_in emended_in assigned_in
       corrigendum_in corrigendum_orphan corrigendum
       edit_description edit_rank edit_notes edit_etymology edit_links edit_type
       edit_redirect autofill_etymology edit_parent
       return validate endorse claim unclaim demote temporary_editable
       transfer_user transfer_user_commit
-      new_correspondence observe unobserve
+      new_correspondence observe unobserve quality_checks
     ]
   )
   before_action(
@@ -256,7 +257,7 @@ def network
 
   # GET /names/1/wiki
   def wiki
-    @crumbs = [['Names', names_path], [@name.name_html, @name], 'Wiki source']
+    @crumbs = [['Names', names_path], [@name.abbr_name, @name], 'Wiki source']
     @name.check_wikispecies if current_user # Force re-check for logged users
   end
 
@@ -559,20 +560,37 @@ def unobserve
     end
   end
 
+  # GET /names/1/quality_checks
+  def quality_checks
+    @crumbs = [
+      ['Names', names_path],
+      [@name.abbr_name, @name],
+      'Quality Checks'
+    ]
+    render('quality_checks', layout: !params[:content].present?)
+  end
+
   private
 
     # Use callbacks to share common setup or constraints between actions
+    def set_name_and_notifications
+      if set_name
+        current_user
+          &.unseen_notifications
+          &.where(notifiable: @name)
+          &.update(seen: true)
+      end
+    end
+
     def set_name
       @name = Name.find(params[:id])
 
       if @name&.can_view?(current_user, cookies[:reviewer_token])
         @register = @name.try(:register)
-        current_user
-          &.unseen_notifications
-          &.where(notifiable: @name)
-          &.update(seen: true)
+        true
       else
         render 'hidden'
+        false
       end
     end
 

app/controllers/page_controller.rb

@@ -1,4 +1,6 @@
 class PageController < ApplicationController
+  include HelpTopics
+
   # GET /page/about
   def about
   end
@@ -123,38 +125,6 @@ def status
   # GET /page/videos
   def videos
   end
-
-  private
-
-    def help_topics
-      {
-        tutorial: {
-          new_genome: 'I have a genome belonging to a novel taxon, how can I ' \
-                      'register it?'
-        },
-        guide: {
-          etymology: 'How do I fill the etymology table?',
-          dictionary: 'How do I use dictionary lookups?',
-          exceptions: 'When and how do I request a genome quality exception?',
-          # SOPs
-          curation: 'How are names internally curated?'
-        },
-        explanation: {
-          open_data: 'What data is publicly released and how?',
-          authorship: 'Can I submit names I didn\'t author?'
-        },
-        reference: {
-          register: 'What are Register Lists?',
-          paths: 'What are the paths to validation?'
-        }
-      }
-    end
-
-    def help_topic_categories
-      Hash[
-        *help_topics.map { |k, v| v.keys.map { |topic| [topic, k] } }.flatten
-      ]
-    end
 end
 
 class SeqCodeDown < Redcarpet::Render::HTML

app/helpers/application_helper.rb

@@ -252,7 +252,15 @@ def modal(title, opts = {})
                 end
             end +
             content_tag(:div, class: opts[:body_class]) do
-              yield if block_given?
+              if block_given?
+                yield
+              elsif opts[:async]
+                content_tag(
+                  :div,
+                  class: 'text-center w-100 p-3',
+                  style: 'font-size: 200%;'
+                ) { fa_icon(:spinner, class: 'fa-spin') + ' Loading...' }
+              end
             end +
             if opts[:footer]
               content_tag(:div, opts[:footer], class: 'modal-footer')