Phase 2: Split names_controller into smaller controllers (rebased)

app/controllers/names/base_controller.rb

@@ -0,0 +1,134 @@
+# frozen_string_literal: true
+
+# Base controller for Names-related controllers.
+# Contains shared logic, before_actions, and private methods.
+class Names::BaseController < ApplicationController
+  before_action :set_tutorial
+
+  # Authentication and authorization methods
+  before_action :authenticate_user!, only: %i[observe unobserve observing]
+  before_action :authenticate_contributor!, only: %i[new create claim]
+  before_action :authenticate_admin!, only: %i[demote temporary_editable]
+  before_action :authenticate_curator!, only: %i[unranked unknown_proposal submitted endorsed draft return validate endorse edit_redirect]
+  before_action :authenticate_owner_or_curator!, only: %i[unclaim new_correspondence transfer_user transfer_user_commit]
+  before_action :authenticate_can_edit!, only: %i[edit destroy proposed_in not_validly_proposed_in emended_in assigned_in corrigendum_in corrigendum_orphan corrigendum edit_description edit_rank edit_notes edit_etymology autofill_etymology edit_parent]
+  before_action :authenticate_can_edit_type!, only: %i[edit_type]
+  before_action :authenticate_can_edit_validated!, only: %i[update edit_links]
+
+  # Setup methods
+  before_action :set_name_and_notifications, only: %i[show]
+  before_action :set_name, only: %i[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 quality_checks]
+
+  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)
+      true
+    else
+      render 'hidden'
+      false
+    end
+  end
+
+  def set_tutorial
+    return if params[:tutorial].blank?
+    @tutorial = Tutorial.find(params[:tutorial])
+  end
+
+  def authenticate_owner_or_curator!
+    unless current_user.try(:curator?) || @name.user?(current_user)
+      flash[:alert] = 'User is not the owner of the name'
+      redirect_to(@name)
+    end
+  end
+
+  def authenticate_can_edit_validated!
+    unless @name.can_edit_validated?(current_user)
+      flash[:alert] = 'User cannot edit this aspect of the name'
+      redirect_to(@name)
+    end
+  end
+
+  def authenticate_can_edit_type!
+    unless @name.can_edit_type?(current_user)
+      flash[:alert] = 'User cannot edit the nomenclatural type'
+      redirect_to(@name)
+    end
+  end
+
+  def authenticate_can_edit!
+    unless @name.can_edit?(current_user)
+      flash[:alert] = 'User cannot edit name'
+      redirect_to(@name)
+    end
+  end
+
+  # Never trust parameters from the scary internet, only allow the white list through
+  def name_params
+    fields = []
+    if @name.can_edit_validated?(current_user)
+      fields += %i[
+        notes ncbi_taxonomy lpsn_url gtdb_accession algaebase_species
+        algaebase_taxonomy wikispecies_entry
+      ]
+      unless @name.type?
+        fields += %i[
+          nomenclatural_type_type nomenclatural_type_id
+          nomenclatural_type_entry
+        ]
+      end
+    end
+
+    if @name.can_edit?(current_user)
+      fields += %i[
+        name rank description syllabication syllabication_reviewed
+        nomenclatural_type_type nomenclatural_type_id nomenclatural_type_entry
+        etymology_text register genome_strain
+      ] + etymology_pars
+    end
+
+    fields << :redirect if current_user.try(:curator?)
+
+    @name_params ||= params.require(:name).permit(*fields.uniq)
+  end
+
+  def etymology_pars
+    Name.etymology_particles.map do |i|
+      Name.etymology_fields.map { |j| :"etymology_#{i}_#{j}" }
+    end.flatten
+  end
+
+  def change_status(fun, success_msg, *extra_opts)
+    if @name.send(fun, *extra_opts)
+      flash[:notice] = success_msg
+    else
+      flash[:alert] = @name.status_alert
+    end
+    redirect_to(@name)
+  rescue ActiveRecord::RecordInvalid => inv
+    flash['alert'] =
+      'An unexpected error occurred while updating the name: ' +
+      inv.record.errors.map { |e| "#{e.attribute} #{e.message}" }.to_sentence
+    redirect_to(inv.record)
+  end
+
+  def add_automatic_correspondence(message)
+    NameCorrespondence.new(
+      message: message, notify: '0', automatic: true,
+      user: current_user, name: @name
+    ).save
+  end
+end

app/controllers/names/editing_controller.rb

@@ -0,0 +1,55 @@
+# frozen_string_literal: true
+
+# Controller for editing actions on names.
+class Names::EditingController < Names::BaseController
+  # GET /names/1/edit
+  def edit
+  end
+
+  # GET /names/1/edit_description
+  def edit_description
+  end
+
+  # GET /names/1/edit_notes
+  def edit_notes
+  end
+
+  # GET /names/1/edit_rank
+  def edit_rank
+  end
+
+  # GET /names/1/edit_links
+  def edit_links
+  end
+
+  # GET /names/1/edit_type
+  def edit_type
+    unless @name.rank?
+      flash[:alert] = 'You must define the rank before the type material'
+      redirect_to(@name)
+    end
+  end
+
+  # GET /names/1/edit_redirect
+  def edit_redirect
+  end
+
+  # GET /names/1/autofill_etymology
+  def autofill_etymology
+    @name.autofill_etymology
+    render :edit_etymology
+  end
+
+  # GET /names/1/edit_etymology
+  def edit_etymology
+  end
+
+  # GET /names/1/edit_parent
+  def edit_parent
+    if @name.placement
+      redirect_to(edit_placement_path(@name.placement))
+    else
+      redirect_to(new_placement_path(@name))
+    end
+  end
+end

app/controllers/names/filtering_controller.rb

@@ -0,0 +1,144 @@
+# frozen_string_literal: true
+
+# Controller for filtering and listing names by status, user, or type.
+class Names::FilteringController < Names::BaseController
+  # GET /names/user
+  # GET /names/user?user=abc
+  def user
+    @user = current_user
+    if params[:user] && current_user&.admin?
+      @user = User.find_by(username: params[:user])
+    end
+    params[:status] ||= 'all'
+    index(where: { created_by: @user })
+    render :index
+  end
+
+  # GET /names/observing
+  def observing
+    user = current_user
+    if params[:user] && current_user.admin?
+      user = User.find_by(username: params[:user])
+    end
+    @title  = 'Names with active alerts'
+    @status = 'user'
+    @names  = user.observing_names.reverse_order
+    index
+    render :index
+  end
+
+  # GET /names/submitted
+  def submitted
+    @submitted = true
+    @status = 'submitted'
+    index(status: 10)
+    render :index
+  end
+
+  # GET /names/endorsed
+  def endorsed
+    @endorsed = true
+    @status = 'endorsed'
+    index(status: 12)
+    render :index
+  end
+
+  # GET /names/draft
+  def draft
+    @draft = true
+    @status = 'draft'
+    index(status: 5)
+    render :index
+  end
+
+  # GET /names/unranked
+  def unranked
+    @names = Name.where(rank: nil).order(created_at: :asc)
+    @names = @names.paginate(page: params[:page], per_page: 30)
+  end
+
+  # GET /names/unknown_proposal
+  def unknown_proposal
+    @names = Name.where(proposed_in: nil).where('name LIKE ?', 'Candidatus %').order(created_at: :asc)
+    @names = @names.paginate(page: params[:page], per_page: 30)
+  end
+
+  # GET /type-genomes
+  # GET /type-genomes.json
+  def type_genomes
+    @names = Name.where(status: 15, nomenclatural_type_type: :Genome)
+                 .reorder(priority_date: :desc, updated_at: :desc)
+                 .paginate(page: params[:page], per_page: 50)
+    @crumbs = [['Genomes', genomes_path], 'Type']
+  end
+
+  private
+
+  # Reuse the index logic from Names::MainController
+  def index(opts = {})
+    @user      ||= nil
+    @submitted ||= false
+    @endorsed  ||= false
+    @draft     ||= false
+    @sort      ||= params[:sort] || 'date'
+    @status    ||= params[:status] || 'public'
+    @status      = 'ICNafp' if @status == 'ICN'
+    @title     ||= [
+      @status == 'all' ? nil : @status.gsub(/^\S/, &:upcase),
+      'Names',
+      @user.present? ? "by #{@user.username}" : nil
+    ].compact.join(' ')
+    opts[:rank] = params[:rank] if params[:rank].present?
+
+    opts[:status] ||=
+      case @status.to_s.downcase
+      when 'public';    Name.public_status
+      when 'automated'; 0
+      when 'seqcode';   15
+      when 'icnp';      20
+      when 'icnafp';    25
+      when 'valid';     Name.valid_status
+      end
+
+    @names ||=
+      case @sort.to_s.downcase
+      when 'date'
+        if opts[:status] == 15
+          Name.order(validated_at: :desc)
+        else
+          Name.order(created_at: :desc)
+        end
+      when 'citations'
+        Name
+          .left_joins(:publication_names).group(:id)
+          .order('COUNT(publication_names.id) DESC')
+      else
+        @sort = 'alphabetically'
+        Name.order(name: :asc)
+      end
+    @names = @names.where(redirect: nil)
+    @names = @names.where(status: opts[:status]) if opts[:status]
+    @names = @names.where(rank: opts[:rank]) if opts[:rank]
+    @names = @names.where(opts[:where]) if opts[:where]
+    @names = @names.paginate(page: params[:page], per_page: 30)
+
+    @count = @names.count
+    @count = @count.size if @count.is_a? Hash
+    @crumbs = [['Names', names_path]]
+    if @user.present?
+      bu = "by #{@user.username}"
+      if @status == 'all'
+        @crumbs << bu
+      else
+        @crumbs << [bu, names_path(user: @user.username)]
+        @crumbs << @status.gsub(/^\S/, &:upcase)
+      end
+    else
+      if @status == 'public'
+        @crumbs[0] = 'Names'
+      else
+        @crumbs << @status.gsub(/^\S/, &:upcase)
+      end
+    end
+  end
+end