Merge branch 'main' into jose

Gemfile

@@ -9,7 +9,7 @@ gem 'google_drive'
 gem 'groupdate'
 gem 'honeybadger', '~> 5.2.0'
 gem 'html-pipeline', '~> 2.14.3'
-gem 'commonmarker', '~> 0.23.8'
+gem 'commonmarker', '~> 0.23.10'
 gem 'net-sftp', '~> 4.0'
 gem 'octicons_helper'
 gem 'omniauth-orcid', '~> 2.1.1'
@@ -18,7 +18,7 @@ gem 'octokit', '~> 6.0'
 gem 'pdf-reader', '~> 2.11.0'
 gem 'pg', '~> 1.4.6'
 gem 'pagy'
-gem 'rails', '7.0.6'
+gem 'rails', '7.0.7'
 gem "importmap-rails"
 gem "turbo-rails"
 gem "stimulus-rails"

Gemfile.lock

@@ -4,70 +4,70 @@ GEM
     Ascii85 (1.1.0)
     aasm (5.5.0)
       concurrent-ruby (~> 1.0)
-    actioncable (7.0.6)
-      actionpack (= 7.0.6)
-      activesupport (= 7.0.6)
+    actioncable (7.0.7)
+      actionpack (= 7.0.7)
+      activesupport (= 7.0.7)
       nio4r (~> 2.0)
       websocket-driver (>= 0.6.1)
-    actionmailbox (7.0.6)
-      actionpack (= 7.0.6)
-      activejob (= 7.0.6)
-      activerecord (= 7.0.6)
-      activestorage (= 7.0.6)
-      activesupport (= 7.0.6)
+    actionmailbox (7.0.7)
+      actionpack (= 7.0.7)
+      activejob (= 7.0.7)
+      activerecord (= 7.0.7)
+      activestorage (= 7.0.7)
+      activesupport (= 7.0.7)
       mail (>= 2.7.1)
       net-imap
       net-pop
       net-smtp
-    actionmailer (7.0.6)
-      actionpack (= 7.0.6)
-      actionview (= 7.0.6)
-      activejob (= 7.0.6)
-      activesupport (= 7.0.6)
+    actionmailer (7.0.7)
+      actionpack (= 7.0.7)
+      actionview (= 7.0.7)
+      activejob (= 7.0.7)
+      activesupport (= 7.0.7)
       mail (~> 2.5, >= 2.5.4)
       net-imap
       net-pop
       net-smtp
       rails-dom-testing (~> 2.0)
-    actionpack (7.0.6)
-      actionview (= 7.0.6)
-      activesupport (= 7.0.6)
+    actionpack (7.0.7)
+      actionview (= 7.0.7)
+      activesupport (= 7.0.7)
       rack (~> 2.0, >= 2.2.4)
       rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.2.0)
-    actiontext (7.0.6)
-      actionpack (= 7.0.6)
-      activerecord (= 7.0.6)
-      activestorage (= 7.0.6)
-      activesupport (= 7.0.6)
+    actiontext (7.0.7)
+      actionpack (= 7.0.7)
+      activerecord (= 7.0.7)
+      activestorage (= 7.0.7)
+      activesupport (= 7.0.7)
       globalid (>= 0.6.0)
       nokogiri (>= 1.8.5)
-    actionview (7.0.6)
-      activesupport (= 7.0.6)
+    actionview (7.0.7)
+      activesupport (= 7.0.7)
       builder (~> 3.1)
       erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.1, >= 1.2.0)
     active_link_to (1.0.5)
       actionpack
       addressable
-    activejob (7.0.6)
-      activesupport (= 7.0.6)
+    activejob (7.0.7)
+      activesupport (= 7.0.7)
       globalid (>= 0.3.6)
-    activemodel (7.0.6)
-      activesupport (= 7.0.6)
-    activerecord (7.0.6)
-      activemodel (= 7.0.6)
-      activesupport (= 7.0.6)
-    activestorage (7.0.6)
-      actionpack (= 7.0.6)
-      activejob (= 7.0.6)
-      activerecord (= 7.0.6)
-      activesupport (= 7.0.6)
+    activemodel (7.0.7)
+      activesupport (= 7.0.7)
+    activerecord (7.0.7)
+      activemodel (= 7.0.7)
+      activesupport (= 7.0.7)
+    activestorage (7.0.7)
+      actionpack (= 7.0.7)
+      activejob (= 7.0.7)
+      activerecord (= 7.0.7)
+      activesupport (= 7.0.7)
       marcel (~> 1.0)
       mini_mime (>= 1.1.0)
-    activesupport (7.0.6)
+    activesupport (7.0.7)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -91,7 +91,7 @@ GEM
       xpath (~> 3.2)
     chartkick (5.0.2)
     coderay (1.1.3)
-    commonmarker (0.23.9)
+    commonmarker (0.23.10)
     concurrent-ruby (1.2.2)
     connection_pool (2.4.1)
     crack (0.4.5)
@@ -204,16 +204,16 @@ GEM
     matrix (0.4.2)
     memoist (0.16.2)
     method_source (1.0.0)
-    mini_mime (1.1.2)
+    mini_mime (1.1.5)
     mini_portile2 (2.8.4)
     mini_racer (0.8.0)
       libv8-node (~> 18.16.0.0)
-    minitest (5.18.1)
+    minitest (5.19.0)
     msgpack (1.7.2)
     multi_json (1.15.0)
     multi_xml (0.6.0)
     multipart-post (2.3.0)
-    net-imap (0.3.6)
+    net-imap (0.3.7)
       date
       net-protocol
     net-pop (0.1.2)
@@ -227,12 +227,12 @@ GEM
     net-ssh (7.1.0)
     newrelic_rpm (9.3.1)
     nio4r (2.5.9)
-    nokogiri (1.15.3)
+    nokogiri (1.15.4)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
-    nokogiri (1.15.3-x86_64-darwin)
+    nokogiri (1.15.4-x86_64-darwin)
       racc (~> 1.4)
-    nokogiri (1.15.3-x86_64-linux)
+    nokogiri (1.15.4-x86_64-linux)
       racc (~> 1.4)
     oauth2 (2.0.9)
       faraday (>= 0.17.3, < 3.0)
@@ -282,39 +282,39 @@ GEM
     puma (6.3.0)
       nio4r (~> 2.0)
     racc (1.7.1)
-    rack (2.2.7)
+    rack (2.2.8)
     rack-protection (3.0.6)
       rack
     rack-test (2.1.0)
       rack (>= 1.3)
-    rails (7.0.6)
-      actioncable (= 7.0.6)
-      actionmailbox (= 7.0.6)
-      actionmailer (= 7.0.6)
-      actionpack (= 7.0.6)
-      actiontext (= 7.0.6)
-      actionview (= 7.0.6)
-      activejob (= 7.0.6)
-      activemodel (= 7.0.6)
-      activerecord (= 7.0.6)
-      activestorage (= 7.0.6)
-      activesupport (= 7.0.6)
+    rails (7.0.7)
+      actioncable (= 7.0.7)
+      actionmailbox (= 7.0.7)
+      actionmailer (= 7.0.7)
+      actionpack (= 7.0.7)
+      actiontext (= 7.0.7)
+      actionview (= 7.0.7)
+      activejob (= 7.0.7)
+      activemodel (= 7.0.7)
+      activerecord (= 7.0.7)
+      activestorage (= 7.0.7)
+      activesupport (= 7.0.7)
       bundler (>= 1.15.0)
-      railties (= 7.0.6)
+      railties (= 7.0.7)
     rails-controller-testing (1.0.5)
       actionpack (>= 5.0.1.rc1)
       actionview (>= 5.0.1.rc1)
       activesupport (>= 5.0.1.rc1)
-    rails-dom-testing (2.1.1)
+    rails-dom-testing (2.2.0)
       activesupport (>= 5.0.0)
       minitest
       nokogiri (>= 1.6)
     rails-html-sanitizer (1.6.0)
       loofah (~> 2.21)
       nokogiri (~> 1.14)
-    railties (7.0.6)
-      actionpack (= 7.0.6)
-      activesupport (= 7.0.6)
+    railties (7.0.7)
+      actionpack (= 7.0.7)
+      activesupport (= 7.0.7)
       method_source
       rake (>= 12.2)
       thor (~> 1.0)
@@ -423,12 +423,12 @@ GEM
       hashdiff (>= 0.4.0, < 2.0.0)
     webrick (1.8.1)
     websocket (1.2.9)
-    websocket-driver (0.7.5)
+    websocket-driver (0.7.6)
       websocket-extensions (>= 0.1.0)
     websocket-extensions (0.1.5)
     xpath (3.2.0)
       nokogiri (~> 1.8)
-    zeitwerk (2.6.8)
+    zeitwerk (2.6.11)
 
 PLATFORMS
   ruby
@@ -441,7 +441,7 @@ DEPENDENCIES
   bootsnap
   capybara (~> 3.38)
   chartkick
-  commonmarker (~> 0.23.8)
+  commonmarker (~> 0.23.10)
   dotenv (~> 2.8.1)
   elasticsearch (< 7.14)
   factory_bot_rails (~> 6.2.0)
@@ -464,7 +464,7 @@ DEPENDENCIES
   pg (~> 1.4.6)
   pry-byebug
   puma
-  rails (= 7.0.6)
+  rails (= 7.0.7)
   rails-controller-testing (~> 1.0.5)
   redis (~> 5.0)
   responders

app/controllers/dispatch_controller.rb

@@ -145,4 +145,53 @@ def api_deposit
       head :forbidden
     end
   end
+
+  def api_retract
+    if params[:secret] == ENV['BOT_SECRET']
+      paper = Paper.find_by_doi!(params[:doi])
+      return head :unprocessable_entity if paper.retracted?
+
+      if params[:metadata]
+        metadata = JSON.parse(Base64.decode64(params[:metadata]))
+      else
+        metadata = {}
+      end
+
+      retraction_paper = Paper.new
+      retraction_paper.doi = metadata[:doi] || "#{paper.doi}R"
+      retraction_paper.retraction_for_id = paper.id
+      retraction_paper.title = metadata[:title] || "Retraction notice for: #{paper.title}"
+      retraction_paper.body = "Retraction notice for: #{paper.title}"
+      retraction_paper.authors = "Editorial Board"
+      retraction_paper.repository_url = paper.repository_url
+      retraction_paper.software_version = paper.software_version
+      retraction_paper.track_id = paper.track_id
+      retraction_paper.citation_string = params[:citation_string]
+      retraction_paper.submission_kind = "new"
+      retraction_paper.state = "accepted"
+      retraction_paper.metadata = metadata
+      retraction_paper.accepted_at = Time.now
+      retraction_paper.review_issue_id = paper.review_issue_id
+
+      if paper.track.nil?
+        submitting_author = Editor.includes(:user).board.select {|e| e.user.present? }.first.user
+      else
+        submitting_author = paper.track.aeics.select {|e| e.user.present? }.first.user
+      end
+      submitting_author = User.where(admin: true).first if submitting_author.nil?
+
+      retraction_paper.submitting_author = submitting_author
+
+      if retraction_paper.save! && retraction_paper.accept!
+        paper.update(retraction_notice: params[:retraction_notice]) if params[:retraction_notice].present?
+        paper.retract!
+        render json: retraction_paper.to_json, status: '201'
+      else
+        head :unprocessable_entity
+      end
+    else
+      head :forbidden
+    end
+  end
+
 end

app/models/paper.rb

@@ -19,6 +19,16 @@ class Paper < ApplicationRecord
              optional: true,
              foreign_key: "eic_id"
 
+  belongs_to :retracted_paper,
+             class_name: 'Paper',
+             optional: true,
+             foreign_key: "retraction_for_id"
+
+  has_one :retraction_paper,
+          class_name: 'Paper',
+          foreign_key: "retraction_for_id",
+          inverse_of: :retracted_paper
+
   has_many :invitations
   has_many :notes
   has_many :votes
@@ -62,6 +72,10 @@ class Paper < ApplicationRecord
     event :withdraw do
       transitions to: :withdrawn
     end
+
+    event :retract do
+      transitions to: :retracted
+    end
   end
 
   VISIBLE_STATES = [
@@ -128,14 +142,14 @@ class Paper < ApplicationRecord
   validates_presence_of :track_id, on: :create, message: "You must select a valid subject for the paper", if: Proc.new { JournalFeatures.tracks? }
   validates :kind, inclusion: { in: Rails.application.settings["paper_types"] }, allow_nil: true
   validates :submission_kind, inclusion: { in: SUBMISSION_KINDS, message: "You must select a submission type" }, allow_nil: false
-  validate :check_repository_address, on: :create
+  validate :check_repository_address, on: :create, unless: Proc.new {|paper| paper.is_a_retraction_notice?}
 
   def notify_editors
-    Notifications.submission_email(self).deliver_now
+    Notifications.submission_email(self).deliver_now unless self.is_a_retraction_notice?
   end
 
   def notify_author
-    Notifications.author_submission_email(self).deliver_now
+    Notifications.author_submission_email(self).deliver_now unless self.is_a_retraction_notice?
   end
 
   # Only index papers that are visible
@@ -172,6 +186,10 @@ def published?
     accepted? || retracted?
   end
 
+  def is_a_retraction_notice?
+    retraction_for_id.present?
+  end
+
   def invite_editor(editor_handle)
     return false unless editor = Editor.find_by_login(editor_handle)
     Notifications.editor_invite_email(self, editor).deliver_now
@@ -296,8 +314,12 @@ def archive_doi_url
 
   # A 5-figure integer used to produce the JOSS DOI
   def joss_id
-    id = "%05d" % review_issue_id
-    "#{setting(:abbreviation).downcase}.#{id}"
+    if self.is_a_retraction_notice?
+      return retracted_paper.joss_id + "R"
+    else
+      id = "%05d" % review_issue_id
+      return "#{setting(:abbreviation).downcase}.#{id}"
+    end
   end
 
   # This URL returns the 'DOI optimized' representation of a URL for a paper