Merge pull request #1256 from openjournals/retraction-papers

Retraction papers
openjournals · Aug 17, 2023 · 154ec00 · 154ec00
2 parents d3bc713 + ed22eb5
commit 154ec00
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Showing 14 changed files with 378 additions and 102 deletions.
diff --git a/app/controllers/dispatch_controller.rb b/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
diff --git a/app/models/paper.rb b/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
@@ -286,8 +304,12 @@ 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

diff --git a/app/views/papers/_show_published.html.erb b/app/views/papers/_show_published.html.erb
@@ -1,5 +1,5 @@
 <div class="container paper-show">
-  <%= render partial: "shared/retraction_notice" if @paper.retracted? %>
+  <%= render partial: "shared/retraction_info" %>
 
   <div class="paper-title">
     <span class="__dimensions_badge_embed__" data-doi="<%= @paper.doi %>" data-hide-zero-citations="true"></span>
@@ -22,58 +22,6 @@
         <embed src="<%= @paper.pdf_url %>#toolbar=0&navpanes=0&scrollbar=0&statusbar=0&messages=0" type="application/pdf"  style="width:100%; height:100%;" />
       </object>
     </div>
-
-    <div class="col-md-3 paper-sidebar">
-      <div class="btn-group-vertical" role="group" aria-label="...">
-        <%= link_to  @paper.repository_url, class: 'btn paper-btn' do %>
-          <%= image_tag "gh-icon.svg" %>
-          Software repository
-        <% end %>
-
-        <%= link_to @paper.review_url, class: 'btn paper-btn' do %>
-          <%= image_tag "icon_docs.svg" %>
-          Paper review
-        <% end %>
-
-        <%= link_to @paper.pdf_url, class: 'btn paper-btn' do %>
-          <%= image_tag "dl-icon.svg" %>
-          Download paper
-        <% end %>
-
-        <%= link_to @paper.archive_doi_url, class: 'btn paper-btn' do %>
-          <%= image_tag "hist-icon.svg" %>
-          Software archive
-        <% end %>
-      </div>
-
-      <div class="label">Review</div>
-      <p>Editor: <%= github_link @paper.metadata_editor %> (<%= link_to "all papers", papers_by_editor_path(@paper.metadata_editor) %>)<br>Reviewers: <%= pretty_reviewers(@paper.metadata_reviewers) %></p>
-
-      <div class="label">Authors</div>
-      <p><%= pretty_authors(@paper.metadata_authors) %></p>
-
-      <div class="label">Citation</div>
-      <p id="citationstring" style="padding-bottom: 0px;margin: 0px;"><%= @paper.citation_string %></p>
-
-      <div id="bibtex" style="position:absolute;left:-10000px;height:0px;padding:0px;"><%= render partial: "bibtex", locals: { paper: @paper } %></div>
-      <div style="margin-bottom: 10px;"><%= link_to "Copy citation string".html_safe, "#", class: "clipboard-btn", "data-clipboard-action": "copy", "data-clipboard-target": "#citationstring" %> &middot; <%= link_to "Copy BibTeX".html_safe, "#", class: "clipboard-btn", "data-clipboard-action": "copy", "data-clipboard-target": "#bibtex" %>&nbsp;&nbsp;<%= octicon "paste", height: 16,  class: "", "aria-label": "Copy" %></div>
-
-      <div class="label">Tags</div>
-      <p>
-        <% @paper.author_tags.compact.each do |tag| %>
-        <span class="badge-lang"><%= link_to tag, papers_by_tag_path(tag: tag) %></span>
-        <% end %>
-      </p>
-      <div class="label">Altmetrics</div>
-      <div style='padding-bottom: 10px;' data-badge-type='donut' class='altmetric-embed' data-badge-popover='right' data-hide-no-mentions='false' data-doi="<%= @paper.doi %>"></div>
-
-      <div class="label">Markdown badge</div>
-      <p><%= image_tag @paper.status_badge_url %> &nbsp; <a href="#" class="clipboard-btn" data-clipboard-action="copy" data-clipboard-text="<%= @paper.markdown_code %>"><%= octicon "paste", height: 16,  class: "", "aria-label": "Copy" %></a></p>
-
-      <div class="label">License</div>
-      <p>Authors of <%= Rails.application.settings['abbreviation'] %> papers retain copyright.</p>
-      <p>This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.</p>
-      <p><a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a></p>
-    </div>
+    <%= render partial: "sidebar_published" %>
   </div>
 </div>
diff --git a/app/views/papers/_sidebar_published.html.erb b/app/views/papers/_sidebar_published.html.erb
@@ -0,0 +1,73 @@
+<div class="col-md-3 paper-sidebar">
+  <div class="btn-group-vertical" role="group" aria-label="...">
+    <% if @paper.is_a_retraction_notice?  %>
+      <%= link_to @paper.pdf_url, class: 'btn paper-btn' do %>
+        <%= image_tag "dl-icon.svg" %>
+        Download Retraction Notice
+      <% end %>
+
+      <%= link_to @paper.retracted_paper.seo_url, class: 'btn paper-btn danger' do %>
+        <%= image_tag "icon_docs.svg" %>
+        Retracted Paper
+      <% end %>
+    <% else %>
+
+      <% if @paper.retracted? && @paper.retraction_paper.present? %>
+        <%= link_to @paper.retraction_paper.seo_url, class: 'btn paper-btn' do %>
+          <%= image_tag "icon_docs.svg" %>
+          Retraction notice
+        <% end %>
+      <% end %>
+      <%= link_to  @paper.repository_url, class: 'btn paper-btn' do %>
+        <%= image_tag "gh-icon.svg" %>
+        Software repository
+      <% end %>
+
+      <%= link_to @paper.review_url, class: 'btn paper-btn' do %>
+        <%= image_tag "icon_docs.svg" %>
+        Paper review
+      <% end %>
+
+      <%= link_to @paper.pdf_url, class: 'btn paper-btn' do %>
+        <%= image_tag "dl-icon.svg" %>
+        Download paper
+      <% end %>
+
+      <%= link_to @paper.archive_doi_url, class: 'btn paper-btn' do %>
+        <%= image_tag "hist-icon.svg" %>
+        Software archive
+      <% end %>
+    <% end %>
+  </div>
+
+  <% unless @paper.is_a_retraction_notice?  %>
+    <div class="label">Review</div>
+    <p>Editor: <%= github_link @paper.metadata_editor %> (<%= link_to "all papers", papers_by_editor_path(@paper.metadata_editor) %>)<br>Reviewers: <%= pretty_reviewers(@paper.metadata_reviewers) %></p>
+  <% end %>
+
+  <div class="label">Authors</div>
+  <p><%= pretty_authors(@paper.metadata_authors) %></p>
+
+  <div class="label">Citation</div>
+  <p id="citationstring" style="padding-bottom: 0px;margin: 0px;"><%= @paper.citation_string %></p>
+
+  <div id="bibtex" style="position:absolute;left:-10000px;height:0px;padding:0px;"><%= render partial: "bibtex", locals: { paper: @paper } %></div>
+  <div style="margin-bottom: 10px;"><%= link_to "Copy citation string".html_safe, "#", class: "clipboard-btn", "data-clipboard-action": "copy", "data-clipboard-target": "#citationstring" %> &middot; <%= link_to "Copy BibTeX".html_safe, "#", class: "clipboard-btn", "data-clipboard-action": "copy", "data-clipboard-target": "#bibtex" %>&nbsp;&nbsp;<%= octicon "paste", height: 16,  class: "", "aria-label": "Copy" %></div>
+
+  <div class="label">Tags</div>
+  <p>
+    <% @paper.author_tags.compact.each do |tag| %>
+    <span class="badge-lang"><%= link_to tag, papers_by_tag_path(tag: tag) %></span>
+    <% end %>
+  </p>
+  <div class="label">Altmetrics</div>
+  <div style='padding-bottom: 10px;' data-badge-type='donut' class='altmetric-embed' data-badge-popover='right' data-hide-no-mentions='false' data-doi="<%= @paper.doi %>"></div>
+
+  <div class="label">Markdown badge</div>
+  <p><%= image_tag @paper.status_badge_url %> &nbsp; <a href="#" class="clipboard-btn" data-clipboard-action="copy" data-clipboard-text="<%= @paper.markdown_code %>"><%= octicon "paste", height: 16,  class: "", "aria-label": "Copy" %></a></p>
+
+  <div class="label">License</div>
+  <p>Authors of <%= Rails.application.settings['abbreviation'] %> papers retain copyright.</p>
+  <p>This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.</p>
+  <p><a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a></p>
+</div>
diff --git a/app/views/papers/show.json.jbuilder b/app/views/papers/show.json.jbuilder
@@ -17,8 +17,8 @@ if @paper.published?
     json.editor_orcid @paper.editor.orcid if @paper.editor.orcid
   end
   json.reviewers @paper.metadata_reviewers
-  json.languages @paper.language_tags.join(', ')
-  json.tags @paper.author_tags.join(', ')
+  json.languages @paper.language_tags
+  json.tags @paper.author_tags
   json.paper_review @paper.review_url
   json.meta_review_issue_id @paper.meta_review_issue_id
   json.pdf_url @paper.seo_pdf_url

diff --git a/app/views/shared/_retraction_info.html.erb b/app/views/shared/_retraction_info.html.erb
@@ -0,0 +1,17 @@
+<% if @paper.retracted? %>
+  <div class="alert alert-danger">
+  <% if @paper.retraction_notice.present? %>
+    <%= @paper.retraction_notice.html_safe %>
+  <% elsif @paper.retraction_paper.present? %>
+    This paper has been retracted, <%= link_to "read details here", @paper.retraction_paper.seo_url %>
+  <% else %>
+    This paper has been retracted
+  <% end %>
+  </div>
+<% end %>
+
+<% if @paper.is_a_retraction_notice? %>
+  <div class="alert alert-danger">
+    This paper is a retraction notice for: <%= link_to @paper.retracted_paper.title, @paper.retracted_paper.seo_url %>
+  </div>
+<% end %>
diff --git a/app/views/shared/_retraction_notice.html.erb b/app/views/shared/_retraction_notice.html.erb
diff --git a/config/routes.rb b/config/routes.rb
@@ -68,9 +68,9 @@
 
   doi_prefix_name = Rails.application.settings[:abbreviation].downcase || "joss"
 
-  get '/papers/:doi/status.svg', to: "papers#status", format: "svg", constraints: { doi: /10.21105\/#{doi_prefix_name}\.\d{5}/}
-  get '/papers/:doi', to: "papers#show", constraints: { doi: /10.21105\/#{doi_prefix_name}\.\d{5}/}
-  get '/papers/:doi.:format', to: "papers#show", constraints: { doi: /10.21105\/#{doi_prefix_name}\.\d{5}/}
+  get '/papers/:doi/status.svg', to: "papers#status", format: "svg", constraints: { doi: /10.21105\/#{doi_prefix_name}\.\d{5}R?/}
+  get '/papers/:doi', to: "papers#show", constraints: { doi: /10.21105\/#{doi_prefix_name}\.\d{5}R?/}
+  get '/papers/:doi.:format', to: "papers#show", constraints: { doi: /10.21105\/#{doi_prefix_name}\.\d{5}R?/}
 
   get '/editor_profile', to: 'editors#profile', as: 'editor_profile'
   patch '/update_editor_profile', to: 'editors#update_profile', as: 'update_editor_profile'
@@ -95,6 +95,7 @@
   post '/papers/api_editor_invite', to: 'dispatch#api_editor_invite'
   post '/papers/api_start_review', to: 'dispatch#api_start_review'
   post '/papers/api_deposit', to: 'dispatch#api_deposit'
+  post '/papers/api_retract', to: 'dispatch#api_retract'
   post '/papers/api_assign_editor', to: 'dispatch#api_assign_editor'
   post '/papers/api_update_paper_info', to: 'dispatch#api_update_paper_info'
   post '/papers/api_assign_reviewers', to: 'dispatch#api_assign_reviewers'

diff --git a/db/migrate/20230609104144_add_retraction_for_id_to_papers.rb b/db/migrate/20230609104144_add_retraction_for_id_to_papers.rb
@@ -0,0 +1,5 @@
+class AddRetractionForIdToPapers < ActiveRecord::Migration[7.0]
+  def change
+    add_reference :papers, :retraction_for, foreign_key: { to_table: :papers }, null: true
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema[7.0].define(version: 2022_06_16_085520) do
+ActiveRecord::Schema[7.0].define(version: 2023_06_09_104144) do
   # These are extensions that must be enabled in order to support this database
   enable_extension "hstore"
   enable_extension "plpgsql"
@@ -110,10 +110,12 @@
     t.string "git_branch"
     t.bigint "track_id"
     t.string "suggested_subject"
+    t.bigint "retraction_for_id"
     t.index ["editor_id"], name: "index_papers_on_editor_id"
     t.index ["eic_id"], name: "index_papers_on_eic_id"
     t.index ["labels"], name: "index_papers_on_labels", using: :gin
     t.index ["last_activity"], name: "index_papers_on_last_activity"
+    t.index ["retraction_for_id"], name: "index_papers_on_retraction_for_id"
     t.index ["reviewers"], name: "index_papers_on_reviewers", using: :gin
     t.index ["sha"], name: "index_papers_on_sha"
     t.index ["track_id"], name: "index_papers_on_track_id"
@@ -178,4 +180,5 @@
     t.index ["paper_id"], name: "index_votes_on_paper_id"
   end
 
+  add_foreign_key "papers", "papers", column: "retraction_for_id"
 end