Publications without doi

app/controllers/publications_controller.rb

@@ -51,41 +51,54 @@ def edit
 
   # POST /publications
   def create
-    @publication = Publication.by_doi(params['publication']['doi'])
-    if @publication.new_record?
-      render('new')
+    if params['publication']['doi'].blank? && current_user.try(:curator?)
+      @publication = Publication.create_without_doi(
+        publication_manual_params,
+        authors: params[:authors_given].to_a.zip(params[:authors_family].to_a)
+      )
+      return render('new') unless @publication.persisted?
     else
-      if params[:link_name] && params[:link_name][:id]
-        @name = Name.find(params[:link_name][:id])
-        par = { publication: @publication, name: @name }
-        pn = PublicationName.find_or_create_by(par)
+      doi = params['publication']['doi']
+      # by_autocomplete resolves either a raw DOI (falling through to
+      # by_doi, so "type a fresh DOI to register it" keeps working
+      # unchanged) or a doi_title-style "key: title" string from selecting
+      # an existing publication in the autocomplete dropdown — including a
+      # DOI-less one via its "id:<id>" key. Only falls back to by_doi
+      # directly for blank input, matching its pre-existing error message.
+      @publication = Publication.by_autocomplete(doi) || Publication.by_doi(doi)
+      return render('new') if @publication.new_record?
+    end
+
+    if params[:link_name] && params[:link_name][:id]
+      @name = Name.find(params[:link_name][:id])
+      par = { publication: @publication, name: @name }
+      pn = PublicationName.find_or_create_by(par)
 
-        case params[:link_name][:as]
-        when 'propose'
-          @name.update(proposed_in: @publication)
-          flash[:notice] = 'Effective publication registered'
-        when 'not_valid_proposal'
-          pn.update(not_valid_proposal: true)
-          flash[:notice] =
-            'Original (not valid) publication registered'
-        when 'corrig'
-          redirect_to(
-            corrigendum_in_name_url(@name, publication_id: @publication.id)
-          )
-          return
-        when 'assign'
-          @name.update(assigned_in: @publication)
-          flash[:notice] = 'Taxonomic assignment publication registered'
-        when 'emend'
-          pn.update(emends: true)
-          flash[:notice] = 'Emending publication registered'
-        else
-          flash[:notice] = 'Publication registered'
-        end
-        redirect_to(@name)
+      case params[:link_name][:as]
+      when 'propose'
+        @name.update(proposed_in: @publication)
+        flash[:notice] = 'Effective publication registered'
+      when 'not_valid_proposal'
+        pn.update(not_valid_proposal: true)
+        flash[:notice] =
+          'Original (not valid) publication registered'
+      when 'corrig'
+        redirect_to(
+          corrigendum_in_name_url(@name, publication_id: @publication.id)
+        )
+        return
+      when 'assign'
+        @name.update(assigned_in: @publication)
+        flash[:notice] = 'Taxonomic assignment publication registered'
+      when 'emend'
+        pn.update(emends: true)
+        flash[:notice] = 'Emending publication registered'
       else
-        redirect_to(@publication)
+        flash[:notice] = 'Publication registered'
       end
+      redirect_to(@name)
+    else
+      redirect_to(@publication)
     end
   end
 
@@ -128,6 +141,15 @@ def set_publication
         params[:doi] ? Publication.find_by(doi: params[:doi]) : nil
     end
 
+    # Fields a curator may hand-enter to register a publication without a
+    # DOI (e.g. an older paper never issued one). Deliberately excludes
+    # crossref_json/datacite_json, which only ever hold verbatim external-API
+    # payloads and have no place in a manually-entered record.
+    def publication_manual_params
+      params.require(:publication)
+        .permit(*%i[title journal journal_loc journal_date doi url pub_type abstract])
+    end
+
     # Never trust parameters from the scary internet, only allow the white list through.
     def publication_params
       params.require(:publication)

app/models/name_paratype.rb

@@ -10,4 +10,17 @@ class NameParatype < ApplicationRecord
   # Per the SeqCode paratype amendment (DOI:10.1093/ismeco/ycaf238), only
   # isolated strains can serve as paratypes
   validates(:nomenclatural_type_type, inclusion: { in: %w[Strain] })
+
+  after_create(:link_publication_to_name)
+
+  private
+
+  # A paratype's registering publication should also be recognized as one
+  # of the name's own publications, same as propose/assign/emend/corrig
+  # already ensure (see PublicationsController#create). Uses find_or_create
+  # so this holds regardless of which code path creates the NameParatype,
+  # and is a no-op if the publication is already linked.
+  def link_publication_to_name
+    PublicationName.find_or_create_by(publication: publication, name: name)
+  end
 end

app/models/publication.rb

@@ -3,6 +3,16 @@
 class Publication < ApplicationRecord
   default_scope { order(journal_date: :desc) }
 
+  # An empty string isn't the same as NULL for the DB's unique index on doi
+  # (two blank-string dois would collide; two NULLs don't), so normalize
+  # blank input before it ever reaches a validation or a save.
+  before_validation { self.doi = nil if doi.blank? }
+
+  validates(:title, presence: true)
+  validates(:journal_date, presence: true)
+  validates(:pub_type, presence: true)
+  validates(:doi, uniqueness: true, allow_nil: true)
+
   has_many(
     :publication_authors, -> { order('publication_authors.id ASC') },
     dependent: :destroy
@@ -34,8 +44,35 @@ class Publication < ApplicationRecord
   class << self
 
     def by_autocomplete(query)
-      doi = query&.sub(/: .*/, '')
-      doi.present? ? by_doi(doi) : nil
+      key = query&.sub(/: .*/, '')
+      return nil unless key.present?
+
+      key.start_with?('id:') ?
+        by_id(key.delete_prefix('id:')) :
+        by_doi(key)
+    end
+
+    def by_id(id)
+      Publication.find_by(id: id) ||
+        Publication.new.tap { |i| i.errors.add(:doi, 'publication not found') }
+    end
+
+    # Creates a Publication without going through DOI lookup (e.g. a
+    # curator-entered legacy paper that never received one), with its
+    # authors, atomically: if either the publication itself is invalid or
+    # an author fails to save, nothing is persisted — avoids ever leaving
+    # behind an author-less publication because add_authors partially
+    # failed after the publication itself saved fine.
+    def create_without_doi(params, authors: [])
+      p = new(params)
+      transaction do
+        if p.save
+          p.add_authors(authors)
+        else
+          raise ActiveRecord::Rollback
+        end
+      end
+      p
     end
 
     def by_doi(doi, force_update = false)
@@ -200,6 +237,39 @@ def journals
       where.not(journal: ['', nil]).select(:journal).reorder(:journal).distinct
     end
 
+    # Curated subset of the Crossref/DataCite `type` vocabulary offered in
+    # the manual-entry dropdown. Values match what by_serrano_work/
+    # by_datacite_work already store, so existing display code (e.g.
+    # #citation, #journal_html) keeps working unchanged either way.
+    def pub_types
+      {
+        'journal-article'     => 'Journal article',
+        'book'                => 'Book',
+        'book-chapter'        => 'Book chapter',
+        'proceedings-article' => 'Conference proceedings',
+        'report'              => 'Report',
+        'other'               => 'Other'
+      }
+    end
+
+  end
+
+  ##
+  # Attach authors given as an array of [given, family] pairs, in
+  # authorship order. Mirrors the author-creation loop in
+  # +by_uniform_hash_work+, so the same dedup/standardization rules
+  # (Author.find_or_create) apply regardless of whether the author list
+  # came from Crossref/DataCite or was hand-entered.
+  def add_authors(pairs)
+    pairs.each_with_index do |(given, family), i|
+      next if family.blank?
+      author = Author.find_or_create(given, family)
+      next if authors.include?(author)
+      PublicationAuthor.create!(
+        publication_id: id, author_id: author.id,
+        sequence: i.zero? ? 'first' : 'additional'
+      )
+    end
   end
 
   def authors_et_al(format = :text)
@@ -248,17 +318,20 @@ def journal_raw
   def long_citation(format = :text)
     case format.to_sym
     when :html
+      doi_html = doi.present? ?
+        %(<a href="#{link}" target="_blank">DOI: #{doi}</a>) : ''
       <<~HTML.html_safe
-        #{authors_et_al(format)} (#{journal_date.year}). #{title_html}. 
+        #{authors_et_al(format)} (#{journal_date.year}). #{title_html}.
         <i>#{journal_html}</i>.
-        <a href="#{link}" target="_blank">DOI: #{doi}</a>
+        #{doi_html}
       HTML
     when :wikispecies
       "#{authors_array(format).join(', ')}. #{journal_date.year}: " \
-        "#{title.gsub(/[\n\r\s]+/, ' ')}. #{journal_raw}. {{Doi|#{doi}}}"
+        "#{title.gsub(/[\n\r\s]+/, ' ')}. #{journal_raw}" \
+        "#{doi.present? ? ". {{Doi|#{doi}}}" : '.'}"
     else
       "#{authors_et_al(format)} (#{journal_date.year}). " \
-        "#{title}. #{journal_raw}. DOI: #{doi}"
+        "#{title}. #{journal_raw}#{doi.present? ? ". DOI: #{doi}" : '.'}"
     end
   end
 
@@ -283,11 +356,12 @@ def prepub?
   end
 
   def link
-    "https://doi.org/#{doi}"
+    "https://doi.org/#{doi}" if doi.present?
   end
 
   def doi_title(html = true)
-    html ? "#{doi}: #{title_html}" : "#{doi}: #{title}"
+    key = doi.presence || "id:#{id}"
+    html ? "#{key}: #{title_html}" : "#{key}: #{title}"
   end
 
   def include_term?(term)

app/models/register/status.rb

@@ -124,9 +124,10 @@ def endorse(user)
   #
   # user: The user notifying the Registry (the current user)
   # params: The notification parameters
-  # doi: DOI of the effective publication
+  # doi: DOI of the effective publication, or a doi_title-style "key: title"
+  #      round-trip string identifying a DOI-less publication
   def notify(user, params, doi)
-    publication = Publication.by_doi(doi)
+    publication = Publication.by_autocomplete(doi) || Publication.by_doi(doi)
     params[:publication] = publication
 
     if publication.new_record?

app/views/contacts/new.html.erb

@@ -25,10 +25,13 @@
     <dd>
       <%= link_to(@publication) do %>
         <%= fa_icon('arrow-circle-right') %> <%= @publication.citation %>
-      <% end %> /
-      <%= link_to(@publication.link, target: '_blank') do %>
-        DOI: <%= @publication.doi %>
-        <%= fa_icon('external-link-alt') %>
+      <% end %>
+      <% if @publication.doi.present? %>
+        /
+        <%= link_to(@publication.link, target: '_blank') do %>
+          DOI: <%= @publication.doi %>
+          <%= fa_icon('external-link-alt') %>
+        <% end %>
       <% end %>
     </dd>
 

app/views/contacts/show.html.erb

@@ -9,10 +9,13 @@
   <dd>
     <%= link_to(@publication) do %>
       <%= fa_icon('arrow-circle-right') %> <%= @publication.citation %>
-    <% end %><br/>
-    <%= link_to(@publication.link, target: '_blank') do %>
-      DOI: <%= @publication.doi %>
-      <%= fa_icon('external-link-alt') %>
+    <% end %>
+    <% if @publication.doi.present? %>
+      <br/>
+      <%= link_to(@publication.link, target: '_blank') do %>
+        DOI: <%= @publication.doi %>
+        <%= fa_icon('external-link-alt') %>
+      <% end %>
     <% end %>
   </dd>
 

app/views/publications/_form.html.erb

@@ -28,7 +28,10 @@
 
   <div class="field">
     <%= form.label :journal_date %>
-    <%= form.date_select :journal_date, id: :publication_journal_date %>
+    <%= form.date_select(
+          :journal_date, { start_year: 1900, end_year: Date.current.year + 1 },
+          id: :publication_journal_date
+        ) %>
   </div>
 
   <div class="field">
@@ -43,7 +46,20 @@
 
   <div class="field">
     <%= form.label :pub_type %>
-    <%= form.text_field :pub_type, id: :publication_pub_type %>
+    <%
+      pub_type_options = Publication.pub_types.to_a.map(&:reverse)
+      if publication.pub_type.present? &&
+          !Publication.pub_types.key?(publication.pub_type)
+        # Preserve an existing value outside the curated list (e.g. a
+        # Crossref/DataCite type like "dataset" or "posted-content") as
+        # its own option, instead of silently losing it on the next save.
+        pub_type_options << [publication.pub_type, publication.pub_type]
+      end
+    %>
+    <%= form.select(
+          :pub_type, pub_type_options, { include_blank: true },
+          id: :publication_pub_type
+        ) %>
   </div>
 
   <div class="field">