Effective publication checks in names

Author: lmrodriguezr

app/models/check.rb

@@ -1,6 +1,6 @@
 class Check < ApplicationRecord
   belongs_to(:name)
-  belongs_to(:user)
+  belongs_to(:user, optional: true)
 
   def fail?
     !pass?

app/models/name/quality_checks.rb

@@ -520,7 +520,12 @@ class QcWarning
         rule_notes: %w[26#1],
         can_endorse: false
       }.merge(@@link_to_edit_parent),
-      # - Rule 26 Note 2 [TODO: Report as check and not as register note]
+      # - Rule 26 Note 2
+      effective_publication_missing_accession: {
+        message: 'The effective publication does not include the SeqCode ' \
+                 'Registry Accession',
+        rule_notes: %w[26#2],
+      },
       # - Rule 26 Note 3 is enforced outside of the SeqCode Registry
       # - Recommendation 26 [Checklist-N]
       missing_description_in_publication: {
@@ -621,6 +626,11 @@ class QcWarning
       # - Rule 50.3 covered in § Rule 50.1
 
       # APPENDIX I
+      name_missing_in_effective_publication: {
+        message:
+          'The reported effective publication does not mention this name',
+        rules: %w[appendix-i]
+      },
       low_genome_sequencing_depth: {
         message:
           'The sequencing depth of the type genome should be 10X or greater',

app/models/register/status.rb

@@ -281,57 +281,47 @@ def automated_validation
   # persistent
   def check_pdf_files
     has_acc = false
-    bnames = Hash[names.map { |n| [n.base_name, false] }]
-    cnames = Hash[names.map { |n| [n.base_name, n.corrigendum_from] }]
+    inames = Hash[names.map { |n| [n, false] }]
     [publication_pdf, supplementary_pdf].each do |as|
-      break if has_acc && bnames.values.all?
+      break if has_acc && inames.values.all?
       next unless as.attached?
 
       as.open do |file|
         render = PDF::Reader.new(file.path)
         render.pages.each do |page|
           txt = page.text
           has_acc = true if txt.index(accession)
-          bnames.each_key do |bn|
-            if txt.index(bn) || (cnames[bn] && txt.index(cnames[bn]))
-              bnames[bn] = true
-            end
+          inames.each_key do |n|
+            bn = n.base_name
+            cn = n.corrigendum_from
+            inames[n] = true if txt.index(bn) || (cn && txt.index(cn))
           end
-          break if has_acc && bnames.values.all?
+          break if has_acc && inames.values.all?
         end
       end
     end
 
     if has_acc
       add_note('The effective publication includes the SeqCode accession')
     else
-      add_note(
-        'The effective publication does not include the accession ' \
-        '(SeqCode, Rule 26, Note 2)'
-      )
+      names.each do |n|
+        Check.find_or_create_by(
+          name: n, kind: :effective_publication_missing_accession, pass: false
+        )
+      end
     end
 
-    if bnames.values.all?
+    if inames.values.all?
       add_note('The effective publication mentions all names in the list')
-    elsif bnames.values.any?
-      if bnames.values.count(&:!) > 5
-        add_note(
-          'The effective publication mentions' \
-            " #{bnames.values.count(&:itself)} out of" \
-            " #{bnames.count} names in the list"
-        )
-      else
-        add_note(
-          'The effective publication mentions some names in the list,' \
-            " but not: #{bnames.select { |_, v| !v }.keys.join(', ')}"
+    else
+      inames.each do |n, v|
+        next if v
+        Check.find_or_create_by(
+          name: n, kind: :name_missing_in_effective_publication, pass: false
         )
       end
-    else
-      add_note(
-        'The effective publication does not mention any names in the list'
-      )
     end
 
-    has_acc && bnames.values.all?
+    has_acc && inames.values.all?
   end
 end

db/migrate/20250902220521_make_checks_user_optional.rb

@@ -0,0 +1,5 @@
+class MakeChecksUserOptional < ActiveRecord::Migration[6.1]
+  def change
+    change_column_null(:checks, :user_id, true)
+  end
+end

db/schema.rb

@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 2025_08_21_140809) do
+ActiveRecord::Schema.define(version: 2025_09_02_220521) do
 
   create_table "action_text_rich_texts", force: :cascade do |t|
     t.string "name", null: false
@@ -60,7 +60,7 @@
 
   create_table "checks", force: :cascade do |t|
     t.integer "name_id", null: false
-    t.integer "user_id", null: false
+    t.integer "user_id"
     t.text "kind", null: false
     t.boolean "pass"
     t.datetime "updated_at", precision: 6, null: false