Validate for DDBJ Record and updating accession

app/controllers/accession_renewals/files_controller.rb

@@ -0,0 +1,7 @@
+class AccessionRenewals::FilesController < ApplicationController
+  def show
+    renewal = current_user.accession_renewals.find(params.expect(:accession_renewal_id))
+
+    redirect_to renewal.file.url, allow_other_host: true
+  end
+end

app/controllers/accession_renewals_controller.rb

@@ -0,0 +1,22 @@
+class AccessionRenewalsController < ApplicationController
+  def show
+    @renewal = current_user.accession_renewals.find(params.expect(:id))
+  end
+
+  def create
+    accession = current_user.accessions.find_by!(number: params.expect(:accession_number))
+    @renewal  = accession.renewals.create!(renewal_params)
+
+    RenewAccessionJob.perform_later @renewal
+
+    render :show, status: :created
+  end
+
+  private
+
+  def renewal_params
+    params.expect(accession_renewal: [
+      :file
+    ])
+  end
+end

app/controllers/validations/via_ddbj_records_controller.rb

@@ -1,10 +1,18 @@
 class Validations::ViaDDBJRecordsController < ApplicationController
   def create
-    @validation = current_user.validations.create!(
+    @validation = create_validation
+
+    ValidateJob.perform_later @validation
+
+    render status: :created
+  end
+
+  private
+
+  def create_validation
+    current_user.validations.create!(
       db:          params.expect(:db),
       via:         :ddbj_record,
-      progress:    :finished,
-      finished_at: Time.current
     ) {|validation|
       validation.objs.build _id: '_base', validity: 'valid'
 
@@ -14,28 +22,23 @@ def create
       if file = record_params[:file]
         validation.objs.build(
           _id:         'DDBJRecord',
-          validity:    'valid',
           file:,
           destination:
         )
       elsif path = record_params['path']
         obj_schema = db[:objects][:ddbj_record].first
 
-        obj = validation.build_obj_from_path(path, **{
+        validation.build_obj_from_path(path, **{
           obj_schema:,
           destination:,
           user:        current_user
         })
-
-        obj.validity = 'valid'
       end
-    }
 
-    render status: :created
+      validation
+    }
   end
 
-  private
-
   def record_params
     params.expect(DDBJRecord: [
       :file,

app/jobs/renew_accession_job.rb

@@ -0,0 +1,26 @@
+class RenewAccessionJob < ApplicationJob
+  def perform(renewal)
+    renewal.update! progress: :running, started_at: Time.current
+
+    sleep 3
+
+    ActiveRecord::Base.transaction do
+      begin
+        JSON.parse renewal.file.download
+      rescue JSON::ParserError => e
+        renewal.validation_details.create!(
+          severity: 'error',
+          message:  e.message
+        )
+      end
+
+      if renewal.validation_details.empty?
+        renewal.validity_valid!
+      else
+        renewal.validity_invalid!
+      end
+    end
+  ensure
+    renewal.update! progress: :finished, finished_at: Time.current unless renewal.canceled?
+  end
+end

app/jobs/validate_job.rb

@@ -3,7 +3,7 @@ def perform(validation)
     validation.update! progress: :running, started_at: Time.current
 
     ActiveRecord::Base.transaction do
-      validator = "Database::#{validation.db}::Validator".constantize.new
+      validator = "Database::#{validation.db}::#{validation.via.camelize}Validator".constantize.new
 
       begin
         validator.validate validation

app/models/accession.rb

@@ -1,3 +1,5 @@
 class Accession < ApplicationRecord
   belongs_to :submission
+
+  has_many :renewals, dependent: :destroy, class_name: 'AccessionRenewal'
 end

app/models/accession_renewal.rb

@@ -0,0 +1,10 @@
+class AccessionRenewal < ApplicationRecord
+  belongs_to :accession, inverse_of: :renewals
+
+  has_many :validation_details, dependent: :destroy, class_name: 'AccessionRenewalValidationDetail', inverse_of: :renewal
+
+  has_one_attached :file
+
+  enum :progress, %w[waiting running finished canceled].index_by(&:to_sym)
+  enum :validity, %w[valid invalid error].index_by(&:to_sym), prefix: true
+end

app/models/accession_renewal_validation_detail.rb

@@ -0,0 +1,3 @@
+class AccessionRenewalValidationDetail < ApplicationRecord
+  belongs_to :renewal, class_name: 'AccessionRenewal'
+end

app/models/database/bioproject/validator.rb → app/models/database/bioproject/file_validator.rb

@@ -1,4 +1,4 @@
-class Database::BioProject::Validator
+class Database::BioProject::FileValidator
   include DDBJValidator
 
   def translate_error(error)

app/models/database/biosample/validator.rb → app/models/database/biosample/file_validator.rb

@@ -1,4 +1,4 @@
-class Database::BioSample::Validator
+class Database::BioSample::FileValidator
   include DDBJValidator
 
   def translate_error(error)

app/models/database/dra/validator.rb → app/models/database/dra/file_validator.rb

@@ -1,4 +1,4 @@
-class Database::DRA::Validator
+class Database::DRA::FileValidator
   def validate(validation)
     objs = validation.objs.without_base.index_by(&:_id)
 

app/models/database/gea/validator.rb → app/models/database/gea/file_validator.rb

@@ -1,4 +1,4 @@
-class Database::GEA::Validator
+class Database::GEA::FileValidator
   def validate(validation)
     objs = validation.objs.without_base.index_by(&:_id)
 

app/models/database/jvar/validator.rb → app/models/database/jvar/file_validator.rb

@@ -1,4 +1,4 @@
-class Database::JVar::Validator
+class Database::JVar::FileValidator
   def validate(validation)
     validation.objs.without_base.each(&:validity_valid!)
   end

app/models/database/metabobank/validator.rb → app/models/database/metabobank/file_validator.rb

@@ -1,4 +1,4 @@
-class Database::MetaboBank::Validator
+class Database::MetaboBank::FileValidator
   def validate(validation)
     objs = validation.objs.without_base.index_by(&:_id)
 

app/models/database/trad/ddbj_record_validator.rb

@@ -0,0 +1,18 @@
+class Database::Trad::DDBJRecordValidator
+  def validate(validation)
+    obj = validation.objs.without_base.last
+
+    begin
+      JSON.parse(obj.file.download)
+
+      obj.validity_valid! if obj.validation_details.empty?
+    rescue JSON::ParserError => e
+      obj.validity_invalid!
+
+      obj.validation_details.create!(
+        severity: 'error',
+        message:  e.message
+      )
+    end
+  end
+end

app/models/database/trad/validator.rb → app/models/database/trad/file_validator.rb

@@ -1,4 +1,4 @@
-class Database::Trad::Validator
+class Database::Trad::FileValidator
   class MissingContactPersonInformation < StandardError; end
   class DuplicateContactPersonInformation < StandardError; end
 

app/models/database/trad2/validator.rb → app/models/database/trad2/file_validator.rb

@@ -1,4 +1,4 @@
-class Database::Trad2::Validator
+class Database::Trad2::FileValidator
   include TradValidation
 
   ASSOC = {

app/models/user.rb

@@ -5,8 +5,9 @@ def self.generate_api_key
 
   has_many :validations, dependent: :destroy
 
-  has_many :submissions, through: :validations
-  has_many :accessions,  through: :submissions
+  has_many :submissions,        through: :validations
+  has_many :accessions,         through: :submissions
+  has_many :accession_renewals, through: :accessions, source: :renewals
 
   before_create do |user|
     user.api_key ||= self.class.generate_api_key

app/views/accession_renewals/_accession_renewal.json.jb

@@ -0,0 +1,25 @@
+{
+  **accession_renewal.slice(
+    :id,
+    :started_at,
+    :finished_at,
+    :progress,
+    :validity,
+    :created_at
+  ),
+
+  file: {
+    filename: accession_renewal.file.filename,
+    url:      accession_renewal_file_url(accession_renewal)
+  },
+
+  validation_details: accession_renewal.validation_details.map {|detail|
+    {
+      **detail.slice(
+        :severity
+      ),
+
+      message: detail.message.scrub
+    }
+  }
+}

app/views/accession_renewals/show.json.jb

@@ -0,0 +1 @@
+render(@renewal)

app/views/accessions/_accession.json.jb

@@ -1,8 +1,12 @@
 # locals: (accession:)
 
-accession.slice(
-  :number,
-  :entry_id,
-  :version,
-  :last_updated_at
-)
+{
+  **accession.slice(
+    :number,
+    :entry_id,
+    :version,
+    :last_updated_at
+  ),
+
+  renewals: render(partial: 'accession_renewals/accession_renewal', collection: accession.renewals)
+}

config/routes.rb

@@ -22,8 +22,15 @@
       end
     end
 
-    resources :submissions, only: %i[index show create]
-    resources :accessions,  only: %i[show update], param: :number
+    resources :submissions, only: %i[index show create] do
+      resources :accessions, only: %i[show update], param: :number, shallow: true do
+        resources :accession_renewals, only: %i[show create] do
+          scope module: 'accession_renewals' do
+            resource :file, only: %i[show], shallow: false
+          end
+        end
+      end
+    end
   end
 
   get 'web/*paths', to: 'webs#show'

db/migrate/20250924000504_create_accession_renewals.rb

@@ -0,0 +1,23 @@
+class CreateAccessionRenewals < ActiveRecord::Migration[8.0]
+  def change
+    create_table :accession_renewals do |t|
+      t.references :accession, null: false, foreign_key: true
+
+      t.string   :progress, null: false, default: "waiting"
+      t.string   :validity
+      t.datetime :started_at
+      t.datetime :finished_at
+
+      t.timestamps
+    end
+
+    create_table :accession_renewal_validation_details do |t|
+      t.references :renewal, null: false, foreign_key: {to_table: :accession_renewals}
+
+      t.string :severity, null: false
+      t.string :message,  null: false
+
+      t.timestamps
+    end
+  end
+end

schema/openapi.d.ts

@@ -999,6 +999,29 @@ export interface components {
             version: number;
             /** Format: date-time */
             last_updated_at: string;
+            renewals?: components["schemas"]["AccessionRenewal"][];
+        };
+        AccessionRenewal: {
+            id: number;
+            /** Format: date-time */
+            created_at: string;
+            /** Format: date-time */
+            started_at: string | null;
+            /** Format: date-time */
+            finished_at: string | null;
+            /** @enum {string} */
+            progress: "waiting" | "running" | "finished" | "canceled";
+            /** @enum {string|null} */
+            validity: "valid" | "invalid" | "error" | null;
+            file: {
+                filename: string;
+                /** Format: url */
+                url: string;
+            } | null;
+            validation_details: {
+                severity: string;
+                message: string;
+            }[];
         };
         ValidationResult: {
             /** @enum {string} */