WIP

Author: ursm

api/Gemfile

@@ -6,11 +6,14 @@ gem "rails", "~> 7.2.0"
 
 gem "aws-sdk-s3"
 gem "base62-rb"
+gem "bcrypt_pbkdf"
 gem "bootsnap", require: false
+gem "ed25519"
 gem "fetch-api"
 gem "jb"
 gem "json"
 gem "metabobank_tools", github: "ddbj/metabobank_tools"
+gem "net-ssh"
 gem "noodles_gff", path: "../noodles_gff-rb"
 gem "openid_connect"
 gem "pagy"

api/Gemfile.lock

@@ -120,6 +120,8 @@ GEM
       aws-eventstream (~> 1, >= 1.0.2)
     base62-rb (0.3.1)
     base64 (0.2.0)
+    bcrypt_pbkdf (1.1.1)
+    bcrypt_pbkdf (1.1.1-arm64-darwin)
     bigdecimal (3.1.8)
     bindata (2.5.0)
     bootsnap (1.18.4)
@@ -141,6 +143,7 @@ GEM
       reline (>= 0.3.8)
     diff-lcs (1.5.1)
     drb (2.2.1)
+    ed25519 (1.3.0)
     email_validator (2.2.4)
       activemodel
     erubi (1.13.0)
@@ -218,6 +221,7 @@ GEM
       timeout
     net-smtp (0.5.0)
       net-protocol
+    net-ssh (7.2.3)
     nio4r (2.7.3)
     nokogiri (1.16.7-aarch64-linux)
       racc (~> 1.4)
@@ -428,15 +432,18 @@ PLATFORMS
 DEPENDENCIES
   aws-sdk-s3
   base62-rb
+  bcrypt_pbkdf
   bootsnap
   brakeman
   climate_control
   debug
+  ed25519
   factory_bot_rails
   fetch-api
   jb
   json
   metabobank_tools!
+  net-ssh
   noodles_gff!
   openid_connect
   pagy

api/app/models/database/dra/submitter.rb

@@ -1,5 +1,46 @@
 class Database::DRA::Submitter
   def submit(submission)
-    # do nothing
+    submitter_id = submission.validation.user.uid
+    user_id      = SubmitterDB::Login.where(submitter_id:).pick(:usr_id)
+
+    DRMDB::Record.transaction isolation: Rails.env.test? ? nil : :serializable do
+      serial        = (DRMDB::Submission.where(submitter_id:).maximum(:serial) || 0) + 1
+      submission_id = "#{submitter_id}-#{serial.to_s.rjust(4, '0')}"
+
+      submission = DRMDB::Submission.create!(
+        usr_id:       user_id,
+        submitter_id:,
+        serial:,
+        create_date:  Date.current
+      )
+
+      submission.status_histories.create!(
+        status: :new
+      )
+
+      DRMDB::OperationHistory.create!(
+        type:         :info,
+        summary:      "Status update to new",
+        usr_id:       user_id,
+        serial:,
+        submitter_id:
+      )
+
+      DRMDB::ExtEntity.create!(
+        acc_type: :submission,
+        ref_name: submission_id,
+        status:   :inputting
+      ) do |entity|
+        entity.ext_permits.build(
+          submitter_id:
+        )
+      end
+
+      host, user, key_data = ENV.values_at("DRA_SSH_HOST", "DRA_SSH_USER", "DRA_SSH_KEY_DATA")
+
+      Net::SSH.start host, user, key_data: [ key_data ] do |ssh|
+        ssh.exec! "sudo /usr/local/sbin/chroot-createdir.sh #{submitter_id} #{submission_id}"
+      end
+    end
   end
 end

api/app/models/drmdb/ext_entity.rb

@@ -4,15 +4,13 @@ class DRMDB::ExtEntity < DRMDB::Record
   has_many :ext_permits, class_name: "DRMDB::ExtPermit", foreign_key: "ext_id"
 
   enum :acc_type, {
-    submission: "1",
-    study:      "2",
-    sample:     "3",
-    experiment: "4",
-    run:        "5",
-    analysis:   "6"
+    study:      "PSUB",
+    sample:     "SSUB",
+    submission: "DRA"
   }, prefix: true
 
   enum :status, {
-    valid: 100
+    inputting: 0,
+    valid:     100
   }, prefix: true
 end

api/app/models/drmdb/operation_history.rb

@@ -1,3 +1,8 @@
 class DRMDB::OperationHistory < DRMDB::Record
-  self.table_name = "operation_history"
+  self.table_name         = "operation_history"
+  self.inheritance_column = nil
+
+  enum :type, {
+    info: 3
+  }
 end

api/app/models/drmdb/status_history.rb

@@ -1,3 +1,9 @@
 class DRMDB::StatusHistory < DRMDB::Record
   self.table_name = "status_history"
+
+  belongs_to :submission, class_name: "DRMDB::Submission", foreign_key: "sub_id"
+
+  enum :status, {
+    new: 100
+  }, prefix: true
 end

api/app/models/drmdb/submission.rb

@@ -1,3 +1,5 @@
 class DRMDB::Submission < DRMDB::Record
   self.table_name = "submission"
+
+  has_many :status_histories, class_name: "DRMDB::StatusHistory", foreign_key: "sub_id"
 end

api/spec/factories/submitterdb_logins.rb

@@ -0,0 +1,5 @@
+FactoryBot.define do
+  factory :submitterdb_login, class: 'SubmitterDB::Login' do
+    password { 'password' }
+  end
+end

api/spec/models/database/dra/submitter_spec.rb

@@ -0,0 +1,59 @@
+require 'rails_helper'
+
+RSpec.describe Database::DRA::Submitter, type: :model do
+  example do
+    submission = create(:submission, {
+      validation: build(:validation, :valid, {
+        user: build(:user, uid: 'alice')
+      })
+    })
+
+    user_id = create(:submitterdb_login, **{
+      submitter_id: 'alice'
+    }).usr_id
+
+    expect(Net::SSH).to receive(:start)
+
+    Database::DRA::Submitter.new.submit submission
+
+    submission = DRMDB::Submission.sole
+
+    expect(submission).to have_attributes(
+      usr_id:       user_id,
+      submitter_id: 'alice',
+      serial:       1
+    )
+
+    status_history = DRMDB::StatusHistory.sole
+
+    expect(status_history).to have_attributes(
+      sub_id: submission[:sub_id],
+      status: 'new'
+    )
+
+    operation_history = DRMDB::OperationHistory.sole
+
+    expect(operation_history).to have_attributes(
+      type:         'info',
+      summary:      'Status update to new',
+      usr_id:       user_id,
+      serial:       1,
+      submitter_id: 'alice'
+    )
+
+    ext_entity = DRMDB::ExtEntity.sole
+
+    expect(ext_entity).to have_attributes(
+      acc_type: 'submission',
+      ref_name: 'alice-0001',
+      status:   'inputting'
+    )
+
+    ext_permit = DRMDB::ExtPermit.sole
+
+    expect(ext_permit).to have_attributes(
+      ext_id:       ext_entity.ext_id,
+      submitter_id: 'alice'
+    )
+  end
+end