WIP

Author: ursm

api/Gemfile

@@ -6,11 +6,14 @@ gem "rails", "~> 7.2.2"
 
 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

@@ -121,6 +121,8 @@ 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)
     benchmark (0.3.0)
     bigdecimal (3.1.8)
     bindata (2.5.0)
@@ -143,6 +145,7 @@ 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)
@@ -221,6 +224,7 @@ GEM
       timeout
     net-smtp (0.5.0)
       net-protocol
+    net-ssh (7.3.0)
     nio4r (2.7.4)
     nokogiri (1.16.7-aarch64-linux)
       racc (~> 1.4)
@@ -430,15 +434,18 @@ 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 +1,72 @@
 class Database::DRA::Submitter
+  ACC_TYPES = {
+    "Submission" => "DRA",
+    "Experiment" => "DRX",
+    "Run"        => "DRR",
+    "Analysis"   => "DRZ"
+  }
+
   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 = 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:
+      )
+
+      submission_id = "#{submitter_id}-#{serial.to_s.rjust(4, '0')}"
+
+      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
+
+      submission.validation.objs.where(_id: ACC_TYPES.keys).each do |obj|
+        DRMDB::AccessionEntity.create!(
+          alias:       "#{submission_id}_#{obj._id}_0001",
+          center_name: "National Institute of Genetics",
+          acc_type:    ACC_TYPES.fetch(obj._id),
+        ) do |accession|
+          accession.create_accession_relation!(
+            grp_id: 42
+          ) do |relation|
+            relation.meta_entities.create!(
+              meta_version: 0,
+              type:         obj._id.downcase,
+              content:      obj.file.download
+            )
+          end
+        end
+      end
+    end
   end
 end

api/app/models/drmdb/accession_entity.rb

@@ -0,0 +1,6 @@
+class DRMDB::AccessionEntity < DRMDB::Record
+  self.table_name         = "accession_entity"
+  self.inheritance_column = nil
+
+  belongs_to :accession_relation, class_name: "DRMDB::AccessionRelation", foreign_key: "acc_id"
+end

api/app/models/drmdb/accession_relation.rb

@@ -0,0 +1,8 @@
+class DRMDB::AccessionRelation < DRMDB::Record
+  self.table_name = "accession_relation"
+
+  belongs_to :submission_group, class_name: "DRMDB::SubmissionGroup", foreign_key: "grp_id"
+
+  has_one  :meta_entity,        class_name: "DRMDB::MetaEntity",      foreign_key: "acc_id"
+  has_many :accession_entities, class_name: "DRMDB::AccessionEntity", foreign_key: "acc_id"
+end

api/app/models/drmdb/ext_entity.rb

@@ -1,7 +1,7 @@
 class DRMDB::ExtEntity < DRMDB::Record
   self.table_name = "ext_entity"
 
-  has_many :ext_permits, class_name: "DRMDB::ExtPermit", foreign_key: "ext_id"
+  belongs_to :ext_relation, class_name: "DRMDB::ExtRelation", foreign_key: "ext_id"
 
   enum :acc_type, {
     study:      "PSUB",

api/app/models/drmdb/ext_permit.rb

@@ -1,3 +1,5 @@
 class DRMDB::ExtPermit < DRMDB::Record
   self.table_name = "ext_permit"
+
+  belongs_to :ext_relation, class_name: "DRMDB::ExtRelation", foreign_key: "ext_id"
 end

api/app/models/drmdb/ext_relation.rb

@@ -0,0 +1,8 @@
+class DRMDB::ExtRelation < DRMDB::Record
+  self.table_name = "ext_relation"
+
+  belongs_to :submission_group, class_name: "DRMDB::SubmissionGroup", foreign_key: "grp_id"
+
+  has_many :ext_entities, class_name: "DRMDB::ExtEntity", foreign_key: "ext_id"
+  has_one  :ext_permit,   class_name: "DRMDB::ExtPermit", foreign_key: "ext_id"
+end

api/app/models/drmdb/meta_entity.rb

@@ -0,0 +1,5 @@
+class DRMDB::MetaEntity < DRMDB::Record
+  self.table_name = "meta_entity"
+
+  belongs_to :accession_relation, class_name: "DRMDB::AccessionRelation", foreign_key: "acc_id"
+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