DRA submission

api/Gemfile

@@ -4,11 +4,14 @@ gem "rails", "~> 8.0.0"
 
 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

@@ -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 (0.4.0)
     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 (1.16.8-aarch64-linux)
       racc (~> 1.4)
@@ -431,15 +435,18 @@ 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/bioproject/submitter.rb

@@ -98,15 +98,16 @@ def submit(submission)
       )
 
       tx.after_commit do
-        DRMDB::ExtEntity.create!(
+        entity = DRMDB::ExtEntity.create!(
           acc_type: :study,
           ref_name: submission_id,
           status:   :valid
-        ) do |entity|
-          entity.ext_permits.build(
-            submitter_id:
-          )
-        end
+        )
+
+        DRMDB::ExtPermit.create!(
+          ext_id: entity.ext_id,
+          submitter_id:
+        )
       end
     end
   end

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

@@ -15,7 +15,6 @@ def submit(submission)
           BioSample::OperationHistory.create!(
             type:         :fatal,
             summary:      "[repository:CreateNewSubmission] Number of submission surpass the upper limit",
-            date:         Time.current,
             submitter_id:
           )
         end
@@ -27,7 +26,6 @@ def submit(submission)
         BioSample::OperationHistory.create!(
           type:         :error,
           summary:      "[repository:CreateNewSubmission] rollback transaction",
-          date:         Time.current,
           submitter_id:
         )
       end
@@ -126,22 +124,22 @@ def submit(submission)
         )
 
         tx.after_commit do
-          DRMDB::ExtEntity.create!(
+          entity = DRMDB::ExtEntity.create!(
             acc_type: :sample,
             ref_name: sample.smp_id,
             status:   :valid
-          ) do |entity|
-            entity.ext_permits.build(
-              submitter_id:
-            )
-          end
+          )
+
+          DRMDB::ExtPermit.create!(
+            ext_id: entity.ext_id,
+            submitter_id:
+          )
         end
       end
 
       BioSample::OperationHistory.create!(
         type:          :info,
         summary:       "[repository:CreateNewSubmission] Create new submission",
-        date:          Time.current,
         submitter_id:,
         submission_id:
       )

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

@@ -1,5 +1,97 @@
 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
+
+      dra_submission = DRMDB::Submission.create!(
+        usr_id:       user_id,
+        submitter_id:,
+        serial:,
+        create_date:  Date.current
+      )
+
+      dra_submission.status_histories.create! status: :data_validated
+
+      submission_group = dra_submission.create_submission_group!(
+        submit_version: 1,
+        valid:          true,
+        serial_version: 1
+      )
+
+      submission_id = "#{submitter_id}-#{serial.to_s.rjust(4, '0')}"
+      center_name   = SubmitterDB::Organization.where(submitter_id:).pick(:center_name)
+      objs          = submission.validation.objs.where(_id: %w(Submission Experiment Run Analysis))
+
+      acc_entities_assoc = objs.map { |obj|
+        DRMDB::AccessionEntity.create!(
+          alias:       "#{submission_id}_#{obj._id}_0001",
+          center_name:,
+          acc_type:    obj._id.downcase
+        )
+      }.index_by(&:acc_type)
+
+      objs.each do |obj|
+        parent_acc_entity = case obj._id
+        when "Submission"
+          nil
+        when "Study", "Sample"
+          acc_entities_assoc["DRA"]
+        when "Sample"
+          acc_entities_assoc["sample"]
+        when "Experiment"
+          acc_entities_assoc["sample"] || acc_entities_assoc["study"]
+        when "Run"
+          acc_entities_assoc["DRX"]
+        when "Analysis"
+          acc_entities_assoc["study"]
+        else
+          raise "must not happen"
+        end
+
+        submission_group.accession_relations.create!(
+          accession_entity:        acc_entity,
+          parent_accession_entity: parent_acc_entity
+        ) do |relation|
+          relation.build_meta_entity(
+            accession_entity: acc_entity,
+            meta_version:     1,
+            type:             obj._id.downcase,
+            content:          obj.file.download
+          )
+        end
+
+        ext_entity = DRMDB::ExtEntity.create!(
+          acc_type: :submission,
+          ref_name: "160053",
+          status:   :valid
+        )
+
+        submission_group.ext_relations.create!(
+          acc_id: acc_entity.acc_id,
+          ext_id: ext_entity.ext_id
+        ) do |relation|
+          relation.build_ext_permit(
+            ext_id:       ext_entity.ext_id,
+            submitter_id:
+          )
+        end
+      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
+
+      DRMDB::OperationHistory.create!(
+        type:         :info,
+        summary:      "Direct submission via repository",
+        usr_id:       user_id,
+        submitter_id:
+      )
+    end
   end
 end

api/app/models/drmdb/accession_entity.rb

@@ -0,0 +1,12 @@
+class DRMDB::AccessionEntity < DRMDB::Record
+  self.table_name = "accession_entity"
+
+  belongs_to :accession_relation, optional: true, class_name: "DRMDB::AccessionRelation", foreign_key: "acc_id", primary_key: "acc_id"
+
+  enum :acc_type, {
+    submission: "DRA",
+    experiment: "DRX",
+    run:        "DRR",
+    analysis:   "DRZ"
+  }
+end

api/app/models/drmdb/accession_relation.rb

@@ -0,0 +1,10 @@
+class DRMDB::AccessionRelation < DRMDB::Record
+  self.table_name = "accession_relation"
+
+  belongs_to :submission_group,        class_name: "DRMDB::SubmissionGroup", foreign_key: "grp_id",   primary_key: "grp_id"
+  belongs_to :accession_entity,        class_name: "DRMDB::AccessionEntity", foreign_key: "acc_id",   primary_key: "acc_id"
+  belongs_to :parent_accession_entity, class_name: "DRMDB::AccessionEntity", foreign_key: "p_acc_id", primary_key: "acc_id", optinal: true
+
+  has_many :accession_entities, class_name: "DRMDB::AccessionEntity", foreign_key: "acc_id", primary_key: "acc_id"
+  has_one  :meta_entity,        class_name: "DRMDB::MetaEntity",      foreign_key: "acc_id", primary_key: "acc_id"
+end

api/app/models/drmdb/batch.rb

@@ -0,0 +1,3 @@
+class DRMDB::Batch < DRMDB::Record
+  self.table_name = 'batch'
+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, optional: true, class_name: "DRMDB::ExtRelation", foreign_key: "ext_id", primary_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, optional: true, class_name: "DRMDB::ExtRelation", foreign_key: "ext_id", primary_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", primary_key: "grp_id"
+
+  has_many :ext_entities, class_name: "DRMDB::ExtEntity", foreign_key: "ext_id", primary_key: "ext_id"
+  has_one  :ext_permit,   class_name: "DRMDB::ExtPermit", foreign_key: "ext_id", primary_key: "ext_id"
+end

api/app/models/drmdb/meta_entity.rb

@@ -0,0 +1,7 @@
+class DRMDB::MetaEntity < DRMDB::Record
+  self.table_name         = "meta_entity"
+  self.inheritance_column = nil
+
+  belongs_to :accession_relation, class_name: "DRMDB::AccessionRelation", foreign_key: "acc_id", primary_key: "acc_id"
+  belongs_to :accession_entity,   class_name: "DRMDB::AccessionEntity",   foreign_key: "acc_id", primary_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

api/app/models/drmdb/status_history.rb

@@ -1,3 +1,20 @@
 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,
+    meta_validated:   300,
+    data_validating:  380,
+    data_error:       390,
+    data_validated:   400,
+    acc_issued:       500,
+    private_complete: 700,
+    release_notifed:  750,
+    public_complete:  800,
+    cancel:           1000,
+    suppress:         1100,
+    killed:           1200
+  }, prefix: true
 end

api/app/models/drmdb/submission.rb

@@ -1,3 +1,6 @@
 class DRMDB::Submission < DRMDB::Record
   self.table_name = "submission"
+
+  has_one  :submission_group, class_name: "DRMDB::SubmissionGroup", foreign_key: "sub_id"
+  has_many :status_histories, class_name: "DRMDB::StatusHistory",   foreign_key: "sub_id"
 end

api/app/models/drmdb/submission_component.rb

@@ -0,0 +1,5 @@
+class DRMDB::SubmissionComponent < DRMDB::Record
+  self.table_name = 'submission_component'
+
+  belongs_to :submission_group, class_name: 'DRMDB::SubmissionGroup', foreign_key: 'grp_id', primary_key: 'grp_id'
+end

api/app/models/drmdb/submission_group.rb

@@ -0,0 +1,21 @@
+class DRMDB::SubmissionGroup < DRMDB::Record
+  self.table_name = "submission_group"
+
+  belongs_to :submission, class_name: "DRMDB::Submission", foreign_key: "sub_id"
+
+  has_many :submission_components, class_name: "DRMDB::SubmissionComponent", foreign_key: "grp_id", primary_key: "grp_id"
+  has_many :accession_relations,   class_name: "DRMDB::AccessionRelation",   foreign_key: "grp_id", primary_key: "grp_id"
+  has_many :ext_relations,         class_name: "DRMDB::ExtRelation",         foreign_key: "grp_id", primary_key: "grp_id"
+
+  has_many :accession_entities, through: :accession_relations
+  has_many :meta_entities,      through: :accession_relations
+  has_many :ext_entities,       through: :ext_relations
+  has_many :ext_permits,        through: :ext_relations
+
+  class << self
+    def instance_method_already_implemented?(method_name)
+      return true if method_name == "valid?"
+      super
+    end
+  end
+end

api/db/bioproject_migrate/20240827022556_bioproject_init.rb

@@ -1,4 +1,4 @@
-class BioProjectInit < ActiveRecord::Migration[7.2]
+class BioProjectInit < ActiveRecord::Migration[8.0]
   def change
     execute 'CREATE SCHEMA mass'
 

api/db/biosample_migrate/20240829001416_biosample_init.rb

@@ -1,4 +1,4 @@
-class BioSampleInit < ActiveRecord::Migration[7.2]
+class BioSampleInit < ActiveRecord::Migration[8.0]
   def change
     execute 'CREATE SCHEMA mass'
 

api/db/drasearch_migrate/20241023004659_dra_search_init.rb

@@ -1,4 +1,4 @@
-class DRASearchInit < ActiveRecord::Migration[7.2]
+class DRASearchInit < ActiveRecord::Migration[8.0]
   def change
     execute 'CREATE SCHEMA sra'