WIP: Add test

api/app/models/database/bioproject.rb

@@ -65,6 +65,25 @@ def submit(submission)
             submitter_id:
           )
         end
+
+        contact      = Dway.submitterdb[:contact].where(submitter_id:, is_pi: true).first
+        organization = Dway.submitterdb[:organization].where(submitter_id:).first
+
+        {
+          first_name:        contact[:first_name],
+          last_name:         contact[:last_name],
+          email:             contact[:email],
+          organization_name: organization.fetch_values(:unit, :affiliation, :department, :organization).compact_blank.join(', '),
+          organization_url:  organization[:url],
+        }.each.with_index 1 do |(key, value), i|
+          Dway.bioproject[:submission_data].insert(
+            submission_id: ,
+            data_name:     key.to_s,
+            data_value:    value.to_s,
+            form_name:     'submitter',
+            t_order:       i
+          )
+        end
       end
     end
 

api/app/models/dway.rb

@@ -2,18 +2,18 @@ class Dway
   include Singleton
 
   class << self
-    delegate :submitterdb, :drmdb, :bioproject, to: :instance
+    delegate :bioproject, :drmdb, :submitterdb, to: :instance
   end
 
-  def submitterdb
-    @submitterdb ||= Sequel.connect(ENV.fetch('SUBMITTERDB_DATABASE_URL'), search_path: 'mass')
+  def bioproject
+    @bioproject ||= Sequel.connect(ENV.fetch('BIOPROJECT_DATABASE_URL'), search_path: 'mass')
   end
 
   def drmdb
     @drmdb ||= Sequel.connect(ENV.fetch('DRMDB_DATABASE_URL'), search_path: 'mass')
   end
 
-  def bioproject
-    @bioproject ||= Sequel.connect(ENV.fetch('BIOPROJECT_DATABASE_URL'), search_path: 'mass')
+  def submitterdb
+    @submitterdb ||= Sequel.connect(ENV.fetch('SUBMITTERDB_DATABASE_URL'), search_path: 'mass')
   end
 end

api/config/environments/test.rb

@@ -62,3 +62,7 @@
   # Raise error when a before_action's only/except options reference missing actions
   config.action_controller.raise_on_missing_callback_actions = true
 end
+
+ENV['BIOPROJECT_DATABASE_URL']  = 'postgres://localhost/bioproject_test'
+ENV['DRMDB_DATABASE_URL']       = 'postgres://localhost/drmdb_test'
+ENV['SUBMITTERDB_DATABASE_URL'] = 'postgres://localhost/submitterdb_test'

api/lib/tasks/dway.rake

@@ -6,7 +6,7 @@ namespace :dway do
     env_keys = %w(DRMDB_DATABASE_URL SUBMITTERDB_DATABASE_URL BIOPROJECT_DATABASE_URL)
 
     desc 'Create databases'
-    task :create do
+    task :create => :environment do
       env_keys.each do |key|
         uri = URI.parse(ENV.fetch(key))
 
@@ -32,7 +32,7 @@ namespace :dway do
     task :prepare => %i[create migrate]
 
     desc 'Drop databases'
-    task :drop do
+    task :drop => :environment do
       env_keys.each do |key|
         uri = URI.parse(ENV.fetch(key))
 

api/spec/fixtures/files/bioproject/valid/1_not_well_format_xml_ok.xml

@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<PackageSet>
+  <Package>
+    <Project>
+      <Project>
+        <ProjectID>
+          <ArchiveID accession="" archive="DDBJ" />
+        </ProjectID>
+        <ProjectDescr>
+          <Title>Title text</Title>
+          <Description>Description text</Description>
+        </ProjectDescr>
+        <ProjectType>
+          <ProjectTypeSubmission>
+            <Target sample_scope="eEnvironment" material="ePartialGenome" capture="eTargetedLocusLoci"></Target>
+            <Method method_type="eSequencing" />
+            <Objectives>
+              <Data data_type="eRawSequenceReads" />
+            </Objectives>
+          </ProjectTypeSubmission>
+        </ProjectType>
+      </Project>
+    </Project>
+  </Package>
+</PackageSet>

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

@@ -0,0 +1,34 @@
+require 'rails_helper'
+
+RSpec.describe Database::BioProject::Submitter do
+  example 'visibility: private' do
+    user = create(:user, uid: 'alice')
+
+    submission = create(:submission, **{
+      visibility: :private,
+
+      validation: build(:validation, :valid, **{
+        user:,
+
+        objs: [
+          build(:obj, **{
+            _id:      'BioProject',
+            file:     file_fixture('bioproject/valid/1_not_well_format_xml_ok.xml'),
+            validity: :valid
+          })
+        ]
+      })
+    })
+
+    Dway.submitterdb[:contact].insert(
+      submitter_id: 'alice',
+      is_pi:        true
+    )
+
+    Dway.submitterdb[:organization].insert(
+      submitter_id: 'alice'
+    )
+
+    Database::BioProject::Submitter.new.submit submission
+  end
+end

api/spec/support/dway.rb

@@ -1,8 +1,5 @@
 require 'sequel/core'
 
-ENV['DRMDB_DATABASE_URL']       = 'postgres://localhost/drmdb_test'
-ENV['SUBMITTERDB_DATABASE_URL'] = 'postgres://localhost/submitterdb_test'
-
 RSpec.configure do |config|
   config.before :suite do
     Rails.application.load_tasks
@@ -11,13 +8,17 @@
   end
 
   config.around do |example|
-    Dway.submitterdb.transaction auto_savepoint: true do
-      Dway.submitterdb.rollback_on_exit
+    Dway.bioproject.transaction auto_savepoint: true do
+      Dway.bioproject.rollback_on_exit
 
       Dway.drmdb.transaction auto_savepoint: true do
         Dway.drmdb.rollback_on_exit
 
-        example.call
+        Dway.submitterdb.transaction auto_savepoint: true do
+          Dway.submitterdb.rollback_on_exit
+
+          example.call
+        end
       end
     end
   end

web/app/components/validation/submit-form.gts

@@ -39,9 +39,9 @@ export default class ValidationSubmitFormComponent extends Component<Signature>
     const res = await safeFetchWithModal(
       `${ENV.apiURL}/submissions`,
       {
-        method:  'POST',
+        method: 'POST',
         headers: this.currentUser.authorizationHeader,
-        body:    formData
+        body: formData,
       },
       this.errorModal,
     );
@@ -53,21 +53,37 @@ export default class ValidationSubmitFormComponent extends Component<Signature>
   });
 
   <template>
-    <form {{on 'submit' this.submit.perform}} class="p-3">
+    <form {{on 'submit' this.submit.perform}} class='p-3'>
       <div class='mb-3'>
         <label class='form-label'>Visibility</label>
 
         <div>
           <div class='form-check form-check-inline'>
             {{#let (uniqueId) as |id|}}
-              <input class='form-check-input' type='radio' name='submission[visibility]' value='public' id={{id}} required />
+              <input
+                class='form-check-input'
+                id={{id}}
+                type='radio'
+                name='submission[visibility]'
+                value='public'
+                required
+              />
+
               <label class='form-check-label' for={{id}}>Public</label>
             {{/let}}
           </div>
 
           <div class='form-check form-check-inline'>
             {{#let (uniqueId) as |id|}}
-              <input class='form-check-input' type='radio' name='submission[visibility]' value='private' id={{id}} required />
+              <input
+                class='form-check-input'
+                id={{id}}
+                type='radio'
+                name='submission[visibility]'
+                value='private'
+                required
+              />
+
               <label class='form-check-label' for={{id}}>Private</label>
             {{/let}}
           </div>