adds rake task to migrate the samples in custom repositories and tests [fixes SCI-2014]

app/services/tasks/samples_to_repository_migration_service.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 # Helper module for dealing with the migration from samples
 # to custom repositories. We need to query with SQL because probably we will not
 # have the "Sample" and other related models at the time this code will execute
@@ -23,7 +25,7 @@ module Tasks
 
       repository_columns = []
       custom_columns.each_with_index do |column, index|
-        repository_column = RepositoryColumn.create(
+        repository_column = RepositoryColumn.create!(
           repository: repository,
           created_by_id: column.fetch('user_id') { repository.created_by_id },
           data_type: :RepositoryTextValue,
@@ -51,16 +53,22 @@ module Tasks
       sample_types = ActiveRecord::Base.connection.execute(sample_types_sql)
       sample_groups = ActiveRecord::Base.connection.execute(sample_groups_sql)
 
-      repository_columns = []
-
-      repository_columns << RepositoryColumn.create(
+      sample_group = RepositoryColumn.create!(
         repository: repository,
         created_by_id: repository.created_by_id,
         data_type: :RepositoryListValue,
         name: 'Sample group'
       )
 
-      repository_columns << RepositoryColumn.create(
+      # needs some random string to prevent duplications error
+      sample_group_color = RepositoryColumn.create!(
+        repository: repository,
+        created_by_id: repository.created_by_id,
+        data_type: :RepositoryTextValue,
+        name: 'Sample group color hex (e980a0f5)'
+      )
+
+      sample_type = RepositoryColumn.create!(
         repository: repository,
         created_by_id: repository.created_by_id,
         data_type: :RepositoryListValue,
@@ -68,28 +76,30 @@ module Tasks
       )
 
       sample_groups.each_with_index do |item, index|
-        RepositoryListItem.create(
+        created_by = item['created_by_id'] || team.created_by_id
+        last_modified_by = item['last_modified_by_id'] || team.created_by_id
+        RepositoryListItem.create!(
           data: item.fetch('name') { "sample group item (#{index})" },
-          created_by_id: item.fetch('created_by_id') { team.created_by_id },
-          last_modified_by_id:
-            item.fetch('last_modified_by_id') { team.created_by_id },
-          repository_column: repository_columns.first,
+          created_by_id: created_by,
+          last_modified_by_id: last_modified_by,
+          repository_column: sample_group,
           repository: repository
         )
       end
 
       sample_types.each_with_index do |item, index|
-        RepositoryListItem.create(
+        created_by = item['created_by_id'] || team.created_by_id
+        last_modified_by = item['last_modified_by_id'] || team.created_by_id
+        RepositoryListItem.create!(
           data: item.fetch('name') { "sample group item (#{index})" },
-          created_by_id: item.fetch('created_by_id') { team.created_by_id },
-          last_modified_by_id:
-            item.fetch('last_modified_by_id') { team.created_by_id },
-          repository_column: repository_columns.last,
+          created_by_id: created_by,
+          last_modified_by_id: last_modified_by,
+          repository_column: sample_type,
           repository: repository
         )
       end
 
-      repository_columns
+      [sample_group, sample_type, sample_group_color]
     end
 
     def self.get_sample_custom_fields(sample_id)
@@ -108,7 +118,7 @@ module Tasks
 
     def self.get_assigned_sample_module(sample_id)
       assigned_samples_sql = <<-SQL
-        SELECT my_module_id, assigned_by_id, assigned_on
+        SELECT my_module_id, assigned_by_id
         FROM sample_my_modules
         WHERE sample_my_modules.sample_id = #{sample_id}
       SQL
@@ -125,12 +135,17 @@ module Tasks
                sample_groups.name AS sample_group_name,
                sample_groups.color AS sample_group_color
         FROM samples
-        JOIN sample_types ON samples.sample_type_id = sample_types.id
-        JOIN sample_groups ON samples.sample_type_id = sample_groups.id
+        LEFT OUTER JOIN sample_types ON samples.sample_type_id = sample_types.id
+        LEFT OUTER JOIN sample_groups ON samples.sample_type_id = sample_groups.id
         WHERE samples.team_id = #{team.id}
       SQL
 
       ActiveRecord::Base.connection.execute(samples_sql).to_a
     end
+
+    def self.get_custom_columns(team, repository)
+      prepare_text_value_custom_columns(team, repository) +
+        prepare_list_value_custom_columns_with_list_items(team, repository)
+    end
   end
 end

lib/tasks/samples_to_repository_migration.rake

@@ -9,19 +9,104 @@ namespace :samples_to_repository_migration do
       params[:start] = args[:last_id].to_i
     end
     Team.find_each(params) do |team|
-      puts "******************************* \n\n\n\n"
-      puts "Processing Team id => [#{team.id}] \n\n\n\n"
+      puts "******************************* \n\n"
+      puts "Processing Team id => [#{team.id}] \n\n"
       puts '*******************************'
-      # byebug
-      migration_service.fetch_all_team_samples(team)
 
-      repository = migration_service.prepare_repository(team)
-      custom_columns = migration_service.prepare_text_value_custom_columns(team, repository) +
-                       migration_service.prepare_list_value_custom_columns_with_list_items(
-                         team,
-                         repository
-                       )
-      # byebug
+      ActiveRecord::Base.transaction do
+        team_samples = migration_service.fetch_all_team_samples(team)
+        repository = migration_service.prepare_repository(team)
+        custom_columns = migration_service.get_custom_columns(team, repository)
+
+        team_samples.each do |item|
+          created_by = item['sample_created_by_id'] || team.created_by_id
+          last_modified_by = item['sample_last_modified_by_id'] || team.created_by_id
+          row = RepositoryRow.create!(name: item['sample_name'],
+                                      created_by_id: created_by,
+                                      last_modified_by_id: last_modified_by,
+                                      repository: repository)
+          # check if sample has sample type assigned
+          if item['sample_type_name']
+            column = custom_columns.detect { |el| el['name'] == 'Sample type' }
+            list_item = column.repository_list_items.where(
+              data: item['sample_type_name']
+            ).take
+            RepositoryListValue.create!(
+              created_by: list_item.created_by,
+              last_modified_by: list_item.last_modified_by,
+              repository_list_item: list_item,
+              repository_cell_attributes: {
+                repository_row: row,
+                repository_column: column
+              }
+            )
+          end
+
+          # check if sample has sample group assigned
+          if item['sample_group_name']
+            column = custom_columns.detect { |el| el['name'] == 'Sample group' }
+            list_item = column.repository_list_items.where(
+              data: item['sample_group_name']
+            ).take
+            RepositoryListValue.create!(
+              created_by: list_item.created_by,
+              last_modified_by: list_item.last_modified_by,
+              repository_list_item: list_item,
+              repository_cell_attributes: {
+                repository_row: row,
+                repository_column: column
+              }
+            )
+
+            # assign sample group color to the sample
+            if item['sample_group_color']
+              column = custom_columns.detect do |el|
+                el['name'] == 'Sample group color hex (e980a0f5)'
+              end
+              RepositoryTextValue.create!(
+                data: item['sample_group_color'],
+                created_by_id: created_by,
+                last_modified_by_id: last_modified_by,
+                repository_cell_attributes: {
+                  repository_row: row,
+                  repository_column: column
+                }
+              )
+            end
+          end
+
+          # append custom fields
+          custom_fields = migration_service.get_sample_custom_fields(
+            item['sample_id']
+          )
+          custom_fields.each do |field|
+            column = custom_columns.detect do |el|
+              el['name'] == field['column_name_reference']
+            end
+            RepositoryTextValue.create!(
+              data: field['value'],
+              created_by_id: created_by,
+              last_modified_by_id: last_modified_by,
+              repository_cell_attributes: {
+                repository_row: row,
+                repository_column: column
+              }
+            )
+          end
+
+          # assign repository item to a tasks
+          assigned_modules = migration_service.get_assigned_sample_module(
+            item['sample_id']
+          )
+          assigned_modules.each do |element|
+            MyModuleRepositoryRow.create!(
+              my_module_id: element['my_module_id'],
+              repository_row: row,
+              assigned_by_id: element['assigned_by_id'] || created_by
+            )
+          end
+        end
+      end
     end
   end
 end

spec/lib/tasks/samples_to_repository_migration_spec.rb

@@ -1,3 +1,76 @@
+require 'rails_helper'
+
 describe 'samples_to_repository_migration:run' do
   include_context 'rake'
+  let!(:user) { create :user, email: 'happy.user@scinote.net' }
+  let!(:team) { create :team, created_by: user }
+  let!(:user_team) { create :user_team, user: user, team: team }
+  let!(:my_module) { create :my_module }
+  let!(:samples_table) { create :samples_table, user: user, team: team }
+  let(:sample_types_names) { %w(type_one type_two type_three) }
+  let(:sample_group_names) { %w(group_one group_two group_three) }
+
+  before do
+    sample_types = []
+    sample_types_names.each do |name|
+      sample_type = create :sample_type, name: name, team: team
+      sample_types << sample_type
+    end
+    sample_groups = []
+    sample_group_names.each do |name|
+      sample_group = create :sample_group, name: name, team: team
+      sample_groups << sample_group
+    end
+    custom_field = create :custom_field, name: 'Banana', team: team, user: user
+    100.times do |index|
+      sample = create :sample, name: "Sample (#{index})", user: user, team: team
+      create :sample_my_module, sample: sample, my_module: my_module
+      sample.sample_type = sample_types[rand(0...2)]
+      sample.sample_group = sample_groups[rand(0...2)]
+      custom_value = create :sample_custom_field,
+                            value: "custom value (#{index})",
+                            custom_field: custom_field,
+                            sample: sample
+      sample.sample_custom_fields << custom_value
+      sample.save
+    end
+  end
+
+  it 'generates a new custom repository with exact copy of samples' do
+    subject.invoke
+    expect(Repository.first.name).to eq 'Samples'
+    expect(RepositoryRow.count).to eq 100
+    RepositoryRow.all.each do |row|
+      row_my_module = MyModuleRepositoryRow.where(repository_row: row,
+                                                  my_module: my_module)
+      expect(row_my_module).to exist
+      expect(row.name).to match(/Sample \([0-9]*\)/)
+      expect(row.created_by).to eq user
+
+      # repository sample_type column
+      sample_type_column = row.repository_cells.first
+      expect(sample_types_names).to include(sample_type_column.value.formatted)
+      expect(sample_type_column.repository_column.name).to eq 'Sample type'
+      expect(sample_type_column.value_type).to eq 'RepositoryListValue'
+
+      # repository sample_group column
+      sample_group_column = row.repository_cells.second
+      expect(sample_group_names).to include(sample_group_column.value.formatted)
+      expect(sample_group_column.repository_column.name).to eq 'Sample group'
+      expect(sample_group_column.value_type).to eq 'RepositoryListValue'
+
+      # repository color column
+      color_column = row.repository_cells.third
+      expect(
+        color_column.repository_column.name
+      ).to eq 'Sample group color hex (e980a0f5)'
+      expect(color_column.value_type).to eq 'RepositoryTextValue'
+
+      # repository custom column
+      custom_column = row.repository_cells.last
+      expect(custom_column.value.formatted).to match(/custom value \([0-9]*\)/)
+      expect(custom_column.repository_column.name).to eq 'Banana'
+      expect(custom_column.value_type).to eq 'RepositoryTextValue'
+    end
+  end
 end

spec/services/tasks/samples_to_repository_migration_service_spec.rb

@@ -81,15 +81,17 @@ describe Tasks::SamplesToRepositoryMigrationService do
       end
 
       it { is_expected.to be_an Array }
-      it { expect(subject.length).to eq 2 }
+      it { expect(subject.length).to eq 3 }
       it { expect(subject.first).to be_an_instance_of(RepositoryColumn) }
       it { expect(subject.first.name).to eq 'Sample group' }
       it { expect(subject.first.data_type).to eq 'RepositoryListValue' }
-      it { expect(subject.last.name).to eq 'Sample type' }
-      it { expect(subject.last.data_type).to eq 'RepositoryListValue' }
+      it { expect(subject.second.name).to eq 'Sample type' }
+      it { expect(subject.second.data_type).to eq 'RepositoryListValue' }
+      it { expect(subject.last.name).to eq 'Sample group color hex (e980a0f5)' }
+      it { expect(subject.last.data_type).to eq 'RepositoryTextValue' }
 
       describe 'generated list items from sample types' do
-        let!(:generated_list_items) { subject.last.repository_list_items }
+        let!(:generated_list_items) { subject.second.repository_list_items }
         it { expect(generated_list_items.count).to eq 10 }
 
         it 'has generated list_items with similar properties' do
@@ -101,6 +103,24 @@ describe Tasks::SamplesToRepositoryMigrationService do
           end
         end
       end
+
+      describe 'sample type without created_at/last_modified_by field' do
+        before do
+          team.sample_types.update_all(created_by_id: nil,
+                                       last_modified_by_id: nil)
+        end
+
+        it 'generates valid list_items' do
+          generated_list_items = subject.second.repository_list_items
+          expect(generated_list_items.count).to eq 10
+          generated_list_items.each_with_index do |item, index|
+            expect(item.data).to eq "Sample Type Item (#{index})"
+            expect(item).to be_an_instance_of RepositoryListItem
+            expect(item.created_by).to eq team.created_by
+            expect(item.last_modified_by).to eq team.created_by
+          end
+        end
+      end
     end
 
     context 'with samples groups' do
@@ -115,13 +135,15 @@ describe Tasks::SamplesToRepositoryMigrationService do
       end
 
       it { is_expected.to be_an Array }
-      it { expect(subject.length).to eq 2 }
+      it { expect(subject.length).to eq 3 }
       it { expect(subject.first).to be_an_instance_of(RepositoryColumn) }
       it { expect(subject.last).to be_an_instance_of(RepositoryColumn) }
       it { expect(subject.first.name).to eq 'Sample group' }
       it { expect(subject.first.data_type).to eq 'RepositoryListValue' }
-      it { expect(subject.last.name).to eq 'Sample type' }
-      it { expect(subject.last.data_type).to eq 'RepositoryListValue' }
+      it { expect(subject.second.name).to eq 'Sample type' }
+      it { expect(subject.second.data_type).to eq 'RepositoryListValue' }
+      it { expect(subject.last.name).to eq 'Sample group color hex (e980a0f5)' }
+      it { expect(subject.last.data_type).to eq 'RepositoryTextValue' }
 
       describe 'generated list items from sample groups' do
         let!(:generated_list_items) { subject.first.repository_list_items }
@@ -136,6 +158,24 @@ describe Tasks::SamplesToRepositoryMigrationService do
           end
         end
       end
+
+      describe 'sample group without created_at/last_modified_by field' do
+        before do
+          team.sample_groups.update_all(created_by_id: nil,
+                                        last_modified_by_id: nil)
+        end
+
+        it 'generates valid list_items' do
+          generated_list_items = subject.first.repository_list_items
+          expect(generated_list_items.count).to eq 10
+          generated_list_items.each_with_index do |item, index|
+            expect(item.data).to eq "Sample Group Item (#{index})"
+            expect(item).to be_an_instance_of RepositoryListItem
+            expect(item.created_by).to eq team.created_by
+            expect(item.last_modified_by).to eq team.created_by
+          end
+        end
+      end
     end
   end
 
@@ -202,9 +242,6 @@ describe Tasks::SamplesToRepositoryMigrationService do
         expect(
           my_module_data.fetch('assigned_by_id')
         ).to eq sample_my_module.assigned_by_id
-        expect(
-          my_module_data.fetch('assigned_on')
-        ).to eq sample_my_module.assigned_on
       end
     end
 

spec/support/shared_contexts/rake.rb

@@ -1,4 +1,4 @@
-require "rake"
+require 'rake'
 
 shared_context 'rake' do
   let(:rake)      { Rake::Application.new }