scinote-web/lib/tasks/samples_to_repository_migration.rake

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require_relative '../../app/services/tasks/samples_to_repository_migration_service'
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namespace :samples_to_repository_migration do
desc 'Migrates all data from samples to custom repository'
task :run, [:last_id] => :environment do |_, args|
include ActiveRecord::Sanitization::ClassMethods
params = { batch_size: 10 }
migration_service = Tasks::SamplesToRepositoryMigrationService
conn = ActiveRecord::Base.connection
if args.present? && args[:last_id].present?
params[:start] = args[:last_id].to_i
end
Team.find_each(params) do |team|
puts "******************************* \n\n"
puts "Processing Team id => [#{team.id}] \n\n"
puts '*******************************'
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)
sample_mappings = {}
team_samples.each do |item|
created_by = item['sample_created_by_id'] || team.created_by_id
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last_modified_by = item['sample_last_modified_by_id']
last_modified_by ||= team.created_by_id
timestamp = conn.quote(Time.now.to_s(:db))
values = [repository.id, created_by, last_modified_by,
conn.quote(item['sample_name']), timestamp, timestamp]
list_item_sql = <<-SQL
INSERT INTO repository_rows
(repository_id, created_by_id, last_modified_by_id, name,
created_at, updated_at)
VALUES (#{values.join(', ')})
RETURNING id
SQL
result = conn.execute(list_item_sql)
row_id = result[0]['id']
sample_mappings[item['sample_id']] = row_id
# 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
migration_service.create_list_cell(
row_id, column.id, list_item.id,
list_item.created_by_id, list_item.last_modified_by_id
)
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
migration_service.create_list_cell(
row_id, column.id, list_item.id,
list_item.created_by_id, list_item.last_modified_by_id
)
# assign sample group color to the sample
if item['sample_group_color']
column = custom_columns.detect do |el|
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el['name'] == 'Sample group color hex'
end
migration_service.create_text_cell(
row_id, column.id, item['sample_group_color'],
created_by, last_modified_by
)
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
migration_service
.create_text_cell(row_id, column.id, field['value'],
created_by, last_modified_by)
end
# assign repository item to a tasks
assigned_modules = migration_service.get_assigned_sample_module(
item['sample_id']
)
assigned_modules.each do |element|
assigned_by = element['assigned_by_id'] || created_by
values = [row_id, element['my_module_id'], assigned_by,
timestamp, timestamp]
cell_sql = <<-SQL
INSERT INTO my_module_repository_rows
(repository_row_id, my_module_id, assigned_by_id,
created_at, updated_at)
VALUES (#{values.join(', ')})
SQL
conn.execute(cell_sql)
end
end
# Now update smart annotations
migration_service.update_smart_annotations(team, sample_mappings)
end
end
end
end