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Merge pull request #1063 from biosistemika/release-1.12.11

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merge release 1.12.11 branch to master
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okriuchykhin 2018-03-27 16:19:57 +02:00 committed by GitHub
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240
app/services/team_exporter.rb Normal file
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require 'fileutils'
class TeamExporter
def initialize(team_id)
@team = Team.includes(:user_teams).find_by_id(team_id)
raise StandardError, 'Can not load team' unless @team
@assets_to_copy = []
@tiny_mce_assets_to_copy = []
end
def export_to_dir
@asset_counter = 0
@team.transaction(isolation: :serializable) do
@dir_to_export = FileUtils.mkdir_p(
File.join("tmp/team_#{@team.id}_export_#{Time.now.to_i}")
).first
# Writing JSON file with team structure
File.write(
File.join(@dir_to_export, 'team_export.json'),
team(@team).to_json
)
# Copying assets
copy_files(@assets_to_copy, :file, File.join(@dir_to_export, 'assets')) do
@asset_counter += 1
end
# Copying tiny_mce_assets
copy_files(@tiny_mce_assets_to_copy,
:image,
File.join(@dir_to_export, 'tiny_mce_assets'))
puts "Exported assets: #{@asset_counter}"
puts "Exported tinyMCE assets: #{@team.tiny_mce_assets.count}"
puts "Exported users: #{@team.users.count}"
puts "Exported repositories: #{@team.repositories.count}"
puts "Exported projects: #{@team.projects.count}"
puts 'Done!'
end
end
private
def copy_files(assets, attachment_name, dir_name)
assets.flatten.each do |a|
next unless a.public_send(attachment_name).present?
unless a.public_send(attachment_name).exists?
raise StandardError,
"File id:#{a.id} of type #{attachment_name} is missing"
end
yield if block_given?
dir = FileUtils.mkdir_p(File.join(dir_name, a.id.to_s)).first
if defined?(S3_BUCKET)
s3_asset =
S3_BUCKET.object(a.public_send(attachment_name).path.remove(%r{^/}))
file_name = a.public_send(attachment_name).original_filename
File.open(File.join(dir, file_name), 'wb') do |f|
s3_asset.get(response_target: f)
end
else
FileUtils.cp(
a.public_send(attachment_name).path,
File.join(dir, a.public_send(attachment_name).original_filename)
)
end
end
end
def team(team)
if team.tiny_mce_assets.present?
@tiny_mce_assets_to_copy.push(team.tiny_mce_assets)
end
{
team: team,
default_admin_id: team.user_teams.where(role: 2).first.user.id,
users: team.users.map { |u| user(u) },
user_teams: team.user_teams,
notifications: Notification
.includes(:user_notifications)
.where('user_notifications.user_id': team.users)
.map { |n| notification(n) },
samples: team.samples.map { |s| sample(s) },
sample_groups: team.sample_groups,
sample_types: team.sample_types,
custom_fields: team.custom_fields,
repositories: team.repositories.map { |r| repository(r) },
tiny_mce_assets: team.tiny_mce_assets,
protocols: team.protocols.where(my_module: nil).map { |pr| protocol(pr) },
protocol_keywords: team.protocol_keywords,
projects: team.projects.map { |p| project(p) }
}
end
def notification(notification)
notification_json = notification.as_json
notification_json['type_of'] = Extends::NOTIFICATIONS_TYPES
.key(notification.read_attribute('type_of'))
.to_s
notification_json
end
def user(user)
user_json = user.as_json
# Looks like Devise doesn't export some fields to JSON, so add it manually
user_json['encrypted_password'] = user.encrypted_password
user_json['confirmed_at'] = user.confirmed_at
user_json['sign_in_count'] = user.sign_in_count
user_json['last_sign_in_at'] = user.last_sign_in_at
user_json['last_sign_in_ip'] = user.last_sign_in_ip
copy_files([user], :avatar, File.join(@dir_to_export, 'avatars'))
{
user: user_json,
user_notifications: user.user_notifications,
user_identities: user.user_identities,
samples_tables: user.samples_tables.where(team: @team),
repository_table_states:
user.repository_table_states.where(repository: @team.repositories)
}
end
def project(project)
{
project: project,
user_projects: project.user_projects,
activities: project.activities,
project_comments: project.project_comments,
reports: project.reports.map { |r| report(r) },
experiments: project.experiments.map { |e| experiment(e) },
tags: project.tags
}
end
def report(report)
{
report: report,
report_elements: report.report_elements
}
end
def experiment(experiment)
{
experiment: experiment,
my_modules: experiment.my_modules.map { |m| my_module(m) },
my_module_groups: experiment.my_module_groups
}
end
def my_module(my_module)
{
my_module: my_module,
outputs: my_module.outputs,
my_module_tags: my_module.my_module_tags,
task_comments: my_module.task_comments,
my_module_repository_rows: my_module.my_module_repository_rows,
sample_my_modules: my_module.sample_my_modules,
user_my_modules: my_module.user_my_modules,
protocols: my_module.protocols.map { |pr| protocol(pr) },
results: my_module.results.map { |res| result(res) }
}
end
def protocol(protocol)
{
protocol: protocol,
protocol_protocol_keywords: protocol.protocol_protocol_keywords,
steps: protocol.steps.map { |s| step(s) }
}
end
def step(step)
@assets_to_copy.push(step.assets.to_a) if step.assets.present?
{
step: step,
checklists: step.checklists.map { |c| checklist(c) },
step_comments: step.step_comments,
step_assets: step.step_assets,
assets: step.assets,
step_tables: step.step_tables,
tables: step.tables.map { |t| table(t) }
}
end
def checklist(checklist)
{
checklist: checklist,
checklist_items: checklist.checklist_items
}
end
def table(table)
return {} if table.nil?
table_json = table.as_json(except: %i(contents data_vector))
table_json['contents'] = Base64.encode64(table.contents)
table_json['data_vector'] = Base64.encode64(table.data_vector)
table_json
end
def result(result)
@assets_to_copy.push(result.asset) if result.asset.present?
{
result: result,
result_comments: result.result_comments,
asset: result.asset,
table: table(result.table),
result_text: result.result_text
}
end
def sample(sample)
{
sample: sample,
sample_custom_fields: sample.sample_custom_fields
}
end
def repository(repository)
{
repository: repository,
repository_columns: repository.repository_columns,
repository_rows: repository.repository_rows.map do |r|
repository_row(r)
end
}
end
def repository_row(repository_row)
{
repository_row: repository_row,
my_module_repository_rows: repository_row.my_module_repository_rows,
repository_cells: repository_row.repository_cells.map do |c|
repository_cell(c)
end
}
end
def repository_cell(cell)
{
repository_cell: cell,
repository_value: cell.value
}
end
end

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class TeamImporter
def initialize
@user_mappings = {}
@notification_mappings = {}
@repository_mappings = {}
@sample_group_mappings = {}
@sample_type_mappings = {}
@custom_field_mappings = {}
@sample_mappings = {}
@project_mappings = {}
@repository_column_mappings = {}
@experiment_mappings = {}
@my_module_group_mappings = {}
@my_module_mappings = {}
@protocol_mappings = {}
@protocol_keyword_mappings = {}
@step_mappings = {}
@asset_mappings = {}
@tag_mappings = {}
@result_text_mappings = {}
@repository_row_mappings = {}
@result_mappings = {}
@checklist_mappings = {}
@table_mappings = {}
@project_counter = 0
@repository_counter = 0
@repository_row_counter = 0
@protocol_counter = 0
@step_counter = 0
@sample_counter = 0
@report_counter = 0
@my_module_counter = 0
@notification_counter = 0
@result_counter = 0
@asset_counter = 0
@user_counter = 0
@mce_asset_counter = 0
end
def import_from_dir(import_dir)
MyModule.skip_callback(:create, :before, :create_blank_protocol)
Activity.skip_callback(:create, :after, :generate_notification)
Protocol.skip_callback(:save, :after, :update_linked_children)
@import_dir = import_dir
team_json = JSON.parse(File.read("#{@import_dir}/team_export.json"))
team = Team.new(team_json['team'].slice(*Team.column_names))
team.id = nil
team.transaction(isolation: :serializable) do
team_creator_id = team.created_by_id
team.created_by_id = nil
team_last_modified_by = team.last_modified_by_id
team.last_modified_by_id = nil
team.save!
create_users(team_json['users'], team)
# Find new id of the first admin in the team
@admin_id = @user_mappings[team_json['default_admin_id']]
create_notifications(team_json['notifications'])
puts 'Assigning users to the team...'
team_json['user_teams'].each do |user_team_json|
user_team = UserTeam.new(user_team_json)
user_team.id = nil
user_team.user_id = find_user(user_team.user_id)
user_team.team_id = team.id
user_team.assigned_by_id = find_user(user_team.assigned_by_id)
user_team.save!
end
create_sample_groups(team_json['sample_groups'], team)
create_sample_types(team_json['sample_types'], team)
create_custom_fields(team_json['custom_fields'], team)
create_samples(team_json['samples'], team)
create_protocol_keywords(team_json['protocol_keywords'], team)
create_protocols(team_json['protocols'], nil, team)
create_projects(team_json['projects'], team)
create_repositories(team_json['repositories'], team)
# Second run, we needed it because of some models should be created
team_json['users'].each do |user_json|
user_json['user_notifications'].each do |user_notification_json|
user_notification = UserNotification.new(user_notification_json)
user_notification.id = nil
user_notification.user_id = find_user(user_notification.user_id)
user_notification.notification_id =
@notification_mappings[user_notification.notification_id]
next if user_notification.notification_id.blank?
user_notification.save!
end
user_json['repository_table_states'].each do |rep_tbl_state_json|
rep_tbl_state = RepositoryTableState.new(rep_tbl_state_json)
rep_tbl_state.id = nil
rep_tbl_state.user_id = find_user(rep_tbl_state.user_id)
rep_tbl_state.repository_id =
@repository_mappings[rep_tbl_state.repository_id]
rep_tbl_state.save!
end
end
team_json['projects'].each do |project_json|
create_activities(project_json['activities'])
create_reports(project_json['reports'])
project_json['experiments'].each do |experiment_json|
experiment_json['my_modules'].each do |my_module_json|
create_task_connections(my_module_json['outputs'])
end
end
end
team_json['repositories'].each do |repository_json|
repository_json['repository_rows'].each do |repository_row_json|
create_repository_cells(repository_row_json['repository_cells'])
end
end
create_tiny_mce_assets(team_json['tiny_mce_assets'], team)
update_smart_annotations(team)
# restoring team's creator
team.created_by_id = find_user(team_creator_id)
team.last_modified_by_id = find_user(team_last_modified_by)
team.save!
puts "Imported users: #{@user_counter}"
puts "Imported notifications: #{@notification_counter}"
puts "Imported projects: #{@project_counter}"
puts "Imported reports: #{@report_counter}"
puts "Imported repositories: #{@repository_counter}"
puts "Imported repository rows: #{@repository_row_counter}"
puts "Imported samples: #{@sample_counter}"
puts "Imported tasks: #{@my_module_counter}"
puts "Imported protocols: #{@protocol_counter}"
puts "Imported steps: #{@step_counter}"
puts "Imported results: #{@result_counter}"
puts "Imported assets: #{@asset_counter}"
puts "Imported tinyMCE assets: #{@mce_asset_counter}"
MyModule.set_callback(:create, :before, :create_blank_protocol)
Activity.set_callback(:create, :after, :generate_notification)
Protocol.set_callback(:save, :after, :update_linked_children)
end
end
private
def update_smart_annotations(team)
team.projects.each do |pr|
pr.project_comments.each do |comment|
comment.save! if update_annotation(comment.message)
end
pr.experiments.each do |exp|
exp.save! if update_annotation(exp.description)
exp.my_modules.each do |task|
task.task_comments.each do |comment|
comment.save! if update_annotation(comment.message)
end
task.save! if update_annotation(task.description)
task.protocol.steps.each do |step|
step.step_comments.each do |comment|
comment.save! if update_annotation(comment.message)
end
step.save! if update_annotation(step.description)
end
task.results.each do |res|
res.result_comments.each do |comment|
comment.save! if update_annotation(comment.message)
end
next unless res.result_text
res.save! if update_annotation(res.result_text.text)
end
end
end
end
team.protocols.where(my_module: nil).each do |protocol|
protocol.steps.each do |step|
step.step_comments.each do |comment|
comment.save! if update_annotation(comment.message)
end
step.save! if update_annotation(step.description)
end
end
team.samples.each do |sample|
sample.sample_custom_fields.find_each do |cf|
cf.save! if update_annotation(cf.value)
end
end
team.repositories.each do |rep|
rep.repository_rows.find_each do |row|
row.repository_cells.each do |cell|
cell.value.save! if update_annotation(cell.value.data)
end
end
end
end
# Returns true if text was updated
def update_annotation(text)
return false if text.nil?
updated = false
%w(prj exp tsk sam).each do |name|
text.scan(/~#{name}~\w+\]/).each do |text_match|
orig_id_encoded = text_match.match(/~#{name}~(\w+)\]/)[1]
orig_id = orig_id_encoded.base62_decode
new_id =
case name
when 'prj'
@project_mappings[orig_id]
when 'exp'
@experiment_mappings[orig_id]
when 'tsk'
@my_module_mappings[orig_id]
when 'sam'
@sample_mappings[orig_id]
end
next unless new_id
new_id_encoded = new_id.base62_encode
text.sub!("~#{name}~#{orig_id_encoded}]", "~#{name}~#{new_id_encoded}]")
updated = true
end
end
text.scan(/\[@[\w+-@?! ]+~\w+\]/).each do |user_match|
orig_id_encoded = user_match.match(/\[@[\w+-@?! ]+~(\w+)\]/)[1]
orig_id = orig_id_encoded.base62_decode
next unless @user_mappings[orig_id]
new_id_encoded = @user_mappings[orig_id].base62_encode
text.sub!("~#{orig_id_encoded}]", "~#{new_id_encoded}]")
updated = true
end
updated
end
def create_task_connections(connections_json)
connections_json.each do |connection_json|
connection = Connection.new(connection_json)
connection.id = nil
connection.input_id = @my_module_mappings[connection.input_id]
connection.output_id = @my_module_mappings[connection.output_id]
connection.save!
end
end
def create_activities(activities_json)
activities_json.each do |activity_json|
activity = Activity.new(activity_json)
activity.id = nil
activity.user_id = find_user(activity.user_id)
activity.project_id = @project_mappings[activity.project_id]
activity.experiment_id =
@experiment_mappings[activity.experiment_id]
activity.my_module_id = @my_module_mappings[activity.my_module_id]
activity.save!
end
end
def create_tiny_mce_assets(tmce_assets_json, team)
tmce_assets_json.each do |tiny_mce_asset_json|
tiny_mce_asset = TinyMceAsset.new(tiny_mce_asset_json)
# Try to find and load file
tiny_mce_file = File.open(
File.join(@import_dir, 'tiny_mce_assets', tiny_mce_asset.id.to_s,
tiny_mce_asset.image_file_name)
)
orig_tmce_id = tiny_mce_asset.id
tiny_mce_asset.id = nil
if tiny_mce_asset.step_id.present?
tiny_mce_asset.step_id = @step_mappings[tiny_mce_asset.step_id]
end
if tiny_mce_asset.result_text_id.present?
tiny_mce_asset.result_text_id =
@result_text_mappings[tiny_mce_asset.result_text_id]
end
tiny_mce_asset.team = team
tiny_mce_asset.image = tiny_mce_file
tiny_mce_asset.save!
@mce_asset_counter += 1
if tiny_mce_asset.step_id.present?
step = Step.find_by_id(tiny_mce_asset.step_id)
step.description.sub!("[~tiny_mce_id:#{orig_tmce_id}]",
"[~tiny_mce_id:#{tiny_mce_asset.id}]")
step.save!
end
if tiny_mce_asset.result_text_id.present?
result_text = ResultText.find_by_id(tiny_mce_asset.result_text_id)
result_text.text.sub!("[~tiny_mce_id:#{orig_tmce_id}]",
"[~tiny_mce_id:#{tiny_mce_asset.id}]")
end
end
end
def create_users(users_json, team)
puts 'Creating users...'
users_json.each do |user_json|
user = User.new(user_json['user'].slice(*User.column_names))
orig_user_id = user.id
user.id = nil
user.password = user_json['user']['encrypted_password']
user.current_team_id = team.id
user.invited_by_id = @user_mappings[user.invited_by_id]
if user.avatar.present?
avatar_path = File.join(@import_dir, 'avatars', orig_user_id.to_s,
user.avatar_file_name)
user.avatar = File.open(avatar_path) if File.exist?(avatar_path)
end
user.save!
@user_counter += 1
user.update_attribute('encrypted_password',
user_json['user']['encrypted_password'])
@user_mappings[orig_user_id] = user.id
user_json['user_identities'].each do |user_identity_json|
user_identity = UserIdentity.new(user_identity_json)
user_identity.id = nil
user_identity.user_id = user.id
user_identity.save!
end
user_json['samples_tables'].each do |samples_table_json|
samples_table = SamplesTable.new(samples_table_json)
samples_table.id = nil
samples_table.user_id = user.id
samples_table.team_id = team.id
samples_table.save!
end
end
end
def create_notifications(notifications_json)
puts 'Creating notifications...'
notifications_json.each do |notification_json|
notification = Notification.new(notification_json)
next if notification.type_of.blank?
orig_notification_id = notification.id
notification.id = nil
notification.generator_user_id = find_user(notification.generator_user_id)
notification.save!
@notification_mappings[orig_notification_id] = notification.id
@notification_counter += 1
end
end
def create_repositories(repositories_json, team)
puts 'Creating repositories...'
repositories_json.each do |repository_json|
repository = Repository.new(repository_json['repository'])
orig_repository_id = repository.id
repository.id = nil
repository.team = team
repository.created_by_id = find_user(repository.created_by_id)
repository.save!
@repository_mappings[orig_repository_id] = repository.id
@repository_counter += 1
repository_json['repository_columns'].each do |repository_column_json|
repository_column = RepositoryColumn.new(repository_column_json)
orig_rep_col_id = repository_column.id
repository_column.id = nil
repository_column.repository = repository
repository_column.created_by_id =
find_user(repository_column.created_by_id)
repository_column.save!
@repository_column_mappings[orig_rep_col_id] = repository_column.id
end
create_repository_rows(repository_json['repository_rows'], repository)
end
end
def create_repository_rows(repository_rows_json, repository)
repository_rows_json.each do |repository_row_json|
repository_row =
RepositoryRow.new(repository_row_json['repository_row'])
orig_rep_row_id = repository_row.id
repository_row.id = nil
repository_row.repository = repository
repository_row.created_by_id = find_user(repository_row.created_by_id)
repository_row.last_modified_by_id =
find_user(repository_row.last_modified_by_id)
repository_row.save!
@repository_row_mappings[orig_rep_row_id] = repository_row.id
@repository_row_counter += 1
repository_row_json['my_module_repository_rows'].each do |mm_rep_row_json|
mm_rep_row = MyModuleRepositoryRow.new(mm_rep_row_json)
mm_rep_row.id = nil
mm_rep_row.repository_row = repository_row
mm_rep_row.my_module_id = @my_module_mappings[mm_rep_row.my_module_id]
mm_rep_row.assigned_by_id = find_user(mm_rep_row.assigned_by_id)
mm_rep_row.save!
end
end
end
def create_repository_cells(repository_cells_json)
repository_cells_json.each do |repository_cell_json|
repository_cell =
RepositoryCell.new(repository_cell_json['repository_cell'])
repository_cell.id = nil
repository_cell.repository_column_id =
@repository_column_mappings[repository_cell.repository_column_id]
repository_cell.repository_row_id =
@repository_row_mappings[repository_cell.repository_row_id]
repository_value =
RepositoryTextValue.new(repository_cell_json['repository_value'])
repository_value.id = nil
repository_value.created_by_id = find_user(repository_value.created_by_id)
repository_value.last_modified_by_id =
find_user(repository_value.last_modified_by_id)
repository_value.repository_cell = repository_cell
repository_value.save!
end
end
def create_sample_groups(sample_groups_json, team)
puts 'Creating sample groups...'
sample_groups_json.each do |sample_group_json|
sample_group = SampleGroup.new(sample_group_json)
orig_group_id = sample_group.id
sample_group.id = nil
sample_group.team = team
sample_group.created_by_id = find_user(sample_group.created_by_id)
sample_group.last_modified_by_id =
find_user(sample_group.last_modified_by_id)
sample_group.save!
@sample_group_mappings[orig_group_id] = sample_group.id
end
end
def create_sample_types(sample_types_json, team)
puts 'Creating sample types...'
sample_types_json.each do |sample_type_json|
sample_type = SampleType.new(sample_type_json)
orig_type_id = sample_type.id
sample_type.id = nil
sample_type.team = team
sample_type.created_by_id = find_user(sample_type.created_by_id)
sample_type.last_modified_by_id =
find_user(sample_type.last_modified_by_id)
sample_type.save!
@sample_type_mappings[orig_type_id] = sample_type.id
end
end
def create_custom_fields(custom_fields_json, team)
puts 'Creating custom fields...'
custom_fields_json.each do |custom_field_json|
custom_field = CustomField.new(custom_field_json)
orig_custom_field_id = custom_field.id
custom_field.id = nil
custom_field.team = team
custom_field.user_id = find_user(custom_field.user_id)
custom_field.last_modified_by_id =
find_user(custom_field.last_modified_by_id)
custom_field.save!
@custom_field_mappings[orig_custom_field_id] = custom_field.id
end
end
def create_samples(samples_json, team)
puts 'Creating samples...'
samples_json.each do |sample_json|
sample = Sample.new(sample_json['sample'])
orig_sample_id = sample.id
sample.id = nil
sample.team = team
sample.user_id = find_user(sample.user_id)
sample.sample_group_id = @sample_group_mappings[sample.sample_group_id]
sample.sample_type_id = @sample_type_mappings[sample.sample_type_id]
sample.last_modified_by_id = find_user(sample.last_modified_by_id)
sample.save!
@sample_mappings[orig_sample_id] = sample.id
@sample_counter += 1
sample_json['sample_custom_fields'].each do |s_custom_field_json|
s_custom_field = SampleCustomField.new(s_custom_field_json)
s_custom_field.id = nil
s_custom_field.sample = sample
s_custom_field.custom_field_id =
@custom_field_mappings[s_custom_field.custom_field_id]
s_custom_field.save!
end
end
end
def create_protocol_keywords(protocol_keywords_json, team)
puts 'Creating keywords...'
protocol_keywords_json.each do |protocol_keyword_json|
protocol_keyword = ProtocolKeyword.new(protocol_keyword_json)
orig_pr_keyword_id = protocol_keyword.id
protocol_keyword.id = nil
protocol_keyword.team = team
protocol_keyword.save!
@protocol_keyword_mappings[orig_pr_keyword_id] = protocol_keyword.id
end
end
def create_projects(projects_json, team)
puts 'Creating projects...'
projects_json.each do |project_json|
project = Project.new(project_json['project'])
orig_project_id = project.id
project.id = nil
project.team = team
project.created_by_id = find_user(project.created_by_id)
project.last_modified_by_id = find_user(project.last_modified_by_id)
project.archived_by_id = find_user(project.archived_by_id)
project.restored_by_id = find_user(project.restored_by_id)
project.save!
@project_mappings[orig_project_id] = project.id
@project_counter += 1
puts 'Creating user_projects...'
project_json['user_projects'].each do |user_project_json|
user_project = UserProject.new(user_project_json)
user_project.id = nil
user_project.project = project
user_project.user_id = find_user(user_project.user_id)
user_project.assigned_by_id = find_user(user_project.assigned_by_id)
user_project.save!
end
puts 'Creating project_comments...'
project_json['project_comments'].each do |project_comment_json|
project_comment = ProjectComment.new(project_comment_json)
project_comment.id = nil
project_comment.user_id = find_user(project_comment.user_id)
project_comment.last_modified_by_id =
find_user(project_comment.last_modified_by_id)
project_comment.project = project
project_comment.save!
end
puts 'Creating tags...'
project_json['tags'].each do |tag_json|
tag = Tag.new(tag_json)
orig_tag_id = tag.id
tag.id = nil
tag.project = project
tag.created_by_id = find_user(tag.created_by_id)
tag.last_modified_by_id = find_user(tag.last_modified_by_id)
tag.save!
@tag_mappings[orig_tag_id] = tag.id
end
create_experiments(project_json['experiments'], project)
end
end
def create_experiments(experiments_json, project)
puts('Creating experiments...')
experiments_json.each do |experiment_json|
experiment = Experiment.new(experiment_json['experiment'])
orig_experiment_id = experiment.id
experiment.id = nil
experiment.project = project
experiment.created_by_id = find_user(experiment.created_by_id)
experiment.last_modified_by_id = find_user(experiment.last_modified_by_id)
experiment.archived_by_id = find_user(experiment.archived_by_id)
experiment.restored_by_id = find_user(experiment.restored_by_id)
experiment.save!
@experiment_mappings[orig_experiment_id] = experiment.id
experiment_json['my_module_groups'].each do |my_module_group_json|
my_module_group = MyModuleGroup.new(my_module_group_json)
orig_module_group_id = my_module_group.id
my_module_group.id = nil
my_module_group.experiment = experiment
my_module_group.created_by_id =
find_user(my_module_group.created_by_id)
my_module_group.save!
@my_module_group_mappings[orig_module_group_id] = my_module_group.id
end
experiment.delay.generate_workflow_img
create_my_modules(experiment_json['my_modules'], experiment)
end
end
def create_my_modules(my_modules_json, experiment)
puts('Creating my_modules...')
my_modules_json.each do |my_module_json|
my_module = MyModule.new(my_module_json['my_module'])
orig_my_module_id = my_module.id
my_module.id = nil
my_module.my_module_group_id =
@my_module_group_mappings[my_module.my_module_group_id]
my_module.created_by_id = find_user(my_module.created_by_id)
my_module.last_modified_by_id =
find_user(my_module.last_modified_by_id)
my_module.archived_by_id = find_user(my_module.archived_by_id)
my_module.restored_by_id = find_user(my_module.restored_by_id)
my_module.experiment = experiment
my_module.save!
@my_module_mappings[orig_my_module_id] = my_module.id
@my_module_counter += 1
my_module_json['my_module_tags'].each do |my_module_tag_json|
my_module_tag = MyModuleTag.new(my_module_tag_json)
my_module_tag.id = nil
my_module_tag.my_module = my_module
my_module_tag.tag_id = @tag_mappings[my_module_tag.tag_id]
my_module_tag.created_by_id =
find_user(my_module_tag.created_by_id)
my_module_tag.save!
end
my_module_json['task_comments'].each do |task_comment_json|
task_comment = TaskComment.new(task_comment_json)
task_comment.id = nil
task_comment.user_id = find_user(task_comment.user_id)
task_comment.last_modified_by_id =
find_user(task_comment.last_modified_by_id)
task_comment.my_module = my_module
task_comment.save!
end
my_module_json['sample_my_modules'].each do |sample_module_json|
sample_module = SampleMyModule.new(sample_module_json)
sample_module.id = nil
sample_module.sample_id =
@sample_mappings[sample_module.sample_id]
sample_module.my_module = my_module
sample_module.assigned_by_id =
find_user(sample_module.assigned_by_id)
sample_module.save!
end
my_module_json['user_my_modules'].each do |user_module_json|
user_module = UserMyModule.new(user_module_json)
user_module.id = nil
user_module.my_module = my_module
user_module.user_id = find_user(user_module.user_id)
user_module.assigned_by_id =
find_user(user_module.assigned_by_id)
user_module.save!
end
create_protocols(my_module_json['protocols'], my_module)
create_results(my_module_json['results'], my_module)
end
end
def create_protocols(protocols_json, my_module = nil, team = nil)
puts 'Creating protocols...'
protocols_json.each do |protocol_json|
protocol = Protocol.new(protocol_json['protocol'])
orig_protocol_id = protocol.id
protocol.id = nil
protocol.added_by_id = find_user(protocol.added_by_id)
protocol.team = team ? team : my_module.experiment.project.team
protocol.archived_by_id = find_user(protocol.archived_by_id)
protocol.restored_by_id = find_user(protocol.restored_by_id)
protocol.my_module = my_module unless protocol.my_module_id.nil?
unless protocol.parent_id.nil?
protocol.parent_id = @protocol_mappings[protocol.parent_id]
end
protocol.save!
@protocol_counter += 1
@protocol_mappings[orig_protocol_id] = protocol.id
protocol_json['protocol_protocol_keywords'].each do |pp_keyword_json|
pp_keyword = ProtocolProtocolKeyword.new(pp_keyword_json)
pp_keyword.id = nil
pp_keyword.protocol = protocol
pp_keyword.protocol_keyword_id =
@protocol_keyword_mappings[pp_keyword.protocol_keyword_id]
pp_keyword.save!
end
create_steps(protocol_json['steps'], protocol)
end
end
def create_steps(steps_json, protocol)
puts('Creating steps...')
steps_json.each do |step_json|
step = Step.new(step_json['step'])
orig_step_id = step.id
step.id = nil
step.user_id = find_user(step.user_id)
step.last_modified_by_id = find_user(step.last_modified_by_id)
step.protocol_id = protocol.id
step.save!
@step_mappings[orig_step_id] = step.id
@step_counter += 1
step_json['step_comments'].each do |step_comment_json|
step_comment = StepComment.new(step_comment_json)
step_comment.id = nil
step_comment.user_id = find_user(step_comment.user_id)
step_comment.last_modified_by_id =
find_user(step_comment.last_modified_by_id)
step_comment.step = step
step_comment.save!
end
step_json['tables'].each do |table_json|
table = Table.new(table_json)
orig_table_id = table.id
table.id = nil
table.created_by_id = find_user(table.created_by_id)
table.last_modified_by_id =
find_user(table.last_modified_by_id)
table.team = protocol.team
table.contents = Base64.decode64(table.contents)
table.data_vector = Base64.decode64(table.data_vector)
table.save!
@table_mappings[orig_table_id] = table.id
StepTable.create!(step: step, table: table)
end
step_json['assets'].each do |asset_json|
asset = create_asset(asset_json, protocol.team)
StepAsset.create!(step: step, asset: asset)
end
create_step_checklists(step_json['checklists'], step)
end
end
def create_results(results_json, my_module)
puts('Creating results...')
results_json.each do |result_json|
result = Result.new(result_json['result'])
orig_result_id = result.id
result.id = nil
result.my_module = my_module
result.user_id = find_user(result.user_id)
result.last_modified_by_id = find_user(result.last_modified_by_id)
result.archived_by_id = find_user(result.archived_by_id)
result.restored_by_id = find_user(result.restored_by_id)
if result_json['table'].present?
table = Table.new(result_json['table'])
orig_table_id = table.id
table.id = nil
table.created_by_id = find_user(table.created_by_id)
table.last_modified_by_id =
find_user(table.last_modified_by_id)
table.team = my_module.experiment.project.team
table.contents = Base64.decode64(table.contents)
table.data_vector = Base64.decode64(table.data_vector)
table.save!
@table_mappings[orig_table_id] = table.id
result.table = table
end
if result_json['asset'].present?
asset = create_asset(result_json['asset'],
my_module.experiment.project.team)
result.asset = asset
end
if result_json['result_text'].present?
result_text = ResultText.new(result_json['result_text'])
orig_result_text_id = result_text.id
result_text.id = nil
result_text.result = result
result_text.save!
@result_text_mappings[orig_result_text_id] = result_text.id
end
result.save!
@result_mappings[orig_result_id] = result.id
@result_counter += 1
result_json['result_comments'].each do |result_comment_json|
result_comment = ResultComment.new(result_comment_json)
result_comment.id = nil
result_comment.user_id = find_user(result_comment.user_id)
result_comment.last_modified_by_id =
find_user(result_comment.last_modified_by_id)
result_comment.result = result
result_comment.save!
end
end
end
# returns asset object
def create_asset(asset_json, team)
asset = Asset.new(asset_json)
orig_asset_id = asset.id
file =
File.open("#{@import_dir}/assets/#{asset.id}/#{asset.file_file_name}")
asset.id = nil
asset.created_by_id = find_user(asset.created_by_id)
asset.last_modified_by_id =
find_user(asset.last_modified_by_id)
asset.team = team
asset.file = file
asset.save!
@asset_mappings[orig_asset_id] = asset.id
@asset_counter += 1
asset
end
def create_step_checklists(step_checklists_json, step)
step_checklists_json.each do |checklist_json|
checklist = Checklist.new(checklist_json['checklist'])
orig_checklist_id = checklist.id
checklist.id = nil
checklist.step = step
checklist.created_by_id = find_user(checklist.created_by_id)
checklist.last_modified_by_id =
find_user(checklist.last_modified_by_id)
checklist.save!
@checklist_mappings[orig_checklist_id] = checklist.id
checklist_json['checklist_items'].each do |checklist_item_json|
checklist_item = ChecklistItem.new(checklist_item_json)
checklist_item.id = nil
checklist_item.checklist = checklist
checklist_item.created_by_id = find_user(checklist_item.created_by_id)
checklist_item.last_modified_by_id =
find_user(checklist_item.last_modified_by_id)
checklist_item.save!
end
end
end
def create_reports(reports_json)
reports_json.each do |report_json|
report_el_parent_mappings = {}
report_element_mappings = {}
report = Report.new(report_json['report'])
report.id = nil
report.project_id = @project_mappings[report.project_id]
report.user_id = find_user(report.user_id)
report.last_modified_by_id = find_user(report.last_modified_by_id)
report.save!
@report_counter += 1
report_json['report_elements'].each do |report_element_json|
report_element = ReportElement.new(report_element_json)
orig_report_element_id = report_element.id
report_element.id = nil
orig_parent_id = report_element.parent_id
report_element.parent_id = nil
report_element.report = report
if report_element.project_id
report_element.project_id =
@project_mappings[report_element.project_id]
end
if report_element.my_module_id
report_element.my_module_id =
@my_module_mappings[report_element.my_module_id]
end
if report_element.step_id
report_element.step_id = @step_mappings[report_element.step_id]
end
if report_element.result_id
report_element.result_id = @result_mappings[report_element.result_id]
end
if report_element.checklist_id
report_element.checklist_id =
@checklist_mappings[report_element.checklist_id]
end
if report_element.asset_id
report_element.asset_id = @asset_mappings[report_element.asset_id]
end
if report_element.table_id
report_element.table_id = @table_mappings[report_element.table_id]
end
if report_element.experiment_id
report_element.experiment_id =
@experiment_mappings[report_element.experiment_id]
end
if report_element.repository_id
report_element.repository_id =
@repository_mappings[report_element.repository_id]
end
report_element.save!
report_element_mappings[orig_report_element_id] = report_element.id
report_el_parent_mappings[report_element.id] = orig_parent_id
end
report_el_parent_mappings.each do |k, v|
re = ReportElement.find_by_id(k)
re.parent_id = report_element_mappings[v]
re.save!
end
end
end
def find_user(user_id)
return nil if user_id.nil?
@user_mappings[user_id] ? @user_mappings[user_id] : @admin_id
end
end

16
lib/tasks/data.rake
View file

@ -80,4 +80,20 @@ namespace :data do
desc "Remove temporary and obsolete data"
task clean: [:environment, :clean_temp_files, :clean_unconfirmed_users]
desc 'Export team to directory'
task :team_export, [:team_id] => [:environment] do |_, args|
Rails.logger.info(
"Exporting team with ID:#{args[:team_id]} to directory in tmp"
)
te = TeamExporter.new(args[:team_id])
te.export_to_dir if te
end
desc 'Import team from directory'
task :team_import, [:dir_path] => [:environment] do |_, args|
Rails.logger.info(
"Importing team from directory #{args[:dir_path]}"
)
TeamImporter.new.import_from_dir(args[:dir_path])
end
end