scinote-eln/scinote-web
1
1
Fork 0
mirror of https://github.com/scinote-eln/scinote-web.git synced 2025-03-03 19:24:48 +08:00
Code Issues Projects Releases Packages Wiki Activity

Add importing of the experiment templates

Browse source
This commit is contained in:
Jure Grabnar 2019-01-16 15:54:03 +01:00
parent 5b496a85d3
commit d1f966ee05
3 changed files with 129 additions and 68 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

2
app/services/model_exporters/experiment_exporter.rb
View file

@ -20,7 +20,7 @@ module ModelExporters
# Writing JSON file with experiment structure
File.write(
File.join(@dir_to_export, 'experiment_export.json'),
experiment.to_json
experiment[0].to_json
)
# Copying assets
copy_files(@assets_to_copy, :file, File.join(@dir_to_export, 'assets')) do

186
app/services/team_importer.rb
View file

@ -1,3 +1,5 @@
require 'digest'
class TeamImporter
def initialize
@user_mappings = {}
@ -139,6 +141,38 @@ class TeamImporter
end
end
def import_template_experiment_from_dir(import_dir, project_id,
user_id)
# Remove callbacks that can cause problems when importing
MyModule.skip_callback(:create, :before, :create_blank_protocol)
Protocol.skip_callback(:save, :after, :update_linked_children)
@import_dir = import_dir
@is_template = true
# Parse the experiment file and save it to DB
project = Project.find_by_id(project_id)
experiment_json = JSON.parse(File.read("#{@import_dir}/experiment_export.json"))
experiment = create_experiment(experiment_json, project, user_id)
# Create connections for modules
experiment_json['my_modules'].each do |my_module_json|
create_task_connections(my_module_json['outputs'])
end
# Create UUID for the template experiment
# TODO: this requires DB migration first
# experiment.template_uid = Digest::SHA256.new("#{expirement.name + experiment.created_at}")
# experiment.save!
# Reset callbacks
MyModule.set_callback(:create, :before, :create_blank_protocol)
Protocol.set_callback(:save, :after, :update_linked_children)
puts "Imported experiment: #{experiment.id}"
experiment
end
private
def update_smart_annotations(team)
@ -483,32 +517,39 @@ class TeamImporter
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)
create_experiment(experiment_json, project)
end
end
def create_my_modules(my_modules_json, experiment)
def create_experiment(experiment_json, project, user_id = nil)
experiment = Experiment.new(experiment_json['experiment'])
orig_experiment_id = experiment.id
experiment.id = nil
experiment.project = project
experiment.created_by_id =
user_id || find_user(experiment.created_by_id)
experiment.last_modified_by_id =
user_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 =
user_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, user_id)
experiment
end
def create_my_modules(my_modules_json, experiment, user_id = nil)
puts('Creating my_modules...')
my_modules_json.each do |my_module_json|
my_module = MyModule.new(my_module_json['my_module'])
@ -516,9 +557,10 @@ class TeamImporter
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.created_by_id =
user_id || find_user(my_module.created_by_id)
my_module.last_modified_by_id =
find_user(my_module.last_modified_by_id)
user_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
@ -526,22 +568,24 @@ class TeamImporter
@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!
unless @is_template
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 =
user_id || find_user(my_module_tag.created_by_id)
my_module_tag.save!
end
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.user_id = user_id || find_user(task_comment.user_id)
task_comment.last_modified_by_id =
find_user(task_comment.last_modified_by_id)
user_id || find_user(task_comment.last_modified_by_id)
task_comment.my_module = my_module
task_comment.save!
end
@ -550,25 +594,27 @@ class TeamImporter
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.user_id = user_id || find_user(user_module.user_id)
user_module.assigned_by_id =
find_user(user_module.assigned_by_id)
user_id || find_user(user_module.assigned_by_id)
user_module.save!
end
create_protocols(my_module_json['protocols'], my_module)
create_protocols(my_module_json['protocols'],
my_module, nil, user_id)
create_results(my_module_json['results'], my_module)
create_results(my_module_json['results'], my_module, user_id)
end
end
def create_protocols(protocols_json, my_module = nil, team = nil)
def create_protocols(protocols_json, my_module = nil, team = nil,
user_id = 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.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?
@ -587,18 +633,19 @@ class TeamImporter
@protocol_keyword_mappings[pp_keyword.protocol_keyword_id]
pp_keyword.save!
end
create_steps(protocol_json['steps'], protocol)
create_steps(protocol_json['steps'], protocol, user_id)
end
end
def create_steps(steps_json, protocol)
def create_steps(steps_json, protocol, user_id = nil)
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.user_id = user_id || find_user(step.user_id)
step.last_modified_by_id =
user_id || find_user(step.last_modified_by_id)
step.protocol_id = protocol.id
step.save!
@step_mappings[orig_step_id] = step.id
@ -607,9 +654,9 @@ class TeamImporter
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.user_id = user_id || find_user(step_comment.user_id)
step_comment.last_modified_by_id =
find_user(step_comment.last_modified_by_id)
user_id || find_user(step_comment.last_modified_by_id)
step_comment.step = step
step_comment.save!
end
@ -618,9 +665,9 @@ class TeamImporter
table = Table.new(table_json)
orig_table_id = table.id
table.id = nil
table.created_by_id = find_user(table.created_by_id)
table.created_by_id = user_id || find_user(table.created_by_id)
table.last_modified_by_id =
find_user(table.last_modified_by_id)
user_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)
@ -630,23 +677,24 @@ class TeamImporter
end
step_json['assets'].each do |asset_json|
asset = create_asset(asset_json, protocol.team)
asset = create_asset(asset_json, protocol.team, user_id)
StepAsset.create!(step: step, asset: asset)
end
create_step_checklists(step_json['checklists'], step)
create_step_checklists(step_json['checklists'], step, user_id)
end
end
def create_results(results_json, my_module)
def create_results(results_json, my_module, user_id = nil)
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.user_id = user_id || find_user(result.user_id)
result.last_modified_by_id =
user_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)
@ -654,9 +702,9 @@ class TeamImporter
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.created_by_id = user_id || find_user(table.created_by_id)
table.last_modified_by_id =
find_user(table.last_modified_by_id)
user_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)
@ -667,7 +715,8 @@ class TeamImporter
if result_json['asset'].present?
asset = create_asset(result_json['asset'],
my_module.experiment.project.team)
my_module.experiment.project.team,
user_id)
result.asset = asset
end
@ -687,9 +736,10 @@ class TeamImporter
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.user_id =
user_id || find_user(result_comment.user_id)
result_comment.last_modified_by_id =
find_user(result_comment.last_modified_by_id)
user_id || find_user(result_comment.last_modified_by_id)
result_comment.result = result
result_comment.save!
end
@ -697,16 +747,16 @@ class TeamImporter
end
# returns asset object
def create_asset(asset_json, team)
def create_asset(asset_json, team, user_id = nil)
asset = Asset.new(asset_json)
File.open(
"#{@import_dir}/assets/#{asset.id}/#{asset.file_file_name}"
) do |file|
orig_asset_id = asset.id
asset.id = nil
asset.created_by_id = find_user(asset.created_by_id)
asset.created_by_id = user_id || find_user(asset.created_by_id)
asset.last_modified_by_id =
find_user(asset.last_modified_by_id)
user_id || find_user(asset.last_modified_by_id)
asset.team = team
asset.file = file
asset.save!
@ -716,24 +766,26 @@ class TeamImporter
asset
end
def create_step_checklists(step_checklists_json, step)
def create_step_checklists(step_checklists_json, step, user_id = nil)
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.created_by_id =
user_id || find_user(checklist.created_by_id)
checklist.last_modified_by_id =
find_user(checklist.last_modified_by_id)
user_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.created_by_id =
user_id || find_user(checklist_item.created_by_id)
checklist_item.last_modified_by_id =
find_user(checklist_item.last_modified_by_id)
user_id || find_user(checklist_item.last_modified_by_id)
checklist_item.save!
end
end

9
lib/tasks/data.rake
View file

@ -117,4 +117,13 @@ namespace :data do
ee&.export_to_dir
end
desc 'Import experiment from directory to given project'
task :experiment_import, %i(dir_path project_id user_id) => [:environment] do |_, args|
Rails.logger.info(
"Importing experiment from directory #{args[:dir_path]}"
)
TeamImporter.new.import_template_experiment_from_dir(args[:dir_path],
args[:project_id],
args[:user_id])
end
end