scinote-web/app/controllers/protocols_controller.rb

1257 lines
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class ProtocolsController < ApplicationController
include RenamingUtil
include ProtocolsImporter
include ProtocolsExporter
include ActionView::Helpers::TextHelper
include ActionView::Helpers::UrlHelper
include ApplicationHelper
include InputSanitizeHelper
include ProtocolsIoHelper
include TeamsHelper
include CommentHelper
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before_action :check_create_permissions, only: %i(
create_new_modal
create
)
before_action :check_clone_permissions, only: [:clone]
before_action :check_view_permissions, only: %i(
protocol_status_bar
updated_at_label
preview
linked_children
linked_children_datatable
)
before_action :check_view_all_permissions, only: %i(
index
datatable
)
# For update_from_parent and update_from_parent_modal we don't need to check
# read permission for the parent protocol
before_action :check_manage_permissions, only: %i(
edit
update_metadata
update_keywords
update_description
edit_name_modal
edit_keywords_modal
edit_authors_modal
edit_description_modal
unlink
unlink_modal
revert
revert_modal
update_from_parent
update_from_parent_modal
)
before_action :check_manage_parent_in_repository_permissions, only: %i(
update_parent
update_parent_modal
)
before_action :check_manage_all_in_repository_permissions, only:
%i(make_private publish archive)
before_action :check_restore_all_in_repository_permissions, only: :restore
before_action :check_load_from_repository_views_permissions, only: %i(
load_from_repository_modal
load_from_repository_datatable
)
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before_action :check_load_from_repository_permissions, only: [
:load_from_repository
]
before_action :check_load_from_file_permissions, only: [
:load_from_file
]
before_action :check_copy_to_repository_permissions, only: %i(
copy_to_repository
copy_to_repository_modal
)
before_action :check_import_permissions, only: :import
before_action :check_export_permissions, only: :export
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before_action :check_protocolsio_import_permissions,
only: %i(protocolsio_import_create protocolsio_import_save)
def index; end
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def datatable
respond_to do |format|
format.json do
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render json: ::ProtocolsDatatable.new(
view_context,
@current_team,
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@type,
current_user
)
end
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end
end
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def preview
respond_to do |format|
format.json do
render json: {
title: I18n.t('protocols.index.preview.title',
protocol: escape_input(@protocol.name)),
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html: render_to_string(
partial: 'protocols/index/protocol_preview_modal_body.html.erb',
locals: { protocol: @protocol }
),
footer: render_to_string(
partial: 'protocols/index/protocol_preview_modal_footer.html.erb',
locals: { protocol: @protocol }
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)
}
end
end
end
def recent_protocols
render json: Protocol.recent_protocols(
current_user,
current_team,
Constants::RECENT_PROTOCOL_LIMIT
).select(:id, :name)
end
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def linked_children
respond_to do |format|
format.json do
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render json: {
title: I18n.t('protocols.index.linked_children.title',
protocol: escape_input(@protocol.name)),
html: render_to_string(partial: 'protocols/index/linked_children_modal_body.html.erb',
locals: { protocol: @protocol })
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}
end
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end
end
def linked_children_datatable
respond_to do |format|
format.json do
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render json: ::ProtocolLinkedChildrenDatatable.new(
view_context,
@protocol,
current_user,
self
)
end
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end
end
def make_private
move_protocol('make_private')
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end
def publish
move_protocol('publish')
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end
def archive
move_protocol('archive')
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end
def restore
move_protocol('restore')
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end
def edit
# Switch to correct team
current_team_switch(@protocol.team)
end
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def update_metadata
@protocol.record_timestamps = false
@protocol.assign_attributes(metadata_params)
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changes = @protocol.changes.keys
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respond_to do |format|
if @protocol.save
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changes.each do |key|
if %w(description authors keywords).include?(key)
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log_activity("edit_#{key}_in_protocol_repository".to_sym, nil, protocol: @protocol.id)
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end
end
format.json do
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render json: {
updated_at_label: render_to_string(
partial: 'protocols/header/updated_at_label.html.erb'
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),
name_label: render_to_string(
partial: 'protocols/header/name_label.html.erb'
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),
authors_label: render_to_string(
partial: 'protocols/header/authors_label.html.erb'
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),
description_label: render_to_string(
partial: 'protocols/header/description_label.html.erb', locals: { edit_mode: true }
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)
}
end
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else
format.json do
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render json: @protocol.errors,
status: :unprocessable_entity
end
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end
end
end
def update_keywords
respond_to do |format|
# sanitize user input
if params[:keywords]
params[:keywords].collect! do |keyword|
escape_input(keyword)
end
end
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if @protocol.update_keywords(params[:keywords])
format.json do
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log_activity(:edit_keywords_in_protocol_repository, nil, protocol: @protocol.id)
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render json: {
updated_at_label: render_to_string(
partial: 'protocols/header/updated_at_label.html.erb'
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),
keywords_label: render_to_string(
partial: 'protocols/header/keywords_label.html.erb'
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)
}
end
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else
format.json { render json: {}, status: :unprocessable_entity }
end
end
end
def update_description
respond_to do |format|
format.json do
if @protocol.update(description: params.require(:protocol)[:description])
TinyMceAsset.update_images(@protocol, params[:tiny_mce_images])
render json: {
html: custom_auto_link(
@protocol.tinymce_render(:description),
simple_format: false,
tags: %w(img),
team: current_team)
}
else
render json: @protocol.errors, status: :unprocessable_entity
end
end
end
end
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def create
@protocol = Protocol.new(
team: @current_team,
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protocol_type: Protocol.protocol_types[@type == :public ? :in_repository_public : :in_repository_private],
added_by: current_user
)
@protocol.assign_attributes(create_params)
ts = Time.now
@protocol.record_timestamps = false
@protocol.created_at = ts
@protocol.updated_at = ts
@protocol.published_on = ts if @type == :public
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respond_to do |format|
if @protocol.save
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log_activity(:create_protocol_in_repository, nil, protocol: @protocol.id)
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TinyMceAsset.update_images(@protocol, params[:tiny_mce_images])
format.json do
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render json: {
url: edit_protocol_path(
@protocol,
team: @current_team,
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type: @type
)
}
end
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else
format.json do
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render json: @protocol.errors,
status: :unprocessable_entity
end
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end
end
end
def clone
cloned = nil
Protocol.transaction do
begin
cloned = @original.deep_clone_repository(current_user)
rescue Exception
raise ActiveRecord:: Rollback
end
end
respond_to do |format|
if !cloned.nil?
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flash[:success] = t(
'protocols.index.clone.success_flash',
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original: @original.name,
new: cloned.name
)
flash.keep(:success)
format.json { render json: {}, status: :ok }
else
flash[:error] = t(
'protocols.index.clone.error_flash',
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original: @original.name
)
flash.keep(:error)
format.json { render json: {}, status: :bad_request }
end
end
end
def copy_to_repository
link_protocols = params[:link] &&
can_manage_protocol_in_module?(@protocol) &&
can_create_protocols_in_repository?(@protocol.team)
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respond_to do |format|
transaction_error = false
Protocol.transaction do
begin
@new = @protocol.copy_to_repository(
copy_to_repository_params[:name],
copy_to_repository_params[:protocol_type],
link_protocols,
current_user
)
rescue Exception
transaction_error = true
raise ActiveRecord:: Rollback
end
end
if transaction_error
# Bad request error
format.json do
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render json: {
message: t('my_modules.protocols.copy_to_repository_modal.error_400')
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},
status: :bad_request
end
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elsif @new.invalid?
# Render errors
format.json do
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render json: @new.errors,
status: :unprocessable_entity
end
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else
# Everything good, render 200
format.json { render json: { refresh: link_protocols }, status: :ok }
end
end
end
def unlink
respond_to do |format|
transaction_error = false
Protocol.transaction do
begin
@protocol.unlink
rescue Exception
transaction_error = true
raise ActiveRecord:: Rollback
end
end
if transaction_error
# Bad request error
format.json do
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render json: {
message: t('my_modules.protocols.unlink_error')
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},
status: :bad_request
end
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else
# Everything good, display flash & render 200
flash[:success] = t(
'my_modules.protocols.unlink_flash'
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)
flash.keep(:success)
format.json { render json: {}, status: :ok }
end
end
end
def revert
respond_to do |format|
if @protocol.can_destroy?
transaction_error = false
Protocol.transaction do
begin
# Revert is basically update from parent
@protocol.update_from_parent(current_user)
rescue Exception
transaction_error = true
raise ActiveRecord:: Rollback
end
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end
if transaction_error
# Bad request error
format.json do
render json: {
message: t('my_modules.protocols.revert_error')
},
status: :bad_request
end
else
# Everything good, display flash & render 200
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log_activity(:update_protocol_in_task_from_repository,
@protocol.my_module.experiment.project,
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my_module: @protocol.my_module.id,
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protocol_repository: @protocol.parent.id)
flash[:success] = t(
'my_modules.protocols.revert_flash'
)
flash.keep(:success)
format.json { render json: {}, status: :ok }
end
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else
format.json do
render json: {
message: t('my_modules.protocols.revert_error_locked')
}, status: :bad_request
end
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end
end
end
def update_parent
respond_to do |format|
if @protocol.parent.can_destroy?
transaction_error = false
Protocol.transaction do
begin
@protocol.update_parent(current_user)
rescue Exception
transaction_error = true
raise ActiveRecord:: Rollback
end
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end
if transaction_error
# Bad request error
format.json do
render json: {
message: t('my_modules.protocols.update_parent_error')
},
status: :bad_request
end
else
# Everything good, record activity, display flash & render 200
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log_activity(:update_protocol_in_repository_from_task,
@protocol.my_module.experiment.project,
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my_module: @protocol.my_module.id,
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protocol_repository: @protocol.parent.id)
flash[:success] = t(
'my_modules.protocols.update_parent_flash'
)
flash.keep(:success)
format.json { render json: {}, status: :ok }
end
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else
format.json do
render json: {
message: t('my_modules.protocols.update_parent_error_locked')
}, status: :bad_request
end
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end
end
end
def update_from_parent
respond_to do |format|
if @protocol.can_destroy?
transaction_error = false
Protocol.transaction do
begin
@protocol.update_from_parent(current_user)
rescue Exception
transaction_error = true
raise ActiveRecord:: Rollback
end
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end
if transaction_error
# Bad request error
format.json do
render json: {
message: t('my_modules.protocols.update_from_parent_error')
},
status: :bad_request
end
else
# Everything good, display flash & render 200
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log_activity(:update_protocol_in_task_from_repository,
@protocol.my_module.experiment.project,
my_module: @protocol.my_module.id,
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protocol_repository: @protocol.parent.id)
flash[:success] = t(
'my_modules.protocols.update_from_parent_flash'
)
flash.keep(:success)
format.json { render json: {}, status: :ok }
end
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else
format.json do
render json: {
message: t('my_modules.protocols.update_from_parent_error_locked')
}, status: :bad_request
end
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end
end
end
def load_from_repository
respond_to do |format|
if @protocol.can_destroy?
transaction_error = false
Protocol.transaction do
begin
@protocol.load_from_repository(@source, current_user)
rescue Exception
transaction_error = true
raise ActiveRecord:: Rollback
end
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end
if transaction_error
# Bad request error
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format.json do
render json: {
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message: t('my_modules.protocols.load_from_repository_error')
},
status: :bad_request
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end
else
# Everything good, record activity, display flash & render 200
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log_activity(:load_protocol_to_task_from_repository,
@protocol.my_module.experiment.project,
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my_module: @protocol.my_module.id,
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protocol_repository: @protocol.parent.id)
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flash[:success] = t('my_modules.protocols.load_from_repository_flash')
flash.keep(:success)
format.json { render json: {}, status: :ok }
end
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else
format.json do
render json: {
message: t('my_modules.protocols.load_from_repository_error_locked')
}, status: :bad_request
end
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end
end
end
def load_from_file
# This is actually very similar to import
respond_to do |format|
if @protocol.can_destroy?
transaction_error = false
Protocol.transaction do
begin
import_into_existing(
@protocol, @protocol_json, current_user, current_team
)
rescue Exception
transaction_error = true
raise ActiveRecord:: Rollback
end
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end
if transaction_error
format.json do
render json: { status: :error }, status: :bad_request
end
else
# Everything good, record activity, display flash & render 200
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log_activity(:load_protocol_to_task_from_file,
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@protocol.my_module.experiment.project,
my_module: @my_module.id)
flash[:success] = t(
'my_modules.protocols.load_from_file_flash'
)
flash.keep(:success)
format.json do
render json: { status: :ok }, status: :ok
end
end
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else
format.json do
render json: { status: :locked }, status: :bad_request
end
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end
end
end
def import
protocol = nil
respond_to do |format|
transaction_error = false
Protocol.transaction do
begin
protocol =
import_new_protocol(@protocol_json, @team, @type, current_user)
rescue StandardError => ex
Rails.logger.error ex.message
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transaction_error = true
raise ActiveRecord:: Rollback
end
end
p_name =
if @protocol_json['name'].present? && !@protocol_json['name'].empty?
escape_input(@protocol_json['name'])
else
t('protocols.index.no_protocol_name')
end
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if transaction_error
format.json do
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render json: { name: p_name, status: :bad_request }, status: :bad_request
end
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else
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Activities::CreateActivityService
.call(activity_type: :import_protocol_in_repository,
owner: current_user,
subject: protocol,
team: current_team,
message_items: {
protocol: protocol.id
})
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format.json do
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render json: {
name: escape_input(p_name), new_name: escape_input(protocol.name), status: :ok
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},
status: :ok
end
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end
end
end
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def protocolsio_import_create
@protocolsio_too_big = false
@protocolsio_invalid_file = false
@protocolsio_no_file = false
if params[:json_file].nil?
@protocolsio_no_file = true
respond_to do |format|
format.js {}
end
return 0 # return 0 stops the rest of the controller code from executing
end
extension = File.extname(params[:json_file].path)
file_size = File.size(params[:json_file].path)
if extension != '.txt' && extension != '.json'
@protocolsio_invalid_file = true
respond_to do |format|
format.js {}
end
return 0 # return 0 stops the rest of the controller code from executing
end
if file_size > Rails.configuration.x.file_max_size_mb.megabytes
@protocolsio_too_big = true
respond_to do |format|
format.js {}
# if file is too big, default to the js.erb file,
# named the same as this controller
# where a javascript alert is called
end
return 0 # return 0 stops the rest of the controller code from executing
end
json_file_contents = File.read(params[:json_file].path)
json_file_contents.gsub! '\"', "'"
# escaped double quotes too stressfull, html works with single quotes too
# json double quotes dont get escaped since they dont match \"
unless valid_protocol_json(json_file_contents)
@protocolsio_invalid_file = true
respond_to do |format|
format.js {}
end
return 0 # return 0 stops the rest of the controller code from executing
end
@json_object = JSON.parse(json_file_contents)
unless step_hash_null?(@json_object['steps'])
@json_object['steps'] = protocols_io_guid_reorder_step_json(
@json_object['steps']
)
end
@protocol = Protocol.new
respond_to do |format|
format.js {} # go to the js.erb file named the same as this controller,
# where a preview modal is rendered,
# and some modals get closed and opened
end
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rescue StandardError => e
Rails.logger.error(e.message)
@protocolsio_general_error = true
respond_to do |format|
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format.js {}
end
end
def protocolsio_import_save
@json_object = JSON.parse(params['json_object'])
@db_json = {}
@toolong = false
@db_json['name'] = pio_eval_title_len(
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sanitize_input(not_null(params['protocol']['name']))
)
# since scinote only has description field, and protocols.io has many others
# ,here i am putting everything important from protocols.io into description
@db_json['authors'] = pio_eval_title_len(
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sanitize_input(not_null(params['protocol']['authors']))
)
@db_json['created_at'] = pio_eval_title_len(
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sanitize_input(not_null(params['protocol']['created_at']))
)
@db_json['updated_at'] = pio_eval_title_len(
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sanitize_input(not_null(params['protocol']['last_modified']))
)
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@db_json['steps'] = {}
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unless step_hash_null?(@json_object['steps'])
@db_json['steps'] = protocols_io_fill_step(
@json_object, @db_json['steps']
)
end
protocol = nil
respond_to do |format|
transaction_error = false
@protocolsio_general_error = false
Protocol.transaction do
begin
protocol = import_new_protocol(
@db_json, current_team, params[:type].to_sym, current_user
)
rescue Exception
transaction_error = true
raise ActiveRecord:: Rollback
end
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end
p_name =
if @db_json['name'].present?
escape_input(@db_json['name'])
else
t('protocols.index.no_protocol_name')
end
if transaction_error
@protocolsio_general_error = true
# General something went wrong, upload to db failed error
# format.json {
# render json: { name: p_name, status: :bad_request },
# status: :bad_request
# }
else
@protocolsio_general_error = false
format.json do
render json:
{ name: @db_json['name'], new_name: @db_json['name'], status: :ok },
status: :ok
end
end
format.js {}
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end
end
def export
# Make a zip output stream and send it to the client
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respond_to do |format|
format.html do
z_output_stream = Zip::OutputStream.write_buffer do |ostream|
ostream.put_next_entry('scinote.xml')
ostream.print(generate_envelope_xml(@protocols))
ostream.put_next_entry('scinote.xsd')
ostream.print(generate_envelope_xsd)
ostream.put_next_entry('eln.xsd')
ostream.print(generate_eln_xsd)
# Create folder and xml file for each protocol and populate it
@protocols.each do |protocol|
protocol_dir = get_guid(protocol.id).to_s
ostream.put_next_entry("#{protocol_dir}/eln.xml")
ostream.print(generate_protocol_xml(protocol))
ostream = protocol.tiny_mce_assets.save_to_eln(ostream, protocol_dir)
# Add assets to protocol folder
next if protocol.steps.count <= 0
protocol.steps.order(:id).each do |step|
step_guid = get_guid(step.id)
step_dir = "#{protocol_dir}/#{step_guid}"
if step.assets.exists?
step.assets.order(:id).each do |asset|
next unless asset.file.exists?
asset_guid = get_guid(asset.id)
asset_file_name = asset_guid.to_s +
File.extname(asset.file_file_name).to_s
ostream.put_next_entry("#{step_dir}/#{asset_file_name}")
input_file = asset.open
ostream.print(input_file.read)
input_file.close
end
end
ostream = step.tiny_mce_assets.save_to_eln(ostream, step_dir)
end
end
end
z_output_stream.rewind
protocol_name = get_protocol_name(@protocols[0])
# Now generate filename of the archive and send file to user
if @protocols.count == 1
# Try to construct an OS-safe file name
file_name = 'protocol.eln'
unless protocol_name.nil?
escaped_name = protocol_name.gsub(/[^0-9a-zA-Z\-.,_]/i, '_')
.downcase[0..Constants::NAME_MAX_LENGTH]
file_name = escaped_name + '.eln' unless escaped_name.empty?
end
elsif @protocols.length > 1
file_name = 'protocols.eln'
end
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@protocols.each do |p|
if params[:my_module_id]
my_module = MyModule.find(params[:my_module_id])
Activities::CreateActivityService
.call(activity_type: :export_protocol_from_task,
owner: current_user,
project: my_module.experiment.project,
subject: my_module,
team: current_team,
message_items: {
my_module: params[:my_module_id].to_i
})
else
Activities::CreateActivityService
.call(activity_type: :export_protocol_in_repository,
owner: current_user,
subject: p,
team: current_team,
message_items: {
protocol: p.id
})
end
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end
send_data(z_output_stream.read, filename: file_name)
end
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end
end
def unlink_modal
respond_to do |format|
format.json do
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render json: {
title: t('my_modules.protocols.confirm_link_update_modal.unlink_title'),
message: t('my_modules.protocols.confirm_link_update_modal.unlink_message'),
btn_text: t('my_modules.protocols.confirm_link_update_modal.unlink_btn_text'),
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url: unlink_protocol_path(@protocol)
}
end
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end
end
def revert_modal
respond_to do |format|
format.json do
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render json: {
title: t('my_modules.protocols.confirm_link_update_modal.revert_title'),
message: t('my_modules.protocols.confirm_link_update_modal.revert_message'),
btn_text: t('my_modules.protocols.confirm_link_update_modal.revert_btn_text'),
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url: revert_protocol_path(@protocol)
}
end
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end
end
def update_parent_modal
respond_to do |format|
format.json do
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render json: {
title: t('my_modules.protocols.confirm_link_update_modal.update_parent_title'),
message: t('my_modules.protocols.confirm_link_update_modal.update_parent_message'),
btn_text: t('general.update'),
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url: update_parent_protocol_path(@protocol)
}
end
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end
end
def update_from_parent_modal
respond_to do |format|
format.json do
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render json: {
title: t('my_modules.protocols.confirm_link_update_modal.update_self_title'),
message: t('my_modules.protocols.confirm_link_update_modal.update_self_message'),
btn_text: t('general.update'),
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url: update_from_parent_protocol_path(@protocol)
}
end
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end
end
def load_from_repository_datatable
@protocol = Protocol.find_by_id(params[:id])
@type = (params[:type] || 'public').to_sym
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respond_to do |format|
format.json do
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render json: ::LoadFromRepositoryProtocolsDatatable.new(
view_context,
@protocol.team,
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@type,
current_user
)
end
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end
end
def load_from_repository_modal
@protocol = Protocol.find_by_id(params[:id])
respond_to do |format|
format.json do
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render json: {
html: render_to_string({
partial: "my_modules/protocols/load_from_repository_modal_body.html.erb"
})
}
end
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end
end
def copy_to_repository_modal
@new = Protocol.new
@original = Protocol.find(params[:id])
respond_to do |format|
format.json do
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render json: {
html: render_to_string({
partial: "my_modules/protocols/copy_to_repository_modal_body.html.erb"
})
}
end
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end
end
def protocol_status_bar
respond_to do |format|
format.json do
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render json: {
html: render_to_string({
partial: "my_modules/protocols/protocol_status_bar.html.erb"
})
}
end
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end
end
def updated_at_label
respond_to do |format|
format.json do
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render json: {
html: render_to_string({
partial: "protocols/header/updated_at_label.html.erb"
})
}
end
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end
end
def create_new_modal
@new_protocol = Protocol.new
respond_to do |format|
format.json do
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render json: {
html: render_to_string({
partial: "protocols/index/create_new_modal_body.html.erb"
})
}
end
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end
end
def edit_name_modal
respond_to do |format|
format.json do
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render json: {
title: I18n.t('protocols.header.edit_name_modal.title',
protocol: escape_input(@protocol.name)),
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html: render_to_string({
partial: "protocols/header/edit_name_modal_body.html.erb"
})
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}
end
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end
end
def edit_keywords_modal
respond_to do |format|
format.json do
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render json: {
title: I18n.t('protocols.header.edit_keywords_modal.title',
protocol: escape_input(@protocol.name)),
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html: render_to_string({
partial: "protocols/header/edit_keywords_modal_body.html.erb"
}),
keywords: @protocol.team.protocol_keywords_list
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}
end
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end
end
def edit_authors_modal
respond_to do |format|
format.json do
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render json: {
title: I18n.t('protocols.header.edit_authors_modal.title',
protocol: escape_input(@protocol.name)),
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html: render_to_string({
partial: "protocols/header/edit_authors_modal_body.html.erb"
})
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}
end
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end
end
def edit_description_modal
respond_to do |format|
format.json do
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render json: {
title: I18n.t('protocols.header.edit_description_modal.title',
protocol: escape_input(@protocol.name)),
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html: render_to_string({
partial: "protocols/header/edit_description_modal_body.html.erb"
})
}
end
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end
end
private
def valid_protocol_json(json)
JSON.parse(json)
return true
rescue JSON::ParserError => e
return false
end
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def move_protocol(action)
rollbacked = false
results = []
begin
Protocol.transaction do
@protocols.find_each do |protocol|
result = {
name: protocol.name
}
success = protocol.method(action).call(current_user)
# Try renaming protocol
unless success
rename_record(protocol, :name)
success = protocol.method(action).call(current_user)
end
result[:new_name] = protocol.name
result[:type] = protocol.protocol_type
result[:success] = success
results << result
end
end
rescue
rollbacked = true
end
respond_to do |format|
if rollbacked
format.json do
render json: {}, status: :bad_request
end
else
format.json do
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render json: {
html: render_to_string({
partial: "protocols/index/results_modal_body.html.erb",
locals: { results: results, en_action: "#{action}_results" }
})
}
end
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end
end
end
def load_team_and_type
@current_team = current_team
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# :public, :private or :archive
@type = (params[:type] || 'public').to_sym
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end
def check_view_all_permissions
load_team_and_type
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render_403 unless can_read_team?(@current_team)
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end
def check_view_permissions
@protocol = Protocol.find_by_id(params[:id])
unless @protocol.present? &&
(can_read_protocol_in_module?(@protocol) ||
can_read_protocol_in_repository?(@protocol))
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respond_to { |f| f.json { render json: {}, status: :unauthorized } }
end
end
def check_create_permissions
load_team_and_type
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if !can_create_protocols_in_repository?(@current_team) || @type == :archive
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render_403
end
end
def check_clone_permissions
load_team_and_type
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@original = Protocol.find_by_id(params[:id])
if @original.blank? ||
!can_clone_protocol_in_repository?(@original) || @type == :archive
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render_403
end
end
def check_manage_permissions
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@protocol = Protocol.find_by_id(params[:id])
render_403 unless @protocol.present? &&
(can_manage_protocol_in_module?(@protocol) ||
can_manage_protocol_in_repository?(@protocol))
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end
def check_manage_parent_in_repository_permissions
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@protocol = Protocol.find_by_id(params[:id])
render_403 unless @protocol.present? &&
can_read_protocol_in_module?(@protocol) &&
can_manage_protocol_in_repository?(@protocol.parent)
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end
def check_manage_all_in_repository_permissions
@protocols = Protocol.where(id: params[:protocol_ids])
@protocols.find_each do |protocol|
unless can_manage_protocol_in_repository?(protocol)
respond_to { |f| f.json { render json: {}, status: :unauthorized } }
break
end
end
end
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def check_restore_all_in_repository_permissions
@protocols = Protocol.where(id: params[:protocol_ids])
@protocols.find_each do |protocol|
unless can_restore_protocol_in_repository?(protocol)
respond_to { |f| f.json { render json: {}, status: :unauthorized } }
break
end
end
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end
def check_load_from_repository_views_permissions
@protocol = Protocol.find_by_id(params[:id])
render_403 if @protocol.blank? || !can_read_protocol_in_module?(@protocol)
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end
def check_load_from_repository_permissions
@protocol = Protocol.find_by_id(params[:id])
@source = Protocol.find_by_id(params[:source_id])
render_403 unless @protocol.present? && @source.present? &&
(can_manage_protocol_in_module?(@protocol) ||
can_read_protocol_in_repository?(@source))
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end
def check_load_from_file_permissions
@protocol_json = params[:protocol]
@protocol = Protocol.find_by_id(params[:id])
@my_module = @protocol.my_module
if @protocol_json.blank? ||
@protocol.blank? ||
@my_module.blank? ||
!can_manage_protocol_in_module?(@protocol)
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render_403
end
end
def check_copy_to_repository_permissions
@protocol = Protocol.find_by_id(params[:id])
@my_module = @protocol.my_module
render_403 unless @my_module.present? &&
(can_read_protocol_in_module?(@protocol) ||
can_create_protocols_in_repository?(@protocol.team))
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end
def check_import_permissions
@protocol_json = params[:protocol]
@team = Team.find(params[:team_id])
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@type = params[:type] ? params[:type].to_sym : nil
unless @protocol_json.present? && @team.present? &&
(@type == :public || @type == :private) &&
can_create_protocols_in_repository?(@team)
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render_403
end
end
def check_export_permissions
@protocols = Protocol.where(id: params[:protocol_ids])
render_403 if @protocols.blank?
@protocols.each do |p|
render_403 unless can_read_protocol_in_module?(p) ||
can_read_protocol_in_repository?(p)
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end
end
def copy_to_repository_params
params.require(:protocol).permit(:name, :protocol_type)
end
def create_params
params.require(:protocol).permit(:name)
end
def metadata_params
params.require(:protocol).permit(:name, :authors, :description)
end
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def check_protocolsio_import_permissions
render_403 unless can_create_protocols_in_repository?(current_team)
end
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def log_activity(type_of, project = nil, message_items = {})
message_items = { protocol: @protocol&.id }.merge(message_items)
Activities::CreateActivityService
.call(activity_type: type_of,
owner: current_user,
subject: @protocol,
team: current_team,
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project: project,
message_items: message_items)
end
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end