mirror of
https://github.com/scinote-eln/scinote-web.git
synced 2024-09-21 07:26:15 +08:00
1301 lines
38 KiB
Ruby
1301 lines
38 KiB
Ruby
class ProtocolsController < ApplicationController
|
|
include RenamingUtil
|
|
include ProtocolsImporter
|
|
include ProtocolsExporter
|
|
include InputSanitizeHelper
|
|
|
|
before_action :check_create_permissions, only: [
|
|
:create_new_modal,
|
|
:create
|
|
]
|
|
before_action :check_clone_permissions, only: [ :clone ]
|
|
before_action :check_view_permissions, only: [
|
|
:protocol_status_bar,
|
|
:updated_at_label,
|
|
:preview,
|
|
:linked_children,
|
|
:linked_children_datatable
|
|
]
|
|
before_action :check_edit_permissions, only: [
|
|
:edit,
|
|
:update_metadata,
|
|
:update_keywords,
|
|
:edit_name_modal,
|
|
:edit_keywords_modal,
|
|
:edit_authors_modal,
|
|
:edit_description_modal
|
|
]
|
|
before_action :check_view_all_permissions, only: [
|
|
:index,
|
|
:datatable
|
|
]
|
|
before_action :check_unlink_permissions, only: [
|
|
:unlink,
|
|
:unlink_modal
|
|
]
|
|
before_action :check_revert_permissions, only: [
|
|
:revert,
|
|
:revert_modal
|
|
]
|
|
before_action :check_update_parent_permissions, only: [
|
|
:update_parent,
|
|
:update_parent_modal
|
|
]
|
|
before_action :check_update_from_parent_permissions, only: [
|
|
:update_from_parent,
|
|
:update_from_parent_modal
|
|
]
|
|
before_action :check_load_from_repository_views_permissions, only: [
|
|
:load_from_repository_modal,
|
|
:load_from_repository_datatable
|
|
]
|
|
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: [
|
|
:copy_to_repository,
|
|
:copy_to_repository_modal
|
|
]
|
|
before_action :check_make_private_permissions, only: [ :make_private ]
|
|
before_action :check_publish_permissions, only: [ :publish ]
|
|
before_action :check_archive_permissions, only: [ :archive ]
|
|
before_action :check_restore_permissions, only: [ :restore ]
|
|
before_action :check_import_permissions, only: [ :import ]
|
|
before_action :check_export_permissions, only: [ :export ]
|
|
|
|
def index
|
|
end
|
|
|
|
def datatable
|
|
respond_to do |format|
|
|
format.json {
|
|
render json: ::ProtocolsDatatable.new(
|
|
view_context,
|
|
@current_team,
|
|
@type,
|
|
current_user
|
|
)
|
|
}
|
|
end
|
|
end
|
|
|
|
def preview
|
|
respond_to do |format|
|
|
format.json do
|
|
render json: {
|
|
title: I18n.t('protocols.index.preview.title',
|
|
protocol: escape_input(@protocol.name)),
|
|
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 }
|
|
)
|
|
}
|
|
end
|
|
end
|
|
end
|
|
|
|
def linked_children
|
|
respond_to do |format|
|
|
format.json {
|
|
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 }
|
|
})
|
|
}
|
|
}
|
|
end
|
|
end
|
|
|
|
def linked_children_datatable
|
|
respond_to do |format|
|
|
format.json {
|
|
render json: ::ProtocolLinkedChildrenDatatable.new(
|
|
view_context,
|
|
@protocol,
|
|
current_user,
|
|
self
|
|
)
|
|
}
|
|
end
|
|
end
|
|
|
|
def make_private
|
|
move_protocol("make_private")
|
|
end
|
|
|
|
def publish
|
|
move_protocol("publish")
|
|
end
|
|
|
|
def archive
|
|
move_protocol("archive")
|
|
end
|
|
|
|
def restore
|
|
move_protocol("restore")
|
|
end
|
|
|
|
def edit
|
|
end
|
|
|
|
def update_metadata
|
|
@protocol.record_timestamps = false
|
|
@protocol.assign_attributes(metadata_params)
|
|
|
|
respond_to do |format|
|
|
if @protocol.save
|
|
format.json {
|
|
render json: {
|
|
updated_at_label: render_to_string(
|
|
partial: "protocols/header/updated_at_label.html.erb"
|
|
),
|
|
name_label: render_to_string(
|
|
partial: "protocols/header/name_label.html.erb"
|
|
),
|
|
authors_label: render_to_string(
|
|
partial: "protocols/header/authors_label.html.erb"
|
|
),
|
|
description_label: render_to_string(
|
|
partial: "protocols/header/description_label.html.erb"
|
|
)
|
|
}
|
|
}
|
|
else
|
|
format.json {
|
|
render json: @protocol.errors,
|
|
status: :unprocessable_entity
|
|
}
|
|
end
|
|
end
|
|
end
|
|
|
|
def update_keywords
|
|
respond_to do |format|
|
|
# sanitize user input
|
|
params[:keywords].collect! do |keyword|
|
|
escape_input(keyword)
|
|
end
|
|
if @protocol.update_keywords(params[:keywords])
|
|
format.json {
|
|
render json: {
|
|
updated_at_label: render_to_string(
|
|
partial: "protocols/header/updated_at_label.html.erb"
|
|
),
|
|
keywords_label: render_to_string(
|
|
partial: "protocols/header/keywords_label.html.erb"
|
|
)
|
|
}
|
|
}
|
|
else
|
|
format.json { render json: {}, status: :unprocessable_entity }
|
|
end
|
|
end
|
|
end
|
|
|
|
def create
|
|
@protocol = Protocol.new(
|
|
team: @current_team,
|
|
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
|
|
if @type == :public
|
|
@protocol.published_on = ts
|
|
end
|
|
|
|
respond_to do |format|
|
|
if @protocol.save
|
|
format.json {
|
|
render json: {
|
|
url: edit_protocol_path(
|
|
@protocol,
|
|
team: @current_team,
|
|
type: @type
|
|
)
|
|
}
|
|
}
|
|
else
|
|
format.json {
|
|
render json: @protocol.errors,
|
|
status: :unprocessable_entity
|
|
}
|
|
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
|
|
flash[:success] = t(
|
|
"protocols.index.clone.success_flash",
|
|
original: @original.name,
|
|
new: cloned.name
|
|
)
|
|
flash.keep(:success)
|
|
format.json { render json: {}, status: :ok }
|
|
else
|
|
flash[:error] = t(
|
|
"protocols.index.clone.error_flash",
|
|
original: @original.name
|
|
)
|
|
flash.keep(:error)
|
|
format.json { render json: {}, status: :bad_request }
|
|
end
|
|
end
|
|
end
|
|
|
|
def copy_to_repository
|
|
link_protocols = can_link_copied_protocol_in_repository(@protocol) && params[:link]
|
|
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 {
|
|
render json: {
|
|
message: t("my_modules.protocols.copy_to_repository_modal.error_400")
|
|
},
|
|
status: :bad_request
|
|
}
|
|
elsif @new.invalid?
|
|
# Render errors
|
|
format.json {
|
|
render json: @new.errors,
|
|
status: :unprocessable_entity
|
|
}
|
|
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 {
|
|
render json: {
|
|
message: t("my_modules.protocols.unlink_error")
|
|
},
|
|
status: :bad_request
|
|
}
|
|
else
|
|
# Everything good, display flash & render 200
|
|
flash[:success] = t(
|
|
"my_modules.protocols.unlink_flash",
|
|
)
|
|
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
|
|
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
|
|
flash[:success] = t(
|
|
'my_modules.protocols.revert_flash'
|
|
)
|
|
flash.keep(:success)
|
|
format.json { render json: {}, status: :ok }
|
|
end
|
|
else
|
|
format.json do
|
|
render json: {
|
|
message: t('my_modules.protocols.revert_error_locked')
|
|
}, status: :bad_request
|
|
end
|
|
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
|
|
end
|
|
|
|
if transaction_error
|
|
# Bad request error
|
|
format.json {
|
|
render json: {
|
|
message: t("my_modules.protocols.update_parent_error")
|
|
},
|
|
status: :bad_request
|
|
}
|
|
else
|
|
# Everything good, record activity, display flash & render 200
|
|
Activity.create(
|
|
type_of: :revert_protocol,
|
|
project: @protocol.my_module.experiment.project,
|
|
experiment: @protocol.my_module.experiment,
|
|
my_module: @protocol.my_module,
|
|
user: current_user,
|
|
message: I18n.t(
|
|
'activities.revert_protocol',
|
|
user: current_user.full_name,
|
|
protocol: @protocol.name
|
|
)
|
|
)
|
|
flash[:success] = t(
|
|
"my_modules.protocols.update_parent_flash",
|
|
)
|
|
flash.keep(:success)
|
|
format.json { render json: {}, status: :ok }
|
|
end
|
|
else
|
|
format.json do
|
|
render json: {
|
|
message: t('my_modules.protocols.update_parent_error_locked')
|
|
}, status: :bad_request
|
|
end
|
|
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
|
|
end
|
|
|
|
if transaction_error
|
|
# Bad request error
|
|
format.json {
|
|
render json: {
|
|
message: t("my_modules.protocols.update_from_parent_error")
|
|
},
|
|
status: :bad_request
|
|
}
|
|
else
|
|
# Everything good, display flash & render 200
|
|
flash[:success] = t(
|
|
"my_modules.protocols.update_from_parent_flash",
|
|
)
|
|
flash.keep(:success)
|
|
format.json { render json: {}, status: :ok }
|
|
end
|
|
else
|
|
format.json do
|
|
render json: {
|
|
message: t('my_modules.protocols.update_from_parent_error_locked')
|
|
}, status: :bad_request
|
|
end
|
|
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
|
|
end
|
|
|
|
if transaction_error
|
|
# Bad request error
|
|
format.json do
|
|
render json: {
|
|
message: t('my_modules.protocols.load_from_repository_error')
|
|
},
|
|
status: :bad_request
|
|
end
|
|
else
|
|
# Everything good, record activity, display flash & render 200
|
|
Activity.create(
|
|
type_of: :load_protocol_from_repository,
|
|
project: @protocol.my_module.experiment.project,
|
|
experiment: @protocol.my_module.experiment,
|
|
my_module: @protocol.my_module,
|
|
user: current_user,
|
|
message: I18n.t(
|
|
'activities.load_protocol_from_repository',
|
|
user: current_user.full_name,
|
|
protocol: @source.name
|
|
)
|
|
)
|
|
flash[:success] = t('my_modules.protocols.load_from_repository_flash')
|
|
flash.keep(:success)
|
|
format.json { render json: {}, status: :ok }
|
|
end
|
|
else
|
|
format.json do
|
|
render json: {
|
|
message: t('my_modules.protocols.load_from_repository_error_locked')
|
|
}, status: :bad_request
|
|
end
|
|
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
|
|
end
|
|
|
|
if transaction_error
|
|
format.json {
|
|
render json: { status: :error }, status: :bad_request
|
|
}
|
|
else
|
|
# Everything good, record activity, display flash & render 200
|
|
Activity.create(
|
|
type_of: :load_protocol_from_file,
|
|
project: @protocol.my_module.experiment.project,
|
|
experiment: @protocol.my_module.experiment,
|
|
my_module: @protocol.my_module,
|
|
user: current_user,
|
|
message: I18n.t(
|
|
'activities.load_protocol_from_file',
|
|
user: current_user.full_name,
|
|
protocol: @protocol_json[:name]
|
|
)
|
|
)
|
|
flash[:success] = t(
|
|
'my_modules.protocols.load_from_file_flash',
|
|
)
|
|
flash.keep(:success)
|
|
format.json {
|
|
render json: { status: :ok }, status: :ok
|
|
}
|
|
end
|
|
else
|
|
format.json do
|
|
render json: { status: :locked }, status: :bad_request
|
|
end
|
|
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 Exception
|
|
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
|
|
if transaction_error
|
|
format.json {
|
|
render json: { name: p_name, status: :bad_request }, status: :bad_request
|
|
}
|
|
else
|
|
format.json {
|
|
render json: {
|
|
name: p_name, new_name: protocol.name, status: :ok
|
|
},
|
|
status: :ok
|
|
}
|
|
end
|
|
end
|
|
end
|
|
|
|
def protocolsio_import_create
|
|
@protocolsio_too_big = false
|
|
file_size = File.size(params[:json_file].path)
|
|
|
|
if file_size / 1000 > Constants::FILE_MAX_SIZE_MB
|
|
@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
|
|
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 \"
|
|
@json_object = JSON.parse(json_file_contents)
|
|
@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
|
|
end
|
|
|
|
def protocolsio_import_save
|
|
@json_object = JSON.parse(params['json_object'])
|
|
@import_object = {}
|
|
@import_object['name'] = 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
|
|
description_array = %w[
|
|
(before_start warning guidelines manuscript_citation publish_date
|
|
created_on vendor_name vendor_link keywords tags link)
|
|
]
|
|
description_string = Sanitize.clean(params['protocol']['description'])
|
|
description_array.each do |element|
|
|
if element == 'created_on'
|
|
if @json_object[element] && @json_object[element] != ''
|
|
new_element = element.slice(0, 1).capitalize + element.slice(1..-1)
|
|
new_element = new_element.tr('_', ' ')
|
|
description_string =
|
|
description_string +
|
|
new_element.to_s + ': ' +
|
|
Sanitize.clean(params['protocol']['created_at'].to_s) + "\n"
|
|
end
|
|
else
|
|
if element == 'tags'
|
|
if @json_object[element].any? && @json_object[element] != ''
|
|
new_element = element.slice(0, 1).capitalize + element.slice(1..-1)
|
|
new_element = new_element.tr('_', ' ')
|
|
description_string = description_string + new_element.to_s + ': '
|
|
@json_object[element].each do |tag|
|
|
description_string =
|
|
description_string +
|
|
Sanitize.clean(tag['tag_name']) + ' , '
|
|
end
|
|
description_string += "\n"
|
|
end
|
|
# Since protocols description field doesnt show html,i just remove it here
|
|
# because its even messier Otherwise
|
|
# what this does is basically appends "FIELD NAME: "+" FIELD VALUE"
|
|
# to description for various fields
|
|
else
|
|
if @json_object[element] && @json_object[element] != ''
|
|
new_element = element.slice(0, 1).capitalize + element.slice(1..-1)
|
|
new_element = new_element.tr('_', ' ')
|
|
description_string +=
|
|
new_element.to_s + ': ' +
|
|
Sanitize.clean(@json_object[element].to_s) + "\n"
|
|
end
|
|
end
|
|
end
|
|
end
|
|
@import_object['authors'] = params['protocol']['authors']
|
|
@import_object['created_at'] = params['protocol']['created_at']
|
|
@import_object['updated_at'] = params['protocol']['last_modified']
|
|
@import_object['description'] = description_string
|
|
@import_object['steps'] = {}
|
|
counter = 0
|
|
step_pos = -1
|
|
# these whitelists are there to not let some useless step components trough,
|
|
# that always have data set to null (data doesnt get imported over to json)
|
|
whitelist_simple = %w(1 6 17)
|
|
# (simple to map) id 1= step description, id 6= section (title),
|
|
# id 17= expected result
|
|
whitelist_complex = %w(8 9 15 18 19 20)
|
|
# (complex mapping with nested hashes) id 8 = software package,
|
|
# id 9 = dataset, id 15 = command, id 18 = attached sub protocol
|
|
# id 19= safety information ,
|
|
# id 20= regents (materials, like scinote samples kind of)
|
|
@json_object['steps'].each do |step|
|
|
step_pos += 1
|
|
counter += 1
|
|
@import_object['steps'][step_pos.to_s] = {}
|
|
@import_object['steps'][step_pos.to_s]['position'] = step_pos
|
|
|
|
step['components'].each do |key,value|
|
|
element_string = nil
|
|
if counter <= 1
|
|
# here i made an if to distinguish the first step from the others,
|
|
# because the first step
|
|
# sometimes has index values as keys instead of hashes, for no good reason
|
|
key = value if value.class == Hash
|
|
end
|
|
if whitelist_simple.include?(key['component_type_id'])
|
|
|
|
case key['component_type_id']
|
|
when '1'
|
|
if !key['data'].nil? && key['data'] != ''
|
|
element_string = '<br>' + (key['data']) + '<br>'
|
|
if @import_object['steps'][step_pos.to_s]['description']
|
|
@import_object['steps'][step_pos.to_s]['description'] << element_string
|
|
else
|
|
@import_object['steps'][step_pos.to_s]['description'] = element_string
|
|
end
|
|
else
|
|
@import_object['steps'][step_pos.to_s]['description'] ||= 'Description missing!'
|
|
end
|
|
when '6'
|
|
if !key['data'].nil? && key['data'] != ''
|
|
@import_object['steps'][step_pos.to_s]['name'] = key['data']
|
|
else
|
|
@import_object['steps'][step_pos.to_s]['name'] = 'Step'
|
|
end
|
|
when '17'
|
|
if !key['data'].nil? && key['data'] != ''
|
|
element_string = '<br><strong>Expected result: </strong>' + (key['data']) + '<br>'
|
|
@import_object['steps'][step_pos.to_s]['description'] << element_string
|
|
|
|
end
|
|
end
|
|
# (complex mapping with nested hashes)
|
|
# id 8 = software package, id 9 = dataset,
|
|
# id 15 = command, id 18 = attached sub protocol
|
|
# id 19= safety information ,
|
|
# id 20= regents (materials, like scinote samples kind of)
|
|
|
|
elsif key && whitelist_complex.include?(key['component_type_id'])
|
|
case key['component_type_id']
|
|
when '8'
|
|
if key['source_data']['name'] && key['source_data']['developer'] && key['source_data']['version'] && key['source_data']['link'] && key['source_data']['repository'] && key['source_data']['os_name'] && key['source_data']['os_version']
|
|
element_string = '<br><strong>Software package: </strong>' + (key['source_data']['name']) + '<br>Developer: ' + (key['source_data']['developer']) + '<br>Version: ' + (key['source_data']['version']) + '<br>Link: ' + (key['source_data']['link']) + '<br>Repository: ' + (key['source_data']['repository']) + '<br> OS name , OS version: ' + (key['source_data']['os_name']) + ' , ' + (key['source_data']['os_version'])
|
|
@import_object['steps'][step_pos.to_s]['description'] << element_string
|
|
end
|
|
when '9'
|
|
if key['source_data']['name'] && key['source_data']['link']
|
|
element_string='<br><strong>Dataset: </strong>' + (key['source_data']['name']) + '<br>Link: ' + (key['source_data']['link'])
|
|
@import_object['steps'][step_pos.to_s]['description'] << element_string
|
|
end
|
|
when '15'
|
|
if key['source_data']['name'] && key['source_data']['description'] && key['source_data']['os_name'] && key['source_data']['os_version']
|
|
element_string = '<br><strong>Command: </strong>' + (key['source_data']['name']) + '<br>Description: ' + (key['source_data']['description']) + '<br>OS name , OS version: ' + (key['source_data']['os_name']) + ' , ' + (key['source_data']['os_version'])
|
|
@import_object['steps'][step_pos.to_s]['description'] << element_string
|
|
end
|
|
when '18'
|
|
if key['source_data']['protocol_name'] && key['source_data']['full_name'] && key['source_data']['link']
|
|
element_string = '<br><strong>This protocol also contains an attached sub-protocol: </strong>' + (key['source_data']['protocol_name']) + '<br>Author: ' + (key['source_data']['full_name']) + '<br>Link: ' + (key['source_data']['link'])
|
|
@import_object['steps'][step_pos.to_s]['description'] << element_string
|
|
|
|
end
|
|
when '19'
|
|
if key['source_data']['body'] && key['source_data']['link']
|
|
element_string = '<br><strong>Safety information: </strong>' + (key['source_data']['body'])+'<br>Link: '+(key['source_data']['link'])
|
|
@import_object['steps'][step_pos.to_s]['description'] << element_string
|
|
end
|
|
# when '20' placeholder za materiale
|
|
end
|
|
end # finished step component iteration
|
|
end # finished looping over step components
|
|
end # steps
|
|
|
|
protocol = nil
|
|
respond_to do |format|
|
|
transaction_error = false
|
|
@protocolsio_general_error = false
|
|
Protocol.transaction do
|
|
begin
|
|
# pass the import_object we made, current team,user
|
|
# and the type (private,public)
|
|
protocol = import_new_protocol(@import_object, current_team, params[:type].to_sym, current_user)
|
|
rescue Exception
|
|
transaction_error = true
|
|
raise ActiveRecord:: Rollback
|
|
end
|
|
end
|
|
|
|
p_name =
|
|
if @import_object['name'].present? && !@import_object['name'].empty?
|
|
escape_input(@import_object['name'])
|
|
else
|
|
t('protocols.index.no_protocol_name')
|
|
end
|
|
|
|
if transaction_error
|
|
@protocolsio_general_error = true
|
|
# format.json {
|
|
# render json: { name: p_name, status: :bad_request },
|
|
# status: :bad_request
|
|
# }
|
|
|
|
else
|
|
# General something went wrong, upload to db failed error
|
|
@protocolsio_general_error = false
|
|
format.json {
|
|
render json:
|
|
{ name: p_name, new_name: protocol.name, status: :ok },
|
|
status: :ok
|
|
}
|
|
end
|
|
format.js {}
|
|
end
|
|
end
|
|
|
|
def export
|
|
# Make a zip output stream and send it to the client
|
|
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))
|
|
# 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}"
|
|
next if step.assets.count <= 0
|
|
step.assets.order(:id).each do |asset|
|
|
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
|
|
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
|
|
send_data(z_output_stream.read, filename: file_name)
|
|
end
|
|
end
|
|
end
|
|
|
|
def unlink_modal
|
|
respond_to do |format|
|
|
format.json {
|
|
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"),
|
|
url: unlink_protocol_path(@protocol)
|
|
}
|
|
}
|
|
end
|
|
end
|
|
|
|
def revert_modal
|
|
respond_to do |format|
|
|
format.json {
|
|
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"),
|
|
url: revert_protocol_path(@protocol)
|
|
}
|
|
}
|
|
end
|
|
end
|
|
|
|
def update_parent_modal
|
|
respond_to do |format|
|
|
format.json {
|
|
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"),
|
|
url: update_parent_protocol_path(@protocol)
|
|
}
|
|
}
|
|
end
|
|
end
|
|
|
|
def update_from_parent_modal
|
|
respond_to do |format|
|
|
format.json {
|
|
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"),
|
|
url: update_from_parent_protocol_path(@protocol)
|
|
}
|
|
}
|
|
end
|
|
end
|
|
|
|
def load_from_repository_datatable
|
|
@protocol = Protocol.find_by_id(params[:id])
|
|
@type = (params[:type] || "public").to_sym
|
|
respond_to do |format|
|
|
format.json {
|
|
render json: ::LoadFromRepositoryProtocolsDatatable.new(
|
|
view_context,
|
|
@protocol.team,
|
|
@type,
|
|
current_user
|
|
)
|
|
}
|
|
end
|
|
end
|
|
|
|
def load_from_repository_modal
|
|
@protocol = Protocol.find_by_id(params[:id])
|
|
respond_to do |format|
|
|
format.json {
|
|
render json: {
|
|
html: render_to_string({
|
|
partial: "my_modules/protocols/load_from_repository_modal_body.html.erb"
|
|
})
|
|
}
|
|
}
|
|
end
|
|
end
|
|
|
|
def copy_to_repository_modal
|
|
@new = Protocol.new
|
|
@original = Protocol.find(params[:id])
|
|
respond_to do |format|
|
|
format.json {
|
|
render json: {
|
|
html: render_to_string({
|
|
partial: "my_modules/protocols/copy_to_repository_modal_body.html.erb"
|
|
})
|
|
}
|
|
}
|
|
end
|
|
end
|
|
|
|
def protocol_status_bar
|
|
respond_to do |format|
|
|
format.json {
|
|
render json: {
|
|
html: render_to_string({
|
|
partial: "my_modules/protocols/protocol_status_bar.html.erb"
|
|
})
|
|
}
|
|
}
|
|
end
|
|
end
|
|
|
|
def updated_at_label
|
|
respond_to do |format|
|
|
format.json {
|
|
render json: {
|
|
html: render_to_string({
|
|
partial: "protocols/header/updated_at_label.html.erb"
|
|
})
|
|
}
|
|
}
|
|
end
|
|
end
|
|
|
|
def create_new_modal
|
|
@new_protocol = Protocol.new
|
|
respond_to do |format|
|
|
format.json {
|
|
render json: {
|
|
html: render_to_string({
|
|
partial: "protocols/index/create_new_modal_body.html.erb"
|
|
})
|
|
}
|
|
}
|
|
end
|
|
end
|
|
|
|
def edit_name_modal
|
|
respond_to do |format|
|
|
format.json {
|
|
render json: {
|
|
title: I18n.t('protocols.header.edit_name_modal.title',
|
|
protocol: escape_input(@protocol.name)),
|
|
html: render_to_string({
|
|
partial: "protocols/header/edit_name_modal_body.html.erb"
|
|
})
|
|
}
|
|
}
|
|
end
|
|
end
|
|
|
|
def edit_keywords_modal
|
|
respond_to do |format|
|
|
format.json {
|
|
render json: {
|
|
title: I18n.t('protocols.header.edit_keywords_modal.title',
|
|
protocol: escape_input(@protocol.name)),
|
|
html: render_to_string({
|
|
partial: "protocols/header/edit_keywords_modal_body.html.erb"
|
|
}),
|
|
keywords: @protocol.team.protocol_keywords_list
|
|
}
|
|
}
|
|
end
|
|
end
|
|
|
|
def edit_authors_modal
|
|
respond_to do |format|
|
|
format.json {
|
|
render json: {
|
|
title: I18n.t('protocols.header.edit_authors_modal.title',
|
|
protocol: escape_input(@protocol.name)),
|
|
html: render_to_string({
|
|
partial: "protocols/header/edit_authors_modal_body.html.erb"
|
|
})
|
|
}
|
|
}
|
|
end
|
|
end
|
|
|
|
def edit_description_modal
|
|
respond_to do |format|
|
|
format.json {
|
|
render json: {
|
|
title: I18n.t('protocols.header.edit_description_modal.title',
|
|
protocol: escape_input(@protocol.name)),
|
|
html: render_to_string({
|
|
partial: "protocols/header/edit_description_modal_body.html.erb"
|
|
})
|
|
}
|
|
}
|
|
end
|
|
end
|
|
|
|
private
|
|
|
|
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|
|
|
unless rollbacked
|
|
format.json {
|
|
render json: {
|
|
html: render_to_string({
|
|
partial: "protocols/index/results_modal_body.html.erb",
|
|
locals: { results: results, en_action: "#{action}_results" }
|
|
})
|
|
}
|
|
}
|
|
else
|
|
format.json {
|
|
render json: {}, status: :bad_request
|
|
}
|
|
end
|
|
end
|
|
end
|
|
|
|
def load_team_and_type
|
|
@current_team = current_team
|
|
# :public, :private or :archive
|
|
@type = (params[:type] || "public").to_sym
|
|
end
|
|
|
|
def check_view_all_permissions
|
|
load_team_and_type
|
|
|
|
render_403 unless can_view_team_protocols(@current_team)
|
|
end
|
|
|
|
def check_view_permissions
|
|
@protocol = Protocol.find_by_id(params[:id])
|
|
if @protocol.blank? || !can_view_protocol(@protocol)
|
|
respond_to { |f| f.json { render json: {}, status: :unauthorized } }
|
|
end
|
|
end
|
|
|
|
def check_create_permissions
|
|
load_team_and_type
|
|
|
|
if !can_create_new_protocol(@current_team) || @type == :archive
|
|
render_403
|
|
end
|
|
end
|
|
|
|
def check_clone_permissions
|
|
load_team_and_type
|
|
@original = Protocol.find_by_id(params[:id])
|
|
|
|
if @original.blank? ||
|
|
!can_clone_protocol(@original) || @type == :archive
|
|
render_403
|
|
end
|
|
end
|
|
|
|
def check_edit_permissions
|
|
load_team_and_type
|
|
@protocol = Protocol.find_by_id(params[:id])
|
|
|
|
unless can_edit_protocol(@protocol)
|
|
render_403
|
|
end
|
|
end
|
|
|
|
def check_unlink_permissions
|
|
@protocol = Protocol.find_by_id(params[:id])
|
|
|
|
if @protocol.blank? || !can_unlink_protocol(@protocol)
|
|
render_403
|
|
end
|
|
end
|
|
|
|
def check_revert_permissions
|
|
@protocol = Protocol.find_by_id(params[:id])
|
|
|
|
if @protocol.blank? || !can_revert_protocol(@protocol)
|
|
render_403
|
|
end
|
|
end
|
|
|
|
def check_update_parent_permissions
|
|
@protocol = Protocol.find_by_id(params[:id])
|
|
|
|
if @protocol.blank? || !can_update_parent_protocol(@protocol)
|
|
render_403
|
|
end
|
|
end
|
|
|
|
def check_update_from_parent_permissions
|
|
@protocol = Protocol.find_by_id(params[:id])
|
|
|
|
if @protocol.blank? || !can_update_protocol_from_parent(@protocol)
|
|
render_403
|
|
end
|
|
end
|
|
|
|
def check_load_from_repository_views_permissions
|
|
@protocol = Protocol.find_by_id(params[:id])
|
|
|
|
if @protocol.blank? || !can_view_protocol(@protocol)
|
|
render_403
|
|
end
|
|
end
|
|
|
|
def check_load_from_repository_permissions
|
|
@protocol = Protocol.find_by_id(params[:id])
|
|
@source = Protocol.find_by_id(params[:source_id])
|
|
|
|
if @protocol.blank? || @source.blank? || !can_load_protocol_from_repository(@protocol, @source)
|
|
render_403
|
|
end
|
|
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_load_protocol_into_module(@my_module)
|
|
render_403
|
|
end
|
|
end
|
|
|
|
def check_copy_to_repository_permissions
|
|
@protocol = Protocol.find_by_id(params[:id])
|
|
@my_module = @protocol.my_module
|
|
|
|
if @my_module.blank? or !can_copy_protocol_to_repository(@my_module)
|
|
render_403
|
|
end
|
|
end
|
|
|
|
def check_make_private_permissions
|
|
@protocols = Protocol.where(id: params[:protocol_ids])
|
|
@protocols.find_each do |protocol|
|
|
unless can_make_protocol_private(protocol) then
|
|
respond_to { |f| f.json { render json: {}, status: :unauthorized } }
|
|
return
|
|
end
|
|
end
|
|
end
|
|
|
|
def check_publish_permissions
|
|
@protocols = Protocol.where(id: params[:protocol_ids])
|
|
@protocols.find_each do |protocol|
|
|
unless can_publish_protocol(protocol) then
|
|
respond_to { |f| f.json { render json: {}, status: :unauthorized } }
|
|
return
|
|
end
|
|
end
|
|
end
|
|
|
|
def check_archive_permissions
|
|
@protocols = Protocol.where(id: params[:protocol_ids])
|
|
@protocols.find_each do |protocol|
|
|
unless can_archive_protocol(protocol) then
|
|
respond_to { |f| f.json { render json: {}, status: :unauthorized } }
|
|
return
|
|
end
|
|
end
|
|
end
|
|
|
|
def check_restore_permissions
|
|
@protocols = Protocol.where(id: params[:protocol_ids])
|
|
@protocols.find_each do |protocol|
|
|
unless can_restore_protocol(protocol) then
|
|
respond_to { |f| f.json { render json: {}, status: :unauthorized } }
|
|
return
|
|
end
|
|
end
|
|
end
|
|
|
|
def check_import_permissions
|
|
@protocol_json = params[:protocol]
|
|
@team = Team.find(params[:team_id])
|
|
@type = params[:type] ? params[:type].to_sym : nil
|
|
if !(
|
|
@protocol_json.present? &&
|
|
@team.present? &&
|
|
(@type == :public || @type == :private) &&
|
|
can_import_protocols(@team)
|
|
)
|
|
render_403
|
|
end
|
|
end
|
|
|
|
def check_export_permissions
|
|
@protocols = Protocol.where(id: params[:protocol_ids])
|
|
if @protocols.blank? || @protocols.any? { |p| !can_export_protocol(p) }
|
|
render_403
|
|
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
|
|
|
|
end
|