scinote-web/app/controllers/protocols_controller.rb

1086 lines
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Ruby
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class ProtocolsController < ApplicationController
include RenamingUtil
include ProtocolsImporter
include ProtocolsExporter
include InputSanitizeHelper
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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,
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:preview,
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: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,
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@type,
current_user
)
}
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
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def linked_children
respond_to do |format|
format.json {
render json: {
title: I18n.t('protocols.index.linked_children.title',
protocol: escape_input(@protocol.name)),
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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
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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,
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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
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,
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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
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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
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 {
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,
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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
)
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)
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 {
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
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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
Activity.create(
type_of: :load_protocol_from_repository,
project: @protocol.my_module.experiment.project,
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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
)
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)
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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 {
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,
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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]
)
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)
flash[:success] = t(
'my_modules.protocols.load_from_file_flash',
)
flash.keep(:success)
format.json {
render json: { status: :ok }, status: :ok
}
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)
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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
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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 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))
# 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
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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,
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@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)),
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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)),
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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
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)),
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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)),
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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
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# :public, :private or :archive
@type = (params[:type] || "public").to_sym
end
def check_view_all_permissions
load_team_and_type
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render_403 unless can_view_team_protocols(@current_team)
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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
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if !can_create_new_protocol(@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(@original) || @type == :archive
render_403
end
end
def check_edit_permissions
load_team_and_type
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@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])
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@type = params[:type] ? params[:type].to_sym : nil
if !(
@protocol_json.present? &&
@team.present? &&
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(@type == :public || @type == :private) &&
can_import_protocols(@team)
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)
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
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end