diff --git a/app/controllers/protocols_controller.rb b/app/controllers/protocols_controller.rb index 62ec530e0..05c55fad1 100644 --- a/app/controllers/protocols_controller.rb +++ b/app/controllers/protocols_controller.rb @@ -600,176 +600,189 @@ class ProtocolsController < ApplicationController end end -def protocolsio_import_create - @protocolsio_too_big=false - file_size=(File.size(params[:json_file].path)) + 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 + 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 {} #if file is too big, default to the js.erb file named the same as this controller - # where a javascript alert is called + 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 - 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 \", they are just " - @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=Hash.new - @import_object["name"]=params["protocol"]["name"] - # since scinote only has description field, while protocols.io has many many others, here i am basically - #putting everything important from protocols.io into description - description_array = [ "before_start","warning","guidelines","manuscript_citation","publish_date","created_on","vendor_name","vendor_link","keywords","tags","link" ] - description_string=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.gsub("_"," ") - description_string=description_string+new_element.to_s+": "+Sanitize.clean(params["protocol"]["created_at"].to_s)+"\n" + 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.gsub("_"," ") - description_string=description_string+new_element.to_s+": " + 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"])+" , " + description_string = + description_string + + Sanitize.clean(tag['tag_name']) + ' , ' end - description_string=description_string+"\n" + 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 + # 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.gsub("_"," ") - description_string=description_string+new_element.to_s+": "+Sanitize.clean(@json_object[element].to_s)+"\n" + 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"]=Hash.new - 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=["1","6","17"] #(simple to map) id 1= step description, id 6= section (title), id 17= expected result - whitelist_complex=["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]=Hash.new - @import_object["steps"][step_pos.to_s]["position"]=step_pos + 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 - if value.class==Hash - key=value - end - end - if whitelist_simple.include?(key["component_type_id"]) + 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="
"+(key["data"])+"
" - if(@import_object["steps"][step_pos.to_s]["description"]) - @import_object["steps"][step_pos.to_s]["description"]<' + 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]["name"]="Step" - end - when "17" - if !key["data"].nil? && key["data"]!="" - - element_string="
Expected result: "+(key["data"])+"
" - @import_object["steps"][step_pos.to_s]["description"]<' + @import_object['steps'][step_pos.to_s]['description'] << element_string - 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) + 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="
Software package: "+(key["source_data"]["name"])+"
Developer: "+(key["source_data"]["developer"])+"
Version: "+(key["source_data"]["version"])+"
Link: "+(key["source_data"]["link"])+"
Repository: "+(key["source_data"]["repository"])+"
OS name , OS version: "+(key["source_data"]["os_name"])+" , "+(key["source_data"]["os_version"]) - @import_object["steps"][step_pos.to_s]["description"]<Link: "+(key["source_data"]["link"]) - @import_object["steps"][step_pos.to_s]["description"]<Description: "+(key["source_data"]["description"])+"
OS name , OS version: "+(key["source_data"]["os_name"])+" , "+(key["source_data"]["os_version"]) - @import_object["steps"][step_pos.to_s]["description"]<Author: "+(key["source_data"]["full_name"])+"
Link: "+(key["source_data"]["link"]) - @import_object["steps"][step_pos.to_s]["description"]<Developer: ' + (key['source_data']['developer']) + '
Version: ' + (key['source_data']['version']) + '
Link: ' + (key['source_data']['link']) + '
Repository: ' + (key['source_data']['repository']) + '
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='
Dataset: ' + (key['source_data']['name']) + '
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 = '
Command: ' + (key['source_data']['name']) + '
Description: ' + (key['source_data']['description']) + '
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 = '
This protocol also contains an attached sub-protocol: ' + (key['source_data']['protocol_name']) + '
Author: ' + (key['source_data']['full_name']) + '
Link: ' + (key['source_data']['link']) + @import_object['steps'][step_pos.to_s]['description'] << element_string - end - #if key["source_data"]["link"]&&key["source_data"]["link"]!="" - #end - when "19" - if(key["source_data"]["body"]&&key["source_data"]["link"]) - element_string="
Safety information: "+(key["source_data"]["body"])+"
Link: "+(key["source_data"]["link"]) - @import_object["steps"][step_pos.to_s]["description"]<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 - end - end #finished step component iteration - - - end #finished looping over step components - end #steps - - protocol = nil - respond_to do |format| + protocol = nil + respond_to do |format| transaction_error = false - #@steps_object=JSON.parse(params["steps"]["steps_object"]) - @protocolsio_general_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 @@ -783,31 +796,25 @@ def protocolsio_import_save end if transaction_error + @protocolsio_general_error = true + # format.json { + # render json: { name: p_name, status: :bad_request }, + # status: :bad_request + # } - @protocolsio_general_error=true - # format.json { - # render json: { name: p_name, status: :bad_request }, status: :bad_request - # } - format.js{} - - #:location => root_url - # protocolsDatatable.ajax.reload(); - # $('#modal-import-json-protocol-preview').modal('hide'); else - @protocolsio_general_error=false + # 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 - }, + render json: + { name: p_name, new_name: protocol.name, status: :ok }, status: :ok } - format.js{} + end + format.js {} end end -end - -# def export # Make a zip output stream and send it to the client respond_to do |format| diff --git a/app/views/protocols/import_export/_import_json_protocol_modal.html.erb b/app/views/protocols/import_export/_import_json_protocol_modal.html.erb index 9caf6750e..cc82e9d53 100644 --- a/app/views/protocols/import_export/_import_json_protocol_modal.html.erb +++ b/app/views/protocols/import_export/_import_json_protocol_modal.html.erb @@ -1,21 +1,29 @@ -