diff --git a/app/controllers/protocols_controller.rb b/app/controllers/protocols_controller.rb
index b0cf788d5..3c3e2cd5d 100644
--- a/app/controllers/protocols_controller.rb
+++ b/app/controllers/protocols_controller.rb
@@ -651,7 +651,7 @@ class ProtocolsController < ApplicationController
end
description_string += "\n"
# Since protocols description field doesnt show html,i just remove it
- # because its even messier
+ # because its even messier (using Sanitize)
# what this does is basically appends "FIELD NAME: "+" FIELD VALUE"
# to description for various fields
elsif @json_object[e] && @json_object[e] != ''
@@ -680,7 +680,6 @@ class ProtocolsController < ApplicationController
# id 20= regents (materials, like scinote samples kind of)
@json_object['steps'].each do |step| # loop over steps
pos += 1 # position of step (first, second.... etc),
- # started at -1 so index is 0
@db_json['steps'][pos.to_s] = {} # the json we will insert into db
@db_json['steps'][pos.to_s]['position'] = pos
step['components'].each do |key, value|
@@ -691,99 +690,41 @@ class ProtocolsController < ApplicationController
# append is the string that we append values into for description
case key['component_type_id']
when '1'
- if !key['data'].nil? && key['data'] != '' &&
- @db_json['steps'][pos.to_s]['description']
- append = '
' + (key['data']) + '
'
- @db_json['steps'][pos.to_s]['description'] << append
- elsif !@db_json['steps'][pos.to_s]['description']
- append = '
' + (key['data']) + '
'
- @db_json['steps'][pos.to_s]['description'] = append
- else
- @db_json['steps'][pos.to_s]['description'] = 'Description missing'
- end
+ @db_json = protocolsio_step_description_populate(@db_json, key, pos)
when '6'
- if !key['data'].nil? && key['data'] != ''
- @db_json['steps'][pos.to_s]['name'] = key['data']
- else
- @db_json['steps'][pos.to_s]['name'] = 'Step'
- end
+ @db_json = protocolsio_step_title_populate(@db_json, key, pos)
when '17'
- if !key['data'].nil? && key['data'] != ''
- append = '
Expected result: '
- + key['data'] + '
'
- @db_json['steps'][pos.to_s]['description'] << append
-
- end
+ @db_json = protocolsio_step_expected_result_populate(
+ @db_json, key, pos
+ )
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']
- append = '
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']
- @db_json['steps'][pos.to_s]['description'] << append
- end
+ @db_json = protocolsio_step_software_package_populate(
+ @db_json, key, pos
+ )
when '9'
- if key['source_data']['name'] && key['source_data']['link']
- append = '
Dataset: ' +
- key['source_data']['name'] + '
Link: ' +
- key['source_data']['link']
- @db_json['steps'][pos.to_s]['description'] << append
- end
+ @db_json = protocolsio_step_dataset_populate(@db_json, key, pos)
when '15'
- if key['source_data']['name'] &&
- key['source_data']['description'] &&
- key['source_data']['os_name'] &&
- key['source_data']['os_version']
- append = '
Command: ' +
- key['source_data']['name'] +
- '
Description: ' + key['source_data']['description'] +
- '
OS name , OS version: ' +
- key['source_data']['os_name'] +
- ' , ' + key['source_data']['os_version']
- @db_json['steps'][pos.to_s]['description'] << append
- end
+ @db_json = protocolsio_step_command_populate(@db_json, key, pos)
when '18'
- if key['source_data']['protocol_name'] &&
- key['source_data']['full_name'] &&
- key['source_data']['link']
- append = '
This protocol also contains an' +
- ' attached sub-protocol: ' +
- key['source_data']['protocol_name'] + '
Author: ' +
- key['source_data']['full_name'] + '
Link: ' +
- key['source_data']['link']
- @db_json['steps'][pos.to_s]['description'] << append
-
- end
+ @db_json = protocolsio_step_attached_sub_protocol_populate(
+ @db_json, key, pos
+ )
when '19'
- if key['source_data']['body'] && key['source_data']['link']
- append = '
Safety information: ' +
- key['source_data']['body'] +
- '
Link: ' + key['source_data']['link']
- @db_json['steps'][pos.to_s]['description'] << append
- end
- # when '20' placeholder za materiale
+ @db_json = protocolsio_step_safety_information_populate(
+ @db_json, key, pos
+ )
end
- end # finished step component iteration
+ end # finished step component case iteration
end # finished looping over step components
end # steps
-
protocol = nil
respond_to do |format|
transaction_error = false
@@ -798,21 +739,18 @@ class ProtocolsController < ApplicationController
raise ActiveRecord:: Rollback
end
end
-
p_name =
if @db_json['name'].present? && !@db_json['name'].empty?
escape_input(@db_json['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
@@ -825,7 +763,15 @@ class ProtocolsController < ApplicationController
format.js {}
end
end
-
+ # epic posodob, success window, upload window
+ # validacije (protocols.io file test), mogoc lahk kdo kej zrusi
+ # excel posodob v epicu in napis da datumi ne grejo
+ # bug no description report
+ # epic napis da datumi grejo v description, datumi pr scinotu so generirani
+ # sortiri buge problem etc da se ve kaj je kaj v dokumentaciji
+ # v excel napis kaj vse od atributov in rtf formata od protocols.io se ne mapira
+ # opis dummy info v protocols io
+ # vse v svoj epik dej
def export
# Make a zip output stream and send it to the client
respond_to do |format|
@@ -1054,6 +1000,116 @@ class ProtocolsController < ApplicationController
private
+ def protocolsio_step_description_populate(result, iterating_key, pos2)
+ if !iterating_key['data'].nil? && iterating_key['data'] != '' &&
+ result['steps'][pos2.to_s]['description']
+ append = '
' + iterating_key['data'] + '
'
+ result['steps'][pos2.to_s]['description'] << append
+ elsif !result['steps'][pos2.to_s]['description']
+ append = '
' + iterating_key['data'] + '
'
+ result['steps'][pos2.to_s]['description'] = append
+ else
+ result['steps'][pos2.to_s]['description'] = 'Description missing'
+ end
+ result
+ end
+
+ def protocolsio_step_title_populate(result, iterating_key, pos2)
+ result['steps'][pos2.to_s]['name'] =
+ if !iterating_key['data'].nil? && iterating_key['data'] != ''
+ iterating_key['data']
+ else
+ 'Step'
+ end
+ result
+ end
+
+ def protocolsio_step_expected_result_populate(result, iterating_key, pos2)
+ if !iterating_key['data'].nil? && iterating_key['data'] != ''
+ append = '
Expected result: '
+ + iterating_key['data'] + '
'
+ result['steps'][pos2.to_s]['description'] << append
+ end
+ result
+ end
+
+ def protocolsio_step_software_package_populate(result, iterating_key, pos2)
+ if iterating_key['source_data']['name'] &&
+ iterating_key['source_data']['developer'] &&
+ iterating_key['source_data']['version'] &&
+ iterating_key['source_data']['link'] &&
+ iterating_key['source_data']['repository'] &&
+ iterating_key['source_data']['os_name'] &&
+ iterating_key['source_data']['os_version']
+ append = '
Software package: ' +
+ iterating_key['source_data']['name'] + '
Developer: ' +
+ iterating_key['source_data']['developer'] + '
Version: ' +
+ iterating_key['source_data']['version'] + '
Link: ' +
+ iterating_key['source_data']['link'] + '
Repository: ' +
+ iterating_key['source_data']['repository'] +
+ '
OS name , OS version: ' +
+ iterating_key['source_data']['os_name'] + ' , ' +
+ iterating_key['source_data']['os_version']
+ result['steps'][pos2.to_s]['description'] << append
+ end
+ result
+ end
+
+ def protocolsio_step_dataset_populate(result, iterating_key, pos2)
+ if iterating_key['source_data']['name'] &&
+ iterating_key['source_data']['link']
+ append = '
Dataset: ' +
+ iterating_key['source_data']['name'] + '
Link: ' +
+ iterating_key['source_data']['link']
+ result['steps'][pos2.to_s]['description'] << append
+ end
+ result
+ end
+
+ def protocolsio_step_command_populate(result, iterating_key, pos2)
+ if iterating_key['source_data']['name'] &&
+ iterating_key['source_data']['description'] &&
+ iterating_key['source_data']['os_name'] &&
+ iterating_key['source_data']['os_version']
+ append = '
Command: ' +
+ iterating_key['source_data']['name'] +
+ '
Description: ' +
+ iterating_key['source_data']['description'] +
+ '
OS name , OS version: ' +
+ iterating_key['source_data']['os_name'] +
+ ' , ' + iterating_key['source_data']['os_version']
+ result['steps'][pos2.to_s]['description'] << append
+ end
+ result
+ end
+
+ def protocolsio_step_attached_sub_protocol_populate(
+ result, iterating_key, pos2
+ )
+ if iterating_key['source_data']['protocol_name'] &&
+ iterating_key['source_data']['full_name'] &&
+ iterating_key['source_data']['link']
+ append = '
This protocol also contains an' +
+ ' attached sub-protocol: ' +
+ iterating_key['source_data']['protocol_name'] + '
Author: ' +
+ iterating_key['source_data']['full_name'] + '
Link: ' +
+ iterating_key['source_data']['link']
+ result['steps'][pos2.to_s]['description'] << append
+ end
+ result
+ end
+
+ def protocolsio_step_safety_information_populate(result, iterating_key, pos2)
+ if iterating_key['source_data']['body'] &&
+ iterating_key['source_data']['link']
+ append = '
Safety information: ' +
+ iterating_key['source_data']['body'] +
+ '
Link: ' + iterating_key['source_data']['link']
+ result['steps'][pos2.to_s]['description'] << append
+ end
+ result
+ end
+
def move_protocol(action)
rollbacked = false
results = []
diff --git a/app/views/protocols/import_export/_import_json_protocol_preview_modal.html.erb b/app/views/protocols/import_export/_import_json_protocol_preview_modal.html.erb
index 576031575..ab75bf9e5 100644
--- a/app/views/protocols/import_export/_import_json_protocol_preview_modal.html.erb
+++ b/app/views/protocols/import_export/_import_json_protocol_preview_modal.html.erb
@@ -47,8 +47,7 @@ CGI.parse(URI.parse(request.referrer).query).fetch("type") %>
<% display_created_at=Time.at(@json_object['created_on'].to_i) %>
- <%= f.text_field :created_at, :value => display_created_at.to_s+"(Protocols.io
- value)",readonly: true, class: "form-control" %>
+ <%= f.text_field :created_at, :value => display_created_at.to_s+"(Protocols.io value)",readonly: true, class: "form-control" %>
@@ -159,7 +158,7 @@ CGI.parse(URI.parse(request.referrer).query).fetch("type") %>
key["data"] %>
<% case key["component_type_id"]
- when "1" %>
+ when "1" %>
Description: