Merge pull request #1000 from Zanz2/null_step_crash_sci2043

Fixed big crash that was caused by invalid or null step hash in protocol [SCI-2043]

app/controllers/protocols_controller.rb

@@ -640,10 +640,11 @@ class ProtocolsController < ApplicationController
       return 0 # return 0 stops the rest of the controller code from executing
     end
     @json_object = JSON.parse(json_file_contents)
-
-    @json_object['steps'] = protocols_io_guid_reorder_step_json(
-      @json_object['steps']
-    )
+    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|
@@ -658,23 +659,26 @@ class ProtocolsController < ApplicationController
     @db_json = {}
     @toolong = false
     @db_json['name'] = pio_eval_title_len(
-      sanitize_input(params['protocol']['name'])
+      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(
-      sanitize_input(params['protocol']['authors'])
+      sanitize_input(not_null(params['protocol']['authors']))
     )
     @db_json['created_at'] = pio_eval_title_len(
-      sanitize_input(params['protocol']['created_at'])
+      sanitize_input(not_null(params['protocol']['created_at']))
     )
     @db_json['updated_at'] = pio_eval_title_len(
-      sanitize_input(params['protocol']['last_modified'])
+      sanitize_input(not_null(params['protocol']['last_modified']))
     )
     @db_json['steps'] = {}
-    @db_json['steps'] = protocols_io_fill_step(
-      @json_object, @db_json['steps']
-    )
+
+    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

app/helpers/protocols_io_helper.rb

@@ -102,6 +102,8 @@ module ProtocolsIoHelper
         @toolong = true
       end
       text
+    else
+      ''
     end
   end
 
@@ -128,6 +130,8 @@ module ProtocolsIoHelper
         @remaining -= text.length - reserved
       end
       text
+    else
+      ''
     end
   end
 
@@ -145,10 +149,15 @@ module ProtocolsIoHelper
     Nokogiri::HTML::DocumentFragment.parse(text).to_html
   end
 
+  def step_hash_null?(step_json)
+    step_json.dig(0, 'components', 0, 'component_type_id').nil?
+  end
+
   # Images are allowed in:
   # Step: description, expected result
   # Protocol description : description before_start warning
   # guidelines manuscript_citation
+
   def prepare_for_view(
     attribute_text1, size, table = 'no_table', image_allowed = false
   )
@@ -321,9 +330,12 @@ module ProtocolsIoHelper
   end
 
   def protocols_io_guid_reorder_step_json(unordered_step_json)
+    return '' if unordered_step_json.blank?
     base_step = unordered_step_json.find { |step| step['previous_guid'].nil? }
     return unordered_step_json if base_step.nil?
     number_of_steps = unordered_step_json.size
+    return unordered_step_json if number_of_steps == 1
+    base_step = unordered_step_json.find { |step| step['previous_guid'].nil? }
     step_order = []
     step_counter = 0
     step_order[step_counter] = base_step

app/views/protocols/import_export/_import_json_protocol_preview_modal.html.erb

@@ -30,7 +30,7 @@
 
           <label><%= t('protocols.import_export.import_modal.name_label') %></label>
 
-          <%= f.text_field :name, :value => pio_eval_title_len(sanitize_input(@json_object['protocol_name'])), class:
+          <%= f.text_field :name, :value => pio_eval_title_len(sanitize_input(not_null(@json_object['protocol_name']))), class:
           "form-control" %>
         </div>
         <div class="form-group">
@@ -52,14 +52,14 @@
             <div class="col-xs-4">
               <label><%= t('protocols.import_export.import_modal.created_at_label') %></label>
 
-              <% display_created_at=Time.at(@json_object['created_on'].to_i) %>
+              <% display_created_at=Time.at(not_null(@json_object['created_on']).to_i) %>
               <%= f.text_field :created_at, :value => display_created_at.to_s,
               readonly: true, class: "form-control" %>
             </div>
             <div class="col-xs-4">
               <label><%= t('protocols.import_export.import_modal.updated_at_label') %></label>
 
-              <% display_last_modified=Time.at(@json_object['last_modified'].to_i) %>
+              <% display_last_modified=Time.at(not_null(@json_object['last_modified']).to_i) %>
               <%= f.text_field :last_modified, :value =>
               display_last_modified.to_s,readonly: true, class:
               "form-control" %>

app/views/protocols/import_export/_import_json_protocol_s_desc.html.erb

@@ -40,13 +40,13 @@
             <br>
             <% case key['component_type_id']
             when '1' %>
-              <% step_info_string += (key['data']) %>
+              <% step_info_string += not_null(key['data']) %>
               <br>
               <strong><%= t('protocols.protocols_io_import.preview.strng_s_desc') %></strong>
               <%= prepare_for_view(key['data'],ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL,'table',true).html_safe %>
               <br>
             <% when '17' %>
-              <% step_info_string += (key['data']) %>
+              <% step_info_string += not_null(key['data']) %>
               <br>
               <strong><%= t('protocols.protocols_io_import.preview.s_exp_res') %></strong>
               <%= prepare_for_view(key['data'],ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL,'table',true).html_safe %>