From 2834edb2861d78418ce4032b4a8be040519d9907 Mon Sep 17 00:00:00 2001
From: Jure Grabnar <jgrabnar@biosistemika.com>
Date: Fri, 23 Nov 2018 20:13:34 +0100
Subject: [PATCH] Add command/subprotocol/safety for PIO

---
 app/helpers/protocols_io_helper.rb            | 12 +++----
 .../_import_json_protocol_s_desc.html.erb     | 32 +++++++++----------
 config/locales/en.yml                         | 14 ++++----
 3 files changed, 30 insertions(+), 28 deletions(-)

diff --git a/app/helpers/protocols_io_helper.rb b/app/helpers/protocols_io_helper.rb
index 50fb921b2..7ea8c58c3 100644
--- a/app/helpers/protocols_io_helper.rb
+++ b/app/helpers/protocols_io_helper.rb
@@ -467,21 +467,21 @@ module ProtocolsIoHelper
           pe_array = %w(
             name description os_name os_version
           )
-          key['source_data']['name'] =
+          key['source']['name'] =
             '<pre><code>' +
-            not_null(key['source_data']['name'].gsub(/\n/, '<br>')) +
+            not_null(key['source']['name'].gsub(/\n/, '<br>')) +
             '</code></pre>'
           trans_text = 'protocols.protocols_io_import.comp_append.command.'
           newj[i.to_s]['description'] += pio_stp(
-            key['source_data'], pe_array, trans_text
+            key['source'], pe_array, trans_text
           )
         when 18
           pe_array = %w(
-            protocol_name full_name link
+            title title_html uri
           )
           trans_text = 'protocols.protocols_io_import.comp_append.sub_protocol.'
           newj[i.to_s]['description'] += pio_stp(
-            key['source_data'], pe_array, trans_text
+            key['source'], pe_array, trans_text
           )
         when 19
           pe_array = %w(
@@ -489,7 +489,7 @@ module ProtocolsIoHelper
           )
           trans_text = 'protocols.protocols_io_import.comp_append.safety_infor.'
           newj[i.to_s]['description'] += pio_stp(
-            key['source_data'], pe_array, trans_text
+            key['source'], pe_array, trans_text
           )
         end # case end
       end # finished looping over step components
diff --git a/app/views/protocols/import_export/_import_json_protocol_s_desc.html.erb b/app/views/protocols/import_export/_import_json_protocol_s_desc.html.erb
index f6777d242..8ce9075a0 100644
--- a/app/views/protocols/import_export/_import_json_protocol_s_desc.html.erb
+++ b/app/views/protocols/import_export/_import_json_protocol_s_desc.html.erb
@@ -85,43 +85,43 @@
             <% when 9 %>
               <% step_info_string += not_null(key['source']['name']).html_safe %>
               <br>
-              <%= t('protocols.protocols_io_import.preview.dataset_name') %>
+              <%= t('protocols.protocols_io_import.preview.dataset_name').html_safe %>
               <%= prepare_for_view(key['source']['name'],ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL,'table').html_safe %>
               <br>
               <%= t('protocols.protocols_io_import.preview.s_link') %>
               <%= prepare_for_view(key['source']['link'],ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL,'table').html_safe %>
             <% when 15 %>
-              <% step_info_string += not_null(key['source_data']['description']) %>
+              <% step_info_string += not_null(key['source']['description']) %>
               <br>
-              <strong><%= key['name']+': ' %></strong>
-              <%= prepare_for_view('<pre><code>'+key['source_data']['name'].gsub(/\n/, '<br>')+'</code></pre>',ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL,'table').html_safe %>
+              <%= t('protocols.protocols_io_import.preview.command_name').html_safe %>
+              <%= prepare_for_view('<pre><code>'+key['source']['name'].gsub(/\n/, '<br>')+'</code></pre>',ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL,'table').html_safe %>
               <br>
               <%= t('protocols.protocols_io_import.preview.s_desc') %>
-              <%= prepare_for_view(key['source_data']['description'],ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL,'table').html_safe %>
+              <%= prepare_for_view(key['source']['description'],ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL,'table').html_safe %>
               <br>
               <%= t('protocols.protocols_io_import.preview.os') %>
-              <%= prepare_for_view(key['source_data']['os_name'],ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL,'table').html_safe + ' , ' +
-              prepare_for_view(key['source_data']['os_version'],ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL,'table').html_safe %>
+              <%= prepare_for_view(key['source']['os_name'],ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL,'table').html_safe + ' , ' +
+              prepare_for_view(key['source']['os_version'],ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL,'table').html_safe %>
             <% when 18 %>
               <br>
-              <strong><%= t('protocols.protocols_io_import.preview.sub_prot') %></strong>
-              <%= pio_eval_title_len(sanitize_input(key['source_data']['protocol_name'])).html_safe %>
+              <%= t('protocols.protocols_io_import.preview.sub_prot').html_safe %>
+              <%= pio_eval_title_len(sanitize_input(key['source']['title'])).html_safe %>
               <br>
               <%= t('protocols.protocols_io_import.preview.auth') %>
-              <%= prepare_for_view(key['source_data']['full_name'],ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL,'table').html_safe %>
+              <%= prepare_for_view(key['source']['title_html'],ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL,'table').html_safe %>
               <br>
-              <% if key['source_data']['link'].present? %>
+              <% if key['source']['uri'].present? %>
                 <%= t('protocols.protocols_io_import.preview.s_nobr_link') %>
-                <%= prepare_for_view(key['source_data']['link'],ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL,'table').html_safe %>
+                <%= prepare_for_view(key['source']['uri'],ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL,'table').html_safe %>
               <% end %>
             <% when 19 %>
-              <% step_info_string += not_null(key['source_data']['body']) %>
+              <% step_info_string += not_null(key['source']['body']) %>
               <br>
-              <strong><%= not_null(key['name'])+': ' %></strong>
-              <%= prepare_for_view(key['source_data']['body'],ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL,'table').html_safe %>
+              <%= t('protocols.protocols_io_import.preview.safety_info').html_safe %>
+              <%= prepare_for_view(key['source']['body'],ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL,'table').html_safe %>
               <br>
               <%= t('protocols.protocols_io_import.preview.s_link') %>
-              <%= prepare_for_view(key['source_data']['link'],ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL,'table').html_safe %>
+              <%= prepare_for_view(key['source']['link'],ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL,'table').html_safe %>
             <% else %>
             <% end #case if%>
           <% end #inner if%>
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 3cd8cd5e5..649788181 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -1547,14 +1547,16 @@ en:
         s_desc: "Description:"
         strng_s_desc: "Description:"
         s_exp_res: "Expected result:"
-        sw_name: "Software package:"
+        sw_name: "<strong>Software package:</strong>"
         dev: "Developer:"
         vers: "Version:"
         repo: "Repository:"
         os: "OS name , OS version:"
-        sub_prot: "This protocol also contains an attached sub-protocol:"
+        command_name: "<strong>Command:</strong>"
+        sub_prot: "<strong>This protocol also contains an attached sub-protocol:</strong>"
+        safety_info: "<strong>Safety information:</strong>"
         auth: "Author:"
-        dataset_name: "Dataset:"
+        dataset_name: "<strong>Dataset:</strong>"
         manuscript_citation: "Manuscript citation:"
         published_on: "Publish date:"
         vendor_name: "Vendor name:"
@@ -1582,9 +1584,9 @@ en:
           description: "<br>Description: "
           os: "<br>OS name , OS version: "
         sub_protocol:
-          protocol_name: "<br><strong>This step also contains an attached sub-protocol: </strong>"
-          full_name: "<br>Author: "
-          link: "<br>Link: "
+          title: "<br><strong>This step also contains an attached sub-protocol: </strong>"
+          title_html: "<br>Author: "
+          uri: "<br>Link: "
         safety_infor:
           body: "<br><strong>Safety information: </strong>"
           link: "<br>Link: "