Fix report saving [SCI-3443] (#1753)

* Fix report saving

* Fix the report saving by using the reports' structures

* Remove uneccesary yarn.lock (mistake)

app/assets/javascripts/reports/new.js

@@ -180,7 +180,7 @@ function initializeNewElement(newEl) {
       switch (parent.data("type")) {
         case "experiment":
           url = dh.data("add-experiment-contents-url"); break;
-        case 'my_module' || 'protocol':
+        case 'my_module':
           url = dh.data("add-module-contents-url"); break;
         case "step":
           url = dh.data("add-step-contents-url"); break;

app/controllers/concerns/report_actions.rb

@@ -70,13 +70,6 @@ module ReportActions
   def generate_module_contents_json(my_module)
     res = []
 
-    res << generate_new_el(false)
-    el = generate_el(
-      'reports/elements/my_module_protocol_element.html.erb',
-      protocol: my_module.protocol
-    )
-    res << el
-
     ReportExtends::MODULE_CONTENTS.each do |contents|
       elements = []
       contents.values.each do |element|

app/helpers/reports_helper.rb

@@ -8,7 +8,6 @@ module ReportsHelper
 
   def render_report_element(element, provided_locals = nil)
     # Determine partial
-
     file_name = element.type_of
     if element.type_of.in? ReportExtends::MY_MODULE_CHILDREN_ELEMENTS
       file_name = "my_module_#{element.type_of.singularize}"

app/models/concerns/tiny_mce_images.rb

@@ -27,6 +27,8 @@ module TinyMceImages
           tm_asset_to_update = html_description.css(
             "img[data-mce-token=\"#{Base62.encode(tm_asset.id)}\"]"
           )[0]
+          next unless tm_asset_to_update
+
           tm_asset_to_update.attributes['src'].value = new_tm_asset_src
           description = html_description.css('body').inner_html.to_s
         ensure

app/models/report.rb

@@ -100,6 +100,7 @@ class Report < ApplicationRecord
       exp.my_modules.each do |my_module|
         module_children = []
 
+        module_children += gen_element_content(my_module, nil, 'my_module_protocol', true)
         my_module.protocol.steps.each do |step|
           step_children =
             gen_element_content(step, step.assets, 'step_asset')

app/views/reports/elements/_my_module_protocol_element.html.erb

@@ -1,5 +1,5 @@
-
-<div class="report-element report-module-protocol-element" data-ts="<%= protocol.created_at %>" data-type="protocol" data-id='{ "protocol_id": <%= protocol.id %> }' data-scroll-id="<%= protocol.id %>">
+<% protocol ||= my_module.protocol %>
+<div class="report-element report-module-protocol-element" data-ts="<%= protocol.created_at %>" data-type="my_module_protocol" data-id='{ "my_module_id": <%= my_module.id %> }' data-scroll-id="<%= protocol.id %>">
   <div class="report-element-header">
     <div class="row">
       <div class="pull-left user-time">
@@ -18,4 +18,5 @@
         <em><%= t('my_modules.protocols.protocol_status_bar.no_description') %></em>
       <% end %>
     </div>
+  </div>
 </div>

app/views/reports/new/modal/_module_contents_inner.html.erb

@@ -1,5 +1,4 @@
 <% my_module_undefined = !defined? my_module or my_module.blank? %>
-
 <div>
   <em>
     <%= t("projects.reports.elements.modals.module_contents_inner.instructions") %>
@@ -12,6 +11,10 @@
       <%= form.check_box :module_all, label: t("projects.reports.elements.modals.module_contents_inner.check_all") %>
       <ul>
 
+        <li>
+          <%= form.check_box :module_protocol, label: t("projects.reports.elements.modals.module_contents_inner.protocol") %>
+        </li>
+
         <% if my_module_undefined or my_module.protocol.steps.exists? %>
           <li>
             <%= form.check_box :module_steps, label: t("projects.reports.elements.modals.module_contents_inner.steps") %>

config/initializers/extends.rb

@@ -38,7 +38,8 @@ class Extends
                            project_samples: 14, # TODO
                            experiment: 15,
                            # Higher number because of addons
-                           my_module_repository: 17 }
+                           my_module_repository: 17,
+                           my_module_protocol: 18 }
 
   # Data type name should match corresponding model's name
   REPOSITORY_DATA_TYPES = { RepositoryTextValue: 0,

config/initializers/extends/report_extends.rb

@@ -59,6 +59,10 @@ module ReportExtends
 
   # Module contents element
   MODULE_CONTENTS = [
+    ModuleElement.new([:protocol],
+                      :protocol,
+                      false,
+                      [:my_module]),
     ModuleElement.new(%i(completed_steps uncompleted_steps),
                       :steps,
                       true,
@@ -114,6 +118,7 @@ module ReportExtends
                        result_comments)
   # sets local :my_module to the listed my_module child elements
   MY_MODULE_ELEMENTS = %w(my_module
+                          my_module_protocol
                           my_module_activity
                           my_module_repository)
 
@@ -153,6 +158,7 @@ module ReportExtends
     ElementReference.new(
       proc do |report_element|
         report_element.my_module? ||
+          report_element.my_module_protocol? ||
           report_element.my_module_activity? ||
           report_element.my_module_samples?
       end,
@@ -198,6 +204,7 @@ module ReportExtends
     ElementReference.new(
       proc do |report_element|
         report_element.my_module? ||
+          report_element.my_module_protocol? ||
           report_element.my_module_activity? ||
           report_element.my_module_samples?
       end,

config/locales/en.yml

@@ -410,6 +410,7 @@ en:
           module_contents_inner:
             instructions: "Select the information from your task that you would like to include to your report."
             check_all: "All tasks content"
+            protocol: "Protocol"
             steps: "Steps"
             completed_steps: "Completed"
             uncompleted_steps: "Uncompleted"