Merge branch 'features/bioeddie-integration' into ma_SCI_5879

app/assets/javascripts/sitewide/bio_eddie.js

@@ -132,6 +132,7 @@ var bioEddieEditor = (function() {
       bioEddieModal.data('update-url', updateUrl);
       bioEddieModal.find('.file-name input').val(name);
       bioEddieModal.modal('show');
+
     }
   };
 }());
@@ -152,5 +153,6 @@ var bioEddieEditor = (function() {
       this.dataset.moleculeDescription,
       this.dataset.updateUrl
     );
+    $.post(this.dataset.editUrl);
   });
 }());

app/controllers/bio_eddie_assets_controller.rb

@@ -1,6 +1,7 @@
 # frozen_string_literal: true
 
 class BioEddieAssetsController < ApplicationController
+  include BioEddieActions
   include ActiveStorage::SetCurrent
 
   before_action :load_vars, except: :create
@@ -12,6 +13,8 @@ class BioEddieAssetsController < ApplicationController
   def create
     asset = BioEddieService.create_molecule(bio_eddie_params, current_user, current_team)
 
+    create_create_bio_eddie_activity(asset, current_user)
+
     if asset && bio_eddie_params[:object_type] == 'Step'
       render json: {
         html: render_to_string(partial: 'assets/asset.html.erb', locals: {
@@ -29,6 +32,8 @@ class BioEddieAssetsController < ApplicationController
   def update
     asset = BioEddieService.update_molecule(bio_eddie_params, current_user, current_team)
 
+    create_edit_bio_eddie_activity(asset, current_user, :finish_editing)
+
     if asset
       render json: { url: rails_representation_url(asset.medium_preview),
                      id: asset.id,
@@ -39,7 +44,7 @@ class BioEddieAssetsController < ApplicationController
   end
 
   def start_editing
-    # Activity here
+    create_edit_bio_eddie_activity(@asset, current_user, :start_editing)
   end
 
   private

app/controllers/concerns/bio_eddie_actions.rb

@@ -0,0 +1,105 @@
+# frozen_string_literal: true
+
+module BioEddieActions
+  extend ActiveSupport::Concern
+
+  private
+
+  def create_edit_bio_eddie_activity(asset, current_user, started_editing)
+    action = case started_editing
+             when :start_editing
+               t('activities.file_editing.started')
+             when :finish_editing
+               t('activities.file_editing.finished')
+             end
+    return unless bio_eddie_asset_validation(asset)
+
+    bio_eddie_find_target_object(asset, current_user, 'edit', action)
+  end
+
+  def create_create_bio_eddie_activity(asset, current_user)
+    return unless bio_eddie_asset_validation(asset)
+
+    bio_eddie_find_target_object(asset, current_user, 'create')
+  end
+
+  def create_delete_bio_eddie_activity(asset, current_user)
+    return unless bio_eddie_asset_validation(asset)
+
+    bio_eddie_find_target_object(asset, current_user, 'delete')
+  end
+
+  def bio_eddie_asset_validation(asset)
+    asset && asset.file.metadata[:asset_type] == 'bio_eddie'
+  end
+
+  def bio_eddie_asset_type(asset, klass)
+    return true if asset.step_asset&.step.instance_of?(klass)
+    return true if asset.result_asset&.result.instance_of?(klass)
+
+    false
+  end
+
+  def bio_eddie_find_target_object(asset, current_user, activity_type, action = nil)
+    if bio_eddie_asset_type(asset, Step)
+      bio_eddie_step_activity(asset, current_user, activity_type, action)
+    elsif bio_eddie_asset_type(asset, Result)
+      bio_eddie_result_activity(asset, current_user, activity_type, action)
+    end
+  end
+
+  def bio_eddie_step_activity(asset, current_user, activity, action = nil)
+    step = asset.step_asset&.step
+    asset_type = 'asset_name'
+    protocol = step&.protocol
+
+    return unless step && protocol
+
+    default_step_items =
+      { step: step.id,
+        step_position: { id: step.id, value_for: 'position_plus_one' },
+        asset_type => { id: asset.id, value_for: 'file_name' } }
+
+    default_step_items[:action] = action if action
+    if protocol.in_module?
+      project = protocol.my_module.experiment.project
+      team = project.team
+      type_of = "#{activity}_molecule_on_step".to_sym
+      message_items = { my_module: protocol.my_module.id }
+    else
+      type_of = "#{activity}_molecule_on_step_in_repository".to_sym
+      team = protocol.team
+      message_items = { protocol: protocol.id }
+    end
+    message_items = default_step_items.merge(message_items)
+    Activities::CreateActivityService
+      .call(activity_type: type_of,
+            owner: current_user,
+            subject: protocol,
+            team: team,
+            project: project,
+            message_items: message_items)
+  end
+
+  def bio_eddie_result_activity(asset, current_user, activity, action = nil)
+    result = asset.result_asset&.result
+    asset_type = 'asset_name'
+    my_module = result&.my_module
+
+    return unless result && my_module
+
+    message_items = {
+      result: result.id,
+      asset_type => { id: asset.id, value_for: 'file_name' }
+    }
+
+    message_items[:action] = action if action
+    Activities::CreateActivityService
+      .call(activity_type: "#{activity}_molecule_on_step_on_result".to_sym,
+            owner: current_user,
+            subject: result,
+            team: my_module.experiment.project.team,
+            project: my_module.experiment.project,
+            message_items: message_items)
+  end
+end

app/controllers/steps_controller.rb

@@ -533,6 +533,10 @@ class StepsController < ApplicationController
       marvin_js_assets_attributes: %i(
         id
         _destroy
+      ),
+       bio_eddie_assets_attributes: %i(
+        id
+        _destroy
       )
     )
   end

app/services/bio_eddie_service.rb

@@ -6,8 +6,8 @@ class BioEddieService
       ApplicationSettings.instance.values['bio_eddie_url']
     end
 
-    def enabled?
-      url.present?
+    def enabled?(current_user)
+      url.present? && current_user.settings.fetch('bio_eddie_enabled', false)
     end
 
     def create_molecule(params, current_user, current_team)

app/views/assets/bio_eddie/_create_bio_eddie_li.html.erb

@@ -1,11 +1,13 @@
-<li>
-  <a
-    class="new-bio-eddie-upload-button"
-    data-object-id="<%= element_id %>"
-    data-object-type="<%= element_type %>"
-    data-assets-container="<%= assets_container %>"
-  >
-    <%= image_tag 'icon_small/bio_eddie.png' %>
-    <%= t('bio_eddie.new_button') %>
-  </a>
-</li>
+<% if BioEddieService.enabled?(current_user) %>
+  <li>
+    <a
+      class="new-bio-eddie-upload-button"
+      data-object-id="<%= element_id %>"
+      data-object-type="<%= element_type %>"
+      data-assets-container="<%= assets_container %>"
+    >
+      <%= image_tag 'icon_small/bio_eddie.png' %>
+      <%= t('bio_eddie.new_button') %>
+    </a>
+  </li>
+<% end %>

app/views/shared/_bio_eddie_modal.html.erb

@@ -1,4 +1,4 @@
-<% if BioEddieService.enabled? %>
+<% if BioEddieService.enabled?(current_user) %>
   <div id="bioEddieModal"
        class="modal modal-bio-eddie"
        role="dialog"

app/views/shared/file_preview/_content.html.erb

@@ -21,10 +21,11 @@
           <span class="fas fa-pencil-alt"></span>
           <%= t('assets.file_preview.edit_in_marvinjs') %>
         </button>
-      <% elsif asset.file.metadata[:asset_type] == 'bio_eddie' %>
+      <% elsif asset.file.metadata[:asset_type] == 'bio_eddie' && BioEddieService.enabled?(current_user) %>
         <button class="btn btn-light bio-eddie-edit-button"
           data-molecule-id="<%= asset.id %>"
           data-update-url="<%= bio_eddie_asset_path(asset) %>"
+          data-edit-url="<%= start_editing_bio_eddie_asset_path(asset) %>"
           data-molecule-name="<%= asset.file.metadata[:name] %>"
           data-molecule-description="<%= asset.file.metadata[:description] %>"
         >

config/initializers/extends.rb

@@ -316,21 +316,30 @@ class Extends
     delete_project_folder: 162,
     generate_pdf_report: 163,
     generate_docx_report: 164,
+    edit_molecule_on_step: 168,
+    edit_molecule_on_result: 169,
+    edit_molecule_on_step_in_repository: 170,
+    create_molecule_on_step: 171,
+    create_molecule_on_result: 172,
+    create_molecule_on_step_in_repository: 173,
+    delete_molecule_on_step: 174,
+    delete_molecule_on_result: 175,
+    delete_molecule_on_step_in_repository: 176,
     register_molecule: 165
   }
 
   ACTIVITY_GROUPS = {
     projects: [*0..7, 32, 33, 34, 95, 108, 65, 109, *158..162],
-    task_results: [23, 26, 25, 42, 24, 40, 41, 99, 110, 122, 116, 128],
+    task_results: [23, 26, 25, 42, 24, 40, 41, 99, 110, 122, 116, 128, 169, 172, 175],
     task: [8, 58, 9, 59, *10..14, 35, 36, 37, 53, 54, *60..63, 138, 139, 140, 64, 66, 106, 126, 120, 132,
-           *146..148],
+           *146..148, 168, 171, 174],
     task_protocol: [15, 22, 16, 18, 19, 20, 21, 17, 38, 39, 100, 111, 45, 46, 47, 121, 124, 115, 118, 127, 130, 137],
     task_inventory: [55, 56, 146, 147],
     experiment: [*27..31, 57],
     reports: [48, 50, 49, 163, 164],
     inventories: [70, 71, 105, 144, 145, 72, 73, 74, 102, 142, 143, 75, 76, 77, 78, 96, 107, 113, 114, *133..136],
     protocol_repository: [80, 103, 89, 87, 79, 90, 91, 88, 85, 86, 84, 81, 82,
-                          83, 101, 112, 123, 125, 117, 119, 129, 131],
+                          83, 101, 112, 123, 125, 117, 119, 129, 131, 170, 173, 176],
     team: [92, 94, 93, 97, 104]
   }
 

config/locales/global_activities/en.yml

@@ -184,6 +184,16 @@ en:
       move_project_folder_html: "%{user} moved folder %{project_folder} from folder %{project_folder_from}</strong> to folder %{project_folder_to}."
       generate_pdf_report_html: "%{user} generated PDF report %{report}."
       generate_docx_report_html: "%{user} generated DOCX report %{report}."
+      edit_molecule_on_step_html: "%{user} edited molecule %{asset_name} on protocol's step %{step_position} %{step} on task %{my_module}: %{action}."
+      edit_molecule_on_result_html: "%{user} edited molecule %{asset_name} on result %{result}: %{action}."
+      edit_molecule_on_step_in_repository_html: "%{user} edited molecule %{asset_name} on protocol %{protocol}'s step %{step_position} %{step}: %{action}."
+      create_molecule_on_step_html: "%{user} created molecule %{asset_name} on protocol's step %{step_position} %{step} on task %{my_module}."
+      create_molecule_on_result_html: "%{user} created molecule %{asset_name} on result %{result}."
+      create_molecule_on_step_in_repository_html: "%{user} created molecule %{asset_name} on protocol %{protocol}'s step %{step_position} %{step}."
+      delete_molecule_on_step_html: "%{user} deleted molecule %{asset_name} on protocol's step %{step_position} %{step} on task %{my_module}."
+      delete_molecule_on_result_html: "%{user} deleted molecule %{asset_name} on result %{result}."
+      delete_molecule_on_step_in_repository_html: "%{user} deleted molecule %{asset_name} on protocol %{protocol}'s step %{step_position} %{step}."
+
 
       register_molecule_html: "%{user} scheduled the %{name} molecule for registration."
 
@@ -334,6 +344,16 @@ en:
       move_project_folder: "Project folder moved"
       generate_pdf_report: "PDF Report generated"
       generate_docx_report: "DOCX Report generated"
+      edit_molecule_on_step: "Molecule on task step edited"
+      edit_molecule_on_result: "Molecule on result edited"
+      edit_molecule_on_step_in_repository: "Molecule on step edited"
+      create_molecule_on_step: "Molecule on task step created"
+      create_molecule_on_result: "Molecule on result created"
+      create_molecule_on_step_in_repository: "Molecule on step created"
+      delete_molecule_on_step: "Molecule on task step deleted"
+      delete_molecule_on_result: "Molecule on result deleted"
+      delete_molecule_on_step_in_repository: "Molecule on step deleted"
+
 
     activity_group:
       projects: "Projects"