Merge pull request #4148 from aignatov-bio/ai-sci-6870-finalize-protocol-repository

Finalize protocol repository [SCI-6870]

app/assets/javascripts/protocols/index.js

@@ -16,7 +16,6 @@ function init() {
   initKeywordFiltering();
   initProtocolPreviewModal();
   initLinkedChildrenModal();
-  initCreateNewModal();
   initModals();
   initImport();
 }

app/assets/stylesheets/protocols/protocol.scss

@@ -7,6 +7,7 @@
 .content-pane.protocols-show {
   background-color: $color-alto;
   margin: 0 -16px;
+  min-height: calc(100vh - var(--navbar-height));
   overflow: hidden;
   padding: 36px 10px 10px;
   width: calc(100% + 31px);

app/controllers/step_elements/base_controller.rb

@@ -35,8 +35,10 @@ module StepElements
     end
 
     def log_step_activity(element_type_of, message_items)
+      message_items[:my_module] = @protocol.my_module.id if @protocol.in_module?
+
       Activities::CreateActivityService.call(
-        activity_type: "#{@step.protocol.in_module? ? 'protocol_step_' : 'task_step_'}#{element_type_of}",
+        activity_type: "#{!@step.protocol.in_module? ? 'protocol_step_' : 'task_step_'}#{element_type_of}",
         owner: current_user,
         team: @protocol.in_module? ? @protocol.my_module.experiment.project.team : @protocol.team,
         project: @protocol.in_module? ? @protocol.my_module.experiment.project : nil,
@@ -47,7 +49,6 @@ module StepElements
             id: @step.id,
             value_for: 'position_plus_one'
           },
-          my_module: @protocol.my_module.id
         }.merge(message_items)
       )
     end

app/controllers/step_elements/checklist_items_controller.rb

@@ -124,7 +124,7 @@ module StepElements
         owner: current_user,
         subject: @step.protocol,
         team: @step.protocol.team,
-        project: @step.protocol.my_module.experiment.project,
+        project: @step.protocol.in_module? ? @step.protocol.my_module.experiment.project : nil,
         message_items: message_items
       )
     end

app/controllers/step_elements/checklists_controller.rb

@@ -23,7 +23,7 @@ module StepElements
         log_step_activity(:checklist_edited, { checklist_name: @checklist.name })
       end
 
-      render json: @checklist, serializer: ChecklistSerializer
+      render json: @checklist, serializer: ChecklistSerializer, user: current_user
     rescue ActiveRecord::RecordInvalid
       head :unprocessable_entity
     end

app/controllers/step_elements/tables_controller.rb

@@ -28,7 +28,7 @@ module StepElements
         log_step_activity(:table_edited, { table_name: @table.name })
       end
 
-      render json: @table, serializer: TableSerializer
+      render json: @table, serializer: TableSerializer, user: current_user
     rescue ActiveRecord::RecordInvalid
       head :unprocessable_entity
     end

app/controllers/step_elements/texts_controller.rb

@@ -24,7 +24,7 @@ module StepElements
         log_step_activity(:text_edited, { text_name: @step_text.name })
       end
 
-      render json: @step_text, serializer: StepTextSerializer
+      render json: @step_text, serializer: StepTextSerializer, user: current_user
     rescue ActiveRecord::RecordInvalid
       head :unprocessable_entity
     end

app/javascript/vue/protocol/container.vue

@@ -38,7 +38,7 @@
             {{ protocol.attributes.name }}
           </span>
         </div>
-        <ProtocolMetadata v-if="protocol.attributes" :protocol="protocol" @update="updateProtocol"/>
+        <ProtocolMetadata v-if="protocol.attributes && protocol.attributes.in_repository" :protocol="protocol" @update="updateProtocol"/>
         <Tinymce
           v-if="urls.update_protocol_description_url"
           :value="protocol.attributes.description"

app/javascript/vue/protocol/mixins/attachments.js

@@ -1,4 +1,4 @@
-/* global ActiveStorage GLOBAL_CONSTANTS Promise i18n */
+/* global ActiveStorage GLOBAL_CONSTANTS Promise I18n */
 
 export default {
   data() {
@@ -40,7 +40,7 @@ export default {
             }
           };
           if (file.size > GLOBAL_CONSTANTS.FILE_MAX_SIZE_MB * 1024 * 1024) {
-            fileObject.error = i18n.t('protocols.steps.attachments.new.file_too_big');
+            fileObject.error = I18n.t('protocols.steps.attachments.new.file_too_big');
             this.attachments.push(fileObject);
             return;
           }
@@ -51,7 +51,7 @@ export default {
 
           upload.create((error, blob) => {
             if (error) {
-              fileObject.error = i18n.t('protocols.steps.attachments.new.general_error');
+              fileObject.error = I18n.t('protocols.steps.attachments.new.general_error');
               reject(error);
             } else {
               const signedId = blob.signed_id;

app/javascript/vue/protocol/step.vue

@@ -69,6 +69,7 @@
           </ul>
         </div>
         <a href="#"
+           v-if="!inRepository"
            ref="comments"
            class="open-comments-sidebar btn icon-btn btn-light"
            data-turbolinks="false"
@@ -111,6 +112,7 @@
           :is="elements[index].attributes.orderable_type"
           :key="index"
           :element.sync="elements[index]"
+          :inRepository="inRepository"
           :reorderElementUrl="urls.reorder_elements_url"
           @component:delete="deleteElement"
           @update="updateElement"

app/javascript/vue/protocol/step_elements/checklist.vue

@@ -47,6 +47,7 @@
           :checklistItem="checklistItem"
           :locked="locked"
           :reorderChecklistItemUrl="element.attributes.orderable.urls.reorder_url"
+          :inRepository="inRepository"
           @editStart="editingItem = true"
           @editEnd="editingItem = false"
           @update="saveItem"
@@ -80,6 +81,10 @@
         type: Object,
         required: true
       },
+      inRepository: {
+        type: Boolean,
+        required: true
+      },
       reorderElementUrl: {
         type: String
       }

app/javascript/vue/protocol/step_elements/checklistItem.vue

@@ -5,7 +5,7 @@
         <i class="fas fa-grip-vertical"></i>
       </div>
       <div class="step-element-name" :class="{ 'done': checklistItem.attributes.checked }">
-        <div class="sci-checkbox-container" :class="{ 'disabled': !checklistItem.attributes.urls.update_url}">
+        <div class="sci-checkbox-container" :class="{ 'disabled': !updateUrl || inRepository}">
           <input ref="checkbox"
                  type="checkbox"
                  class="sci-checkbox"
@@ -15,7 +15,7 @@
         </div>
         <div class="step-checklist-text">
           <InlineEdit
-            v-if="checklistItem.attributes.urls.update_url"
+            v-if="!checklistItem.attributes.urls || updateUrl"
             :value="checklistItem.attributes.text"
             :characterLimit="10000"
             :placeholder="''"
@@ -35,10 +35,10 @@
         </div>
       </div>
       <div class="step-element-controls">
-        <button v-if="checklistItem.attributes.urls.update_url" class="btn icon-btn btn-light" @click="enableTextEdit">
+        <button v-if="!checklistItem.attributes.urls || updateUrl" class="btn icon-btn btn-light" @click="enableTextEdit">
           <i class="fas fa-pen"></i>
         </button>
-        <button v-if="checklistItem.attributes.urls.delete_url" class="btn icon-btn btn-light" @click="showDeleteModal">
+        <button v-if="!checklistItem.attributes.urls || deleteUrl" class="btn icon-btn btn-light" @click="showDeleteModal">
           <i class="fas fa-trash"></i>
         </button>
       </div>
@@ -65,6 +65,10 @@
         type: Boolean,
         default: false
       },
+      inRepository: {
+        type: Boolean,
+        required: true
+      },
       reorderChecklistItemUrl: {
         type: String
       }
@@ -82,6 +86,16 @@
             position: this.checklistItem.attributes.position
          }
         });
+      },
+      updateUrl() {
+        if (!this.checklistItem.attributes.urls) return
+
+        return this.checklistItem.attributes.urls.update_url;
+      },
+      deleteUrl() {
+        if (!this.checklistItem.attributes.urls) return
+
+        return this.checklistItem.attributes.urls.delete_url;
       }
     },
     methods: {
@@ -94,7 +108,7 @@
         this.$emit('editEnd');
       },
       toggleChecked(e) {
-        if (!this.checklistItem.attributes.urls.update_url) return
+        if (!this.updateUrl) return
         this.checklistItem.attributes.checked = this.$refs.checkbox.checked;
         this.update();
       },

app/javascript/vue/protocol/step_elements/table.vue

@@ -66,6 +66,10 @@
         type: Object,
         required: true
       },
+      inRepository: {
+        type: Boolean,
+        required: true
+      },
       reorderElementUrl: {
         type: String
       }

app/javascript/vue/protocol/step_elements/text.vue

@@ -46,6 +46,10 @@
         type: Object,
         required: true
       },
+      inRepository: {
+        type: Boolean,
+        required: true
+      },
       reorderElementUrl: {
         type: String
       }

app/serializers/checklist_serializer.rb

@@ -12,7 +12,7 @@ class ChecklistSerializer < ActiveModel::Serializer
   end
 
   def urls
-    return {} if object.destroyed? || !can_manage_step?(scope[:user], object.step)
+    return {} if object.destroyed? || !can_manage_step?(scope[:user] || @instance_options[:user], object.step)
 
     {
       delete_url: step_checklist_path(object.step, object),

app/serializers/protocol_serializer.rb

@@ -15,8 +15,8 @@ class ProtocolSerializer < ActiveModel::Serializer
 
   def added_by
     {
-      avatar: object.added_by.avatar_url(:icon_small),
+      avatar: object.added_by&.avatar_url(:icon_small),
-      name: object.added_by.full_name
+      name: object.added_by&.full_name
     }
   end
 

app/serializers/step_text_serializer.rb

@@ -29,7 +29,7 @@ class StepTextSerializer < ActiveModel::Serializer
   end
 
   def urls
-    return {} if object.destroyed? || !can_manage_step?(scope[:user], object.step)
+    return {} if object.destroyed? || !can_manage_step?(scope[:user] || @instance_options[:user], object.step)
 
     {
       delete_url: step_text_path(object.step, object),

app/serializers/table_serializer.rb

@@ -19,7 +19,7 @@ class TableSerializer < ActiveModel::Serializer
 
     object.reload unless object.step
 
-    return {} unless can_manage_step?(scope[:user], object.step)
+    return {} unless can_manage_step?(scope[:user] || @instance_options[:user], object.step)
 
     {
       delete_url: step_table_path(object.step, object),