Merge branch 'features/protocol_versioning' into sb_SCI-8007

app/assets/javascripts/my_modules/protocols.js

@@ -38,19 +38,19 @@ function initEditProtocolDescription() {
 function initLinkUpdate() {
   var modal = $('#confirm-link-update-modal');
   var modalTitle = modal.find('.modal-title');
-  var modalBody = modal.find('.modal-body');
+  var modalMessage = modal.find('.modal-body .message');
   var updateBtn = modal.find(".modal-footer [data-action='submit']");
   $("[data-action='unlink'], [data-action='revert'], [data-action='update-parent'], [data-action='update-self']")
     .on('ajax:success', function(e, data) {
       modalTitle.html(data.title);
-      modalBody.html(data.message);
+      modalMessage.html(data.message);
       updateBtn.text(data.btn_text);
       modal.attr('data-url', data.url);
       modal.modal('show');
     });
 
   modal.on('hidden.bs.modal', function() {
-    modalBody.html('');
+    modalMessage.html('');
   });
 
   if (!$._data(updateBtn[0], 'events')) {

app/assets/javascripts/protocols/index.js

@@ -135,9 +135,30 @@ var ProtocolsIndex = (function() {
     });
   }
 
-  function initManageAccessButton() {
+  function initManageAccess() {
-    $('.protocols-index').on('click', '#manageProtocolAccess', function() {
+    let protocolsContainer = '.protocols-container';
-      $(`tr[data-row-id=${rowsSelected[0]}] .protocol-users-link`).click();
+    let manageAccessModal = '.protocol-assignments-modal';
+
+    function loadManageAccessModal(href) {
+      $.get(href, function(data) {
+        $(protocolsContainer).append($.parseHTML(data.html));
+        $(manageAccessModal).modal('show');
+
+        // Remove modal when it gets closed
+        $(manageAccessModal).on('hidden.bs.modal', function() {
+          $(manageAccessModal).remove();
+        });
+      });
+    }
+
+    protocolsTableEl.on('click', '.protocol-users-link', function(e) {
+      loadManageAccessModal(this.href);
+      e.stopPropagation();
+      e.preventDefault();
+    });
+
+    $(protocolsContainer).on('click', '#manageProtocolAccess', function() {
+      loadManageAccessModal($(`tr[data-row-id=${rowsSelected[0]}] .protocol-users-link`).attr('href'));
     });
   }
 
@@ -180,8 +201,8 @@ var ProtocolsIndex = (function() {
         targets: 0,
         searchable: false,
         orderable: false,
-        sWidth: "1%",
+        sWidth: '1%',
-        render: function (data, type, full, meta) {
+        render: function() {
           return `<div class="sci-checkbox-container">
                     <input type="checkbox" class="sci-checkbox">
                     <span class="sci-checkbox-label"></span>
@@ -244,7 +265,7 @@ var ProtocolsIndex = (function() {
       fnInitComplete: function(e) {
         var dataTableWrapper = $(e.nTableWrapper);
         DataTableHelpers.initLengthAppearance(dataTableWrapper);
-        DataTableHelpers.initSearchField(dataTableWrapper, 'Enter...');
+        DataTableHelpers.initSearchField(dataTableWrapper, I18n.t('protocols.index.search_bar_placeholder'));
         dataTableWrapper.find('.main-actions, .pagination-row').removeClass('hidden');
 
         let actionToolBar = $($('#protocolActionToolbar').html());
@@ -675,29 +696,18 @@ var ProtocolsIndex = (function() {
   }
 
   function updateDataTableSelectAllCheckbox() {
-    var table = protocolsDatatable.table().node();
+    var table = $('.protocols-datatable');
-    var checkboxesAll = $("tbody input[type='checkbox']", protocolsTableEl);
+    var checkboxes = table.find("tbody input[type='checkbox']");
-    var checkboxesChecked = $("tbody input[type='checkbox']:checked", protocolsTableEl);
+    var selectedCheckboxes = table.find("tbody input[type='checkbox']:checked");
-    var checkboxSelectAll = $("thead input[name='select_all']", table).get(0);
+    var selectAllCheckbox = table.find("thead input[name='select_all']");
 
-    if (checkboxesChecked.length === 0) {
+    selectAllCheckbox.prop('indeterminate', false);
-      // If none of the checkboxes are checked
+    if (selectedCheckboxes.length === 0) {
-      checkboxSelectAll.checked = false;
+      selectAllCheckbox.prop('checked', false);
-      if ('indeterminate' in checkboxSelectAll) {
+    } else if (selectedCheckboxes.length === checkboxes.length) {
-        checkboxSelectAll.indeterminate = false;
+      selectAllCheckbox.prop('checked', true);
-      }
-    } else if (checkboxesChecked.length === checkboxesAll.length) {
-      // If all of the checkboxes are checked
-      checkboxSelectAll.checked = true;
-      if ('indeterminate' in checkboxSelectAll) {
-        checkboxSelectAll.indeterminate = false;
-      }
     } else {
-      // If some of the checkboxes are checked
+      selectAllCheckbox.prop('indeterminate', true);
-      checkboxSelectAll.checked = true;
-      if ('indeterminate' in checkboxSelectAll) {
-        checkboxSelectAll.indeterminate = true;
-      }
     }
   }
 
@@ -1002,7 +1012,7 @@ var ProtocolsIndex = (function() {
   }
 
   init();
-  initManageAccessButton();
+  initManageAccess();
   initArchiveProtocols();
   initRestoreProtocols();
   initExportProtocols();

app/assets/javascripts/protocols/new_protocol.js

@@ -1,10 +1,16 @@
 /* global dropdownSelector HelperModule */
 (function() {
-  $('#newProtocolModal').on('change', '#protocol_visibility', function() {
+  const protocolModal = '#newProtocolModal';
-    $('#roleSelectWrapper').toggleClass('hidden', !$(this)[0].checked);
+  $(protocolModal)
-  });
+    .on('change', '#protocol_visibility', function() {
+      $('#roleSelectWrapper').toggleClass('hidden', !$(this)[0].checked);
+    })
+    .on('show.bs.modal', function() {
+      $(`${protocolModal} #protocol_name`).parent().removeClass('error');
+      $(`${protocolModal} form[data-action="new"] #protocol_name`).val('');
+    });
 
-  let roleSelector = '#newProtocolModal #protocol_role_selector';
+  let roleSelector = `${protocolModal} #protocol_role_selector`;
   dropdownSelector.init(roleSelector, {
     noEmptyOption: true,
     singleSelect: true,
@@ -15,16 +21,16 @@
     }
   });
 
-  $('#newProtocolModal')
+  $(protocolModal)
     .on('ajax:error', 'form', function(e, error) {
       let msg = error.responseJSON.error;
-      $('#newProtocolModal #protocol_name').parent().addClass('error').attr('data-error-text', msg);
+      $(`${protocolModal} #protocol_name`).parent().addClass('error').attr('data-error-text', msg);
     })
     .on('ajax:success', 'form', function(e, data) {
       if (data.message) {
         HelperModule.flashAlertMsg(data.message, 'success');
       }
-      $('#newProtocolModal #protocol_name').parent().removeClass('error');
+      $(`${protocolModal} #protocol_name`).parent().removeClass('error');
-      $('#newProtocolModal').modal('hide');
+      $(protocolModal).modal('hide');
     });
 }());

app/assets/stylesheets/access_permissions/access_modal.scss

@@ -22,7 +22,8 @@
   }
 
   .modal-body {
-    min-height: calc(100vh - 200px);
+    max-height: calc(100vh - 190px);
+    min-height: 370px;
     overflow: auto;
     padding-top: 0;
   }

app/assets/stylesheets/my_modules/protocol.scss

@@ -14,6 +14,10 @@
     align-items: baseline;
     display: flex;
 
+    a:first-of-type:focus {
+      outline: none;
+    }
+
     .task-section-caret {
       padding-right: .25em;
     }

app/assets/stylesheets/my_modules/protocols/index.scss

@@ -428,9 +428,14 @@
     width: 506px;
     padding: 15px 0;
 
+    .dropdown-content {
+      padding: 24px;
+    }
+
     .dropdown-header,
-    .dropdown-body {
+    .dropdown-body,
-      padding: 10px 24px;
+    .dropdown-footer {
+      padding: 12px 0;
     }
 
     .dropdown-header {
@@ -508,7 +513,6 @@
 
     .dropdown-footer {
       border-top: $border-tertiary;
-      padding: 12px 0 0;
     }
   }
 }
@@ -670,8 +674,14 @@
   margin-left: 4px;
 }
 
-#confirm-link-update-modal {
+#confirm-link-update-modal,
+.delete-steps-modal {
+  .modal-body p {
+    margin: 1.2em 0;
+  }
+
   .warning {
-    margin: 0 15px 15px;
+    font-weight: bold;
+    margin-bottom: 1.2em;
   }
 }

app/assets/stylesheets/protocols/index.scss

@@ -27,6 +27,18 @@
           white-space: nowrap;
         }
       }
+
+      .table.dataTable .sorting {
+        &::after {
+          opacity: 0;
+        }
+
+        &:hover {
+          &::after {
+            opacity: 1;
+          }
+        }
+      }
     }
 
     .toolbar {
@@ -61,6 +73,10 @@
     .dataTables_scrollBody {
       height: 100%;
 
+      td:first-child {
+        padding-top: 13px;
+      }
+
       td:not(:first-child) {
         padding: 14px 8px;
       }

app/assets/stylesheets/protocols/protocol.scss

@@ -89,7 +89,7 @@
       padding-left: 20px;
     }
   }
-  .details-container {
+  .protocol-details {
     .protocol-metadata {
       margin-bottom: 2em;
 

app/controllers/access_permissions/projects_controller.rb

@@ -53,21 +53,36 @@ module AccessPermissions
         permitted_create_params[:resource_members].each do |_k, user_assignment_params|
           next unless user_assignment_params[:assign] == '1'
 
-          user_assignment = UserAssignment.find_or_initialize_by(
+          if user_assignment_params[:user_id] == 'all'
-            assignable: @project,
+            @project.update!(visibility: :visible, default_public_user_role_id: user_assignment_params[:user_role_id])
-            user_id: user_assignment_params[:user_id],
+            Activities::CreateActivityService
-            team: current_team
+              .call(activity_type: :change_project_visibility,
-          )
+                    owner: current_user,
+                    subject: @project,
+                    team: @project.team,
+                    project: @project,
+                    message_items: {
+                      project: @project.id,
+                      visibility: t('projects.activity.visibility_visible')
+                    })
+          else
 
-          user_assignment.update!(
+            user_assignment = UserAssignment.find_or_initialize_by(
-            user_role_id: user_assignment_params[:user_role_id],
+              assignable: @project,
-            assigned_by: current_user,
+              user_id: user_assignment_params[:user_id],
-            assigned: :manually
+              team: current_team
-          )
+            )
 
-          log_activity(:assign_user_to_project, user_assignment)
+            user_assignment.update!(
-          created_count += 1
+              user_role_id: user_assignment_params[:user_role_id],
-          propagate_job(user_assignment)
+              assigned_by: current_user,
+              assigned: :manually
+            )
+
+            log_activity(:assign_user_to_project, user_assignment)
+            created_count += 1
+            propagate_job(user_assignment)
+          end
         end
 
         respond_to do |format|

app/controllers/access_permissions/protocols_controller.rb

@@ -51,25 +51,31 @@ module AccessPermissions
         permitted_create_params[:resource_members].each do |_k, user_assignment_params|
           next unless user_assignment_params[:assign] == '1'
 
-          user_assignment = UserAssignment.find_or_initialize_by(
+          if user_assignment_params[:user_id] == 'all'
-            assignable: @protocol,
+            @protocol.update!(visibility: :visible, default_public_user_role_id: user_assignment_params[:user_role_id])
-            user_id: user_assignment_params[:user_id],
+          else
-            team: current_team
+            user_assignment = UserAssignment.find_or_initialize_by(
-          )
+              assignable: @protocol,
+              user_id: user_assignment_params[:user_id],
+              team: current_team
+            )
 
-          user_assignment.update!(
+            user_assignment.update!(
-            user_role_id: user_assignment_params[:user_role_id],
+              user_role_id: user_assignment_params[:user_role_id],
-            assigned_by: current_user,
+              assigned_by: current_user,
-            assigned: :manually
+              assigned: :manually
-          )
+            )
 
-          created_count += 1
+            created_count += 1
-          log_activity(:protocol_template_access_granted, user_assignment)
+            log_activity(:protocol_template_access_granted, user_assignment)
+          end
         end
+
         respond_to do |format|
           @message = t('access_permissions.create.success', count: created_count)
           format.json { render :edit }
         end
+
       rescue ActiveRecord::RecordInvalid
         respond_to do |format|
           @message = t('access_permissions.create.failure')

app/datatables/protocols_datatable.rb

@@ -127,10 +127,7 @@ class ProtocolsDatatable < CustomDatatable
     records = records.where(protocols: { published_by_id: params[:published_by] }) if params[:published_by].present?
 
     if params[:members].present?
-      records = records.joins('LEFT OUTER JOIN "user_assignments" "all_user_assignments" '\
+      records = records.where(all_user_assignments: { user_id: params[:members] })
-                              'ON "all_user_assignments"."assignable_type" = \'Protocol\' '\
-                              'AND "all_user_assignments"."assignable_id" = "protocols"."id"')
-                       .where(all_user_assignments: { user_id: params[:members] })
     end
 
     if params[:archived_on_from].present?
@@ -141,7 +138,13 @@ class ProtocolsDatatable < CustomDatatable
     records = records.where(protocols: { archived_by_id: params[:archived_by] }) if params[:archived_by].present?
 
     if params[:has_draft].present?
-      records = records.where(protocols: { protocol_type: Protocol.protocol_types[:in_repository_draft] })
+      records =
+        records
+        .joins("LEFT OUTER JOIN protocols protocol_drafts " \
+               "ON protocol_drafts.protocol_type = #{Protocol.protocol_types[:in_repository_draft]} " \
+               "AND (protocol_drafts.parent_id = protocols.id OR protocol_drafts.parent_id = protocols.parent_id)")
+        .where('protocols.protocol_type = ? OR protocol_drafts.id IS NOT NULL',
+               Protocol.protocol_types[:in_repository_draft])
     end
 
     records
@@ -199,6 +202,9 @@ class ProtocolsDatatable < CustomDatatable
              'ON "protocol_protocol_keywords"."protocol_keyword_id" = "protocol_keywords"."id"')
       .joins('LEFT OUTER JOIN "users" "archived_users" ON "archived_users"."id" = "protocols"."archived_by_id"')
       .joins('LEFT OUTER JOIN "users" ON "users"."id" = "protocols"."published_by_id"')
+      .joins('LEFT OUTER JOIN "user_assignments" "all_user_assignments" '\
+        'ON "all_user_assignments"."assignable_type" = \'Protocol\' '\
+        'AND "all_user_assignments"."assignable_id" = "protocols"."id"')
       .group('"protocols"."id"')
 
     records = filter_protocols_records(records)
@@ -212,7 +218,7 @@ class ProtocolsDatatable < CustomDatatable
       '(COUNT(DISTINCT("self_linked_task_protocols"."id")) + ' \
       'COUNT(DISTINCT("parent_linked_task_protocols"."id")) + ' \
       'COUNT(DISTINCT("version_linked_task_protocols"."id"))) AS nr_of_linked_tasks',
-      'COUNT("user_assignments"."id") AS "nr_of_assigned_users"',
+      'COUNT(DISTINCT("all_user_assignments"."id")) AS "nr_of_assigned_users"',
       'MAX("users"."full_name") AS "full_username_str"', # "Hack" to get single username
       'MAX("archived_users"."full_name") AS "archived_full_username_str"'
     )

app/helpers/user_roles_helper.rb

@@ -1,8 +1,11 @@
 # frozen_string_literal: true
 
 module UserRolesHelper
-  def user_roles_collection(with_inherit: false)
+  def user_roles_collection(object, with_inherit: false)
-    roles = UserRole.order(id: :asc).pluck(:name, :id)
+    permission_group = "#{object.class.name}Permissions".constantize
+    permissions = permission_group.constants.map { |const| permission_group.const_get(const) }
+
+    roles = user_roles_subset_by_permissions(permissions).order(id: :asc).pluck(:name, :id)
     roles = [[t('access_permissions.reset'), 'reset']] + roles if with_inherit
     roles
   end
@@ -12,9 +15,10 @@ module UserRolesHelper
       PermissionExtends::TeamPermissions.constants.map { |const| TeamPermissions.const_get(const) } +
       ProtocolPermissions.constants.map { |const| ProtocolPermissions.const_get(const) } +
       RepositoryPermissions.constants.map { |const| RepositoryPermissions.const_get(const) }
-    UserRole.where('permissions && ARRAY[?]::varchar[]', team_permissions)
+
-            .sort_by { |user_role| (user_role.permissions & team_permissions).length }
+    user_roles_subset_by_permissions(team_permissions)
-            .reverse!
+      .sort_by { |user_role| (user_role.permissions & team_permissions).length }
+      .reverse!
   end
 
   def team_user_roles_for_select
@@ -22,6 +26,12 @@ module UserRolesHelper
   end
 
   def managing_team_user_roles_collection
-    UserRole.where('permissions && ARRAY[?]::varchar[]', [TeamPermissions::USERS_MANAGE])
+    user_roles_subset_by_permissions([TeamPermissions::USERS_MANAGE])
+  end
+
+  private
+
+  def user_roles_subset_by_permissions(permissions)
+    UserRole.where('permissions && ARRAY[?]::varchar[]', permissions)
   end
 end

app/javascript/vue/protocol/modals/delete_steps.vue

@@ -10,8 +10,7 @@
         </div>
         <div class="modal-body">
           <p>{{ i18n.t('protocols.steps.modals.delete_steps.description_1')}}</p>
-          <p><b>{{ i18n.t('protocols.steps.modals.delete_steps.description_2')}}</b></p>
+          <p class="warning">{{ i18n.t('protocols.steps.modals.delete_steps.description_2')}}</p>
-
         </div>
         <div class="modal-footer">
           <button class="btn btn-secondary" @click="cancel">{{ i18n.t('general.cancel') }}</button>

app/javascript/vue/protocol/protocolMetadata.vue

@@ -19,6 +19,7 @@
         <button class="btn btn-light" @click="openVersionsModal">{{ i18n.t("protocols.header.versions") }}</button>
         <button v-if="protocol.attributes.urls.publish_url" @click="$emit('publish')" class="btn btn-primary">{{ i18n.t("protocols.header.publish") }}</button>
         <button v-if="protocol.attributes.urls.save_as_draft_url" @click="saveAsdraft" class="btn btn-secondary">{{ i18n.t("protocols.header.save_as_draft") }}</button>
+        <button v-bind:disabled="protocol.attributes.disabled_drafting" v-if="protocol.attributes.disabled_drafting" @click="saveAsdraft" class="btn btn-secondary">{{ i18n.t("protocols.header.save_as_draft") }}</button>
       </div>
     </div>
     <div id="details-container" class="protocol-details collapse in">

app/models/protocol.rb

@@ -21,6 +21,7 @@ class Protocol < ApplicationRecord
   after_save :update_user_assignments, if: -> { saved_change_to_visibility? && in_repository? }
   after_save :update_linked_children
   skip_callback :create, :after, :create_users_assignments, if: -> { in_module? }
+  before_update :sync_protocol_assignments, if: :visibility_changed?
 
   enum visibility: { hidden: 0, visible: 1 }
   enum protocol_type: {
@@ -230,6 +231,11 @@ class Protocol < ApplicationRecord
     teams.blank? ? self : where(team: teams)
   end
 
+  def original_code
+    # returns linked protocol code, or code of the original version of the linked protocol
+    parent&.parent&.code || parent&.code || code
+  end
+
   def insert_step(step, position)
     ActiveRecord::Base.transaction do
       steps.where('position >= ?', position).desc_order.each do |s|
@@ -793,4 +799,12 @@ class Protocol < ApplicationRecord
       errors.add(:base, I18n.t('activerecord.errors.models.protocol.wrong_parent_draft_number'))
     end
   end
+
+  def sync_protocol_assignments
+    if visible?
+      auto_assign_protocol_members
+    else
+      user_assignments.where(assigned: :automatically).destroy_all
+    end
+  end
 end

app/permissions/team.rb

@@ -105,11 +105,11 @@ Canaid::Permissions.register_for(Protocol) do
 
   # protocol in repository: restore
   can :restore_protocol_in_repository do |user, protocol|
-    protocol.archived? && protocol.permission_granted?(user, ProtocolPermissions::MANAGE)
+    protocol.archived? && protocol.permission_granted?(user, ProtocolPermissions::RESTORE)
   end
 
   can :archive_protocol_in_repository do |user, protocol|
-    protocol.active? && protocol.permission_granted?(user, ProtocolPermissions::MANAGE)
+    protocol.active? && protocol.permission_granted?(user, ProtocolPermissions::ARCHIVE)
   end
 
   # protocol in repository: copy
@@ -119,7 +119,7 @@ Canaid::Permissions.register_for(Protocol) do
 
   can :publish_protocol_in_repository do |user, protocol|
     protocol.in_repository_draft? &&
-      protocol.permission_granted?(user, ProtocolPermissions::MANAGE)
+      protocol.permission_granted?(user, ProtocolPermissions::PUBLISH)
   end
 
   can :delete_protocol_draft_in_repository do |user, protocol|

app/serializers/protocol_serializer.rb

@@ -8,7 +8,7 @@ class ProtocolSerializer < ActiveModel::Serializer
 
   attributes :name, :id, :urls, :description, :description_view, :updated_at, :in_repository,
              :created_at_formatted, :updated_at_formatted, :added_by, :authors, :keywords, :version, :code,
-             :published, :version_comment, :archived
+             :published, :version_comment, :archived, :disabled_drafting
 
   def updated_at
     object.updated_at.to_i
@@ -84,6 +84,14 @@ class ProtocolSerializer < ActiveModel::Serializer
     !object.in_module?
   end
 
+  def disabled_drafting
+    protocol_types = Protocol.where(name: object.name).pluck(:protocol_type)
+    object.protocol_type != 'in_repository_draft' &&
+      !object.archived &&
+      protocol_types.length > 1 &&
+      protocol_types.include?('in_repository_draft')
+  end
+
   private
 
   def load_from_repo_url

app/views/access_permissions/partials/_default_public_user_role_form.html.erb

@@ -21,7 +21,7 @@
               </button>
               <%= f.hidden_field :default_public_user_role_id, value: f.object.default_public_user_role.id, class: "default-public-user-role-id" %>
               <ul class="dropdown-menu dropdown-menu-right user-assignment-dropdown" aria-labelledby="defaultPublicUserRole">
-                <% user_roles_collection.each do |role| %>
+                <% user_roles_collection(assignable).each do |role| %>
                   <li>
                     <a href="#" data-turbolinks="false" class="user-role-selector" data-role-id="<%= role[1] %>">
                       <%= role[0] %>

app/views/access_permissions/partials/_member_field.html.erb

@@ -27,7 +27,7 @@
           </button>
           <%= f.hidden_field :user_role_id, value: f.object.user_role.id %>
           <ul class="dropdown-menu dropdown-menu-right user-assignment-dropdown" aria-labelledby="userAccess_<%= user.id %>">
-            <% user_roles_collection(with_inherit: with_inherit).each do |role| %>
+            <% user_roles_collection(assignable, with_inherit: with_inherit).each do |role| %>
               <li>
                 <a href="#" data-turbolinks="false" class="user-role-selector" data-role-id="<%= role[1] %>">
                   <%= role[0] %>

app/views/access_permissions/partials/_new_assignments_form.html.erb

@@ -16,9 +16,14 @@
         <%= text_field_tag :search_users, '', placeholder: t('.find_people_html'), class: 'sci-input-field', data: { action: 'filter-list', target: 'new-user-assignment-to-project-form' } %>
         <i class="fas fa-search"></i>
       </div>
+      <% if assignable.visibility && assignable.visibility == 'hidden' %>
+        <%= f.fields_for :users, UserAssignment.new do |user_form| %>
+          <%= render 'access_permissions/partials/public_assignment_field.html.erb', user_form: user_form, assignable: assignable  %>
+        <% end %>
+      <% end %>
       <% users.each do |user| %>
         <%= f.fields_for :users, UserAssignment.new(user: user) do |user_form| %>
-          <%= render 'access_permissions/partials/user_assignment_field.html.erb', user_form: user_form  %>
+          <%= render 'access_permissions/partials/user_assignment_field.html.erb', user_form: user_form, assignable: assignable  %>
         <% end %>
       <% end %>
     </div>

app/views/access_permissions/partials/_public_assignment_field.html.erb

@@ -0,0 +1,31 @@
+<% # frozen_string_literal: true %>
+
+<div class="member-item new-member-item">
+  <%= user_form.hidden_field :user_id, value: :all, name:"access_permissions_new_user_form[resource_members][0][user_id]"  %>
+  <div class="user-assignment-info">
+    <div class="sci-checkbox-container">
+      <%= user_form.check_box :assign,
+                        name: "access_permissions_new_user_form[resource_members][0][assign]",
+                        data: { action: 'toggle-visibility', target: 'usersAll' },
+                        class: "sci-checkbox"
+        %>
+      <span class="sci-checkbox-label"></span>
+    </div>
+    <div class="global-avatar-container">
+        <%= image_tag "icon/team.png", class: 'img-circle pull-left' %>
+      </div>
+    <div>
+      <%= t('user_assignment.assign_all_team_members') %>
+    </div>
+  </div>
+  <div class="user-assignment-controls">
+    <div class="user-assignment-role hidden" id="usersAll">
+      <%= user_form.select :user_role_id,
+                options_for_select(user_roles_collection(assignable)),
+                {},
+                name: "access_permissions_new_user_form[resource_members][0][user_role_id]",
+                class: 'form-control selectpicker pull-right',
+                title: t('user_assignment.select_role')  %>
+    </div>
+  </div>
+</div>

app/views/access_permissions/partials/_user_assignment_field.html.erb

@@ -26,7 +26,7 @@
   <div class="user-assignment-controls">
     <div class="user-assignment-role hidden" id="<%= id %>">
       <%= user_form.select :user_role_id,
-                options_for_select(user_roles_collection),
+                options_for_select(user_roles_collection(assignable)),
                 {},
                 name: "access_permissions_new_user_form[resource_members][#{user.id}][user_role_id]",
                 class: 'form-control selectpicker pull-right',

app/views/my_modules/protocols/_confirm_link_update_modal.html.erb

@@ -5,8 +5,10 @@
         <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
         <h4 class="modal-title" id="confirm-link-update-modal-label"></h4>
       </div>
-      <div class="modal-body"></div>
+      <div class="modal-body">
-      <h3 class="warning"><%= t('my_modules.protocols.confirm_link_update_modal.warning') %></h3>
+        <p class="message"></p>
+        <p class="warning"><%= t('my_modules.protocols.confirm_link_update_modal.warning') %></p>
+      </div>
       <div class="modal-footer">
         <button type="button" class="btn btn-default" data-dismiss="modal"><%= t("general.cancel") %></button>
         <button type="button" class="btn btn-success" data-action="submit"></button>

app/views/my_modules/protocols/_protocol_status_bar.html.erb

@@ -15,53 +15,57 @@
     <i class="fas fa-info-circle"></i>
   </a>
   <div class="dropdown-menu status-info-dropdown" aria-labelledby="my-module-protocol-info-button">
-    <div class="dropdown-header">
+    <div class="dropdown-content">
-      <h2 class="protocol-name">
+        <div class="dropdown-header">
-        <%= @protocol.parent&.name || @protocol.name %>
+          <h2 class="protocol-name">
-      </h2>
+            <%= @protocol.parent&.name || @protocol.name %>
-      <% if @protocol.linked? %>
+          </h2>
-        <div class="protocol-header-info">
+          <% if @protocol.linked? %>
-          <span><%= t('my_modules.protocols.protocol_status_bar.protocol_id_label') %> <%= @protocol.parent&.code %></span>
+            <div class="protocol-header-info">
-          <span><%= t('my_modules.protocols.protocol_status_bar.protocol_version_label') %> <%= @protocol.parent&.version_number %></span>
+              <span><%= t('my_modules.protocols.protocol_status_bar.protocol_id_label') %> <%= @protocol.original_code %></span>
+              <span><%= t('my_modules.protocols.protocol_status_bar.protocol_version_label') %> <%= @protocol.parent&.version_number %></span>
+            </div>
+          <% end %>
         </div>
-      <% end %>
+        <div class="dropdown-body">
-    </div>
+          <% if @protocol.unlinked? %>
-    <div class="dropdown-body">
+            <div class="info-line">
-      <% if @protocol.unlinked? %>
+              <div class="description"><%= t("my_modules.protocols.protocol_status_bar.protocol_created") %></div>
-        <div class="info-line">
+              <div class="value"><%= I18n.l(@protocol.created_at, format: :full) %></div>
-          <div class="description"><%= t("my_modules.protocols.protocol_status_bar.protocol_created") %></div>
+            </div>
-          <div class="value"><%= I18n.l(@protocol.created_at, format: :full) %></div>
+          <% end %>
-        </div>
+          <div class="info-line">
-      <% end %>
+            <div class="description"><%= t("my_modules.protocols.protocol_status_bar.protocol_updated") %></div>
-      <div class="info-line">
+            <div class="value"><%= I18n.l(@protocol.updated_at, format: :full) %></div>
-        <div class="description"><%= t("my_modules.protocols.protocol_status_bar.protocol_updated") %></div>
+          </div>
-        <div class="value"><%= I18n.l(@protocol.updated_at, format: :full) %></div>
+          <% if @protocol.linked?%>
-      </div>
+            <div class="info-line">
-      <% if @protocol.linked?%>
+              <div class="description"><%= t("my_modules.protocols.protocol_status_bar.protocol_loaded") %></div>
-        <div class="info-line">
+              <div class="value"><%= @protocol.linked_at ? I18n.l(@protocol.linked_at, format: :full) : '' %></div>
-          <div class="description"><%= t("my_modules.protocols.protocol_status_bar.protocol_loaded") %></div>
+            </div>
-          <div class="value"><%= @protocol.linked_at ? I18n.l(@protocol.linked_at, format: :full) : '' %></div>
+            <div class="info-line">
-        </div>
+              <div class="description"><%= t("my_modules.protocols.protocol_status_bar.protocol_published") %></div>
-        <div class="info-line">
+              <div class="value"><%= I18n.l(@protocol&.parent&.published_on, format: :full) %></div>
-          <div class="description"><%= t("my_modules.protocols.protocol_status_bar.protocol_published") %></div>
+            </div>
-          <div class="value"><%= I18n.l(@protocol&.parent&.published_on, format: :full) %></div>
+          <% end %>
         </div>
         <div class="dropdown-footer">
-          <% if @protocol.parent_newer? %>
+          <% if @protocol.linked? %>
-            <div class="notification-line new-parent-version">
+            <% if @protocol.parent_newer? %>
-              <i class="fas fa-info-circle"></i>
+              <div class="notification-line new-parent-version">
-              <div class="description"><%= t("my_modules.protocols.protocol_status_bar.messages.template_updated_html") %></div>
+                <i class="fas fa-info-circle"></i>
-            </div>
+                <div class="description"><%= t("my_modules.protocols.protocol_status_bar.messages.template_updated_html") %></div>
-          <% end %>
+              </div>
-          <% if @protocol.newer_than_parent? %>
+            <% end %>
-            <div class="notification-line new-protocol-version">
+            <% if @protocol.newer_than_parent? %>
-              <i class="fas fa-info-circle"></i>
+              <div class="notification-line new-protocol-version">
-              <div class="description"><%= t("my_modules.protocols.protocol_status_bar.messages.protocol_updated") %></div>
+                <i class="fas fa-info-circle"></i>
-            </div>
+                <div class="description"><%= t("my_modules.protocols.protocol_status_bar.messages.protocol_updated") %></div>
+              </div>
+            <% end %>
           <% end %>
         </div>
-      <% end %>
+      </div>
     </div>
-  </div>
 </div>
 <%= javascript_include_tag("my_modules/protocols/protocol_status_bar") %>

app/views/projects/index/modals/_edit_project_contents.html.erb

@@ -26,7 +26,7 @@
     <div class="row <%= f.object.hidden? ? 'hidden' : '' %>" id="role_select_wrapper">
       <div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
         <%= f.select :default_public_user_role_id,
-                     options_for_select(user_roles_collection, selected: f.object.default_public_user_role_id),
+                     options_for_select(user_roles_collection(@project), selected: f.object.default_public_user_role_id),
                      { label: t('user_assignment.select_default_user_role') },
                      class: 'form-control selectpicker'%>
       </div>

app/views/projects/index/modals/_new_project.html.erb

@@ -26,7 +26,7 @@
           <div class="row hidden" id="role_select_wrapper">
             <div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
               <%= f.select :default_public_user_role_id,
-                           options_for_select(user_roles_collection, UserRole.find_by(name: I18n.t('user_roles.predefined.viewer')).id),
+                           options_for_select(user_roles_collection(@project), UserRole.find_by(name: I18n.t('user_roles.predefined.viewer')).id),
                            class: 'form-control selectpicker'%>
             </div>
           </div>

app/views/protocol_importers/_preview_modal_footer.html.erb

@@ -14,7 +14,7 @@
         <%= label_tag :default_public_user_role_id, t("protocols.new_protocol_modal.role_label") %>
         <% default_role = UserRole.find_by(name: I18n.t('user_roles.predefined.viewer')).id %>
         <%= hidden_field_tag :default_public_user_role_id, value: default_role %>
-        <%= select_tag :role_selector, options_for_select(user_roles_collection, default_role) %>
+        <%= select_tag :role_selector, options_for_select(user_roles_collection(@protocol), default_role) %>
       </div>
     </div>
   </div>

app/views/protocols/index/_general_toolbar.html.erb

@@ -1,25 +1,25 @@
 <template id="protocolGeneralToolbar">
   <div class="left-general-toolbar">
-    <button data-toggle="modal"
+    <% if can_create_protocols_in_repository?(@current_team) %>
-            data-target="#newProtocolModal"
-            <%= 'disabled' if !can_create_protocols_in_repository?(@current_team) %>
-            class="btn btn-primary only-active"
-    >
-      <span class="fas fa-plus"></span>
-      <span class="hidden-xs"><%= t("protocols.index.create_new") %></span>
-    </button>
 
-    <div id="protocol-import-group" class="sci-btn-group  only-active" role="group">
+      <button data-toggle="modal"
-      <button class="btn btn-light btn-open-file <%= 'disabled' unless can_create_protocols_in_repository?(@current_team) %>"
+              data-target="#newProtocolModal"
-        data-toggle="dropdown"
+              class="btn btn-primary only-active"
-        aria-haspopup="true"
+      >
-        aria-expanded="false">
+        <span class="fas fa-plus"></span>
-        <span class="fas fa-upload"></span><span class="hidden-xs"><%= t("protocols.index.import") %></span>
+        <span class="hidden-xs"><%= t("protocols.index.create_new") %></span>
       </button>
-      <% if can_create_protocols_in_repository?(@current_team) %>
+
+      <div id="protocol-import-group" class="sci-btn-group  only-active" role="group">
+        <button class="btn btn-light btn-open-file"
+          data-toggle="dropdown"
+          aria-haspopup="true"
+          aria-expanded="false">
+          <span class="fas fa-upload"></span><span class="hidden-xs"><%= t("protocols.index.import") %></span>
+        </button>
         <ul class="dropdown-menu">
           <li>
-            <a class="btn-link-alt btn-default-link btn-open-file" <%= can_create_protocols_in_repository?(@current_team) ? 'data-action="import"' : 'disabled="disabled"' %>>
+            <a class="btn-link-alt btn-default-link btn-open-file" data-action="import">
               <span><%= t("protocols.index.import_alt") %></span>
               <input type="file" value="" accept=".eln" data-role="import-file-input"
               data-team-id="<%= @current_team.id %>" data-import-url="<%= import_protocols_path %>"
@@ -30,7 +30,7 @@
             <%= link_to t("protocols.index.import_protocols_io"), '', data: { target: '#protocolsioModal', toggle: 'modal' } %>
           </li>
         </ul>
-      <% end %>
+      </div>
-    </div>
+    <% end %>
   </div>
 </template>

app/views/protocols/index/_new_protocol_modal.html.erb

@@ -1,5 +1,5 @@
 <div class="modal" id="newProtocolModal" tabindex="-1" role="dialog">
-  <%= form_with model: @protocol || Protocol.new, url: type == 'new' ? protocols_path : copy_to_repository_protocol_path(@protocol), method: :post  do |f| %>
+  <%= form_with model: @protocol || Protocol.new, url: type == 'new' ? protocols_path : copy_to_repository_protocol_path(@protocol), method: :post, data: { action: type }  do |f| %>
     <div class="modal-dialog" role="document">
       <div class="modal-content">
         <div class="modal-header">
@@ -32,7 +32,7 @@
               <%= f.label :default_public_user_role_id, t("protocols.new_protocol_modal.role_label") %>
               <% default_role = UserRole.find_by(name: I18n.t('user_roles.predefined.viewer')).id %>
               <%= f.hidden_field :default_public_user_role_id, value: default_role %>
-              <%= f.select :role_selector, options_for_select(user_roles_collection, default_role) %>
+              <%= f.select :role_selector, options_for_select(team_user_roles_for_select, default_role) %>
             </div>
           </div>
         </div>

app/views/protocols/index/_protocol_versions_modal.html.erb

@@ -56,7 +56,7 @@
                   >
                   <div class="protocol-comment-message">
                     <div class="view-mode" data-placeholder="<%= t('protocols.index.versions.comment_placeholder') %>"><%= draft.version_comment %></div>
-                    <%= text_area_tag 'version_comment', draft.version_comment, disabled: true, class: 'smart-text-area hidden' %>
+                    <%= text_area_tag 'version_comment', draft.version_comment, disabled: can_publish_protocol_in_repository?(@protocol), class: 'smart-text-area hidden' %>
                   </div>
                   <div class="edit-buttons">
                     <span class="cancel-button btn btn-secondary"><%= t('general.cancel') %></span>

app/views/protocols/index/_protocolsio_modal_body.html.erb

@@ -31,10 +31,10 @@
                   <span><i class="fas fa-sort-amount-down"></i></span>
                 </button>
                 <ul id="sortMenuDropdown" class="dropdown-menu sort-projects-menu dropdown-menu-right" aria-labelledby="sortMenu">
-                  <% {new: :newest, old: :oldest, atoz: :alpha_asc, ztoa: :alpha_desc}.each do |name, value| %>
+                  <% {atoz: :alpha_asc, ztoa: :alpha_desc, new: :newest, old: :oldest}.each do |name, value| %>
                     <li>
                       <input type='radio' name='sort_by' value='<%= value %>' <%= name == :new ? 'checked' : '' %> />
-                      <label for="<%= value %>"><%= t("general.sort.#{name.to_s}_html") %></label>
+                      <label for="<%= value %>"><%= t("protocols.index.protocolsio.sort.#{name.to_s}_html") %></label>
                     </li>
                   <% end %>
                 </ul>

config/initializers/extends/permission_extends.rb

@@ -19,6 +19,9 @@ module PermissionExtends
     %w(
       READ
       READ_ARCHIVED
+      ARCHIVE
+      RESTORE
+      PUBLISH
       MANAGE
       USERS_MANAGE
       MANAGE_DRAFT

config/locales/en.yml

@@ -2707,6 +2707,7 @@ en:
       head_title_archived: "Archived protocol templates"
       default_name: 'New protocol'
       back_to_active_protocols: 'Back to active protocols'
+      search_bar_placeholder: 'Filter protocols'
       navigation:
         public: "Team protocols"
         private: "My protocols"
@@ -2740,7 +2741,7 @@ en:
         name: "Name"
         id: "ID"
         keywords: "Keywords"
-        nr_of_linked_children: "No. of linked tasks"
+        nr_of_linked_children: "Linked tasks"
         versions: "Versions"
         access: "Access"
         published_by: "Published by"
@@ -2853,6 +2854,11 @@ en:
           public: "Team protocols"
           private: "My protocols"
           success_flash: 'Protocol <strong>%{name}</strong> successfully imported.'
+        sort:
+          new_html: "<i class=\"fas fa-sort-numeric-up\"></i>&nbsp;&nbsp;Newest first"
+          old_html: "<i class=\"fas fa-sort-numeric-down\"></i>&nbsp;&nbsp;Oldest first"
+          atoz_html: "<i class=\"fas fa-sort-alpha-down\"></i>&nbsp;&nbsp;Name A to Z"
+          ztoa_html: "<i class=\"fas fa-sort-alpha-up\"></i>&nbsp;&nbsp;Name Z to A"
 
     steps:
       placeholder: 'Enter step name'
@@ -3207,6 +3213,7 @@ en:
     change_experiment_role: "Change experiment role"
     change_my_module_role: "Change task role"
     select_role: "Select role"
+    assign_all_team_members: "Grant access to all team members"
     from_project: "%{user_role} [from project]"
     from_experiment: "%{user_role} [from experiment]"
     experiment_select_role: "Change experiment role"