Merge branch 'master' of https://github.com/biosistemika/scinote-web into zz_tooltip_settings_enable_sci2663

Merging to update db, so i dont have to docker-clean my whole environment 2 times to switch between this branch and up to date ones

VERSION

@@ -1 +1 @@
-1.14.3
+1.14.4

app/assets/javascripts/application.js.erb

@@ -262,4 +262,9 @@ var HelperModule = (function(){
       $('.modal').modal('hide');
     });
   });
-})();
+
+  /* Fix .selectpicker (bootstrap-select) to work with Turbolinks 5.x */
+  $(document).on('turbolinks:load', function() {
+    $(window).trigger('load.bs.select.data-api');
+  });
+})();

app/assets/javascripts/repositories/forms/repository_item_edit.js

@@ -115,6 +115,7 @@
   RepositoryItemEditForm.prototype.parseToFormObject = function(tableID, selectedRecord) {
     var formData = this.formData;
     var formDataObj = new FormData();
+    var removeFileColumns = [];
     formDataObj.append('request_url', $(tableID).data('current-uri'));
     formDataObj.append('repository_row_id', $(selectedRecord).attr('id'));
 
@@ -125,18 +126,25 @@
       } else {
         var colId = element.replace('colId-', '');
         var $el   = $('#' + element);
+        // don't save anything if element is not visible
+        if($el.length == 0) {
+          return true;
+        }
         if($el.attr('type') === 'file') {
-          // don't save anything if element is deleted
+          // handle deleting of element
           if($el.attr('remove') === "true") {
-            return true;
+            removeFileColumns.push(colId);
+            formDataObj.append('repository_cells[' + colId + ']', null);
+          } else {
+            formDataObj.append('repository_cells[' +  colId + ']',
+                               getFileValue($el));
           }
-          formDataObj.append('repository_cells[' +  colId + ']',
-                             getFileValue($el));
-        } else if(value.length > 0) {
+        } else if(value.length >= 0) {
           formDataObj.append('repository_cells[' +  colId + ']', value);
         }
       }
     });
+    formDataObj.append('remove_file_columns', JSON.stringify(removeFileColumns));
     return formDataObj;
   }
   /**

app/assets/javascripts/sitewide/drag_n_drop.js.erb

@@ -270,7 +270,7 @@
     function _uploadedAssetPreview(asset, i) {
       var html = '<div class="panel panel-default panel-step-attachment-new">';
       html += '<div class="panel-heading">';
-      html += '<span class="fas fa-file"></span>';
+      html += '<span class="fas fa-paperclip"></span>';
       html += '<%= I18n.t 'assets.drag_n_drop.file_label' %>';
       html += '<div class="pull-right">';
       html += '<a data-item-id="' + i + '" href="#">';
@@ -442,7 +442,7 @@
     function _uploadedAssetPreview(asset, i) {
       var html = '<div class="panel panel-default panel-result-attachment-new">';
       html += '<div class="panel-heading">';
-      html += '<span class="fas fa-file"></span>';
+      html += '<span class="fas fa-paperclip"></span>';
       html += '<%= I18n.t 'assets.drag_n_drop.file_label' %>';
       html += '<div class="pull-right">';
       html += '<a data-item-id="' + i + '" href="#">';

app/assets/javascripts/users/settings/teams/invite_users_modal.js

@@ -164,15 +164,20 @@
   }
 
   function initializeModalsToggle() {
-    $("[data-trigger='invite-users']").on('click', function() {
+    $("[data-trigger='invite-users']").on('click', function(event) {
       var id = $(this).attr('data-modal-id');
+      event.preventDefault();
+      event.stopPropagation();
       $('[data-role=invite-users-modal][data-id=' + id + ']')
         .modal('show');
     });
   }
 
-  $('[data-role=invite-users-modal]').each(function() {
-    initializeModal($(this));
+  $(document).on('turbolinks:load', function() {
+    $('[data-role=invite-users-modal]').each(function() {
+      initializeModal($(this));
+    });
+
+    initializeModalsToggle();
   });
-  initializeModalsToggle();
 }());

app/assets/javascripts/users/settings/teams/show.js

@@ -1,5 +1,3 @@
-//= require users/settings/teams/invite_users_modal
-
 (function() {
   'use strict';
 

app/controllers/activities_controller.rb

@@ -23,7 +23,7 @@ class ActivitiesController < ApplicationController
     activities = current_user.last_activities
                              .page(page)
                              .per(Constants::ACTIVITY_AND_NOTIF_SEARCH_LIMIT)
-    unless activities.last_page?
+    unless activities.blank? || activities.last_page?
       more_url = url_for(
         activities_url(
           format: :json,

app/controllers/api/api_controller.rb

@@ -34,6 +34,8 @@ module Api
     end
 
     def health
+      User.new && Team.new && Project.new
+      User.first if params[:db]
       render plain: 'RUNNING'
     end
 

app/controllers/repository_rows_controller.rb

@@ -134,7 +134,7 @@ class RepositoryRowsController < ApplicationController
                 existing.delete
               end
             elsif existing.value_type == 'RepositoryAssetValue'
-              next if value.blank?
+              existing.value.destroy && next if remove_file_columns_params.include?(key)
               if existing.value.asset.update(file: value)
                 existing.value.asset.created_by = current_user
                 existing.value.asset.last_modified_by = current_user
@@ -145,6 +145,7 @@ class RepositoryRowsController < ApplicationController
                 }
               end
             else
+              existing.value.destroy && next if value == ''
               existing.value.data = value
               if existing.value.save
                 record_annotation_notification(@record, existing)
@@ -156,17 +157,12 @@ class RepositoryRowsController < ApplicationController
               end
             end
           else
+            next if value == ''
             # Looks like it is a new cell, so we need to create new value, cell
             # will be created automatically
             next if create_cell_value(@record, key, value, errors).nil?
           end
         end
-        # Clean up empty cells, not present in updated record
-        @record.repository_cells.each do |cell|
-          next if cell.value_type == 'RepositoryListValue'
-          cell.value.destroy unless cell_params
-                                    .key?(cell.repository_column_id.to_s)
-        end
       else
         @record.repository_cells.each { |c| c.value.destroy }
       end
@@ -369,6 +365,10 @@ class RepositoryRowsController < ApplicationController
     params.permit(repository_cells: {}).to_h[:repository_cells]
   end
 
+  def remove_file_columns_params
+    JSON.parse(params.fetch(:remove_file_columns) { '[]' })
+  end
+
   def selected_params
     params.permit(selected_rows: []).to_h[:selected_rows]
   end

app/services/api.rb

@@ -16,12 +16,14 @@ module Api
     attr_accessor :core_api_token_ttl
     attr_accessor :core_api_token_iss
     attr_accessor :azure_ad_apps
+    attr_accessor :core_api_v1_preview
 
     def initialize
       @core_api_sign_alg = 'HS256'
       @core_api_token_ttl = 30.minutes
       @core_api_token_iss = 'SciNote'
       @azure_ad_apps = {}
+      @core_api_v1_preview = false
     end
   end
 end

app/views/my_modules/archive/_result.html.erb

@@ -39,7 +39,7 @@
         <% if result.asset.is_image? %>
           <span class="fas fa-image"></span>
         <% else %>
-          <span class="fas fa-file"></span>
+          <span class="fas fa-paperclip"></span>
         <% end %>
       <% elsif result.is_text %>
         <span class="fas fa-asterisk"></span>

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

@@ -17,12 +17,12 @@
       <% if can_manage_protocol_in_module?(@protocol) %>
         <li>
           <a class="btn-open-file" href="#" data-action="load-from-file" data-import-url="<%= load_from_file_protocol_path(@protocol, format: :json) %>">
-            <span class="fas fa-file"></span>&nbsp;<%= t("my_modules.protocols.buttons.load_protocol_from_file") %>
+            <span class="fas fa-paperclip"></span>&nbsp;<%= t("my_modules.protocols.buttons.load_protocol_from_file") %>
             <input type="file" value="" accept=".eln" data-turbolinks="false">
           </a>
         </li>
       <% else %>
-        <li class="disabled"><a href="#"><span class="fas fa-file"></span>&nbsp;<%= t("my_modules.protocols.buttons.load_protocol_from_file") %></a></li>
+        <li class="disabled"><a href="#"><span class="fas fa-paperclip"></span>&nbsp;<%= t("my_modules.protocols.buttons.load_protocol_from_file") %></a></li>
       <% end %>
     </ul>
   </div>

app/views/protocols/index.html.erb

@@ -61,7 +61,7 @@
               <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"' %>>
-                    <span class="fas fa-file"></span>
+                    <span class="fas fa-paperclip"></span>
                     <span class="hidden-xs"><%= t("protocols.index.import_alt") %></span>
                     <input type="file" value="" accept=".eln" data-role="import-file-input"
                     data-team-id="<%= @current_team.id %>"
@@ -70,8 +70,8 @@
                   </a>
                 </li>
                 <li>
-                <%= link_to "#modal-import-json-protocol", data: { toggle: 'modal', remote: true } do %>
-                  <span class="fas fa-file"></span>
+                <%= link_to "#modal-import-json-protocol", data: { toggle: 'modal' } do %>
+                  <span class="fas fa-paperclip"></span>
                   <span class="hidden-xs"><%= t("protocols.index.import_json") %></span>
                 <% end %>
                 </li>
@@ -85,7 +85,7 @@
 
           <div class="btn-group" role="group">
             <a class="btn btn-default" data-action="archive" data-url="<%= archive_protocols_path %>">
-              <span class="fas fa-briefcase"></span>
+              <span class="fas fa-archive"></span>
               <span class="hidden-xs">&nbsp;<%= t("protocols.index.archive_action") %></span>
             </a>
           </div>

app/views/reports/new/_report_navigation.html.erb

@@ -8,8 +8,8 @@
         <span class="caret"></span>
       </button>
       <ul class="dropdown-menu" aria-labelledby="dropdownMenu1">
-        <li><a href="#" data-sort="desc"><%= t('projects.reports.new.nav_sort_desc') %></a></li>
-        <li><a href="#" data-sort="asc"><%= t('projects.reports.new.nav_sort_asc') %></a></li>
+        <li><a href="#" data-sort="desc" data-turbolinks="false"><%= t('projects.reports.new.nav_sort_desc') %></a></li>
+        <li><a href="#" data-sort="asc" data-turbolinks="false"><%= t('projects.reports.new.nav_sort_asc') %></a></li>
       </ul>
     </div>
 
@@ -21,7 +21,7 @@
       <div class="form-group">
       <%= hidden_field_tag "html", "" %>
       <%= link_to "", class: "btn btn-default", remote: true, id: "get-report-pdf" do %>
-        <span class="fas fa-file-download"></span>
+        <span class="fas fa-upload"></span>
         <span class="hidden-xs"><%=t "projects.reports.new.nav_pdf" %></span>
       <% end %>
       </div>
@@ -30,6 +30,8 @@
     <button
       onclick="$('#savePDFtoInventory').modal('show')"
       class="btn btn-default">
+      <span class="fas fa-save">
+      </span>
       <%=t 'projects.reports.new.save_PDF_to_inventory'%>
     </button>
 

app/views/search/index.html.erb

@@ -182,7 +182,7 @@
                            match_case: @search_case, utf8: '✓',
                            search_id: @search_id}.to_query %>">
               <span class="badge pull-right"><%= @asset_search_count %></span>
-              <span class="fas fa-file"></span>
+              <span class="fas fa-paperclip"></span>
               <%= t'Assets' %>
             </a>
           </li>

app/views/search/results/_assets.html.erb

@@ -6,7 +6,7 @@
       <% if wopi_file?(asset) %>
         <%= file_extension_icon(asset) %>
       <% else %>
-        <span class="fas fa-file"></span>
+        <span class="fas fa-paperclip"></span>
       <% end %>
     <% end %>
     <%= render partial: "search/results/partials/asset_text.html.erb", locals: { asset: asset, query: search_query } %>

app/views/search/results/_results.html.erb

@@ -8,7 +8,7 @@
       <% if result.asset.is_image? %>
         <span class="fas fa-image"></span>
       <% else %>
-        <span class="fas fa-file"></span>
+        <span class="fas fa-paperclip"></span>
       <% end %>
     <% end %>
     <%= render partial: "search/results/partials/result_text.html.erb", locals: { result: result, query: search_query, target: nil } %>

app/views/steps/_empty_step.html.erb

@@ -14,7 +14,7 @@
       id="new-step-assets-tab"
       onClick="dragNdropAssetsInit('steps')">
     <a href="#new-step-assets" data-toggle="tab" data-no-turbolink="true">
-      <span class="fas fa-file"></span>
+      <span class="fas fa-paperclip"></span>
       <%= t("protocols.steps.new.tab_assets") %>
     </a>
   </li>

app/views/steps/_form_assets.html.erb

@@ -1,6 +1,6 @@
 <div class="panel panel-default panel-step-attachment">
   <div class="panel-heading">
-    <span class="fas fa-file"></span>
+    <span class="fas fa-paperclip"></span>
     <%= t("protocols.steps.new.asset_panel_title") %>
     <div class="pull-right">
       <% unless ff.object.file.exists? && ff.object.locked? %>

app/views/users/settings/teams/show.html.erb

@@ -93,7 +93,7 @@
       <div class="panel-body">
         <div class="col-xs-24 col-sm-12">
           <a href="#" class="btn btn-primary pull-right row" data-trigger="invite-users"
-             data-modal-id="team-invite-users-modal" data-remote="true">
+             data-modal-id="team-invite-users-modal">
             <span class="fas fa-plus"></span>
             <%= t("users.settings.teams.edit.add_user") %>
           </a>
@@ -137,4 +137,5 @@
 <%= render partial: 'users/settings/user_teams/destroy_user_team_modal.html.erb' %>
 <%= stylesheet_link_tag 'datatables' %>
 <%= javascript_include_tag 'users/settings/teams/show' %>
+<%= javascript_include_tag 'users/settings/teams/invite_users_modal' %>
 <span data-hook="team-bottom"></span>

config/initializers/api.rb

@@ -9,6 +9,8 @@ Api.configure do |config|
     config.core_api_token_iss = ENV['CORE_API_TOKEN_ISS']
   end
 
+  config.core_api_v1_preview = true if ENV['CORE_API_V1_PREVIEW']
+
   vars = ENV.select { |name, _| name =~ /^[[:alnum:]]*_AZURE_AD_APP_ID/ }
   vars.each do |name, value|
     app_name = name.sub('_AZURE_AD_APP_ID', '')

config/initializers/assets.rb

@@ -28,6 +28,8 @@ Rails.application.config.assets.precompile +=
 Rails.application.config.assets.precompile +=
   %w(users/settings/teams/add_user_modal.js)
 Rails.application.config.assets.precompile += %w(users/settings/teams/show.js)
+Rails.application.config.assets.precompile +=
+  %w(users/settings/teams/invite_users_modal.js)
 Rails.application.config.assets.precompile += %w(my_modules/activities.js)
 Rails.application.config.assets.precompile += %w(my_modules/protocols.js)
 Rails.application.config.assets.precompile +=

config/initializers/extends.rb

@@ -61,7 +61,7 @@ class Extends
                                 repository_asset_value: :asset]
 
   # List of implemented core API versions
-  API_VERSIONS = ['20170715']
+  API_VERSIONS = %w(20170715 v1)
 
   # Array used for injecting names of additional authentication methods for API
   API_PLUGABLE_AUTH_METHODS = [:azure_jwt_auth]

config/initializers/silencer.rb

@@ -7,7 +7,8 @@ Rails.application.configure do
     config.log_tags,
     silence: [
       # Silence WickedPDF rendering in logs
-      %r{/projects/[0-9]*/reports/generate.pdf}
+      %r{/projects/[0-9]*/reports/generate.pdf},
+      '/api/health'
     ]
   )
 end

config/routes.rb

@@ -540,8 +540,10 @@ Rails.application.routes.draw do
       get 'health', to: 'api#health'
       get 'status', to: 'api#status'
       post 'auth/token', to: 'api#authenticate'
-      namespace :v1 do
-        resources :teams, only: %i(index show) do
+      if Api.configuration.core_api_v1_preview
+        namespace :v1 do
+          resources :teams, only: %i(index show) do
+          end
         end
       end
     end

docker-compose.yml

@@ -2,7 +2,7 @@ version: '2'
 services:
   db:
     container_name: scinote_db_development
-    image: postgres:9.4
+    image: postgres:9.6
     volumes:
       - scinote_development_postgres:/var/lib/postgresql/data
 

spec/controllers/api/api_controller_spec.rb

@@ -1,6 +1,18 @@
 require 'rails_helper'
 
 describe Api::ApiController, type: :controller do
+  describe 'GET #health' do
+    before do
+      get :health
+    end
+
+    it 'Returns HTTP success and with correct text' do
+      expect(response).to be_success
+      expect(response).to have_http_status(200)
+      expect(response.body).to match('RUNNING')
+    end
+  end
+
   describe 'GET #status' do
     before do
       get :status
@@ -17,7 +29,9 @@ describe Api::ApiController, type: :controller do
       expect(hash_body).to match(
         'message' => I18n.t('api.core.status_ok'),
         'versions' => [{ 'version' => '20170715',
-                         'baseUrl' => '/api/20170715/' }]
+                         'baseUrl' => '/api/20170715/' },
+                       { 'version' => 'v1',
+                         'baseUrl' => '/api/v1/' }]
       )
     end
   end

spec/rails_helper.rb

@@ -5,6 +5,9 @@ require 'database_cleaner'
 require 'devise'
 require_relative 'support/controller_macros'
 ENV['RAILS_ENV'] = 'test'
+
+ENV['CORE_API_V1_PREVIEW'] = 'true'
+
 require File.expand_path('../../config/environment', __FILE__)
 # Prevent database truncation if the environment is production
 abort('The Rails environment is running in production mode!') if Rails.env.production?