Merge branch 'master' into rails-5.1

Conflicts:
	Gemfile.lock
	app/datatables/repository_datatable.rb
	app/models/repository_cell.rb

Gemfile

@@ -51,7 +51,7 @@ gem 'ajax-datatables-rails', '~> 0.3.1'
 gem 'commit_param_routing' # Enables different submit actions in the same form to route to different actions in controller
 gem 'kaminari'
 gem "i18n-js", ">= 3.0.0.rc11" # Localization in javascript files
-gem 'roo', '~> 2.1.0' # Spreadsheet parser
+gem 'roo', '~> 2.7.1' # Spreadsheet parser
 gem 'wicked_pdf'
 gem 'silencer' # Silence certain Rails logs
 gem 'wkhtmltopdf-heroku'
@@ -64,6 +64,7 @@ gem 'sneaky-save', git: 'https://github.com/einzige/sneaky-save'
 gem 'rails_autolink', '~> 1.1', '>= 1.1.6'
 gem 'delayed_paperclip'
 gem 'rubyzip'
+gem 'activerecord-import'
 
 gem 'paperclip', '~> 5.1' # File attachment, image attachment library
 gem 'aws-sdk', '~> 2'

Gemfile.lock

@@ -7,7 +7,7 @@ GIT
 
 GIT
   remote: https://github.com/einzige/sneaky-save
-  revision: e7c77674abe74d598dfd58db7c680dd85936f207
+  revision: 7e7596720e76a3c243042be2f5f916525b143a54
   specs:
     sneaky-save (0.1.2)
       activerecord (>= 3.2.0)
@@ -56,6 +56,8 @@ GEM
       activemodel (= 5.1.1)
       activesupport (= 5.1.1)
       arel (~> 8.0)
+    activerecord-import (0.19.1)
+      activerecord (>= 3.2)
     activesupport (5.1.1)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (~> 0.7)
@@ -70,26 +72,28 @@ GEM
     ast (2.3.0)
     auto_strip_attributes (2.1.0)
       activerecord (>= 3.0)
-    autoprefixer-rails (7.1.1.2)
+    autoprefixer-rails (7.1.2.4)
       execjs
     autosize-rails (1.18.17)
       rails (>= 3.1)
     awesome_print (1.8.0)
-    aws-sdk (2.2.37)
+    aws-sdk (2.10.21)
-      aws-sdk-resources (= 2.2.37)
+      aws-sdk-resources (= 2.10.21)
-    aws-sdk-core (2.2.37)
+    aws-sdk-core (2.10.21)
+      aws-sigv4 (~> 1.0)
       jmespath (~> 1.0)
-    aws-sdk-resources (2.2.37)
+    aws-sdk-resources (2.10.21)
-      aws-sdk-core (= 2.2.37)
+      aws-sdk-core (= 2.10.21)
+    aws-sigv4 (1.0.1)
     babel-source (5.8.35)
     babel-transpiler (0.7.0)
       babel-source (>= 4.0, < 6)
       execjs (~> 2.0)
     base62 (1.0.0)
     bcrypt (3.1.11)
-    better_errors (2.1.1)
+    better_errors (2.3.0)
       coderay (>= 1.0.0)
-      erubis (>= 2.6.6)
+      erubi (>= 1.0.0)
       rack (>= 0.9.0)
     binding_of_caller (0.7.2)
       debug_inspector (>= 0.0.1)
@@ -102,9 +106,9 @@ GEM
     bootstrap_form (2.7.0)
     builder (3.2.3)
     byebug (9.0.6)
-    capybara (2.14.4)
+    capybara (2.15.1)
       addressable
-      mime-types (>= 1.16)
+      mini_mime (>= 0.1.3)
       nokogiri (>= 1.3.3)
       rack (>= 1.0.0)
       rack-test (>= 0.5.4)
@@ -169,15 +173,14 @@ GEM
       devise (>= 4.0.0)
     diff-lcs (1.3)
     docile (1.1.5)
-    erubi (1.6.0)
+    erubi (1.6.1)
-    erubis (2.7.0)
     execjs (2.7.0)
     factory_girl (4.8.0)
       activesupport (>= 3.0.0)
     factory_girl_rails (4.8.0)
       factory_girl (~> 4.8.0)
       railties (>= 3.0.0)
-    faker (1.7.3)
+    faker (1.8.4)
       i18n (~> 0.5)
     ffi (1.9.18)
     figaro (1.1.1)
@@ -188,8 +191,8 @@ GEM
     globalid (0.4.0)
       activesupport (>= 4.2.0)
     hammerjs-rails (2.0.4)
-    i18n (0.8.4)
+    i18n (0.8.6)
-    i18n-js (3.0.0)
+    i18n-js (3.0.1)
       i18n (~> 0.6, >= 0.6.6)
     introjs-rails (1.0.0)
       sass-rails (>= 3.2)
@@ -236,17 +239,18 @@ GEM
     method_source (0.8.2)
     mime-types (1.25.1)
     mimemagic (0.3.2)
+    mini_mime (0.1.3)
     mini_portile2 (2.2.0)
-    minitest (5.10.2)
+    minitest (5.10.3)
     momentjs-rails (2.17.1)
       railties (>= 3.1)
     multi_json (1.12.1)
     multi_test (0.1.2)
-    nested_form_fields (0.8)
+    nested_form_fields (0.8.1)
       coffee-rails (>= 3.2.1)
       jquery-rails
       rails (>= 3.2.0)
-    newrelic_rpm (4.2.0.334)
+    newrelic_rpm (4.3.0.335)
     nio4r (2.1.0)
     nokogiri (1.8.0)
       mini_portile2 (~> 2.2.0)
@@ -260,7 +264,7 @@ GEM
       cocaine (~> 0.5.5)
       mime-types
       mimemagic (~> 0.3.0)
-    parallel (1.11.2)
+    parallel (1.12.0)
     parser (2.4.0.0)
       ast (~> 2.2)
     pg (0.21.0)
@@ -318,7 +322,7 @@ GEM
     rainbow (2.2.2)
       rake
     rake (12.0.0)
-    rb-fsevent (0.9.8)
+    rb-fsevent (0.10.2)
     rb-inotify (0.9.10)
       ffi (>= 0.5.0, < 2)
     rdoc (4.3.0)
@@ -332,7 +336,7 @@ GEM
       lazy_priority_queue (~> 0.1.0)
       stream (~> 0.5.0)
     rkelly-remix (0.0.7)
-    roo (2.1.1)
+    roo (2.7.1)
       nokogiri (~> 1)
       rubyzip (~> 1.1, < 2.0.0)
     rspec-core (3.6.0)
@@ -367,7 +371,7 @@ GEM
       crass (~> 1.0.2)
       nokogiri (>= 1.4.4)
       nokogumbo (~> 1.4.1)
-    sass (3.4.24)
+    sass (3.4.25)
     sass-rails (5.0.6)
       railties (>= 4.0.0, < 6)
       sass (~> 3.1)
@@ -380,7 +384,7 @@ GEM
     sdoc (0.4.2)
       json (~> 1.7, >= 1.7.7)
       rdoc (~> 4.0)
-    shoulda-matchers (3.1.1)
+    shoulda-matchers (3.1.2)
       activesupport (>= 4.0.0)
     silencer (1.0.1)
     simple_token_authentication (1.15.1)
@@ -413,8 +417,8 @@ GEM
     stream (0.5)
     thor (0.19.4)
     thread_safe (0.3.6)
-    tilt (2.0.7)
+    tilt (2.0.8)
-    tinymce-rails (4.6.4)
+    tinymce-rails (4.6.5)
       railties (>= 3.1.1)
     turbolinks (5.0.1)
       turbolinks-source (~> 5)
@@ -446,6 +450,7 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
+  activerecord-import
   ajax-datatables-rails (~> 0.3.1)
   aspector
   auto_strip_attributes (~> 2.1)
@@ -506,7 +511,7 @@ DEPENDENCIES
   recaptcha
   remotipart (~> 1.2)
   rgl
-  roo (~> 2.1.0)
+  roo (~> 2.7.1)
   rspec-rails
   rubocop
   ruby-graphviz (~> 1.2)
@@ -536,4 +541,4 @@ RUBY VERSION
    ruby 2.4.1p111
 
 BUNDLED WITH
-   1.15.1
+   1.15.3

VERSION

@@ -0,0 +1 @@
+1.12.3

app/assets/javascripts/repositories/index.js

@@ -18,7 +18,7 @@
     $('#form-records-file').on('ajax:success', function(ev, data) {
       $('#modal-import-records').modal('hide');
       $(data.html).appendTo('body').promise().done(function() {
-        $('#parse-records_modal')
+        $('#parse-records-modal')
           .modal('show')
           .on('hidden.bs.modal', function() {
             animateSpinner();
@@ -26,6 +26,11 @@
           });
         repositoryRecordsImporter();
       });
+    }).on('ajax:error', function(ev, data) {
+      $(this).find('.form-group').addClass('has-error');
+      $(this).find('.form-group').find('.help-block').remove();
+      $(this).find('.form-group').append("<span class='help-block'>" +
+                                         data.responseJSON.message + '</span>');
     });
   }
 
@@ -41,8 +46,10 @@
         success: function (data) {
         	var tabBody = $(pane.context.hash).find(".tab-content-body");
           tabBody.html(data.html);
-          pane.tab('show').promise().done(function() {
+          pane.tab('show').promise().done(function(el) {
             initImportRecordsModal();
+            RepositoryDatatable.destroy()
+            RepositoryDatatable.init(el.attr('data-repo-table'));
           });
         },
         error: function (error) {

app/assets/javascripts/repositories/my_module_repository.js

@@ -0,0 +1,10 @@
+(function() {
+  'use strict';
+
+  // initialze repository datatable
+  $(document).ready(function() {
+    RepositoryDatatable.destroy()
+    RepositoryDatatable.init($('#content').attr('data-repo-id'));
+    onClickToggleAssignedRecords();
+  });
+})();

app/assets/javascripts/sitewide/about_modal.js

@@ -0,0 +1,9 @@
+(function() {
+  'use strict';
+
+  $(document).ready(function() {
+    $("[data-trigger='about-modal']").on('click', function() {
+      $('[data-role=about-modal]').modal('show');
+    });
+  });
+})();

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

@@ -424,6 +424,11 @@ var SmartAnnotation = (function() {
       init: init
     };
   }
+  // Closes the atwho popup * needed in repositories to close the popup
+  // if nothing is selected and the user leaves the form *
+  function closePopup() {
+    $('.atwho-header-res').find('.glyphicon-remove').click();
+  }
 
   function initialize(field) {
     var atWho = new setAtWho(field);
@@ -432,7 +437,8 @@ var SmartAnnotation = (function() {
 
   var publicApi = Object.freeze({
     init: initialize,
-    preventPropagation: atwhoStopPropagation
+    preventPropagation: atwhoStopPropagation,
+    closePopup: closePopup
   });
 
   return publicApi;

app/controllers/repositories_controller.rb

@@ -184,27 +184,27 @@ class RepositoriesController < ApplicationController
 
   def parse_sheet
     repository = current_team.repositories.find_by_id(params[:id])
-    parsed_file = ImportRepository::ParseRepository.new(
-      file: params[:file],
-      repository: repository,
-      session: session
-    )
 
-    respond_to do |format|
+    unless params[:file]
-      unless params[:file]
+      repository_response(t('teams.parse_sheet.errors.no_file_selected'))
-        repository_response(t('teams.parse_sheet.errors.no_file_selected'))
+      return
-        return
+    end
-      end
+    begin
-      begin
+      parsed_file = ImportRepository::ParseRepository.new(
-        if parsed_file.too_large?
+        file: params[:file],
-          repository_response(t('general.file.size_exceeded',
+        repository: repository,
-                                file_size: Constants::FILE_MAX_SIZE_MB))
+        session: session
-        elsif parsed_file.empty?
+      )
-          flash[:notice] = t('teams.parse_sheet.errors.empty_file')
+      if parsed_file.too_large?
-          redirect_to back and return
+        repository_response(t('general.file.size_exceeded',
-        else
+                              file_size: Constants::FILE_MAX_SIZE_MB))
-          @import_data = parsed_file.data
+      elsif parsed_file.empty?
-          if parsed_file.generated_temp_file?
+        flash[:notice] = t('teams.parse_sheet.errors.empty_file')
+        redirect_to back and return
+      else
+        @import_data = parsed_file.data
+        if parsed_file.generated_temp_file?
+          respond_to do |format|
             format.json do
               render json: {
                 html: render_to_string(
@@ -212,16 +212,16 @@ class RepositoriesController < ApplicationController
                 )
               }
             end
-          else
-            repository_response(t('teams.parse_sheet.errors.temp_file_failure'))
           end
+        else
+          repository_response(t('teams.parse_sheet.errors.temp_file_failure'))
         end
-      rescue ArgumentError, CSV::MalformedCSVError
-        repository_response(t('teams.parse_sheet.errors.invalid_file',
-                              encoding: ''.encoding))
-      rescue TypeError
-        repository_response(t('teams.parse_sheet.errors.invalid_extension'))
       end
+    rescue ArgumentError, CSV::MalformedCSVError
+      repository_response(t('teams.parse_sheet.errors.invalid_file',
+                            encoding: ''.encoding))
+    rescue TypeError
+      repository_response(t('teams.parse_sheet.errors.invalid_extension'))
     end
   end
 
@@ -238,8 +238,9 @@ class RepositoriesController < ApplicationController
                                 number_of_rows: status[:nr_of_added])
             render json: {}, status: :ok
           else
-            flash[:alert] = t('repositories.import_records.error_flash',
+            flash[:alert] =
-                              message: status[:errors])
+              t('repositories.import_records.partial_success_flash',
+                nr: status[:nr_of_added], total_nr: status[:total_nr])
             render json: {}, status: :unprocessable_entity
           end
         else
@@ -320,13 +321,15 @@ class RepositoriesController < ApplicationController
   end
 
   def repository_response(message)
-    format.html do
+    respond_to do |format|
-      flash[:alert] = message
+      format.html do
-      redirect_to :back
+        flash[:alert] = message
-    end
+        redirect_to :back
-    format.json do
+      end
-      render json: { message: message },
+      format.json do
-        status: :unprocessable_entity
+        render json: { message: message },
+          status: :unprocessable_entity
+      end
     end
   end
 

app/controllers/repository_rows_controller.rb

@@ -19,9 +19,7 @@ class RepositoryRowsController < ApplicationController
 
     record.transaction do
       record.name = record_params[:name] unless record_params[:name].blank?
-      unless record.save
+      errors[:default_fields] = record.errors.messages unless record.save
-        errors[:default_fields] = record.errors.messages
-      end
       if params[:repository_cells]
         params[:repository_cells].each do |key, value|
           column = @repository.repository_columns.detect do |c|
@@ -94,9 +92,7 @@ class RepositoryRowsController < ApplicationController
 
     @record.transaction do
       @record.name = record_params[:name].blank? ? nil : record_params[:name]
-      unless @record.save
+      errors[:default_fields] = @record.errors.messages unless @record.save
-        errors[:default_fields] = @record.errors.messages
-      end
       if params[:repository_cells]
         params[:repository_cells].each do |key, value|
           existing = @record.repository_cells.detect do |c|
@@ -119,7 +115,7 @@ class RepositoryRowsController < ApplicationController
             column = @repository.repository_columns.detect do |c|
               c.id == key.to_i
             end
-            value = RepositoryTextValue.new(
+            cell_value = RepositoryTextValue.new(
               data: value,
               created_by: current_user,
               last_modified_by: current_user,
@@ -128,15 +124,15 @@ class RepositoryRowsController < ApplicationController
                 repository_column: column
               }
             )
-            if value.save
+            if cell_value.save
-              record_annotation_notification(@record, value.repository_cell)
+              record_annotation_notification(@record,
+                                             cell_value.repository_cell)
             else
               errors[:repository_cells] << {
-                "#{column.id}": value.errors.messages
+                "#{column.id}": cell_value.errors.messages
               }
             end
           end
-          raise ActiveRecord::Rollback if errors[:repository_cells].any?
         end
         # Clean up empty cells, not present in updated record
         @record.repository_cells.each do |cell|

app/controllers/teams_controller.rb

@@ -36,8 +36,7 @@ class TeamsController < ApplicationController
 
             # Get data (it will trigger any errors as well)
             @header = sheet.row(1)
-            @rows = [];
+            @columns = sheet.row(2)
-            @rows << Hash[[@header, sheet.row(2)].transpose]
 
             # Fill in fields for dropdown
             @available_fields = @team.get_available_sample_fields

app/controllers/wopi_controller.rb

@@ -70,11 +70,11 @@ class WopiController < ActionController::Base
       UserCanNotWriteRelative:       true,
       CloseUrl:                      @close_url,
       DownloadUrl: url_for(controller: 'assets', action: 'download',
-                           id: @asset.id),
+                           id: @asset.id, host: ENV['WOPI_USER_HOST']),
       HostEditUrl: url_for(controller: 'assets', action: 'edit',
-                           id: @asset.id),
+                           id: @asset.id, host: ENV['WOPI_USER_HOST']),
       HostViewUrl: url_for(controller: 'assets', action: 'view',
-                           id: @asset.id),
+                           id: @asset.id, host: ENV['WOPI_USER_HOST']),
       BreadcrumbBrandName:  @breadcrumb_brand_name,
       BreadcrumbBrandUrl:   @breadcrumb_brand_url,
       BreadcrumbFolderName: @breadcrumb_folder_name,
@@ -82,7 +82,7 @@ class WopiController < ActionController::Base
     }
     response.headers['X-WOPI-HostEndpoint'] = ENV['WOPI_ENDPOINT_URL']
     response.headers['X-WOPI-MachineName'] = ENV['WOPI_ENDPOINT_URL']
-    response.headers['X-WOPI-ServerVersion'] = Constants::APP_VERSION
+    response.headers['X-WOPI-ServerVersion'] = Scinote::Application::VERSION
     render json: msg and return
   end
 
@@ -286,21 +286,21 @@ class WopiController < ActionController::Base
       if @protocol.in_module?
         @close_url = protocols_my_module_url(@protocol.my_module,
                                              only_path: false,
-                                             host: ENV['WOPI_BREADCRUMBS_HOST'])
+                                             host: ENV['WOPI_USER_HOST'])
 
         project = @protocol.my_module.experiment.project
         @breadcrumb_brand_name  = project.name
         @breadcrumb_brand_url   = project_url(project,
                                               only_path: false,
-                                              host: ENV['WOPI_BREADCRUMBS_HOST'])
+                                              host: ENV['WOPI_USER_HOST'])
         @breadcrumb_folder_name = @protocol.my_module.name
       else
         @close_url = protocols_url(only_path: false,
-                                   host: ENV['WOPI_BREADCRUMBS_HOST'])
+                                   host: ENV['WOPI_USER_HOST'])
 
         @breadcrump_brand_name  = 'Projects'
         @breadcrumb_brand_url   = root_url(only_path: false,
-                                           host: ENV['WOPI_BREADCRUMBS_HOST'])
+                                           host: ENV['WOPI_USER_HOST'])
         @breadcrumb_folder_name = 'Protocol managament'
       end
       @breadcrumb_folder_url  = @close_url
@@ -310,12 +310,12 @@ class WopiController < ActionController::Base
 
       @close_url = results_my_module_url(@my_module,
                                          only_path: false,
-                                         host: ENV['WOPI_BREADCRUMBS_HOST'])
+                                         host: ENV['WOPI_USER_HOST'])
 
       @breadcrumb_brand_name  = @my_module.experiment.project.name
       @breadcrumb_brand_url   = project_url(@my_module.experiment.project,
                                             only_path: false,
-                                            host: ENV['WOPI_BREADCRUMBS_HOST'])
+                                            host: ENV['WOPI_USER_HOST'])
       @breadcrumb_folder_name = @my_module.name
       @breadcrumb_folder_url  = @close_url
     end

app/datatables/repository_datatable.rb

@@ -152,7 +152,7 @@ class RepositoryDatatable < CustomDatatable
     # Make mappings of custom columns, so we have same id for every column
     i = 5
     @columns_mappings = {}
-    @repository.repository_columns.each do |column|
+    @repository.repository_columns.order(:id).each do |column|
       @columns_mappings[column.id] = i.to_s
       i += 1
     end
@@ -230,13 +230,68 @@ class RepositoryDatatable < CustomDatatable
 
   # Override default sort method if needed
   def sort_records(records)
-    if sort_column(order_params) == ASSIGNED_SORT_COL
+    if params[:order].present? && params[:order].length == 1
-      # If "assigned" column is sorted
+      if sort_column(params[:order].values[0]) == ASSIGNED_SORT_COL
-      direction = sort_null_direction(order_params)
+        # If "assigned" column is sorted when viewing assigned items
-      if @my_module
+        return records if @my_module && params[:assigned] == 'assigned'
-        # Depending on the sort, order nulls first or
+        # If "assigned" column is sorted
-        # nulls last on repository_cells association
+        direction = sort_null_direction(params[:order].values[0])
-        return records if dt_params[:assigned] == 'assigned'
+        if @my_module
+          # Depending on the sort, order nulls first or
+          # nulls last on repository_cells association
+          records.joins(
+            "LEFT OUTER JOIN my_module_repository_rows ON
+            (repository_rows.id = my_module_repository_rows.repository_row_id
+            AND (my_module_repository_rows.my_module_id = #{@my_module.id} OR
+                              my_module_repository_rows.id IS NULL))"
+          ).order("my_module_repository_rows.id NULLS #{direction}")
+        else
+          sort_assigned_records(records, params[:order].values[0]['dir'])
+        end
+      elsif sorting_by_custom_column
+        # Check if have to filter records first
+        # if params[:search].present? && params[:search][:value].present?
+        #   # Couldn't force ActiveRecord to yield the same query as below because
+        #   # Rails apparently forgets to join stuff in subqueries -
+        #   # #justrailsthings
+        #   conditions = build_conditions_for(params[:search][:value])
+        #
+        #   filter_query = %(SELECT "samples"."id" FROM "samples"
+        #     LEFT OUTER JOIN "sample_custom_fields" ON
+        #     "sample_custom_fields"."sample_id" = "samples"."id"
+        #     LEFT OUTER JOIN "users" ON "users"."id" = "repository_row"."user_id"
+        #     WHERE "samples"."team_id" = #{@team.id} AND #{conditions.to_sql})
+        #
+        #   records = records.where("samples.id IN (#{filter_query})")
+        # end
+
+        ci = sortable_displayed_columns[
+          params[:order].values[0][:column].to_i - 1
+        ]
+        column_id = @columns_mappings.key((ci.to_i + 1).to_s)
+        dir = sort_direction(params[:order].values[0])
+
+        # Because repository records can have multiple custom cells,
+        # we first group them by samples.id and inside that group we sort them by column_id. Because
+        # we sort them ASC, sorted columns will be on top. Distinct then only
+        # takes the first row and cuts the rest of every group and voila we have
+        # 1 row for every sample, which are not sorted yet ...
+        # records = records.select('DISTINCT ON (repository_rows.id) *')
+        # .order("repository_rows.id, CASE WHEN repository_cells.repository_column_id = #{column_id} THEN 1 ELSE 2 END ASC")
+
+        # ... this little gem (pun intended) then takes the records query, sorts it again
+        # and paginates it. sq.t0_* are determined empirically and are crucial -
+        # imagine A -> B -> C transitive relation but where A and C are the
+        # same. Useless right? But not when you acknowledge that find_by_sql
+        # method does some funky stuff when your query spans multiple queries -
+        # Sample object might have id from SampleType, name from
+        # User ... chaos ensues basically. If something changes in db this might
+        # change.
+        # formated_date = (I18n.t 'time.formats.datatables_date').gsub!(/^\"|\"?$/, '')
+        # Sample.find_by_sql("SELECT sq.t0_r0 as id, sq.t0_r1 as name, to_char( sq.t0_r4, '#{ formated_date }' ) as created_at, sq.t0_r5, s, sq.t0_r2 as user_id, sq.custom_field_id FROM (#{records.to_sql})
+        #                              as sq ORDER BY CASE WHEN sq.custom_field_id = #{column_id} THEN 1 ELSE 2 END #{dir}, sq.value #{dir}
+        #                              LIMIT #{per_page} OFFSET #{offset}")
+
         records.joins(
           "LEFT OUTER JOIN my_module_repository_rows ON
           (repository_rows.id = my_module_repository_rows.repository_row_id
@@ -307,4 +362,21 @@ class RepositoryDatatable < CustomDatatable
 
     @sortable_displayed_columns = sort_order
   end
+
+  def sort_assigned_records(records, direction)
+    assigned = records.joins(:my_module_repository_rows).distinct.pluck(:id)
+    unassigned = records.where.not(id: assigned).pluck(:id)
+    if direction == 'asc'
+      ids = assigned + unassigned
+    elsif direction == 'desc'
+      ids = unassigned + assigned
+    end
+
+    order_by_index = ActiveRecord::Base.send(
+      :sanitize_sql_array,
+      ["position((',' || repository_rows.id || ',') in ?)",
+      ids.join(',') + ',']
+    )
+    records.order(order_by_index)
+  end
 end

app/helpers/addons_helper.rb

@@ -0,0 +1,8 @@
+module AddonsHelper
+  def list_all_addons
+    Rails::Engine
+      .subclasses
+      .select { |c| c.name.start_with?('Scinote') }
+      .map(&:parent)
+  end
+end

app/helpers/permission_helper.rb

@@ -1075,11 +1075,13 @@ module PermissionHelper
   end
 
   def can_delete_column_in_repository(column)
-    is_normal_user_or_admin_of_team(column.repository.team)
+    column.created_by == current_user ||
+      is_admin_of_team(column.repository.team)
   end
 
   def can_edit_column_in_repository(column)
-    is_normal_user_or_admin_of_team(column.repository.team)
+    column.created_by == current_user ||
+      is_admin_of_team(column.repository.team)
   end
 
   def can_create_repository_records(repository)

app/models/asset.rb

@@ -384,10 +384,17 @@ class Asset < ApplicationRecord
     action = get_action(file_ext, action)
     if !action.nil?
       action_url = action.urlsrc
-      action_url = action_url.gsub(/<IsLicensedUser=BUSINESS_USER&>/,
+      if ENV['WOPI_BUSINESS_USERS'] && ENV['WOPI_BUSINESS_USERS']=='true'
-                                   'IsLicensedUser=0&')
+        action_url = action_url.gsub(/<IsLicensedUser=BUSINESS_USER&>/,
-      action_url = action_url.gsub(/<IsLicensedUser=BUSINESS_USER>/,
+                                     'IsLicensedUser=1&')
-                                   'IsLicensedUser=0')
+        action_url = action_url.gsub(/<IsLicensedUser=BUSINESS_USER>/,
+                                     'IsLicensedUser=1')
+      else
+        action_url = action_url.gsub(/<IsLicensedUser=BUSINESS_USER&>/,
+                                     'IsLicensedUser=0&')
+        action_url = action_url.gsub(/<IsLicensedUser=BUSINESS_USER>/,
+                                     'IsLicensedUser=0')
+      end
       action_url = action_url.gsub(/<.*?=.*?>/, '')
 
       rest_url = Rails.application.routes.url_helpers.wopi_rest_endpoint_url(

app/models/repository.rb

@@ -111,57 +111,82 @@ class Repository < ApplicationRecord
 
   # Imports records
   def import_records(sheet, mappings, user)
-    errors = []
+    errors = false
-    custom_fields = []
+    columns = []
     name_index = -1
+    total_nr = 0
     nr_of_added = 0
 
     mappings.each.with_index do |(_k, value), index|
       if value == '-1'
         # Fill blank space, so our indices stay the same
-        custom_fields << nil
+        columns << nil
         name_index = index
       else
-        cf = repository_columns.find_by_id(value)
+        columns << repository_columns.find_by_id(value)
-        custom_fields << cf
       end
     end
 
+    # Check for duplicate columns
+    col_compact = columns.compact
+    unless col_compact.map(&:id).uniq.length == col_compact.length
+      return { status: :error, nr_of_added: nr_of_added, total_nr: total_nr }
+    end
+
     # Now we can iterate through record data and save stuff into db
-    (2..sheet.last_row).each do |i|
+    transaction do
-      error = []
+      (2..sheet.last_row).each do |i|
-      record_row = RepositoryRow.new(name: sheet.row(i)[name_index],
+        total_nr += 1
-                                 repository: self,
+        record_row = RepositoryRow.new(name: sheet.row(i)[name_index],
-                                 created_by: user,
+                                   repository: self,
-                                 last_modified_by: user)
+                                   created_by: user,
+                                   last_modified_by: user)
+        record_row.transaction(requires_new: true) do
+          unless record_row.save
+            errors = true
+            raise ActiveRecord::Rollback
+          end
 
-      next unless record_row.valid?
+          row_cell_values = []
-      sheet.row(i).each.with_index do |value, index|
+
-        if custom_fields[index] && value
+          sheet.row(i).each.with_index do |value, index|
-          rep_column = RepositoryTextValue.new(
+            if columns[index] && value
-            data: value,
+              cell_value = RepositoryTextValue.new(
-            created_by: user,
+                data: value,
-            last_modified_by: user,
+                created_by: user,
-            repository_cell_attributes: {
+                last_modified_by: user,
-              repository_row: record_row,
+                repository_cell_attributes: {
-              repository_column: custom_fields[index]
+                  repository_row: record_row,
-            }
+                  repository_column: columns[index]
-          )
+                }
-          error << rep_column.errors.messages unless rep_column.save
+              )
+              cell = RepositoryCell.new(repository_row: record_row,
+                                        repository_column: columns[index],
+                                        value: cell_value)
+              cell.skip_on_import = true
+              cell_value.repository_cell = cell
+              unless cell.valid? && cell_value.valid?
+                errors = true
+                raise ActiveRecord::Rollback
+              end
+              row_cell_values << cell_value
+            end
+          end
+          if RepositoryTextValue.import(row_cell_values,
+                                        recursive: true,
+                                        validate: false).failed_instances.any?
+            errors = true
+            raise ActiveRecord::Rollback
+          end
+          nr_of_added += 1
         end
       end
-      if error.any?
-        record_row.destroy
-      else
-        nr_of_added += 1
-        record_row.save
-      end
     end
 
-    if errors.count > 0
+    if errors
-      return { status: :error, errors: errors, nr_of_added: nr_of_added }
+      return { status: :error, nr_of_added: nr_of_added, total_nr: total_nr }
     end
-    { status: :ok, nr_of_added: nr_of_added }
+    { status: :ok, nr_of_added: nr_of_added, total_nr: total_nr }
   end
 
   private
@@ -170,13 +195,11 @@ class Repository < ApplicationRecord
     case File.extname(filename)
     when '.csv'
       Roo::CSV.new(file_path, extension: :csv)
-    when '.tdv'
+    when '.tsv'
-      Roo::CSV.new(file_path, nil, :ignore, csv_options: { col_sep: '\t' })
+      Roo::CSV.new(file_path, csv_options: { col_sep: "\t" })
     when '.txt'
       # This assumption is based purely on biologist's habits
-      Roo::CSV.new(file_path, csv_options: { col_sep: '\t' })
+      Roo::CSV.new(file_path, csv_options: { col_sep: "\t" })
-    when '.xls'
-      Roo::Excel.new(file_path)
     when '.xlsx'
       Roo::Excelx.new(file_path)
     else

app/models/repository_cell.rb

@@ -1,11 +1,15 @@
-class RepositoryCell < ApplicationRecord
+class RepositoryCell < ActiveRecord::Base
-  belongs_to :repository_row, optional: true
+  attr_accessor :skip_on_import
-  belongs_to :repository_column, optional: true
+
-  belongs_to :value, polymorphic: true, dependent: :destroy, optional: true
+  belongs_to :repository_row
+  belongs_to :repository_column
+  belongs_to :value, polymorphic: true, dependent: :destroy
 
   validates :repository_column, presence: true
   validate :repository_column_data_type
-  validates :repository_row, uniqueness: { scope: :repository_column }
+  validates :repository_row,
+            uniqueness: { scope: :repository_column },
+            unless: :skip_on_import
 
   private
 

app/models/team.rb

@@ -43,16 +43,14 @@ class Team < ApplicationRecord
     end
 
     case File.extname(filename)
-    when ".csv" then
+    when '.csv' then
       Roo::CSV.new(file_path, extension: :csv)
-    when ".tdv" then
+    when '.tsv' then
-      Roo::CSV.new(file_path, nil, :ignore, csv_options: {col_sep: "\t"})
+      Roo::CSV.new(file_path, csv_options: { col_sep: "\t" })
-    when ".txt" then
+    when '.txt' then
       # This assumption is based purely on biologist's habits
-      Roo::CSV.new(file_path, csv_options: {col_sep: "\t"})
+      Roo::CSV.new(file_path, csv_options: { col_sep: "\t" })
-    when ".xls" then
+    when '.xlsx' then
-      Roo::Excel.new(file_path)
-    when ".xlsx" then
       Roo::Excelx.new(file_path)
     else
       raise TypeError
@@ -71,7 +69,7 @@ class Team < ApplicationRecord
   # -3 == sample_group
   # TODO: use constants
   def import_samples(sheet, mappings, user)
-    errors = []
+    errors = false
     nr_of_added = 0
     total_nr = 0
 
@@ -80,17 +78,17 @@ class Team < ApplicationRecord
     sname_index = -1
     stype_index = -1
     sgroup_index = -1
-    mappings.each.with_index do |(k, v), i|
+    mappings.each.with_index do |(_, v), i|
-      if v == "-1"
+      if v == '-1'
         # Fill blank space, so our indices stay the same
         custom_fields << nil
         sname_index = i
-      elsif v == "-2"
+      elsif v == '-2'
         custom_fields << nil
         stype_index = i
-      elsif v == "-3"
+      elsif v == '-3'
         custom_fields << nil
-        sgroup_index =  i
+        sgroup_index = i
       else
         cf = CustomField.find_by_id(v)
 
@@ -99,87 +97,70 @@ class Team < ApplicationRecord
         custom_fields << cf
       end
     end
-
     # Now we can iterate through sample data and save stuff into db
     (2..sheet.last_row).each do |i|
-      error = []
       total_nr += 1
+      sample = Sample.new(name: sheet.row(i)[sname_index],
+                          team: self,
+                          user: user)
 
-      sample = Sample.new(
+      sample.transaction do
-        name: sheet.row(i)[sname_index],
+        unless sample.valid?
-        team_id: id,
+          errors = true
-        user: user
+          raise ActiveRecord::Rollback
-      )
+        end
 
-      if sample.save
         sheet.row(i).each.with_index do |value, index|
-          # We need to have sample saved before messing with custom fields (they
-          # need sample id)
           if index == stype_index
-            stype = SampleType.where(name: value, team_id: id).take
+            stype = SampleType.where(name: value, team: self).take
 
-            if stype
+            unless stype
-              sample.sample_type = stype
+              stype = SampleType.new(name: value, team: self)
-            else
+              unless stype.save
-              sample.create_sample_type(
+                errors = true
-                name: value,
+                raise ActiveRecord::Rollback
-                team_id: id
-              )
-            end
-            sample.save
-          elsif index == sgroup_index
-            sgroup = SampleGroup.where(name: value, team_id: id).take
-
-            if sgroup
-              sample.sample_group = sgroup
-            else
-              sample.create_sample_group(
-                name: value,
-                team_id: id
-              )
-            end
-            sample.save
-          elsif value and mappings[index.to_s].strip.present? and index != sname_index
-            if custom_fields[index]
-              # we're working with CustomField
-              scf = SampleCustomField.new(
-                sample_id: sample.id,
-                custom_field_id: custom_fields[index].id,
-                value: value
-              )
-
-              if !scf.save
-                error << scf.errors.messages
               end
-            else
-              # This custom_field does not exist
-              error << {"#{mappings[index]}": "Does not exists"}
             end
+            sample.sample_type = stype
+          elsif index == sgroup_index
+            sgroup = SampleGroup.where(name: value, team: self).take
+
+            unless sgroup
+              sgroup = SampleGroup.new(name: value, team: self)
+              unless sgroup.save
+                errors = true
+                raise ActiveRecord::Rollback
+              end
+            end
+            sample.sample_group = sgroup
+          elsif value && custom_fields[index]
+            # we're working with CustomField
+            scf = SampleCustomField.new(
+              sample: sample,
+              custom_field: custom_fields[index],
+              value: value
+            )
+            unless scf.valid?
+              errors = true
+              raise ActiveRecord::Rollback
+            end
+            sample.sample_custom_fields << scf
           end
         end
-      else
+        if Sample.import([sample],
-        error << sample.errors.messages
+                         recursive: true,
-      end
+                         validate: false).failed_instances.any?
-      if error.present?
+          errors = true
-        errors << { "#{i}": error}
+          raise ActiveRecord::Rollback
-      else
+        end
         nr_of_added += 1
       end
     end
 
-    if errors.count > 0 then
+    if errors
-      return {
+      return { status: :error, nr_of_added: nr_of_added, total_nr: total_nr }
-        status: :error,
-        errors: errors,
-        nr_of_added: nr_of_added,
-        total_nr: total_nr
-      }
     else
-      return {
+      return { status: :ok, nr_of_added: nr_of_added, total_nr: total_nr }
-        status: :ok,
-        nr_of_added: nr_of_added,
-        total_nr: total_nr
-      }
     end
   end
 

app/services/import_repository/parse_repository.rb

@@ -11,15 +11,14 @@ module ImportRepository
     def data
       # Get data (it will trigger any errors as well)
       header = @sheet.row(1)
-      rows = []
+      columns = @sheet.row(2)
-      rows << Hash[[header, @sheet.row(2)].transpose]
       # Fill in fields for dropdown
       @repository.available_repository_fields.transform_values! do |name|
         truncate(name, length: Constants::NAME_TRUNCATION_LENGTH_DROPDOWN)
       end
       @temp_file = TempFile.create(session_id: @session.id, file: @file)
       Data.new(header,
-               rows,
+               columns,
                @repository.available_repository_fields,
                @repository,
                @temp_file)
@@ -47,7 +46,7 @@ module ImportRepository
     end
 
     Data = Struct.new(
-      :header, :rows, :available_fields, :repository, :temp_file
+      :header, :columns, :available_fields, :repository, :temp_file
     )
   end
 end

app/views/layouts/application.html.erb

@@ -45,6 +45,9 @@
       </div>
     </div>
 
+    <!-- About us modal -->
+    <%= render "shared/about_modal" %>
+
     <%= render "shared/navigation" %>
 
     <div id="notifications">

app/views/my_modules/repository.html.erb

@@ -31,7 +31,8 @@
   <% end %>
 </div>
 
-<div id="content">
+<div id="content"
+     data-repo-id="#repository-table-<%= @repository.id %>">
 	<%= render partial: "repositories/repository_table",
              locals: {
                repository: @repository,
@@ -40,3 +41,7 @@
              }
   %>
 </div>
+
+<%= stylesheet_link_tag 'datatables' %>
+<%= javascript_include_tag 'repositories/repository_datatable' %>
+<%= javascript_include_tag 'repositories/my_module_repository' %>

app/views/repositories/_parse_records_modal.html.erb

@@ -1,5 +1,5 @@
 <div class="modal fade"
-     id="parse-records_modal"
+     id="parse-records-modal"
      aria-labelledby="parse-modal-title"
      role="dialog">
   <div class="modal-dialog modal-lg">
@@ -30,29 +30,31 @@
                                include_blank: t('teams.parse_sheet.do_not_include_column'),
                                hide_label: true) %>
                   <br />
-                  <% if th.length > Constants::NAME_TRUNCATION_LENGTH_DROPDOWN %>
+                  <% if th.nil? %>
-                    <div class="modal-tooltip">
+                    <i><%= t('repositories.import_records.no_header_name') %></i>
-                      <%= truncate(th, length: Constants::NAME_TRUNCATION_LENGTH_DROPDOWN) %>
-                    </div>
                   <% else %>
-                    <%= th %>
+                    <% if th.length > Constants::NAME_TRUNCATION_LENGTH_DROPDOWN %>
+                      <div class="modal-tooltip">
+                        <%= truncate(th, length: Constants::NAME_TRUNCATION_LENGTH_DROPDOWN) %>
+                      </div>
+                    <% else %>
+                      <%= th %>
+                    <% end %>
                   <% end %>
                 </th>
               <% end %>
             </thead>
             <tbody>
-              <%  @import_data.rows.each do |row| %>
+              <tr>
-                <tr>
+                <td>
+                  <p><%= t('teams.parse_sheet.example_value') %></p>
+                </td>
+                <% @import_data.columns.each do |td| %>
                   <td>
-                    <p><%= t('teams.parse_sheet.example_value') %></p>
+                    <%= td %>
                   </td>
-                  <% row.each do |td| %>
+                <% end %>
-                    <td>
+              </tr>
-                      <%= td[1] %>
-                    </td>
-                  <% end %>
-                </tr>
-              <% end %>
             </tbody>
           </table>
         </div>

app/views/repositories/_repository_table.html.erb

@@ -1,5 +1,5 @@
 <div class="repository-table">
-  <table id="repository-table" class="table"
+  <table id="repository-table-<%= repository.id %>" class="table"
     data-current-uri="<%= request.original_url %>"
     data-repository-id="<%= repository.id %>"
     data-source="<%= repository_index_link %>"
@@ -19,7 +19,7 @@
         <th id="row-name"><%= t("repositories.table.row_name") %></th>
         <th id="added-on"><%= t("repositories.table.added_on") %></th>
         <th id="added-by"><%= t("repositories.table.added_by") %></th>
-        <% repository.repository_columns.each do |column| %>
+        <% repository.repository_columns.order(:id).each do |column| %>
           <th class="repository-column" id="<%= column.id %>"
             <%= 'data-editable' if can_edit_column_in_repository(column) %>
             <%= 'data-deletable' if can_delete_column_in_repository(column) %>
@@ -35,6 +35,3 @@
     <tbody></tbody>
   </table>
 </div>
-
-<%= stylesheet_link_tag 'datatables' %>
-<%= javascript_include_tag('repositories/repository_datatable') %>

app/views/repositories/index.html.erb

@@ -10,6 +10,7 @@
       <li role="presentation">
         <a href="#custom_repo_<%= repo.id %>"
            data-toggle="tab"
+           data-repo-table="#repository-table-<%= repo.id %>"
            aria-controls="custom_repo_<%= repo.id %>"
            data-url="<%=team_repository_show_tab_path(current_team, repo)%>"
            title="<%=repo.name%>"><%= truncate(repo.name, length: Constants::NAME_TRUNCATION_LENGTH) %></a>
@@ -53,4 +54,6 @@
   </div>
 <% end %>
 
+<%= stylesheet_link_tag 'datatables' %>
+<%= javascript_include_tag 'repositories/repository_datatable' %>
 <%= javascript_include_tag "repositories/index", "data-turbolinks-track" => true %>

app/views/samples/_parse_samples_modal.html.erb

@@ -25,29 +25,31 @@
                              include_blank: t('teams.parse_sheet.do_not_include_column'),
                              hide_label: true) %>
                 <br />
-                <% if th.length > Constants::NAME_TRUNCATION_LENGTH_DROPDOWN %>
+                <% if th.nil? %>
-                  <div class="modal-tooltip">
+                  <i><%= t('samples.modal_import.no_header_name') %></i>
-                    <%= truncate(th, length: Constants::NAME_TRUNCATION_LENGTH_DROPDOWN) %>
-                  </div>
                 <% else %>
-                  <%= th %>
+                  <% if th.length > Constants::NAME_TRUNCATION_LENGTH_DROPDOWN %>
+                    <div class="modal-tooltip">
+                      <%= truncate(th, length: Constants::NAME_TRUNCATION_LENGTH_DROPDOWN) %>
+                    </div>
+                  <% else %>
+                    <%= th %>
+                  <% end %>
                 <% end %>
               </th>
             <% end %>
           </thead>
           <tbody>
-            <% @rows.each do |row| %>
+            <tr>
-              <tr>
+              <td>
+                <p><%= t('teams.parse_sheet.example_value') %></p>
+              </td>
+              <% @columns.each do |td| %>
                 <td>
-                  <p><%= t('teams.parse_sheet.example_value') %></p>
+                  <%= td %>
                 </td>
-                <% row.each do |td| %>
+              <% end %>
-                  <td>
+            </tr>
-                    <%= td[1] %>
-                  </td>
-                <% end %>
-              </tr>
-            <% end %>
           </tbody>
         </table>
       </div>

app/views/shared/_about_modal.html.erb

@@ -0,0 +1,28 @@
+<div class="modal" id="aboutModal" tabindex="-1" role="dialog" aria-labelledby="aboutModal" data-role="about-modal">
+  <div class="modal-dialog" role="document">
+    <div class="modal-content">
+      <div class="modal-header">
+        <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
+        <h4 class="modal-title"><%= t('about.modal_title') %></h4>
+      </div>
+      <div class="modal-body">
+        <strong><%= t('about.core_version') %></strong>
+        <br />
+        <%= Scinote::Application::VERSION %>
+        <br />
+        <br />
+        <div data-hook="about-modal-addon-versions">
+          <strong><%= t('about.addon_versions') %></strong>
+          <br />
+          <% list_all_addons.each do |addon| %>
+            <%= "#{addon.name}:" %>
+            <br />
+            <%= addon::VERSION %>
+            <br />
+            <br />
+          <% end %>
+        </div>
+      </div>
+    </div>
+  </div>
+</div>

app/views/shared/_navigation.html.erb

@@ -19,7 +19,7 @@
         <% if show_version %>
           <%= image_tag('/images/logo.png', class: 'with-version', id: 'logo') %>
           <span class="version">
-            <%= Constants::APP_VERSION %>
+            <%= Scinote::Application::VERSION %>
           </span>
         <% else %>
           <%= image_tag('/images/logo.png', id: 'logo') %>
@@ -234,6 +234,12 @@
             <li><%= link_to t('nav.help.contact'),
                               Constants::CONTACT_URL,
                               target: "_blank" %></li>
+            <li role="separator" class="divider"></li>
+            <li>
+              <%= link_to '#', data: { trigger: 'about-modal' } do %>
+                <%= t('nav.help.about') %>
+              <% end %>
+            </li>
           </ul>
         </li>
 

app/views/shared/_secondary_navigation.html.erb

@@ -203,7 +203,10 @@
               <ul class="dropdown-menu repositories-dropdown-menu" aria-labelledby="repositoriesDropdownMenuLink">
                 <% @my_module.experiment.project.team.repositories.order(created_at: :asc).each do |repository| %>
                   <li>
-                    <a class="dropdown-item" href="<%= repository_my_module_url(id: @my_module, repository_id: repository) %>" title="<%= repository.name %>">
+                    <a class="dropdown-item"
+                       href="<%= repository_my_module_url(id: @my_module, repository_id: repository) %>"
+                       title="<%= repository.name %>"
+                       data-no-turbolink="true">
                       <%= truncate(repository.name) %>
                     </a>
                   </li>

config/application.rb

@@ -29,5 +29,8 @@ module Scinote
       csv: 'text/plain',
       wopitest: ['text/plain', 'inode/x-empty']
     }
+
+    # sciNote Core Application version
+    VERSION = File.read(Rails.root.join('VERSION')).strip.freeze
   end
 end

config/initializers/assets.rb

@@ -80,6 +80,8 @@ Rails.application.config.assets.precompile += %w(repositories/index.js)
 Rails.application.config.assets.precompile += %w(repositories/edit.js)
 Rails.application.config.assets.precompile +=
   %w(repositories/repository_datatable.js)
+Rails.application.config.assets.precompile +=
+  %w(repositories/my_module_repository.js)
 
 # Libraries needed for Handsontable formulas
 Rails.application.config.assets.precompile += %w(lodash.js)

config/initializers/constants.rb

@@ -196,9 +196,6 @@ class Constants
   # Other
   #=============================================================================
 
-  # Application version
-  APP_VERSION = '1.12.1'.freeze
-
   TEXT_EXTRACT_FILE_TYPES = [
     'application/pdf',
     'application/rtf',

config/initializers/devise.rb

@@ -105,7 +105,7 @@ Devise.setup do |config|
   # The period the generated invitation token is valid, after
   # this period, the invited resource won't be able to accept the invitation.
   # When invite_for is 0 (the default), the invitation won't expire.
-  config.invite_for = 3.days
+  config.invite_for = 7.days
 
   # Number of invitations users can send.
   # - If invitation_limit is nil, there is no limit for invitations, users can
@@ -163,7 +163,7 @@ Devise.setup do |config|
   # their account can't be confirmed with the token any more.
   # Default is nil, meaning there is no restriction on how long a user can take
   # before confirming their account.
-  config.confirm_within = 3.days
+  config.confirm_within = 7.days
 
   # If true, requires any email changes to be confirmed (exactly the same way as
   # initial account confirmation) to be applied. Requires additional unconfirmed_email

config/initializers/paperclip.rb

@@ -81,7 +81,7 @@ module Paperclip
     # Determine file content type from its name
     def content_types_from_name
       @content_types_from_name ||=
-        Paperclip.run('mimetype', '-b :file_name', file_name: @name).chomp
+        Paperclip.run('mimetype', '-b -- :file_name', file_name: @name).chomp
     end
 
     # Determine file media type from its name
@@ -92,7 +92,7 @@ module Paperclip
     # Determine file content type from mimetype command
     def type_from_mimetype_command
       @type_from_mimetype_command ||=
-        Paperclip.run('mimetype', '-b :file', file: @file.path).chomp
+        Paperclip.run('mimetype', '-b -- :file', file: @file.path).chomp
     end
 
     # Determine file media type from mimetype command
@@ -105,7 +105,7 @@ module Paperclip
     def type_from_file_command
       unless defined? @type_from_file_command
         @type_from_file_command =
-          Paperclip.run('file', '-b --mime :file', file: @file.path)
+          Paperclip.run('file', '-b --mime -- :file', file: @file.path)
                    .split(/[:;]\s+/).first
 
         if allowed_spoof_exception?(@type_from_file_command,

config/locales/en.yml

@@ -72,6 +72,7 @@ en:
       support: "Customer support"
       premium: "Premium"
       contact: "Contact us"
+      about: "About sciNote"
     activities:
       none: "No activities!"
     label:
@@ -87,6 +88,11 @@ en:
       info: "Info"
       account: "Account"
 
+  about:
+    modal_title: "About sciNote"
+    core_version: "sciNote core version"
+    addon_versions: "Addon versions"
+
   sidebar:
     title: "Navigation"
     no_module_group: "No workflow"
@@ -905,8 +911,9 @@ en:
     add_new_record: "Add new item"
     import_records:
       import: 'Import'
+      no_header_name: 'No column name'
       success_flash: "%{number_of_rows} new item(s) successfully imported."
-      error_flash: "Something went wrong: %{message}"
+      partial_success_flash: "%{nr} of %{total_nr} successfully imported. Other rows contained errors."
       error_message:
         temp_file_not_found: "This file could not be found. Your session might expire."
         session_expired: "Your session expired. Please try again."
@@ -944,7 +951,7 @@ en:
       title: 'Import items'
     modal_import:
       title: 'Import items'
-      notice: 'You may upload .csv file (comma separated) or tab separated file (.txt or .tdv) or Excel file (.xls, .xlsx). First row should include header names, followed by rows with sample data.'
+      notice: 'You may upload .csv file (comma separated) or tab separated file (.txt or .tsv) or Excel file (.xlsx). First row should include header names, followed by rows with sample data.'
       upload: 'Upload file'
     js:
       permission_error: "You don't have permission to edit this item."
@@ -1002,7 +1009,8 @@ en:
       sample_type: "Sample type:"
     modal_import:
       title: "Import samples"
-      notice: "You may upload .csv file (comma separated) or tab separated file (.txt or .tdv) or Excel file (.xls, .xlsx). First row should include header names, followed by rows with sample data."
+      notice: "You may upload .csv file (comma separated) or tab separated file (.txt or .tsv) or Excel file (.xlsx). First row should include header names, followed by rows with sample data."
+      no_header_name: 'No column name'
       upload: "Upload file"
     modal_delete:
       title: "Delete samples"

lib/generators/addon/addon_generator.rb

@@ -114,12 +114,16 @@ class AddonGenerator < Rails::Generators::NamedBase
     gsub_file(file_path, '${ADDON_NAME}', @addon_name)
 
     # lib/.../version.rb
+    dots = @modules.map { '/..' }.join
     create_file(
       "addons/#{@addon_name}/lib/" \
       "#{@folders_path}/version.rb"
     ) do
       embed_into_modules do
-        "VERSION = '0.0.1'.freeze\n"
+        "VERSION =\n" \
+        "  File.read(\n" \
+        "    \"\#{File.dirname(__FILE__)}#{dots}/../VERSION\"\n" \
+        "  ).strip.freeze\n"
       end
     end
 
@@ -182,6 +186,7 @@ class AddonGenerator < Rails::Generators::NamedBase
     gsub_file(file_path, '${FULL_UNDERSCORE_NAME}', @full_underscore_name)
     gsub_file(file_path, '${NAME}', name)
     gsub_file(file_path, '${FOLDERS_PATH}', @folders_path)
+    create_file("addons/#{@addon_name}/VERSION") { '0.0.1' }
 
     # Rakefile
     file_path = "addons/#{@addon_name}/Rakefile"