1) {
var colIndex = $(el).attr('data-column-index');
- var visible = table.column(colIndex).visible();
+ var visible = TABLE.column(colIndex).visible();
var editable = $(el).is('[data-editable]');
var deletable = $(el).is('[data-deletable]');
@@ -993,19 +997,19 @@ function changeToEditMode() {
'form-control" style="display: none;" />' +
'' +
'' +
+ 'title="' + $(TABLE_ID).data('save-text') + '">' +
'' +
'' +
+ $(TABLE_ID).data('columns-visibility-text') + '">' +
' ' +
'' +
'' +
'
';
dropdownList.append(html);
@@ -1037,27 +1041,27 @@ function changeToEditMode() {
event.stopPropagation();
var self = $(this);
var li = self.closest('li');
- var column = table.column(li.attr('data-position'));
+ var column = TABLE.column(li.attr('data-position'));
if (column.visible()) {
self.addClass('glyphicon-eye-close');
self.removeClass('glyphicon-eye-open');
li.addClass('col-invisible');
column.visible(false);
- table.setColumnSearchable(column.index(), false);
+ TABLE.setColumnSearchable(column.index(), false);
} else {
self.addClass('glyphicon-eye-open');
self.removeClass('glyphicon-eye-close');
li.removeClass('col-invisible');
column.visible(true);
- table.setColumnSearchable(column.index(), true);
+ TABLE.setColumnSearchable(column.index(), true);
initHeaderTooltip();
}
// Re-filter/search if neccesary
var searchText = $('div.dataTables_filter input').val();
if (!_.isEmpty(searchText)) {
- table.search(searchText).draw();
+ TABLE.search(searchText).draw();
}
initRowSelection();
});
@@ -1069,7 +1073,7 @@ function changeToEditMode() {
cancel: '.new-repository-column',
axis: 'y',
update: function() {
- var reorderer = table.colReorder;
+ var reorderer = TABLE.colReorder;
var listIds = [];
// We skip first two columns
listIds.push(0, 1);
@@ -1106,7 +1110,7 @@ function changeToEditMode() {
dropdownList.sortable('enable');
$(li).clearFormErrors();
text.html(generateColumnNameTooltip(newName));
- $(table.columns().header()).filter('#' + id)
+ $(TABLE.columns().header()).filter('#' + id)
.html(generateColumnNameTooltip(newName));
originalHeader.find('#' + id).html(newName);
cancelEditMode();
@@ -1290,28 +1294,28 @@ function changeToEditMode() {
$('div.toolbarButtons').hide();
// Destroy datatable
- table.destroy();
+ TABLE.destroy();
// Subtract number of columns
- $('#repository-table').data(
+ $(TABLE_ID).data(
'num-columns',
- $('#repository-table').data('num-columns') - 1
+ $(TABLE_ID).data('num-columns') - 1
);
// Remove column from table (=table header) & rows
var th = originalHeader.find('#' + id);
var index = th.index();
th.remove();
- $('#repository-table tbody td:nth-child(' + (index + 1) + ')').remove();
+ $(TABLE_ID + ' tbody td:nth-child(' + (index + 1) + ')').remove();
// Remove all event handlers as we re-initialize them later with
// new table
- $('#repository-table').off();
- $('#repository-table thead').empty();
- $('#repository-table thead').append(originalHeader);
+ $(TABLE_ID).off();
+ $(TABLE_ID + ' thead').empty();
+ $(TABLE_ID + ' thead').append(originalHeader);
// Re-initialize datatable
- table = dataTableInit();
+ TABLE = dataTableInit();
loadColumnsNames();
// Hide modal
@@ -1343,7 +1347,7 @@ function changeToEditMode() {
}
function generateColumnNameTooltip(name) {
- var maxLength = $('#repository-table').data('max-dropdown-length');
+ var maxLength = $(TABLE_ID).data('max-dropdown-length');
if ($.trim(name).length > maxLength) {
return '' +
truncateLongString(name, maxLength) +
@@ -1354,7 +1358,9 @@ function changeToEditMode() {
// initialze dropdown after the table is loaded
function initDropdown() {
- table.on('init.dt', function() {
+ TABLE.on('init.dt', function() {
+ dropdown = $('#repository-columns-dropdown');
+ dropdownList = $('#repository-columns-list');
initNewColumnForm();
initSorting();
toggleColumnVisibility();
@@ -1371,5 +1377,19 @@ function changeToEditMode() {
});
}
- initDropdown();
-})(table);
+ function init(id) {
+ TABLE_ID = id;
+ TABLE = dataTableInit();
+ initDropdown();
+ }
+
+ function destroy() {
+ TABLE = {};
+ TABLE_ID = '';
+ }
+
+ return Object.freeze({
+ init: init,
+ destroy: destroy
+ });
+})(window);
diff --git a/app/assets/javascripts/sitewide/about_modal.js b/app/assets/javascripts/sitewide/about_modal.js
new file mode 100644
index 000000000..ca558059a
--- /dev/null
+++ b/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');
+ });
+ });
+})();
diff --git a/app/assets/javascripts/sitewide/atwho_res.js.erb b/app/assets/javascripts/sitewide/atwho_res.js.erb
index 377918eb3..24889894f 100644
--- a/app/assets/javascripts/sitewide/atwho_res.js.erb
+++ b/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;
diff --git a/app/controllers/repositories_controller.rb b/app/controllers/repositories_controller.rb
index ca41b2ed4..bb56e7938 100644
--- a/app/controllers/repositories_controller.rb
+++ b/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]
- repository_response(t('teams.parse_sheet.errors.no_file_selected'))
- return
- end
- begin
- if parsed_file.too_large?
- repository_response(t('general.file.size_exceeded',
- file_size: Constants::FILE_MAX_SIZE_MB))
- elsif parsed_file.empty?
- 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?
+ unless params[:file]
+ repository_response(t('teams.parse_sheet.errors.no_file_selected'))
+ return
+ end
+ begin
+ parsed_file = ImportRepository::ParseRepository.new(
+ file: params[:file],
+ repository: repository,
+ session: session
+ )
+ if parsed_file.too_large?
+ repository_response(t('general.file.size_exceeded',
+ file_size: Constants::FILE_MAX_SIZE_MB))
+ elsif parsed_file.empty?
+ 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',
- message: status[:errors])
+ flash[:alert] =
+ 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
- flash[:alert] = message
- redirect_to :back
- end
- format.json do
- render json: { message: message },
- status: :unprocessable_entity
+ respond_to do |format|
+ format.html do
+ flash[:alert] = message
+ redirect_to :back
+ end
+ format.json do
+ render json: { message: message },
+ status: :unprocessable_entity
+ end
end
end
diff --git a/app/controllers/repository_rows_controller.rb b/app/controllers/repository_rows_controller.rb
index f971ae73f..9526bcc71 100644
--- a/app/controllers/repository_rows_controller.rb
+++ b/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
- end
+ errors[:default_fields] = record.errors.messages unless record.save
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
- end
+ errors[:default_fields] = @record.errors.messages unless @record.save
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
- record_annotation_notification(@record, value.repository_cell)
+ if cell_value.save
+ 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|
diff --git a/app/controllers/teams_controller.rb b/app/controllers/teams_controller.rb
index 244128f11..622cff038 100644
--- a/app/controllers/teams_controller.rb
+++ b/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 = [];
- @rows << Hash[[@header, sheet.row(2)].transpose]
+ @columns = sheet.row(2)
# Fill in fields for dropdown
@available_fields = @team.get_available_sample_fields
diff --git a/app/controllers/wopi_controller.rb b/app/controllers/wopi_controller.rb
index dd7b30192..8639bb80c 100644
--- a/app/controllers/wopi_controller.rb
+++ b/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
diff --git a/app/datatables/repository_datatable.rb b/app/datatables/repository_datatable.rb
index f0e94aaba..e48ca85cc 100644
--- a/app/datatables/repository_datatable.rb
+++ b/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 "assigned" column is sorted
- direction = sort_null_direction(order_params)
- if @my_module
- # Depending on the sort, order nulls first or
- # nulls last on repository_cells association
- return records if dt_params[:assigned] == 'assigned'
+ if params[:order].present? && params[:order].length == 1
+ if sort_column(params[:order].values[0]) == ASSIGNED_SORT_COL
+ # If "assigned" column is sorted when viewing assigned items
+ return records if @my_module && params[:assigned] == 'assigned'
+ # If "assigned" column is sorted
+ direction = sort_null_direction(params[:order].values[0])
+ 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
diff --git a/app/helpers/addons_helper.rb b/app/helpers/addons_helper.rb
new file mode 100644
index 000000000..150af4976
--- /dev/null
+++ b/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
diff --git a/app/helpers/permission_helper.rb b/app/helpers/permission_helper.rb
index 16bbd8a4b..907cb2ac8 100644
--- a/app/helpers/permission_helper.rb
+++ b/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)
diff --git a/app/models/asset.rb b/app/models/asset.rb
index 7d3eb30b3..d17976213 100644
--- a/app/models/asset.rb
+++ b/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=0&')
- action_url = action_url.gsub(//,
- 'IsLicensedUser=0')
+ if ENV['WOPI_BUSINESS_USERS'] && ENV['WOPI_BUSINESS_USERS']=='true'
+ action_url = action_url.gsub(//,
+ 'IsLicensedUser=1&')
+ action_url = action_url.gsub(//,
+ 'IsLicensedUser=1')
+ else
+ action_url = action_url.gsub(//,
+ 'IsLicensedUser=0&')
+ action_url = action_url.gsub(//,
+ 'IsLicensedUser=0')
+ end
action_url = action_url.gsub(/<.*?=.*?>/, '')
rest_url = Rails.application.routes.url_helpers.wopi_rest_endpoint_url(
diff --git a/app/models/repository.rb b/app/models/repository.rb
index c2ac03add..e9ec2fc51 100644
--- a/app/models/repository.rb
+++ b/app/models/repository.rb
@@ -111,57 +111,82 @@ class Repository < ApplicationRecord
# Imports records
def import_records(sheet, mappings, user)
- errors = []
- custom_fields = []
+ errors = false
+ 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)
- custom_fields << cf
+ columns << repository_columns.find_by_id(value)
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|
- error = []
- record_row = RepositoryRow.new(name: sheet.row(i)[name_index],
- repository: self,
- created_by: user,
- last_modified_by: user)
+ transaction do
+ (2..sheet.last_row).each do |i|
+ total_nr += 1
+ record_row = RepositoryRow.new(name: sheet.row(i)[name_index],
+ repository: self,
+ 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?
- sheet.row(i).each.with_index do |value, index|
- if custom_fields[index] && value
- rep_column = RepositoryTextValue.new(
- data: value,
- created_by: user,
- last_modified_by: user,
- repository_cell_attributes: {
- repository_row: record_row,
- repository_column: custom_fields[index]
- }
- )
- error << rep_column.errors.messages unless rep_column.save
+ row_cell_values = []
+
+ sheet.row(i).each.with_index do |value, index|
+ if columns[index] && value
+ cell_value = RepositoryTextValue.new(
+ data: value,
+ created_by: user,
+ last_modified_by: user,
+ repository_cell_attributes: {
+ repository_row: record_row,
+ repository_column: columns[index]
+ }
+ )
+ 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
- return { status: :error, errors: errors, nr_of_added: nr_of_added }
+ if errors
+ 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'
- Roo::CSV.new(file_path, nil, :ignore, csv_options: { col_sep: '\t' })
+ when '.tsv'
+ 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' })
- when '.xls'
- Roo::Excel.new(file_path)
+ Roo::CSV.new(file_path, csv_options: { col_sep: "\t" })
when '.xlsx'
Roo::Excelx.new(file_path)
else
diff --git a/app/models/repository_cell.rb b/app/models/repository_cell.rb
index a3c12dccc..ad034e160 100644
--- a/app/models/repository_cell.rb
+++ b/app/models/repository_cell.rb
@@ -1,11 +1,15 @@
-class RepositoryCell < ApplicationRecord
- belongs_to :repository_row, optional: true
- belongs_to :repository_column, optional: true
- belongs_to :value, polymorphic: true, dependent: :destroy, optional: true
+class RepositoryCell < ActiveRecord::Base
+ attr_accessor :skip_on_import
+
+ 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
diff --git a/app/models/team.rb b/app/models/team.rb
index 1e61f1ea8..74f3d3841 100644
--- a/app/models/team.rb
+++ b/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
- Roo::CSV.new(file_path, nil, :ignore, csv_options: {col_sep: "\t"})
- when ".txt" then
+ when '.tsv' then
+ Roo::CSV.new(file_path, csv_options: { col_sep: "\t" })
+ when '.txt' then
# This assumption is based purely on biologist's habits
- Roo::CSV.new(file_path, csv_options: {col_sep: "\t"})
- when ".xls" then
- Roo::Excel.new(file_path)
- when ".xlsx" then
+ Roo::CSV.new(file_path, csv_options: { col_sep: "\t" })
+ 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|
- if v == "-1"
+ mappings.each.with_index do |(_, v), i|
+ 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(
- name: sheet.row(i)[sname_index],
- team_id: id,
- user: user
- )
+ sample.transaction do
+ unless sample.valid?
+ errors = true
+ 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
- sample.sample_type = stype
- else
- sample.create_sample_type(
- name: value,
- 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
+ unless stype
+ stype = SampleType.new(name: value, team: self)
+ unless stype.save
+ errors = true
+ raise ActiveRecord::Rollback
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
- error << sample.errors.messages
- end
- if error.present?
- errors << { "#{i}": error}
- else
+ if Sample.import([sample],
+ recursive: true,
+ validate: false).failed_instances.any?
+ errors = true
+ raise ActiveRecord::Rollback
+ end
nr_of_added += 1
end
end
- if errors.count > 0 then
- return {
- status: :error,
- errors: errors,
- nr_of_added: nr_of_added,
- total_nr: total_nr
- }
+ if errors
+ return { status: :error, nr_of_added: nr_of_added, total_nr: total_nr }
else
- return {
- status: :ok,
- nr_of_added: nr_of_added,
- total_nr: total_nr
- }
+ return { status: :ok, nr_of_added: nr_of_added, total_nr: total_nr }
end
end
diff --git a/app/services/import_repository/parse_repository.rb b/app/services/import_repository/parse_repository.rb
index e40c91280..192f4b61e 100644
--- a/app/services/import_repository/parse_repository.rb
+++ b/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 = []
- rows << Hash[[header, @sheet.row(2)].transpose]
+ columns = @sheet.row(2)
# 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
diff --git a/app/views/layouts/application.html.erb b/app/views/layouts/application.html.erb
index 4b7027acf..a508c5f48 100644
--- a/app/views/layouts/application.html.erb
+++ b/app/views/layouts/application.html.erb
@@ -45,6 +45,9 @@
+
+ <%= render "shared/about_modal" %>
+
<%= render "shared/navigation" %>
diff --git a/app/views/my_modules/repository.html.erb b/app/views/my_modules/repository.html.erb
index 35f6427a4..0c09e6d50 100644
--- a/app/views/my_modules/repository.html.erb
+++ b/app/views/my_modules/repository.html.erb
@@ -31,7 +31,8 @@
<% end %>
-
+
<%= render partial: "repositories/repository_table",
locals: {
repository: @repository,
@@ -40,3 +41,7 @@
}
%>
+
+<%= stylesheet_link_tag 'datatables' %>
+<%= javascript_include_tag 'repositories/repository_datatable' %>
+<%= javascript_include_tag 'repositories/my_module_repository' %>
diff --git a/app/views/repositories/_parse_records_modal.html.erb b/app/views/repositories/_parse_records_modal.html.erb
index 05925e6c5..ccab285b1 100644
--- a/app/views/repositories/_parse_records_modal.html.erb
+++ b/app/views/repositories/_parse_records_modal.html.erb
@@ -1,5 +1,5 @@
@@ -30,29 +30,31 @@
include_blank: t('teams.parse_sheet.do_not_include_column'),
hide_label: true) %>
- <% if th.length > Constants::NAME_TRUNCATION_LENGTH_DROPDOWN %>
-
- <%= truncate(th, length: Constants::NAME_TRUNCATION_LENGTH_DROPDOWN) %>
-
+ <% if th.nil? %>
+ <%= t('repositories.import_records.no_header_name') %>
<% else %>
- <%= th %>
+ <% if th.length > Constants::NAME_TRUNCATION_LENGTH_DROPDOWN %>
+
+ <%= truncate(th, length: Constants::NAME_TRUNCATION_LENGTH_DROPDOWN) %>
+
+ <% else %>
+ <%= th %>
+ <% end %>
<% end %>
|
<% end %>