diff --git a/Gemfile b/Gemfile
index cae686400..75fadeeee 100644
--- a/Gemfile
+++ b/Gemfile
@@ -46,7 +46,7 @@ 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'
diff --git a/Gemfile.lock b/Gemfile.lock
index 40a51e8f3..eb70da5f8 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -190,9 +190,8 @@ GEM
jquery-rails
rails (>= 3.2.0)
newrelic_rpm (4.0.0.332)
- nokogiri (1.6.8)
+ nokogiri (1.6.8.1)
mini_portile2 (~> 2.1.0)
- pkg-config (~> 1.1.7)
nokogumbo (1.4.10)
nokogiri
oj (2.17.4)
@@ -206,7 +205,6 @@ GEM
parser (2.4.0.0)
ast (~> 2.2)
pg (0.18.4)
- pkg-config (1.1.7)
polyglot (0.3.5)
powerpack (0.1.1)
puma (2.15.3)
@@ -257,7 +255,7 @@ GEM
algorithms (~> 0.6.1)
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)
rubocop (0.48.1)
@@ -268,7 +266,7 @@ GEM
unicode-display_width (~> 1.0, >= 1.0.1)
ruby-graphviz (1.2.2)
ruby-progressbar (1.8.1)
- rubyzip (1.1.7)
+ rubyzip (1.2.1)
sanitize (4.4.0)
crass (~> 1.0.2)
nokogiri (>= 1.4.4)
@@ -390,7 +388,7 @@ DEPENDENCIES
recaptcha
remotipart (~> 1.2)
rgl
- roo (~> 2.1.0)
+ roo (~> 2.7.1)
rubocop
ruby-graphviz (~> 1.2)
rubyzip
diff --git a/app/assets/javascripts/repositories/index.js b/app/assets/javascripts/repositories/index.js
index d6150415e..3ff5474cf 100644
--- a/app/assets/javascripts/repositories/index.js
+++ b/app/assets/javascripts/repositories/index.js
@@ -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("" +
+ data.responseJSON.message + '');
});
}
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/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/models/repository.rb b/app/models/repository.rb
index e47e79501..0e6c193c3 100644
--- a/app/models/repository.rb
+++ b/app/models/repository.rb
@@ -109,9 +109,10 @@ class Repository < ActiveRecord::Base
# Imports records
def import_records(sheet, mappings, user)
- errors = []
+ errors = false
custom_fields = []
name_index = -1
+ total_nr = 0
nr_of_added = 0
mappings.each.with_index do |(_k, value), index|
@@ -127,13 +128,17 @@ class Repository < ActiveRecord::Base
# Now we can iterate through record data and save stuff into db
(2..sheet.last_row).each do |i|
- error = []
+ total_nr += 1
+ cell_error = false
record_row = RepositoryRow.new(name: sheet.row(i)[name_index],
repository: self,
created_by: user,
last_modified_by: user)
- next unless record_row.valid?
+ unless record_row.valid?
+ errors = true
+ next
+ end
sheet.row(i).each.with_index do |value, index|
if custom_fields[index] && value
rep_column = RepositoryTextValue.new(
@@ -145,10 +150,11 @@ class Repository < ActiveRecord::Base
repository_column: custom_fields[index]
}
)
- error << rep_column.errors.messages unless rep_column.save
+ cell_error = true unless rep_column.save
end
end
- if error.any?
+ if cell_error
+ errors = true
record_row.destroy
else
nr_of_added += 1
@@ -156,10 +162,12 @@ class Repository < ActiveRecord::Base
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
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/repositories/_parse_records_modal.html.erb b/app/views/repositories/_parse_records_modal.html.erb
index 05925e6c5..c582b8bbe 100644
--- a/app/views/repositories/_parse_records_modal.html.erb
+++ b/app/views/repositories/_parse_records_modal.html.erb
@@ -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 %>
- <% @import_data.rows.each do |row| %>
-
+
+ |
+ <%= t('teams.parse_sheet.example_value') %>
+ |
+ <% @import_data.columns.each do |td| %>
- <%= t('teams.parse_sheet.example_value') %>
+ <%= td %>
|
- <% row.each do |td| %>
-
- <%= td[1] %>
- |
- <% end %>
-
- <% end %>
+ <% end %>
+
diff --git a/app/views/samples/_parse_samples_modal.html.erb b/app/views/samples/_parse_samples_modal.html.erb
index 31a946b88..613c3d444 100644
--- a/app/views/samples/_parse_samples_modal.html.erb
+++ b/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) %>
- <% if th.length > Constants::NAME_TRUNCATION_LENGTH_DROPDOWN %>
-
- <%= truncate(th, length: Constants::NAME_TRUNCATION_LENGTH_DROPDOWN) %>
-
+ <% if th.nil? %>
+ <%= t('samples.modal_import.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 %>
- <% @rows.each do |row| %>
-
+
+ |
+ <%= t('teams.parse_sheet.example_value') %>
+ |
+ <% @columns.each do |td| %>
- <%= t('teams.parse_sheet.example_value') %>
+ <%= td %>
|
- <% row.each do |td| %>
-
- <%= td[1] %>
- |
- <% end %>
-
- <% end %>
+ <% end %>
+
diff --git a/config/initializers/paperclip.rb b/config/initializers/paperclip.rb
index 2cdeb718e..4f91e6ce7 100644
--- a/config/initializers/paperclip.rb
+++ b/config/initializers/paperclip.rb
@@ -80,7 +80,7 @@ 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
@@ -91,7 +91,7 @@ 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
@@ -104,7 +104,7 @@ 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,
diff --git a/config/locales/en.yml b/config/locales/en.yml
index fa31517ed..af6c491fe 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -911,8 +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."
@@ -1009,6 +1010,7 @@ en:
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."
+ no_header_name: 'No column name'
upload: "Upload file"
modal_delete:
title: "Delete samples"