class TeamsController < ApplicationController
before_action :load_vars, only: [:parse_sheet, :import_samples, :export_samples]
before_action :check_create_sample_permissions, only: [:parse_sheet, :import_samples]
before_action :check_view_samples_permission, only: [:export_samples]
def parse_sheet
session[:return_to] ||= request.referer
respond_to do |format|
if params[:file]
begin
if params[:file].size > Constants::FILE_MAX_SIZE_MB.megabytes
error = t 'general.file.size_exceeded',
file_size: Constants::FILE_MAX_SIZE_MB
format.html {
flash[:alert] = error
redirect_to session.delete(:return_to)
}
format.json {
render json: {message: error},
status: :unprocessable_entity
}
else
sheet = Team.open_spreadsheet(params[:file])
# Check if we actually have any rows (last_row > 1)
if sheet.last_row.between?(0, 1)
flash[:notice] = t(
"teams.parse_sheet.errors.empty_file")
redirect_to session.delete(:return_to) and return
end
# Get data (it will trigger any errors as well)
@header = sheet.row(1)
@columns = sheet.row(2)
# Fill in fields for dropdown
@available_fields = @team.get_available_sample_fields
# Truncate long fields
@available_fields.update(@available_fields) do |_k, v|
v.truncate(Constants::NAME_TRUNCATION_LENGTH_DROPDOWN)
end
# Save file for next step (importing)
@temp_file = TempFile.new(
session_id: session.id,
file: params[:file]
)
if @temp_file.save
@temp_file.destroy_obsolete
# format.html
format.json {
render :json => {
:html => render_to_string({
:partial => "samples/parse_samples_modal.html.erb"
})
}
}
else
error = t("teams.parse_sheet.errors.temp_file_failure")
format.html {
flash[:alert] = error
redirect_to session.delete(:return_to)
}
format.json {
render json: {message: error},
status: :unprocessable_entity
}
end
end
rescue ArgumentError, CSV::MalformedCSVError
error = t('teams.parse_sheet.errors.invalid_file',
encoding: ''.encoding)
format.html {
flash[:alert] = error
redirect_to session.delete(:return_to)
}
format.json {
render json: {message: error},
status: :unprocessable_entity
}
rescue TypeError
error = t("teams.parse_sheet.errors.invalid_extension")
format.html {
flash[:alert] = error
redirect_to session.delete(:return_to)
}
format.json {
render json: {message: error},
status: :unprocessable_entity
}
end
else
error = t("teams.parse_sheet.errors.no_file_selected")
format.html {
flash[:alert] = error
session[:return_to] ||= request.referer
redirect_to session.delete(:return_to)
}
format.json {
render json: {message: error},
status: :unprocessable_entity
}
end
end
end
def import_samples
session[:return_to] ||= request.referer
respond_to do |format|
if params[:file_id]
@temp_file = TempFile.find_by_id(params[:file_id])
if @temp_file
# Check if session_id is equal to prevent file stealing
if @temp_file.session_id == session.id
# Check if mappings exists or else we don't have anything to parse
if params[:mappings]
@sheet = Team.open_spreadsheet(@temp_file.file)
# Check for duplicated values
h1 = params[:mappings].clone.delete_if { |k, v| v.empty? }
if h1.length == h1.invert.length
# Check if there exist mapping for sample name (it's mandatory)
if params[:mappings].has_value?("-1")
result = @team.import_samples(@sheet, params[:mappings], current_user)
nr_of_added = result[:nr_of_added]
total_nr = result[:total_nr]
if result[:status] == :ok
# If no errors are present, redirect back
# to samples table
flash[:success] = t(
"teams.import_samples.success_flash",
nr: nr_of_added,
samples: t(
"teams.import_samples.sample",
count: total_nr
)
)
@temp_file.destroy
format.html {
redirect_to session.delete(:return_to)
}
format.json {
flash.keep(:success)
render json: { status: :ok }
}
else
# Otherwise, also redirect back,
# but display different message
flash[:alert] = t(
"teams.import_samples.partial_success_flash",
nr: nr_of_added,
samples: t(
"teams.import_samples.sample",
count: total_nr
)
)
@temp_file.destroy
format.html {
redirect_to session.delete(:return_to)
}
format.json {
flash.keep(:alert)
render json: { status: :unprocessable_entity }
}
end
else
# This is currently the only AJAX error response
flash_alert = t(
"teams.import_samples.errors.no_sample_name")
format.html {
flash[:alert] = flash_alert
redirect_to session.delete(:return_to)
}
format.json {
render json: {
html: render_to_string({
partial: "parse_error.html.erb",
locals: { error: flash_alert }
})
},
status: :unprocessable_entity
}
end
else
# This code should never execute unless user tampers with
# JS (selects same column in more than one dropdown)
flash_alert = t(
"teams.import_samples.errors.duplicated_values")
format.html {
flash[:alert] = flash_alert
redirect_to session.delete(:return_to)
}
format.json {
render json: {
html: render_to_string({
partial: "parse_error.html.erb",
locals: { error: flash_alert }
})
},
status: :unprocessable_entity
}
end
else
@temp_file.destroy
flash[:alert] = t(
"teams.import_samples.errors.no_data_to_parse")
format.html {
redirect_to session.delete(:return_to)
}
format.json {
flash.keep(:alert)
render json: { status: :unprocessable_entity }
}
end
else
@temp_file.destroy
flash[:alert] = t(
"teams.import_samples.errors.session_expired")
format.html {
redirect_to session.delete(:return_to)
}
format.json {
flash.keep(:alert)
render json: { status: :unprocessable_entity }
}
end
else
# No temp file to begin with, so no need to destroy it
flash[:alert] = t(
"teams.import_samples.errors.temp_file_not_found")
format.html {
redirect_to session.delete(:return_to)
}
format.json {
flash.keep(:alert)
render json: { status: :unprocessable_entity }
}
end
else
flash[:alert] = t(
"teams.import_samples.errors.temp_file_not_found")
format.html {
redirect_to session.delete(:return_to)
}
format.json {
flash.keep(:alert)
render json: { status: :unprocessable_entity }
}
end
end
end
def export_samples
if params[:sample_ids] && params[:header_ids]
generate_samples_zip
else
flash[:alert] = t('zip_export.export_error')
end
redirect_to :back
end
def routing_error(error = 'Routing error', status = :not_found, exception=nil)
redirect_to root_path
end
private
def load_vars
@team = Team.find_by_id(params[:id])
unless @team
render_404
end
end
def check_create_sample_permissions
unless can_create_samples(@team)
render_403
end
end
def check_view_samples_permission
unless can_view_samples(@team)
render_403
end
end
def generate_samples_zip
zip = ZipExport.create(user: current_user)
zip.generate_exportable_zip(
current_user,
@team.to_csv(Sample.where(id: params[:sample_ids]), params[:header_ids]),
:samples
)
end
end