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Merge pull request #940 from okriuchykhin/ok_SCI_1946

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Fix samples import [SCI-1946]
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okriuchykhin 2018-01-17 12:51:35 +01:00 committed by GitHub
commit 8ccb361525
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1 changed files with 25 additions and 12 deletions
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37
app/controllers/teams_controller.rb
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@ -7,17 +7,17 @@ class TeamsController < ApplicationController
def parse_sheet def parse_sheet
session[:return_to] ||= request.referer session[:return_to] ||= request.referer
unless params[:file] unless import_params[:file]
return parse_sheet_error(t('teams.parse_sheet.errors.no_file_selected')) return parse_sheet_error(t('teams.parse_sheet.errors.no_file_selected'))
end end
if params[:file].size > Constants::FILE_MAX_SIZE_MB.megabytes if import_params[:file].size > Constants::FILE_MAX_SIZE_MB.megabytes
error = t('general.file.size_exceeded', error = t('general.file.size_exceeded',
file_size: Constants::FILE_MAX_SIZE_MB) file_size: Constants::FILE_MAX_SIZE_MB)
return parse_sheet_error(error) return parse_sheet_error(error)
end end
begin begin
sheet = SpreadsheetParser.open_spreadsheet(params[:file]) sheet = SpreadsheetParser.open_spreadsheet(import_params[:file])
@header, @columns = SpreadsheetParser.first_two_rows(sheet) @header, @columns = SpreadsheetParser.first_two_rows(sheet)
if @header.empty? || @columns.empty? if @header.empty? || @columns.empty?
@ -34,7 +34,7 @@ class TeamsController < ApplicationController
# Save file for next step (importing) # Save file for next step (importing)
@temp_file = TempFile.new( @temp_file = TempFile.new(
session_id: session.id, session_id: session.id,
file: params[:file] file: import_params[:file]
) )
if @temp_file.save if @temp_file.save
@ -65,23 +65,25 @@ class TeamsController < ApplicationController
session[:return_to] ||= request.referer session[:return_to] ||= request.referer
respond_to do |format| respond_to do |format|
if params[:file_id] if import_params[:file_id]
@temp_file = TempFile.find_by_id(params[:file_id]) @temp_file = TempFile.find_by_id(import_params[:file_id])
if @temp_file if @temp_file
# Check if session_id is equal to prevent file stealing # Check if session_id is equal to prevent file stealing
if @temp_file.session_id == session.id if @temp_file.session_id == session.id
# Check if mappings exists or else we don't have anything to parse # Check if mappings exists or else we don't have anything to parse
if params[:mappings] if import_params[:mappings]
@sheet = SpreadsheetParser.open_spreadsheet(@temp_file.file) @sheet = SpreadsheetParser.open_spreadsheet(@temp_file.file)
# Check for duplicated values # Check for duplicated values
h1 = params[:mappings].clone.delete_if { |k, v| v.empty? } h1 = import_params[:mappings].clone.delete_if { |_, v| v.empty? }
if h1.length == h1.invert.length if h1.length == h1.invert.length
# Check if there exist mapping for sample name (it's mandatory) # Check if there exist mapping for sample name (it's mandatory)
if params[:mappings].has_value?("-1") if import_params[:mappings].value?('-1')
result = @team.import_samples(@sheet, params[:mappings], current_user) result = @team.import_samples(@sheet,
import_params[:mappings],
current_user)
nr_of_added = result[:nr_of_added] nr_of_added = result[:nr_of_added]
total_nr = result[:total_nr] total_nr = result[:total_nr]
@ -212,7 +214,7 @@ class TeamsController < ApplicationController
end end
def export_samples def export_samples
if params[:sample_ids] && params[:header_ids] if export_params[:sample_ids] && export_params[:header_ids]
generate_samples_zip generate_samples_zip
else else
flash[:alert] = t('zip_export.export_error') flash[:alert] = t('zip_export.export_error')
@ -248,6 +250,14 @@ class TeamsController < ApplicationController
end end
end end
def import_params
params.permit(:id, :file, :file_id, mappings: {}).to_h
end
def export_params
params.permit(sample_ids: [], header_ids: []).to_h
end
def check_create_sample_permissions def check_create_sample_permissions
unless can_manage_samples?(@team) unless can_manage_samples?(@team)
render_403 render_403
@ -264,7 +274,10 @@ class TeamsController < ApplicationController
zip = ZipExport.create(user: current_user) zip = ZipExport.create(user: current_user)
zip.generate_exportable_zip( zip.generate_exportable_zip(
current_user, current_user,
@team.to_csv(Sample.where(id: params[:sample_ids]), params[:header_ids]), @team.to_csv(
Sample.where(id: export_params[:sample_ids]),
export_params[:header_ids]
),
:samples :samples
) )
end end