forked from MIRRI/mirri_utils
183 lines
7.3 KiB
Python
183 lines
7.3 KiB
Python
#!/usr/bin/env python3
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import argparse
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import sys
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from collections import Counter
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from mirri.biolomics.pipelines.growth_medium import get_or_create_or_update_growth_medium
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from mirri.biolomics.pipelines.strain import get_or_create_or_update_strain
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from mirri.biolomics.remote.biolomics_client import BiolomicsMirriClient
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from mirri.io.parsers.mirri_excel import parse_mirri_excel
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from mirri.validation.excel_validator import validate_mirri_excel
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TEST_SERVER_URL = 'https://webservices.bio-aware.com/mirri_test'
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PROD_SERVER_URL = 'https://webservices.bio-aware.com/mirri'
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def get_cmd_args():
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desc = "Upload strains to MIRRI-IS"
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parser = argparse.ArgumentParser(description=desc)
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parser.add_argument('-i', '--input', help='Validated Excel file',
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type=argparse.FileType('rb'), required=True)
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parser.add_argument('-v', '--spec_version', default='20200601',
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help='Version of he specification of the given excel file')
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parser.add_argument('-u', '--ws_user', help='Username of the web service',
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required=True)
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parser.add_argument('-p', '--ws_password', required=True,
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help='Password of the web service user')
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parser.add_argument('-c', '--client_id', required=True,
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help='Client id of the web service')
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parser.add_argument('-s', '--client_secret', required=True,
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help='Client secret of the web service')
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parser.add_argument('--force_update', required=False,
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action='store_true',
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help='Use it if you want to update the existing strains')
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parser.add_argument('--verbose', action='store_true',
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help='use it if you want a verbose output')
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parser.add_argument('--prod', action='store_true',
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help='Use production server')
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parser.add_argument('--dont_add_gm', action='store_false',
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help="Don't add growth media", default=True)
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parser.add_argument('--dont_add_strains', action='store_false',
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help="Don't add growth media", default=True)
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parser.add_argument('--skip_first_num', type=int,
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help='skip first X strains to the tool')
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args = parser.parse_args()
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return {'input_fhand': args.input, 'user': args.ws_user,
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'version': args.spec_version,
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'password': args.ws_password, 'client_id': args.client_id,
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'client_secret': args.client_secret, 'update': args.force_update,
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'verbose': args.verbose, 'use_production_server': args.prod,
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'add_gm': args.dont_add_gm, 'add_strains': args.dont_add_strains,
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'skip_first_num': args.skip_first_num}
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def write_errors_in_screen(errors, fhand=sys.stderr):
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for key, errors_by_type in errors.items():
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fhand.write(f'{key}\n')
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fhand.write('-' * len(key) + '\n')
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for error in errors_by_type:
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if error.pk:
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fhand.write(f'{error.pk}: ')
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fhand.write(f'{error.message} - {error.code}\n')
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fhand.write('\n')
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def create_or_upload_strains(client, strains, update=False, counter=None,
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out_fhand=None, seek=None):
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for index, strain in enumerate(strains):
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if seek is not None and index < seek:
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continue
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# if strain.id.strain_id != 'CECT 5766':
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# continue
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result = get_or_create_or_update_strain(client, strain, update=update)
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new_strain = result['record']
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created = result['created']
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updated = result.get('updated', False)
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if updated:
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result_state = 'updated'
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elif created:
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result_state = 'created'
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else:
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result_state = 'not modified'
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if counter is not None:
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counter[result_state] += 1
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if out_fhand is not None:
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out_fhand.write(f'{index}: Strain {new_strain.id.strain_id}: {result_state}\n')
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# break
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def create_or_upload_growth_media(client, growth_media, update=False, counter=None,
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out_fhand=None):
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for gm in growth_media:
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result = get_or_create_or_update_growth_medium(client, gm, update)
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new_gm = result['record']
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created = result['created']
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updated = result.get('updated', False)
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if updated:
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result_state = 'updated'
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elif created:
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result_state = 'created'
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else:
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result_state = 'not modified'
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if counter is not None:
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counter[result_state] += 1
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if out_fhand is not None:
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out_fhand.write(f'Growth medium {new_gm.record_name}: {result_state}\n')
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def main():
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args = get_cmd_args()
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input_fhand = args['input_fhand']
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spec_version = args['version']
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out_fhand = sys.stdout
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error_log = validate_mirri_excel(input_fhand, version=spec_version)
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errors = error_log.get_errors()
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skip_first_num = args['skip_first_num']
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if errors:
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write_errors_in_screen(errors, out_fhand)
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sys.exit(1)
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input_fhand.seek(0)
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parsed_objects = parse_mirri_excel(input_fhand, version=spec_version)
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strains = list(parsed_objects['strains'])
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growth_media = list(parsed_objects['growth_media'])
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server_url = PROD_SERVER_URL if args['use_production_server'] else TEST_SERVER_URL
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client = BiolomicsMirriClient(server_url=server_url, api_version='v2',
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client_id=args['client_id'],
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client_secret=args['client_secret'],
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username=args['user'],
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password=args['password'],
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verbose=args['verbose'])
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if args['add_gm']:
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client.start_transaction()
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counter = Counter()
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try:
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create_or_upload_growth_media(client, growth_media, update=args['update'],
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counter=counter, out_fhand=out_fhand)
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except (Exception, KeyboardInterrupt) as error:
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out_fhand.write('There were some errors in the Growth media upload\n')
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out_fhand.write(str(error) + '\n')
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out_fhand.write('Rolling back\n')
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client.rollback()
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raise
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client.finish_transaction()
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show_stats(counter, 'Growth Media', out_fhand)
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if args['add_strains']:
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client.start_transaction()
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counter = Counter()
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try:
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create_or_upload_strains(client, strains, update=args['update'],
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counter=counter,
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out_fhand=out_fhand, seek=skip_first_num)
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client.finish_transaction()
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except (Exception, KeyboardInterrupt) as error:
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out_fhand.write('There were some errors in the Strain upload\n')
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out_fhand.write(str(error) + '\n')
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out_fhand.write('rolling back\n')
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# client.rollback()
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raise
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client.finish_transaction()
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show_stats(counter, 'Strains', out_fhand)
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def show_stats(counter, kind, out_fhand):
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out_fhand.write(f'{kind}\n')
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line = ''.join(['-'] * len(kind))
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out_fhand.write(f"{line}\n")
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for kind2, value in counter.most_common(5):
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out_fhand.write(f'{kind2}: {value}\n')
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out_fhand.write('\n')
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if __name__ == '__main__':
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main()
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