forked from MIRRI/mirri_utils
92 lines
3.6 KiB
Python
92 lines
3.6 KiB
Python
#!/usr/bin/env python3
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import argparse
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import sys
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from mirri.biolomics.pipelines.strain import retrieve_strain_by_accession_number
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from mirri.biolomics.remote.biolomics_client import BiolomicsMirriClient
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from mirri.biolomics.remote.endoint_names import GROWTH_MEDIUM_WS, STRAIN_WS
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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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SERVER_URL = 'https://webservices.bio-aware.com/mirri_test'
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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('-f', '--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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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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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 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.stderr
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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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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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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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for gm in growth_media:
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try:
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client.delete_by_name(GROWTH_MEDIUM_WS, gm.acronym)
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except ValueError as error:
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print(error)
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continue
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print(f'Growth medium {gm.acronym} deleted')
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for strain in strains:
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ws_strain = retrieve_strain_by_accession_number(client, strain.id.strain_id)
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if ws_strain is not None:
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client.delete_by_id(STRAIN_WS, ws_strain.record_id)
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print(f'Strain {strain.id.strain_id} deleted')
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else:
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print(f'Strain {strain.id.strain_id} not in database')
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if __name__ == '__main__':
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main()
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