forked from MIRRI/mirri_utils
224 lines
8.5 KiB
Python
224 lines
8.5 KiB
Python
#!/usr/bin/env python3
|
|
import argparse
|
|
from cmath import nan
|
|
import sys
|
|
from collections import Counter
|
|
|
|
#
|
|
from mirri.biolomics.pipelines.growth_medium import get_or_create_or_update_growth_medium
|
|
from mirri.biolomics.pipelines.strain import get_or_create_or_update_strain
|
|
from mirri.biolomics.remote.biolomics_client import BiolomicsMirriClient
|
|
from mirri.io.parsers.mirri_excel import parse_mirri_excel
|
|
from mirri.validation.excel_validator import validate_mirri_excel
|
|
|
|
##Database
|
|
from sqlalchemy import create_engine, MetaData
|
|
import pymysql
|
|
import pandas as pd
|
|
from pathlib import Path
|
|
import numpy as np
|
|
|
|
# DEFINE THE DATABASE CREDENTIALS
|
|
user = 'mirridev'
|
|
password = 'estramboticandolotodo'
|
|
host = 'mirri-is.mirri.org'
|
|
port = 33066
|
|
database = 'mirri-db'
|
|
|
|
TEST_SERVER_URL = 'https://webservices.bio-aware.com/mirri_test'
|
|
PROD_SERVER_URL = 'https://webservices.bio-aware.com/mirri'
|
|
|
|
def show_stats(counter, kind, out_fhand):
|
|
out_fhand.write(f'{kind}\n')
|
|
line = ''.join(['-'] * len(kind))
|
|
out_fhand.write(f"{line}\n")
|
|
for kind2, value in counter.most_common(5):
|
|
out_fhand.write(f'{kind2}: {value}\n')
|
|
out_fhand.write('\n')
|
|
|
|
|
|
def get_cmd_args():
|
|
desc = "Upload strains to MIRRI-IS"
|
|
parser = argparse.ArgumentParser(description=desc)
|
|
parser.add_argument('-i' , '--input', required=True, help='Validated Excel file', type=argparse.FileType('rb'))
|
|
parser.add_argument('-v' , '--spec_version', default='20200601', help='Version of he specification of the given excel file')
|
|
parser.add_argument('-u' , '--ws_user', help='Username of the web service')
|
|
parser.add_argument('-p' , '--ws_password', required=True, help='Password of the web service user')
|
|
parser.add_argument('-c' , '--client_id', required=True, help='Client id of the web service')
|
|
parser.add_argument('-s' , '--client_secret', required=True, help='Client secret of the web service')
|
|
parser.add_argument('--force_update' , required=False, action='store_true', help='Use it if you want to update the existing strains')
|
|
parser.add_argument('--verbose' , action='store_true', help='use it if you want a verbose output')
|
|
parser.add_argument('--prod' , action='store_true', help='Use production server')
|
|
parser.add_argument('--dont_add_gm' , default=True, action='store_false', help="Don't add growth media")
|
|
parser.add_argument('--dont_add_strains', default=True, action='store_false', help="Don't add growth media")
|
|
parser.add_argument('--skip_first_num' , type=int, help='skip first X strains to the tool')
|
|
|
|
args = parser.parse_args()
|
|
|
|
return {'input_fhand': args.input
|
|
,'user': args.ws_user
|
|
,'version': args.spec_version
|
|
,'password': args.ws_password
|
|
,'client_id': args.client_id
|
|
,'client_secret': args.client_secret
|
|
,'update': args.force_update
|
|
,'verbose': args.verbose
|
|
,'use_production_server': args.prod
|
|
,'add_gm': args.dont_add_gm
|
|
,'add_strains': args.dont_add_strains
|
|
,'skip_first_num': args.skip_first_num
|
|
}
|
|
|
|
|
|
def write_errors_in_screen(errors, fhand=sys.stderr):
|
|
for key, errors_by_type in errors.items():
|
|
fhand.write(f'{key}\n')
|
|
fhand.write('-' * len(key) + '\n')
|
|
for error in errors_by_type:
|
|
if error.pk:
|
|
fhand.write(f'{error.pk}: ')
|
|
fhand.write(f'{error.message} - {error.code}\n')
|
|
fhand.write('\n')
|
|
|
|
|
|
def create_or_upload_strains(client, strains, update=False, counter=None, out_fhand=None, seek=None):
|
|
|
|
for index, strain in enumerate(strains):
|
|
if seek is not None and index < seek:
|
|
continue
|
|
# if strain.id.strain_id != 'CECT 5766':
|
|
# continue
|
|
result = get_or_create_or_update_strain(client, strain, update=update)
|
|
|
|
new_strain = result['record']
|
|
created = result['created']
|
|
updated = result.get('updated', False)
|
|
if updated:
|
|
result_state = 'updated'
|
|
elif created:
|
|
result_state = 'created'
|
|
else:
|
|
result_state = 'not modified'
|
|
|
|
if counter is not None:
|
|
counter[result_state] += 1
|
|
if out_fhand is not None:
|
|
out_fhand.write(f'{index}: Strain {new_strain.id.strain_id}: {result_state}\n')
|
|
# break
|
|
|
|
|
|
def create_or_upload_growth_media(client, growth_media, update=False, counter=None, out_fhand=None):
|
|
|
|
for gm in growth_media:
|
|
result = get_or_create_or_update_growth_medium(client, gm, update)
|
|
|
|
new_gm = result['record']
|
|
created = result['created']
|
|
updated = result.get('updated', False)
|
|
if updated:
|
|
result_state = 'updated'
|
|
elif created:
|
|
result_state = 'created'
|
|
else:
|
|
result_state = 'not modified'
|
|
if counter is not None:
|
|
counter[result_state] += 1
|
|
if out_fhand is not None:
|
|
out_fhand.write(f'Growth medium {new_gm.record_name}: {result_state}\n')
|
|
|
|
|
|
def get_connection():
|
|
# PYTHON FUNCTION TO CONNECT TO THE MYSQL DATABASE AND
|
|
# RETURN THE SQLACHEMY ENGINE OBJECT
|
|
return create_engine(url="mysql+pymysql://{0}:{1}@{2}:{3}/{4}".format(user, password, host, port, database))
|
|
|
|
def main():
|
|
## Load Excel
|
|
path = Path('C://data//brclims_excel.xlsx')
|
|
Excel_Data = pd.read_excel(path, sheet_name = None)
|
|
cc_id=1
|
|
|
|
## Load Database
|
|
sqlEngine = get_connection()
|
|
engine = sqlEngine.connect()
|
|
|
|
## Create new file upload
|
|
with engine.connect() as conn:
|
|
metaDats = MetaData(conn, schema=database)
|
|
metaDats.reflect(bind=conn)
|
|
table = metaDats.tables['mirri-db.file_upload']
|
|
stmt = table.insert().values(filename=path.name,cc_id=cc_id)
|
|
aux=conn.execute(stmt).inserted_primary_key[0]
|
|
|
|
## Load all Sheet from Excel to DB
|
|
for key in Excel_Data.keys():
|
|
#print(key)
|
|
n=Excel_Data[key].replace(np.nan, '', regex=True).astype(str)
|
|
n.columns = n.columns.str.replace(' ','_')
|
|
n['f_id']=aux
|
|
n.to_sql(key, engine, index=False, if_exists='append')
|
|
|
|
|
|
|
|
"""
|
|
args = get_cmd_args()
|
|
input_fhand = args['input_fhand']
|
|
spec_version = args['version']
|
|
out_fhand = sys.stdout
|
|
error_log = validate_mirri_excel(input_fhand, version=spec_version)
|
|
errors = error_log.get_errors()
|
|
skip_first_num = args['skip_first_num']
|
|
if errors:
|
|
write_errors_in_screen(errors, out_fhand)
|
|
sys.exit(1)
|
|
|
|
input_fhand.seek(0)
|
|
parsed_objects = parse_mirri_excel(input_fhand, version=spec_version)
|
|
strains = list(parsed_objects['strains'])
|
|
growth_media = list(parsed_objects['growth_media'])
|
|
|
|
server_url = PROD_SERVER_URL if args['use_production_server'] else TEST_SERVER_URL
|
|
|
|
client = BiolomicsMirriClient(server_url=server_url, api_version='v2',
|
|
client_id=args['client_id'],
|
|
client_secret=args['client_secret'],
|
|
username=args['user'],
|
|
password=args['password'],
|
|
verbose=args['verbose'])
|
|
|
|
if args['add_gm']:
|
|
client.start_transaction()
|
|
counter = Counter()
|
|
try:
|
|
create_or_upload_growth_media(client, growth_media, update=args['update'],
|
|
counter=counter, out_fhand=out_fhand)
|
|
except (Exception, KeyboardInterrupt) as error:
|
|
out_fhand.write('There were some errors in the Growth media upload\n')
|
|
out_fhand.write(str(error) + '\n')
|
|
out_fhand.write('Rolling back\n')
|
|
client.rollback()
|
|
raise
|
|
client.finish_transaction()
|
|
show_stats(counter, 'Growth Media', out_fhand)
|
|
|
|
if args['add_strains']:
|
|
client.start_transaction()
|
|
counter = Counter()
|
|
try:
|
|
create_or_upload_strains(client, strains, update=args['update'],
|
|
counter=counter,
|
|
out_fhand=out_fhand, seek=skip_first_num)
|
|
client.finish_transaction()
|
|
except (Exception, KeyboardInterrupt) as error:
|
|
out_fhand.write('There were some errors in the Strain upload\n')
|
|
out_fhand.write(str(error) + '\n')
|
|
out_fhand.write('rolling back\n')
|
|
# client.rollback()
|
|
raise
|
|
client.finish_transaction()
|
|
show_stats(counter, 'Strains', out_fhand)
|
|
"""
|
|
|
|
if __name__ == '__main__':
|
|
main()
|