MIRRI/mirri_utils
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Antonio Vara 2022-09-01 14:15:40 +02:00
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.gitignore vendored Normal file
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mirri/biolomics/secrets.py
.vscode/launch.json
*.pyc

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bin/upload_strains_to_mirri_is_NEWDB.py Normal file
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#!/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()

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#!/usr/bin/env python
import sys
from pathlib import Path
from mirri.validation.excel_validator import validate_mirri_excel
import warnings
warnings.simplefilter("ignore")
def main():
# path = Path(sys.argv[1])
path = Path( 'C:/data/brclims_excel.xlsx')
error_log = validate_mirri_excel(path.open("rb"))
for errors in error_log.get_errors().values():
for error in errors:
print(error.pk, error.message, error.code)
if __name__ == "__main__":
main()