9189630163

Committed 22 May 2024 10:26AM UTC coverage: 94.311%. Remained the same

Build # 9189630163

Build Type

Pull #121

github

Committed by

web-flow

Commit Message

Merge 389cf0ae7 into fcdb3ce6a

Pull Request Pull Request #121: ⬆️ Bump jinja2 from 3.1.2 to 3.1.4

Run Details

2984 of 3164 relevant lines covered (94.31%)

0.94 hits per line

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85.19

/src/data/add_breed.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Apr  1 12:28:31 2021

@author: Paolo Cozzi <paolo.cozzi@ibba.cnr.it>

Add or update a breed in smarter database using CLI
"""

import click
import logging

from pathlib import Path

from src.features.smarterdb import (
    global_connection, get_or_create_breed, BreedAlias, Dataset)

logger = logging.getLogger(__name__)


@click.command()
@click.option(
    '--species_class',
    type=click.Choice(
        ['Sheep', 'Goat'],
        case_sensitive=False),
    required=True,
    help="The generic species of this breed (Sheep or Goat)")
@click.option(
    '--name',
    type=str,
    required=True,
    help="The breed name")
@click.option(
    '--code',
    type=str,
    required=True,
    help="The breed code")
@click.option(
    '--alias',
    type=str,
    multiple=True,
    help="The FID used as a breed code in genotype file")
@click.option(
    '--dataset', type=str, required=True,
    help="The raw dataset file name (zip archive)"
)
def main(species_class, name, code, alias, dataset):
    """Add or update a breed into SMARTER database"""

    logger.info(f"{Path(__file__).name} started")

    # get the dataset object
    dataset = Dataset.objects(file=dataset).get()

    # fix input parameters
    aliases = [BreedAlias(fid=fid, dataset=dataset) for fid in alias]
    species_class = species_class.capitalize()
    code = code.upper()

    # get a breed object relying on parameters
    breed, modified = get_or_create_breed(
        species_class=species_class, name=name, code=code, aliases=aliases)

    if modified:
        logger.info(f"{breed} added to database")

    logger.info(f"{Path(__file__).name} ended")


if __name__ == '__main__':
    log_fmt = '%(asctime)s - %(name)s - %(levelname)s - %(message)s'
    logging.basicConfig(level=logging.INFO, format=log_fmt)

    # connect to database
    global_connection()

    main()

1	#!/usr/bin/env python3
2	# -- coding: utf-8 --
3	"""	1✔
4	Created on Thu Apr 1 12:28:31 2021
5
6	@author: Paolo Cozzi <paolo.cozzi@ibba.cnr.it>
7
8	Add or update a breed in smarter database using CLI
9	"""
10
11	import click	1✔
12	import logging	1✔
13
14	from pathlib import Path	1✔
15
16	from src.features.smarterdb import (	1✔
17	global_connection, get_or_create_breed, BreedAlias, Dataset)
18
19	logger = logging.getLogger(__name__)	1✔
20
21
22	@click.command()	1✔
23	@click.option(	1✔
24	'--species_class',
25	type=click.Choice(
26	['Sheep', 'Goat'],
27	case_sensitive=False),
28	required=True,
29	help="The generic species of this breed (Sheep or Goat)")
30	@click.option(	1✔
31	'--name',
32	type=str,
33	required=True,
34	help="The breed name")
35	@click.option(	1✔
36	'--code',
37	type=str,
38	required=True,
39	help="The breed code")
40	@click.option(	1✔
41	'--alias',
42	type=str,
43	multiple=True,
44	help="The FID used as a breed code in genotype file")
45	@click.option(	1✔
46	'--dataset', type=str, required=True,
47	help="The raw dataset file name (zip archive)"
48	)
49	def main(species_class, name, code, alias, dataset):	1✔
50	"""Add or update a breed into SMARTER database"""
51
52	logger.info(f"{Path(__file__).name} started")	1✔
53
54	# get the dataset object
55	dataset = Dataset.objects(file=dataset).get()	1✔
56
57	# fix input parameters
58	aliases = [BreedAlias(fid=fid, dataset=dataset) for fid in alias]	1✔
59	species_class = species_class.capitalize()	1✔
60	code = code.upper()	1✔
61
62	# get a breed object relying on parameters
63	breed, modified = get_or_create_breed(	1✔
64	species_class=species_class, name=name, code=code, aliases=aliases)
65
66	if modified:	1✔
67	logger.info(f"{breed} added to database")	1✔
68
69	logger.info(f"{Path(__file__).name} ended")	1✔
70
71
72	if __name__ == '__main__':	1✔
73	log_fmt = '%(asctime)s - %(name)s - %(levelname)s - %(message)s'	×
74	logging.basicConfig(level=logging.INFO, format=log_fmt)	×
75
76	# connect to database
77	global_connection()	×
78
79	main()	×

cnr-ibba / SMARTER-database / 9189630163

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