1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
|
"""Load genotypes from R/qtl2 bundle into the database."""
import sys
import uuid
import logging
import traceback
from pathlib import Path
from zipfile import ZipFile
from argparse import ArgumentParser
import MySQLdb as mdb
from redis import Redis
from r_qtl import r_qtl2 as rqtl2
from quality_control.parsing import take
from qc_app.db_utils import database_connection
from qc_app.check_connections import check_db, check_redis
from scripts.redis_logger import RedisLogger
stderr_handler = logging.StreamHandler(stream=sys.stderr)
logger = logging.getLogger("install_genotypes")
logger.addHandler(stderr_handler)
def insert_markers(dbconn: mdb.Connection,
speciesid: int,
markers: tuple[str, ...]) -> int:
"""Insert genotype and genotype values into the database."""
with dbconn.cursor() as cursor:
cursor.executemany(
"INSERT INTO Geno(SpeciesId, Name, Marker_Name) "
"VALUES (%(speciesid)s, %(marker)s, %(marker)s) "
"ON DUPLICATE KEY UPDATE SpeciesId=SpeciesId",
tuple({"speciesid": speciesid, "marker": marker}
for marker in markers))
return cursor.rowcount
# TODO: Install geno data: GenoData
return cursor.rowcount
def install_genotypes(dbconn: mdb.Connection,
speciesid: int,
populationid: int,
rqtl2bundle: Path) -> int:
"""Load any existing genotypes into the database."""
count = 0
with ZipFile(str(rqtl2bundle.absolute()), "r") as zfile:
try:
logger.info("Validating bundle")
rqtl2.validate_bundle(zfile)
logger.info("Bundle validated successfully.")
logger.info(("Loading genotypes. This could take a while. "
"Please be patient."))
cdata = rqtl2.control_data(zfile)
genotypes = rqtl2.file_data(zfile,
"geno",
cdata,
rqtl2.make_process_data_geno(cdata))
while True:
batch = tuple(take(genotypes, 5000))
if len(batch) == 0:
logger.info("Loading Genotypes complete!")
logger.info(
"Total rows processed: %s", count)
break
insert_markers(
dbconn,
speciesid,
tuple(key for key in batch[0].keys() if key != "id"))
count = count + len(batch)
if "gmap" in cdata:
logger.info("Loading genetic mapping info.")
# TODO: load gmap files
logger.info("Successfully loaded genetic mapping.")
if "pmap" in cdata:
logger.info("Loading physical mapping info.")
# TODO: load pmap files
logger.info("Successfully loaded physical mapping.")
except rqtl2.InvalidFormat as exc:
logger.error(str(exc))
logger.info("There are no genotypes to load.")
except Exception as _exc:
logger.error("Failing with exception: %s", traceback.format_exc())
return 3
return 0
if __name__ == "__main__":
def cli_args():
"""Process command-line arguments for install_genotypes"""
parser = ArgumentParser(
prog="install_genotypes",
description="Parse genotypes from R/qtl2 bundle into the database.")
parser.add_argument("databaseuri", help="URL to MariaDB")
parser.add_argument("redisuri", help="URL to Redis")
parser.add_argument("jobid",
help="Job ID that this belongs to.",
type=uuid.UUID)
parser.add_argument("speciesid",
help="Species to which bundle relates.")
parser.add_argument("populationid",
help="Population to group data under")
parser.add_argument("rqtl2bundle",
help="Path to R/qtl2 bundle zip file.",
type=Path)
parser.add_argument("--redisexpiry",
help="How long to keep any redis keys around.",
type=int,
default=86400)
return parser.parse_args()
def main():
"""Run `install_genotypes` scripts."""
args = cli_args()
check_db(args.databaseuri)
check_redis(args.redisuri)
if not args.rqtl2bundle.exists():
logging.error("File not found: '%s'.", args.rqtl2bundle)
return 2
with (Redis.from_url(args.redisuri, decode_responses=True) as rconn,
database_connection(args.databaseuri) as dbconn):
formatter = logging.Formatter(
"%(asctime)s - %(name)s - %(levelname)s: %(message)s")
job_messagelist = f"{str(args.jobid)}:log-messages"
rconn.hset(name=str(args.jobid),
key="log-messagelist",
value=job_messagelist)
redislogger = RedisLogger(
rconn, args.jobid, expiry=args.redisexpiry)
redislogger.setFormatter(formatter)
logger.addHandler(redislogger)
logger.setLevel("INFO")
return install_genotypes(dbconn,
args.speciesid,
args.populationid,
args.rqtl2bundle)
sys.exit(main())
|
