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mpievolbio-scicomp
RepinPop
Commits
456a0d16
Commit
456a0d16
authored
Dec 13, 2021
by
Carsten
Browse files
Cleaning up logging.
parent
3c13cb81
Pipeline
#257489
failed with stages
in 8 minutes and 22 seconds
Changes
2
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
app/__init__.py
View file @
456a0d16
import
logging
import
os
import
rq
from
.config
import
Config
...
...
@@ -8,7 +7,6 @@ from flask_mail import Mail
from
flask_mongoengine
import
MongoEngine
,
MongoEngineSessionInterface
from
redis
import
Redis
logging
.
basicConfig
(
level
=
logging
.
DEBUG
)
app
=
Flask
(
__name__
,
instance_relative_config
=
True
,
static_url_path
=
'/static'
)
upload_dir
=
os
.
path
.
join
(
app
.
static_folder
,
'uploads'
)
...
...
app/routes.py
View file @
456a0d16
...
...
@@ -35,21 +35,14 @@ import logging
from
Bio
import
SeqIO
import
datetime
import
logging
logging
.
basicConfig
(
level
=
logging
.
DEBUG
)
def
get_logger
():
logger
=
logging
.
getLogger
(
__name__
)
formatter
=
logging
.
Formatter
(
'%(asctime)s [%(levelname)s] %(module)s: %(message)s'
)
timestamp
=
datetime
.
datetime
.
now
().
strftime
(
format
=
"%Y%m%d-%H%M%S"
)
handler
=
logging
.
FileHandler
(
"/tmp/rarefan_{}.log"
.
format
(
timestamp
))
handler
.
setFormatter
(
formatter
)
handler
.
setLevel
(
logging
.
DEBUG
)
logger
.
addHandler
(
handler
)
return
logger
logger
=
get_logger
()
logger
=
logging
.
getLogger
(
__name__
)
formatter
=
logging
.
Formatter
(
'%(asctime)s [%(levelname)s] %(module)s: %(message)s'
)
timestamp
=
datetime
.
datetime
.
now
().
strftime
(
format
=
"%Y%m%d-%H%M%S"
)
handler
=
logging
.
FileHandler
(
"/tmp/rarefan.log"
.
format
(
timestamp
))
handler
.
setFormatter
(
formatter
)
handler
.
setLevel
(
logging
.
DEBUG
)
logger
.
addHandler
(
handler
)
def
get_status_code
(
run_id_path
):
...
...
@@ -69,13 +62,13 @@ def validate_fasta(filename):
:param filename: The filename of the file to validate.
"""
logg
er
.
info
(
"Validating fasta file %s."
,
filename
)
logg
ing
.
info
(
"Validating fasta file %s."
,
filename
)
with
open
(
filename
,
'r'
)
as
fp
:
fasta
=
SeqIO
.
parse
(
fp
,
"fasta"
)
is_fasta
=
any
(
fasta
)
if
not
is_fasta
:
logg
er
.
warning
(
"%s is not a valid fasta file."
,
filename
)
logg
ing
.
warning
(
"%s is not a valid fasta file."
,
filename
)
return
is_fasta
...
...
@@ -95,7 +88,7 @@ def upload():
)
seqs
=
[
v
for
k
,
v
in
request
.
files
.
items
()
if
k
.
startswith
(
'file'
)]
logg
er
.
info
(
"Uploading %s."
,
str
(
seqs
))
logg
ing
.
info
(
"Uploading %s."
,
str
(
seqs
))
dna_extensions
=
[
'fn'
,
'fna'
,
'fastn'
,
'fas'
,
'fasta'
]
aa_extensions
=
[
'fa'
,
'faa'
]
...
...
@@ -202,12 +195,12 @@ def submit():
session
[
'analyse_repins'
]
=
request
.
form
.
get
(
'analyse_repins'
)
session
[
'email'
]
=
request
.
form
.
get
(
'email'
,
None
)
logg
er
.
info
(
"Session parameters:"
)
logg
er
.
info
(
"tmpdir: %s"
,
session
[
'tmpdir'
])
logg
er
.
info
(
"outdir: %s"
,
session
[
'outdir'
])
logg
er
.
info
(
"reference_strain: %s"
,
session
[
'reference_strain'
])
logg
er
.
info
(
"treefile: %s"
,
session
[
'treefile'
])
logg
er
.
info
(
"email: %s"
,
session
[
'email'
])
logg
ing
.
info
(
"Session parameters:"
)
logg
ing
.
info
(
"tmpdir: %s"
,
session
[
'tmpdir'
])
logg
ing
.
info
(
"outdir: %s"
,
session
[
'outdir'
])
logg
ing
.
info
(
"reference_strain: %s"
,
session
[
'reference_strain'
])
logg
ing
.
info
(
"treefile: %s"
,
session
[
'treefile'
])
logg
ing
.
info
(
"email: %s"
,
session
[
'email'
])
# Store session in db.
run_id
=
os
.
path
.
basename
(
session
[
'tmpdir'
])
...
...
@@ -408,7 +401,7 @@ def files(req_path):
# Remove trailing '/'
if
req_path
.
endswith
(
'/'
):
req_path
=
req_path
[:
-
1
]
logg
er
.
warning
(
"Request dir is %s in (%s)."
,
req_path
,
os
.
path
.
dirname
(
req_path
))
logg
ing
.
warning
(
"Request dir is %s in (%s)."
,
req_path
,
os
.
path
.
dirname
(
req_path
))
# Save the target for the 'back to results' link.
tmp_dir
=
session
.
get
(
'tmpdir'
,
None
)
...
...
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