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mpievolbio-scicomp
RepinPop
Commits
c8ee8025
Commit
c8ee8025
authored
Dec 17, 2021
by
c.fortmanngrote
Browse files
Module level logging and basicConfig in __init__.
parent
674a3c73
Pipeline
#258964
failed with stages
in 3 minutes and 50 seconds
Changes
9
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
app/__init__.py
View file @
c8ee8025
...
...
@@ -21,16 +21,15 @@ app.config.from_object(Config)
app
.
config
[
'UPLOAD_DIR'
]
=
upload_dir
# Logging
logger
=
logging
.
getLogger
(
'rarefan'
)
formatter
=
logging
.
Formatter
(
'%(asctime)s [%(levelname)s] %(module)s: %(message)s'
)
handler
=
logging
.
FileHandler
(
"/tmp/rarefan.log"
)
handler
=
logging
.
FileHandler
(
filename
=
"/tmp/rarefan.log"
)
handler
.
setFormatter
(
formatter
)
if
app
.
debug
:
logger
.
setLevel
(
logging
.
DEBUG
)
else
:
logger
.
setLevel
(
logging
.
INFO
)
logger
.
addHandler
(
handler
)
# Configure root logger (this config will trickle down to all module loggers.)
logging
.
basicConfig
(
handlers
=
[
handler
],
filemode
=
'a'
,
level
=
logging
.
DEBUG
)
logger
=
logging
.
getLogger
(
__name__
)
if
app
.
debug
:
logger
.
debug
(
"****************** Debug mode is active ******************"
)
...
...
app/models.py
View file @
c8ee8025
...
...
@@ -7,7 +7,7 @@ import rq
from
rq.exceptions
import
NoSuchJobError
import
logging
logger
=
logging
.
getLogger
(
'rarefan'
)
logger
=
logging
.
getLogger
(
__name__
)
from
app
import
app
,
db
...
...
app/routes.py
View file @
c8ee8025
...
...
@@ -34,7 +34,7 @@ import subprocess
import
tempfile
import
time
logger
=
logging
.
getLogger
(
'rarefan'
)
logger
=
logging
.
getLogger
(
__name__
)
def
get_status_code
(
run_id_path
):
# Check if the run has finished.
...
...
app/tasks/email.py
View file @
c8ee8025
...
...
@@ -20,7 +20,7 @@ from app.models import Job as DBJob
import
jinja2
import
logging
logger
=
logging
.
getLogger
(
'rarefan'
)
logger
=
logging
.
getLogger
(
__name__
)
app
.
app_context
().
push
()
...
...
app/tasks/rarefan.py
View file @
c8ee8025
...
...
@@ -8,7 +8,7 @@ import subprocess
from
app.models
import
Job
as
DBJob
from
rq
import
get_current_job
import
logging
logger
=
logging
.
getLogger
(
'rarefan'
)
logger
=
logging
.
getLogger
(
__name__
)
from
app.utilities.rarefan_cli
import
rarefan_command
...
...
app/tasks/redis_tests.py
View file @
c8ee8025
...
...
@@ -2,7 +2,7 @@
import
time
import
logging
logger
=
logging
.
getLogger
()
logger
=
logging
.
getLogger
(
__name__
)
def
example
(
seconds
):
seconds
=
int
(
seconds
)
...
...
app/tasks/tree.py
View file @
c8ee8025
...
...
@@ -7,7 +7,7 @@ from app.models import Job as DBJob
from
rq
import
get_current_job
import
logging
logger
=
logging
.
getLogger
(
'rarefan'
)
logger
=
logging
.
getLogger
(
__name__
)
def
tree_task
(
run_dir
,
treefile
=
None
):
""" Generate a phylogenetic tree from all DNA sequence files in given directory.
...
...
app/tasks/zip.py
View file @
c8ee8025
...
...
@@ -7,7 +7,7 @@ import shutil
from
app.models
import
Job
as
DBJob
from
rq
import
get_current_job
import
logging
logger
=
logging
.
getLogger
(
'rarefan'
)
logger
=
logging
.
getLogger
(
__name__
)
def
zip_task
(
run_dir
):
...
...
app/utilities/checkers.py
View file @
c8ee8025
import
sys
import
os
import
logging
logger
=
logging
.
getLogger
(
'rarefan'
)
logger
=
logging
.
getLogger
(
__name__
)
def
count_lines
(
fname
):
...
...
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