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mpievolbio-scicomp
RepinPop
Commits
dde8f83a
Commit
dde8f83a
authored
Dec 17, 2021
by
c.fortmanngrote
Browse files
Utilize app.logger everywhere.
parent
eebfc57e
Pipeline
#258999
failed with stages
in 4 minutes and 19 seconds
Changes
9
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
app/__init__.py
View file @
dde8f83a
...
...
@@ -24,14 +24,13 @@ app.config['UPLOAD_DIR'] = upload_dir
formatter
=
logging
.
Formatter
(
'%(asctime)s [%(levelname)s] %(module)s: %(message)s'
)
handler
=
logging
.
FileHandler
(
filename
=
"/tmp/rarefan.log"
)
handler
.
setFormatter
(
formatter
)
handler
.
setLevel
(
logging
.
DEBUG
)
# Configure root logger (this config will trickle down to all module loggers.)
logging
.
basicConfig
(
handlers
=
[
handler
],
level
=
logging
.
DEBUG
)
logger
=
logging
.
getLogger
(
__name__
)
app
.
logger
.
addHandler
(
handler
)
if
app
.
debug
:
logger
.
debug
(
"****************** Debug mode is active ******************"
)
app
.
logger
.
debug
(
"****************** Debug mode is active ******************"
)
# csrf = CSRFProtect()
...
...
app/callbacks/callbacks.py
View file @
dde8f83a
...
...
@@ -4,9 +4,9 @@ from app.models import Job as DBJob
from
app.utilities.checkers
import
parse_results
from
app.tasks.email
import
email_task
from
app.tasks.zip
import
zip_task
from
app
import
app
import
logging
logger
=
logging
.
getLogger
(
'rarefan'
)
logger
=
app
.
logger
def
rarefan_on_success
(
job
,
result
):
""" Callback for the 'rarefan' task if completed successfully. """
...
...
app/models.py
View file @
dde8f83a
...
...
@@ -5,11 +5,8 @@ import os
import
sys
import
rq
from
rq.exceptions
import
NoSuchJobError
import
logging
logger
=
logging
.
getLogger
(
__name__
)
from
app
import
app
,
db
logger
=
app
.
logger
class
Job
(
db
.
Document
):
...
...
app/routes.py
View file @
dde8f83a
...
...
@@ -34,7 +34,7 @@ import subprocess
import
tempfile
import
time
logger
=
logging
.
getLogger
(
__name__
)
logger
=
app
.
logger
def
get_status_code
(
run_id_path
):
# Check if the run has finished.
...
...
@@ -520,7 +520,9 @@ def test_task():
@
app
.
route
(
'/test_mail'
)
def
test_mail
():
logger
.
debug
(
"Attempting to send mail throug redis queue."
)
job
=
app
.
queue
.
enqueue
(
email_test
)
logger
.
debug
(
job
)
time
.
sleep
(
3
)
...
...
app/tasks/email.py
View file @
dde8f83a
...
...
@@ -19,14 +19,15 @@ from app.views import AnalysisForm
from
app.models
import
Job
as
DBJob
import
jinja2
import
logging
logger
=
logging
.
getLogger
(
__name__
)
app
.
app_context
().
push
()
logger
=
app
.
logger
def
email_test
():
recipients
=
[
'grotec@evolbio.mpg.de'
]
logger
.
debug
(
"Attempting to send email to %s"
,
recipients
[
0
])
message
=
Message
(
"Test from flask"
,
sender
=
"rarefan@evolbio.mpg.de"
,
...
...
@@ -39,7 +40,7 @@ def email_test():
logger
.
debug
(
"Mail was sent: %s"
,
str
(
success
))
logger
.
debug
(
"Mail message was: %s"
,
str
(
message
))
return
success
,
message
return
success
,
str
(
message
)
def
email_task
(
run_id
):
...
...
@@ -99,3 +100,6 @@ def email_task(run_id):
dbjob
.
save
()
logger
.
debug
(
"Mail sent? %s"
,
str
(
is_sent
))
if
__name__
==
"__main__"
:
email_test
()
app/tasks/rarefan.py
View file @
dde8f83a
...
...
@@ -7,8 +7,10 @@ import subprocess
from
app.models
import
Job
as
DBJob
from
rq
import
get_current_job
import
logging
logger
=
logging
.
getLogger
(
__name__
)
from
app
import
app
app
.
app_context
().
push
()
logger
=
app
.
logger
from
app.utilities.rarefan_cli
import
rarefan_command
...
...
app/tasks/redis_tests.py
View file @
dde8f83a
# usage: $> rq enqueue -p app.tasks.redis_tests example 10
import
time
import
logging
logger
=
logging
.
getLogger
(
__name__
)
from
app
import
app
app
.
app_context
().
push
()
logger
=
app
.
logger
def
example
(
seconds
):
seconds
=
int
(
seconds
)
...
...
app/tasks/tree.py
View file @
dde8f83a
...
...
@@ -5,9 +5,9 @@ import shlex
import
shutil
from
app.models
import
Job
as
DBJob
from
rq
import
get_current_job
import
logging
logger
=
logging
.
getLogger
(
__name__
)
from
app
import
app
app
.
app_context
().
push
()
logger
=
app
.
logger
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 @
dde8f83a
...
...
@@ -6,8 +6,9 @@ import shutil
from
app.models
import
Job
as
DBJob
from
rq
import
get_current_job
import
logging
logger
=
logging
.
getLogger
(
__name__
)
from
app
import
app
app
.
app_context
().
push
()
logger
=
app
.
logger
def
zip_task
(
run_dir
):
...
...
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