Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Metagenomics
metagenedb
Commits
bbde253f
Commit
bbde253f
authored
Aug 07, 2020
by
Kenzo-Hugo Hillion
♻
Browse files
update README and try to restore celery worker on kubernetes
parent
126032cf
Pipeline
#35260
passed with stages
in 3 minutes and 46 seconds
Changes
6
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
README.md
View file @
bbde253f
...
...
@@ -14,4 +14,4 @@ It is composed of both an API and a client side for visualization and interactio
## Wiki & Documentation
For more information, please have a look at our
[
Wiki
](
https://gitlab.pasteur.fr/metagenomics/metagenedb/-/wikis/
MetageneDB
)
For more information, please have a look at our
[
Wiki
](
https://gitlab.pasteur.fr/metagenomics/metagenedb/-/wikis/
home
)
backend/metagenedb/api/catalog/urls.py
View file @
bbde253f
...
...
@@ -4,7 +4,7 @@ from rest_framework.routers import DefaultRouter, DynamicRoute, Route
from
metagenedb.api.catalog
import
views
#
from metagenedb.api.catalog.views.celery_test import
celery_test_view,
test_task_view
from
metagenedb.api.catalog.views.celery_test
import
test_task_view
class
CustomRouter
(
DefaultRouter
):
...
...
@@ -66,6 +66,5 @@ api_router.register(r'statistics', views.StatisticsViewSet, basename='statistics
urlpatterns
=
[
url
(
r
'v1/'
,
include
((
api_router
.
urls
,
'v1'
))),
path
(
'admin/'
,
include
((
'metagenedb.api.catalog.admin_urls'
,
'admin'
))),
# path('celery-test/', celery_test_view, name='celery-test'),
# path('celery-task-test/', test_task_view, name='celery-task-test'),
path
(
'celery-task-test/'
,
test_task_view
,
name
=
'celery-task-test'
),
]
backend/metagenedb/api/catalog/views/celery_test.py
View file @
bbde253f
...
...
@@ -4,17 +4,9 @@ from celery.decorators import task
from
rest_framework.decorators
import
api_view
from
rest_framework.response
import
Response
from
metagenedb.celery_app
import
debug_task
logger
=
logging
.
getLogger
(
__name__
)
@
api_view
()
def
celery_test_view
(
request
):
debug_task
.
delay
()
return
Response
({
"message"
:
"Your task is being processed!"
})
@
task
(
name
=
"test_celery_task"
)
def
test_task
(
msg
):
logger
.
info
(
"Test Celery Task"
)
...
...
@@ -28,6 +20,6 @@ def mul(x, y):
@
api_view
()
def
test_task_view
(
request
):
msg
=
test_task
.
delay
(
"poooouet"
)
msg
=
test_task
.
delay
(
"p
iro
oooouet
tee
"
)
muli
=
mul
.
delay
(
2
,
4
)
return
Response
({
"message"
:
f
"Tested celery task:
{
msg
.
get
(
timeout
=
1
)
}
{
muli
.
get
(
timeout
=
1
)
}
"
})
backend/metagenedb/apps/catalog/management/commands/create_light_db.py
View file @
bbde253f
...
...
@@ -23,12 +23,10 @@ def empty_db():
def
create_taxonomy_db
():
Taxonomy
.
objects
.
all
().
delete
()
gen_tax_db
()
def
create_genes_db
():
Gene
.
objects
.
all
().
delete
()
GeneFactory
.
create_batch
(
50
)
GeneWithEggNOGFactory
.
create_batch
(
15
)
GeneWithKeggFactory
.
create_batch
(
12
)
...
...
backend/metagenedb/celery_app.py
View file @
bbde253f
...
...
@@ -12,8 +12,3 @@ app.conf.beat_schedule = {
'schedule'
:
20.0
},
}
@
app
.
task
(
bind
=
True
)
def
debug_task
(
self
):
print
(
'Request: {0!r}'
.
format
(
self
.
request
))
ci/deploy/deploy.sh
View file @
bbde253f
...
...
@@ -27,7 +27,7 @@ kubectl -n ${NAMESPACE} wait --for=condition=available --timeout=600s deployment
envsubst < ci/kubernetes/backend.yaml | kubectl apply
-n
${
NAMESPACE
}
-f
-
kubectl
-n
${
NAMESPACE
}
patch deployment backend
-p
"{
\"
spec
\"
:{
\"
template
\"
:{
\"
metadata
\"
:{
\"
labels
\"
:{
\"
date
\"
:
\"
`
date
+
'%s'
`
\"
}}}}}"
## Celery worker
#
envsubst < ci/kubernetes/celery-worker.yaml | kubectl apply -n ${NAMESPACE} -f -
envsubst < ci/kubernetes/celery-worker.yaml | kubectl apply
-n
${
NAMESPACE
}
-f
-
## Frontend
envsubst < ci/kubernetes/frontend.yaml | kubectl apply
-n
${
NAMESPACE
}
-f
-
kubectl
-n
${
NAMESPACE
}
patch deployment frontend
-p
"{
\"
spec
\"
:{
\"
template
\"
:{
\"
metadata
\"
:{
\"
labels
\"
:{
\"
date
\"
:
\"
`
date
+
'%s'
`
\"
}}}}}"
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment