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Commit c3aefece authored by Remi  PLANEL's avatar Remi PLANEL
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set all galaxy env in secrete or configmap

parent 5d709d9a
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......@@ -58,6 +58,11 @@ variables:
--set djangoninja.postgresql.teamId=${TEAM_ID}
--set djangoninja.django.secret=${SECRET_KEY}
--set djangoninja.galaxy.key=${GALAXY_API_KEY}
--set djangoninja.galaxy.email=${GALAXY_EMAIL}
--set djangoninja.galaxy.workflowId=${GALAXY_WORKFLOW_ID}
--set djangoninja.galaxy.instance="https://galaxy.pasteur.fr"
--set djangoninja.galaxy.instanceName="Galaxy@Pasteur"
--set djangoninja.galaxy.workflowName=defense-finder
--set nuxt.imagePullSecrets[0].name="registry-pull-secret-${CI_COMMIT_REF_SLUG}"
--set nuxt.image.repository="$CI_REGISTRY_IMAGE/$NUXT_IMG_NAME"
--set nuxt.image.tag="$CI_COMMIT_SHORT_SHA"
......
import os
import tarfile
from tempfile import mkstemp
from django.conf import settings
from ninja import Router, File, Form
from ninja.files import UploadedFile
......@@ -59,7 +60,7 @@ def add(
session_key = request.session.session_key
session = Session.objects.get(session_key=session_key)
aw = AnalysisWorkflow.objects.get(pk=1)
aw = AnalysisWorkflow.objects.get(galaxy_id=settings.GALAXY_WORKFLOW_ID)
input_files = [
genome_path,
......
......@@ -9,22 +9,20 @@ class Command(BaseCommand):
def handle(self, *args, **options):
gi, _ = GalaxyInstance.objects.get_or_create(
url="https://galaxy.pasteur.fr", name="Galaxy@Pasteur"
url=settings.GALAXY_INSTANCE, name=settings.GALAXY_INSTANCE_NAME
)
print(gi)
print(settings.GALAXY_API_KEY)
gu, _ = AnalysisGalaxyUser.objects.get_or_create(
email="remi.planel@pasteur.fr",
email=settings.GALAXY_EMAIL,
api_key=settings.GALAXY_API_KEY,
galaxy_instance=gi,
)
print(gu)
gw, _ = AnalysisWorkflow.objects.get_or_create(
galaxy_id="24c630a7c1056e18",
galaxy_id=settings.GALAXY_WORKFLOW_ID,
galaxy_owner=gu,
analysis_owner=gu,
name="defense-finder",
name=settings.GALAXY_WORKFLOW_NAME,
published=False,
)
print(gw)
......@@ -148,6 +148,12 @@ DEFAULT_AUTO_FIELD = "django.db.models.BigAutoField"
# GALAXY env
GALAXY_API_KEY = env("GALAXY_API_KEY")
GALAXY_EMAIL = env("GALAXY_EMAIL")
GALAXY_INSTANCE = env("GALAXY_INSTANCE")
GALAXY_INSTANCE_NAME = env("GALAXY_INSTANCE_NAME")
GALAXY_WORKFLOW_ID = env("GALAXY_WORKFLOW_ID")
GALAXY_WORKFLOW_NAME = env("GALAXY_WORKFLOW_NAME")
# CSRF token
......
......@@ -49,13 +49,18 @@ spec:
- name: http
containerPort: {{ .Values.service.port }}
protocol: TCP
envFrom:
- secretRef:
name: galaxy-secret
- configMapRef:
name: galaxy-config-map
env:
- name: DEBUG
value: "True"
- name: SECRET_KEY
value: {{ .Values.django.secret }}
- name: GALAXY_API_KEY
value: {{ .Values.galaxy.key }}
# - name: GALAXY_API_KEY
# value: {{ .Values.galaxy.key }}
- name: DF_HOSTNAME
value: {{ .Release.Name }}
- name: POSTGRES_PASSWORD
......
apiVersion: v1
kind: ConfigMap
metadata:
name: galaxy-config-map
data:
GALAXY_EMAIL: {{ .Values.galaxy.email }}
GALAXY_INSTANCE: {{ .Values.galaxy.instance }}
GALAXY_INSTANCE_NAME: {{ .Values.galaxy.instanceName }}
GALAXY_WORKFLOW_ID: {{ .Values.galaxy.workflowId }}
GALAXY_WORKFLOW_NAME: {{ .Values.galaxy.workflowName }}
apiVersion: v1
kind: Secret
metadata:
name: galaxy-secret
data:
GALAXY_API_KEY: {{ .Values.galaxy.key }}
......@@ -94,3 +94,8 @@ django:
galaxy:
key: "api-key"
email: email@example.com
instance: "galaxy-instance"
instanceName: "galaxyName"
workflowId: "workflowId"
workflowName: "workflowName"
\ No newline at end of file
......@@ -36,6 +36,13 @@ djangoninja:
galaxy:
key: "api-key"
email: email@example.com
instance: "galaxy-instance"
instanceName: "galaxyName"
workflowId: "workflowId"
workflowName: "workflowName"
nuxt:
......
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