From 6f84535f15bfda7cf4d7cf090a864bb9be8a883f Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Mon, 4 Mar 2024 10:23:50 +0100
Subject: [PATCH] Resolve "Cron Job to clean database and galaxy"
---
backend/analysis/api.py | 3 ++-
.../commands/clear-sessions-history.py | 24 +++++++++++++++++--
.../djangoninja/templates/deployment.yaml | 10 ++++----
deploy/templates/pvc-uploaded-files.yaml | 12 ----------
4 files changed, 29 insertions(+), 20 deletions(-)
delete mode 100644 deploy/templates/pvc-uploaded-files.yaml
diff --git a/backend/analysis/api.py b/backend/analysis/api.py
index ce4129e..e9cdc15 100644
--- a/backend/analysis/api.py
+++ b/backend/analysis/api.py
@@ -29,7 +29,8 @@ from analysis.model_schemas import (
SystemOutSchema,
)
-session_expiry = 2628000
+# session_expiry = 2628000
+session_expiry = 10
router = Router()
diff --git a/backend/analysis/management/commands/clear-sessions-history.py b/backend/analysis/management/commands/clear-sessions-history.py
index 8a53fc6..928615d 100644
--- a/backend/analysis/management/commands/clear-sessions-history.py
+++ b/backend/analysis/management/commands/clear-sessions-history.py
@@ -30,11 +30,31 @@ class Command(BaseCommand):
email=options["galaxyemail"],
galaxy_instance=gi,
).first()
- print(gu)
histories = AnalysisHistory.objects.filter(
analysis_owner=gu, session__expire_date__lt=datetime.now().astimezone()
)
for h in histories:
print(f"Delete expire history {h.name} expired : {h.session.expire_date}")
- h.delete()
+
+ try:
+ h.analysis_owner.obj_gi.histories.delete(id_=h.galaxy_id, purge=True)
+ except ConnectionError as e:
+ print(e)
+ raise e
+ else:
+ h.delete()
+
+ # clean orphan galaxy histories
+ histories = gu.obj_gi.gi.histories.get_histories()
+ histories_from_host = [
+ h for h in histories if settings.DF_HOSTNAME in h["tags"]
+ ]
+ for h in histories_from_host:
+ galaxy_id = h["id"]
+ # check if in database.
+ # if not, purge it
+ history = AnalysisHistory.objects.filter(galaxy_id=galaxy_id)
+ if not history.exists():
+ print(f"Delete orphan history {h['name']}.")
+ gu.obj_gi.gi.histories.delete_history(galaxy_id, purge=True)
diff --git a/deploy/charts/djangoninja/templates/deployment.yaml b/deploy/charts/djangoninja/templates/deployment.yaml
index e92f4dd..7eb4b59 100644
--- a/deploy/charts/djangoninja/templates/deployment.yaml
+++ b/deploy/charts/djangoninja/templates/deployment.yaml
@@ -89,8 +89,8 @@ spec:
resources:
{{- toYaml .Values.resources | nindent 12 }}
volumeMounts:
- - mountPath: /code/public/static
- name: server-static
+ # - mountPath: /code/public/static
+ # name: server-static
- mountPath: /uploaded-files
name: uploaded-files
{{- with .Values.nodeSelector }}
@@ -106,9 +106,9 @@ spec:
{{- toYaml . | nindent 8 }}
{{- end }}
volumes:
- - name: server-static
- persistentVolumeClaim:
- claimName: server-static
+ # - name: server-static
+ # persistentVolumeClaim:
+ # claimName: server-static
- name: uploaded-files
emptyDir:
sizeLimit: 5Gi
diff --git a/deploy/templates/pvc-uploaded-files.yaml b/deploy/templates/pvc-uploaded-files.yaml
deleted file mode 100644
index 8319f66..0000000
--- a/deploy/templates/pvc-uploaded-files.yaml
+++ /dev/null
@@ -1,12 +0,0 @@
-apiVersion: v1
-kind: PersistentVolumeClaim
-metadata:
- name: "uploaded-files"
-spec:
- accessModes:
- - ReadWriteOnce
- resources:
- requests:
- storage: 10Gi
- storageClassName: {{ .Values.uploadedFile.storageClassName }}
-status: {}
--
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