fix: nan in dataframe

Author: xgui3783

.helm/adhoc/cronjob-kubectl-top-pod.yaml

@@ -39,3 +39,35 @@ spec:
 
 # to enable/disable
 # kubectl patch cronjobs cronjob-pod-usage -p '{"spec" : {"suspend" : true }}'
+
+---
+apiVersion: batch/v1
+kind: CronJob
+metadata:
+  name: cronjob-trim-old-log-usage
+spec:
+  # run two month
+  schedule: "41 1 */5 */2 *"
+  concurrencyPolicy: Replace
+  jobTemplate:
+    spec:
+      template:
+        spec:
+          containers:
+          - name: cronjob-trim-old-log-usage
+            image: docker-registry.ebrains.eu/monitoring/kubectl:v1.29.2
+            imagePullPolicy: Always
+            command:
+            - /bin/ash
+            - -c
+            # delete all files over 30 days of modification date
+            - "find /siibra_api_logs -mindepth 1 -maxdepth 1 -mtime +30 -delete"
+            volumeMounts:
+              - mountPath: /siibra_api_logs
+                name: log-volume
+
+          restartPolicy: OnFailure
+          volumes:
+          - name: log-volume
+            persistentVolumeClaim:
+              claimName: log-volume-claim

.helm/siibra-api-v4-server/Chart.yaml

@@ -21,4 +21,4 @@ version: 0.1.0
 # incremented each time you make changes to the application. Versions are not expected to
 # follow Semantic Versioning. They should reflect the version the application is using.
 # It is recommended to use it with quotes.
-appVersion: "0.3.21-rc9"
+appVersion: "0.3.21-hotfix2"

.helm/siibra-api-v4-worker/Chart.yaml

@@ -21,4 +21,4 @@ version: 0.1.0
 # incremented each time you make changes to the application. Versions are not expected to
 # follow Semantic Versioning. They should reflect the version the application is using.
 # It is recommended to use it with quotes.
-appVersion: "0.3.21-rc9"
+appVersion: "0.3.21-hotfix2"

.helm/siibra-api-v4-worker/templates/_helpers.tpl

@@ -5,6 +5,13 @@ Expand the name of the chart.
 {{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" }}
 {{- end }}
 
+{{- define "siibra-api-v4-worker.image-full-spec" -}}
+{{- if eq (substr 0 7 .Values.image.spec) "sha256:" -}}
+{{- printf "%s@%s" .Values.image.repository .Values.image.spec }}
+{{- else -}}
+{{- printf "%s:%s" .Values.image.repository .Values.image.spec }}
+{{- end -}}
+
 
 {{/*
 Define cache-dir. append -rc if is rc

.helm/siibra-api-v4-worker/values.yaml

@@ -21,6 +21,7 @@ image:
   pullPolicy: IfNotPresent
   # Overrides the image tag whose default is the chart appVersion.
   tag: 0.3-worker
+  spec: 0.3-worker # can be 1/ tag 2/ sha256:<sha-hash>
 
 imagePullSecrets: []
 nameOverride: ""

api/serialization/_common.py

@@ -51,7 +51,7 @@ def pdseries_to_model(series: Series, **kwargs) -> SeriesModel:
         name=series.name,
         dtype=str(series.dtype),
         index=[instance_to_model(el) for el in series.index],
-        data=series.values.tolist()
+        data=instance_to_model(series.values.tolist())
     )
 
 @serialize(DataFrame)

api/serialization/util/__init__.py

@@ -7,6 +7,7 @@
     NonStrKeyException,
 )
 from typing import Any, Dict, _GenericAlias
+import math
 
 REGISTER: Dict[Type, Callable[..., ConfigBaseModel]] = {}
 
@@ -50,6 +51,8 @@ def instance_to_model(instance: Any, * , use_class: Type=None, skip_classes: Lis
     if instance is None:
         return None
     if isinstance(instance, (str, int, float)):
+        if math.isnan(instance):
+            return None
         return instance
     if isinstance(instance, (list, tuple)):
         return [instance_to_model(item) for item in instance]