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fix(helm): Medcat trainer helm chart run as single pod (#40)
* fix(helm): Fix medcat-trainer log buffer. Fix load examples * fix(helm): Medcat trainer deployment should run as one pod with both nginx and the api * fix(helm): Trainer service selectorlabels fix * feat(helm): Medcat-trainer helm to restart pod when configmap changes
1 parent 98ff6ac commit e7773e3

11 files changed

Lines changed: 79 additions & 149 deletions

‎deployment/kubernetes/charts/medcat-trainer-helm/templates/NOTES.txt‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -15,8 +15,8 @@
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export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "medcat-trainer-helm.fullname" . }} --template "{{"{{ range (index .status.loadBalancer.ingress 0) }}{{.}}{{ end }}"}}")
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echo http://$SERVICE_IP:{{ .Values.service.port }}
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{{- else if contains "ClusterIP" .Values.service.type }}
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export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app.kubernetes.io/name={{ include "medcat-trainer-helm.name" . }},app.kubernetes.io/instance={{ .Release.Name }},app.kubernetes.io/component=nginx" -o jsonpath="{.items[0].metadata.name}")
19-
export CONTAINER_PORT=$(kubectl get pod --namespace {{ .Release.Namespace }} $POD_NAME -o jsonpath="{.spec.containers[0].ports[0].containerPort}")
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export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app.kubernetes.io/name={{ include "medcat-trainer-helm.name" . }},app.kubernetes.io/instance={{ .Release.Name }},app.kubernetes.io/component=medcat-trainer" -o jsonpath="{.items[0].metadata.name}")
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export CONTAINER_PORT=$(kubectl get pod --namespace {{ .Release.Namespace }} $POD_NAME -o jsonpath="{.spec.containers[?(@.name==\"nginx\")].ports[0].containerPort}")
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echo "Visit http://127.0.0.1:8080 to use your application"
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kubectl --namespace {{ .Release.Namespace }} port-forward $POD_NAME 8080:$CONTAINER_PORT
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{{- end }}

‎deployment/kubernetes/charts/medcat-trainer-helm/templates/ingress.yaml‎

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@@ -35,7 +35,7 @@ spec:
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{{- end }}
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backend:
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service:
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name: {{ include "medcat-trainer-helm.fullname" $ }}-nginx
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name: {{ include "medcat-trainer-helm.fullname" $ }}-medcat-trainer
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port:
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number: {{ $.Values.service.port }}
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{{- end }}

‎deployment/kubernetes/charts/medcat-trainer-helm/templates/medcat-trainer-configmap.yaml‎

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Original file line numberDiff line numberDiff line change
@@ -17,23 +17,23 @@ data:
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pidfile=/var/run/supervisord.pid
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[program:medcattrainer]
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command=sh -c "exec /home/scripts/run.sh 2>&1 | sed 's/^/[medcattrainer] /'"
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command=sh -c "exec /home/scripts/run.sh 2>&1 | sed -u 's/^/[medcattrainer] /'"
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stdout_logfile=/dev/stdout
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stdout_logfile_maxbytes=0
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stderr_logfile=/dev/stderr
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stderr_logfile_maxbytes=0
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autorestart=true
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[program:bg-process]
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command=sh -c "exec /home/scripts/run-bg-process.sh 2>&1 | sed 's/^/[bg-process] /'"
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command=sh -c "exec /home/scripts/run-bg-process.sh 2>&1 | sed -u 's/^/[bg-process] /'"
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stdout_logfile=/dev/stdout
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stdout_logfile_maxbytes=0
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stderr_logfile=/dev/stderr
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stderr_logfile_maxbytes=0
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autorestart=true
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[program:db-backup]
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command=sh -c "exec cron -f -l 2 2>&1 | sed 's/^/[db-backup] /'"
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command=sh -c "exec cron -f -l 2 2>&1 | sed -u 's/^/[db-backup] /'"
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stdout_logfile=/dev/stdout
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stdout_logfile_maxbytes=0
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stderr_logfile=/dev/stderr

‎deployment/kubernetes/charts/medcat-trainer-helm/templates/medcat-trainer-deployment.yaml‎

Lines changed: 47 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -4,25 +4,26 @@ metadata:
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name: {{ include "medcat-trainer-helm.fullname" . }}-medcat-trainer
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labels:
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{{- include "medcat-trainer-helm.labels" . | nindent 4 }}
7-
app.kubernetes.io/component: medcat-trainer
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spec:
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{{- if not .Values.autoscaling.enabled }}
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replicas: {{ .Values.replicaCount }}
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{{- end }}
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selector:
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matchLabels:
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{{- include "medcat-trainer-helm.selectorLabels" . | nindent 6 }}
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app.kubernetes.io/component: medcat-trainer
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strategy: {{ toYaml .Values.updateStrategy | nindent 4 }}
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template:
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metadata:
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{{- with .Values.podAnnotations }}
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annotations:
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{{- with .Values.podAnnotations }}
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{{- toYaml . | nindent 8 }}
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{{- end }}
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checksum/medcat-trainer-configmap: {{ include (print $.Template.BasePath "/medcat-trainer-configmap.yaml") . | sha256sum }}
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checksum/medcat-trainer-env-configmap: {{ include (print $.Template.BasePath "/medcat-trainer-env-configmap.yaml") . | sha256sum }}
23+
checksum/medcat-trainer-secret: {{ include (print $.Template.BasePath "/medcat-trainer-secret.yaml") . | sha256sum }}
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checksum/nginx-configmap: {{ include (print $.Template.BasePath "/nginx-configmap.yaml") . | sha256sum }}
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labels:
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{{- include "medcat-trainer-helm.labels" . | nindent 8 }}
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app.kubernetes.io/component: medcat-trainer
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{{- with .Values.podLabels }}
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{{- toYaml . | nindent 8 }}
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{{- end }}
@@ -45,8 +46,8 @@ spec:
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image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
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imagePullPolicy: {{ .Values.image.pullPolicy }}
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ports:
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- name: http
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containerPort: 8000
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- name: api
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containerPort: {{ .Values.service.apiPort }}
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protocol: TCP
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args:
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- /usr/bin/supervisord
@@ -93,6 +94,43 @@ spec:
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{{- with .Values.volumeMounts }}
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{{- toYaml . | nindent 12 }}
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{{- end }}
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- name: nginx
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{{- with .Values.securityContext }}
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securityContext:
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{{- toYaml . | nindent 12 }}
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{{- end }}
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image: "{{ .Values.nginxImage.repository }}:{{ .Values.nginxImage.tag }}"
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imagePullPolicy: {{ .Values.nginxImage.pullPolicy }}
104+
ports:
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- name: http
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containerPort: {{ .Values.service.port }}
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protocol: TCP
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{{- with .Values.nginx.livenessProbe }}
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livenessProbe:
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{{- toYaml . | nindent 12 }}
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{{- end }}
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{{- with .Values.nginx.readinessProbe }}
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readinessProbe:
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{{- toYaml . | nindent 12 }}
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{{- end }}
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{{- with .Values.resources }}
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resources:
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{{- toYaml . | nindent 12 }}
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{{- end }}
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volumeMounts:
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- name: nginx-config
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mountPath: /etc/nginx/nginx.conf
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subPath: nginx.conf
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- name: nginx-config
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mountPath: /etc/nginx/sites-enabled/medcattrainer
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subPath: sitesenabled.medcattrainer
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- mountPath: /home/api/media
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name: api-media
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- mountPath: /home/api/static
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name: api-static
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{{- with .Values.volumeMounts }}
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{{- toYaml . | nindent 12 }}
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{{- end }}
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volumes:
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- name: medcat-trainer-config
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configMap:
@@ -111,6 +149,9 @@ spec:
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persistentVolumeClaim:
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claimName: {{ include "medcat-trainer-helm.fullname" . }}-api-db-backup
113151
{{- end }}
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- name: nginx-config
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configMap:
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name: {{ include "medcat-trainer-helm.fullname" . }}-nginx-config
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{{- with .Values.volumes }}
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{{- toYaml . | nindent 8 }}
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{{- end }}

‎deployment/kubernetes/charts/medcat-trainer-helm/templates/medcat-trainer-env-configmap.yaml‎

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@@ -12,6 +12,8 @@ data:
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DB_BACKUP_DIR: "/home/api/db-backup"
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DB_DIR: "/home/api/db"
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DB_PATH: "/home/api/db/db.sqlite3"
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MCT_VERSION: {{ .Values.image.tag | default .Chart.AppVersion }}
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API_URL: http://localhost:{{ .Values.service.apiPort }}/api/
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{{- range $key, $value := .Values.env }}
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{{ $key }}: {{ $value | quote }}
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{{- end }}

‎deployment/kubernetes/charts/medcat-trainer-helm/templates/medcat-trainer-secret.yaml‎

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Original file line numberDiff line numberDiff line change
@@ -4,6 +4,7 @@ metadata:
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name: {{ include "medcat-trainer-helm.fullname" . }}-secret
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labels:
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{{- include "medcat-trainer-helm.labels" . | nindent 4 }}
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app.kubernetes.io/component: medcat-trainer
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stringData:
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DB_NAME: {{ .Values.postgresql.auth.database }}
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DB_USER: "{{ .Values.postgresql.auth.username }}"

‎deployment/kubernetes/charts/medcat-trainer-helm/templates/nginx-configmap.yaml‎

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Original file line numberDiff line numberDiff line change
@@ -165,7 +165,7 @@ data:
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}
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location / {
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proxy_pass http://{{ include "medcat-trainer-helm.fullname" . }}-medcat-trainer:8000;
168+
proxy_pass http://localhost:8000;
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proxy_set_header Host $host;
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proxy_set_header X-Real-IP $remote_addr;
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proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;

‎deployment/kubernetes/charts/medcat-trainer-helm/templates/nginx-deployment.yaml‎

Lines changed: 0 additions & 102 deletions
This file was deleted.

‎deployment/kubernetes/charts/medcat-trainer-helm/templates/service.yaml‎

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Original file line numberDiff line numberDiff line change
@@ -4,25 +4,6 @@ metadata:
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name: {{ include "medcat-trainer-helm.fullname" . }}-medcat-trainer
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labels:
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{{- include "medcat-trainer-helm.labels" . | nindent 4 }}
7-
app.kubernetes.io/component: medcat-trainer
8-
spec:
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type: ClusterIP
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ports:
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- port: 8000
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targetPort: http
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protocol: TCP
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name: http
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selector:
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{{- include "medcat-trainer-helm.selectorLabels" . | nindent 4 }}
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app.kubernetes.io/component: medcat-trainer
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---
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apiVersion: v1
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kind: Service
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metadata:
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name: {{ include "medcat-trainer-helm.fullname" . }}-nginx
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labels:
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{{- include "medcat-trainer-helm.labels" . | nindent 4 }}
25-
app.kubernetes.io/component: nginx
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spec:
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type: {{ .Values.service.type }}
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ports:
@@ -33,7 +14,10 @@ spec:
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targetPort: http
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protocol: TCP
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name: http
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- port: {{ .Values.service.apiPort }}
18+
targetPort: api
19+
protocol: TCP
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name: api
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selector:
3722
{{- include "medcat-trainer-helm.selectorLabels" . | nindent 4 }}
38-
app.kubernetes.io/component: nginx
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---

‎deployment/kubernetes/charts/medcat-trainer-helm/values.yaml‎

Lines changed: 17 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@ replicaCount: 1
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image:
1010
repository: cogstacksystems/medcat-trainer
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# This sets the pull policy for images.
12-
pullPolicy: IfNotPresent
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pullPolicy: Always
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# Overrides the image tag whose default is the chart appVersion.
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tag: "latest"
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nginxImage:
@@ -33,6 +33,7 @@ env:
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OPENBLAS_NUM_THREADS: "1"
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RESUBMIT_ALL_ON_STARTUP: "0"
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UNIQUE_DOC_NAMES_IN_DATASETS: "True"
36+
VITE_USE_OIDC: "0"
3637

3738
# TODO: Support custom DB overrides#
3839
# DB_ENGINE: "sqlite3"
@@ -162,8 +163,10 @@ service:
162163
# This sets the service type more information can be found here: https://kubernetes.io/docs/concepts/services-networking/service/#publishing-services-service-types
163164
type: ClusterIP
164165
# This sets the ports more information can be found here: https://kubernetes.io/docs/concepts/services-networking/service/#field-spec-ports
165-
port: 8000
166-
166+
port: 8001
167+
apiPort: 8000 # Note medcat-trainer API is currently hardcoded on 8000 in the run.sh script
168+
# nodePort: 30001
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167170
# This block is for setting up the ingress for more information can be found here: https://kubernetes.io/docs/concepts/services-networking/ingress/
168171
ingress:
169172
enabled: false
@@ -188,27 +191,28 @@ resources: {}
188191
# lines, adjust them as necessary, and remove the curly braces after 'resources:'.
189192
# limits:
190193
# cpu: 3 # Recommended to leave unset. If desired to set note service performance has been found to improve up to around 3 CPU.
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# memory: 2Gi
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# memory: 4Gi
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# requests:
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# cpu: 1
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# memory: 1Gi
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# cpu: 2 # For reference loading the examples on startup measured to use 2CPU and 2Gi memory
197+
# memory: 2Gi
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196199
# This is to setup the liveness and readiness probes more information can be found here: https://kubernetes.io/docs/tasks/configure-pod-container/configure-liveness-readiness-startup-probes/
197200
livenessProbe:
198201
httpGet:
199-
path: /api/health/live/
200-
port: http
202+
path: /api/health/live/?format=json
203+
port: api
204+
failureThreshold: 30
201205
readinessProbe:
202206
httpGet:
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path: /api/health/ready/
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port: http
207+
path: /api/health/ready/?format=json
208+
port: api
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startupProbe:
206210
httpGet:
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path: /api/health/startup/
208-
port: http
211+
path: /api/health/startup/?format=json
212+
port: api
209213
failureThreshold: 30
210214
periodSeconds: 10
211-
initialDelaySeconds: 5
215+
initialDelaySeconds: 15
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nginx:
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livenessProbe:

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