fix(helm): Medcat trainer helm chart run as single pod

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

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

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

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

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

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

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

@@ -4,15 +4,13 @@ metadata:
   name: {{ include "medcat-trainer-helm.fullname" . }}-medcat-trainer
   labels:
     {{- include "medcat-trainer-helm.labels" . | nindent 4 }}
-    app.kubernetes.io/component: medcat-trainer
 spec:
   {{- if not .Values.autoscaling.enabled }}
   replicas: {{ .Values.replicaCount }}
   {{- end }}
   selector:
     matchLabels:
       {{- include "medcat-trainer-helm.selectorLabels" . | nindent 6 }}
-      app.kubernetes.io/component: medcat-trainer
   strategy: {{ toYaml .Values.updateStrategy | nindent 4 }}
   template:
     metadata:
@@ -22,7 +20,6 @@ spec:
       {{- end }}
       labels:
         {{- include "medcat-trainer-helm.labels" . | nindent 8 }}
-        app.kubernetes.io/component: medcat-trainer
         {{- with .Values.podLabels }}
         {{- toYaml . | nindent 8 }}
         {{- end }}
@@ -45,8 +42,8 @@ spec:
           image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
           imagePullPolicy: {{ .Values.image.pullPolicy }}
           ports:
-            - name: http
-              containerPort: 8000
+            - name: api
+              containerPort: {{ .Values.service.apiPort }}
               protocol: TCP
           args:
             - /usr/bin/supervisord
@@ -93,6 +90,43 @@ spec:
           {{- with .Values.volumeMounts }}
           {{- toYaml . | nindent 12 }}
           {{- end }}
+        - name: nginx
+          {{- with .Values.securityContext }}
+          securityContext:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          image: "{{ .Values.nginxImage.repository }}:{{ .Values.nginxImage.tag }}"
+          imagePullPolicy: {{ .Values.nginxImage.pullPolicy }}
+          ports:
+            - name: http
+              containerPort: {{ .Values.service.port }}
+              protocol: TCP
+          {{- with .Values.nginx.livenessProbe }}
+          livenessProbe:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          {{- with .Values.nginx.readinessProbe }}
+          readinessProbe:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          {{- with .Values.resources }}
+          resources:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          volumeMounts:
+            - name: nginx-config
+              mountPath: /etc/nginx/nginx.conf
+              subPath: nginx.conf 
+            - name: nginx-config
+              mountPath: /etc/nginx/sites-enabled/medcattrainer
+              subPath: sitesenabled.medcattrainer 
+            - mountPath: /home/api/media
+              name: api-media
+            - mountPath: /home/api/static
+              name: api-static
+          {{- with .Values.volumeMounts }}
+          {{- toYaml . | nindent 12 }}
+          {{- end }}
       volumes:
         - name: medcat-trainer-config
           configMap:
@@ -111,6 +145,9 @@ spec:
           persistentVolumeClaim:
             claimName: {{ include "medcat-trainer-helm.fullname" . }}-api-db-backup
         {{- end }}
+        - name: nginx-config
+          configMap:
+            name: {{ include "medcat-trainer-helm.fullname" . }}-nginx-config
         {{- with .Values.volumes }}
         {{- toYaml . | nindent 8 }}
         {{- end }}

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

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

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

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

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

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

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

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

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

@@ -9,7 +9,7 @@ replicaCount: 1
 image:
   repository: cogstacksystems/medcat-trainer
   # This sets the pull policy for images.
-  pullPolicy: IfNotPresent
+  pullPolicy: Always
   # Overrides the image tag whose default is the chart appVersion.
   tag: "latest"
 nginxImage:
@@ -33,6 +33,7 @@ env:
   OPENBLAS_NUM_THREADS: "1"
   RESUBMIT_ALL_ON_STARTUP: "0"
   UNIQUE_DOC_NAMES_IN_DATASETS: "True"
+  VITE_USE_OIDC: "0"
 
   # TODO: Support custom DB overrides#
   # DB_ENGINE: "sqlite3"
@@ -162,8 +163,10 @@ service:
   # This sets the service type more information can be found here: https://kubernetes.io/docs/concepts/services-networking/service/#publishing-services-service-types
   type: ClusterIP
   # This sets the ports more information can be found here: https://kubernetes.io/docs/concepts/services-networking/service/#field-spec-ports
-  port: 8000
-
+  port: 8001
+  apiPort: 8000 # Note medcat-trainer API is currently hardcoded on 8000 in the run.sh script
+  # nodePort: 30001
+
 # This block is for setting up the ingress for more information can be found here: https://kubernetes.io/docs/concepts/services-networking/ingress/
 ingress:
   enabled: false
@@ -188,27 +191,28 @@ resources: {}
   # lines, adjust them as necessary, and remove the curly braces after 'resources:'.
   # limits:
   #   cpu: 3 # Recommended to leave unset. If desired to set note service performance has been found to improve up to around 3 CPU.
-  #   memory: 2Gi
+  #   memory: 4Gi
   # requests:
-  #   cpu: 1
-  #   memory: 1Gi
+  #   cpu: 2  # For reference loading the examples on startup measured to use 2CPU and 2Gi memory
+  #   memory: 2Gi
 
 # 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/
 livenessProbe:
   httpGet:
-    path: /api/health/live/
-    port: http
+    path: /api/health/live/?format=json
+    port: api
+  failureThreshold: 30
 readinessProbe:
   httpGet:
-    path: /api/health/ready/
-    port: http
+    path: /api/health/ready/?format=json
+    port: api
 startupProbe:
   httpGet:
-    path: /api/health/startup/
-    port: http
+    path: /api/health/startup/?format=json
+    port: api
   failureThreshold: 30
   periodSeconds: 10
-  initialDelaySeconds: 5
+  initialDelaySeconds: 15
 
 nginx:
   livenessProbe:

deployment/kubernetes/local_dev_startup.sh

@@ -21,7 +21,7 @@ helm test medcat-service --logs
 # Test medcat trainer
 # kubectl port-forward svc/nginx 8000:8000
 
-helm upgrade my-test ./medcat-trainer-helm --install --recreate-pods  --wait --timeout 5m0s # Install if it doesnt already exist, else upgrade
+helm upgrade x ./medcat-trainer-helm --install  --wait --timeout 5m0s # Install if it doesnt already exist, else upgrade
 # kubectl port-forward svc/medcat-trainer-solr 8983:8983
 
 ## helm install trainer-registry oci://registry-1.docker.io/cogstacksystems/medcat-trainer-helm --wait --timeout 5m0s