ops: CU-869adnv5w Add health checks to trainer helm

deployment/kubernetes/charts/medcat-service-helm/README.md

@@ -60,3 +60,14 @@ or
 ```sh
 helm install my-medcat ./medcat-chart -f values-model-download.yaml
 ```
+
+### DeID Mode
+
+The service can perform DeID of EHRs by swithcing to the following values
+
+```
+env:
+  APP_MEDCAT_MODEL_PACK: "/cat/models/examples/example-deid-model-pack.zip"
+  DEID_MODE: "true"
+  DEID_REDACT: "true"
+```

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

@@ -26,6 +26,11 @@ env:
   # MODEL_META_URL: "https://cogstack-medcat-example-models.s3.eu-west-2.amazonaws.com/medcat-example-models/mc_status.zip"
   # APP_MODEL_CDB_PATH: "/cat/models/medmen/cdb.dat"
 
+  # Enable DeID mode with the following
+  # APP_MEDCAT_MODEL_PACK: "/cat/models/examples/example-deid-model-pack.zip"
+  # DEID_MODE: true
+  # DEID_REDACT: true
+
 # This is for the secrets for pulling an image from a private repository more information can be found here: https://kubernetes.io/docs/tasks/configure-pod-container/pull-image-private-registry/
 imagePullSecrets: []
 # This is to override the chart name.

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

@@ -72,6 +72,10 @@ spec:
           readinessProbe:
             {{- toYaml . | nindent 12 }}
           {{- end }}
+          {{- with .Values.startupProbe }}
+          startupProbe:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
           {{- with .Values.resources }}
           resources:
             {{- toYaml . | nindent 12 }}

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

@@ -178,22 +178,20 @@ resources: {}
   #   memory: 128Mi
 
 # 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/
-# TODO Add liveness and readiness to django app
-# https://github.com/CogStack/cogstack-nlp/pull/131/files
-# livenessProbe:
-#   httpGet:
-#     path: /api/health/live/
-#     port: http
-# readinessProbe:
-#   httpGet:
-#     path: /api/health/ready/
-#     port: http
-# startupProbe:
-#   httpGet:
-#     path: /api/health/startup/
-#     port: http
-#   failureThreshold: 30
-#   periodSeconds: 10
+livenessProbe:
+  httpGet:
+    path: /api/health/live/
+    port: http
+readinessProbe:
+  httpGet:
+    path: /api/health/ready/
+    port: http
+startupProbe:
+  httpGet:
+    path: /api/health/startup/
+    port: http
+  failureThreshold: 30
+  periodSeconds: 10
 
 nginx:
   livenessProbe: