diff --git a/deployment/kubernetes/charts/medcat-service-helm/README.md b/deployment/kubernetes/charts/medcat-service-helm/README.md index 68fba10..0001f0d 100644 --- a/deployment/kubernetes/charts/medcat-service-helm/README.md +++ b/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" +``` diff --git a/deployment/kubernetes/charts/medcat-service-helm/values.yaml b/deployment/kubernetes/charts/medcat-service-helm/values.yaml index 0cfa56b..59a7452 100644 --- a/deployment/kubernetes/charts/medcat-service-helm/values.yaml +++ b/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. diff --git a/deployment/kubernetes/charts/medcat-trainer-helm/templates/medcat-trainer-deployment.yaml b/deployment/kubernetes/charts/medcat-trainer-helm/templates/medcat-trainer-deployment.yaml index 03cf3cc..0949545 100644 --- a/deployment/kubernetes/charts/medcat-trainer-helm/templates/medcat-trainer-deployment.yaml +++ b/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 }} diff --git a/deployment/kubernetes/charts/medcat-trainer-helm/values.yaml b/deployment/kubernetes/charts/medcat-trainer-helm/values.yaml index 845e579..40b909f 100644 --- a/deployment/kubernetes/charts/medcat-trainer-helm/values.yaml +++ b/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: