MedCAT Trainer Helm Chart

This Helm chart deploys MedCAT Trainer and infrastructure to a Kubernetes cluster.

By default the chart will:

• Run MedCAT Trainer Django server
• Run NGINX for static site hosting and routing
• Run a SOLR and Zookeeper cluster for the Concept DB
• Run a Postgres database for persistence

Installation

helm install my-medcat-trainer oci://registry-1.docker.io/cogstacksystems/medcat-trainer-helm

Configuration

See these values for common configurations to change:

Setting	description
env	Environment variables as defined in the MedCAT Trainer docs.
medcatConfig	MedCAT config file as described here
env.CSRF_TRUSTED_ORIGINS	The Host and Port to access the application on

Use Sqlite instead of Postgres

Sqlite can be used for smaller single instance deployments

Set these values:

DB_ENGINE: "sqlite3"

postgresql:
  enabled: false

Missing features

These features are not yet existing but to be added in future:

• Use a pre existing postgres db
• Use a pre existing SOLR instance
• Migrate from supervisord to standalone deployment for background tasks for better scaling
• Support SOLR authentication from medcat trainer
• Support passing DB OPTIONS to medcat trainer for use in cloud environments

Requirements

Repository	Name	Version
oci://registry-1.docker.io/bitnamicharts	postgresql	16.7.27
oci://registry-1.docker.io/bitnamicharts	solr	9.6.10

Values

Key	Type	Default	Description
affinity	object	{}
autoscaling.enabled	bool	false
autoscaling.maxReplicas	int	100
autoscaling.minReplicas	int	1
autoscaling.targetCPUUtilizationPercentage	int	80
env	object	{"CSRF_TRUSTED_ORIGINS":"http://localhost:8080","DB_ENGINE":"postgresql","DB_PORT":"5432","DEBUG":"1","EMAIL_HOST":"mail.cogstack.org","EMAIL_PASS":"to-be-changed","EMAIL_PORT":"465","EMAIL_USER":"example@cogstack.org","ENV":"non-prod","LOAD_NUM_DOC_PAGES":"10","MAX_DATASET_SIZE":"10000","MAX_MEDCAT_MODELS":"2","OPENBLAS_NUM_THREADS":"1","RESUBMIT_ALL_ON_STARTUP":"0","UNIQUE_DOC_NAMES_IN_DATASETS":"True","VITE_USE_OIDC":"0"}	Add any environment variables here that should be set in the medcat-trainer container
env.CSRF_TRUSTED_ORIGINS	string	"http://localhost:8080"	This sets the CSRF trusted origins for the medcat-trainer container. Change to allow access from other domains
envValueFrom	object	{"K8S_NODE_NAME":{"fieldRef":{"fieldPath":"spec.nodeName"}},"K8S_POD_NAME":{"fieldRef":{"fieldPath":"metadata.name"}},"K8S_POD_NAMESPACE":{"fieldRef":{"fieldPath":"metadata.namespace"}},"K8S_POD_UID":{"fieldRef":{"fieldPath":"metadata.uid"}}}	Allow setting env values from field/configmap/secret references @default -- Adds K8s downward API values for tracing
fullnameOverride	string	""
hostAliases	list	[]	Host aliases for the pod
image.pullPolicy	string	"IfNotPresent"	This sets the pull policy for images.
image.repository	string	"cogstacksystems/medcat-trainer"	Image repository for the MedCAT service container
imagePullSecrets	list	[]	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/
ingress.annotations	object	{}
ingress.className	string	""
ingress.enabled	bool	false
ingress.hosts[0].host	string	"chart-example.local"
ingress.hosts[0].paths[0].path	string	"/"
ingress.hosts[0].paths[0].pathType	string	"ImplementationSpecific"
ingress.tls	list	[]
livenessProbe.failureThreshold	int	30
livenessProbe.httpGet.path	string	"/api/health/live/?format=json"
livenessProbe.httpGet.port	string	"api"
medcatConfig	string	Default config for MedCAT Trainer	MedCAT config as described here: MedCAT config
nameOverride	string	""	This is to override the chart name.
nginx.livenessProbe.httpGet.path	string	"/nginx/health/live"
nginx.livenessProbe.httpGet.port	string	"http"
nginx.readinessProbe.httpGet.path	string	"/nginx/health/live"
nginx.readinessProbe.httpGet.port	string	"http"
nginxImage	object	{"pullPolicy":"IfNotPresent","repository":"nginx","tag":"1.29.1"}	This sets the container image for the nginx server more information can be found here: https://kubernetes.io/docs/concepts/containers/images/
nginxImage.pullPolicy	string	"IfNotPresent"	This sets the pull policy for images.
nginxImage.repository	string	"nginx"	Image repository for the nginx server
nginxImage.tag	string	"1.29.1"	This sets the image tag for the nginx server
nginxUpdateStrategy.type	string	"RollingUpdate"
nodeSelector	object	{}
persistence.media.size	string	"8Gi"
persistence.sqlite.backupDbSize	string	"300Mi"
persistence.sqlite.size	string	"100Mi"
persistence.static.size	string	"100Mi"
persistence.storageClassName	string	""
podAnnotations	object	{}	This is for setting Kubernetes Annotations to a Pod. For more information checkout: https://kubernetes.io/docs/concepts/overview/working-with-objects/annotations/
podLabels	object	{}	This is for setting Kubernetes Labels to a Pod. For more information checkout: https://kubernetes.io/docs/concepts/overview/working-with-objects/labels/
podSecurityContext	object	{}
postgresql.auth.database	string	"postgres"
postgresql.auth.password	string	"postgres"
postgresql.auth.username	string	"postgres"
postgresql.enabled	bool	true
postgresql.fullnameOverride	string	"medcat-trainer-postgresql"
postgresql.image.repository	string	"bitnamilegacy/postgresql"
postgresql.image.tag	string	"17.6.0-debian-12-r4"
postgresql.primary.persistence.size	string	"500Mi"
provisioning.config	object	Config to load example project from github	Provisioning Config Yaml contents. Can be templated See https://docs.cogstack.org/projects/medcat-trainer/en/latest/provisioning/
provisioning.enabled	bool	false	Set to true to enable provisioning of projects and models on startup..
provisioning.existingConfigMap	object	{}	Optional: Reference an existing configmap for the provisioning config.
readinessProbe.httpGet.path	string	"/api/health/ready/?format=json"
readinessProbe.httpGet.port	string	"api"
replicaCount	int	1	This will set the replicaset count more information can be found here: https://kubernetes.io/docs/concepts/workloads/controllers/replicaset/
resources	object	{}	Resources for the pod. More information can be found here: https://kubernetes.io/docs/concepts/containers/ Recommendation for a minimal production setup is { requests: { cpu: 2, memory: 2Gi }, limits: { cpu: null , memory: 4Gi } }
runtimeClassName	string	""	Runtime class name for the pod (e.g., "nvidia" for GPU workloads)
securityContext	object	{}
service.apiPort	int	8000
service.port	int	8001	This sets the ports more information can be found here: https://kubernetes.io/docs/concepts/services-networking/service/#field-spec-ports
service.type	string	"ClusterIP"	This sets the service type more information can be found here: https://kubernetes.io/docs/concepts/services-networking/service/#publishing-services-service-types
serviceAccount.annotations	object	{}	Annotations to add to the service account
serviceAccount.automount	bool	true	Automatically mount a ServiceAccount's API credentials?
serviceAccount.create	bool	true	Specifies whether a service account should be created
serviceAccount.name	string	""	The name of the service account to use. If not set and create is true, a name is generated using the fullname template
solr.auth.enabled	bool	false
solr.collectionReplicas	int	1
solr.collectionShards	int	1
solr.image.repository	string	"bitnamilegacy/solr"
solr.image.tag	string	"9.9.0-debian-12-r1"
solr.persistence.size	string	"1Gi"
solr.podLabels."app.kubernetes.io/component"	string	"solr"
solr.podLabels."app.kubernetes.io/part-of"	string	"cogstack"
solr.replicaCount	int	1
solr.zookeeper.image.repository	string	"bitnamilegacy/zookeeper"
solr.zookeeper.image.tag	string	"3.9.3-debian-12-r22"
solr.zookeeper.persistence.size	string	"1Gi"
solr.zookeeper.replicaCount	int	1
startupProbe.failureThreshold	int	30
startupProbe.httpGet.path	string	"/api/health/startup/?format=json"
startupProbe.httpGet.port	string	"api"
startupProbe.initialDelaySeconds	int	15
startupProbe.periodSeconds	int	10
tolerations	list	[]
tracing.disabledInstrumentations	string	"psycopg,sqlite3"
tracing.experimentalResourceDetectors	string	"containerid,os"
tracing.otlp.enabled	bool	false
tracing.otlp.grpc.enabled	bool	false
tracing.otlp.grpc.endpoint	string	"http://unused:4317"
tracing.otlp.http.enabled	bool	false
tracing.otlp.http.endpoint	string	"http://unused:4318"
tracing.resourceAttributes	object	Adds semantic k8s attributes for tracing	Resource attributes to add to the traces. Can be templated
tracing.serviceName	string	"medcat-trainer"
updateStrategy.type	string	"RollingUpdate"	Used for Kubernetes deployment .spec.strategy.type. Allowed values are "Recreate" or "RollingUpdate".
volumeMounts	list	[]	Additional volumeMounts on the output Deployment definition.
volumes	list	[]	Additional volumes on the output Deployment definition.

---

Autogenerated from chart metadata using helm-docs v1.14.2