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docs(helm): Add helm docs for medcat-trainer
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‎.pre-commit-config.yaml‎

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files: helm-charts/medcat-service-helm/.*
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args:
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# Make the tool search for charts only under the `example-charts` directory
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- --chart-search-root=helm-charts/medcat-service-helm
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- --chart-search-root=helm-charts/medcat-service-helm
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- id: helm-docs-container
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files: helm-charts/medcat-trainer-helm/.*
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args:
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# Make the tool search for charts only under the `example-charts` directory
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- --chart-search-root=helm-charts/medcat-trainer-helm

‎helm-charts/medcat-trainer-helm/README.md‎

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- Run a SOLR and Zookeeper cluster for the Concept DB
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- Run a Postgres database for persistence
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## Installation
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```sh
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See these values for common configurations to change:
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| Setting |description |
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| -------- | -------- |
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| `env` | Environment variables as defined in the [MedCAT Trainer docs](https://docs.cogstack.org/projects/medcat-trainer/en/latest/installation.html). |
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|`medcatConfig`|MedCAT config file as described [here](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/medcat/config/config.py)|
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| `env.CSRF_TRUSTED_ORIGINS` | The Host and Port to access the application on |
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| Setting | description |
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| -------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------- |
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| `env` | Environment variables as defined in the [MedCAT Trainer docs](https://docs.cogstack.org/projects/medcat-trainer/en/latest/installation.html). |
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| `medcatConfig` | MedCAT config file as described [here](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/medcat/config/config.py) |
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| `env.CSRF_TRUSTED_ORIGINS` | The Host and Port to access the application on |
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### Use Sqlite instead of Postgres
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```
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## Missing features
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These features are not yet existing but to be added in future:
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- Use a pre existing postgres db
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- Use a pre existing SOLR instance
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- Migrate from supervisord to standalone deployment for background tasks for better scaling
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- Support SOLR authentication from medcat trainer
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- Support passing DB OPTIONS to medcat trainer for use in cloud environments
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## Requirements
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| Repository | Name | Version |
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|------------|------|---------|
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| oci://registry-1.docker.io/bitnamicharts | postgresql | 16.7.27 |
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| oci://registry-1.docker.io/bitnamicharts | solr | 9.6.10 |
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## Values
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| Key | Type | Default | Description |
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|-----|------|---------|-------------|
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| affinity | object | `{}` | |
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| autoscaling.enabled | bool | `false` | |
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| autoscaling.maxReplicas | int | `100` | |
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| autoscaling.minReplicas | int | `1` | |
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| autoscaling.targetCPUUtilizationPercentage | int | `80` | |
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| 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 |
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| 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 |
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| 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 |
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| fullnameOverride | string | `""` | |
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| hostAliases | list | `[]` | Host aliases for the pod |
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| image.pullPolicy | string | `"IfNotPresent"` | This sets the pull policy for images. |
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| image.repository | string | `"cogstacksystems/medcat-trainer"` | Image repository for the MedCAT service container |
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| 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/ |
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| ingress.annotations | object | `{}` | |
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| ingress.className | string | `""` | |
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| ingress.enabled | bool | `false` | |
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| ingress.hosts[0].host | string | `"chart-example.local"` | |
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| ingress.hosts[0].paths[0].path | string | `"/"` | |
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| ingress.hosts[0].paths[0].pathType | string | `"ImplementationSpecific"` | |
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| ingress.tls | list | `[]` | |
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| livenessProbe.failureThreshold | int | `30` | |
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| livenessProbe.httpGet.path | string | `"/api/health/live/?format=json"` | |
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| livenessProbe.httpGet.port | string | `"api"` | |
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| medcatConfig | string | Default config for MedCAT Trainer | MedCAT config as described here: [MedCAT config](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/medcat/config/config.py) |
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| nameOverride | string | `""` | This is to override the chart name. |
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| nginx.livenessProbe.httpGet.path | string | `"/nginx/health/live"` | |
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| nginx.livenessProbe.httpGet.port | string | `"http"` | |
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| nginx.readinessProbe.httpGet.path | string | `"/nginx/health/live"` | |
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| nginx.readinessProbe.httpGet.port | string | `"http"` | |
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| 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/ |
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| nginxImage.pullPolicy | string | `"IfNotPresent"` | This sets the pull policy for images. |
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| nginxImage.repository | string | `"nginx"` | Image repository for the nginx server |
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| nginxImage.tag | string | `"1.29.1"` | This sets the image tag for the nginx server |
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| nginxUpdateStrategy.type | string | `"RollingUpdate"` | |
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| nodeSelector | object | `{}` | |
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| persistence.media.size | string | `"8Gi"` | |
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| persistence.sqlite.backupDbSize | string | `"300Mi"` | |
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| persistence.sqlite.size | string | `"100Mi"` | |
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| persistence.static.size | string | `"100Mi"` | |
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| persistence.storageClassName | string | `""` | |
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| 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/ |
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| 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/ |
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| podSecurityContext | object | `{}` | |
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| postgresql.auth.database | string | `"postgres"` | |
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| postgresql.auth.password | string | `"postgres"` | |
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| postgresql.auth.username | string | `"postgres"` | |
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| postgresql.enabled | bool | `true` | |
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| postgresql.image.repository | string | `"bitnamilegacy/postgresql"` | |
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| postgresql.image.tag | string | `"17.6.0-debian-12-r4"` | |
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| postgresql.primary.persistence.size | string | `"500Mi"` | |
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| 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/ |
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| provisioning.enabled | bool | `false` | Set to true to enable provisioning of projects and models on startup.. |
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| provisioning.existingConfigMap | object | `{}` | Optional: Reference an existing configmap for the provisioning config. |
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| readinessProbe.httpGet.path | string | `"/api/health/ready/?format=json"` | |
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| readinessProbe.httpGet.port | string | `"api"` | |
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| replicaCount | int | `1` | This will set the replicaset count more information can be found here: https://kubernetes.io/docs/concepts/workloads/controllers/replicaset/ |
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| 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 <unset>, memory: 4Gi } } |
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| runtimeClassName | string | `""` | Runtime class name for the pod (e.g., "nvidia" for GPU workloads) |
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| securityContext | object | `{}` | |
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| service.apiPort | int | `8000` | |
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| 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 |
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| 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 |
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| serviceAccount.annotations | object | `{}` | Annotations to add to the service account |
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| serviceAccount.automount | bool | `true` | Automatically mount a ServiceAccount's API credentials? |
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| serviceAccount.create | bool | `true` | Specifies whether a service account should be created |
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| 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 |
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| solr.auth.enabled | bool | `false` | |
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| solr.collectionReplicas | int | `1` | |
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| solr.collectionShards | int | `1` | |
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| solr.image.repository | string | `"bitnamilegacy/solr"` | |
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| solr.image.tag | string | `"9.9.0-debian-12-r1"` | |
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| solr.persistence.size | string | `"1Gi"` | |
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| solr.podLabels."app.kubernetes.io/component" | string | `"solr"` | |
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| solr.podLabels."app.kubernetes.io/part-of" | string | `"cogstack"` | |
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| solr.replicaCount | int | `1` | |
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| solr.zookeeper.image.repository | string | `"bitnamilegacy/zookeeper"` | |
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| solr.zookeeper.image.tag | string | `"3.9.3-debian-12-r22"` | |
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| solr.zookeeper.persistence.size | string | `"1Gi"` | |
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| solr.zookeeper.replicaCount | int | `1` | |
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| startupProbe.failureThreshold | int | `30` | |
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| startupProbe.httpGet.path | string | `"/api/health/startup/?format=json"` | |
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| startupProbe.httpGet.port | string | `"api"` | |
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| startupProbe.initialDelaySeconds | int | `15` | |
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| startupProbe.periodSeconds | int | `10` | |
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| tolerations | list | `[]` | |
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| tracing.disabledInstrumentations | string | `"psycopg,sqlite3"` | |
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| tracing.experimentalResourceDetectors | string | `"containerid,os"` | |
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| tracing.otlp.enabled | bool | `false` | |
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| tracing.otlp.grpc.enabled | bool | `false` | |
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| tracing.otlp.grpc.endpoint | string | `"http://unused:4317"` | |
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| tracing.otlp.http.enabled | bool | `false` | |
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| tracing.otlp.http.endpoint | string | `"http://unused:4318"` | |
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| tracing.resourceAttributes | object | Adds semantic k8s attributes for tracing | Resource attributes to add to the traces. Can be templated |
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| tracing.serviceName | string | `"medcat-trainer"` | |
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| updateStrategy.type | string | `"RollingUpdate"` | Used for Kubernetes deployment .spec.strategy.type. Allowed values are "Recreate" or "RollingUpdate". |
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| volumeMounts | list | `[]` | Additional volumeMounts on the output Deployment definition. |
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| volumes | list | `[]` | Additional volumes on the output Deployment definition. |
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----------------------------------------------
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Autogenerated from chart metadata using [helm-docs v1.14.2](https://github.com/norwoodj/helm-docs/releases/v1.14.2)

‎helm-charts/medcat-trainer-helm/README.md.gotmpl‎

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# MedCAT Trainer Helm Chart
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This Helm chart deploys MedCAT Trainer and infrastructure to a Kubernetes cluster.
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By default the chart will:
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- Run MedCAT Trainer Django server
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- Run NGINX for static site hosting and routing
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- Run a SOLR and Zookeeper cluster for the Concept DB
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- Run a Postgres database for persistence
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## Installation
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```sh
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helm install my-medcat-trainer oci://registry-1.docker.io/cogstacksystems/medcat-trainer-helm
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```
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## Configuration
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See these values for common configurations to change:
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| Setting | description |
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| -------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------- |
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| `env` | Environment variables as defined in the [MedCAT Trainer docs](https://docs.cogstack.org/projects/medcat-trainer/en/latest/installation.html). |
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| `medcatConfig` | MedCAT config file as described [here](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/medcat/config/config.py) |
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| `env.CSRF_TRUSTED_ORIGINS` | The Host and Port to access the application on |
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### Use Sqlite instead of Postgres
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Sqlite can be used for smaller single instance deployments
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Set these values:
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```yaml
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DB_ENGINE: "sqlite3"
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postgresql:
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enabled: false
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```
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## Missing features
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These features are not yet existing but to be added in future:
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- Use a pre existing postgres db
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- Use a pre existing SOLR instance
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- Migrate from supervisord to standalone deployment for background tasks for better scaling
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- Support SOLR authentication from medcat trainer
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- Support passing DB OPTIONS to medcat trainer for use in cloud environments
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{{ template "chart.requirementsSection" . }}
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{{ template "chart.valuesSection" . }}
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{{ template "helm-docs.versionFooter" . }}

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