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feat(helm): Setup helm-docs and generate readme files for helm charts (#62)
* feat(helm): Create git precommit hook for helm docs
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‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/norwoodj/helm-docs
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rev: v1.14.2
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hooks:
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- id: helm-docs-container
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files: helm-charts/(.*)/values.yaml
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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

‎helm-charts/cogstack-helm-ce/README.md‎

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```bash
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kubectl delete namespace cogstack
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```
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## Requirements
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| Repository | Name | Version |
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|------------|------|---------|
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| file://../medcat-service-helm | medcat-service(medcat-service-helm) | 0.0.1 |
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| file://../medcat-service-helm | anoncat-service(medcat-service-helm) | 0.0.1 |
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| file://../medcat-trainer-helm | medcat-trainer(medcat-trainer-helm) | 0.0.1 |
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| file://charts/jupyterhub | cogstack-jupyterhub | 0.1.0 |
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| https://opensearch-project.github.io/helm-charts/ | opensearch | 3.5.0 |
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| https://opensearch-project.github.io/helm-charts/ | opensearch-dashboards | 3.5.0 |
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## Values
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| Key | Type | Default | Description |
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|-----|------|---------|-------------|
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| anoncat-service.enabled | bool | `true` | Enable AnonCAT service deployment. |
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| anoncat-service.env.APP_MEDCAT_MODEL_PACK | string | `"/cat/models/examples/example-deid-model-pack.zip"` | Model pack used by the MedCAT service when running in DeID mode. |
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| anoncat-service.env.DEID_MODE | bool | `true` | Enable DeID mode. |
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| anoncat-service.env.DEID_REDACT | bool | `false` | Enable redaction behaviour for DeID. |
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| anoncat-service.image.repository | string | `"cogstacksystems/medcat-service"` | MedCAT service image repository for AnonCAT. |
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| anoncat-service.image.tag | string | `"1.2.0"` | MedCAT service image tag used by AnonCAT. |
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| anoncat-service.replicasCount | int | `1` | Number of AnonCAT (medcat-service in DeID mode) replicas. |
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| cogstack-jupyterhub.enabled | bool | `true` | Enable JupyterHub (with hub and singleuser components). |
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| cogstack-jupyterhub.jupyterhub.hub.config.Authenticator.admin_users | list | `["admin"]` | Allowed admin users for the dummy authenticator. |
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| cogstack-jupyterhub.jupyterhub.hub.config.Authenticator.admin_users[0] | string | `"admin"` | Admin user entry for the dummy authenticator. |
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| cogstack-jupyterhub.jupyterhub.hub.config.DummyAuthenticator.password | string | `"SuperSecret"` | Password for the dummy authenticator (do not use in production). |
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| cogstack-jupyterhub.jupyterhub.hub.config.JupyterHub.authenticator_class | string | `"dummy"` | Authenticator class used by JupyterHub (dummy authenticator for demo/non-prod). |
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| cogstack-jupyterhub.jupyterhub.hub.image.name | string | `"cogstacksystems/jupyter-hub"` | JupyterHub hub image name. |
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| cogstack-jupyterhub.jupyterhub.hub.image.tag | string | `"2.2.2"` | JupyterHub hub image tag. |
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| cogstack-jupyterhub.jupyterhub.singleuser.image.name | string | `"cogstacksystems/jupyter-singleuser"` | JupyterHub singleuser image name. |
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| cogstack-jupyterhub.jupyterhub.singleuser.image.pullPolicy | string | `"IfNotPresent"` | JupyterHub singleuser image pull policy. |
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| cogstack-jupyterhub.jupyterhub.singleuser.image.tag | string | `"2.2.2"` | JupyterHub singleuser image tag. |
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| fullnameOverride | string | `""` | Fully override the chart fullname. |
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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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| medcat-service.enabled | bool | `true` | Enable MedCAT service deployment. |
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| medcat-service.image.repository | string | `"cogstacksystems/medcat-service"` | MedCAT service image repository. |
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| medcat-service.image.tag | string | `"1.2.0"` | MedCAT service image tag. |
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| medcat-service.replicasCount | int | `1` | Number of MedCAT service replicas. |
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| medcat-trainer.enabled | bool | `true` | Enable MedCAT Trainer deployment. |
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| medcat-trainer.env.CSRF_TRUSTED_ORIGINS | string | `"http://localhost:8080"` | CSRF trusted origins for the MedCAT Trainer frontend (set for your deployment/port-forward). |
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| medcat-trainer.image.tag | string | `"latest@sha256:103215a7540ad614c32866f4cb00ddd91e7aff37cea9abc25dc226c577f9506d"` | MedCAT Trainer image tag (can be a digest-pinned tag). |
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| medcat-trainer.provisioning.enabled | bool | `true` | Enable provisioning of projects and models on startup. |
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| medcat-trainer.provisioning.existingConfigMap.name | string | `"cogstack-helm-ce-example-trainer-provisioining"` | Existing ConfigMap name containing the provisioning configuration. |
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| nameOverride | string | `""` | This is to override the chart name. |
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| opensearch-dashboards.enabled | bool | `true` | Deploy an opensearch-dashboards instance |
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| opensearch.enabled | bool | `true` | Deploy an opensearch cluster |
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| opensearch.extraEnvs | list | Sets the initial admin password for OpenSearch | Extra environment variables to pass to OpenSearch. |
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| provisioning.enabled | bool | `true` | Enable provisioning for supporting services (e.g. OpenSearch templates/documents). |
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| provisioning.opensearch.createExampleDocuments | bool | `true` | Create example documents in OpenSearch on startup. |
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| provisioning.opensearch.createIndexTemplate | bool | `true` | Create the OpenSearch index template on startup. |
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| provisioning.opensearchDashboards.createDashboards | bool | `true` | Create dashboards on startup. |
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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/cogstack-helm-ce/README.md.gotmpl‎

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# CogStack Helm Community Edition
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This is a all in one helm chart that runs CogStack on Kubernetes
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## Overview
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This chart is an umbrella chart that deploys:
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| Component | Description |
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|------------------|-------------|
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| **MedCAT** | Medical Concept Annotation Tool — NER and linking for clinical text. |
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| **AnonCAT** | De-identification service (MedCAT in DEID mode) for anonymising text. |
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| **MedCAT Trainer** | Training and model management for MedCAT, with Solr and PostgreSQL. |
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## Prerequisites
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- Kubernetes cluster
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- Helm 3+
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## Installation
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```sh
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helm install cogstack oci://registry-1.docker.io/cogstacksystems/cogstack-helm-ce
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```
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## Configuration
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These are some values that are likely to need customization for your deployment:
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| Value | Default | Description |
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|-------|---------|-------------|
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| `medcat-service.replicasCount` | `1` | Number of MedCAT service replicas. |
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| `anoncat-service.replicasCount` | `1` | Number of AnonCAT service replicas. |
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| `anoncat-service.env.DEID_REDACT` | `false` | Redaction behaviour for de-identification. |
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| `medcat-trainer.env.CSRF_TRUSTED_ORIGINS` | `"http://localhost:8080"` | CSRF trusted origins for MedCAT Trainer frontend (set correct value for your deployment, this default works for port forwarding). |
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Subcharts (MedCAT service, AnonCAT service, MedCAT Trainer) support additional options; see their respective charts under `../medcat-service-helm` and `../medcat-trainer-helm`. Pass them under the same keys as in this chart’s `values.yaml` (e.g. `medcat-service.*`, `anoncat-service.*`, `medcat-trainer-helm.*`).
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Example override file:
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```yaml
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# my-values.yaml
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medcat-service:
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replicasCount: 2
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anoncat-service:
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replicasCount: 1
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env:
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APP_ENABLE_DEMO_UI: true
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DEID_MODE: true
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```
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Install with overrides:
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```bash
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helm install cogstack . -f my-values.yaml --namespace cogstack --create-namespace
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```
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## Dependencies
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The chart uses local subcharts via relative paths:
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- `medcat-service-helm` (as `medcat-service` and `anoncat-service`)
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- `medcat-trainer-helm`
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## Uninstall
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```bash
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helm uninstall cogstack-ce --namespace cogstack
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```
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If the namespace was created only for this release, remove it with:
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```bash
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kubectl delete namespace cogstack
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```
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{{ template "chart.requirementsSection" . }}
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{{ template "chart.valuesSection" . }}
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{{ template "helm-docs.versionFooter" . }}

‎helm-charts/cogstack-helm-ce/charts/jupyterhub/README.md‎

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# cogstack-jupyterhub
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![Version: 0.1.0](https://img.shields.io/badge/Version-0.1.0-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: latest](https://img.shields.io/badge/AppVersion-latest-informational?style=flat-square)
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A Helm chart for CogStack Jupyter Hub using official JupyterHub chart
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## Requirements
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| Repository | Name | Version |
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|------------|------|---------|
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| https://hub.jupyter.org/helm-chart/ | jupyterhub | 4.3.2 |
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## Values
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| Key | Type | Default | Description |
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|-----|------|---------|-------------|
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| jupyterhub.cull.enabled | bool | false, so pods stay running indefinitely d | Enable culling of user pods |
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| jupyterhub.hub.config.Authenticator.admin_users[0] | string | `"admin"` | |
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| jupyterhub.hub.config.DummyAuthenticator.password | string | `"SuperSecret"` | |
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| jupyterhub.hub.config.JupyterHub.authenticator_class | string | `"dummy"` | |
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| jupyterhub.hub.config.KubeSpawner.fs_gid | int | `0` | |
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| jupyterhub.hub.config.KubeSpawner.http_timeout | int | `120` | |
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| jupyterhub.hub.config.KubeSpawner.notebook_dir | string | `"/home/jovyan/work"` | |
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| jupyterhub.hub.config.KubeSpawner.start_timeout | int | `300` | |
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| jupyterhub.hub.config.KubeSpawner.uid | int | `0` | |
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| jupyterhub.hub.config.Spawner.default_url | string | `"/lab/"` | |
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| jupyterhub.hub.config.Spawner.notebook_dir | string | `"/home/jovyan/work"` | |
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| jupyterhub.hub.extraConfig | object | `{"00-custom-spawner":"# Custom environment variables for user pods\nc.KubeSpawner.environment = {\n 'GRANT_SUDO': '1',\n 'CHOWN_HOME': 'yes',\n 'CHOWN_HOME_OPTS': '-R',\n}\n# Allow root in notebooks\nc.KubeSpawner.args = ['--allow-root']\n"}` | Extra hub configuration for custom spawner settings |
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| jupyterhub.hub.extraConfig.00-log-level | string | `"c.Application.log_level = 'DEBUG'\n"` | |
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| jupyterhub.hub.image.name | string | `"cogstacksystems/jupyter-hub"` | Image repository for the JupyterHub hub. |
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| jupyterhub.hub.image.pullPolicy | string | `"IfNotPresent"` | Pull policy for the JupyterHub hub. |
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| jupyterhub.hub.image.tag | string | `"2.2.2"` | Image tag for the JupyterHub hub. |
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| jupyterhub.prePuller.continuous.enabled | bool | `false` | |
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| jupyterhub.prePuller.hook | object | `{"enabled":false}` | Enable pulling the singleuser image before they are used to improve startup time |
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| jupyterhub.proxy.service.type | string | `"ClusterIP"` | |
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| jupyterhub.scheduling.userScheduler.replicas | int | `1` | |
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| jupyterhub.singleuser.cmd[0] | string | `"jupyterhub-singleuser"` | |
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| jupyterhub.singleuser.extraPodConfig | object | `{"securityContext":{"runAsGroup":0,"runAsUser":0}}` | Extra arguments passed to jupyterhub-singleuser |
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| jupyterhub.singleuser.fsGid | int | `0` | |
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| jupyterhub.singleuser.image.name | string | `"cogstacksystems/jupyter-singleuser"` | |
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| jupyterhub.singleuser.image.pullPolicy | string | `"IfNotPresent"` | |
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| jupyterhub.singleuser.image.tag | string | `"2.2.2"` | |
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| jupyterhub.singleuser.lifecycleHooks.postStart | object | `{"exec":{"command":["sh","-c","if [ ! -f /home/jovyan/work/.notebooks_initialized ]; then\n echo \"First run - copying notebooks and medcat-scripts...\";\n cp -r /srv/jupyterhub/notebooks/* /home/jovyan/work/;\n cp -r /srv/jupyterhub/medcat-scripts /home/jovyan/work/;\n touch /home/jovyan/work/.notebooks_initialized;\n echo \"Notebooks initialized successfully\";\nelse\n echo \"Notebooks already initialized - skipping\";\nfi\n"]}}` | Lifecycle hook to copy notebooks from image to PVC on first run |
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| jupyterhub.singleuser.networkPolicy.enabled | bool | `false` | |
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| jupyterhub.singleuser.startTimeout | int | `600` | |
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| jupyterhub.singleuser.storage.capacity | string | `"5Gi"` | Capacity of the storage for the user pods. |
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| jupyterhub.singleuser.storage.extraVolumeMounts.jupyter-examples.mountPath | string | `"/home/jovyan/work/examples"` | |
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| jupyterhub.singleuser.storage.extraVolumeMounts.jupyter-examples.name | string | `"jupyter-examples"` | |
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| jupyterhub.singleuser.storage.extraVolumeMounts.jupyter-examples.readOnly | bool | `true` | |
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| jupyterhub.singleuser.storage.extraVolumes | object | `{"jupyter-examples":{"configMap":{"name":"jupyter-examples"},"name":"jupyter-examples"}}` | NOTE: Prefer dictionary-form here to avoid Helm merge issues when this subchart is configured by a parent chart. |
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| jupyterhub.singleuser.uid | int | `0` | |
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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/cogstack-helm-ce/charts/jupyterhub/README.md.gotmpl‎

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{{ template "chart.header" . }}
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{{ template "chart.deprecationWarning" . }}
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{{ template "chart.badgesSection" . }}
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{{ template "chart.description" . }}
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{{ template "chart.homepageLine" . }}
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{{ template "chart.maintainersSection" . }}
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{{ template "chart.sourcesSection" . }}
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{{ template "chart.requirementsSection" . }}
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{{ template "chart.valuesSection" . }}
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{{ template "helm-docs.versionFooter" . }}

‎helm-charts/cogstack-helm-ce/charts/jupyterhub/values.yaml‎

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jupyterhub:
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hub:
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image:
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# -- Image repository for the JupyterHub hub.
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name: cogstacksystems/jupyter-hub
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# -- Image tag for the JupyterHub hub.
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tag: "2.2.2"
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# -- Pull policy for the JupyterHub hub.
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pullPolicy: IfNotPresent
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extraConfig:
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00-log-level: |
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default_url: /lab/
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notebook_dir: /home/jovyan/work
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# Extra hub configuration for custom spawner settings
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# -- Extra hub configuration for custom spawner settings
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extraConfig:
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00-custom-spawner: |
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# Custom environment variables for user pods
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name: cogstacksystems/jupyter-singleuser
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tag: "2.2.2"
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pullPolicy: IfNotPresent
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# Lifecycle hook to copy notebooks from image to PVC on first run
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lifecycleHooks:
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# -- Lifecycle hook to copy notebooks from image to PVC on first run
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postStart:
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exec:
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command:
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fsGid: 0
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cmd: ["jupyterhub-singleuser"]
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# Extra arguments passed to jupyterhub-singleuser
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# -- Extra arguments passed to jupyterhub-singleuser
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extraPodConfig:
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securityContext:
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runAsUser: 0
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runAsGroup: 0
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storage:
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# -- Capacity of the storage for the user pods.
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capacity: 5Gi
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# NOTE: Prefer dictionary-form here to avoid Helm merge issues
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# -- NOTE: Prefer dictionary-form here to avoid Helm merge issues
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# when this subchart is configured by a parent chart.
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extraVolumes:
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jupyter-examples:
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mountPath: /home/jovyan/work/examples
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readOnly: true
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cull:
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# -- Enable culling of user pods
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# @default -- false, so pods stay running indefinitely
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enabled: false
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scheduling:
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userScheduler:
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replicas: 1
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prePuller:
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# -- Enable pulling the singleuser image before they are used to improve startup time
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hook:
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enabled: false
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continuous:

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