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feat(helm): Create Cogstack Community Edition Chart
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‎.github/workflows/kubernetes-charts-build.yaml‎

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echo "chart_version=$CHART_VERSION" >> "$GITHUB_OUTPUT"
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- name: Package Helm Charts
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# TODO: List the dir instead of hardcoding each one
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run: |
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helm package ./charts/medcat-service-helm --version ${{ steps.version.outputs.chart_version }}
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helm package ./charts/medcat-trainer-helm --version ${{ steps.version.outputs.chart_version }} --dependency-update
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helm package ./charts/cogstack-helm-ce --version ${{ steps.version.outputs.chart_version }} --dependency-update
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- name: Helm OCI login to Docker Hub
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run: helm registry login registry-1.docker.io -u ${{ secrets.DOCKERHUB_USERNAME }} -p ${{ secrets.DOCKERHUB_TOKEN }}
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run: |
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helm push ./medcat-service-helm-${{ steps.version.outputs.chart_version }}.tgz oci://registry-1.docker.io/cogstacksystems
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helm push ./medcat-trainer-helm-${{ steps.version.outputs.chart_version }}.tgz oci://registry-1.docker.io/cogstacksystems
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helm push ./cogstack-helm-ce-${{ steps.version.outputs.chart_version }}.tgz oci://registry-1.docker.io/cogstacksystems
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- name: Release
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uses: softprops/action-gh-release@v2
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if: github.ref_type == 'tag'
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with:
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draft: true
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files: |
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./deployment/kubernetes/medcat-service-helm-${{ steps.version.outputs.chart_version }}.tgz
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./deployment/kubernetes/medcat-trainer-helm-${{ steps.version.outputs.chart_version }}.tgz
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./deployment/kubernetes/*.tgz

‎deployment/kubernetes/charts/cogstack-helm-ce/.helmignore‎

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# Patterns to ignore when building packages.
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# This supports shell glob matching, relative path matching, and
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# negation (prefixed with !). Only one pattern per line.
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.DS_Store
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# Common VCS dirs
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.git/
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.gitignore
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.bzr/
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.bzrignore
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.hg/
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.hgignore
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.svn/
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# Common backup files
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*.swp
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*.bak
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*.tmp
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*.orig
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*~
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# Various IDEs
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.project
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.idea/
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*.tmproj
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.vscode/

‎deployment/kubernetes/charts/cogstack-helm-ce/Chart.lock‎

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dependencies:
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- name: medcat-service-helm
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repository: file://../medcat-service-helm
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version: 0.0.1
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- name: medcat-service-helm
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repository: file://../medcat-service-helm
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version: 0.0.1
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- name: medcat-trainer-helm
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repository: file://../medcat-trainer-helm
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version: 0.0.1
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digest: sha256:ed3f7c95117421145affc912bbec79151b7dd55062c7358b837074f0e0bf4641
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generated: "2026-02-26T12:55:11.318221565Z"

‎deployment/kubernetes/charts/cogstack-helm-ce/Chart.yaml‎

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apiVersion: v2
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name: cogstack-helm-ce
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description: CogStack Community Edition Helm Chart
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# A chart can be either an 'application' or a 'library' chart.
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#
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# Application charts are a collection of templates that can be packaged into versioned archives
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# to be deployed.
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#
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# Library charts provide useful utilities or functions for the chart developer. They're included as
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# a dependency of application charts to inject those utilities and functions into the rendering
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# pipeline. Library charts do not define any templates and therefore cannot be deployed.
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type: application
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# This is the chart version. This version number should be incremented each time you make changes
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# to the chart and its templates, including the app version.
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# Versions are expected to follow Semantic Versioning (https://semver.org/)
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version: 0.1.0
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# This is the version number of the application being deployed. This version number should be
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# incremented each time you make changes to the application. Versions are not expected to
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# follow Semantic Versioning. They should reflect the version the application is using.
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# It is recommended to use it with quotes.
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appVersion: "1.0.0"
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maintainers:
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- name: alhendrickson
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email: alistair@cogstack.org
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dependencies:
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- name: medcat-service-helm
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alias: medcat-service
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version: "0.0.1"
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repository: "file://../medcat-service-helm"
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- name: medcat-service-helm
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alias: anoncat-service
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version: "0.0.1"
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repository: "file://../medcat-service-helm"
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- name: medcat-trainer-helm
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version: "0.0.1"
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repository: "file://../medcat-trainer-helm"

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

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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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From the chart directory (or repo root), update dependencies and install:
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```bash
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cd deployment/kubernetes/charts/cogstack-helm-ce
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helm dependency update
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helm install cogstack-ce . --namespace cogstack --create-namespace
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```
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Or from the repo root:
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```bash
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helm dependency update deployment/kubernetes/charts/cogstack-helm-ce
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helm install cogstack-ce deployment/kubernetes/charts/cogstack-helm-ce --namespace cogstack --create-namespace
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```
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## Configuration
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Key values in `values.yaml`:
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| Value | Default | Description |
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|-------|---------|-------------|
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| `imagePullSecrets` | `[]` | Secrets for pulling images from a private registry. |
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| `nameOverride` | `""` | Override the chart name used in resource names. |
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| `fullnameOverride` | `""` | Override the full name used in resource names. |
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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.APP_ENABLE_DEMO_UI` | `true` | Enable AnonCAT demo UI. |
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| `anoncat-service.env.DEID_MODE` | `true` | Run AnonCAT in de-identification mode. |
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| `anoncat-service.env.DEID_REDACT` | `false` | Redaction behaviour for de-identification. |
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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-ce . -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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```

‎deployment/kubernetes/charts/cogstack-helm-ce/templates/NOTES.txt‎

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‎deployment/kubernetes/charts/cogstack-helm-ce/templates/_helpers.tpl‎

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{{/*
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Expand the name of the chart.
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*/}}
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{{- define "cogstack-helm-ce.name" -}}
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{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" }}
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{{- end }}
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{{/*
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Create a default fully qualified app name.
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We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
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If release name contains chart name it will be used as a full name.
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*/}}
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{{- define "cogstack-helm-ce.fullname" -}}
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{{- if .Values.fullnameOverride }}
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{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" }}
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{{- else }}
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{{- $name := default .Chart.Name .Values.nameOverride }}
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{{- if contains $name .Release.Name }}
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{{- .Release.Name | trunc 63 | trimSuffix "-" }}
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{{- else }}
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{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" }}
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{{- end }}
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{{- end }}
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{{- end }}
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{{/*
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Create chart name and version as used by the chart label.
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*/}}
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{{- define "cogstack-helm-ce.chart" -}}
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{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
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{{- end }}
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{{/*
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Common labels
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*/}}
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{{- define "cogstack-helm-ce.labels" -}}
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helm.sh/chart: {{ include "cogstack-helm-ce.chart" . }}
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{{ include "cogstack-helm-ce.selectorLabels" . }}
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{{- if .Chart.AppVersion }}
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app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
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{{- end }}
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app.kubernetes.io/managed-by: {{ .Release.Service }}
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{{- end }}
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{{/*
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Selector labels
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*/}}
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{{- define "cogstack-helm-ce.selectorLabels" -}}
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app.kubernetes.io/name: {{ include "cogstack-helm-ce.name" . }}
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app.kubernetes.io/instance: {{ .Release.Name }}
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{{- end }}
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{{/*
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Create the name of the service account to use
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*/}}
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{{- define "cogstack-helm-ce.serviceAccountName" -}}
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{{- if .Values.serviceAccount.create }}
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{{- default (include "cogstack-helm-ce.fullname" .) .Values.serviceAccount.name }}
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{{- else }}
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{{- default "default" .Values.serviceAccount.name }}
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{{- end }}
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{{- end }}

‎deployment/kubernetes/charts/cogstack-helm-ce/values.yaml‎

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# Default values for cogstack-helm-ce.
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# This is a YAML-formatted file.
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# Declare variables to be passed into your templates.
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# 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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imagePullSecrets: []
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# This is to override the chart name.
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nameOverride: ""
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fullnameOverride: ""
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anoncat-service:
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replicasCount: 1
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env:
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APP_MEDCAT_MODEL_PACK: "/cat/models/examples/example-deid-model-pack.zip"
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DEID_MODE: true
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DEID_REDACT: false
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image:
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repository: cogstacksystems/medcat-service
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tag: "1.2.0"
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medcat-service:
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replicasCount: 1
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image:
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repository: cogstacksystems/medcat-service
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tag: "1.2.0"

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