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ops: Create Helm Chart for Medcat Service (#14)
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‎.github/workflows/kubernetes-charts-build.yaml‎

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name: Kubernetes - Lint, Test, and Publish Helm Charts
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on: pull_request
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defaults:
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run:
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working-directory: ./deployment/kubernetes
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jobs:
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helm-lint-test:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- name: Set up Helm
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uses: azure/[email protected]
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with:
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version: v3.17.0
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- uses: actions/[email protected]
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with:
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python-version: '3.x'
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check-latest: true
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- name: Set up chart-testing
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uses: helm/[email protected]
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- name: Run chart-testing (list-changed)
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id: list-changed
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run: |
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changed=$(ct list-changed --target-branch ${{ github.event.repository.default_branch}})
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if [[ -n "$changed" ]]; then
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echo "changed=true" >> "$GITHUB_OUTPUT"
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fi
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- name: Run chart-testing (lint)
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if: steps.list-changed.outputs.changed == 'true'
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run: ct lint --target-branch ${{ github.event.repository.default_branch }}
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- name: Create kind cluster
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if: steps.list-changed.outputs.changed == 'true'
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uses: helm/[email protected]
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- name: Run chart-testing (install)
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if: steps.list-changed.outputs.changed == 'true'
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run: ct install --target-branch ${{ github.event.repository.default_branch }}
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helm-publish:
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runs-on: ubuntu-latest
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needs: helm-lint-test
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env:
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CHART_VERSION: 0.0.1
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steps:
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- name: Log in to Docker Hub
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uses: docker/login-action@v1
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with:
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username: ${{ secrets.DOCKERHUB_USERNAME }}
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password: ${{ secrets.DOCKERHUB_TOKEN }}
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- name: Set up Helm
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uses: azure/[email protected]
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with:
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version: v3.17.0
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- name: Checkout
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uses: actions/checkout@v5
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- name: Package Helm Charts
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run: helm package ./charts/medcat-service-helm --version $CHART_VERSION
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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 ${{ secrets.DOCKERHUB_TOKEN }}
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- name: Push Helm Chart to Docker Hub OCI
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run: |
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helm push ./medcat-service-helm-${CHART_VERSION}.tgz oci://registry-1.docker.io/cogstacksystems

‎README.md‎

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@@ -7,4 +7,5 @@ See the latest documentation on [Readthedocs](https://docs.cogstack.org/en/lates
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## Project contents
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- Source for the official cogstack documentation. This git repo stores the top level documetation that hosts on https://docs.cogstack.org
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- CogStack deployment instructions and examples
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- Helm Charts for deployments
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- CogStack platform tools eg Observability.

‎deployment/kubernetes/charts/.gitignore‎

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# Ignore packaged helm charts
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*.tgz

‎deployment/kubernetes/charts/medcat-service-helm/.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/medcat-service-helm/Chart.yaml‎

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apiVersion: v2
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name: medcat-service-helm
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description: A Helm chart to deploy CogStack medcat-service
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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: 0.0.1
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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: "latest"
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maintainers:
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- name: alhendrickson
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email: [email protected]
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icon: "https://avatars.githubusercontent.com/u/28688163"

‎deployment/kubernetes/charts/medcat-service-helm/README.md‎

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# MedCAT Service Helm Chart
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This Helm chart deploys the MedCAT service to a Kubernetes cluster.
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## Installation
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```sh
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helm install my-medcat-service oci://registry-1.docker.io/cogstacksystems/medcat-service-helm
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```
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## Configuration
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You should specify a model pack to be used by the service. By default it will use a small bundled model, which can be used for testing
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---
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### Option 1: Use the demo model pack
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There is a model pack already bundled into medcat service, and is the default in this chart.
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This pack is only really used for testing, and has just a few concepts built in.
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### Option 2: Download Model on Startup
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Enable MedCAT to download the model from a remote URL on container startup.
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Create a values file like `values-model-download.yaml` and update the env vars with:
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```yaml
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env:
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ENABLE_MODEL_DOWNLOAD: "true"
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MODEL_NAME: "medmen"
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MODEL_VOCAB_URL: "https://cogstack-medcat-example-models.s3.eu-west-2.amazonaws.com/medcat-example-models/vocab.dat"
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MODEL_CDB_URL: "https://cogstack-medcat-example-models.s3.eu-west-2.amazonaws.com/medcat-example-models/cdb-medmen-v1.dat"
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MODEL_META_URL: "https://cogstack-medcat-example-models.s3.eu-west-2.amazonaws.com/medcat-example-models/mc_status.zip"
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APP_MODEL_CDB_PATH: "/cat/models/medmen/cdb.dat"
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```
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Use this if you prefer dynamic loading of models at runtime.
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### Option 3: Get a model into a k8s volume, and mount it
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The service can use a model pack if you want to setup your own download flow. For example, setup an initContainer pattern that downloads to a volume, then mount the volume yourself.
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Use this env variable to point to the file:
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Create a values file like `values-model-pack.yaml` and update the env vars with:
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```yaml
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env:
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# This defines the Model Pack used by the medcat service
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APP_MEDCAT_MODEL_PACK: "/cat/models/examples/example-medcat-v1-model-pack.zip"
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```
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## Example
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```sh
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helm install my-medcat ./medcat-chart -f values-model-pack.yaml
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```
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or
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```sh
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helm install my-medcat ./medcat-chart -f values-model-download.yaml
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```

‎deployment/kubernetes/charts/medcat-service-helm/templates/NOTES.txt‎

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1. Get the application URL by running these commands:
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{{- if .Values.ingress.enabled }}
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{{- range $host := .Values.ingress.hosts }}
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{{- range .paths }}
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http{{ if $.Values.ingress.tls }}s{{ end }}://{{ $host.host }}{{ .path }}
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{{- end }}
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{{- end }}
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{{- else if contains "NodePort" .Values.service.type }}
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export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ include "medcat-service.fullname" . }})
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export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
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echo http://$NODE_IP:$NODE_PORT
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{{- else if contains "LoadBalancer" .Values.service.type }}
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NOTE: It may take a few minutes for the LoadBalancer IP to be available.
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You can watch its status by running 'kubectl get --namespace {{ .Release.Namespace }} svc -w {{ include "medcat-service.fullname" . }}'
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export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "medcat-service.fullname" . }} --template "{{"{{ range (index .status.loadBalancer.ingress 0) }}{{.}}{{ end }}"}}")
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echo http://$SERVICE_IP:{{ .Values.service.port }}
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{{- else if contains "ClusterIP" .Values.service.type }}
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export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app.kubernetes.io/name={{ include "medcat-service.name" . }},app.kubernetes.io/instance={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
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export CONTAINER_PORT=$(kubectl get pod --namespace {{ .Release.Namespace }} $POD_NAME -o jsonpath="{.spec.containers[0].ports[0].containerPort}")
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echo "Visit http://127.0.0.1:8080 to use your application"
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kubectl --namespace {{ .Release.Namespace }} port-forward $POD_NAME 8080:$CONTAINER_PORT --pod-running-timeout=5m0s
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{{- end }}

‎deployment/kubernetes/charts/medcat-service-helm/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 "medcat-service.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 "medcat-service.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 "medcat-service.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 "medcat-service.labels" -}}
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helm.sh/chart: {{ include "medcat-service.chart" . }}
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{{ include "medcat-service.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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app.kubernetes.io/part-of: cogstack
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{{- end }}
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{{/*
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Selector labels
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*/}}
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{{- define "medcat-service.selectorLabels" -}}
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app.kubernetes.io/name: {{ include "medcat-service.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 "medcat-service.serviceAccountName" -}}
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{{- if .Values.serviceAccount.create }}
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{{- default (include "medcat-service.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/medcat-service-helm/templates/deployment.yaml‎

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apiVersion: apps/v1
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kind: Deployment
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metadata:
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name: {{ include "medcat-service.fullname" . }}
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labels:
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{{- include "medcat-service.labels" . | nindent 4 }}
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spec:
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{{- if not .Values.autoscaling.enabled }}
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replicas: {{ .Values.replicaCount }}
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{{- end }}
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selector:
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matchLabels:
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{{- include "medcat-service.selectorLabels" . | nindent 6 }}
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template:
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metadata:
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{{- with .Values.podAnnotations }}
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annotations:
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{{- toYaml . | nindent 8 }}
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{{- end }}
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labels:
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{{- include "medcat-service.labels" . | nindent 8 }}
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{{- with .Values.podLabels }}
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{{- toYaml . | nindent 8 }}
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{{- end }}
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spec:
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{{- with .Values.imagePullSecrets }}
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imagePullSecrets:
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{{- toYaml . | nindent 8 }}
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{{- end }}
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serviceAccountName: {{ include "medcat-service.serviceAccountName" . }}
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{{- with .Values.podSecurityContext }}
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securityContext:
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{{- toYaml . | nindent 8 }}
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{{- end }}
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containers:
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- name: {{ .Chart.Name }}
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{{- with .Values.securityContext }}
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securityContext:
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{{- toYaml . | nindent 12 }}
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{{- end }}
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image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
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imagePullPolicy: {{ .Values.image.pullPolicy }}
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ports:
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- name: http
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containerPort: {{ .Values.service.port }}
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protocol: TCP
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env:
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{{- range $key, $value := .Values.envValueFrom }}
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- name: {{ $key | quote }}
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valueFrom:
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{{- tpl (toYaml $value) $ | nindent 10 }}
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{{- end }}
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{{- range $key, $value := .Values.env }}
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- name: "{{ tpl $key $ }}"
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value: "{{ tpl (print $value) $ }}"
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{{- end }}
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{{- with .Values.livenessProbe }}
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livenessProbe:
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{{- toYaml . | nindent 12 }}
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{{- end }}
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{{- with .Values.readinessProbe }}
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readinessProbe:
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{{- toYaml . | nindent 12 }}
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{{- end }}
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{{- with .Values.startupProbe }}
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startupProbe:
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{{- toYaml . | nindent 12 }}
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{{- end }}
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{{- with .Values.resources }}
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resources:
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{{- toYaml . | nindent 12 }}
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{{- end }}
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{{- with .Values.volumeMounts }}
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volumeMounts:
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{{- toYaml . | nindent 12 }}
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{{- end }}
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{{- with .Values.volumes }}
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volumes:
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{{- toYaml . | nindent 8 }}
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{{- end }}
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{{- with .Values.nodeSelector }}
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nodeSelector:
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{{- toYaml . | nindent 8 }}
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{{- end }}
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{{- with .Values.affinity }}
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affinity:
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{{- toYaml . | nindent 8 }}
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{{- end }}
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{{- with .Values.tolerations }}
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tolerations:
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{{- toYaml . | nindent 8 }}
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{{- end }}

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