ops: Create Helm Chart for Medcat Service

.github/workflows/kubernetes-charts-build.yaml

@@ -0,0 +1,80 @@
+name: Kubernetes - Lint, Test, and Publish Helm Charts
+
+on: pull_request
+defaults:
+  run:
+    working-directory: ./deployment/kubernetes
+
+
+jobs:
+  helm-lint-test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up Helm
+        uses: azure/setup-helm@v4.2.0
+        with:
+          version: v3.17.0
+
+      - uses: actions/setup-python@v5.3.0
+        with:
+          python-version: '3.x'
+          check-latest: true
+
+      - name: Set up chart-testing
+        uses: helm/chart-testing-action@v2.7.0
+
+      - name: Run chart-testing (list-changed)
+        id: list-changed
+        run: |
+          changed=$(ct list-changed --target-branch ${{ github.event.repository.default_branch}})
+          if [[ -n "$changed" ]]; then
+            echo "changed=true" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: Run chart-testing (lint)
+        if: steps.list-changed.outputs.changed == 'true'
+        run: ct lint --target-branch ${{ github.event.repository.default_branch }}
+
+      - name: Create kind cluster
+        if: steps.list-changed.outputs.changed == 'true'
+        uses: helm/kind-action@v1.12.0
+
+      - name: Run chart-testing (install)
+        if: steps.list-changed.outputs.changed == 'true'
+        run: ct install --target-branch ${{ github.event.repository.default_branch }}
+
+  helm-publish:
+    runs-on: ubuntu-latest
+    needs: helm-lint-test
+    env:
+      CHART_VERSION: 0.0.1
+    steps:
+    - name: Log in to Docker Hub
+      uses: docker/login-action@v1
+      with:
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+    - name: Set up Helm
+      uses: azure/setup-helm@v4.2.0
+      with:
+        version: v3.17.0
+
+    - name: Checkout
+      uses: actions/checkout@v5
+
+    - name: Package Helm Charts
+      run: helm package ./charts/medcat-service-helm --version $CHART_VERSION
+
+    - name: Helm OCI login to Docker Hub
+      run: helm registry login registry-1.docker.io -u ${{ secrets.DOCKERHUB_USERNAME }} -p ${{ secrets.DOCKERHUB_TOKEN }}
+
+    - name: Push Helm Chart to Docker Hub OCI
+      run: |
+        helm push ./medcat-service-helm-${CHART_VERSION}.tgz oci://registry-1.docker.io/cogstacksystems

README.md

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

deployment/kubernetes/charts/.gitignore

@@ -0,0 +1,3 @@
+
+# Ignore packaged helm charts
+*.tgz

deployment/kubernetes/charts/medcat-service-helm/.helmignore

@@ -0,0 +1,23 @@
+# Patterns to ignore when building packages.
+# This supports shell glob matching, relative path matching, and
+# negation (prefixed with !). Only one pattern per line.
+.DS_Store
+# Common VCS dirs
+.git/
+.gitignore
+.bzr/
+.bzrignore
+.hg/
+.hgignore
+.svn/
+# Common backup files
+*.swp
+*.bak
+*.tmp
+*.orig
+*~
+# Various IDEs
+.project
+.idea/
+*.tmproj
+.vscode/

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

@@ -0,0 +1,30 @@
+apiVersion: v2
+name: medcat-service-helm
+description: A Helm chart to deploy CogStack medcat-service
+
+# A chart can be either an 'application' or a 'library' chart.
+#
+# Application charts are a collection of templates that can be packaged into versioned archives
+# to be deployed.
+#
+# Library charts provide useful utilities or functions for the chart developer. They're included as
+# a dependency of application charts to inject those utilities and functions into the rendering
+# pipeline. Library charts do not define any templates and therefore cannot be deployed.
+type: application
+
+# This is the chart version. This version number should be incremented each time you make changes
+# to the chart and its templates, including the app version.
+# Versions are expected to follow Semantic Versioning (https://semver.org/)
+version: 0.0.1
+
+# This is the version number of the application being deployed. This version number should be
+# incremented each time you make changes to the application. Versions are not expected to
+# follow Semantic Versioning. They should reflect the version the application is using.
+# It is recommended to use it with quotes.
+appVersion: "latest"
+
+maintainers:
+  - name: alhendrickson
+    email: alistair@cogstack.org
+
+icon: "https://avatars.githubusercontent.com/u/28688163"

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

@@ -0,0 +1,62 @@
+# MedCAT Service Helm Chart
+
+This Helm chart deploys the MedCAT service to a Kubernetes cluster.
+
+## Installation
+
+```sh
+helm install my-medcat-service oci://registry-1.docker.io/cogstacksystems/medcat-service-helm
+```
+
+## Configuration
+
+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
+
+---
+### Option 1: Use the demo model pack
+
+There is a model pack already bundled into medcat service, and is the default in this chart.
+
+This pack is only really used for testing, and has just a few concepts built in. 
+
+###  Option 2: Download Model on Startup
+
+Enable MedCAT to download the model from a remote URL on container startup.
+
+Create a values file like `values-model-download.yaml` and update the env vars with: 
+```yaml
+env:
+  ENABLE_MODEL_DOWNLOAD: "true"
+  MODEL_NAME: "medmen"
+  MODEL_VOCAB_URL: "https://cogstack-medcat-example-models.s3.eu-west-2.amazonaws.com/medcat-example-models/vocab.dat"
+  MODEL_CDB_URL: "https://cogstack-medcat-example-models.s3.eu-west-2.amazonaws.com/medcat-example-models/cdb-medmen-v1.dat"
+  MODEL_META_URL: "https://cogstack-medcat-example-models.s3.eu-west-2.amazonaws.com/medcat-example-models/mc_status.zip"
+  APP_MODEL_CDB_PATH: "/cat/models/medmen/cdb.dat"
+```
+
+Use this if you prefer dynamic loading of models at runtime.
+
+### Option 3: Get a model into a k8s volume, and mount it
+
+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.
+
+Use this env variable to point to the file:
+
+Create a values file like `values-model-pack.yaml` and update the env vars with: 
+```yaml
+env:
+  # This defines the Model Pack used by the medcat service
+  APP_MEDCAT_MODEL_PACK: "/cat/models/examples/example-medcat-v1-model-pack.zip"
+```
+
+## Example
+
+```sh
+helm install my-medcat ./medcat-chart -f values-model-pack.yaml
+```
+
+or
+
+```sh
+helm install my-medcat ./medcat-chart -f values-model-download.yaml
+```

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

@@ -0,0 +1,22 @@
+1. Get the application URL by running these commands:
+{{- if .Values.ingress.enabled }}
+{{- range $host := .Values.ingress.hosts }}
+  {{- range .paths }}
+  http{{ if $.Values.ingress.tls }}s{{ end }}://{{ $host.host }}{{ .path }}
+  {{- end }}
+{{- end }}
+{{- else if contains "NodePort" .Values.service.type }}
+  export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ include "medcat-service.fullname" . }})
+  export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
+  echo http://$NODE_IP:$NODE_PORT
+{{- else if contains "LoadBalancer" .Values.service.type }}
+     NOTE: It may take a few minutes for the LoadBalancer IP to be available.
+           You can watch its status by running 'kubectl get --namespace {{ .Release.Namespace }} svc -w {{ include "medcat-service.fullname" . }}'
+  export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "medcat-service.fullname" . }} --template "{{"{{ range (index .status.loadBalancer.ingress 0) }}{{.}}{{ end }}"}}")
+  echo http://$SERVICE_IP:{{ .Values.service.port }}
+{{- else if contains "ClusterIP" .Values.service.type }}
+  export POD_NAME=$(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}")
+  export CONTAINER_PORT=$(kubectl get pod --namespace {{ .Release.Namespace }} $POD_NAME -o jsonpath="{.spec.containers[0].ports[0].containerPort}")
+  echo "Visit http://127.0.0.1:8080 to use your application"
+  kubectl --namespace {{ .Release.Namespace }} port-forward $POD_NAME 8080:$CONTAINER_PORT --pod-running-timeout=5m0s
+{{- end }}

deployment/kubernetes/charts/medcat-service-helm/templates/_helpers.tpl

@@ -0,0 +1,63 @@
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "medcat-service.name" -}}
+{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Create a default fully qualified app name.
+We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
+If release name contains chart name it will be used as a full name.
+*/}}
+{{- define "medcat-service.fullname" -}}
+{{- if .Values.fullnameOverride }}
+{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" }}
+{{- else }}
+{{- $name := default .Chart.Name .Values.nameOverride }}
+{{- if contains $name .Release.Name }}
+{{- .Release.Name | trunc 63 | trimSuffix "-" }}
+{{- else }}
+{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" }}
+{{- end }}
+{{- end }}
+{{- end }}
+
+{{/*
+Create chart name and version as used by the chart label.
+*/}}
+{{- define "medcat-service.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Common labels
+*/}}
+{{- define "medcat-service.labels" -}}
+helm.sh/chart: {{ include "medcat-service.chart" . }}
+{{ include "medcat-service.selectorLabels" . }}
+{{- if .Chart.AppVersion }}
+app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
+{{- end }}
+app.kubernetes.io/managed-by: {{ .Release.Service }}
+app.kubernetes.io/part-of: cogstack
+{{- end }}
+
+{{/*
+Selector labels
+*/}}
+{{- define "medcat-service.selectorLabels" -}}
+app.kubernetes.io/name: {{ include "medcat-service.name" . }}
+app.kubernetes.io/instance: {{ .Release.Name }}
+{{- end }}
+
+{{/*
+Create the name of the service account to use
+*/}}
+{{- define "medcat-service.serviceAccountName" -}}
+{{- if .Values.serviceAccount.create }}
+{{- default (include "medcat-service.fullname" .) .Values.serviceAccount.name }}
+{{- else }}
+{{- default "default" .Values.serviceAccount.name }}
+{{- end }}
+{{- end }}

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

@@ -0,0 +1,92 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ include "medcat-service.fullname" . }}
+  labels:
+    {{- include "medcat-service.labels" . | nindent 4 }}
+spec:
+  {{- if not .Values.autoscaling.enabled }}
+  replicas: {{ .Values.replicaCount }}
+  {{- end }}
+  selector:
+    matchLabels:
+      {{- include "medcat-service.selectorLabels" . | nindent 6 }}
+  template:
+    metadata:
+      {{- with .Values.podAnnotations }}
+      annotations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      labels:
+        {{- include "medcat-service.labels" . | nindent 8 }}
+        {{- with .Values.podLabels }}
+        {{- toYaml . | nindent 8 }}
+        {{- end }}
+    spec:
+      {{- with .Values.imagePullSecrets }}
+      imagePullSecrets:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      serviceAccountName: {{ include "medcat-service.serviceAccountName" . }}
+      {{- with .Values.podSecurityContext }}
+      securityContext:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      containers:
+        - name: {{ .Chart.Name }}
+          {{- with .Values.securityContext }}
+          securityContext:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
+          imagePullPolicy: {{ .Values.image.pullPolicy }}
+          ports:
+            - name: http
+              containerPort: {{ .Values.service.port }}
+              protocol: TCP
+          env:
+          {{- range $key, $value := .Values.envValueFrom }}
+          - name: {{ $key | quote }}
+            valueFrom:
+              {{- tpl (toYaml $value) $ | nindent 10 }}
+          {{- end }}
+          {{- range $key, $value := .Values.env }}
+          - name: "{{ tpl $key $ }}"
+            value: "{{ tpl (print $value) $ }}"
+          {{- end }}
+          {{- with .Values.livenessProbe }}
+          livenessProbe:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          {{- with .Values.readinessProbe }}
+          readinessProbe:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          {{- with .Values.startupProbe }}
+          startupProbe:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          {{- with .Values.resources }}
+          resources:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          {{- with .Values.volumeMounts }}
+          volumeMounts:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+      {{- with .Values.volumes }}
+      volumes:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.nodeSelector }}
+      nodeSelector:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.affinity }}
+      affinity:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.tolerations }}
+      tolerations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}