Add helm chart for taxonium backend (#615)

* update * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add ingress and svc * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update ingress.yaml * Update ingress.yaml --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
theosanderson · Oct 6, 2024 · e8bff46 · e8bff46
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diff --git a/helm_charts/taxonium-backend/Chart.yaml b/helm_charts/taxonium-backend/Chart.yaml
@@ -0,0 +1,4 @@
+apiVersion: v2
+name: taxonium-backend
+description: A Helm chart for the Taxonium backend
+version: 0.1.0
diff --git a/helm_charts/taxonium-backend/templates/deployment.yaml b/helm_charts/taxonium-backend/templates/deployment.yaml
@@ -0,0 +1,55 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ .Release.Name }}-taxonium-backend
+  labels:
+    app: {{ .Release.Name }}-taxonium-backend
+spec:
+  replicas: {{ .Values.replicaCount }}
+  selector:
+    matchLabels:
+      app: {{ .Release.Name }}-taxonium-backend
+  strategy:
+    type: RollingUpdate
+    rollingUpdate:
+      maxSurge: {{ .Values.maxSurge | default "25%" }}
+      maxUnavailable: {{ .Values.maxUnavailable | default "25%" }}
+  template:
+    metadata:
+      labels:
+        app: {{ .Release.Name }}-taxonium-backend
+      annotations:
+        kubectl.kubernetes.io/restartedAt: {{ now | date "2006-01-02T15:04:05Z" | quote }}
+    spec:
+      containers:
+      - name: taxonium-backend
+        image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
+        imagePullPolicy: {{ .Values.image.pullPolicy }}
+        env:
+        - name: DATA_URL
+          value: {{ .Values.dataUrl }}
+        - name: CONFIG_JSON
+          value: {{ .Values.configJson }}
+        - name: MAXMEM
+          value: {{ .Values.maxmem | quote }}
+        ports:
+        - containerPort: 80
+          protocol: TCP
+        livenessProbe:
+          httpGet:
+            path: /
+            port: 80
+          initialDelaySeconds: {{ .Values.livenessProbe.initialDelaySeconds }}
+          periodSeconds: {{ .Values.livenessProbe.periodSeconds }}
+          timeoutSeconds: {{ .Values.livenessProbe.timeoutSeconds }}
+          failureThreshold: {{ .Values.livenessProbe.failureThreshold }}
+        readinessProbe:
+          httpGet:
+            path: /
+            port: 80
+          initialDelaySeconds: {{ .Values.readinessProbe.initialDelaySeconds }}
+          periodSeconds: {{ .Values.readinessProbe.periodSeconds }}
+          timeoutSeconds: {{ .Values.readinessProbe.timeoutSeconds }}
+          failureThreshold: {{ .Values.readinessProbe.failureThreshold }}
+        resources:
+          {{- toYaml .Values.resources | nindent 12 }}
diff --git a/helm_charts/taxonium-backend/templates/ingress.yaml b/helm_charts/taxonium-backend/templates/ingress.yaml
@@ -0,0 +1,33 @@
+{{- if .Values.ingress.enabled -}}
+apiVersion: networking.k8s.io/v1
+kind: Ingress
+metadata:
+  name: {{ .Release.Name }}-taxonium-backend
+  labels:
+    app: {{ .Release.Name }}-taxonium-backend
+  {{- with .Values.ingress.annotations }}
+  annotations:
+    {{- toYaml . | nindent 4 }}
+  {{- end }}
+spec:
+  {{- if .Values.ingress.className }}
+  ingressClassName: {{ .Values.ingress.className }}
+  {{- end }}
+  rules:
+    - host: {{ .Values.hostname | quote }}
+      http:
+        paths:
+          - path: /
+            pathType: Prefix
+            backend:
+              service:
+                name: {{ .Release.Name }}-taxonium-backend
+                port:
+                  number: {{ .Values.service.port }}
+  {{- with .Values.ingress.tls }}
+  tls:
+    - hosts:
+        - {{ $.Values.hostname | quote }}
+      secretName: {{ .secretName }}
+  {{- end }}
+{{- end }}
diff --git a/helm_charts/taxonium-backend/templates/service.yaml b/helm_charts/taxonium-backend/templates/service.yaml
@@ -0,0 +1,14 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ .Release.Name }}-taxonium-backend
+  labels:
+    app: {{ .Release.Name }}-taxonium-backend
+spec:
+  type: {{ .Values.service.type }}
+  ports:
+    - port: {{ .Values.service.port }}
+      targetPort: 80
+      protocol: TCP
+  selector:
+    app: {{ .Release.Name }}-taxonium-backend
diff --git a/helm_charts/taxonium-backend/values.yaml b/helm_charts/taxonium-backend/values.yaml
@@ -0,0 +1,44 @@
+replicaCount: 1
+
+image:
+  repository: theosanderson/taxonium_backend
+  tag: master
+  pullPolicy: Always
+
+maxSurge: "25%"
+maxUnavailable: "25%"
+
+dataUrl: "https://cov2tree.nyc3.cdn.digitaloceanspaces.com/latest_public.jsonl.gz"
+configJson: "config_public.json"
+maxmem: "7000"
+
+livenessProbe:
+  initialDelaySeconds: 120
+  periodSeconds: 30
+  timeoutSeconds: 10
+  failureThreshold: 3
+
+readinessProbe:
+  initialDelaySeconds: 30
+  periodSeconds: 10
+  timeoutSeconds: 1
+  failureThreshold: 3
+
+resources:
+  requests:
+    cpu: "1"
+    memory: 6500Mi
+
+ingress:
+  enabled: true
+  className: ""
+  annotations:
+    {}
+    # kubernetes.io/ingress.class: nginx
+    # kubernetes.io/tls-acme: "true"
+  hosts:
+    - host: chart-example.local
+      paths:
+        - path: /
+          pathType: ImplementationSpecific
+  tls: []
diff --git a/taxonium_component/src/components/Key.jsx b/taxonium_component/src/components/Key.jsx
@@ -149,7 +149,7 @@ const Key = ({
       </h3>
 
       {!collapsed &&
-        ((colorRamps && colorByField in colorRamps) ? (
+        (colorRamps && colorByField in colorRamps ? (
           <ColorRamp ramp={colorRamps[colorByField]} />
         ) : (
           <KeyContent