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@@ -21,5 +21,5 @@ EventWriters: | |
| - log | ||
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| Server: | ||
| HostName: < funnel service clusterIP > | ||
| HostName: "${HOSTNAME}" | ||
| RPCPort: 9090 | ||
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| # 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/ |
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| apiVersion: v2 | ||
| name: funnel | ||
| description: A Helm chart for Kubernetes | ||
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| # 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 | ||
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| # 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: 0.1.0 | ||
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| # 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: "1.16.0" |
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| 1. To access the Funnel application, use the following instructions: | ||
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| To access the service locally, use: | ||
| kubectl --namespace {{ .Release.Namespace }} port-forward svc/{{ include "funnel.fullname" . }} 8080:8000 | ||
| echo "Visit http://127.0.0.1:8080" |
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| {{/* | ||
| Expand the name of the chart. | ||
| */}} | ||
| {{- define "funnel.name" -}} | ||
| {{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" }} | ||
| {{- end }} | ||
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| {{/* | ||
| 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 "funnel.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 }} | ||
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| {{/* | ||
| Create chart name and version as used by the chart label. | ||
| */}} | ||
| {{- define "funnel.chart" -}} | ||
| {{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }} | ||
| {{- end }} | ||
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||
| {{/* | ||
| Common labels | ||
| */}} | ||
| {{- define "funnel.labels" -}} | ||
| helm.sh/chart: {{ include "funnel.chart" . }} | ||
| {{ include "funnel.selectorLabels" . }} | ||
| {{- if .Chart.AppVersion }} | ||
| app.kubernetes.io/version: {{ .Chart.AppVersion | quote }} | ||
| {{- end }} | ||
| app.kubernetes.io/managed-by: {{ .Release.Service }} | ||
| {{- end }} | ||
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||
| {{/* | ||
| Selector labels | ||
| */}} | ||
| {{- define "funnel.selectorLabels" -}} | ||
| app.kubernetes.io/name: {{ include "funnel.name" . }} | ||
| app.kubernetes.io/instance: funnel | ||
| {{- end }} | ||
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| {{/* | ||
| Create the name of the service account to use | ||
| */}} | ||
| {{- define "funnel.serviceAccountName" -}} | ||
| {{- if .Values.serviceAccount.create }} | ||
| {{- default (include "funnel.fullname" .) .Values.serviceAccount.name }} | ||
| {{- else }} | ||
| {{- default "default" .Values.serviceAccount.name }} | ||
| {{- end }} | ||
| {{- end }} |
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| apiVersion: v1 | ||
| kind: ConfigMap | ||
| metadata: | ||
| name: funnel-config | ||
| data: | ||
| funnel-server-config.yaml: |- | ||
| Database: boltdb | ||
| Compute: kubernetes | ||
| Logger: | ||
| Level: debug | ||
| Kubernetes: | ||
| # The executor used to execute tasks. Available executors: docker, kubernetes | ||
| Executor: "kubernetes" | ||
| DisableJobCleanup: false | ||
| DisableReconciler: false | ||
| ReconcileRate: 5m | ||
| Namespace: default | ||
| Template: | | ||
| apiVersion: batch/v1 | ||
| kind: Job | ||
| metadata: | ||
| ## DO NOT CHANGE NAME | ||
| name: {{.TaskId}} | ||
| namespace: {{.Namespace}} | ||
| spec: | ||
| backoffLimit: 0 | ||
| completions: 1 | ||
| template: | ||
| spec: | ||
| restartPolicy: Never | ||
| serviceAccountName: funnel-sa | ||
| containers: | ||
| - name: {{printf "funnel-worker-%s" .TaskId}} | ||
| image: quay.io/ohsu-comp-bio/funnel:latest | ||
| imagePullPolicy: IfNotPresent | ||
| args: | ||
| - "worker" | ||
| - "run" | ||
| - "--config" | ||
| - "/etc/config/funnel-worker-config.yaml" | ||
| - "--taskID" | ||
| - {{.TaskId}} | ||
| resources: | ||
| requests: | ||
| cpu: {{if ne .Cpus 0 -}}{{.Cpus}}{{ else }}{{"100m"}}{{end}} | ||
| memory: {{if ne .RamGb 0.0 -}}{{printf "%.0fG" .RamGb}}{{else}}{{"16M"}}{{end}} | ||
| ephemeral-storage: {{if ne .DiskGb 0.0 -}}{{printf "%.0fG" .DiskGb}}{{else}}{{"100M"}}{{end}} | ||
| volumeMounts: | ||
| - name: {{printf "funnel-storage-%s" .TaskId}} | ||
| mountPath: {{printf "/opt/funnel/funnel-work-dir/%s" .TaskId}} | ||
| - name: config-volume | ||
| mountPath: /etc/config | ||
| securityContext: | ||
| privileged: true | ||
| volumes: | ||
| - name: {{printf "funnel-storage-%s" .TaskId}} | ||
| emptyDir: {} | ||
| - name: config-volume | ||
| configMap: | ||
| name: funnel-config | ||
| funnel-worker-config.yaml: |- | ||
| Database: boltdb | ||
| BoltDB: | ||
| Path: /opt/funnel/funnel-work-dir/funnel.bolt.db | ||
| Compute: kubernetes | ||
| Kubernetes: | ||
| Executor: "kubernetes" | ||
| Logger: | ||
| Level: debug | ||
| RPCClient: | ||
| MaxRetries: 3 | ||
| Timeout: 30s | ||
| EventWriters: | ||
| - rpc | ||
| - log | ||
| Server: | ||
| HostName: "" | ||
| RPCPort: 9090 |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,51 @@ | ||
| apiVersion: apps/v1 | ||
| kind: Deployment | ||
| metadata: | ||
| name: {{ include "funnel.fullname" . }} | ||
| labels: | ||
| {{- include "funnel.labels" . | nindent 4 }} | ||
| spec: | ||
| replicas: 1 | ||
| selector: | ||
| matchLabels: | ||
| {{- include "funnel.selectorLabels" . | nindent 6 }} | ||
| template: | ||
| metadata: | ||
| labels: | ||
| {{- include "funnel.labels" . | nindent 8 }} | ||
| spec: | ||
| serviceAccountName: {{ include "funnel.serviceAccountName" . }} | ||
| containers: | ||
| - name: funnel | ||
| image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}" | ||
| imagePullPolicy: Always | ||
| command: | ||
| - 'funnel' | ||
| - 'server' | ||
| - 'run' | ||
| - '--config' | ||
| - '/etc/config/funnel-server-config.yaml' | ||
| resources: | ||
| requests: | ||
| cpu: {{ .Values.resources.requests.cpu }} | ||
| memory: {{ .Values.resources.requests.memory }} | ||
| limits: | ||
| cpu: {{ .Values.resources.limits.cpu }} | ||
| memory: {{ .Values.resources.limits.memory }} | ||
| ports: | ||
| - name: http | ||
| containerPort: 8000 | ||
| - name: rpc | ||
| containerPort: 9090 | ||
| volumeMounts: | ||
| - name: funnel-deployment-storage | ||
| mountPath: /opt/funnel/funnel-work-dir | ||
| - name: config-volume | ||
| mountPath: /etc/config | ||
| volumes: | ||
| - name: funnel-deployment-storage | ||
| persistentVolumeClaim: | ||
| claimName: funnel-pvc | ||
| - name: config-volume | ||
| configMap: | ||
| name: funnel-config |
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| @@ -0,0 +1,16 @@ | ||
| {{- if .Values.rbac.create }} | ||
| apiVersion: rbac.authorization.k8s.io/v1 | ||
| kind: Role | ||
| metadata: | ||
| name: {{ include "funnel.fullname" . }}-role | ||
| rules: | ||
| - apiGroups: [""] | ||
| resources: ["pods", "pods/log"] | ||
| verbs: ["get", "list", "watch"] | ||
| - apiGroups: ["batch", "extensions"] | ||
| resources: ["jobs"] | ||
| verbs: ["get", "list", "watch", "create", "update", "patch", "delete"] | ||
| - apiGroups: ["extensions", "apps"] | ||
| resources: ["deployments"] | ||
| verbs: ["get", "list", "watch", "create", "update", "patch", "delete"] | ||
| {{- end }} |
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| {{- if .Values.rbac.create }} | ||
| apiVersion: rbac.authorization.k8s.io/v1 | ||
| kind: RoleBinding | ||
| metadata: | ||
| name: funnel-rolebinding | ||
| subjects: | ||
| - kind: ServiceAccount | ||
| name: funnel-sa | ||
| roleRef: | ||
| kind: Role | ||
| name: funnel-role | ||
| apiGroup: rbac.authorization.k8s.io | ||
| {{- end }} |
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