added initial helm charts

.gitignore

+*.tgz

cermine/.helmignore

+# 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
+*~
+# Various IDEs
+.project
+.idea/
+*.tmproj
+.vscode/

cermine/Chart.yaml

+apiVersion: v1
+appVersion: "1.0"
+description: A Helm chart for CERMINE
+name: cermine
+version: 0.1.0

cermine/templates/NOTES.txt

+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 }}://{{ $host.host }}{{ . }}
+  {{- end }}
+{{- end }}
+{{- else if contains "NodePort" .Values.service.type }}
+  export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ include "cermine-chart.fullname" . }})
+  export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
+  echo http://$NODE_IP:$NODE_PORT
+{{- else if contains "LoadBalancer" .Values.service.type }}
+     NOTE: It may take a few minutes for the LoadBalancer IP to be available.
+           You can watch the status of by running 'kubectl get --namespace {{ .Release.Namespace }} svc -w {{ include "cermine-chart.fullname" . }}'
+  export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "cermine-chart.fullname" . }} -o jsonpath='{.status.loadBalancer.ingress[0].ip}')
+  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 "cermine-chart.name" . }},app.kubernetes.io/instance={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
+  echo "Visit http://127.0.0.1:8072 to use your application"
+  kubectl port-forward $POD_NAME 8070:8072
+{{- end }}

cermine/templates/_helpers.tpl

+{{/* vim: set filetype=mustache: */}}
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "cermine-chart.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 "cermine-chart.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 "cermine-chart.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
+{{- end -}}

cermine/templates/deployment.yaml

+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ include "cermine-chart.fullname" . }}
+  labels:
+    app.kubernetes.io/name: {{ include "cermine-chart.name" . }}
+    helm.sh/chart: {{ include "cermine-chart.chart" . }}
+    app.kubernetes.io/instance: {{ .Release.Name }}
+    app.kubernetes.io/managed-by: {{ .Release.Service }}
+spec:
+  replicas: {{ .Values.replicaCount }}
+  selector:
+    matchLabels:
+      app.kubernetes.io/name: {{ include "cermine-chart.name" . }}
+      app.kubernetes.io/instance: {{ .Release.Name }}
+  template:
+    metadata:
+      labels:
+        app.kubernetes.io/name: {{ include "cermine-chart.name" . }}
+        app.kubernetes.io/instance: {{ .Release.Name }}
+    spec:
+      containers:
+        - name: {{ .Chart.Name }}
+          image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
+          imagePullPolicy: {{ .Values.image.pullPolicy }}
+          ports:
+            - name: http
+              containerPort: 8080
+              protocol: TCP
+          livenessProbe:
+            httpGet:
+              path: /
+              port: http
+            failureThreshold: {{ .Values.livenessProbe.failureThreshold }}
+          readinessProbe:
+            httpGet:
+              path: /
+              port: http
+            failureThreshold: {{ .Values.readinessProbe.failureThreshold }}
+          resources:
+            {{- toYaml .Values.resources | nindent 12 }}
+      {{- with .Values.nodeSelector }}
+      nodeSelector:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+    {{- with .Values.affinity }}
+      affinity:
+        {{- toYaml . | nindent 8 }}
+    {{- end }}
+    {{- with .Values.tolerations }}
+      tolerations:
+        {{- toYaml . | nindent 8 }}
+    {{- end }}

cermine/templates/hpa.yaml

+apiVersion: autoscaling/v2beta1
+kind: HorizontalPodAutoscaler
+metadata:
+  name: {{ include "cermine-chart.fullname" . }}
+  labels:
+    app.kubernetes.io/name: {{ include "cermine-chart.name" . }}
+    helm.sh/chart: {{ include "cermine-chart.chart" . }}
+    app.kubernetes.io/instance: {{ .Release.Name }}
+    app.kubernetes.io/managed-by: {{ .Release.Service }}
+spec:
+  scaleTargetRef:
+    apiVersion: apps/v1
+    kind: Deployment
+    name: {{ include "cermine-chart.fullname" . }}
+  minReplicas: {{ .Values.replicaCount }}
+  maxReplicas: {{ .Values.autoscaling.maxReplicas }}
+  metrics:
+  - type: Resource
+    resource:
+      name: cpu
+      targetAverageUtilization: {{ .Values.autoscaling.targetAverageCpuUtilization }}

cermine/templates/ingress.yaml

+{{- if .Values.ingress.enabled -}}
+{{- $fullName := include "cermine-chart.fullname" . -}}
+apiVersion: extensions/v1beta1
+kind: Ingress
+metadata:
+  name: {{ $fullName }}
+  labels:
+    app.kubernetes.io/name: {{ include "cermine-chart.name" . }}
+    helm.sh/chart: {{ include "cermine-chart.chart" . }}
+    app.kubernetes.io/instance: {{ .Release.Name }}
+    app.kubernetes.io/managed-by: {{ .Release.Service }}
+  {{- with .Values.ingress.annotations }}
+  annotations:
+    {{- toYaml . | nindent 4 }}
+  {{- end }}
+spec:
+{{- if .Values.ingress.tls }}
+  tls:
+  {{- range .Values.ingress.tls }}
+    - hosts:
+      {{- range .hosts }}
+        - {{ . | quote }}
+      {{- end }}
+      secretName: {{ .secretName }}
+  {{- end }}
+{{- end }}
+  rules:
+  {{- range .Values.ingress.hosts }}
+    - host: {{ .host | quote }}
+      http:
+        paths:
+        {{- range .paths }}
+          - path: {{ . }}
+            backend:
+              serviceName: {{ $fullName }}
+              servicePort: http
+        {{- end }}
+  {{- end }}
+{{- end }}

cermine/templates/service.yaml

+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ include "cermine-chart.fullname" . }}
+  labels:
+    app.kubernetes.io/name: {{ include "cermine-chart.name" . }}
+    helm.sh/chart: {{ include "cermine-chart.chart" . }}
+    app.kubernetes.io/instance: {{ .Release.Name }}
+    app.kubernetes.io/managed-by: {{ .Release.Service }}
+spec:
+  type: {{ .Values.service.type }}
+  ports:
+    - port: {{ .Values.service.port }}
+      targetPort: http
+      protocol: TCP
+      name: http
+  selector:
+    app.kubernetes.io/name: {{ include "cermine-chart.name" . }}
+    app.kubernetes.io/instance: {{ .Release.Name }}

cermine/templates/tests/test-connection.yaml

+apiVersion: v1
+kind: Pod
+metadata:
+  name: "{{ include "cermine-chart.fullname" . }}-test-connection"
+  labels:
+    app.kubernetes.io/name: {{ include "cermine-chart.name" . }}
+    helm.sh/chart: {{ include "cermine-chart.chart" . }}
+    app.kubernetes.io/instance: {{ .Release.Name }}
+    app.kubernetes.io/managed-by: {{ .Release.Service }}
+  annotations:
+    "helm.sh/hook": test-success
+spec:
+  containers:
+    - name: wget
+      image: busybox
+      command: ['wget']
+      args:  ['{{ include "cermine-chart.fullname" . }}:{{ .Values.service.port }}']
+  restartPolicy: Never

cermine/values.yaml

+# Default values for cermine-chart.
+# This is a YAML-formatted file.
+# Declare variables to be passed into your templates.
+
+replicaCount: 1
+
+image:
+  repository: elifesciences/cermine
+  tag: 1.13
+  pullPolicy: IfNotPresent
+
+nameOverride: ""
+fullnameOverride: ""
+
+livenessProbe:
+  failureThreshold: 120  # just under 60s startup time seems to be normal
+
+readinessProbe:
+  failureThreshold: 120  # just under 60s startup time seems to be normal
+
+service:
+  type: ClusterIP
+  port: 8072
+
+ingress:
+  enabled: false
+  annotations: {}
+    # kubernetes.io/ingress.class: nginx
+    # kubernetes.io/tls-acme: "true"
+  hosts:
+    - #host: chart-example.local
+      paths: []
+
+  tls: []
+  #  - secretName: chart-example-tls
+  #    hosts:
+  #      - chart-example.local
+
+resources:
+  limits:
+    cpu: 1
+    memory: 4Gi
+  requests:
+    cpu: 1
+    memory: 4Gi
+
+autoscaling:
+  maxReplicas: 16
+  targetAverageCpuUtilization: 80 # default of HPA
+
+nodeSelector: {}
+
+tolerations: []
+
+affinity: {}

grobid/.helmignore

+# 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
+*~
+# Various IDEs
+.project
+.idea/
+*.tmproj
+.vscode/

grobid/Chart.yaml

+apiVersion: v1
+appVersion: "1.0"
+description: A Helm chart for GROBID
+name: grobid
+version: 0.1.0

grobid/templates/NOTES.txt

+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 }}://{{ $host.host }}{{ . }}
+  {{- end }}
+{{- end }}
+{{- else if contains "NodePort" .Values.service.type }}
+  export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ include "grobid-chart.fullname" . }})
+  export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
+  echo http://$NODE_IP:$NODE_PORT
+{{- else if contains "LoadBalancer" .Values.service.type }}
+     NOTE: It may take a few minutes for the LoadBalancer IP to be available.
+           You can watch the status of by running 'kubectl get --namespace {{ .Release.Namespace }} svc -w {{ include "grobid-chart.fullname" . }}'
+  export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "grobid-chart.fullname" . }} -o jsonpath='{.status.loadBalancer.ingress[0].ip}')
+  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 "grobid-chart.name" . }},app.kubernetes.io/instance={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
+  echo "Visit http://127.0.0.1:8070 to use your application"
+  kubectl port-forward $POD_NAME 8070:8070
+{{- end }}

grobid/templates/_helpers.tpl

+{{/* vim: set filetype=mustache: */}}
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "grobid-chart.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 "grobid-chart.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 "grobid-chart.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
+{{- end -}}

grobid/templates/deployment.yaml

+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ include "grobid-chart.fullname" . }}
+  labels:
+    app.kubernetes.io/name: {{ include "grobid-chart.name" . }}
+    helm.sh/chart: {{ include "grobid-chart.chart" . }}
+    app.kubernetes.io/instance: {{ .Release.Name }}
+    app.kubernetes.io/managed-by: {{ .Release.Service }}
+spec:
+  replicas: {{ .Values.replicaCount }}
+  selector:
+    matchLabels:
+      app.kubernetes.io/name: {{ include "grobid-chart.name" . }}
+      app.kubernetes.io/instance: {{ .Release.Name }}
+  template:
+    metadata:
+      labels:
+        app.kubernetes.io/name: {{ include "grobid-chart.name" . }}
+        app.kubernetes.io/instance: {{ .Release.Name }}
+    spec:
+      {{- if not .Values.crossref.enabled }}
+      hostAliases:
+      - ip: "127.0.0.1"
+        hostnames:
+        - "api.crossref.org"
+      {{- end }}
+      containers:
+        - name: {{ .Chart.Name }}
+          image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
+          imagePullPolicy: {{ .Values.image.pullPolicy }}
+          env:
+          - name: JAVA_OPTS
+            value: "{{ .Values.maxJavaHeap }}"
+          ports:
+            - name: http
+              containerPort: 8070
+              protocol: TCP
+          livenessProbe:
+            httpGet:
+              path: /
+              port: http
+            #timeoutSeconds: 5
+            #failureThreshold: 3 # default
+          readinessProbe:
+            httpGet:
+              path: /
+              port: http
+          resources:
+            {{- toYaml .Values.resources | nindent 12 }}
+        {{- if .Values.warmup.enabled }}
+        - name: warmup
+          image: pstauffer/curl
+          command: ['/bin/sh']
+          args: ['-c', 'curl https://upload.wikimedia.org/wikipedia/commons/5/5b/I-20_Sample.pdf -o sample.pdf && sleep 168h']
+          readinessProbe:
+            exec:
+              command:
+                  - '/bin/sh'
+                  - '-c'
+                  - 'curl -v --form input=@sample.pdf --form consolidateHeader=0 --form consolidateCitations=0 -o /dev/null http://localhost:8070/api/processFulltextDocument'
+            periodSeconds: 60
+        {{- 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 }}

grobid/templates/hpa.yaml

+apiVersion: autoscaling/v2beta1
+kind: HorizontalPodAutoscaler
+metadata:
+  name: {{ include "grobid-chart.fullname" . }}
+  labels:
+    app.kubernetes.io/name: {{ include "grobid-chart.name" . }}
+    helm.sh/chart: {{ include "grobid-chart.chart" . }}
+    app.kubernetes.io/instance: {{ .Release.Name }}
+    app.kubernetes.io/managed-by: {{ .Release.Service }}
+spec:
+  scaleTargetRef:
+    apiVersion: apps/v1
+    kind: Deployment
+    name: {{ include "grobid-chart.fullname" . }}
+  minReplicas: {{ .Values.replicaCount }}
+  maxReplicas: {{ .Values.autoscaling.maxReplicas }}
+  metrics:
+  - type: Resource
+    resource:
+      name: cpu
+      targetAverageUtilization: {{ .Values.autoscaling.targetAverageCpuUtilization }}

grobid/templates/ingress.yaml

+{{- if .Values.ingress.enabled -}}
+{{- $fullName := include "grobid-chart.fullname" . -}}
+apiVersion: extensions/v1beta1
+kind: Ingress
+metadata:
+  name: {{ $fullName }}
+  labels:
+    app.kubernetes.io/name: {{ include "grobid-chart.name" . }}
+    helm.sh/chart: {{ include "grobid-chart.chart" . }}
+    app.kubernetes.io/instance: {{ .Release.Name }}
+    app.kubernetes.io/managed-by: {{ .Release.Service }}
+  {{- with .Values.ingress.annotations }}
+  annotations:
+    {{- toYaml . | nindent 4 }}
+  {{- end }}
+spec:
+{{- if .Values.ingress.tls }}
+  tls:
+  {{- range .Values.ingress.tls }}
+    - hosts:
+      {{- range .hosts }}
+        - {{ . | quote }}
+      {{- end }}
+      secretName: {{ .secretName }}
+  {{- end }}
+{{- end }}
+  rules:
+  {{- range .Values.ingress.hosts }}
+    - host: {{ .host | quote }}
+      http:
+        paths:
+        {{- range .paths }}
+          - path: {{ . }}
+            backend:
+              serviceName: {{ $fullName }}
+              servicePort: http
+        {{- end }}
+  {{- end }}
+{{- end }}

grobid/templates/poddisruptionbudget.yaml

+apiVersion: policy/v1beta1
+kind: PodDisruptionBudget
+metadata:
+  name: {{ include "grobid-chart.fullname" . }}
+  labels:
+    app.kubernetes.io/name: {{ include "grobid-chart.name" . }}
+    helm.sh/chart: {{ include "grobid-chart.chart" . }}
+    app.kubernetes.io/instance: {{ .Release.Name }}
+    app.kubernetes.io/managed-by: {{ .Release.Service }}
+spec:
+  selector:
+    matchLabels:
+      app.kubernetes.io/name: {{ include "grobid-chart.name" . }}
+      app.kubernetes.io/instance: {{ .Release.Name }}
+  minAvailable: "50%"

grobid/templates/service.yaml

+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ include "grobid-chart.fullname" . }}
+  labels:
+    app.kubernetes.io/name: {{ include "grobid-chart.name" . }}
+    helm.sh/chart: {{ include "grobid-chart.chart" . }}
+    app.kubernetes.io/instance: {{ .Release.Name }}
+    app.kubernetes.io/managed-by: {{ .Release.Service }}
+spec:
+  type: {{ .Values.service.type }}
+  ports:
+    - port: {{ .Values.service.port }}
+      targetPort: http
+      protocol: TCP
+      name: http
+  selector:
+    app.kubernetes.io/name: {{ include "grobid-chart.name" . }}
+    app.kubernetes.io/instance: {{ .Release.Name }}