Add basic api local k8s deployment

api/.env_template

@@ -5,5 +5,5 @@ MONGO_INITDB_ROOT_PASSWORD=should_match_connstring
 DB_NAME=bia_integrator
 # run: 'openssl rand -hex 32' to generate a secret key for testing
 JWT_SECRET_KEY="long_key"
-# token needs to end in ==
+# token needs to be b64 encoded
 USER_CREATE_SECRET_TOKEN="some_long_secret_token"

api/local/.env_template

@@ -0,0 +1,6 @@
+MONGO_ROOT_USER=root
+MONGO_ROOT_PASSWORD=example
+# run: 'openssl rand -hex 32' to generate a secret key for testing
+JWT_SECRET_KEY=5aaacd0471b95e32ecb75693f785225472b9f3e57b6ad480619c8449fb2fc885
+# token needs to be b64 encoded
+USER_CREATE_TOKEN=00123456789==

api/local/README.md

@@ -0,0 +1,14 @@
+```sh
+minikube start --memory=10000 --cpus=4 --extra-config=apiserver.service-node-port-range=1-65535
+
+
+# create RO classic token for minikube here https://github.com/settings/tokens
+kubectl create secret --namespace api docker-registry ghcr-creds \
+    --docker-server=https://ghcr.io \
+    --docker-username=GITHUB_USERNAME \
+    --docker-password=SEE_COMMENT \
+    --docker-email=GITHUB_EMAIL
+```
+
+* `cp .env_template .env`
+* helmsman --apply -f helmsman_local.yml -e .env

api/local/api/.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/

api/local/api/Chart.yaml

@@ -0,0 +1,24 @@
+apiVersion: v2
+name: api
+description: A Helm chart for Kubernetes
+
+# 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: 0.1.0
+
+# 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"

api/local/api/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 "api.fullname" . }})
+  export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
+  echo http://$NODE_IP:$NODE_PORT
+{{- else if contains "LoadBalancer" .Values.service.type }}
+     NOTE: It may take a few minutes for the LoadBalancer IP to be available.
+           You can watch the status of by running 'kubectl get --namespace {{ .Release.Namespace }} svc -w {{ include "api.fullname" . }}'
+  export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "api.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 "api.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
+{{- end }}

api/local/api/templates/_helpers.tpl

@@ -0,0 +1,62 @@
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "api.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 "api.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 "api.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Common labels
+*/}}
+{{- define "api.labels" -}}
+helm.sh/chart: {{ include "api.chart" . }}
+{{ include "api.selectorLabels" . }}
+{{- if .Chart.AppVersion }}
+app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
+{{- end }}
+app.kubernetes.io/managed-by: {{ .Release.Service }}
+{{- end }}
+
+{{/*
+Selector labels
+*/}}
+{{- define "api.selectorLabels" -}}
+app.kubernetes.io/name: {{ include "api.name" . }}
+app.kubernetes.io/instance: {{ .Release.Name }}
+{{- end }}
+
+{{/*
+Create the name of the service account to use
+*/}}
+{{- define "api.serviceAccountName" -}}
+{{- if .Values.serviceAccount.create }}
+{{- default (include "api.fullname" .) .Values.serviceAccount.name }}
+{{- else }}
+{{- default "default" .Values.serviceAccount.name }}
+{{- end }}
+{{- end }}

api/local/api/templates/deployment.yaml

@@ -0,0 +1,59 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ include "api.fullname" . }}
+spec:
+  selector:
+    matchLabels:
+      {{- include "api.selectorLabels" . | nindent 6 }}
+  template:
+    metadata:
+      labels:
+        {{- include "api.labels" . | nindent 8 }}
+    spec:
+      {{- with .Values.imagePullSecrets }}
+      imagePullSecrets:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      containers:
+        - name: {{ .Chart.Name }}
+          image: "ghcr.io/bioimage-archive/integrator-api:{{ .Values.image.tag }}"
+          imagePullPolicy: {{ .Values.image.pullPolicy }}
+          resources:
+            {{- toYaml .Values.resources | nindent 12 }}
+          ports:
+            - name: http
+              containerPort: 8080
+              protocol: TCP
+          livenessProbe:
+            httpGet:
+              path: /v1/search/studies?limit=1
+              port: http
+            initialDelaySeconds: 10
+            failureThreshold: 10
+            periodSeconds: 60
+          readinessProbe:
+            httpGet:
+              path: /v1/openapi.json
+              port: http
+            initialDelaySeconds: 10
+            failureThreshold: 10
+            periodSeconds: 60
+          env:
+            - name: DB_NAME
+              value: {{ .Values.api_env.dbName }}
+            - name: JWT_SECRET_KEY
+              valueFrom:
+                secretKeyRef:
+                  name: {{ include "api.fullname" . }}
+                  key: jwtSecretKey
+            - name: USER_CREATE_SECRET_TOKEN
+              valueFrom:
+                secretKeyRef:
+                  name: {{ include "api.fullname" . }}
+                  key: userCreateSecretToken
+            - name: MONGO_CONNSTRING
+              valueFrom:
+                secretKeyRef:
+                  name: {{ include "api.fullname" . }}
+                  key: mongoConnstring

api/local/api/templates/ingress.yaml

@@ -0,0 +1,61 @@
+{{- if .Values.ingress.enabled -}}
+{{- $fullName := include "api.fullname" . -}}
+{{- $svcPort := .Values.service.port -}}
+{{- if and .Values.ingress.className (not (semverCompare ">=1.18-0" .Capabilities.KubeVersion.GitVersion)) }}
+  {{- if not (hasKey .Values.ingress.annotations "kubernetes.io/ingress.class") }}
+  {{- $_ := set .Values.ingress.annotations "kubernetes.io/ingress.class" .Values.ingress.className}}
+  {{- end }}
+{{- end }}
+{{- if semverCompare ">=1.19-0" .Capabilities.KubeVersion.GitVersion -}}
+apiVersion: networking.k8s.io/v1
+{{- else if semverCompare ">=1.14-0" .Capabilities.KubeVersion.GitVersion -}}
+apiVersion: networking.k8s.io/v1beta1
+{{- else -}}
+apiVersion: extensions/v1beta1
+{{- end }}
+kind: Ingress
+metadata:
+  name: {{ $fullName }}
+  labels:
+    {{- include "api.labels" . | nindent 4 }}
+  {{- with .Values.ingress.annotations }}
+  annotations:
+    {{- toYaml . | nindent 4 }}
+  {{- end }}
+spec:
+  {{- if and .Values.ingress.className (semverCompare ">=1.18-0" .Capabilities.KubeVersion.GitVersion) }}
+  ingressClassName: {{ .Values.ingress.className }}
+  {{- end }}
+  {{- 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: {{ .path }}
+            {{- if and .pathType (semverCompare ">=1.18-0" $.Capabilities.KubeVersion.GitVersion) }}
+            pathType: {{ .pathType }}
+            {{- end }}
+            backend:
+              {{- if semverCompare ">=1.19-0" $.Capabilities.KubeVersion.GitVersion }}
+              service:
+                name: {{ $fullName }}
+                port:
+                  number: {{ $svcPort }}
+              {{- else }}
+              serviceName: {{ $fullName }}
+              servicePort: {{ $svcPort }}
+              {{- end }}
+          {{- end }}
+    {{- end }}
+{{- end }}

api/local/api/templates/secrets.yaml

@@ -0,0 +1,9 @@
+apiVersion: v1
+kind: Secret
+metadata:
+  name: {{ include "api.fullname" . }}
+type: Opaque
+stringData:
+  mongoConnstring: "mongodb://{{ .Values.api_env.mongoRootUser }}:{{ .Values.api_env.mongoRootPassword }}@{{ .Values.api_env.mongoHost }}:27017"
+  jwtSecretKey: {{ .Values.api_env.jwtSecretKey }}
+  userCreateSecretToken: {{ .Values.api_env.userCreateSecretToken }}

api/local/api/templates/service.yaml

@@ -0,0 +1,12 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ include "api.fullname" . }}
+  labels:
+spec:
+  type: {{ .Values.service.type }}
+  ports:
+    - port: {{ .Values.service.port }}
+      nodePort: {{ .Values.service.port }}
+  selector:
+    {{- include "api.selectorLabels" . | nindent 4 }}

api/local/api/templates/tests/test-connection.yaml

@@ -0,0 +1,15 @@
+apiVersion: v1
+kind: Pod
+metadata:
+  name: "{{ include "api.fullname" . }}-test-connection"
+  labels:
+    {{- include "api.labels" . | nindent 4 }}
+  annotations:
+    "helm.sh/hook": test
+spec:
+  containers:
+    - name: wget
+      image: busybox
+      command: ['wget']
+      args: ['{{ include "api.fullname" . }}:{{ .Values.service.port }}']
+  restartPolicy: Never

api/local/api/values.yaml

@@ -0,0 +1,36 @@
+replicaCount: 1
+
+imagePullSecrets:
+  - name: ghcr-creds
+
+image:
+  tag: "0.1"
+  pullPolicy: IfNotPresent
+
+service:
+  type: NodePort
+  port: 8080
+
+ingress:
+  # TODO
+  enabled: false
+  className: ""
+  annotations: {}
+  hosts:
+    - host: chart-example.local
+      paths:
+        - path: /
+          pathType: ImplementationSpecific
+
+resources: 
+  limits:
+    memory: "1G"
+    cpu: "1"
+
+api_env:
+  mongoRootUser: ""
+  mongoRootPassword: ""
+  mongoHost: ""
+  dbName: "bia-integrator"
+  jwtSecretKey: ""
+  userCreateSecretToken: ""