Merge branch 'feature/image-viewer' into feature/fix-mongodb

helm/gen3/Chart.yaml

@@ -107,6 +107,10 @@ dependencies:
   version: 0.1.0
   repository: "file://../image-viewer"
   condition: image-viewer.enabled
+- name: viv
+  version: 0.1.0
+  repository: "file://../viv"
+  condition: viv.enabled
 
 # A chart can be either an 'application' or a 'library' chart.
 #

helm/image-viewer/templates/deployment.yaml

@@ -59,7 +59,7 @@ spec:
             - "/bin/sh"
             - "-c"
             - >
-              uvicorn image_viewer.app:app --host 0.0.0.0 --port 8000 --reload
+              uvicorn image_viewer.app:app --host 0.0.0.0 --port {{ .Values.service.port }} --reload
 
       {{- with .Values.nodeSelector }}
       nodeSelector:

helm/image-viewer/values.yaml

@@ -6,8 +6,10 @@ replicaCount: 1
 serviceName: image-viewer-service
 
 image:
-  repository: gen3-image-viewer
+  repository: quay.io/ohsu-comp-bio/gen3-image-viewer
   pullPolicy: Always
+  tag: "latest"
+
 
 imagePullSecrets: []
 nameOverride: ""
@@ -59,3 +61,7 @@ nodeSelector: {}
 tolerations: []
 
 affinity: {}
+
+env:
+  BASE_URL: "/aviator/?image_url="
+

helm/revproxy/gen3.nginx.conf/viv-service.conf

@@ -0,0 +1,9 @@
+location /aviator/ {
+    proxy_connect_timeout 600s;
+    proxy_send_timeout 600s;
+    proxy_read_timeout 600s;
+    send_timeout 600s;
+
+#   maintain the /aviator prefix in the proxied request
+    proxy_pass http://viv-service.$namespace.svc.cluster.local:8000;
+}

helm/viv/.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/

helm/viv/Chart.yaml

@@ -0,0 +1,24 @@
+apiVersion: v2
+name: viv
+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: "0.14.2"

helm/viv/README.md

@@ -0,0 +1,3 @@
+# To get viv to be discoverable to other microservices run the following command
+
+kc expose deployment local-viv 

helm/viv/templates/_helpers.tpl

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

helm/viv/templates/deployment.yaml

@@ -0,0 +1,72 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: viv-deployment
+  labels:
+    {{- include "viv.labels" . | nindent 4 }}
+spec:
+  {{- if not .Values.autoscaling.enabled }}
+  replicas: {{ .Values.replicaCount }}
+  {{- end }}
+  selector:
+    matchLabels:
+      {{- include "viv.selectorLabels" . | nindent 6 }}
+  template:
+    metadata:
+      {{- with .Values.podAnnotations }}
+      annotations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      labels:
+        {{- include "viv.selectorLabels" . | nindent 8 }}
+    spec:
+      {{- with .Values.imagePullSecrets }}
+      imagePullSecrets:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      serviceAccountName: {{ include "viv.serviceAccountName" . }}
+      securityContext:
+        {{- toYaml .Values.podSecurityContext | nindent 8 }}
+      volumes: []
+      containers:
+        - name: {{ .Chart.Name }}
+          securityContext:
+            {{- toYaml .Values.securityContext | nindent 12 }}
+          image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
+          imagePullPolicy: {{ .Values.image.pullPolicy }}
+          ports:
+            - name: http
+              containerPort: {{ .Values.service.port }}
+              protocol: TCP
+          livenessProbe:
+            httpGet:
+              path: /
+              port: 8000
+            initialDelaySeconds: 10
+            periodSeconds: 60
+            timeoutSeconds: 30
+          readinessProbe:
+            httpGet:
+              path: /
+              port: 8000
+            initialDelaySeconds: 10
+          resources:
+            {{- toYaml .Values.resources | nindent 12 }}
+          command:
+            - "/bin/sh"
+            - "-c"
+            - >
+              pnpm dev --host 0.0.0.0 --port {{ .Values.service.port }}  --base /aviator
+
+      {{- with .Values.nodeSelector }}
+      nodeSelector:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.affinity }}
+      affinity:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.tolerations }}
+      tolerations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}

helm/viv/templates/hpa.yaml

@@ -0,0 +1,32 @@
+{{- if .Values.autoscaling.enabled }}
+apiVersion: autoscaling/v2
+kind: HorizontalPodAutoscaler
+metadata:
+  name: {{ include "viv.fullname" . }}
+  labels:
+    {{- include "viv.labels" . | nindent 4 }}
+spec:
+  scaleTargetRef:
+    apiVersion: apps/v1
+    kind: Deployment
+    name: {{ include "viv.fullname" . }}
+  minReplicas: {{ .Values.autoscaling.minReplicas }}
+  maxReplicas: {{ .Values.autoscaling.maxReplicas }}
+  metrics:
+    {{- if .Values.autoscaling.targetCPUUtilizationPercentage }}
+    - type: Resource
+      resource:
+        name: cpu
+        target:
+          type: Utilization
+          averageUtilization: {{ .Values.autoscaling.targetCPUUtilizationPercentage }}
+    {{- end }}
+    {{- if .Values.autoscaling.targetMemoryUtilizationPercentage }}
+    - type: Resource
+      resource:
+        name: memory
+        target:
+          type: Utilization
+          averageUtilization: {{ .Values.autoscaling.targetMemoryUtilizationPercentage }}
+    {{- end }}
+{{- end }}

helm/viv/templates/service.yaml

@@ -0,0 +1,16 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ .Values.serviceName}}
+  labels:
+    {{- include "viv.labels" . | nindent 4 }}
+spec:
+  type: {{ .Values.service.type }}
+  ports:
+    - port: {{ .Values.service.port }}
+      targetPort: http
+      protocol: TCP
+      name: http
+  selector:
+    {{- include "viv.selectorLabels" . | nindent 4 }}
+

helm/viv/templates/serviceaccount.yaml

@@ -0,0 +1,12 @@
+{{- if .Values.serviceAccount.create -}}
+apiVersion: v1
+kind: ServiceAccount
+metadata:
+  name: {{ include "viv.serviceAccountName" . }}
+  labels:
+    {{- include "viv.labels" . | nindent 4 }}
+  {{- with .Values.serviceAccount.annotations }}
+  annotations:
+    {{- toYaml . | nindent 4 }}
+  {{- end }}
+{{- end }}

helm/viv/templates/tests/test-connection.yaml

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

helm/viv/templates/viv-values.yaml

@@ -0,0 +1,6 @@
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: viv-values
+data:
+  serviceName: {{ .Values.serviceName | quote }}

helm/viv/values.yaml

@@ -0,0 +1,62 @@
+# Default values for viv.
+# This is a YAML-formatted file.
+# Declare variables to be passed into your templates.
+
+replicaCount: 1
+serviceName: viv-service
+
+image:
+  repository: quay.io/ohsu-comp-bio/viv
+  pullPolicy: Always
+  tag: "latest"
+
+imagePullSecrets: []
+nameOverride: ""
+fullnameOverride: ""
+
+serviceAccount:
+  # Specifies whether a service account should be created
+  create: true
+  # Annotations to add to the service account
+  annotations: {}
+  # The name of the service account to use.
+  # If not set and create is true, a name is generated using the fullname template
+  name: ""
+
+podAnnotations: {}
+
+podSecurityContext: {}
+  # fsGroup: 2000
+
+securityContext: {}
+  # capabilities:
+  #   drop:
+  #   - ALL
+  # readOnlyRootFilesystem: true
+  # runAsNonRoot: true
+  # runAsUser: 1000
+
+service:
+  type: ClusterIP
+  port: 8000
+
+resources:
+  limits:
+    cpu: 2.0
+    memory: 2Gi
+  requests:
+    cpu: 0.2
+    memory: 256Mi
+
+autoscaling:
+  enabled: false
+  minReplicas: 1
+  maxReplicas: 100
+  targetCPUUtilizationPercentage: 80
+  # targetMemoryUtilizationPercentage: 80
+
+nodeSelector: {}
+
+tolerations: []
+
+affinity: {}