Feature/grip

etl.yaml

@@ -1,5 +1,5 @@
-kind: Pod 
-apiVersion: v1 
+kind: Pod
+apiVersion: v1
 metadata:
   name: etl
 
@@ -29,7 +29,8 @@ spec:
 
   containers:
     - name: container-configmap
-      image: quay.io/ohsu-comp-bio/aced-etl:latest
+      image: quay.io/ohsu-comp-bio/aced-etl:feature_grip
+      imagePullPolicy: Always
       volumeMounts:
         # Gen3 credentials file
         - name: gen3-credentials
@@ -56,7 +57,7 @@ spec:
       command: ["/bin/bash" ]
       args:
         - "-c"
-        - | 
+        - |
           # Until we fix in helm env, setup well known postgres env variables
           # TODO - set GLOBAL_HOSTNAME to value from values.yaml
           cat  << EOF >> ~/.bashrc
@@ -71,18 +72,18 @@ spec:
           # link back to mounted volumes
           ln -s /studies /data_model/studies
           ln -s /output /data_model/output
-          
+
           echo "Done setting up data_model"
 
           # link back to mounted volumes
           ln -s /studies /data_model/studies
           ln -s /output /data_model/output
-          
+
           echo "Done setting up data_model"
 
           # For development purposes, extends the lifespan of the pod to let us exec into it.
           while true; do sleep 30; done;
 
   # TODO - read nodegroup from values.yaml
-  nodeSelector:
-        eks.amazonaws.com/nodegroup: aced-commons-development-etl-node-group-large
+  #nodeSelector:
+  #      eks.amazonaws.com/nodegroup: aced-commons-development-etl-node-group-large

helm/fhir-server/.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/fhir-server/Chart.yaml

@@ -0,0 +1,24 @@
+apiVersion: v2
+name: fhir-server
+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"

helm/fhir-server/templates/NOTES.txt

@@ -0,0 +1 @@
+{{ .Chart.Name }} has been deployed successfully.

helm/fhir-server/templates/_helpers.tpl

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

helm/fhir-server/templates/deployment.yaml

@@ -0,0 +1,72 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ include "fhir-server.fullname" . }}
+  labels:
+    {{- include "fhir-server.labels" . | nindent 4 }}
+spec:
+  {{- if not .Values.autoscaling.enabled }}
+  replicas: {{ .Values.replicaCount }}
+  {{- end }}
+  selector:
+    matchLabels:
+      {{- include "fhir-server.selectorLabels" . | nindent 6 }}
+  template:
+    metadata:
+      {{- with .Values.podAnnotations }}
+      annotations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      labels:
+        {{- include "fhir-server.selectorLabels" . | nindent 8 }}
+    spec:
+      {{- with .Values.imagePullSecrets }}
+      imagePullSecrets:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      serviceAccountName: {{ include "fhir-server.serviceAccountName" . }}
+      securityContext:
+        {{- toYaml .Values.podSecurityContext | nindent 8 }}
+      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: /_status
+              port: http
+            initialDelaySeconds: 30
+            periodSeconds: 60
+            timeoutSeconds: 30
+          readinessProbe:
+            httpGet:
+              path: /_status
+              port: http
+            initialDelaySeconds: 30
+
+          resources:
+            {{- toYaml .Values.resources | nindent 12 }}
+          command:
+            - "/bin/sh"
+            - "-c"
+            - >
+              uvicorn bundle_service.main:app --host 0.0.0.0 --port 8000 --reload
+
+      {{- 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/fhir-server/templates/hpa.yaml

@@ -0,0 +1,32 @@
+{{- if .Values.autoscaling.enabled }}
+apiVersion: autoscaling/v2
+kind: HorizontalPodAutoscaler
+metadata:
+  name: {{ include "fhir-server.fullname" . }}
+  labels:
+    {{- include "fhir-server.labels" . | nindent 4 }}
+spec:
+  scaleTargetRef:
+    apiVersion: apps/v1
+    kind: Deployment
+    name: {{ include "fhir-server.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/fhir-server/templates/serviceaccount.yaml

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

helm/fhir-server/templates/tests/test-connection.yaml

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

helm/fhir-server/values.yaml

@@ -0,0 +1,66 @@
+# Default values for fhir-server.
+# This is a YAML-formatted file.
+# Declare variables to be passed into your templates.
+
+replicaCount: 1
+
+image:
+  repository: quay.io/ohsu-comp-bio/fhir_server
+  pullPolicy: Always
+  # Overrides the image tag whose default is the chart appVersion.
+  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: {}
+  # We usually recommend not to specify default resources and to leave this as a conscious
+  # choice for the user. This also increases chances charts run on environments with little
+  # resources, such as Minikube. If you do want to specify resources, uncomment the following
+  # lines, adjust them as necessary, and remove the curly braces after 'resources:'.
+  # limits:
+  #   cpu: 100m
+  #   memory: 128Mi
+  # requests:
+  #   cpu: 100m
+  #   memory: 128Mi
+
+autoscaling:
+  enabled: false
+  minReplicas: 1
+  maxReplicas: 100
+  targetCPUUtilizationPercentage: 80
+  # targetMemoryUtilizationPercentage: 80
+
+nodeSelector: {}
+
+tolerations: []
+
+affinity: {}