Merge pull request #7 from chgl/updated-ohdsi

Updated ohdsi
chgl · Dec 19, 2020 · ca38fa1 · ca38fa1
2 parents 6d847cc + b497dea
commit ca38fa1
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diff --git a/README.md b/README.md
@@ -9,13 +9,20 @@ helm repo update
 
 ## Development
 
-1. Install the [pre-commit](https://pre-commit.com/) hooks
+1. (Optional) Install the [pre-commit](https://pre-commit.com/) hooks
 
    ```sh
    pip install pre-commit
    pre-commit install
    ```
 
+1. (Optional) Setup a KinD cluster with Nginx ingress support
+
+   ```sh
+   kind create cluster --config=hack/kind-config.yaml
+   kubectl apply -f https://raw.githubusercontent.com/kubernetes/ingress-nginx/master/deploy/static/provider/kind/deploy.yaml
+   ```
+
 1. Make changes to the charts
 
 1. Mount the folder in the [kube-powertools](https://github.com/chgl/kube-powertools) container to easily run linters and checks

diff --git a/charts/ohdsi/Chart.yaml b/charts/ohdsi/Chart.yaml
@@ -2,7 +2,7 @@ apiVersion: v2
 name: ohdsi
 description: A Helm chart for deploying OHDSI ATLAS and the WebAPI
 type: application
-version: 0.1.4
+version: 0.1.5
 home: https://github.com/OHDSI
 keywords:
   - ohdsi

diff --git a/charts/ohdsi/README.md b/charts/ohdsi/README.md
diff --git a/charts/ohdsi/templates/NOTES.txt b/charts/ohdsi/templates/NOTES.txt
@@ -1,21 +1,21 @@
-{{- if .Values.webapi.enabled }}
+{{- if .Values.webApi.enabled }}
 - Get the application URL for the WebAPI running these commands:
-{{- if .Values.webapi.ingress.enabled }}
-{{- range $host := .Values.webapi.ingress.hosts }}
+{{- if .Values.webApi.ingress.enabled }}
+{{- range $host := .Values.webApi.ingress.hosts }}
   {{- range .paths }}
-  http{{ if $.Values.webapi.ingress.tls }}s{{ end }}://{{ $host.host }}{{ . }}
+  http{{ if $.Values.webApi.ingress.tls }}s{{ end }}://{{ $host.host }}{{ . }}
   {{- end }}
 {{- end }}
-{{- else if contains "NodePort" .Values.webapi.service.type }}
+{{- else if contains "NodePort" .Values.webApi.service.type }}
   export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ include "ohdsi.fullname" . }})
   export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
   echo http://$NODE_IP:$NODE_PORT
-{{- else if contains "LoadBalancer" .Values.webapi.service.type }}
+{{- else if contains "LoadBalancer" .Values.webApi.service.type }}
      NOTE: It may take a few minutes for the LoadBalancer IP to be available.
            You can watch the status of by running 'kubectl get --namespace {{ .Release.Namespace }} svc -w {{ include "ohdsi.fullname" . }}'
   export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "ohdsi.fullname" . }} --template "{{"{{ range (index .status.loadBalancer.ingress 0) }}{{.}}{{ end }}"}}")
-  echo http://$SERVICE_IP:{{ .Values.webapi.service.port }}
-{{- else if contains "ClusterIP" .Values.webapi.service.type }}
+  echo http://$SERVICE_IP:{{ .Values.webApi.service.port }}
+{{- else if contains "ClusterIP" .Values.webApi.service.type }}
   export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app.kubernetes.io/name={{ include "ohdsi.name" . }}-webapi,app.kubernetes.io/instance={{ .Release.Name }}-webapi" -o jsonpath="{.items[0].metadata.name}")
   echo "Visit http://127.0.0.1:8080 to use your application"
   kubectl --namespace {{ .Release.Namespace }} port-forward $POD_NAME 8080:80

diff --git a/charts/ohdsi/templates/_helpers.tpl b/charts/ohdsi/templates/_helpers.tpl
@@ -52,8 +52,8 @@ Get the name of the secret containing the DB password
 {{- else -}}
 {{ printf "%s-%s" $fullname "postgresqlha-postgresql" }}
 {{- end -}}
-{{- else if .Values.webapi.db.existingSecret -}}
-{{ .Values.webapi.db.existingSecret | quote }}
+{{- else if .Values.webApi.db.existingSecret -}}
+{{ .Values.webApi.db.existingSecret | quote }}
 {{- else -}}
 {{ printf "%s-%s" $fullname "webapi-db-secret" }}
 {{- end -}}
@@ -68,6 +68,6 @@ Create the JDBC URL from the host, port and database name.
 {{- $pgpoolServiceName := ( printf "%s-%s" $fullname "postgresqlha-pgpool") -}}
 {{ printf "jdbc:postgresql://%s:%d/%s" $pgpoolServiceName 5432 .Values.global.postgresql.database }}
 {{- else -}}
-{{ printf "jdbc:postgresql://%s:%d/%s" .Values.webapi.db.host (int64 .Values.webapi.db.port) .Values.webapi.db.database }}
+{{ printf "jdbc:postgresql://%s:%d/%s" .Values.webApi.db.host (int64 .Values.webApi.db.port) .Values.webApi.db.database }}
 {{- end -}}
 {{- end -}}
diff --git a/charts/ohdsi/templates/atlas-deployment.yaml b/charts/ohdsi/templates/atlas-deployment.yaml
@@ -62,9 +62,14 @@ spec:
           resources:
             {{- toYaml .resources | nindent 12 }}
           env:
-            {{- if .ingress.enabled }}
+            {{- if .webApiUrl }}
             - name: WEBAPI_URL
-              value: http{{ if .ingress.tls }}s{{ end }}://{{ (index .ingress.hosts 0).host }}/atlas
+              value: {{ .webApiUrl }}
+            {{- else if $.Values.webApi.ingress.enabled }}
+            - name: WEBAPI_URL
+              {{- $host := (index $.Values.webApi.ingress.hosts 0) }}
+              {{- $path := index (index $.Values.webApi.ingress.hosts 0).paths 0 }}
+              value: http{{ if $.Values.webApi.ingress.tls }}s{{ end }}://{{ $host.host }}{{ $path }}
             {{- end }}
           {{- if .extraEnv }}
           {{- toYaml .extraEnv | nindent 12 }}

diff --git a/charts/ohdsi/templates/atlas-ingress.yaml b/charts/ohdsi/templates/atlas-ingress.yaml
@@ -1,26 +1,29 @@
-{{- if and .Values.atlas.ingress.enabled .Values.atlas.enabled -}}
-{{- $fullName := include "ohdsi.fullname" . -}}
-{{- $svcPort := .Values.service.port -}}
-{{- if semverCompare ">=1.14-0" .Capabilities.KubeVersion.GitVersion -}}
+{{- with .Values.atlas }}
+{{- if and .ingress.enabled .enabled -}}
+{{- $fullName := include "ohdsi.fullname" $ -}}
+{{- $svcPort := .service.port -}}
+{{- 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 -}}
+{{ else }}
 apiVersion: extensions/v1beta1
 {{- end }}
 kind: Ingress
 metadata:
-  name: {{ $fullName }}
+  name: {{ $fullName }}-atlas
   labels:
-    {{- include "ohdsi.labels" . | nindent 4 }}
+    {{- include "ohdsi.labels" $ | nindent 4 }}
     app.kubernetes.io/name: {{ include "ohdsi.name" $ }}-atlas
     app.kubernetes.io/instance: {{ $.Release.Name }}-atlas
-  {{- with .Values.ingress.annotations }}
+  {{- with .ingress.annotations }}
   annotations:
     {{- toYaml . | nindent 4 }}
   {{- end }}
 spec:
-  {{- if .Values.ingress.tls }}
+  {{- if .ingress.tls }}
   tls:
-    {{- range .Values.ingress.tls }}
+    {{- range .ingress.tls }}
     - hosts:
         {{- range .hosts }}
         - {{ . | quote }}
@@ -29,15 +32,27 @@ spec:
     {{- end }}
   {{- end }}
   rules:
-    {{- range .Values.ingress.hosts }}
+    {{- range .ingress.hosts }}
+    {{- $pathType := .pathType }}
     - host: {{ .host | quote }}
       http:
         paths:
           {{- range .paths }}
           - path: {{ . }}
+            {{- if semverCompare ">=1.19-0" $.Capabilities.KubeVersion.GitVersion }}
+            pathType: {{ $pathType | default "ImplementationSpecific" }}
+            {{- 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 }}
   {{- end }}
+{{- end }}
diff --git a/charts/ohdsi/templates/tests/test-connection.yaml b/charts/ohdsi/templates/tests/test-connection.yaml
@@ -13,7 +13,7 @@ spec:
       image: busybox:1
       imagePullPolicy: Always
       command: ['wget', '-O', '-']
-      args: ['{{ include "ohdsi.fullname" . }}-webapi:{{ .Values.webapi.service.port }}/atlas/']
+      args: ['{{ include "ohdsi.fullname" . }}-webapi:{{ .Values.webApi.service.port }}/atlas/']
       securityContext:
         readOnlyRootFilesystem: true
         runAsUser: 1111

diff --git a/charts/ohdsi/templates/webapi-db-secret.yaml b/charts/ohdsi/templates/webapi-db-secret.yaml
@@ -1,4 +1,4 @@
-{{- if .Values.webapi.enabled }}
+{{- if .Values.webApi.enabled }}
 {{- if not .Values.postgresqlha.enabled -}}
 apiVersion: v1
 kind: Secret
@@ -10,6 +10,6 @@ metadata:
     app.kubernetes.io/instance: {{ .Release.Name }}-webapi-db-secret
 type: Opaque
 data:
-  postgresql-password: {{ .Values.webapi.db.password | b64enc | quote }}
+  postgresql-password: {{ .Values.webApi.db.password | b64enc | quote }}
 {{- end -}}
 {{- end -}}
diff --git a/charts/ohdsi/templates/webapi-deployment.yaml b/charts/ohdsi/templates/webapi-deployment.yaml
@@ -1,4 +1,4 @@
-{{- with .Values.webapi }}
+{{- with .Values.webApi }}
 {{- if .enabled }}
 apiVersion: apps/v1
 kind: Deployment

diff --git a/charts/ohdsi/templates/webapi-ingress.yaml b/charts/ohdsi/templates/webapi-ingress.yaml
@@ -1,26 +1,29 @@
-{{- if and .Values.webapi.ingress.enabled .Values.webapi.enabled -}}
-{{- $fullName := include "ohdsi.fullname" . -}}
-{{- $svcPort := .Values.service.port -}}
-{{- if semverCompare ">=1.14-0" .Capabilities.KubeVersion.GitVersion -}}
+{{- with .Values.webApi }}
+{{- if and .ingress.enabled .enabled -}}
+{{- $fullName := include "ohdsi.fullname" $ -}}
+{{- $svcPort := .service.port -}}
+{{- 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 -}}
+{{ else }}
 apiVersion: extensions/v1beta1
 {{- end }}
 kind: Ingress
 metadata:
-  name: {{ $fullName }}
+  name: {{ $fullName }}-webapi
   labels:
-    {{- include "ohdsi.labels" . | nindent 4 }}
+    {{- include "ohdsi.labels" $ | nindent 4 }}
     app.kubernetes.io/name: {{ include "ohdsi.name" $ }}-webapi
     app.kubernetes.io/instance: {{ $.Release.Name }}-webapi
-  {{- with .Values.ingress.annotations }}
+  {{- with .ingress.annotations }}
   annotations:
     {{- toYaml . | nindent 4 }}
   {{- end }}
 spec:
-  {{- if .Values.ingress.tls }}
+  {{- if .ingress.tls }}
   tls:
-    {{- range .Values.ingress.tls }}
+    {{- range .ingress.tls }}
     - hosts:
         {{- range .hosts }}
         - {{ . | quote }}
@@ -29,15 +32,27 @@ spec:
     {{- end }}
   {{- end }}
   rules:
-    {{- range .Values.ingress.hosts }}
+    {{- range .ingress.hosts }}
+    {{- $pathType := .pathType }}
     - host: {{ .host | quote }}
       http:
         paths:
           {{- range .paths }}
           - path: {{ . }}
+            {{- if semverCompare ">=1.19-0" $.Capabilities.KubeVersion.GitVersion }}
+            pathType: {{ $pathType | default "ImplementationSpecific" }}
+            {{- 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 }}
   {{- end }}
+{{- end }}
diff --git a/charts/ohdsi/templates/webapi-service.yaml b/charts/ohdsi/templates/webapi-service.yaml
@@ -1,4 +1,4 @@
-{{- with .Values.webapi }}
+{{- with .Values.webApi }}
 {{- if .enabled }}
 apiVersion: v1
 kind: Service

diff --git a/charts/ohdsi/values.yaml b/charts/ohdsi/values.yaml
@@ -15,7 +15,7 @@ postgresqlha:
   postgresqlImage:
     tag: 13.1.0
 
-webapi:
+webApi:
   enabled: true
   replicaCount: 1
   image:
@@ -116,6 +116,11 @@ atlas:
     tag: 2.8.0-dev
     pullPolicy: Always
 
+  # the base URL of the OHDSI WebAPI, e.g. https://example.com/WebAPI
+  # if this value is not set but `webapi.ingress.enabled=true`, then this
+  # URL is constructed from `webapi.ingress`
+  webApiUrl: ""
+
   podAnnotations: {}
 
   podSecurityContext:

diff --git a/hack/kind-config.yaml b/hack/kind-config.yaml
@@ -0,0 +1,17 @@
+kind: Cluster
+apiVersion: kind.x-k8s.io/v1alpha4
+nodes:
+  - role: control-plane
+    kubeadmConfigPatches:
+      - |
+        kind: InitConfiguration
+        nodeRegistration:
+          kubeletExtraArgs:
+            node-labels: "ingress-ready=true"
+    extraPortMappings:
+      - containerPort: 80
+        hostPort: 80
+        protocol: TCP
+      - containerPort: 443
+        hostPort: 443
+        protocol: TCP