Include instance configurations in Helm values (#790)

* change how helm is configured * up * fix * fix * fix * f * f * f * up * u * up * Update lapis-ingress.yaml * fix lapis urls * up * add docs * add values file arg to deploy.py * fix * up
loculus-project · Jan 19, 2024 · 812c2f5 · 812c2f5
1 parent a7cf2b3
commit 812c2f5
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Showing 16 changed files with 174 additions and 157 deletions.
diff --git a/deploy.py b/deploy.py
@@ -11,6 +11,7 @@
 CLUSTER_NAME = 'testCluster'
 HELM_RELEASE_NAME = 'preview'
 HELM_CHART_DIR = ROOT_DIR / 'kubernetes' / 'loculus'
+HELM_VALUES_FILE = HELM_CHART_DIR / 'values.yaml'
 
 WEBSITE_PORT_MAPPING = '-p 3000:30081@agent:0'
 BACKEND_PORT_MAPPING = '-p 8079:30082@agent:0'
@@ -37,6 +38,8 @@
 helm_parser.add_argument('--uninstall', action='store_true', help='Uninstall installation')
 helm_parser.add_argument('--enablePreprocessing', action='store_true',
                          help='Include deployment of preprocessing pipelines')
+helm_parser.add_argument('--values', help='Values file for helm chart',
+                         default=HELM_VALUES_FILE)
 
 upgrade_parser = subparsers.add_parser('upgrade', help='Upgrade helm installation')
 
@@ -112,6 +115,7 @@ def handle_helm():
 
     parameters = [
         'helm', 'install', HELM_RELEASE_NAME, HELM_CHART_DIR,
+        '-f', args.values,
         '--set', "environment=local",
         '--set', f"branch={branch}",
         '--set', f"dockerconfigjson={docker_config_json}",
@@ -136,7 +140,11 @@ def get_docker_config_json():
 
 
 def handle_helm_upgrade():
-    subprocess.run(['helm', 'upgrade', HELM_RELEASE_NAME, HELM_CHART_DIR], check=True)
+    parameters = [
+        'helm', 'upgrade', HELM_RELEASE_NAME, HELM_CHART_DIR,
+        '-f', args.values
+    ]
+    subprocess.run(parameters, check=True)
 
 
 if __name__ == '__main__':

diff --git a/kubernetes/README.md b/kubernetes/README.md
@@ -5,6 +5,26 @@ The Helm variable `environment` reflects those purposes:
 * `local`: Running locally with ports
 * `server`: Running on a server with domain name
 
+## Deploying on a Kubernetes cluster
+
+### Prerequisites
+
+Install [helm](https://helm.sh/) and use [traefik](https://traefik.io/traefik/) for ingress.
+
+Create a long-lived managed database: [to be documented as part of: https://github.com/loculus-project/loculus/issues/793]
+
+Create your own configuration, by copying the `loculus/values.yaml` file and editing it as appropriate.
+
+### Deployment
+
+Install the Helm chart:
+
+```
+helm install loculus kubernetes/loculus -f my-values.yaml
+```
+
+# Local development/testing with k3d
+
 ## Prerequisites
 
 Install [k3d](https://k3d.io/v5.6.0/) and [helm](https://helm.sh/).
@@ -20,7 +40,7 @@ Install [k3d](https://k3d.io/v5.6.0/) and [helm](https://helm.sh/).
 
 Start the [backend](/backend/README.md) and the [website](/website/README.md) locally.
 
-### The `deploy.py` script
+#### The `deploy.py` script
 
 The `deploy.py` script wraps the most important `k3d` and `helm` commands.
 Check the help for more information:
@@ -75,6 +95,7 @@ You can also delete the cluster with:
 ../deploy.py cluster --delete
 ```
 
+With helm based commands you can customise the values yaml file with `--values [file.yaml]`.
 ## Argo CD
 
 ArgoCD will aim to build preview instances for any open PR with the `preview` label. It may take 5 minutes for an instance to appear. The preview will appear at `[branch_name].preview.k3s.loculus.org`. Very long branch names, and some special characters, are not supported.

diff --git a/kubernetes/loculus/config.yaml b/kubernetes/loculus/config.yaml
diff --git a/kubernetes/loculus/templates/_common-metadata.tpl b/kubernetes/loculus/templates/_common-metadata.tpl
@@ -28,7 +28,7 @@ fields:
 {{- define "loculus.generateWebsiteConfig" }}
 {{- $commonMetadata := (include "loculus.commonMetadata" . | fromYaml).fields }}
 instances:
-  {{- range $key, $instance := .instances }}
+  {{- range $key, $instance := $.Values.instances }}
   {{ $key }}:
     schema:
       {{- with $instance.schema }}
@@ -65,7 +65,7 @@ fields:
 {{/* Generate backend config from passed config object */}}
 {{- define "loculus.generateBackendConfig" }}
 instances:
-  {{- range $key, $instance := .instances }}
+  {{- range $key, $instance := $.Values.instances }}
   {{ $key }}:
     schema:
       {{- with $instance.schema }}

diff --git a/kubernetes/loculus/templates/_lapis-urls.tpl b/kubernetes/loculus/templates/_lapis-urls.tpl
@@ -1,6 +1,6 @@
 {{/* generates internal LAPIS urls from given config object */}}
 {{ define "loculus.generateInternalLapisUrls"}}
-{{ range $key, $_ := .instances }}
+{{ range $key, $_ := $.Values.instances }}
 "{{ $key -}}": "http://{{ template "loculus.lapisServiceName" $key }}:8080"
 {{ end }}
 {{ end }}

diff --git a/kubernetes/loculus/templates/ingressroute.yaml b/kubernetes/loculus/templates/ingressroute.yaml
@@ -1,6 +1,5 @@
 {{- if eq .Values.environment "server" }}
 {{- $backendHost := printf "backend.%s" .Values.host }}
-{{- $configFile := .Files.Get "config.yaml" | fromYaml }}
 {{- $keycloakHost := printf "authentication.%s" .Values.host }}
 
 apiVersion: traefik.containo.us/v1alpha1

diff --git a/kubernetes/loculus/templates/lapis-ingress.yaml b/kubernetes/loculus/templates/lapis-ingress.yaml
@@ -1,6 +1,5 @@
 {{- $lapisHost := printf "lapis.%s" .Values.host }}
-{{- $configFile := .Files.Get "config.yaml" | fromYaml }}
-{{- range $key, $_ := $configFile.instances }}
+{{- range $key, $_ := $.Values.instances }}
 
 ---
 apiVersion: traefik.containo.us/v1alpha1

diff --git a/kubernetes/loculus/templates/lapis-service.yaml b/kubernetes/loculus/templates/lapis-service.yaml
@@ -1,6 +1,4 @@
-{{- $configFile := .Files.Get "config.yaml" | fromYaml }}
-
-{{- range $key, $_ := $configFile.instances }}
+{{- range $key, $_ := $.Values.instances }}
 ---
 apiVersion: v1
 kind: Service

diff --git a/kubernetes/loculus/templates/lapis-silo-database-config.yaml b/kubernetes/loculus/templates/lapis-silo-database-config.yaml
@@ -1,8 +1,7 @@
-{{- $configFile := .Files.Get "config.yaml" | fromYaml }}
 {{- $commonMetadata := (include "loculus.commonMetadata" . | fromYaml).fields }}
 {{- $importScriptLines := .Files.Lines "silo_import_job.sh" }}
 
-{{- range $key, $instance := $configFile.instances }}
+{{- range $key, $instance := $.Values.instances }}
 ---
 apiVersion: v1
 kind: ConfigMap

diff --git a/kubernetes/loculus/templates/lapis-silo-deployment.yaml b/kubernetes/loculus/templates/lapis-silo-deployment.yaml
@@ -1,6 +1,4 @@
-{{- $configFile := .Files.Get "config.yaml" | fromYaml }}
-
-{{- range $key, $_ := $configFile.instances }}
+{{- range $key, $_ := $.Values.instances }}
 ---
 apiVersion: apps/v1
 kind: Deployment

diff --git a/kubernetes/loculus/templates/lapis-silo-import-cronjob.yaml b/kubernetes/loculus/templates/lapis-silo-import-cronjob.yaml
@@ -1,9 +1,7 @@
-{{- $configFile := .Files.Get "config.yaml" | fromYaml }}
-
 {{- $keycloakTokenUrl := "http://loculus-keycloak-service:8083/realms/loculusRealm/protocol/openid-connect/token" }}
 
 
-{{- range $key, $_ := $configFile.instances }}
+{{- range $key, $_ := $.Values.instances }}
 ---
 apiVersion: batch/v1
 kind: CronJob

diff --git a/kubernetes/loculus/templates/lapis-silo-shared-data.yaml b/kubernetes/loculus/templates/lapis-silo-shared-data.yaml
@@ -1,6 +1,4 @@
-{{- $configFile := .Files.Get "config.yaml" | fromYaml }}
-
-{{- range $key, $_ := $configFile.instances }}
+{{- range $key, $_ := $.Values.instances }}
 ---
 apiVersion: v1
 kind: PersistentVolumeClaim

diff --git a/kubernetes/loculus/templates/loculus-backend-config.yaml b/kubernetes/loculus/templates/loculus-backend-config.yaml
@@ -6,4 +6,4 @@ metadata:
   namespace: {{ .Values.namespace }}
 data:
   backend_config.json: |
-    {{ .Files.Get "config.yaml" | fromYaml | include "loculus.generateBackendConfig" | fromYaml | toJson }}
+    {{ include "loculus.generateBackendConfig" . | fromYaml | toJson }}
diff --git a/kubernetes/loculus/templates/loculus-preprocessing-deployment.yaml b/kubernetes/loculus/templates/loculus-preprocessing-deployment.yaml
@@ -1,5 +1,4 @@
 {{- $dockerTag := include "loculus.dockerTag" .Values }}
-{{ $configFile := .Files.Get "config.yaml" | fromYaml }}
 {{ $backendHost := .Values.disableBackend | ternary
     "http://host.k3d.internal:8079"
     "http://loculus-backend-service:8079"
@@ -28,7 +27,7 @@ spec:
         component: loculus-preprocessing
     spec:
       containers:
-        {{- range $key, $_ := $configFile.instances }}
+        {{- range $key, $_ := $.Values.instances }}
         - name: preprocessing-{{ $key }}
           image: ghcr.io/loculus-project/preprocessing-dummy:{{ $dockerTag }}
           imagePullPolicy: Always

diff --git a/kubernetes/loculus/templates/loculus-website-config.yaml b/kubernetes/loculus/templates/loculus-website-config.yaml
@@ -1,13 +1,12 @@
 {{- $keycloakHost := printf "authentication.%s" .Values.host }}
-{{- $config := .Files.Get "config.yaml" | fromYaml }}
 {{- $lapisHost := (
   eq .Values.environment "server" | ternary
     (printf "https://lapis.%s" .Values.host)
     "http://localhost:8080"
 ) }}
 {{- $externalLapisUrlConfig := dict
   "host" $lapisHost
-  "config" $config
+  "config" $.Values
 }}
 
 ---
@@ -18,7 +17,7 @@ metadata:
   namespace: {{ .Values.namespace }}
 data:
   website_config.json: |
-    {{ .Files.Get "config.yaml" | fromYaml | include "loculus.generateWebsiteConfig" | fromYaml | toJson }}
+    {{ include "loculus.generateWebsiteConfig" . | fromYaml | toJson }}
 
   runtime_config.json: |
     {
@@ -28,7 +27,7 @@ data:
             {{- else }}
             "backendUrl": "http://localhost:8079",
             {{- end }}
-            "lapisUrls": {{- include "loculus.generateInternalLapisUrls" $config | fromYaml | toJson }},
+            "lapisUrls": {{- include "loculus.generateInternalLapisUrls" . | fromYaml | toJson }},
             "keycloakUrl": "http://loculus-keycloak-service:8083"
         },
         "public": {

diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml