introduce concept of default organisms

loculus-project · Mar 1, 2024 · df8b146 · df8b146
1 parent 9174be7
commit df8b146
Show file tree

Hide file tree

Showing 12 changed files with 15 additions and 15 deletions.
diff --git a/kubernetes/loculus/templates/_common-metadata.tpl b/kubernetes/loculus/templates/_common-metadata.tpl
@@ -35,7 +35,7 @@ logo: {{ $.Values.logo | toYaml | nindent 6 }}
 accessionPrefix: {{ $.Values.accessionPrefix }}
 {{- $commonMetadata := (include "loculus.commonMetadata" . | fromYaml).fields }}
 organisms:
-  {{- range $key, $instance := $.Values.organisms }}
+  {{- range $key, $instance := default $.Values.defaultOrganisms $.Values.organisms }}
   {{ $key }}:
 
     schema:
@@ -81,7 +81,7 @@ fields:
 accessionPrefix: {{$.Values.accessionPrefix}}
 name: {{ $.Values.name }}
 organisms:
-  {{- range $key, $instance := $.Values.organisms }}
+  {{- range $key, $instance := default $.Values.defaultOrganisms $.Values.organisms }}
   {{ $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, $_ := $.Values.organisms }}
+  {{ range $key, $_ := default $.Values.defaultOrganisms $.Values.organisms }}
     "{{ $key }}": "{{ if not $.Values.disableWebsite }}http://{{ template "loculus.lapisServiceName" $key }}:8080{{ else -}}http://localhost:8080/{{ $key }}{{ end }}"
   {{ end }}
 {{ end }}

diff --git a/kubernetes/loculus/templates/lapis-ingress.yaml b/kubernetes/loculus/templates/lapis-ingress.yaml
@@ -5,13 +5,13 @@ kind: Ingress
 metadata:
   name: lapis-ingress
   annotations:
-    traefik.ingress.kubernetes.io/router.middlewares: "{{- $first := true }}{{- range $key, $_ := $.Values.organisms }}{{ if $first }}{{ $first = false }}{{ else }},{{ end }}{{ $.Release.Namespace }}-strip-{{ $key }}-prefix@kubernetescrd{{- end }}"
+    traefik.ingress.kubernetes.io/router.middlewares: "{{- $first := true }}{{- range $key, $_ := default $.Values.defaultOrganisms $.Values.organisms }}{{ if $first }}{{ $first = false }}{{ else }},{{ end }}{{ $.Release.Namespace }}-strip-{{ $key }}-prefix@kubernetescrd{{- end }}"
 spec:
   rules:
   - host: {{ if eq $.Values.environment "server" }}{{ $lapisHost }}{{ end }}
     http:
       paths:
-      {{- range $key, $_ := $.Values.organisms }}
+      {{- range $key, $_ := default $.Values.defaultOrganisms $.Values.organisms }}
       - path: /{{ $key }}/
         pathType: Prefix
         backend:
@@ -30,7 +30,7 @@ spec:
   {{- end }}
 
 
-{{- range $key, $_ := $.Values.organisms }}
+{{- range $key, $_ := default $.Values.defaultOrganisms $.Values.organisms }}
 ---
 apiVersion: traefik.containo.us/v1alpha1
 kind: Middleware

diff --git a/kubernetes/loculus/templates/lapis-service.yaml b/kubernetes/loculus/templates/lapis-service.yaml
@@ -1,4 +1,4 @@
-{{- range $key, $_ := $.Values.organisms }}
+{{- range $key, $_ := default $.Values.defaultOrganisms $.Values.organisms }}
 ---
 apiVersion: v1
 kind: Service

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

diff --git a/kubernetes/loculus/templates/lapis-silo-deployment.yaml b/kubernetes/loculus/templates/lapis-silo-deployment.yaml
@@ -1,5 +1,5 @@
 {{- $dockerTag := include "loculus.dockerTag" $.Values }}
-{{- range $key, $_ := $.Values.organisms }}
+{{- range $key, $_ := default $.Values.defaultOrganisms $.Values.organisms }}
 ---
 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
@@ -2,7 +2,7 @@
 {{- $keycloakTokenUrl := "http://loculus-keycloak-service:8083/realms/loculusRealm/protocol/openid-connect/token" }}
 
 
-{{- range $key, $_ := $.Values.organisms }}
+{{- range $key, $_ := default $.Values.defaultOrganisms $.Values.organisms }}
 ---
 apiVersion: batch/v1
 kind: CronJob

diff --git a/kubernetes/loculus/templates/lapis-silo-input-data-cache.yaml b/kubernetes/loculus/templates/lapis-silo-input-data-cache.yaml
@@ -1,4 +1,4 @@
-{{- range $key, $_ := $.Values.organisms }}
+{{- range $key, $_ := default $.Values.defaultOrganisms $.Values.organisms }}
 ---
 apiVersion: v1
 kind: PersistentVolumeClaim

diff --git a/kubernetes/loculus/templates/lapis-silo-shared-data.yaml b/kubernetes/loculus/templates/lapis-silo-shared-data.yaml
@@ -1,4 +1,4 @@
-{{- range $key, $_ := $.Values.organisms }}
+{{- range $key, $_ := default $.Values.defaultOrganisms $.Values.organisms }}
 ---
 apiVersion: v1
 kind: PersistentVolumeClaim

diff --git a/kubernetes/loculus/templates/loculus-preprocessing-config.yaml b/kubernetes/loculus/templates/loculus-preprocessing-config.yaml
@@ -1,4 +1,4 @@
-{{- range $key, $values := .Values.organisms }}
+{{- range $key, $values := default $.Values.defaultOrganisms $.Values.organisms }}
 {{- if $values.preprocessing.configFile }}
 ---
 apiVersion: v1

diff --git a/kubernetes/loculus/templates/loculus-preprocessing-deployment.yaml b/kubernetes/loculus/templates/loculus-preprocessing-deployment.yaml
@@ -8,7 +8,7 @@
     "http://loculus-keycloak-service:8083"
 }}
 {{- if not .Values.disablePreprocessing }}
-{{- range $key, $value := .Values.organisms }}
+{{- range $key, $value := default $.Values.defaultOrganisms $.Values.organisms }}
 ---
 apiVersion: apps/v1
 kind: Deployment

diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
@@ -9,7 +9,7 @@ logo:
   url: "/favicon.svg"
   width: 100
   height: 100
-organisms:
+defaultOrganisms:
   dummy-organism:
     schema:
       image: "https://www.un.org/sites/un2.un.org/files/field/image/1583952355.1997.jpg"