diff --git a/kubernetes/loculus/templates/_common-metadata.tpl b/kubernetes/loculus/templates/_common-metadata.tpl index 45a38de46..a146f4b5c 100644 --- 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 index cf868f104..61036b616 100644 --- 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 index 09149f5ae..e45f61e3c 100644 --- 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 index a5c528804..3749f66e1 100644 --- 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 index d3045ddf4..b15ec7293 100644 --- 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 index 259ce7133..9eee098d7 100644 --- 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 index 90f876953..cebddc5e7 100644 --- 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 index 2dfa5af0c..2664d151c 100644 --- 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 index 34df11cce..6b2ed05e4 100644 --- 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 index 543f81055..0a33cddb5 100644 --- 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 index 4638f2875..86e6a0a61 100644 --- 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 index 6da5f6ea7..b18c856c1 100644 --- 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"