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feat(website): link from groupid to group page in seq details page #2013

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merged 4 commits into from
May 22, 2024
Merged

feat(website): link from groupid to group page in seq details page #2013

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5a5116b
fix(k8s): check if backendExtraArgs is set, add test for default temp…
corneliusroemer May 22, 2024
826ae05
fix spacing
corneliusroemer May 22, 2024
104040f
f
corneliusroemer May 22, 2024
aae3739
feat(website): link from groupid to group page in seq details page
corneliusroemer May 22, 2024
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8 changes: 7 additions & 1 deletion .github/workflows/e2e-k3d.yml
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Expand Up @@ -61,7 +61,12 @@ jobs:
run: |
./deploy.py --verbose cluster

- name: Template with helm
- name: Default template with helm
uses: WyriHaximus/github-action-helm3@v4
with:
exec: helm template loculus kubernetes/loculus

- name: E2E Template with helm
uses: WyriHaximus/github-action-helm3@v4
with:
exec: ./deploy.py --verbose helm --branch ${{ github.ref_name }} --sha ${{ env.sha }} --for-e2e --template > /tmp/helm_template.yaml
Expand All @@ -71,6 +76,7 @@ jobs:
with:
name: helm-template
path: /tmp/helm_template.yaml

- name: Deploy with helm
run: |
./deploy.py --verbose helm --branch ${{ github.ref_name }} --sha ${{ env.sha }} --for-e2e
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16 changes: 16 additions & 0 deletions kubernetes/loculus/templates/_common-metadata.tpl
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@@ -1,3 +1,16 @@
{{- define "loculus.websiteUrl" -}}
{{- $websiteHost := "" }}
{{- if $.Values.codespaceName }}
{{- $websiteHost = printf "https://%s-3000.app.github.dev" $.Values.codespaceName }}
{{- else if eq $.Values.environment "server" }}
{{- $websiteHost = printf "https://%s" $.Values.host }}
{{- else }}
{{- $websiteHost = "http://localhost:3000" }}
{{- end }}
{{- printf $websiteHost }}
{{- end }}


{{/* Get common metadata fields */}}
{{- define "loculus.commonMetadata" }}
fields:
Expand Down Expand Up @@ -29,6 +42,9 @@ fields:
type: int
autocomplete: true
header: Submission details
customDisplay:
type: link
url: {{ include "loculus.websiteUrl" $ -}} /group/__value__
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- name: groupName
type: string
generateIndex: true
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4 changes: 3 additions & 1 deletion kubernetes/loculus/templates/loculus-backend.yaml
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Expand Up @@ -59,7 +59,9 @@ spec:
- "--spring.datasource.username=$(DB_USERNAME)"
- "--spring.security.oauth2.resourceserver.jwt.jwk-set-uri=http://loculus-keycloak-service:8083/realms/loculus/protocol/openid-connect/certs"
- "--loculus.cleanup.task.reset-stale-in-processing-after-seconds={{- .Values.preprocessingTimeout | default 120 }}"
{{ .Values.backendExtraArgs | toYaml | nindent 12 }}
{{- if .Values.backendExtraArgs }}
{{- .Values.backendExtraArgs | toYaml | nindent 12 }}
{{- end }}
env:
- name: JVM_OPTS
value: -XX:+UseContainerSupport -XX:+UseG1GC -XX:MaxHeapFreeRatio=5 -XX:MinHeapFreeRatio=2
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