Helm v2t3 update

charts/jupyterhub/dick.yaml

@@ -0,0 +1,103 @@
+#jupyterhub:
+  ingress:
+    enabled: true
+    hosts:
+      - jupyter.koudekoffie.nl
+    annotations:
+      kubernetes.io/ingress.class: "nginx"
+      cert-manager.io/cluster-issuer: letsencrypt
+    tls:
+      - hosts:
+        - jupyter.koudekoffie.nl
+        secretName: jupyterhub-secret
+
+  hub:
+    config:
+      JupyterHub:
+        admin_access: true
+        authenticator_class: generic-oauth
+      Authenticator:
+        auto_login: false
+      GenericOAuthenticator:
+        client_id: abaa320f-9e12-487d-b484-ea4c5b71dbef
+        client_secret: QfMUyyQl30I-tGQDK6v6gY45JTXUmiQ62r7mL9vZ5nw 
+        login_service: MOLGENIS
+        authorize_url: https://lifecycle-auth.molgenis.org/oauth2/authorize
+        token_url: https://lifecycle-auth.molgenis.org/oauth2/token
+        userdata_url: https://lifecycle-auth.molgenis.org/oauth2/userinfo
+        userdata_method: GET
+        username_key: email
+        oauth_callback_url: http://jupyter.koudekoffie.nl/hub/oauth_callback
+        scope:
+          - openid
+          - name
+          - profile
+          - email
+    extraConfig:
+      checkRolesConfig: |
+        def check_roles(authenticator, handler, authentication):
+            if ("roles" in authentication["auth_state"]["oauth_user"]):
+                if ("ADMIN" in authentication["auth_state"]["oauth_user"]["roles"]):
+                    authentication["admin"] = True
+                    return authentication
+                elif ("USER" in authentication["auth_state"]["oauth_user"]["roles"]):
+                    return authentication
+                else:
+                    return None
+            else:
+                return None
+        c.Authenticator.post_auth_hook = check_roles
+
+        #  scheduling:
+        #    userScheduler:
+        #      enabled: true
+        #    podPriority:
+        #      enabled: true
+        #    userPlaceholder:
+        #      enabled: true
+        #      replicas: 3
+        #    userPods:
+        #      nodeAffinity:
+        #        matchNodePurpose: require
+
+  singleuser:
+    image:
+      name: datashield/rstudio-jupyter
+      tag: 1.2.0
+    cpu:
+      limit: 2
+      guarantee: 2
+    memory:
+      limit: 3G
+      guarantee: 1500M
+    startTimeout: 800
+    profileList: 
+        - 
+          display_name: "DataSHIELD - dsBaseClient v6.1.0"
+          description: "RStudio analysis environment dsBaseClient v6.1.0"
+          kubespawner_override: 
+            image: "datashield/rstudio-jupyter:1.2.0"
+          default: true
+
+  proxy:
+    secretToken: xxxxxxxxxzxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+    service:
+      type: NodePort
+        #https:
+        #  enabled: true
+        #  hosts: 
+        #    - jupyter.koudekoffie.nl
+        #  letsencrypt:
+        #    contactEmail: [email protected]
+  prePuller:
+    hook:
+      podSchedulingWaitDuration: -1
+  # https://github.com/jupyterhub/jupyterhub-idle-culler#as-a-standalone-script
+  cull:
+    enabled: true
+    users: false
+    removeNamedServers: false
+    timeout: 3600
+    every: 2400
+    concurrency: 10
+    maxAge: 0

charts/variant-formatter/Chart.lock

@@ -0,0 +1,6 @@
+dependencies:
+- name: postgresql
+  repository: https://charts.bitnami.com/bitnami
+  version: 11.1.9
+digest: sha256:02b3dd33a3dc9149c40b3d835db5db99d29c71e00e8907a065bf00b619e3fa0f
+generated: "2022-10-05T09:16:57.306708801+02:00"

charts/variant-formatter/Chart.yaml

@@ -1,11 +1,16 @@
-apiVersion: v1
+apiVersion: v2
 appVersion: "1.1"
 description: Format variants using biocommons tools
 name: variant-formatter
 home: https://github.com/biocommons/hgvs
-version: 0.3.1
+version: 0.4.0
 icon: https://raw.githubusercontent.com/molgenis/molgenis-ops-helm/master/charts/variant-formatter/catalogIcon-variant-formatter.png
 maintainers:
 - name: fdlk
 sources:
 - https://github.com/molgenis/molgenis-ops-helm.git
+dependencies:
+- name: postgresql
+  version: 11.1.9 
+  repository: https://charts.bitnami.com/bitnami 
+

charts/variant-formatter/templates/deployment.yaml

@@ -43,7 +43,7 @@ spec:
             - name: HGVS_SEQREPO_DIR
               value: /usr/local/share/seqrepo/{{ .Values.seqrepo.dataRelease }}
             - name: UTA_DB_URL
-              value: postgresql://{{ .Values.postgresql.postgresqlUsername }}:{{ .Values.postgresql.postgresqlPassword }}@{{ include "call-nested" (list . "postgresql" "postgresql.fullname") }}/{{ .Values.postgresql.postgresqlDatabase }}/{{ .Values.uta.version }}
+              value: postgresql://{{ .Values.postgresql.postgresqlUsername }}:{{ .Values.postgresql.postgresqlPassword }}@{{ .Release.Name }}-postgresql/{{ .Values.postgresql.postgresqlDatabase }}/{{ .Values.uta.version }}
           ports:
             - name: http
               containerPort: 1234

charts/variant-formatter/templates/ingress.yaml

@@ -1,6 +1,6 @@
 {{- if .Values.ingress.enabled -}}
 {{- $fullName := include "variant-formatter.fullname" . -}}
-apiVersion: networking.k8s.io/v1beta1
+apiVersion: networking.k8s.io/v1
 kind: Ingress
 metadata:
   name: {{ $fullName }}
@@ -27,8 +27,11 @@ spec:
       http:
         paths:
           - path: {{ $.Values.ingress.path }}
+            pathType: Prefix
             backend:
-              serviceName: {{ $fullName }}
-              servicePort: http
+              service:
+                name: {{ $fullName }}
+                port:
+                  name: http
   {{- end }}
 {{- end }}

charts/variant-formatter/values.yaml

@@ -6,6 +6,10 @@ uta:
   version: "uta_20190927"
 
 postgresql:
+  image:
+    registry: docker.io
+    repository: bitnami/postgresql
+    tag: "11.9.0-debian-10-r16"
   initdbScriptsConfigMap: "{{ .Release.Name }}-uta-config"
   postgresqlUsername: uta_admin
   postgresqlPassword: uta_admin

resources/assets/vault/resources/l

@@ -0,0 +1,9 @@
+10.10.12.4 armadillo_backend04 :
+  armadillopft.molgeniscloud.org 
+  armadillopft-auth.molgeniscloud.org 
+  armadillopft-storage.molgeniscloud.org 
+  armadillopft-storage-console.molgeniscloud.org 
+
+10.10.12.5 armadillo_backend05 :
+  opalpft.molgeniscloud.org 
+