Remove PV from MySQL component (#1527)

andreyvelich · web-flow · commit d0d9c8d80e0a · 2021-05-06T18:59:06.000-07:00
Add startupProbe to mySQL
diff --git a/manifests/v1beta1/components/cert-generator/kustomization.yaml b/manifests/v1beta1/components/cert-generator/kustomization.yaml
@@ -2,5 +2,5 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 
 resources:
-- cert-generator.yaml
-- rbac.yaml
+  - cert-generator.yaml
+  - rbac.yaml
diff --git a/manifests/v1beta1/components/controller/kustomization.yaml b/manifests/v1beta1/components/controller/kustomization.yaml
@@ -2,8 +2,8 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 
 resources:
-- controller.yaml
-- katib-config.yaml
-- rbac.yaml
-- service.yaml
-- trial-templates.yaml
+  - controller.yaml
+  - katib-config.yaml
+  - rbac.yaml
+  - service.yaml
+  - trial-templates.yaml
diff --git a/manifests/v1beta1/components/crd/kustomization.yaml b/manifests/v1beta1/components/crd/kustomization.yaml
@@ -2,6 +2,6 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 
 resources:
-- experiment.yaml
-- suggestion.yaml
-- trial.yaml
+  - experiment.yaml
+  - suggestion.yaml
+  - trial.yaml
diff --git a/manifests/v1beta1/components/db-manager/db-manager.yaml b/manifests/v1beta1/components/db-manager/db-manager.yaml
@@ -34,10 +34,6 @@ spec:
           ports:
             - name: api
               containerPort: 6789
-          readinessProbe:
-            exec:
-              command: ["/bin/grpc_health_probe", "-addr=:6789"]
-            initialDelaySeconds: 5
           livenessProbe:
             exec:
               command: ["/bin/grpc_health_probe", "-addr=:6789"]
diff --git a/manifests/v1beta1/components/db-manager/kustomization.yaml b/manifests/v1beta1/components/db-manager/kustomization.yaml
@@ -2,5 +2,5 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 
 resources:
-- db-manager.yaml
-- service.yaml
+  - db-manager.yaml
+  - service.yaml
diff --git a/manifests/v1beta1/components/mysql/kustomization.yaml b/manifests/v1beta1/components/mysql/kustomization.yaml
@@ -2,8 +2,7 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 
 resources:
-- mysql.yaml
-- pv.yaml
-- pvc.yaml
-- secret.yaml
-- service.yaml
+  - mysql.yaml
+  - pvc.yaml
+  - secret.yaml
+  - service.yaml
diff --git a/manifests/v1beta1/components/mysql/mysql.yaml b/manifests/v1beta1/components/mysql/mysql.yaml
@@ -45,18 +45,24 @@ spec:
                 - "/bin/bash"
                 - "-c"
                 - "mysql -D ${MYSQL_DATABASE} -u root -p${MYSQL_ROOT_PASSWORD} -e 'SELECT 1'"
-            initialDelaySeconds: 5
-            periodSeconds: 10
-            timeoutSeconds: 1
+            periodSeconds: 2
+            failureThreshold: 10
           livenessProbe:
             exec:
               command:
                 - "/bin/bash"
                 - "-c"
                 - "mysqladmin ping -u root -p${MYSQL_ROOT_PASSWORD}"
-            initialDelaySeconds: 30
-            periodSeconds: 10
-            timeoutSeconds: 5
+            periodSeconds: 2
+            failureThreshold: 10
+          startupProbe:
+            exec:
+              command:
+                - "/bin/bash"
+                - "-c"
+                - "mysqladmin ping -u root -p${MYSQL_ROOT_PASSWORD}"
+            periodSeconds: 15
+            failureThreshold: 60
           volumeMounts:
             - name: katib-mysql
               mountPath: /var/lib/mysql
diff --git a/manifests/v1beta1/components/mysql/pv.yaml b/manifests/v1beta1/components/mysql/pv.yaml
diff --git a/manifests/v1beta1/components/mysql/pvc.yaml b/manifests/v1beta1/components/mysql/pvc.yaml
@@ -4,7 +4,6 @@ metadata:
   name: katib-mysql
   namespace: kubeflow
 spec:
-  storageClassName: katib
   accessModes:
     - ReadWriteOnce
   resources:
diff --git a/manifests/v1beta1/components/ui/kustomization.yaml b/manifests/v1beta1/components/ui/kustomization.yaml
@@ -2,6 +2,6 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 
 resources:
-- rbac.yaml
-- service.yaml
-- ui.yaml
+  - rbac.yaml
+  - service.yaml
+  - ui.yaml
diff --git a/manifests/v1beta1/components/webhook/kustomization.yaml b/manifests/v1beta1/components/webhook/kustomization.yaml
@@ -2,4 +2,4 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 
 resources:
-- webhooks.yaml
+  - webhooks.yaml
diff --git a/manifests/v1beta1/installs/katib-cert-manager/certificate.yaml b/manifests/v1beta1/installs/katib-cert-manager/certificate.yaml
@@ -6,15 +6,13 @@ spec:
   isCA: true
   commonName: $(KATIB_SERVICE_NAME).$(KATIB_NAMESPACE).svc
   dnsNames:
-  - $(KATIB_SERVICE_NAME).$(KATIB_NAMESPACE).svc
-  - $(KATIB_SERVICE_NAME).$(KATIB_NAMESPACE).svc.cluster.local
+    - $(KATIB_SERVICE_NAME).$(KATIB_NAMESPACE).svc
+    - $(KATIB_SERVICE_NAME).$(KATIB_NAMESPACE).svc.cluster.local
   issuerRef:
     kind: Issuer
     name: katib-selfsigned-issuer
   secretName: katib-webhook-cert
-
 ---
-
 apiVersion: cert-manager.io/v1alpha2
 kind: Issuer
 metadata:
diff --git a/manifests/v1beta1/installs/katib-cert-manager/kustomization.yaml b/manifests/v1beta1/installs/katib-cert-manager/kustomization.yaml
@@ -33,28 +33,28 @@ patchesStrategicMerge:
   - patches/katib-cert-injection.yaml
 
 vars:
-- fieldref:
-    fieldPath: metadata.namespace
-  name: KATIB_NAMESPACE
-  objref:
-    apiVersion: v1
-    kind: Service
-    name: katib-controller
-- fieldref:
-    fieldPath: metadata.name
-  name: KATIB_SERVICE_NAME
-  objref:
-    apiVersion: v1
-    kind: Service
-    name: katib-controller
-- name: KATIB_CERT_NAME
-  objref:
+  - fieldref:
+      fieldPath: metadata.namespace
+    name: KATIB_NAMESPACE
+    objref:
+      apiVersion: v1
+      kind: Service
+      name: katib-controller
+  - fieldref:
+      fieldPath: metadata.name
+    name: KATIB_SERVICE_NAME
+    objref:
+      apiVersion: v1
+      kind: Service
+      name: katib-controller
+  - name: KATIB_CERT_NAME
+    objref:
       kind: Certificate
       group: cert-manager.io
       version: v1alpha2
       name: katib-webhook-cert
-  fieldref:
-    fieldpath: metadata.name
+    fieldref:
+      fieldpath: metadata.name
 
 configurations:
   - params.yaml
diff --git a/manifests/v1beta1/installs/katib-cert-manager/params.yaml b/manifests/v1beta1/installs/katib-cert-manager/params.yaml
@@ -1,20 +1,18 @@
 varReference:
-- path: spec/http/route/destination/host
-  kind: VirtualService
-- path: spec/commonName
-  kind: Certificate
-- path: spec/dnsNames
-  kind: Certificate
-- path: spec/issuerRef/name
-  kind: Certificate
-- path: metadata/annotations
-  kind: MutatingWebhookConfiguration
-- path: metadata/annotations
-  kind: ValidatingWebhookConfiguration
+  - path: spec/commonName
+    kind: Certificate
+  - path: spec/dnsNames
+    kind: Certificate
+  - path: spec/issuerRef/name
+    kind: Certificate
+  - path: metadata/annotations
+    kind: MutatingWebhookConfiguration
+  - path: metadata/annotations
+    kind: ValidatingWebhookConfiguration
 nameReference:
-- kind: Issuer
-  group: cert-manager.io
-  fieldSpecs:
-  - kind: Certificate
+  - kind: Issuer
     group: cert-manager.io
-    path: spec/issuerRef/name
+    fieldSpecs:
+      - kind: Certificate
+        group: cert-manager.io
+        path: spec/issuerRef/name
diff --git a/manifests/v1beta1/installs/katib-external-db/kustomization.yaml b/manifests/v1beta1/installs/katib-external-db/kustomization.yaml
@@ -30,7 +30,7 @@ images:
     newName: docker.io/kubeflowkatib/cert-generator
     newTag: latest
 patchesStrategicMerge:
-  - db-manager-patch.yaml
+  - patches/db-manager.yaml
 # Modify katib-mysql-secrets with parameters for the DB.
 secretGenerator:
   - name: katib-mysql-secrets
diff --git a/manifests/v1beta1/installs/katib-external-db/patches/db-manager.yaml b/manifests/v1beta1/installs/katib-external-db/patches/db-manager.yaml
diff --git a/manifests/v1beta1/installs/katib-openshift/kustomization.yml b/manifests/v1beta1/installs/katib-openshift/kustomization.yml
@@ -2,16 +2,11 @@
 #  - No Job is spawned to generate TLS key for `katib-controller` Service
 #  - Instead, the Service and WebhookConfigurations linked to it are annotated
 #    for OpenShift service controller to handle TLS certification.
-#  - PersistentVolumeClaim has empty `.spec.storageClassName` to allow dynamic
-#    provisioning with default StorageClass
 #
 # Requires OpenShift version: 4.4+
-#  
-# Note: PersistentVolume should not be created, as OpenShift installations typically
-# have PVC dynamic provisioning configured or need some extra administrative effort
-# to provision a PV manually.
+#
 # To achieve this, run:
-# 
+#
 # `kustomize build ./manifests/v1beta1/installs/katib-openshift | oc apply -f - -l type!=local`
 ---
 apiVersion: kustomize.config.k8s.io/v1beta1
@@ -51,6 +46,7 @@ patchesJson6902:
       version: v1
       kind: Service
       name: katib-controller
+      namespace: kubeflow
     path: patches/service-serving-cert.yaml
   # Annotate WebhookConfigurations to delegate `caBundle` population to OpenShift service controller
   # https://docs.openshift.com/container-platform/4.6/security/certificates/service-serving-certificate.html#add-service-certificate-mutating-webhook_service-serving-certificate
@@ -66,10 +62,3 @@ patchesJson6902:
       kind: MutatingWebhookConfiguration
       name: katib.kubeflow.org
     path: patches/webhook-inject-cabundle.yaml
-  # Remove PVC's storageClassName to provision it with the default StorageClass by default
-  - target:
-      group: ""
-      version: v1
-      kind: PersistentVolumeClaim
-      name: katib-mysql
-    path: patches/pvc-unset-storageClass.yaml
diff --git a/manifests/v1beta1/installs/katib-openshift/patches/pvc-unset-storageClass.yaml b/manifests/v1beta1/installs/katib-openshift/patches/pvc-unset-storageClass.yaml
diff --git a/manifests/v1beta1/installs/katib-openshift/patches/service-serving-cert.yaml b/manifests/v1beta1/installs/katib-openshift/patches/service-serving-cert.yaml
@@ -1,5 +1,3 @@
----
 - op: "add"
-  path: "/metadata/annotations"
-  value:
-    service.beta.openshift.io/serving-cert-secret-name: katib-webhook-cert
+  path: "/metadata/annotations/service.beta.openshift.io~1serving-cert-secret-name"
+  value: katib-webhook-cert
diff --git a/manifests/v1beta1/installs/katib-openshift/patches/webhook-inject-cabundle.yaml b/manifests/v1beta1/installs/katib-openshift/patches/webhook-inject-cabundle.yaml
@@ -1,4 +1,3 @@
----
 - op: "add"
   path: "/metadata/annotations"
   value:
diff --git a/manifests/v1beta1/installs/katib-with-kubeflow/kustomization.yaml b/manifests/v1beta1/installs/katib-with-kubeflow/kustomization.yaml
@@ -18,24 +18,16 @@ images:
     newTag: latest
 
 patchesStrategicMerge:
-  - patches/remove-resources-patch.yaml
-
-patchesJson6902:
-  - path: patches/mysql-pvc.yaml
-    target:
-      version: v1
-      name: katib-mysql
-      kind: PersistentVolumeClaim
-      namespace: kubeflow
+  - patches/remove-namespace.yaml
 
 vars:
-- fieldref:
-    fieldPath: metadata.namespace
-  name: KATIB_UI_NAMESPACE
-  objref:
-    apiVersion: apps/v1
-    kind: Deployment
-    name: katib-ui
+  - fieldref:
+      fieldPath: metadata.namespace
+    name: KATIB_UI_NAMESPACE
+    objref:
+      apiVersion: apps/v1
+      kind: Deployment
+      name: katib-ui
 
 configurations:
   - params.yaml
diff --git a/manifests/v1beta1/installs/katib-with-kubeflow/patches/mysql-pvc.yaml b/manifests/v1beta1/installs/katib-with-kubeflow/patches/mysql-pvc.yaml
diff --git a/manifests/v1beta1/installs/katib-with-kubeflow/patches/remove-namespace.yaml b/manifests/v1beta1/installs/katib-with-kubeflow/patches/remove-namespace.yaml
@@ -0,0 +1,5 @@
+$patch: delete
+apiVersion: v1
+kind: Namespace
+metadata:
+  name: kubeflow
diff --git a/manifests/v1beta1/installs/katib-with-kubeflow/patches/remove-resources-patch.yaml b/manifests/v1beta1/installs/katib-with-kubeflow/patches/remove-resources-patch.yaml
diff --git a/scripts/v1beta1/deploy.sh b/scripts/v1beta1/deploy.sh
@@ -19,4 +19,4 @@ set -o xtrace
 SCRIPT_ROOT=$(dirname ${BASH_SOURCE})/../..
 
 cd ${SCRIPT_ROOT}
-kustomize build manifests/v1beta1/installs/katib-standalone --load_restrictor none | kubectl apply -f -
+kustomize build manifests/v1beta1/installs/katib-standalone | kubectl apply -f -
diff --git a/scripts/v1beta1/undeploy.sh b/scripts/v1beta1/undeploy.sh
@@ -23,4 +23,4 @@ sleep 10
 SCRIPT_ROOT=$(dirname ${BASH_SOURCE})/../..
 
 cd ${SCRIPT_ROOT}
-kustomize build manifests/v1beta1/installs/katib-standalone --load_restrictor none | kubectl delete -f -
+kustomize build manifests/v1beta1/installs/katib-standalone | kubectl delete -f -
