Merge branch 'helm-1.19-compatibility'

OpenNeuroOrg · May 27, 2021 · 3f0e9ba · 3f0e9ba
2 parents 16aaf9d + b83d259
commit 3f0e9ba
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diff --git a/helm/README.md b/helm/README.md
@@ -122,6 +122,11 @@ Other values which can be overridden are found in the chart version of [values.y
 
 Installing a chart deploys it to a cluster. This creates an initial release by generating the configuration templates and applying them to the cluster.
 
+```bash
+# Add an ssh key for GitHub remotes
+kubectl create secret generic openneuro-my-dev-ssh-key --from-file=datalad-key=datalad-key
+```
+
 ```bash
 # Make sure you're in the helm directory and run
 helm install -f values.yaml -f secrets.yaml openneuro-my-dev openneuro/

diff --git a/helm/manual-old-indexer b/helm/manual-old-indexer
@@ -0,0 +1,36 @@
+apiVersion: batch/v1
+kind: Job
+metadata:
+  annotations:
+    cronjob.kubernetes.io/instantiate: manual
+  name: openneuro-prod-indexer-manual-1
+  namespace: default
+spec:
+  backoffLimit: 6
+  completions: 1
+  parallelism: 1
+  template:
+    spec:
+      containers:
+      - envFrom:
+        - configMapRef:
+            name: openneuro-prod-configmap
+        - secretRef:
+            name: openneuro-prod-secret
+        image: openneuro/indexer:v3.31.1
+        imagePullPolicy: IfNotPresent
+        name: openneuro-indexer
+        resources:
+          limits:
+            cpu: 500m
+            memory: 512Mi
+          requests:
+            cpu: 100m
+            memory: 256Mi
+        terminationMessagePath: /dev/termination-log
+        terminationMessagePolicy: File
+      dnsPolicy: ClusterFirst
+      restartPolicy: OnFailure
+      schedulerName: default-scheduler
+      securityContext: {}
+      terminationGracePeriodSeconds: 30
diff --git a/helm/openneuro/Chart.yaml b/helm/openneuro/Chart.yaml
@@ -5,7 +5,7 @@ description: OpenNeuro production deployment chart
 home: https://openneuro.org
 sources:
   - https://github.com/openNeuroOrg/openneuro
-appVersion: 3.33.2
+appVersion: 3.33.5
 dependencies:
   - name: redis
     version: 10.6.17

diff --git a/helm/openneuro/templates/api-deployment.yaml b/helm/openneuro/templates/api-deployment.yaml
@@ -28,7 +28,7 @@ spec:
               cpu: "1.2"
               memory: "2Gi"
             requests:
-              cpu: ".5"
+              cpu: ".3"
               memory: "768Mi"
           ports:
             - containerPort: 8111

diff --git a/helm/openneuro/templates/dataset-worker-stateful-set.yaml b/helm/openneuro/templates/dataset-worker-stateful-set.yaml
@@ -30,6 +30,8 @@ spec:
       - key: "storage"
         operator: "Exists"
         effect: "NoSchedule"
+      nodeSelector:
+        role: storage
       volumes:
       - name: ssh-key
         secret:
@@ -41,13 +43,13 @@ spec:
       containers:
       - name: {{ .Release.Name }}-dataset-worker
         image: 'openneuro/datalad-service:v{{ .Chart.AppVersion }}'
-        command: ["gunicorn", "--bind", "0.0.0.0:80", "--reload", "datalad_service.app:create_app('/datasets')", "--workers", "8", "--worker-class", "gevent", "--timeout", "60", "--keep-alive", "30"]
+        command: ["gunicorn", "--bind", "0.0.0.0:80", "--reload", "datalad_service.app:create_app('/datasets')", "--workers", "4", "--worker-class", "gevent", "--timeout", "60", "--keep-alive", "30"]
         resources:
           limits:
-            cpu: "2"
-            memory: "8Gi"
+            cpu: "1.6"
+            memory: "10Gi"
           requests:
-            cpu: "0.5"
+            cpu: "0.3"
             memory: "1Gi"
         ports:
         - containerPort: 80

diff --git a/helm/openneuro/templates/ingress.yaml b/helm/openneuro/templates/ingress.yaml
@@ -1,4 +1,4 @@
-apiVersion: extensions/v1beta1
+apiVersion: networking.k8s.io/v1
 kind: Ingress
 metadata:
   name: {{ .Release.Name }}
@@ -18,47 +18,74 @@ spec:
       http:
         paths:
           - path: /*
+            pathType: ImplementationSpecific
             backend:
-              serviceName: www-redirect
-              servicePort: use-annotation
+              service:
+                name: www-redirect
+                port:
+                  name: use-annotation
     - host: {{ .Values.hostname }}
       http:
         paths:
           - path: /*
+            pathType: ImplementationSpecific
             backend:
-              serviceName: ssl-redirect
-              servicePort: use-annotation
+              service:
+                name: ssl-redirect
+                port:
+                  name: use-annotation
           - path: /graphql-subscriptions
+            pathType: ImplementationSpecific
             backend:
-              serviceName: {{ .Release.Name }}-api
-              servicePort: 8111
+              service:
+                name: {{ .Release.Name }}-api
+                port:
+                  number: 8111
           - path: /crn/*
+            pathType: ImplementationSpecific
             backend:
-              serviceName: {{ .Release.Name }}-api
-              servicePort: 8111
+              service:
+                name: {{ .Release.Name }}-api
+                port:
+                  number: 8111
           - path: /sitemap.xml
+            pathType: ImplementationSpecific
             backend:
-              serviceName: {{ .Release.Name }}-api
-              servicePort: 8111
+              service:
+                name: {{ .Release.Name }}-api
+                port:
+                  number: 8111
           {{- $relname := .Release.Name -}}
           {{- range until ( .Values.dataladWorkers | int ) }}
           - path: /uploads/{{ . }}/*
+            pathType: ImplementationSpecific
             backend:
-              serviceName: {{ $relname }}-dataset-worker-{{ . }}
-              servicePort: 80
+              service:
+                name: {{ $relname }}-dataset-worker-{{ . }}
+                port:
+                  number: 80
           {{- end }}
           {{- $relname := .Release.Name -}}
           {{- range until ( .Values.dataladWorkers | int ) }}
           - path: /git/{{ . }}/*
+            pathType: ImplementationSpecific
             backend:
-              serviceName: {{ $relname }}-dataset-worker-{{ . }}
-              servicePort: 80
+              service:
+                name: {{ $relname }}-dataset-worker-{{ . }}
+                port:
+                  number: 80
           {{- end }}
           - path: /intake/*
+            pathType: ImplementationSpecific
             backend:
-              serviceName: {{ .Release.Name }}-apm-server
-              servicePort: 8200
+              service:
+                name: {{ .Release.Name }}-apm-server
+                port:
+                  number: 8200
           - path: /*
+            pathType: ImplementationSpecific
             backend:
-              serviceName: {{ .Release.Name }}-web
-              servicePort: 80
+              service:
+                name: {{ .Release.Name }}-web
+                port:
+                  number: 80
diff --git a/helm/openneuro/templates/openebs-pool-statefulset.yaml b/helm/openneuro/templates/openebs-pool-statefulset.yaml
diff --git a/helm/openneuro/templates/openebs-pool-storageclass.yaml b/helm/openneuro/templates/openebs-pool-storageclass.yaml
diff --git a/helm/openneuro/templates/openebs-volume-storageclass.yaml b/helm/openneuro/templates/openebs-volume-storageclass.yaml
@@ -3,15 +3,17 @@ kind: StorageClass
 metadata:
   name: {{ .Release.Name }}-datasets
 parameters:
+  scheduler: "VolumeWeighted"
   fstype: 'zfs'
   poolname: 'zfspv-pool'
   compression: 'lz4'
   recordsize: '16k'
 reclaimPolicy: Retain
+volumeBindingMode: WaitForFirstConsumer
 allowVolumeExpansion: true
 provisioner: zfs.csi.openebs.io
 allowedTopologies:
   - matchLabelExpressions:
-      - key: alpha.eksctl.io/nodegroup-name
+      - key: role
         values:
           - storage
diff --git a/helm/openneuro/values-production.yaml b/helm/openneuro/values-production.yaml
@@ -59,7 +59,7 @@ efs-provisioner:
 aws-alb-ingress-controller:
   awsRegion: us-west-2
   autoDiscoverAwsVpcID: true
-  clusterName: openneuro-prod
+  clusterName: openneuro-prod-2021
 
 # Disable Redis password for testing
 redis: