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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/

helm/eksctl-cluster-prod.yaml

@@ -34,10 +34,11 @@ nodeGroups:
     preBootstrapCommands:
       - apt update
       - apt install -y nfs-common zfsutils-linux
-  - name: storage
+  - name: storage-m5
     amiFamily: Ubuntu2004
-    instanceType: r5ad.large
+    instanceType: m5ad.2xlarge
     desiredCapacity: 2
+    labels: { role: storage }
     availabilityZones:
       - us-west-2b
       - us-west-2c

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

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

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

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:
@@ -44,11 +46,11 @@ spec:
         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"]
         resources:
           limits:
-            cpu: "2"
-            memory: "8Gi"
+            cpu: "3"
+            memory: "10Gi"
           requests:
-            cpu: "0.5"
-            memory: "1Gi"
+            cpu: "1"
+            memory: "4Gi"
         ports:
         - containerPort: 80
         envFrom:

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