Add rclone push example without credentials

inst/helm-chart/templates/_helpers.tpl

@@ -17,3 +17,24 @@ csi:
 {{- end -}}
 {{- end -}}
 {{- end -}}
+
+{{/*
+Extract the filename portion from a file path
+*/}}
+{{- define "biockubeinstall.getFilenameFromPath" -}}
+{{- printf "%s" (. | splitList "/" | last) -}}
+{{- end -}}
+
+{{/*
+Make string DNS-compliant by turning to lowercase then removing all noncompliant characters
+*/}}
+{{- define "biockubeinstall.makeDnsCompliant" -}}
+{{- (printf "%s" (regexReplaceAll "[^a-z0-9-]" (. | lower) "")) | trunc 63 | trimSuffix "-"  }}
+{{- end -}}
+
+{{/*
+Get unique name for extra files
+*/}}
+{{- define "biockubeinstall.getExtraFilesUniqueName" -}}
+{{- (printf "%s" (include "biockubeinstall.makeDnsCompliant" (printf "extra-%s-%s" (include "biockubeinstall.getFilenameFromPath" .) (. | sha256sum))))  }}
+{{- end -}}

inst/helm-chart/templates/extrafilemappings.yaml

@@ -0,0 +1,23 @@
+{{- range $key, $entry := .Values.extraFileMappings -}}
+{{- if $entry }}
+apiVersion: v1
+metadata:
+  # Extract the filename portion only
+  name: {{ printf "%s-%s" "extrafiles" (include "biockubeinstall.getExtraFilesUniqueName" $key) }}
+{{- if $entry.useSecret }}
+kind: Secret
+type: Opaque
+stringData:
+{{- else }}
+kind: ConfigMap
+data:
+{{- end }}
+  {{- include "biockubeinstall.getFilenameFromPath" $key | nindent 2 }}: |
+  {{- if $entry.tpl }}
+    {{- tpl (tpl $entry.content $) $ | nindent 4 }}
+  {{- else }}
+    {{- $entry.content | nindent 4 }}
+  {{- end }}
+---
+{{- end }}
+{{- end }}

inst/helm-chart/templates/manager-deployment.yaml

@@ -5,7 +5,7 @@ metadata:
   labels:
     app: rstudio
 spec:
-  containers:
+  initContainers:
     - name: manager
       image: {{ .Values.manager.image.repository }}:{{ .Values.manager.image.tag }}
       imagePullPolicy: {{ .Values.pullPolicy }}
@@ -14,6 +14,13 @@ spec:
       volumeMounts:
         - name: nfs-data
           mountPath: {{ .Values.persistence.mountPath }}
+        {{- range $key, $entry := .Values.extraFileMappings -}}
+        {{- if $entry.applyToManager }}
+        - name: {{ include "biockubeinstall.getExtraFilesUniqueName" $key }}
+          mountPath: {{ $key }}
+          subPath: {{ include "biockubeinstall.getFilenameFromPath" $key }}
+        {{- end }}
+        {{- end }}
       env:
         - name: PASSWORD
           value: {{ .Values.rstudioPassword | quote }}
@@ -26,8 +33,82 @@ spec:
           {{- tpl .Values.manager.extraCommand $ }};
           {{- end -}}
           {{ tpl .Values.manager.defaultCommand . }}
+  containers:
+    - name: osn-rclone-copy
+      image: rclone/rclone:latest
+      command:
+        - /bin/sh
+        - -c
+      args:
+        - rclone copyto /host/binary_{{ .Values.biocVersion | replace "." "_" }} osn:bir190004-bucket01/bioconductor-packages/{{ .Values.biocVersion }}/container-binaries/bioconductor_docker -v && rclone copyto /host/library_{{ .Values.biocVersion | replace "." "_" }} osn:bir190004-bucket01/bioconductor-packages/{{ .Values.biocVersion }}/container-binaries/bioconductor_docker/src/contrib -v && rclone copyto /host/logs_{{ .Values.biocVersion | replace "." "_" }} osn:bir190004-bucket01/bioconductor-packages/{{ .Values.biocVersion }}/container-binaries/bioconductor_docker/src/package_logs -v
+      volumeMounts:
+        - name: nfs-data
+          mountPath: {{ .Values.persistence.mountPath }}
+        {{- range $key, $entry := .Values.extraFileMappings -}}
+        {{- if $entry.applyToRclone }}
+        - name: {{ include "biockubeinstall.getExtraFilesUniqueName" $key }}
+          mountPath: {{ $key }}
+          subPath: {{ include "biockubeinstall.getFilenameFromPath" $key }}
+        {{- end }}
+        {{- end }}
+      resources:
+        requests:
+          memory: 100Mi
+          cpu: 100m
+    - name: azure-rclone-copy
+      image: rclone/rclone:latest
+      command:
+        - /bin/sh
+        - -c
+      args:
+        - rclone copyto /host/binary_{{ .Values.biocVersion | replace "." "_" }} azurebuckets:bioconductor-packages/{{ .Values.biocVersion }}/container-binaries/bioconductor_docker -v && rclone copyto /host/library_{{ .Values.biocVersion | replace "." "_" }} azurebuckets:bioconductor-packages/{{ .Values.biocVersion }}/container-binaries/bioconductor_docker/src/contrib -v && rclone copyto /host/logs_{{ .Values.biocVersion | replace "." "_" }} azurebuckets:bioconductor-packages/{{ .Values.biocVersion }}/container-binaries/bioconductor_docker/src/package_logs -v
+      volumeMounts:
+        - name: nfs-data
+          mountPath: {{ .Values.persistence.mountPath }}
+        {{- range $key, $entry := .Values.extraFileMappings -}}
+        {{- if $entry.applyToRclone }}
+        - name: {{ include "biockubeinstall.getExtraFilesUniqueName" $key }}
+          mountPath: {{ $key }}
+          subPath: {{ include "biockubeinstall.getFilenameFromPath" $key }}
+        {{- end }}
+        {{- end }}
+      resources:
+        requests:
+          memory: 100Mi
+          cpu: 100m
+    - name: gcp-rclone-copy
+      image: rclone/rclone:latest
+      command:
+        - /bin/sh
+        - -c
+      args:
+        - rclone copyto /host/binary_{{ .Values.biocVersion | replace "." "_" }} gcpbuckets:bioconductor-packages/{{ .Values.biocVersion }}/container-binaries/bioconductor_docker -v && rclone copyto /host/library_{{ .Values.biocVersion | replace "." "_" }} gcpbuckets:bioconductor-packages/{{ .Values.biocVersion }}/container-binaries/bioconductor_docker/src/contrib -v && rclone copyto /host/logs_{{ .Values.biocVersion | replace "." "_" }} gcpbuckets:bioconductor-packages/{{ .Values.biocVersion }}/container-binaries/bioconductor_docker/src/package_logs -v
+      volumeMounts:
+        - name: nfs-data
+          mountPath: {{ .Values.persistence.mountPath }}
+        {{- range $key, $entry := .Values.extraFileMappings -}}
+        {{- if $entry.applyToRclone }}
+        - name: {{ include "biockubeinstall.getExtraFilesUniqueName" $key }}
+          mountPath: {{ $key }}
+          subPath: {{ include "biockubeinstall.getFilenameFromPath" $key }}
+        {{- end }}
+        {{- end }}
+      resources:
+        requests:
+          memory: 100Mi
+          cpu: 100m
   restartPolicy: {{ .Values.restartPolicy | quote}}
   volumes:
   - name: nfs-data
     persistentVolumeClaim:
-      claimName: {{.Release.Namespace}}-nfs
+      claimName: {{.Release.Namespace}}-nfs
+  {{- range $key, $entry := .Values.extraFileMappings }}
+  - name: {{ include "biockubeinstall.getExtraFilesUniqueName" $key }}
+    {{- if $entry.useSecret }}
+    secret:
+      secretName: {{ printf "%s-%s" "extrafiles" (include "biockubeinstall.getExtraFilesUniqueName" $key) }}
+    {{- else }}
+    configMap:
+      name: {{ printf "%s-%s" "extrafiles" (include "biockubeinstall.getExtraFilesUniqueName" $key) }}
+    {{- end }}
+  {{- end }}

inst/helm-chart/values.yaml

@@ -90,3 +90,37 @@ redis:
   redisImage: redis
   redisImageTag: '5.0'
   containerPort: 6379
+
+extraFileMappings:
+  /root/.rclone.conf:
+    useSecret: true
+    applyToRclone: true
+    applyToManager: false
+    tpl: false
+    content: |
+      [azurebuckets]
+      sas_url = https://bioconductorhubs.blob.core.windows.net/bucketname?sp=rl&sas-secret
+      type = azureblob
+
+      [osn]
+      type = s3
+      provider = AWS
+      access_key_id = accesskey
+      secret_access_key = secretkey
+      endpoint = https://mghp.osn.xsede.org
+      acl = private
+      no_check_bucket = true
+
+      [awsopendata]
+      type = s3
+      provider = AWS
+      access_key_id = accesskey
+      secret_access_key = secretkey
+      acl = private
+
+      [gcpbuckets]
+      type = google cloud storage
+      service_account_file = /path/to/service_account
+      project_number = 12345678 
+      object_acl = private
+      bucket_acl = private