feat: Add Backup Helm Chart to Gen3-Helm

.github/workflows/lint_test.yaml

@@ -36,7 +36,7 @@ jobs:
       - name: Run chart-testing (lint)
         run: ct lint --config .github/ct.yaml
 
-  # TODO: add back in when we have tests
+  # TODO: add back in when tests are re-enabled
   # deploy-and-test-chart:
   #   name: Deploy and Test Chart
   #   timeout-minutes: 20

helm/aws-es-proxy/values.yaml

@@ -109,6 +109,11 @@ resources:
     # -- (string) The maximum amount of memory the container can use
     memory: 2Gi
 
+# Added default to resolve nil pointer error with `ct` linting:
+# <.Values.persistence.capacity>: nil pointer evaluating interface {}.capacity
+persistence:
+  capacity: 1Gi
+
 # -- (map) Kubernetes service information.
 service:
   # -- (string) Type of service. Valid values are "ClusterIP", "NodePort", "LoadBalancer", "ExternalName".

helm/backups/.helmignore

@@ -0,0 +1,23 @@
+# Patterns to ignore when building packages.
+# This supports shell glob matching, relative path matching, and
+# negation (prefixed with !). Only one pattern per line.
+.DS_Store
+# Common VCS dirs
+.git/
+.gitignore
+.bzr/
+.bzrignore
+.hg/
+.hgignore
+.svn/
+# Common backup files
+*.swp
+*.bak
+*.tmp
+*.orig
+*~
+# Various IDEs
+.project
+.idea/
+*.tmproj
+.vscode/

helm/backups/Chart.yaml

@@ -0,0 +1,25 @@
+apiVersion: v2
+name: backups
+description: A Helm chart for Kubernetes
+
+# A chart can be either an 'application' or a 'library' chart.
+#
+# Application charts are a collection of templates that can be packaged into versioned archives
+# to be deployed.
+#
+# Library charts provide useful utilities or functions for the chart developer. They're included as
+# a dependency of application charts to inject those utilities and functions into the rendering
+# pipeline. Library charts do not define any templates and therefore cannot be deployed.
+type: application
+
+# This is the chart version. This version number should be incremented each time you make changes
+# to the chart and its templates, including the app version.
+# Versions are expected to follow Semantic Versioning (https://semver.org/)
+version: 0.5.1
+
+# This is the version number of the application being deployed. This version number should be
+# incremented each time you make changes to the application. Versions are not expected to
+# follow Semantic Versioning. They should reflect the version the application is using.
+# It is recommended to use it with quotes.
+# Ref: https://github.com/calypr/backup-service/releases
+appVersion: "1.15.1"

helm/backups/README.md

@@ -0,0 +1,24 @@
+# backups
+
+![Version: 0.5.0](https://img.shields.io/badge/Version-0.5.0-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 1.15.0](https://img.shields.io/badge/AppVersion-1.15.0-informational?style=flat-square)
+
+A Helm chart for Kubernetes
+
+## Values
+
+| Key | Type | Default | Description |
+|-----|------|---------|-------------|
+| backups.grip.graph | string | `"CALYPR"` |  |
+| backups.grip.host | string | `"grip-service.default.svc.cluster.local"` |  |
+| backups.image | string | `"quay.io/ohsu-comp-bio/backup-service:main"` |  |
+| backups.postgres.host | string | `"local-postgresql.default.svc.cluster.local"` |  |
+| backups.postgres.secret | string | `"local-postgresql"` |  |
+| backups.postgres.user | string | `"postgres"` |  |
+| backups.s3.bucket | string | `"calypr-backups"` |  |
+| backups.s3.dir | string | `"calypr-dev"` |  |
+| backups.s3.endpoint | string | `"https://aced-storage.ohsu.edu"` |  |
+| backups.s3.secret | string | `"s3-credentials"` |  |
+| backups.schedule | string | `"0 2 * * *"` |  |
+
+----------------------------------------------
+Autogenerated from chart metadata using [helm-docs v1.14.2](https://github.com/norwoodj/helm-docs/releases/v1.14.2)

helm/backups/templates/cronjob.yaml

@@ -0,0 +1,77 @@
+# templates/cronjob.yaml (or the new CronJob.yaml location in a Helm chart)
+apiVersion: batch/v1
+kind: CronJob
+metadata:
+  name: backup-service-cronjob
+spec:
+  # Use the schedule from values.yaml
+  schedule: "{{ .Values.backups.schedule }}"
+  jobTemplate:
+    spec:
+      template:
+        spec:
+          restartPolicy: OnFailure
+          containers:
+            - name: backup-service
+              image: "{{ .Values.backups.image }}"
+              imagePullPolicy: Always
+
+              env:
+                # GRIP Host
+                - name: GRIP_HOST
+                  value: "{{ .Values.backups.grip.host }}"
+
+                # GRIP Graph
+                - name: GRIP_GRAPH
+                  value: "{{ .Values.backups.grip.graph }}"
+
+                # Postgres Host
+                - name: PGHOST
+                  value: "{{ .Values.backups.postgres.host }}"
+
+                # Postgres User
+                - name: PGUSER
+                  value: "{{ .Values.backups.postgres.user }}"
+
+                # Postgres Password
+                # Note: this secret relies on the existing Gen3 Postgres secret
+                #       and is not expected to be created separately.
+                - name: PGPASSWORD
+                  valueFrom:
+                    secretKeyRef:
+                      name: "{{ .Values.backups.postgres.secret }}"
+                      key: postgres-password
+
+                # S3 Endpoint
+                - name: ENDPOINT
+                  value: "{{ .Values.backups.s3.endpoint }}"
+
+                # S3 Bucket
+                - name: BUCKET
+                  value: "{{ .Values.backups.s3.bucket }}"
+
+                # S3 Directory
+                - name: DIR
+                  value: "{{ .Values.backups.s3.dir }}"
+
+                # S3 Access Key
+                # TODO: This secret requires creation; it is not part of Gen3 by default.
+                #
+                # MinIO client requires the Access Key to be set to AWS_ACCESS_KEY
+                # Ref: https://github.com/minio/minio-py/blob/7.2.20/minio/credentials/providers.py#L251
+                - name: AWS_ACCESS_KEY
+                  valueFrom:
+                    secretKeyRef:
+                      name: "{{ .Values.backups.s3.secret }}"
+                      key: ACCESS_KEY
+
+                # S3 Secret Key
+                # TODO: This secret requires creation; it is not part of Gen3 by default.
+                #
+                # MinIO client requires the Secret Key to be set to AWS_SECRET_KEY
+                # Ref: https://github.com/minio/minio-py/blob/7.2.20/minio/credentials/providers.py#L258
+                - name: AWS_SECRET_KEY
+                  valueFrom:
+                    secretKeyRef:
+                      name: "{{ .Values.backups.s3.secret }}"
+                      key: SECRET_KEY

helm/backups/values.yaml

@@ -0,0 +1,23 @@
+# values.yaml
+backups:
+  # CronJob configuration (Daily at 2am)
+  schedule: "0 2 * * *"
+  image: "quay.io/ohsu-comp-bio/backup-service:main"
+
+  # GRIP
+  grip:
+    host: grip-service.default.svc.cluster.local
+    graph: CALYPR
+
+  # Postgres
+  postgres:
+    host: local-postgresql.default.svc.cluster.local
+    user: postgres
+    secret: local-postgresql
+
+  # S3
+  s3:
+    endpoint: https://aced-storage.ohsu.edu
+    bucket: calypr-backups
+    dir: "calypr-dev"
+    secret: s3-credentials

helm/funnel/.helmignore

@@ -0,0 +1,23 @@
+# Patterns to ignore when building packages.
+# This supports shell glob matching, relative path matching, and
+# negation (prefixed with !). Only one pattern per line.
+.DS_Store
+# Common VCS dirs
+.git/
+.gitignore
+.bzr/
+.bzrignore
+.hg/
+.hgignore
+.svn/
+# Common backup files
+*.swp
+*.bak
+*.tmp
+*.orig
+*~
+# Various IDEs
+.project
+.idea/
+*.tmproj
+.vscode/

helm/funnel/Chart.yaml

@@ -0,0 +1,37 @@
+apiVersion: v2
+name: funnel
+description: A toolkit for distributed task execution ⚙️
+keywords:
+  - funnel
+
+# A chart can be either an 'application' or a 'library' chart.
+#
+# Application charts are a collection of templates that can be packaged into versioned archives
+# to be deployed.
+#
+# Library charts provide useful utilities or functions for the chart developer. They're included as
+# a dependency of application charts to inject those utilities and functions into the rendering
+# pipeline. Library charts do not define any templates and therefore cannot be deployed.
+type: application
+
+# This is the chart version. This version number should be incremented each time you make changes
+# to the chart and its templates, including the app version.
+# Versions are expected to follow Semantic Versioning (https://semver.org/)
+version: 0.1.76
+
+# This is the version number of the application being deployed. This version number should be
+# incremented each time you make changes to the application. Versions are not expected to
+# follow Semantic Versioning. They should reflect the version the application is using.
+# It is recommended to use it with quotes.
+appVersion: "2025-12-22"
+
+dependencies:
+  - name: postgresql
+    version: 18.1.15
+    repository: https://charts.bitnami.com/bitnami
+    condition: postgresql.enabled
+
+  - name: mongodb
+    version: 13.9.4
+    repository: https://charts.bitnami.com/bitnami
+    condition: mongodb.enabled