chore(k8s): configure prod overlay for quantms-ddalfq deployment

[t0mdavid-m]

Wire the prod Kustomize overlay to the OpenMS Traefik cluster:

• namePrefix/commonLabels: quantms-ddalfq
• image: ghcr.io/openms/quantms-web:main-full
• IngressRoute: opendda.webapps.openms.{de,org}
• Redis URL pointed at quantms-ddalfq-redis
• memory-tier-high component (heavy DIA/LFQ workloads)
• Workspace PVC sized to 3Ti

Summary by CodeRabbit

Release Notes

• Chores
  • Increased workspace storage capacity to 3 terabytes
  • Updated production environment configuration with new service names and hostnames
  • Modified Redis connection settings for production deployments
  • Enhanced production memory tier configuration

[coderabbitai]

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ℹ️ Review info

⚙️ Run configuration

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📥 Commits

Reviewing files that changed from the base of the PR and between 7ca8dbe and cb1bd20.

📒 Files selected for processing (1)

• .github/workflows/build-and-test.yml

📝 Walkthrough

Walkthrough

Updates Kubernetes manifests to increase workspace storage capacity from 500Gi to 3Ti and reconfigure the production overlay environment with new application naming, memory tier settings, image references, and service connections.

Changes

Cohort / File(s)	Summary
Kubernetes Base Configuration k8s/base/workspace-pvc.yaml	Increases PersistentVolumeClaim storage capacity from 500Gi to 3Ti.
Production Deployment Configuration k8s/overlays/prod/kustomization.yaml	Migrates prod overlay from template-app to quantms-ddalfq naming, upgrades memory tier to high, updates image reference to ghcr.io/openms/quantms-web, changes IngressRoute hostnames from template.webapps.openms.* to opendda.webapps.openms.*, and updates Redis service connections in streamlit and rq-worker deployments.

Poem

🐰 From template's days to quantms new,
Storage swells to three tiers through,
Redis redirects with proper care,
Production infrastructure, debonair!

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and concisely summarizes the main change: configuring the production Kustomize overlay for the quantms-ddalfq deployment, which aligns with the primary objectives of the changeset.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch setup_deployment

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[coderabbitai]

Actionable comments posted: 1

🧹 Nitpick comments (3)

k8s/overlays/prod/kustomization.yaml (3)

31-44: Positional env/0 JSON patch is brittle — prefer a strategic merge by env name.

Both Redis patches target /spec/template/spec/containers/0/env/0/value, which silently depends on REDIS_URL remaining the first entry in the base deployments' env list (k8s/base/streamlit-deployment.yaml and k8s/base/rq-worker-deployment.yaml). If anyone reorders env vars in base, these patches will quietly overwrite the wrong variable instead of failing. A strategic merge patch keyed by name: REDIS_URL is safer and self-documenting.

♻️ Proposed refactor

-  - target:
-      kind: Deployment
-      name: streamlit
-    patch: |
-      - op: replace
-        path: /spec/template/spec/containers/0/env/0/value
-        value: "redis://quantms-ddalfq-redis:6379/0"
-  - target:
-      kind: Deployment
-      name: rq-worker
-    patch: |
-      - op: replace
-        path: /spec/template/spec/containers/0/env/0/value
-        value: "redis://quantms-ddalfq-redis:6379/0"
+  - patch: |-
+      apiVersion: apps/v1
+      kind: Deployment
+      metadata:
+        name: streamlit
+      spec:
+        template:
+          spec:
+            containers:
+              - name: streamlit
+                env:
+                  - name: REDIS_URL
+                    value: "redis://quantms-ddalfq-redis:6379/0"
+  - patch: |-
+      apiVersion: apps/v1
+      kind: Deployment
+      metadata:
+        name: rq-worker
+      spec:
+        template:
+          spec:
+            containers:
+              - name: rq-worker
+                env:
+                  - name: REDIS_URL
+                    value: "redis://quantms-ddalfq-redis:6379/0"

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@k8s/overlays/prod/kustomization.yaml` around lines 31 - 44, The JSON patches
currently replace /spec/template/spec/containers/0/env/0/value which is brittle;
update the two patches for the Deployment targets named streamlit and rq-worker
to use a strategic merge patch (or patchStrategicMerge) that matches the env
entry by name "REDIS_URL" and sets its value to
"redis://quantms-ddalfq-redis:6379/0" instead of using positional env/0; locate
the patches referencing those Deployment names (streamlit, rq-worker) and
replace the positional JSON patch with a strategic merge fragment that contains
the container env entry { name: REDIS_URL, value:
"redis://quantms-ddalfq-redis:6379/0" } so the patch is resilient to env
reordering.

---

12-13: Migrate commonLabels to the labels field for full Kustomize compatibility.

commonLabels is deprecated in recent Kustomize releases (v5.3+) and generates warnings. While still functional, migrating to the labels field with explicit control is recommended. Use kustomize edit fix to automate this migration, or manually update as shown below.

♻️ Suggested migration (to preserve current behavior)

-commonLabels:
-  app: quantms-ddalfq
+labels:
+  - pairs:
+      app: quantms-ddalfq
+    includeSelectors: true
+    includeTemplates: true

Set both includeSelectors: true and includeTemplates: true to maintain full parity with the original commonLabels behavior (labels applied to metadata, selectors, and templates). Omit includeTemplates or set includeSelectors: false if you only want labels added to metadata without selector injection.

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@k8s/overlays/prod/kustomization.yaml` around lines 12 - 13, Replace the
top-level commonLabels mapping with a new labels block: remove the commonLabels:
app: quantms-ddalfq entry and create labels containing includeSelectors: true
and includeTemplates: true plus the label mapping (app: quantms-ddalfq) so the
label is applied to metadata, selectors and templates; use the symbols
commonLabels, labels, includeSelectors and includeTemplates to find and update
the kustomization YAML.

---

21-30: Hardcoded quantms-ddalfq-streamlit couples the IngressRoute patch to namePrefix.

Since Traefik's IngressRoute is a CRD, Kustomize's default nameReference transformer doesn't rewrite the services[].name field, so the explicit value here is necessary. However, it now has to be kept in sync manually with namePrefix (Line 10)—changing one without the other will silently route to a non-existent service.

Consider either:

1. Adding a short comment noting the coupling, or
2. Registering a configurations: entry with a nameReference for IngressRoute.spec.routes[].services[].name so Kustomize rewrites it automatically (the standard pattern for custom resources without builtin support).

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@k8s/overlays/prod/kustomization.yaml` around lines 21 - 30, The IngressRoute
patch hardcodes the service name ("quantms-ddalfq-streamlit") which must stay in
sync with the kustomize namePrefix; replace this brittle approach by registering
a nameReference in kustomize configurations so Kustomize rewrites
IngressRoute.spec.routes[].services[].name automatically (or at minimum add a
clear inline comment noting the coupling). Update the kustomization to include a
configurations: entry that maps the custom resource kind IngressRoute and the
field spec.routes[].services[].name as a nameReference, or add a short comment
next to the patch mentioning it must match namePrefix whenever namePrefix
changes.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@k8s/base/workspace-pvc.yaml`:
- Line 11: The base PersistentVolumeClaim "workspaces-pvc" was changed to
request 3Ti at spec.resources.requests.storage, which will affect all
environments; instead revert that change in the base and add a prod-only
strategic merge patch that updates "workspaces-pvc" to storage: 3Ti in the prod
overlay. Create a new overlay patch (e.g., workspace-pvc-patch.yaml) containing
the PersistentVolumeClaim metadata name: workspaces-pvc and
spec.resources.requests.storage: 3Ti, then reference it from the prod
kustomization under patchesStrategicMerge so only the prod overlay receives the
increased size.

---

Nitpick comments:
In `@k8s/overlays/prod/kustomization.yaml`:
- Around line 31-44: The JSON patches currently replace
/spec/template/spec/containers/0/env/0/value which is brittle; update the two
patches for the Deployment targets named streamlit and rq-worker to use a
strategic merge patch (or patchStrategicMerge) that matches the env entry by
name "REDIS_URL" and sets its value to "redis://quantms-ddalfq-redis:6379/0"
instead of using positional env/0; locate the patches referencing those
Deployment names (streamlit, rq-worker) and replace the positional JSON patch
with a strategic merge fragment that contains the container env entry { name:
REDIS_URL, value: "redis://quantms-ddalfq-redis:6379/0" } so the patch is
resilient to env reordering.
- Around line 12-13: Replace the top-level commonLabels mapping with a new
labels block: remove the commonLabels: app: quantms-ddalfq entry and create
labels containing includeSelectors: true and includeTemplates: true plus the
label mapping (app: quantms-ddalfq) so the label is applied to metadata,
selectors and templates; use the symbols commonLabels, labels, includeSelectors
and includeTemplates to find and update the kustomization YAML.
- Around line 21-30: The IngressRoute patch hardcodes the service name
("quantms-ddalfq-streamlit") which must stay in sync with the kustomize
namePrefix; replace this brittle approach by registering a nameReference in
kustomize configurations so Kustomize rewrites
IngressRoute.spec.routes[].services[].name automatically (or at minimum add a
clear inline comment noting the coupling). Update the kustomization to include a
configurations: entry that maps the custom resource kind IngressRoute and the
field spec.routes[].services[].name as a nameReference, or add a short comment
next to the patch mentioning it must match namePrefix whenever namePrefix
changes.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 1e7abc86-f080-482d-87a1-21efd0028c6b

📥 Commits

Reviewing files that changed from the base of the PR and between 076351b and 7ca8dbe.

📒 Files selected for processing (2)

• k8s/base/workspace-pvc.yaml
• k8s/overlays/prod/kustomization.yaml

[coderabbitai]

⚠️ Potential issue | 🟠 Major

Scope drift: this base PVC change applies to all overlays, not just prod.

Line 11 raises the base request to 3Ti, which affects every environment inheriting k8s/base. The PR objective is prod-only sizing, so this should be done as an overlay patch in production to avoid unintended cost/capacity impact elsewhere.

Suggested direction

# k8s/base/workspace-pvc.yaml
-      storage: 3Ti
+      storage: 500Gi

# k8s/overlays/prod/workspace-pvc-patch.yaml (new)
apiVersion: v1
kind: PersistentVolumeClaim
metadata:
  name: workspaces-pvc
spec:
  resources:
    requests:
      storage: 3Ti

# k8s/overlays/prod/kustomization.yaml
patchesStrategicMerge:
  - workspace-pvc-patch.yaml

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@k8s/base/workspace-pvc.yaml` at line 11, The base PersistentVolumeClaim
"workspaces-pvc" was changed to request 3Ti at spec.resources.requests.storage,
which will affect all environments; instead revert that change in the base and
add a prod-only strategic merge patch that updates "workspaces-pvc" to storage:
3Ti in the prod overlay. Create a new overlay patch (e.g.,
workspace-pvc-patch.yaml) containing the PersistentVolumeClaim metadata name:
workspaces-pvc and spec.resources.requests.storage: 3Ti, then reference it from
the prod kustomization under patchesStrategicMerge so only the prod overlay
receives the increased size.