Merge pull request #19 from FNNDSC/dev

Support adding of podAnnotations for linkerd

charts/chris/Chart.yaml

@@ -17,7 +17,7 @@ keywords:
 icon: ./logo_chris.png
 
 type: application
-version: "0.10.2"
+version: "0.11.0"
 appVersion: "5.0.0"
 
 maintainers:

charts/chris/templates/server.yml

@@ -17,7 +17,7 @@ spec:
   template:
     metadata:
       name: {{ .Release.Name }}-server
-      {{- with .Values.podAnnotations }}
+      {{- with .Values.cube.server.podAnnotations }}
       annotations:
         {{- toYaml . | nindent 8 }}
       {{- end }}
@@ -74,4 +74,4 @@ spec:
       targetPort: 8000
       {{- if .Values.cube.server.service.nodePort }}
       nodePort: {{ .Values.cube.server.service.nodePort }}
-      {{- end }}
+      {{- end }}

charts/chris/values.yaml

@@ -162,6 +162,7 @@ cube:
       # nodePort:
       ## nodePortHost does nothing. It is simply used to print the URL of CUBE in the NOTES
       # nodePortHost:
+    podAnnotations: {}
     ## resources for the HTTP server (WSGI).
     ## Default values should be okay. About 256Mi of memory is needed per idle worker.
     resources:

extra/pfdcm-linkerd-service-profile.yml

@@ -0,0 +1,27 @@
+apiVersion: linkerd.io/v1alpha2
+kind: ServiceProfile
+metadata:
+  name: name-needs-to-be-changed
+  namespace: chris
+  labels:
+    app.kubernetes.io/part-of: chris
+spec:
+  routes:
+    - name: '/api/v1/PACS/thread/pypx/'
+      condition:
+        pathRegex: '/api/v1/PACS/thread/pypx/'
+        method: POST
+      isRetryable: true
+      timeout: 10s
+    - name: '/api/v1/PACS/sync/pypx/'
+      condition:
+        pathRegex: '/api/v1/PACS/sync/pypx/'
+        method: POST
+      isRetryable: true
+      timeout: 10s
+  # https://linkerd.io/2.15/reference/service-profiles/#retry-budget
+  retryBudget:
+    retryRatio: 0.2
+    minRetriesPerSecond: 10
+    ttl: 10s
+

testing/default-values.yaml

@@ -8,6 +8,8 @@ cube:
     service:
       type: NodePort
       nodePort: 32000
+    podAnnotations:
+      linkerd.io/inject: enabled
     resources:
       limits:
         cpu: 1
@@ -18,6 +20,14 @@ cube:
   config:
     GUNICORN_CMD_ARGS: "--workers=4 --timeout=3600"
 
+postgresql:
+  primary:
+    podAnnotations:
+      linkerd.io/inject: enable
+    service:
+      annotations:
+        config.linkerd.io/opaque-ports: "5432"
+
 pfcon:
   storage:
     size: 10Gi
@@ -27,6 +37,8 @@ pfdcm:
   service:
     type: NodePort
     nodePort: 32001
+  podAnnotations:
+    linkerd.io/inject: enabled
   listener:
     service:
       type: NodePort
@@ -39,15 +51,17 @@ pfdcm:
       - name: OTEL_RESOURCE_ATTRIBUTES
         value: service.name=oxidicom
       - name: OTEL_EXPORTER_OTLP_ENDPOINT
-        value: http://tempo.grafana.svc.cluster.local:4318
+        value: http://otel-collector-opentelemetry-collector.observe.svc.cluster.local:4318
     resources:
       limits:
         cpu: 500m
         memory: 2Gi
       requests:
         cpu: 500m
         memory: 2Gi
+
 orthanc:
+  enabled: true
   service:
     type: NodePort
     nodePort: 32003

testing/justfile

@@ -96,6 +96,13 @@ observe:
     kubectl wait --for=condition=ready -n observe pod -l app.kubernetes.io/name=grafana --timeout=300s
     helm upgrade --install -n observe -f observe/opentelemetry-collector.yaml otel-collector open-telemetry/opentelemetry-collector
 
+linkerd:
+    linkerd check --pre
+    linkerd install --crds | kubectl apply -f -
+    linkerd install | kubectl apply -f -
+    linkerd viz install | kubectl apply -f -
+    linkerd check
+
 # Helper Functions
 # --------------------------------------------------------------------------------
 

testing/observe/opentelemetry-collector.yaml

@@ -20,7 +20,8 @@ presets:
     extractAllPodAnnotations: false
   # See https://opentelemetry.io/docs/kubernetes/collector/components/#kubeletstats-receiver for details on the receiver.
   kubeletMetrics:
-    enabled: true
+    # The kube-prometheus-stack is already collecting this data.
+    enabled: false
   # See https://opentelemetry.io/docs/kubernetes/collector/components/#kubernetes-objects-receiver for details on the receiver.
   kubernetesEvents:
     enabled: false
@@ -61,7 +62,6 @@ config:
           endpoint: ${env:MY_POD_IP}:4318
     kubeletstats:
       insecure_skip_verify: true
-
     # prometheus:
     #   config:
     #     scrape_configs:

testing/observe/prom-stack.yaml

@@ -1,10 +1,4 @@
-# TODO replace with Grafana and Mimir
-
-# disable most stuff, we get metrics from the OpenTelemetry collector instead.
-defaultRules:
-  create: false
-kubernetesServiceMonitors:
-  enabled: false
+# Consider replacing kube-prometheus-stack with just Grafana and Mimir?
 
 alertmanager:
   enabled: false