Refactor pgstacbootstrap job and ConfigMaps to use Helm hooks for execution order (#207)

emmanuelmathot · web-flow · commit 0cbb6d7c1566 · 2025-04-09T17:14:11.000+02:00
* Refactor pgstacbootstrap job and ConfigMaps to use Helm hooks for execution order

* Update PGO_VERSION to 5.7.4 in helm-tests workflow

* Enhance debugging output for failed service boot and test failures in CI workflow

* Remove unnecessary Helm hook annotations for deployment order management

* ensure non empty annotations
diff --git a/.github/workflows/helm-tests.yml b/.github/workflows/helm-tests.yml
@@ -118,7 +118,40 @@ jobs:
       - name: cleanup if services fail to boot
         if: steps.watchservices.outcome == 'failure'
         run: |
-          echo "The previous step failed or timed out."
+          echo "The watchservices step failed or timed out. Extracting pod logs for debugging..."
+          
+          # Get and display all pods status
+          echo "===== Pod Status ====="
+          kubectl get pods
+          
+          # Extract logs from database pod
+          echo "===== Database Pod Logs ====="
+          kubectl get pod | grep "^db-$RELEASE_NAME" | cut -d' ' -f1 | xargs -I{} kubectl logs pod/{} --tail=100 || echo "Could not get database logs"
+          
+          # Extract logs from pgstacbootstrap pod
+          echo "===== PGSTACBootstrap Pod Logs ====="
+          kubectl get pod | grep "^pgstacbootstrap-$RELEASE_NAME" | cut -d' ' -f1 | xargs -I{} kubectl logs pod/{} --tail=100 || echo "Could not get pgstacbootstrap logs"
+          
+          # Extract logs from raster pod init container (wait-for-pgstacbootstrap)
+          echo "===== Raster Pod Init Container Logs (wait-for-pgstacbootstrap) ====="
+          kubectl get pod | grep "^raster-$RELEASE_NAME" | cut -d' ' -f1 | xargs -I{} kubectl logs pod/{} -c wait-for-pgstacbootstrap --tail=100 || echo "Could not get raster init container logs"
+          
+          # Extract logs from raster pod main container
+          echo "===== Raster Pod Main Container Logs ====="
+          kubectl get pod | grep "^raster-$RELEASE_NAME" | cut -d' ' -f1 | xargs -I{} kubectl logs pod/{} --tail=100 || echo "Could not get raster main container logs"
+          
+          # Extract logs from vector pod
+          echo "===== Vector Pod Logs ====="
+          kubectl get pod | grep "^vector-$RELEASE_NAME" | cut -d' ' -f1 | xargs -I{} kubectl logs pod/{} --tail=100 || echo "Could not get vector logs"
+          
+          # Extract logs from stac pod
+          echo "===== STAC Pod Logs ====="
+          kubectl get pod | grep "^stac-$RELEASE_NAME" | cut -d' ' -f1 | xargs -I{} kubectl logs pod/{} --tail=100 || echo "Could not get STAC logs"
+          
+          # Check if pods are in pending state or have issues
+          echo "===== Pod Descriptions for Troubleshooting ====="
+          kubectl get pod | grep "$RELEASE_NAME" | cut -d' ' -f1 | xargs -I{} kubectl describe pod/{} || echo "Could not describe pods"
+          
           # force GH action to show failed result
           exit 128
 
@@ -145,18 +178,51 @@ jobs:
           echo $RASTER_ENDPOINT
           echo '#################################'
 
-          pytest .github/workflows/tests/test_vector.py || kubectl logs svc/vector-$RELEASE_NAME
-          pytest .github/workflows/tests/test_stac.py
+          pytest .github/workflows/tests/test_vector.py || kubectl logs svc/vector
+          pytest .github/workflows/tests/test_stac.py || kubectl logs svc/stac
           # TODO: fix raster tests
-          #pytest .github/workflows/tests/test_raster.py
+          #pytest .github/workflows/tests/test_raster.py || kubectl logs svc/raster
 
       - name: error if tests failed
         if: steps.testrunner.outcome == 'failure'
         run: |
-          echo "The previous step failed or timed out."
+          echo "The tests failed. Extracting pod logs for debugging..."
+          
+          # Get and display all pods status
+          echo "===== Pod Status ====="
+          kubectl get pods
+          
+          # Extract logs from database pod
+          echo "===== Database Pod Logs ====="
+          kubectl get pod | grep "^db-$RELEASE_NAME" | cut -d' ' -f1 | xargs -I{} kubectl logs pod/{} --tail=100 || echo "Could not get database logs"
+          
+          # Extract logs from pgstacbootstrap pod
+          echo "===== PGSTACBootstrap Pod Logs ====="
+          kubectl get pod | grep "^pgstacbootstrap-$RELEASE_NAME" | cut -d' ' -f1 | xargs -I{} kubectl logs pod/{} --tail=100 || echo "Could not get pgstacbootstrap logs"
+          
+          # Extract logs from raster pod init container (wait-for-pgstacbootstrap)
+          echo "===== Raster Pod Init Container Logs (wait-for-pgstacbootstrap) ====="
+          kubectl get pod | grep "^raster-$RELEASE_NAME" | cut -d' ' -f1 | xargs -I{} kubectl logs pod/{} -c wait-for-pgstacbootstrap --tail=100 || echo "Could not get raster init container logs"
+          
+          # Extract logs from raster pod main container
+          echo "===== Raster Pod Main Container Logs ====="
+          kubectl get pod | grep "^raster-$RELEASE_NAME" | cut -d' ' -f1 | xargs -I{} kubectl logs pod/{} --tail=100 || echo "Could not get raster main container logs"
+          
+          # Extract logs from vector pod
+          echo "===== Vector Pod Logs ====="
+          kubectl get pod | grep "^vector-$RELEASE_NAME" | cut -d' ' -f1 | xargs -I{} kubectl logs pod/{} --tail=100 || echo "Could not get vector logs"
+          
+          # Extract logs from stac pod
+          echo "===== STAC Pod Logs ====="
+          kubectl get pod | grep "^stac-$RELEASE_NAME" | cut -d' ' -f1 | xargs -I{} kubectl logs pod/{} --tail=100 || echo "Could not get STAC logs"
+          
+          # Check if pods are in pending state or have issues
+          echo "===== Pod Descriptions for Troubleshooting ====="
+          kubectl get pod | grep "$RELEASE_NAME" | cut -d' ' -f1 | xargs -I{} kubectl describe pod/{} || echo "Could not describe pods"
+          
           # force GH action to show failed result
           exit 128
 
       - name: helm uninstall eoapi templates
         run: |
-          helm uninstall $RELEASE_NAME
+          helm uninstall $RELEASE_NAME
diff --git a/helm-chart/eoapi/templates/pgstacboostrap/configmap.yaml b/helm-chart/eoapi/templates/pgstacboostrap/configmap.yaml
@@ -1,9 +1,16 @@
 {{- if .Values.pgstacBootstrap.enabled }}
 ---
+# These ConfigMaps provide the necessary data and scripts for the pgstacbootstrap job.
+# They use Helm hooks with a weight of "-6" (lower than the job's "-5") to ensure
+# they are created before the job that depends on them.
 apiVersion: v1
 kind: ConfigMap
 metadata:
   name: initdb-sql-config-{{ $.Release.Name }}
+  annotations:
+    helm.sh/hook: "post-install,post-upgrade"
+    helm.sh/hook-weight: "-6"
+    helm.sh/hook-delete-policy: "before-hook-creation,hook-succeeded"
 data:
   initdb.sql: |
     {{- range $path, $bytes := $.Files.Glob "initdb-data/*.sql"  -}}
@@ -14,6 +21,10 @@ apiVersion: v1
 kind: ConfigMap
 metadata:
   name: initdb-json-config-{{ $.Release.Name }}
+  annotations:
+    helm.sh/hook: "post-install,post-upgrade"
+    helm.sh/hook-weight: "-6"
+    helm.sh/hook-delete-policy: "before-hook-creation,hook-succeeded"
 data:
   {{- range $path, $bytes := $.Files.Glob "initdb-data/*.json"  -}}
   {{- base $path | nindent 2 -}}: | {{- $.Files.Get $path | nindent 4 -}}
@@ -23,6 +34,10 @@ apiVersion: v1
 kind: ConfigMap
 metadata:
   name: pgstac-setup-config-{{ $.Release.Name }}
+  annotations:
+    helm.sh/hook: "post-install,post-upgrade"
+    helm.sh/hook-weight: "-6"
+    helm.sh/hook-delete-policy: "before-hook-creation,hook-succeeded"
 data:
   pgstac-migrate.py: |
     {{- range $path, $bytes := $.Files.Glob "initdb-data/*.py"  -}}
@@ -33,6 +48,10 @@ apiVersion: v1
 kind: ConfigMap
 metadata:
   name: initdb-sh-config-{{ $.Release.Name }}
+  annotations:
+    helm.sh/hook: "post-install,post-upgrade"
+    helm.sh/hook-weight: "-6"
+    helm.sh/hook-delete-policy: "before-hook-creation,hook-succeeded"
 data:
   run-forever.sh: |
     #!/bin/bash
diff --git a/helm-chart/eoapi/templates/pgstacboostrap/job.yaml b/helm-chart/eoapi/templates/pgstacboostrap/job.yaml
@@ -1,27 +1,32 @@
 {{- if .Values.pgstacBootstrap.enabled }}
 ---
+# This job initializes the PostgreSQL database with the necessary schema and data.
+# Instead of using an initContainer in the deployment to wait for this job to complete,
+# we use Helm hooks to control the execution order:
+# 
+# 1. The "post-install,post-upgrade" hook ensures this job runs after the postgres 
+#    dependency is installed but before other resources (like deployments)
+# 2. The "-5" hook-weight ensures this job runs after its ConfigMaps (weight -6)
+# 3. The "before-hook-creation,hook-succeeded" delete policy ensures the job is recreated
+#    on each helm install/upgrade and is cleaned up after successful completion
+#
 apiVersion: batch/v1
 kind: Job
 metadata:
   name: pgstacbootstrap
   labels:
     app: pgstacbootstrap
+  annotations:
+    helm.sh/hook: "post-install,post-upgrade"
+    helm.sh/hook-weight: "-5"
+    helm.sh/hook-delete-policy: "before-hook-creation,hook-succeeded"
 spec:
   template:
     metadata:
       labels:
         app: pgstacbootstrap
     spec:
       restartPolicy: Never
-      initContainers:
-        - name: wait-for-db
-          image: busybox
-          command:
-            {{ if .Values.testing }}
-            ['sh', '-c', 'until nc -z {{ $.Release.Name }}-pgbouncer 5432; do echo waiting for db; sleep 10; done;']
-            {{ else }}
-            ['sh', '-c', 'until nc -z eoapi-pgbouncer 5432; do echo waiting for db; sleep 10; done;']
-            {{ end }}
       containers:
         - name: pgstacbootstrap
           image: {{ .Values.pgstacBootstrap.image.name }}:{{ .Values.pgstacBootstrap.image.tag }}
diff --git a/helm-chart/eoapi/templates/services/deployment.yaml b/helm-chart/eoapi/templates/services/deployment.yaml
@@ -9,9 +9,11 @@ metadata:
     app: {{ $serviceName }}-{{ $.Release.Name }}
     gitsha: {{ $.Values.gitSha }}
   name: {{ $serviceName }}-{{ $.Release.Name }}
-  {{- with index $v "annotations" }}
+  {{- if index $v "annotations" }}
   annotations:
+    {{- with index $v "annotations" }}
     {{- toYaml . | nindent 4 }}
+    {{- end }}
   {{- end }}
 spec:
   progressDeadlineSeconds: 600
@@ -30,19 +32,6 @@ spec:
         app: {{ $serviceName }}-{{ $.Release.Name }}
     spec:
       serviceAccountName: eoapi-sa-{{ $.Release.Name }}
-      initContainers:
-      - name: wait-for-pgstacbootstrap
-        image: bitnami/kubectl:latest
-        command:
-        - /bin/sh
-        - -c
-        - |
-          echo "Waiting for pgstacbootstrap job to complete..."
-          while ! kubectl -n {{ $.Release.Namespace }} wait --for=condition=complete job/pgstacbootstrap --timeout=5s; do
-            echo "pgstacbootstrap job not completed yet. Checking again in 10 seconds..."
-            sleep 10
-          done
-          echo "pgstacbootstrap job completed successfully"
       containers:
       - image: {{ index $v "image" "name" }}:{{ index $v "image" "tag" }}
         name: {{ $serviceName }}
