Merge branch 'master' into fix/dicom-setup

uc-cdis · May 1, 2024 · a9d20e9 · a9d20e9
2 parents 45c4846 + 4d346ff
commit a9d20e9
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Showing 3 changed files with 100 additions and 13 deletions.
diff --git a/kube/services/argo-events/workflows/sensor-created.yaml b/kube/services/argo-events/workflows/sensor-created.yaml
@@ -59,12 +59,22 @@ spec:
                         args:
                           - "-c"
                           - |
+                            #!/bin/bash
+                            if [ -z "$PROVISIONER_TEMPLATE" ]; then
+                              PROVISIONER_TEMPLATE="provisioner.yaml"
+                            fi
+
+                            if [ -z "$AWSNODETEMPLATE_TEMPLATE" ]; then
+                              AWSNODETEMPLATE_TEMPLATE="nodetemplate.yaml"
+                            fi
+
+
                             if ! kubectl get awsnodetemplate workflow-$WORKFLOW_NAME >/dev/null 2>&1; then
-                              sed -e "s/WORKFLOW_NAME/$workflow_name/" -e "s/GEN3_USERNAME/$workflow_user/" -e "s/ENVIRONMENT/$ENVIRONMENT/"  | kubectl apply -f - 
+                              sed -e "s/WORKFLOW_NAME/$WORKFLOW_NAME/" -e "s/GEN3_USERNAME/$GEN3_USERNAME/" -e "s/ENVIRONMENT/$ENVIRONMENT/" "$AWSNODETEMPLATE_TEMPLATE" | kubectl apply -f - 
                             fi
 
                             if ! kubectl get provisioner workflow-$WORKFLOW_NAME >/dev/null 2>&1; then
-                              sed -e "s/WORKFLOW_NAME/$workflow_name/" -e "s/GEN3_USERNAME/$workflow_user/" -e "s/ENVIRONMENT/$ENVIRONMENT/"  | kubectl apply -f - 
+                              sed -e "s/WORKFLOW_NAME/$WORKFLOW_NAME/" -e "s/GEN3_USERNAME/$GEN3_USERNAME/" -e "s/ENVIRONMENT/$ENVIRONMENT/"  "$PROVISIONER_TEMPLATE" | kubectl apply -f - 
                             fi
                         env:
                           - name: WORKFLOW_NAME
@@ -76,9 +86,13 @@ spec:
                               configMapKeyRef:
                                 name: environment
                                 key: environment
+                          - name: PROVISIONER_TEMPLATE
+                            value: /manifests/provisioner.yaml
+                          - name: AWSNODETEMPLATE_TEMPLATE
+                            value: /manifests/nodetemplate.yaml
                         volumeMounts:
                           - name: karpenter-templates-volume
-                            mountPath: /home/manifests
+                            mountPath: /manifests
                     volumes:
                       - name: karpenter-templates-volume
                         configMap:

diff --git a/kube/services/karpenter-reconciler/karpenter-reconciler-cronjob-va-testing.yaml b/kube/services/karpenter-reconciler/karpenter-reconciler-cronjob-va-testing.yaml
@@ -0,0 +1,71 @@
+apiVersion: batch/v1
+kind: CronJob
+metadata:
+  name: karpenter-reconciler-cronjob-va-testing
+  namespace: argo-events
+spec:
+  schedule: "*/5 * * * *"
+  jobTemplate:
+    spec:
+      template:
+        metadata:
+          labels:
+            app: gen3job
+        spec:
+          serviceAccount: karpenter-reconciler
+          volumes:
+            - name: karpenter-templates-volume
+              configMap:
+                name: karpenter-templates
+          containers:
+            - name: karpenter-reconciler
+              image: quay.io/cdis/awshelper
+              volumeMounts:
+                - name: karpenter-templates-volume
+                  mountPath: /manifests
+              env:
+                - name: PROVISIONER_TEMPLATE
+                  value: /manifests/provisioner.yaml
+                - name: AWSNODETEMPLATE_TEMPLATE
+                  value: /manifests/nodetemplate.yaml
+              command: ["/bin/bash"]
+              args:
+                - "-c"
+                - |
+                  #!/bin/bash
+                  if [ -z "$PROVISIONER_TEMPLATE" ]; then
+                    PROVISIONER_TEMPLATE="provisioner.yaml"
+                  fi
+
+                  if [ -z "$AWSNODETEMPLATE_TEMPLATE" ]; then
+                    AWSNODETEMPLATE_TEMPLATE="nodetemplate.yaml"
+                  fi
+
+                  ENVIRONMENT=$(kubectl -n va-testing get configmap global -o jsonpath="{.data.environment}")
+
+                  WORKFLOWS=$(kubectl get workflows -n argo -o=jsonpath='{range .items[*]}{.metadata.name}{" "}{.metadata.labels.gen3username}{"\n"}')
+
+                  WORKFLOW_ARRAY=()
+
+                  while IFS= read -r line; do
+                    WORKFLOW_ARRAY+=("$line")
+                  done <<< "$WORKFLOWS"
+
+                  for workflow in "${WORKFLOW_ARRAY[@]}"
+                  do
+                    echo "Running loop for workflow: $workflow"
+                    workflow_name=$(echo "$workflow" | awk '{print $1}')
+                    workflow_user=$(echo "$workflow" | awk '{print $2}')
+
+                    if ! kubectl get awsnodetemplate workflow-$workflow_name >/dev/null 2>&1; then
+                      echo "No awsnodetemplate found for ${workflow_name}, creating one"
+                      sed -e "s/WORKFLOW_NAME/$workflow_name/" -e "s/GEN3_USERNAME/$workflow_user/" -e "s/ENVIRONMENT/$ENVIRONMENT/" "$AWSNODETEMPLATE_TEMPLATE" | kubectl apply -f -
+                    fi
+
+                    if ! kubectl get provisioner workflow-$workflow_name >/dev/null 2>&1; then
+                      echo "No provisioner found for ${workflow_name}, creating one"
+                      sed -e "s/WORKFLOW_NAME/$workflow_name/" -e "s/GEN3_USERNAME/$workflow_user/" -e "s/ENVIRONMENT/$ENVIRONMENT/" "$PROVISIONER_TEMPLATE" | kubectl apply -f -
+
+                    fi
+                  done
+          restartPolicy: OnFailure
diff --git a/kube/services/karpenter-reconciler/karpenter-reconciler-cronjob.yaml b/kube/services/karpenter-reconciler/karpenter-reconciler-cronjob.yaml
@@ -43,30 +43,32 @@ spec:
 
                   ENVIRONMENT=$(kubectl -n default get configmap global -o jsonpath="{.data.environment}")
 
-                  RAW_WORKFLOWS=$(kubectl get workflows -n argo -o yaml)
-
-                  WORKFLOWS=$(echo "${RAW_WORKFLOWS}" | yq -r '.items[] | [.metadata.name, .metadata.labels.gen3username] | join(" ")')
+                  WORKFLOWS=$(kubectl get workflows -n argo -o=jsonpath='{range .items[*]}{.metadata.name}{" "}{.metadata.labels.gen3username}{"\n"}')
 
                   WORKFLOW_ARRAY=()
 
                   while IFS= read -r line; do
                     WORKFLOW_ARRAY+=("$line")
                   done <<< "$WORKFLOWS"
 
+                  echo $WORKFLOWS
+
                   for workflow in "${WORKFLOW_ARRAY[@]}"
                   do
                     workflow_name=$(echo "$workflow" | awk '{print $1}')
                     workflow_user=$(echo "$workflow" | awk '{print $2}')
 
-                    if ! kubectl get awsnodetemplate workflow-$workflow_name >/dev/null 2>&1; then
-                      echo "No awsnodetemplate found for ${workflow_name}, creating one"
-                      sed -e "s/WORKFLOW_NAME/$workflow_name/" -e "s/GEN3_USERNAME/$workflow_user/" -e "s/ENVIRONMENT/$ENVIRONMENT/" "$AWSNODETEMPLATE_TEMPLATE" | kubectl apply -f -
-                    fi
+                    if [ ! -z "$workflow_name" ]; then
+                      if ! kubectl get awsnodetemplate workflow-$workflow_name >/dev/null 2>&1; then
+                        echo "No awsnodetemplate found for ${workflow_name}, creating one"
+                        sed -e "s/WORKFLOW_NAME/$workflow_name/" -e "s/GEN3_USERNAME/$workflow_user/" -e "s/ENVIRONMENT/$ENVIRONMENT/" "$AWSNODETEMPLATE_TEMPLATE" | kubectl apply -f -
+                      fi
 
-                    if ! kubectl get provisioner workflow-$workflow_name >/dev/null 2>&1; then
-                      echo "No provisioner found for ${workflow_name}, creating one"
-                      sed -e "s/WORKFLOW_NAME/$workflow_name/" -e "s/GEN3_USERNAME/$workflow_user/" -e "s/ENVIRONMENT/$ENVIRONMENT/" "$PROVISIONER_TEMPLATE" | kubectl apply -f -
+                      if ! kubectl get provisioner workflow-$workflow_name >/dev/null 2>&1; then
+                        echo "No provisioner found for ${workflow_name}, creating one"
+                        sed -e "s/WORKFLOW_NAME/$workflow_name/" -e "s/GEN3_USERNAME/$workflow_user/" -e "s/ENVIRONMENT/$ENVIRONMENT/" "$PROVISIONER_TEMPLATE" | kubectl apply -f -
 
+                      fi
                     fi
                   done
           restartPolicy: OnFailure