Chore/clean up (#1320)

* chore(cleanup): minor * feat(status): refactor code for checking status
uc-cdis · Jul 14, 2020 · b552fd6 · b552fd6
1 parent 0805e00
commit b552fd6
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Showing 3 changed files with 23 additions and 8 deletions.
diff --git a/gen3/bin/bucket-manifest.sh b/gen3/bin/bucket-manifest.sh
@@ -142,8 +142,8 @@ EOF
 
   # Run k8s jobs to submitting jobs and consuming sqs
   local sqsUrl=$(aws sqs get-queue-url --queue-name $sqs_name | jq -r .QueueUrl)
-  gen3 gitops filter $HOME/cloud-automation/kube/services/jobs/bucket-manifest-job.yaml BUCKET $bucket JOB_QUEUE $job_queue JOB_DEFINITION $job_definition SQS $sqsUrl AUTHZ "$authz" OUT_BUCKET $temp_bucket | sed "s|sa-#SA_NAME_PLACEHOLDER#|$saName|g" | sed "s|bucket-manifest#PLACEHOLDER#|bucket-manifest-${jobId}|g" > ./bucket-manifest-${jobId}-job.yaml
-  gen3 job run ./bucket-manifest-${jobId}-job.yaml
+  gen3 gitops filter $HOME/cloud-automation/kube/services/jobs/bucket-manifest-job.yaml BUCKET $bucket JOB_QUEUE $job_queue JOB_DEFINITION $job_definition SQS $sqsUrl AUTHZ "$authz" OUT_BUCKET $temp_bucket | sed "s|sa-#SA_NAME_PLACEHOLDER#|$saName|g" | sed "s|bucket-manifest#PLACEHOLDER#|bucket-manifest-${jobId}|g" > ./aws-bucket-manifest-${jobId}-job.yaml
+  gen3 job run ./aws-bucket-manifest-${jobId}-job.yaml
   gen3_log_info "The job is started. Job ID: ${jobId}"
 
 }
@@ -153,7 +153,17 @@ EOF
 # @param job-id
 #
 gen3_manifest_generating_status() {
-  gen3_log_info "Please use kubectl logs -f bucket-manifest-{jobid}-xxx command"
+  if [[ $# -lt 1 ]]; then
+    gen3_log_info "An jobId is required"
+    exit 1
+  fi
+  jobid=$1
+  pod_name=$(g3kubectl get pod | grep aws-bucket-manifest-$jobid | grep -e Completed -e Running | cut -d' ' -f1)
+  if [[ $? != 0 ]]; then
+    gen3_log_err "The job has not been started. Check it again"
+    exit 0
+  fi
+  g3kubectl logs -f ${pod_name}
 }
 
 
@@ -205,8 +215,10 @@ gen3_batch_cleanup() {
   gen3 cd
   gen3_load "gen3/lib/terraform"
   gen3_terraform destroy
-  gen3 trash --apply
-
+  if [[ $? == 0 ]]; then
+    gen3 trash --apply
+  fi
+
   # Delete service acccount, role and policy attached to it
   role=$(g3kubectl describe serviceaccount $saName | grep Annotations | sed -n "s/^.*:role\/\(\S*\)$/\1/p")
   policyName=$(gen3_aws_run aws iam list-role-policies --role-name $role | jq -r .PolicyNames[0])
@@ -229,7 +241,7 @@ case "$command" in
     gen3_batch_cleanup "$@"
     ;;
   'status')
-    gen3_manifest_generating_status
+    gen3_manifest_generating_status "$@"
     ;;
   'list' )
     gen3_bucket_manifest_list

diff --git a/gen3/bin/gcp-bucket-manifest.sh b/gen3/bin/gcp-bucket-manifest.sh
@@ -177,7 +177,10 @@ gen3_batch_cleanup() {
   gen3 cd
   gen3_load "gen3/lib/terraform"
   gen3_terraform destroy
-  gen3 trash --apply
+
+  if [[ $? == 0 ]]; then
+    gen3 trash --apply
+  fi
 
   gsutil rm -r gs://"${temp_bucket}"
   g3kubectl delete job google-bucket-manifest-${jobId}

diff --git a/kube/services/jobs/bucket-manifest-job.yaml b/kube/services/jobs/bucket-manifest-job.yaml
@@ -2,7 +2,7 @@
 apiVersion: batch/v1
 kind: Job
 metadata:
-  name: bucket-manifest#PLACEHOLDER#
+  name: aws-bucket-manifest#PLACEHOLDER#
 spec:
   template:
     metadata: