Merge pull request #172 from broadinstitute/sn_fix_hard_clone_to_exte…

…rnal_bucket

Sn fix hard clone to external bucket

python/hard_clone_workspace.py

@@ -111,7 +111,7 @@ def run(self) -> None:
             file_extensions_to_ignore=self.extensions_to_ignore,
             file_name_only=True,
             # Ignore log files for this workflow since could be updating as running
-            file_strings_to_ignore=["/HardCloneTerraWorkspace/"]
+            file_strings_to_ignore=["/HardCloneTerraWorkspace/", "/HardCloneWithExternalBucket/"]
         )
 
         files_to_copy = [
@@ -200,7 +200,7 @@ def make_bucket_files(src_bucket: str, dest_bucket: str) -> None:
         if not external_bucket.startswith("gs://") or not external_bucket.endswith("/"):
             raise ValueError("gcp_bucket must start with gs:// and end with /")
         # Remove the gs:// prefix and trailing slash to match what is returned by the Terra API
-        external_bucket = external_bucket.lstrip("gs://").rstrip("/")
+        external_bucket = external_bucket.replace("gs://", "").rstrip("/")
 
     token = Token(cloud=GCP)
     request_util = RunRequest(token=token)

wdl/HardCloneWithExternalBucket/HardCloneWithExternalBucket.wdl

@@ -8,7 +8,7 @@ workflow HardCloneWithExternalBucket {
 		String source_workspace_name
 		String dest_billing_project
 		String dest_workspace_name
-        String external_bucket
+		String external_bucket
 		Boolean allow_already_created
 		Boolean rsync_workspace
 		Boolean do_not_update_acls
@@ -21,7 +21,7 @@ workflow HardCloneWithExternalBucket {
 
 	String docker_name = select_first([docker, "us-central1-docker.pkg.dev/operations-portal-427515/ops-toolbox/ops_terra_utils_slim:latest"])
 	# Ignore HardCloneTerraWorkspace submisisons files so do not write to src as copying to dest
-	String rysnc_regex_exclude = ".*/HardCloneTerraWorkspace/.*"
+	String rysnc_regex_exclude = ".*/HardCloneWithExternalBucket/.*"
 	Int memory = select_first([memory_gb, 8])
 
 	call HardCloneWithExternalBucketTask {
@@ -31,7 +31,7 @@ workflow HardCloneWithExternalBucket {
 			dest_billing_project=dest_billing_project,
 			dest_workspace_name=dest_workspace_name,
 			allow_already_created=allow_already_created,
-            external_bucket=external_bucket,
+			external_bucket=external_bucket,
 			workers=workers,
 			extensions_to_ignore=extensions_to_ignore,
 			docker_name=docker_name,
@@ -58,7 +58,7 @@ task HardCloneWithExternalBucketTask {
 		String dest_billing_project
 		String dest_workspace_name
 		Boolean allow_already_created
-        String external_bucket
+		String external_bucket
 		Int? workers
 		String? extensions_to_ignore
 		String docker_name