Don't prepull containers if extensions are enabled

See common-workflow-language/cwl-utils#309
DataBiosphere · Jul 16, 2024 · c264a0d · c264a0d
1 parent 2b559cb
commit c264a0d
Showing 1 changed file with 9 additions and 4 deletions.
diff --git a/src/toil/cwl/cwltoil.py b/src/toil/cwl/cwltoil.py
@@ -102,7 +102,7 @@
 from toil.batchSystems.registry import DEFAULT_BATCH_SYSTEM
 from toil.common import Toil, addOptions
 from toil.cwl import check_cwltool_version
-from toil.lib.misc import call_command
+from toil.lib.misc import call_command, CalledProcessErrorStderr
 from toil.provisioners.clusterScaler import JobTooBigError
 
 check_cwltool_version()
@@ -247,14 +247,14 @@ def try_prepull(cwl_tool_uri: str, runtime_context: cwltool.context.RuntimeConte
     """
     if runtime_context.singularity:
         if "CWL_SINGULARITY_CACHE" in os.environ:
-            logger.info("Prepulling containers with Singularity...")
+            logger.info("Prepulling the workflow's containers with Singularity...")
             call_command(["cwl-docker-extract", "--singularity", "--dir", os.environ['CWL_SINGULARITY_CACHE'], cwl_tool_uri])
     elif not runtime_context.user_space_docker_cmd and not runtime_context.podman:
         # For udocker and podman prefetching is unimplemented
         # This is docker
         if batchsystem == "single_machine":
             # Only on single machine will the docker daemon be accessible by all workers and the leader
-            logger.info("Prepulling containers with Docker...")
+            logger.info("Prepulling the workflow's containers with Docker...")
             call_command(["cwl-docker-extract", cwl_tool_uri])
 
 
@@ -3768,7 +3768,12 @@ def main(args: Optional[List[str]] = None, stdout: TextIO = sys.stdout) -> int:
 
                 # Attempt to prepull the containers
                 if not options.no_prepull:
-                    try_prepull(uri, runtime_context, toil.config.batchSystem)
+                    if not options.enable_ext:
+                        # The CWL utils parser does not support cwltool extensions and will crash if encountered, so don't prepull if extensions are enabled
+                        # See https://github.com/common-workflow-language/cwl-utils/issues/309
+                        try_prepull(uri, runtime_context, toil.config.batchSystem)
+                    else:
+                        logger.debug("Not prepulling containers as cwltool extensions are not supported.")
 
                 options.tool_help = None
                 options.debug = options.logLevel == "DEBUG"