Fixed the path of the config file stored in the DataManager. Before…

… this commit, it was saved the path defined in the `StreamFlow file`, which can be a relative path

streamflow/cwl/translator.py

@@ -7,7 +7,7 @@
 import urllib.parse
 from collections.abc import MutableMapping, MutableSequence
 from enum import Enum
-from pathlib import PurePosixPath
+from pathlib import Path, PurePosixPath
 from types import ModuleType
 from typing import Any, cast, get_args
 
@@ -1411,6 +1411,13 @@ def __init__(
             | cwl_utils.parser.Workflow
         ) = cwl_definition
         self.cwl_inputs: MutableMapping[str, Any] = cwl_inputs
+
+        if cwl_inputs_path is not None:
+            uri = urllib.parse.urlparse(cwl_inputs_path)
+            if not uri.scheme or uri.scheme == "file":
+                cwl_inputs_path = _get_path(
+                    Path(urllib.parse.unquote_plus(uri.path)).resolve().as_uri()
+                )
         self.cwl_inputs_path: str | None = cwl_inputs_path
         self.default_map: MutableMapping[str, Any] = {}
         self.deployment_map: MutableMapping[str, DeployStep] = {}

streamflow/cwl/utils.py

@@ -672,7 +672,7 @@ def process_inner_element(
     context: MutableMapping[str, Any],
 ):
     run_command = cwl_element.run
-    inner_context = {**context}
+    inner_context = dict(context)
     if cwl_utils.parser.is_process(run_command):
         run_command.cwlVersion = context["version"]
         cwl_utils.parser.utils.convert_stdstreams_to_files(run_command)

streamflow/data/manager.py

@@ -356,6 +356,12 @@ async def transfer_data(
             ).resolve()
         ) is None:
             logger.info(f"Remote file system: {repr(self.path_mapper)}")
+
+            src_res, _ = await src_connector.run(src_location, ["ls", "-lhaR", "/tmp"])
+            logger.info(f"src_res: {src_res}")
+            dst_res = await dst_connector.run(dst_locations[0], ["ls", "-lhaR", "/tmp"])
+            logger.info(f"dst_res: {dst_res}")
+
             raise WorkflowExecutionException(
                 f"Error retrieving realpath for {src_path} on location {src_location} "
                 f"while transferring it to {dst_path} on deployment {dst_connector.deployment_name}"