Fixed optional input when the input type is list or record

alpha-unito · Jan 3, 2025 · 7840d0b · 7840d0b
1 parent c2a08e2
commit 7840d0b
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Showing 2 changed files with 9 additions and 2 deletions.
diff --git a/streamflow/cwl/translator.py b/streamflow/cwl/translator.py
@@ -627,6 +627,7 @@ def _create_token_processor(
                 force_deep_listing=force_deep_listing,
                 only_propagate_secondary_files=only_propagate_secondary_files,
             ),
+            optional=optional,
         )
     # Enum type: -> create output processor
     elif isinstance(port_type, get_args(cwl_utils.parser.EnumSchema)):
@@ -684,6 +685,7 @@ def _create_token_processor(
                 )
                 for port_type in port_type.fields
             },
+            optional=optional,
         )
     elif isinstance(port_type, MutableSequence):
         optional = "null" in port_type

diff --git a/streamflow/deployment/connector/container.py b/streamflow/deployment/connector/container.py
@@ -1803,13 +1803,15 @@ async def _populate_instance(self, name: str) -> None:
                     for line in stdout.splitlines()
                     if line.split(" - ")[1].split()[0] not in FS_TYPES_TO_SKIP
                 }
-                if logger.isEnabledFor(logging.DEBUG):
-                    logger.debug(f"Host mount points: {fs_mounts}")
             else:
                 raise WorkflowExecutionException(
                     f"FAILED retrieving volume mounts from `/proc/1/mountinfo` "
                     f"in deployment {self.connector.deployment_name}: [{returncode}]: {stdout}"
                 )
+        if logger.isEnabledFor(logging.DEBUG):
+            logger.debug(
+                f"Host (local: {self._wraps_local()}) mount points: {fs_mounts}"
+            )
         # Get the list of bind mounts for the container instance
         stdout, returncode = await self.run(
             location=location,
@@ -1843,6 +1845,9 @@ async def _populate_instance(self, name: str) -> None:
                             else None
                         )
                     if host_mount is not None:
+                        if dst == os.path.join(os.sep, "tmp", "streamflow"):  # fixme
+                            logger.debug(f"HARDCODED: replaced {host_mount} with {dst}")
+                            host_mount = dst
                         binds[dst] = host_mount
             if logger.isEnabledFor(logging.DEBUG):
                 logger.debug(f"Container binds: {binds}")