Error executing tool with id '__EXTRACT_DATASET__': 'Dataset collection has no element_identifier with key None.'

[bgruening]

I found that while debugging some workflow execution of a user. I'm sure the workflows is wrong, but it should probably not fail this way, but not start at all in the first place. Or return some meaningful error message?

Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]: Traceback (most recent call last):
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:   File "/opt/galaxy/server/lib/galaxy/tools/__init__.py", line 1937, in handle_single_execution
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:     rval = self.execute(
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:            ^^^^^^^^^^^^^
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:   File "/opt/galaxy/server/lib/galaxy/tools/__init__.py", line 2034, in execute
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:     return self.tool_action.execute(
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:            ^^^^^^^^^^^^^^^^^^^^^^^^^
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:   File "/opt/galaxy/server/lib/galaxy/tools/actions/model_operations.py", line 88, in execute
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:     self._produce_outputs(
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:   File "/opt/galaxy/server/lib/galaxy/tools/actions/model_operations.py", line 119, in _produce_outputs
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:     tool.produce_outputs(
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:   File "/opt/galaxy/server/lib/galaxy/tools/__init__.py", line 3308, in produce_outputs
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:     extracted_element = collection[incoming["which"]["identifier"]]
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:                         ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:   File "/opt/galaxy/server/lib/galaxy/model/__init__.py", line 6394, in __getitem__
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:     raise KeyError(error_message)
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]: KeyError: 'Dataset collection has no element_identifier with key None.'
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]: galaxy.tools.execute WARNING 2023-09-23 14:20:28,474 [pN:workflow_scheduler_sn06_0,p:3387131,tN:WorkflowRequestMonitor.monitor_thread] There was a failure executing a job for tool [__EXTRACT_DATASET__] - Error executing tool with id '__EXTRACT_DATASET__': 'Dataset collection has no element_identifier with key None.'
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]: galaxy.tools.execute DEBUG 2023-09-23 14:20:28,481 [pN:workflow_scheduler_sn06_0,p:3387131,tN:WorkflowRequestMonitor.monitor_thread] Created 1 job(s) for tool __EXTRACT_DATASET__ request (93.894 ms)
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]: galaxy.workflow.run ERROR 2023-09-23 14:20:28,498 [pN:workflow_scheduler_sn06_0,p:3387131,tN:WorkflowRequestMonitor.monitor_thread] Failed to schedule Workflow[id=224248,name=IceNet], problem occurred on WorkflowStep[index=20,type=tool,label=None,uuid=7876109a-7cb5-426d-8d1d-ab5bb88ba818,id=3437276].
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]: Traceback (most recent call last):
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:   File "/opt/galaxy/server/lib/galaxy/workflow/run.py", line 233, in invoke
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:     incomplete_or_none = self._invoke_step(workflow_invocation_step)
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:   File "/opt/galaxy/server/lib/galaxy/workflow/run.py", line 309, in _invoke_step
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:     incomplete_or_none = invocation_step.workflow_step.module.execute(
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:   File "/opt/galaxy/server/lib/galaxy/workflow/modules.py", line 2323, in execute
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]:     raise exceptions.MessageException(message)
Sep 23 14:20:28 sn06.galaxyproject.eu python[3387131]: galaxy.exceptions.MessageException: Failed to create 1 job(s) for workflow step 21: Error executing tool with id '__EXTRACT_DATASET__': 'Dataset collection has no element_identifier with key None.'

Describe the bug
A clear and concise description of what the bug is.

Galaxy Version and/or server at which you observed the bug
Galaxy Version: (check <galaxy_url>/api/version if you don't know)
Commit: (run git rev-parse HEAD if you run this Galaxy server)

To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Additional context
Add any other context about the problem here.

[mvdbeek]

but not start at all in the first place.

I don't think that's possible, that is a usage error where the identifier read in by __EXTRACT_DATASET__ is actually None. Does the error message appear when you open the invocation ?

[mvdbeek]

Should be easier to see for users after #16917