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[BUG] fivettgen_hsvs_.py #281

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arkiev opened this issue Mar 5, 2024 · 0 comments
Open

[BUG] fivettgen_hsvs_.py #281

arkiev opened this issue Mar 5, 2024 · 0 comments
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bug Something isn't working pipelines

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@arkiev
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arkiev commented Mar 5, 2024

Description

When 5TTgen hsvs is executed, the task runs to completion. However, after the task finishes, the following error occurs.

How to reproduce

Here's the code for the task:

    wf.add(
            FivettGen_Hsvs(
                in_file=wf.FastSurfer_task.lzout.subjects_dir_output, 
                out_file="5TT_hsvs.mif",
                name="fTTgen_task",
                nocrop=True,
                sgm_amyg_hipp=True,
                nocleanup=True,
                white_stem=True
            )
        )

Note that the default fivettgen_hsvs_.py file was used here, with the exception being:

output_fields = [
    ("out_file", ImageOut, {"help_string": "The output 5TT image"}),
    (
        "scratch",
        Directory,
        {
            **"mandatory": False,**
            "help_string": "manually specify the path in which to generate the scratch directory."
        },
    ),
]

Screenshots

Exception has occurred: Exception
Metadata for 'scratch', does not not contain any of the required fields ("callable", "output_file_template" or "value"): {'mandatory': False, 'help_string': 'manually specify the path in which to generate the scratch directory.'}.
  File "/Users/arkievdsouza/git/pydra/pydra/engine/specs.py", line 612, in _field_metadata
    raise Exception(
  File "/Users/arkievdsouza/git/pydra/pydra/engine/specs.py", line 481, in collect_additional_outputs
    additional_out[fld.name] = self._field_metadata(
                               ^^^^^^^^^^^^^^^^^^^^^
  File "/Users/arkievdsouza/git/pydra/pydra/engine/core.py", line 590, in _collect_outputs
    other_output = output.collect_additional_outputs(
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/arkievdsouza/git/pydra/pydra/engine/core.py", line 562, in _run
    result.output = self._collect_outputs(output_dir=output_dir)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/arkievdsouza/git/pydra/pydra/engine/workers.py", line 146, in exec_serial
    return runnable._run(rerun, environment=environment)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/arkievdsouza/git/pydra/pydra/engine/workers.py", line 152, in fetch_finished
    await asyncio.gather(*futures)
  File "/Users/arkievdsouza/git/pydra/pydra/engine/submitter.py", line 251, in expand_workflow
    task_futures = await self.worker.fetch_finished(task_futures)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/arkievdsouza/git/pydra/pydra/engine/core.py", line 1339, in _run_task
    await submitter.expand_workflow(self, rerun=rerun)
  File "/Users/arkievdsouza/git/pydra/pydra/engine/core.py", line 1310, in _run
    await self._run_task(submitter, rerun=rerun)
  File "/Users/arkievdsouza/git/pydra/pydra/engine/submitter.py", line 84, in submit_from_call
    await runnable._run(self, rerun=rerun)
  File "/Users/arkievdsouza/git/pydra/pydra/engine/submitter.py", line 55, in __call__
    self.loop.run_until_complete(
  File "/Users/arkievdsouza/git/pydra/pydra/engine/core.py", line 461, in __call__
    res = sub(self, environment=environment)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/arkievdsouza/git/t1-pipeline/T1_ProcessingPipeline_v1.py", line 347, in <module>
    result = wf(
             ^^^
Exception: Metadata for 'scratch', does not not contain any of the required fields ("callable", "output_file_template" or "value"): {'mandatory': False, 'help_string': 'manually specify the path in which to generate the scratch directory.'}.
@arkiev arkiev added bug Something isn't working pipelines labels Mar 5, 2024
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