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FIX: Copy interface before running to prevent task mutation on run #12

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FIX: Copy interface before running to prevent task mutation on run #12

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effigies
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Test still needed.

@effigies
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effigies commented May 1, 2021

@JW-96 Do you happen to remember an interface that was changing hash before and after run? I can't remember how to create this condition to write a test.

@JeffWigger
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I think it was due to the paths in the docker image, on which I run the workflow, being different to the paths on my system. However, I will rerun the workflow and check again.

@JeffWigger
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Originally we had the problem with ApplyTransforms of Ants, but I did not get it again. However, for Normalize12 of SPM I get:

>>> t = load_task("/home/cache_part1_fix_chris_test2/Nipype1Task_d9baecc08957742c186ec5f8c5f1cbfe1b8f6624eae11dc73ef0222d54199afa/_task.pklz")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/pydra/pydra/engine/helpers.py", line 819, in load_task
    task = cp.loads(task_pkl.read_bytes())
  File "/opt/miniconda-latest/envs/fcbg38/lib/python3.8/site-packages/traits/has_traits.py", line 1341, in __setstate__
    self.trait_set(trait_change_notify=trait_change_notify, **state)
  File "/opt/miniconda-latest/envs/fcbg38/lib/python3.8/site-packages/traits/has_traits.py", line 1434, in trait_set
    setattr(self, name, value)
  File "/opt/miniconda-latest/envs/fcbg38/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
    value = super(File, self).validate(objekt, name, value, return_pathlike=True)
  File "/opt/miniconda-latest/envs/fcbg38/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
    self.error(objekt, name, str(value))
  File "/opt/miniconda-latest/envs/fcbg38/lib/python3.8/site-packages/traits/base_trait_handler.py", line 74, in error
    raise TraitError(
traits.trait_errors.TraitError: The 'image_to_align' trait of a Normalize12InputSpec instance must be a pathlike object or string representing an existing file, but a value of '/home/cache_part1_fix_chris_test2/Nipype1Task_d9baecc08957742c186ec5f8c5f1cbfe1b8f6624eae11dc73ef0222d54199afa/normalize2_con/sub-04_t1w_preproc.nii' <class 'str'> was specified.

With the directory looking like this:

root@a11df7db765e:/home/pydra-glm-example/pydra_version# ls /home/cache_part1_fix_chris_test2/Nipype1Task_d9baecc08957742c186ec5f8c5f1cbfe1b8f6624eae11dc73ef0222d54199afa/
normalize2_con	_result.pklz  _task.pklz
root@a11df7db765e:/home/pydra-glm-example/pydra_version# ls /home/cache_part1_fix_chris_test2/Nipype1Task_d9baecc08957742c186ec5f8c5f1cbfe1b8f6624eae11dc73ef0222d54199afa/normalize2_con/
_0x1befbbe3d820fb023e02fa5c28d41651.json  _node.pklz		  _report		      wcon_0001.nii  wcon_0003.nii  wcon_0005.nii  wcon_0007.nii  wess_0009.nii		   y_sub-04_t1w_preproc.nii
_inputs.pklz				  pyscript_normalize12.m  result_normalize2_con.pklz  wcon_0002.nii  wcon_0004.nii  wcon_0006.nii  wess_0008.nii  wsub-04_t1w_preproc.nii
root@a11df7db765e:/home/pydra-glm-example/pydra_version#

@effigies
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effigies commented May 1, 2021

Does this pr address that?

@JeffWigger
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I rerun my workflow again with this pull request and the above issue with loading the Normalize12 task does no longer occur.

@effigies
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effigies commented May 4, 2021

Ah, right. Thanks for the reminder of how this was exhibiting.

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codecov-commenter commented Oct 19, 2022 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 95.38%. Comparing base (4c08fab) to head (1df2696).

Additional details and impacted files 
@@            Coverage Diff             @@
##             main      #12      +/-   ##
==========================================
+ Coverage   95.31%   95.38%   +0.07%     
==========================================
  Files           4        4              
  Lines          64       65       +1     
  Branches        7        7              
==========================================
+ Hits           61       62       +1     
  Misses          2        2              
  Partials        1        1

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@effigies @JeffWigger @codecov-commenter