No information about function_str in the report from JoinNode with Function interface

[achetverikov]

Summary

When interfaces.utility.Function is used in combination with JoinNode, report.rst shows that function_str is <undefined>. With normal nodes, everything is OK. I'm not sure, but I have a suspicion that it also affects caching. Here's an example Node and a part of its report:

combine_plots = nipype.JoinNode(interface = util.Function(input_names = ['data_list','subject_id'], 
                                                          output_names = ['out_plot', 'out_data'],
                                                          function=combine_plots_fun),
                                name = 'combine_plots', joinfield = ['data_list'], 
                                joinsource='samples_pars',
                                run_without_submitting = True)

Node: combine_plots (utility)
=============================

 Hierarchy : decoding.combine_plots
 Exec ID : combine_plots.a0

Original Inputs
---------------

* data_list : <undefined>
* data_listJ1 : file1.csv
* data_listJ2 : file2.csv
* data_listJ3 : file3.csv
* data_listJ4 : file4.csv
* function_str : <undefined>
* ignore_exception : <undefined>
* subject_id : P01

Execution Inputs
----------------

* data_list : <undefined>
* data_listJ1 : file1.csv
* data_listJ2 : file2.csv
* data_listJ3 : file3.csv
* data_listJ4 : file4.csv
* function_str : <undefined>
* ignore_exception : <undefined>
* subject_id : P01

Platform details:

620 $ python -c "import nipype; print(nipype.get_info()); print(nipype.__version__)"
{'pkg_path': '/home/visual/andche/.conda/envs/demo/lib/python3.6/site-packages/nipype', 'commit_source': 'archive substitution', 'commit_hash': '%h', 'nipype_version': '0.14.0', 'sys_version': '3.6.3 | packaged by conda-forge | (default, Dec  9 2017, 16:18:26) \n[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]', 'sys_executable': '/home/visual/andche/.conda/envs/demo/bin/python', 'sys_platform': 'linux', 'numpy_version': '1.13.3', 'scipy_version': '1.0.0', 'networkx_version': '2.0', 'nibabel_version': '2.2.1', 'traits_version': '4.6.0'}
0.14.0

[mgxd]

@achetverikov

is this still a problem with our latest release?

As a workaround, could you try breaking this up into two nodes? An IdentiyInterface JoinNode that collects and merges data_list (similar to this), and then your custom Function Node that interacts with data_list.

[oesteban]

I don't recall to have any special treatment for JoinNodes when writing the report so I'm guessing that this has not been addressed.

[achetverikov]

@mgxd not sure about the latest release, this one is the latest on conda, and I don't wanna install another one with pip. I think your workaround will work as outside of JoinNode, Function interface works and reports as it should. I also found that declaring function_str explicitly after node initialization works as well:

from nipype.utils.functions import getsource
combine_plots.inputs.function_str = getsource(combine_plots_fun)

And the caching works as intended with this workaround.

As a side issue, I think reporting that "data_list" (the joinfield) is undefined is misleading as well. I think it should be data_list : ['file1.csv', 'file2.csv', 'file3.csv', 'file4.csv'] rather than separate data_listJ1 etc.

[djarecka]

I can confirm that I have function_str : <undefined> with the current version. However, it looks to me that caching is working properly.

[djarecka]

@oesteban - I'm searching for a place that should be change and trying to understand _override_join_traits with only partial success. I suspect that we shouldn't set undefined here without checking if dyntraits has already the specific trait. Any thoughts? Am I right?