FIX: Correctly populate output spec for ICA_AROMA #2027
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effigies
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effigies
approved these changes
May 17, 2017
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@jdkent Can you verify that you are able to run ICA_AROMA with this interface? |
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@effigies Sure, what is the best way to do this? copy terminal output? |
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If you like. Just for you to verify that you can run it without errors is the main thing I'm looking for. So something like: >>> aroma = ICA_AROMA(...)
>>> res = aroma.run()
>>> res.outputs
{'out_dir': <out_dir>, ...} |
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and this version for a workflow execution: |
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Okay, this did not fix the problem: |
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Can you show the full command sequence you gave? I'm surprised by that result. Edit: Oh, if you want a dictionary, I think you need |
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I'm looking at how the CommandLine interface is defined, but I can't seem to figure out what's going wrong. Here's how I set up the command. |
Codecov Report
@@ Coverage Diff @@
## master #2027 +/- ##
=========================================
- Coverage 72.2% 72.2% -0.01%
=========================================
Files 1132 1132
Lines 57023 57024 +1
Branches 8165 8165
=========================================
Hits 41173 41173
- Misses 14566 14567 +1
Partials 1284 1284
Continue to review full report at Codecov.
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Codecov Report
@@ Coverage Diff @@
## master #2027 +/- ##
=========================================
- Coverage 72.2% 72.2% -0.01%
=========================================
Files 1132 1132
Lines 57023 57024 +1
Branches 8165 8165
=========================================
Hits 41173 41173
- Misses 14566 14567 +1
Partials 1284 1284
Continue to review full report at Codecov.
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Nothing's jumping out at me as to why that's not working. I might need to look with fresh eyes tomorrow. If somebody else does see something, can you help @jdkent? |
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@effigies I will help. Nothing is jumping out at me either, but I'll keep looking. |
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Many apologies, the version of nipype I was using with my virtual environment wasn't the most up to date version. After squaring that away I got the correct output with @effigies code structure However, I did not get the behavior expected by @satra when constructing a node. There was no result attribute, but there still was the outputs attribute. Is it because of how I imported Node? |
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@jdkent - my instructions were off. i meant to say node.result.outputs. but this output looks fine. |
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Fixes #2026
Changes proposed in this pull request
added
outputs = self.output_spec().getto _list_outputsMay or may not fix the other error message.