FIX: Add desc=preproc as filter when finding preproc BOLD files #204
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Hello @adelavega, Thank you for updating! Cheers! There are no style issues detected in this Pull Request. 🍻 To test for issues locally, Comment last updated at 2019-12-11 22:03:14 UTC |
adelavega
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Tested, and neuroscout-cli models are running with this change. Not sure why this didn't come up before, but I think I hadn't rebuilt my fitlins image in a while, and maybe it was on a previous pybids version or something. Upgrading to 0.6.0 did it though. I guess bugfix release will be needed, ugh. |
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I suspect it's because I only used |
Codecov Report
@@ Coverage Diff @@
## master #204 +/- ##
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Coverage 77.35% 77.35%
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Files 18 18
Lines 1042 1042
Branches 187 187
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Hits 806 806
- Misses 147 148 +1
+ Partials 89 88 -1
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| @@ -231,7 +231,7 @@ def _load_level1(self, runtime, analysis): | |||
| TR = ents.pop('RepetitionTime', None) # Required field in seconds | |||
| if TR is None: # But is unreliable (for now?) | |||
| preproc_files = analysis.layout.get( | |||
| extension=['.nii', '.nii.gz'], **ents) | |||
| extension=['.nii', '.nii.gz'], desc='preproc', **ents) | |||
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Is there any chance ents could already contain 'desc'? If so, this is setting us up for an error.
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It doesn't, I checked. Makes sense because the entities are coming from the design matrix which doesn't have that key.
| bold_file = layout.get(**selectors) | ||
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| if len(bold_file) == 0: | ||
| raise FileNotFoundError( | ||
| "Could not find BOLD file in {} with entities {}" | ||
| "".format(self.inputs.bids_dir, selectors)) |
Yep, that's exactly what happened. |
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I'm not too happy about |
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What if we enable validation but package our own config that handles |
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That's probably the best thing to do yeah |
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Merging, hope that's allright. |
adelavega
changed the title
Related issue: bids-standard/pybids#557
Stems from having
validate=False, which we only used to do when necessary, but now is applied across the whole master Layout