.get returns double results when validate=False #557
Description
Let's say I set up a derivative as a root directory, as a derivative (because I want it to use derivative entities, such as desc): Let's say I also said validate=False:
layout = BIDSLayout('/data/fmriprep', derivatives=['/data/fmriprep'], validate=False)
Then if I ask for the following:
layout.get(task='sherlockPart1', subject='01', datatype='func', suffix='bold')
I will get two results:
[<BIDSImageFile filename='/work/Sherlock/preproc/fmriprep/sub-01/func/sub-01_task-sherlockPart1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'>,
<BIDSImageFile filename='/work/Sherlock/preproc/fmriprep/sub-01/func/sub-01_task-sherlockPart1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'>]
What is happening is that both the root layout, and the derivative layout are returning results.
This happens even if I ask for results only from derivatives:
layout.get(task='sherlockPart1', subject='01', datatype='func', suffix='bold', scope='derivatives')
This happens because _in_scope determines if a layout is in the scope of derivatives based on the PipelineDescription, which the root derivative has, even though derivative results were not applied when indexing.
If I validate the layout, then I only get one result, because the preproc file is not indexed at all by the root layout.
The reason this is relevant for fitlins, is that as @effigies pointed out, BIDS Model are not valid BIDS yet so we have to run with validate=False.
I think the simple solution for fitlins is to add desc=preproc as a entity to filter that get call on, so that we only get 1 preproc file returned.
But I think it's a bug to say the root derivative is in the derivatives scope, even when that set of entities were not applied during indexing.