make the changes to use niworkflows BIDSDataGrabber

Author: bpinsard

fmriprep/cli/run.py

@@ -512,7 +512,6 @@ def build_workflow(opts, retval):
     from niworkflows.reports import generate_reports
     from ..__about__ import __version__
     from ..workflows.base import init_fmriprep_wf
-    from nipype.interfaces.base import Undefined
 
     build_log = nlogging.getLogger('nipype.workflow')
 
@@ -527,7 +526,7 @@ def build_workflow(opts, retval):
     output_dir = opts.output_dir.resolve()
     work_dir = opts.work_dir.resolve()
     bids_filters_file = opts.bids_filters.resolve()
-    bids_filters = json.load(open(bids_filters_file)) if bids_filters_file else Undefined
+    bids_filters = json.load(open(bids_filters_file)) if bids_filters_file else None
 
     retval['return_code'] = 1
     retval['workflow'] = None

fmriprep/workflows/base.py

@@ -471,7 +471,7 @@ def init_single_subject_wf(
             'bold': ['/completely/made/up/path/sub-01_task-nback_bold.nii.gz']
         }
     else:
-        subject_data = collect_data(layout, subject_id, task_id, echo_idx)[0]
+        subject_data = collect_data(layout, subject_id, task_id, echo_idx, bids_filters=bids_filters)[0]
 
     # Make sure we always go through these two checks
     if not anat_only and subject_data['bold'] == []:
@@ -523,7 +523,7 @@ def init_single_subject_wf(
     inputnode = pe.Node(niu.IdentityInterface(fields=['subjects_dir']),
                         name='inputnode')
 
-    bidssrc = pe.Node(BIDSDataGrabber(subject_data=subject_data, anat_only=anat_only, output_query=bids_filters),
+    bidssrc = pe.Node(BIDSDataGrabber(subject_data=subject_data, anat_only=anat_only),
                       name='bidssrc')
 
     bids_info = pe.Node(BIDSInfo(