Throw a warning when BIDS compliance fails.

CoBrALab · Sep 26, 2023 · 792cd55 · 792cd55
1 parent 6d54e97
commit 792cd55
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Showing 2 changed files with 8 additions and 2 deletions.
diff --git a/rabies/preprocess_pkg/main_wf.py b/rabies/preprocess_pkg/main_wf.py
@@ -133,7 +133,14 @@ def init_main_wf(data_dir_path, output_folder, opts, name='main_wf'):
 
     import bids
     bids.config.set_option('extension_initial_dot', True)
-    layout = bids.layout.BIDSLayout(data_dir_path, validate=False)
+    try:
+        layout = bids.layout.BIDSLayout(data_dir_path, validate=True)
+    except Exception as e:
+        from nipype import logging
+        log = logging.getLogger('nipype.workflow')
+        log.warning(f"The BIDS compliance failed: {e} \n\nRABIES will run anyway; double-check that the right files were picked up for processing.\n")
+        layout = bids.layout.BIDSLayout(data_dir_path, validate=False)
+
     split_name, scan_info, run_iter, scan_list, bold_scan_list = prep_bids_iter(
         layout, opts.bold_only, inclusion_list=opts.inclusion_ids, exclusion_list=opts.exclusion_ids)
 

diff --git a/rabies/preprocess_pkg/utils.py b/rabies/preprocess_pkg/utils.py
@@ -6,7 +6,6 @@
     traits, TraitedSpec, BaseInterfaceInputSpec,
     File, BaseInterface
 )
-from rabies.utils import run_command
 
 def prep_bids_iter(layout, bold_only=False, inclusion_list=['all'], exclusion_list=['none']):
     '''