Merge pull request #240 from nipreps/fix/239

FIX: Add ``.bidsignore`` file writing

Author: oesteban

dmriprep/cli/run.py

@@ -163,23 +163,24 @@ def main():
             config.execution.participant_label,
             config.execution.output_dir,
             config.execution.run_uuid,
-            config=load('config/reports-spec.yml'),
+            config=load('reports-spec.yml'),
             packagename='dmriprep',
         )
-        write_derivative_description(
-            config.execution.bids_dir,
-            config.execution.dmriprep_dir,
-            dataset_links=config.execution.dataset_links,
-        )
-        write_bidsignore(config.execution.dmriprep_dir)
-
+        # Report errors in report generation immediately
         if failed_reports:
             msg = (
                 'Report generation was not successful for the following participants '
                 f': {", ".join(failed_reports)}.'
             )
             config.loggers.cli.error(msg)
 
+        write_derivative_description(
+            config.execution.bids_dir,
+            config.execution.output_dir,
+            dataset_links=config.execution.dataset_links,
+        )
+        write_bidsignore(config.execution.output_dir)
+
         sys.exit(int((errno + len(failed_reports)) > 0))
 
 

dmriprep/config/reports-spec.yml renamed to dmriprep/data/reports-spec.yml

@@ -37,6 +37,16 @@
 
 from dmriprep.data import load as load_data
 
+DEFAULT_BIDS_IGNORE = {
+    '*.html',
+    'logs/',
+    'figures/',  # Reports
+    '*_xfm.*',  # Unspecified transform files
+    '*.surf.gii',  # Unspecified structural outputs
+    # Unspecified diffusion outputs
+    '*_dwiref.nii.gz',
+}
+
 
 @cache
 def _get_layout(derivatives_dir: Path) -> BIDSLayout:
@@ -252,5 +262,9 @@ def validate_input_dir(exec_env, bids_dir, participant_label, need_T1w=True):
             print('bids-validator does not appear to be installed', file=sys.stderr)
 
 
+def write_bidsignore(deriv_dir, bids_ignore=DEFAULT_BIDS_IGNORE):
+    (Path(deriv_dir) / '.bidsignore').write_text('\n'.join(bids_ignore) + '\n')
+
+
 def _get_shub_version(singularity_url):
     return NotImplemented