Merge pull request nipreps#141 from oesteban/fix/NoScansFound

[FIX] mriqc crashes if no anatomical scans are found

mriqc/utils/mriqc_run.py

@@ -3,7 +3,7 @@
 # @Author: oesteban
 # @Date:   2015-11-19 16:44:27
 # @Last Modified by:   oesteban
-# @Last Modified time: 2016-05-06 11:14:22
+# @Last Modified time: 2016-07-20 18:28:25
 
 """
 =====
@@ -24,11 +24,14 @@
 from argparse import ArgumentParser
 from argparse import RawTextHelpFormatter
 from nipype import config as ncfg
+from nipype import logging
 
 from mriqc.reports.generators import workflow_report
 from mriqc.workflows import core as mwc
 from mriqc import __version__
 
+LOGGER = logging.getLogger('workflow')
+
 
 def main():
     """Entry point"""
@@ -131,6 +134,10 @@ def main():
         ms_func = getattr(mwc, 'ms_' + dtype)
         workflow = ms_func(subject_id=opts.subject_id, session_id=opts.session_id,
                            run_id=opts.run_id, settings=settings)
+        if workflow is None:
+            LOGGER.warn('No {} scans were found in {}', dtype, settings['bids_root'])
+            continue
+
         workflow.base_dir = settings['work_dir']
         if settings.get('write_graph', False):
             workflow.write_graph()

mriqc/workflows/core.py

@@ -7,7 +7,7 @@
 # @Date:   2016-01-05 11:24:05
 # @Email:  code@oscaresteban.es
 # @Last modified by:   oesteban
-# @Last Modified time: 2016-05-04 14:53:43
+# @Last Modified time: 2016-07-20 17:32:24
 """ The core module combines the existing workflows """
 from six import string_types
 from nipype.pipeline import engine as pe
@@ -17,6 +17,7 @@
 from mriqc.workflows.functional import fmri_qc_workflow
 from mriqc.utils.misc import gather_bids_data
 
+
 def ms_anat(settings=None, subject_id=None, session_id=None, run_id=None):
     """ Multi-subject anatomical workflow wrapper """
     # Run single subject mode if only one subject id is provided
@@ -33,7 +34,7 @@ def ms_anat(settings=None, subject_id=None, session_id=None, run_id=None):
         sub_list = [s for s in sub_list if s[2] == run_id]
 
     if not sub_list:
-        raise RuntimeError('No scans found in %s' % settings['bids_root'])
+        return None
 
     inputnode = pe.Node(niu.IdentityInterface(fields=['data']),
                         name='inputnode')
@@ -70,7 +71,7 @@ def ms_func(settings=None, subject_id=None, session_id=None, run_id=None):
         sub_list = [s for s in sub_list if s[2] == run_id]
 
     if not sub_list:
-        raise RuntimeError('No scans found in %s' % settings['bids_root'])
+        return None
 
     inputnode = pe.Node(niu.IdentityInterface(fields=['data']),
                         name='inputnode')