🔧 Add fail_fast to expose Nipype's stop_on_first_crash

CHANGELOG.md

@@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Added the ability to use TotalReadoutTime of epi field maps in the calculation of FSL topup distortion correction.
 - Difference method (``-``) for ``CPAC.utils.configuration.Configuration`` instances
 - Calculate reho and alff when timeseries in template space
+- Added ``fail_fast`` configuration setting and CLI flag
 
 ### Changed
 - Added a level of depth to `working` directories to match `log` and `output` directory structure

CPAC/pipeline/cpac_pipeline.py

@@ -281,9 +281,9 @@ def run_workflow(sub_dict, c, run, pipeline_timing_info=None, p_name=None,
         },
         'execution': {
             'crashfile_format': 'txt',
-            'resource_monitor_frequency': 0.2
-        }
-    })
+            'resource_monitor_frequency': 0.2,
+            'stop_on_first_crash': c['pipeline_setup', 'system_config',
+                                     'fail_fast']}})
 
     config.enable_resource_monitor()
     logging.update_logging(config)

CPAC/pipeline/schema.py

@@ -265,6 +265,7 @@ def sanitize(filename):
             'path': Maybe(str),
         },
         'system_config': {
+            'fail_fast': bool1_1,
             'FSLDIR': Maybe(str),
             'on_grid': {
                 'run': bool1_1,

CPAC/resources/configs/pipeline_config_blank.yml

@@ -57,6 +57,9 @@ pipeline_setup:
 
   system_config:
 
+    # Stop worklow execution on first crash?
+    fail_fast: Off
+
     # Random seed used to fix the state of execution.
     # If unset, each process uses its own default.
     # If set, a `random.log` file will be generated logging the random seed and each node to which that seed was applied.
@@ -1191,8 +1194,7 @@ functional_preproc:
     # this is a fork point
     #   run: [On, Off] - this will run both and fork the pipeline
     run: [Off]
-
-    space: 'native'
+    space: native
 
 nuisance_corrections:
   2-nuisance_regression:

CPAC/resources/configs/pipeline_config_default.yml

@@ -85,7 +85,8 @@ pipeline_setup:
     path: /outputs/crash
 
   system_config:
-
+    # Stop worklow execution on first crash?
+    fail_fast: Off
     # Random seed used to fix the state of execution.
     # If unset, each process uses its own default.
     # If set, a `random.log` file will be generated logging the random seed and each node to which that seed was applied.

CPAC/resources/configs/pipeline_config_rbc-options.yml

@@ -23,6 +23,9 @@ pipeline_setup:
 
   system_config:
 
+    # Stop worklow execution on first crash?
+    fail_fast: On
+
     # Random seed used to fix the state of execution.
     # If unset, each process uses its own default.
     # If set, a `random.log` file will be generated logging the random seed and each node to which that seed was applied.
@@ -110,7 +113,7 @@ functional_preproc:
     # this is a fork point
     #   run: [On, Off] - this will run both and fork the pipeline
     run: [On]
-    space: 'template'
+    space: template
 
 nuisance_corrections:
   2-nuisance_regression:

dev/docker_data/run.py

@@ -28,6 +28,7 @@
 from CPAC import license_notice, __version__
 from CPAC.pipeline import AVAILABLE_PIPELINE_CONFIGS
 from CPAC.pipeline.random_state import set_up_random_state
+from CPAC.pipeline.schema import str_to_bool1_1
 from CPAC.utils.bids_utils import create_cpac_data_config, \
                                   load_cpac_data_config, \
                                   load_yaml_config, \
@@ -248,6 +249,8 @@ def run_main():
                         help='Save the contents of the working directory.',
                         default=False)
 
+    parser.add_argument('--fail_fast', type=str.title,
+                        help='Stop worklow execution on first crash?')
     parser.add_argument('--participant_label',
                         help='The label of the participant that should be '
                              'analyzed. The label corresponds to '
@@ -604,6 +607,10 @@ def run_main():
                            'Either change the output directory to something '
                            'local or turn off the --save_working_dir flag')
 
+        if args.fail_fast is not None:
+            c['pipeline_setup', 'system_config',
+              'fail_fast'] = str_to_bool1_1(args.fail_fast)
+
         if c['pipeline_setup']['output_directory']['quality_control'][
                 'generate_xcpqc_files']:
             c['functional_preproc']['motion_estimates_and_correction'][