add the extractors description in the acquisition description file

iblrig/__init__.py

@@ -1 +1 @@
-__version__ = "8.6.1"
+__version__ = "8.7.0"

iblrig/base_tasks.py

@@ -47,6 +47,7 @@ class BaseSession(ABC):
     protocol_name = None
     base_parameters_file = None
     is_mock = False
+    extractor_tasks = None
 
     def __init__(self, subject=None, task_parameter_file=None, file_hardware_settings=None,
                  hardware_settings=None, file_iblrig_settings=None, iblrig_settings=None,
@@ -119,7 +120,7 @@ def __init__(self, subject=None, task_parameter_file=None, file_hardware_setting
         # Prepare the experiment description dictionary
         self.experiment_description = self.make_experiment_description_dict(
             self.protocol_name, self.paths.TASK_COLLECTION,
-            procedures, projects, self.hardware_settings, stub)
+            procedures, projects, self.hardware_settings, stub, extractors=self.extractor_tasks)
 
     def _init_paths(self, append: bool = False):
         """
@@ -191,8 +192,9 @@ def _setup_loggers(self, level='INFO', file=None):
             self.logger = logger
 
     @staticmethod
-    def make_experiment_description_dict(task_protocol: str, task_collection: str, procedures: list = None, projects: list = None,
-                                         hardware_settings: dict = None, stub: Path = None):
+    def make_experiment_description_dict(task_protocol: str, task_collection: str, procedures: list = None,
+                                         projects: list = None, hardware_settings: dict = None,
+                                         stub: Path = None, extractors: list = None):
         """
         Construct an experiment description dictionary.
 
@@ -210,6 +212,8 @@ def make_experiment_description_dict(task_protocol: str, task_collection: str, p
             An optional dict of hardware devices, loaded from the hardware_settings.yaml file.
         stub : dict
             An optional experiment description stub to update.
+        extractors: list
+            An optional list of extractor names for the task.
 
         Returns
         -------
@@ -238,6 +242,9 @@ def make_experiment_description_dict(task_protocol: str, task_collection: str, p
                 'bpod': {'collection': task_collection, 'acquisition_software': 'pybpod', 'extension': '.jsonable'}}
         # Add task
         task = {task_protocol: {'collection': task_collection, 'sync_label': 'bpod'}}
+        if extractors:
+            assert isinstance(extractors, list), 'extractors parameter must be a list of strings'
+            task[task_protocol].update({'extractors': extractors})
         if 'tasks' not in description:
             description['tasks'] = [task]
         else:

iblrig/test/base.py

@@ -58,6 +58,11 @@ def test_graphviz(self) -> None:
                 pdf_out = Path(inspect.getfile(self.task.__class__)).parent.joinpath('state_machine_graph')
                 self.task.get_graphviz_task(output_file=pdf_out, view=False)
 
+        def test_acquisition_description(self) -> None:
+            # This makes sure that the task has a defined set of extractors
+            description_task = self.task.experiment_description['tasks'][0][self.task.protocol_name]
+            self.assertEqual(description_task['extractors'], self.task.extractor_tasks)
+
 
 class TestIntegrationFullRuns(BaseTestCases.CommonTestTask):
     """

iblrig/test/tasks/test_training_choice_world.py

@@ -42,8 +42,12 @@ def test_acquisition_description(self):
                 'cameras': {'left': {'collection': 'raw_video_data', 'sync_label': 'audio'}},
                 'microphone': {'microphone': {'collection': 'raw_task_data_00', 'sync_label': 'audio'}},
             },
-            'tasks': [
-                {'_iblrig_tasks_trainingChoiceWorld': {'collection': 'raw_task_data_00', 'sync_label': 'bpod'}}],
+            'tasks': [{
+                '_iblrig_tasks_trainingChoiceWorld': {
+                    'collection': 'raw_task_data_00',
+                    'sync_label': 'bpod',
+                    'extractors': ['TrialRegisterRaw', 'TrainingTrials', 'TrainingStatus']}}
+            ],
         }
         for k in ed:
             assert ad[k] == ed[k], f"Failed on {k}"

iblrig/test/test_base_tasks.py

@@ -84,7 +84,11 @@ def test_valve_mixin(self):
 
 
 class TestExperimentDescription(unittest.TestCase):
-    """Test creation of experiment description dictionary."""
+    """
+    Test creation of experiment description dictionary
+    Note: another part of testing is done in test/base.py, where the specific extractor classes
+    are passed on to the acquisition description and tested for each task.
+    """
 
     def setUp(self) -> None:
         self.stub = {

iblrig_tasks/_iblrig_tasks_advancedChoiceWorld/task.py

@@ -4,6 +4,7 @@
 
 class Session(ActiveChoiceWorldSession):
     protocol_name = "_iblrig_tasks_advancedChoiceWorld"
+    extractor_tasks = ['TrialRegisterRaw', 'TrainingTrials', 'TrainingStatus']
 
     def next_trial(self):
         # update counters

iblrig_tasks/_iblrig_tasks_biasedChoiceWorld/task.py

@@ -3,7 +3,7 @@
 
 
 class Session(BiasedChoiceWorldSession):
-    pass
+    extractor_tasks = ['TrialRegisterRaw', 'BiasedTrials', 'TrainingStatus']
 
 
 if __name__ == "__main__":  # pragma: no cover

iblrig_tasks/_iblrig_tasks_ephysChoiceWorld/task.py

@@ -13,6 +13,7 @@
 
 class Session(BiasedChoiceWorldSession):
     protocol_name = "_iblrig_tasks_ephysChoiceWorld"
+    extractor_tasks = ['TrialRegisterRaw', 'BiasedTrials', 'TrainingStatus']
 
     def __init__(self, *args, session_template_id=0, delay_secs=0, **kwargs):
         super(Session, self).__init__(*args, **kwargs)

iblrig_tasks/_iblrig_tasks_habituationChoiceWorld/task.py

@@ -3,7 +3,7 @@
 
 
 class Session(HabituationChoiceWorldSession):
-    pass
+    extractor_tasks = ['TrialRegisterRaw', 'HabituationTrials']
 
 
 if __name__ == "__main__":  # pragma: no cover

iblrig_tasks/_iblrig_tasks_neuroModulatorChoiceWorld/task.py

@@ -11,6 +11,7 @@
 
 class Session(BiasedChoiceWorldSession):
     protocol_name = "_iblrig_tasks_neuromodulatorChoiceWorld"
+    extractor_tasks = ['TrialRegisterRaw', 'TrialsTableNeuromodulator', 'TrainingStatus']
 
     def __init__(self, *args, **kwargs):
         super(Session, self).__init__(*args, **kwargs)

iblrig_tasks/_iblrig_tasks_passiveChoiceWorld/task.py

@@ -10,6 +10,7 @@
 
 class Session(ChoiceWorldSession):
     protocol_name = "_iblrig_tasks_passiveChoiceWorld"
+    extractor_tasks = ['PassiveRegisterRaw', 'PassiveChoiceWorld']
 
     def __init__(self, **kwargs):
         super(ChoiceWorldSession, self).__init__(**kwargs)

iblrig_tasks/_iblrig_tasks_trainingChoiceWorld/task.py

@@ -4,6 +4,7 @@
 
 
 class Session(TrainingChoiceWorldSession):
+    extractor_tasks = ['TrialRegisterRaw', 'TrainingTrials', 'TrainingStatus']
 
     @staticmethod
     def extra_parser():

iblrig_tasks/_iblrig_tasks_trainingPhaseChoiceWorld/task.py

@@ -4,6 +4,7 @@
 
 class Session(TrainingChoiceWorldSession):
     protocol_name = "_iblrig_tasks_trainingPhaseChoiceWorld"
+    extractor_tasks = ['TrialRegisterRaw', 'TrainingTrials', 'TrainingStatus']
 
     def __init__(self, *args, **kwargs):
         super(Session, self).__init__(*args, **kwargs)