Custom configuration allowed for testing

Author: bclenet

narps_open/data/task.py

@@ -12,13 +12,16 @@
 class TaskInformation(dict, metaclass=SingletonMeta):
     """ This class allows to access information about the task performed in NARPS """
 
-    task_information_file = join(Configuration()['directories']['dataset'], 'task-MGT_bold.json')
-
-    def __init__(self):
+    def __init__(self, task_file=''):
         super().__init__()
 
         # Load information from the task-MGT_bold.json file
-        with open(self.task_information_file, 'rb') as file:
+        if task_file:
+            task_information_file = task_file # For testing purpose only
+        else:            
+            task_information_file = join(
+                Configuration()['directories']['dataset'], 'task-MGT_bold.json')
+        with open(task_information_file, 'rb') as file:
             self.update(load(file))
 
         # Compute derived information

narps_open/utils/configuration/docker_testing_config.toml

@@ -0,0 +1,26 @@
+[general]
+title = "Testing configuration for the NARPS open pipelines project, to be used inside the nipype/nipype:py38 docker container"
+config_type = "custom"
+
+[directories]
+dataset = "/work/data/original/ds001734/"
+reproduced_results = "/work/run/reproduced/"
+narps_results = "/work/data/results/"
+test_data = "/work/tests/test_data/"
+test_runs = "/work/run/"
+
+[runner]
+nb_procs = 8 # Maximum number of threads executed by the runner
+nb_trials = 3 # Maximum number of executions to have the pipeline executed completely
+
+[pipelines]
+remove_unused_data = true # set to true to activate remove nodes of pipelines
+
+[results]
+neurovault_naming = true # true if results files are saved using the neurovault naming, false if they use naming of narps
+
+[testing]
+
+[testing.pipelines]
+nb_subjects_per_group = 4 # Compute first level analyses by subgroups of N subjects, to avoid lacking of disk and memory
+correlation_thresholds = [0.30, 0.70, 0.78, 0.85, 0.93] # Correlation between reproduced hypotheses files and results, respectively for [20, 40, 60, 80, 108] subjects.

tests/conftest.py

@@ -24,8 +24,24 @@
 from narps_open.data.results import ResultsCollection
 from narps_open.data.participants import get_participants_subset
 
-# Init configuration, to ensure it is in testing mode
-Configuration(config_type='testing')
+def pytest_addoption(parser):
+    """ Add a configuration option for narps_open to the pytest command line """
+    parser.addoption('--narps_open_config',
+        action='store', help='NARPS Open Pipelines configuration file')
+
+@fixture(scope='session', autouse=True)
+def load_configuration(request):
+    """ Automatically load narps_open configuration from the corresponding
+        pytest command line argument.
+    """
+    config_file = request.config.getoption('--narps_open_config')
+
+    if config_file:
+        # Init configuration with custom file
+        Configuration(config_type='custom').config_file = config_file
+    else:
+        # Ensure it is in testing mode
+        Configuration(config_type='testing')
 
 @fixture
 def temporary_data_dir():

tests/data/test_task.py

@@ -18,10 +18,9 @@
 from narps_open.data import task
 
 @fixture(scope='function', autouse=True)
-def mock_task_data(mocker):
-    """ Patch the json.load method to mock task data """
-    mocker.patch.object(
-        task.TaskInformation, 'task_information_file',
+def load_test_task_data():
+    """ Init the TaskInformation class with task data for testing """
+    task.TaskInformation(
         join(Configuration()['directories']['test_data'], 'data', 'task', 'task-info.json')
         )