98BT bug with subject IDs (#183)

* [BUG] inside unit_tests workflow

* Refactoring pipeline 98BT

* [TEST] update tests [REFAC] pep8 and bug correction

* Using narps_open.data.task module inside 98BT

* [TEST] update + dependancy to niflow

* [REFAC][skip ci]

* [BUG] input of get_contrats [skip ci]

* Light bugs + remove large files [skip ci]

* [TEST] adding tests for 98BT

* [TEST] adding tests for 98BT

* [TEST] adding tests for 98BT

* Output names for 98BT

* Preprocessing output names

* Subject info issue + output names

* 98BT - Refac get_parameters_files

* [TEST] 98BT get_parameters_file

* Using fixture for temporary test dir creation / removal

* Linting pipelines test files

* Bug with regressors naming

* pylintrc for pylint config

* Subject ID completion in get_contrast

narps_open/pipelines/team_98BT.py

@@ -706,6 +706,11 @@ def get_group_level_analysis_sub_workflow(self, method):
         get_equal_indifference_subjects.inputs.list_1 = get_group('equalIndifference')
         get_equal_indifference_subjects.inputs.list_2 = self.subject_list
 
+        # Create a function to complete the subject ids out from the get_equal_*_subjects nodes
+        #   If not complete, subject id '001' in search patterns
+        #   would match all contrast files with 'con_0001.nii'.
+        complete_subject_ids = lambda l : [f'_subject_id_{a}' for a in l]
+
         # Function Node elements_in_string
         #   Get contrast files for required subjects
         # Note : using a MapNode with elements_in_string requires using clean_list to remove
@@ -778,14 +783,16 @@ def get_group_level_analysis_sub_workflow(self, method):
                 ])
 
         if method == 'equalRange':
-            group_level_analysis.connect([
-                (get_equal_range_subjects, get_contrasts, [('out_list', 'elements')])
-                ])
+            group_level_analysis.connect(
+                get_equal_range_subjects, ('out_list', complete_subject_ids),
+                get_contrasts, 'elements'
+                )
 
         elif method == 'equalIndifference':
-            group_level_analysis.connect([
-                (get_equal_indifference_subjects, get_contrasts, [('out_list', 'elements')])
-                ])
+            group_level_analysis.connect(
+                get_equal_indifference_subjects, ('out_list', complete_subject_ids),
+                get_contrasts, 'elements'
+                )
 
         elif method == 'groupComp':
             estimate_contrast.inputs.contrasts = [
@@ -812,8 +819,12 @@ def get_group_level_analysis_sub_workflow(self, method):
 
             group_level_analysis.connect([
                 (select_files, get_contrasts_2, [('contrasts', 'input_str')]),
-                (get_equal_range_subjects, get_contrasts, [('out_list', 'elements')]),
-                (get_equal_indifference_subjects, get_contrasts_2, [('out_list', 'elements')]),
+                (get_equal_range_subjects, get_contrasts, [
+                    (('out_list', complete_subject_ids), 'elements')
+                    ]),
+                (get_equal_indifference_subjects, get_contrasts_2, [
+                    (('out_list', complete_subject_ids), 'elements')
+                    ]),
                 (get_contrasts, two_sample_t_test_design, [
                     (('out_list', clean_list), 'group1_files')
                     ]),