From 299b5262bf7d9b6ce01fd76592cfed50827c1bb5 Mon Sep 17 00:00:00 2001
From: elodiegermani1 <elodie.germani@irisa.fr>
Date: Tue, 15 Aug 2023 10:07:48 -0400
Subject: [PATCH] Start reproduction of pipeline 43FJ

---
 .../{team_43FJ_debug.py => team_43FJ.py}      |  0
 tests/pipelines/test_team_43FJ.py             | 93 +++++++++++++++++++
 2 files changed, 93 insertions(+)
 rename narps_open/pipelines/{team_43FJ_debug.py => team_43FJ.py} (100%)
 create mode 100644 tests/pipelines/test_team_43FJ.py

diff --git a/narps_open/pipelines/team_43FJ_debug.py b/narps_open/pipelines/team_43FJ.py
similarity index 100%
rename from narps_open/pipelines/team_43FJ_debug.py
rename to narps_open/pipelines/team_43FJ.py
diff --git a/tests/pipelines/test_team_43FJ.py b/tests/pipelines/test_team_43FJ.py
new file mode 100644
index 00000000..f343777a
--- /dev/null
+++ b/tests/pipelines/test_team_43FJ.py
@@ -0,0 +1,93 @@
+#!/usr/bin/python
+# coding: utf-8
+
+""" Tests of the 'narps_open.pipelines.team_1KB2' module.
+
+Launch this test with PyTest
+
+Usage:
+======
+    pytest -q test_team_2T6S.py
+    pytest -q test_team_2T6S.py -k <selected_test>
+"""
+
+from statistics import mean
+from os import environ
+
+from pytest import raises, helpers, mark
+from nipype import Workflow
+
+from narps_open.pipelines.team_1KB2 import PipelineTeam1KB2
+
+class TestPipelinesTeam1KB2:
+    """ A class that contains all the unit tests for the PipelineTeam1KB2 class."""
+
+    @staticmethod
+    @mark.unit_test
+    def test_create(mocker): # Add mocker as argument
+        """ Test the creation of a PipelineTeam1KB2 object """
+        # Defines fake environment variable
+        mocker.patch.dict(environ, {'FSLDIR': '/fake/path/to/fsl'})
+
+        pipeline = PipelineTeam1KB2()
+
+        # 1 - check the parameters
+        assert pipeline.team_id == '1KB2'
+
+        # 2 - check workflows
+        assert isinstance(pipeline.get_preprocessing(), Workflow)
+        assert isinstance(pipeline.get_run_level_analysis(), Workflow)
+        assert isinstance(pipeline.registration(), Workflow)
+        assert isinstance(pipeline.get_subject_level_analysis(), Workflow)
+        group_level = pipeline.get_group_level_analysis()
+
+        assert len(group_level) == 3
+        for sub_workflow in group_level:
+            assert isinstance(sub_workflow, Workflow)
+
+    @staticmethod
+    @mark.unit_test
+    def test_outputs():
+        """ Test the expected outputs of a PipelineTeam1KB2 object """
+        pipeline = PipelineTeam1KB2()
+        # 1 - 1 suject outputs, 1 run
+        pipeline.subject_list = ['001']
+        pipeline.run_list = ['01']
+        pipeline.contrast_list = ['1','2']
+        assert len(pipeline.get_preprocessing_outputs()) == 6
+        #assert len(pipeline.get_run_level_outputs()) == 0
+        #assert len(pipeline.get_registration()) == 0
+        #assert len(pipeline.get_subject_level_outputs()) == 
+        #assert len(pipeline.get_group_level_outputs()) == 84
+
+        # 2 - 1 suject outputs, 4 runs
+        pipeline.subject_list = ['001']
+        pipeline.run_list = ['01', '02', '03', '04']
+        pipeline.contrast_list = ['1','2']
+        assert len(pipeline.get_preprocessing_outputs()) == 24
+        #assert len(pipeline.get_run_level_outputs()) == 0
+        #assert len(pipeline.get_registration()) == 0
+        #assert len(pipeline.get_subject_level_outputs()) == 36
+        #assert len(pipeline.get_group_level_outputs()) == 84
+
+        # 3 - 4 suject outputs, 4 runs
+        pipeline.subject_list = ['001', '002', '003', '004']
+        pipeline.run_list = ['01', '02', '03', '04']
+        pipeline.contrast_list = ['1','2']
+        assert len(pipeline.get_preprocessing_outputs()) == 96
+        #assert len(pipeline.get_run_level_outputs()) == 0
+        #assert len(pipeline.get_registration()) == 0
+        #assert len(pipeline.get_subject_level_outputs()) == 36
+        #assert len(pipeline.get_group_level_outputs()) == 84
+
+    @staticmethod
+    @mark.pipeline_test
+    def test_execution():
+        """ Test the execution of a PipelineTeam1KB2 and compare results """
+        results_4_subjects = helpers.test_pipeline(
+            '1KB2',
+            '/references/',
+            '/data/',
+            '/output/',
+            4)
+        assert mean(results_4_subjects) > .003