[TEST] change pipeline test_utils to avoid having to rewrite it at ev…

…ery repro

tests/pipelines/test_pipelines.py

@@ -135,8 +135,8 @@ class TestUtils:
     @mark.unit_test
     def test_utils():
         """ Test the utils methods of PipelineRunner """
-        # 1 - Get number of not implemented pipelines
-        assert len(get_not_implemented_pipelines()) == 69
+        # 1 - Get not implemented pipelines
+        assert '1K0E' in get_not_implemented_pipelines()
 
-        # 2 - Get number of implemented pipelines
-        assert len(get_implemented_pipelines()) == 1
+        # 2 - Get implemented pipelines
+        assert '2T6S' in get_implemented_pipelines()

tests/test_conftest.py

@@ -0,0 +1,139 @@
+#!/usr/bin/python
+# coding: utf-8
+
+""" Tests of the 'conftest.py' module.
+
+Launch this test with PyTest
+
+Usage:
+======
+    pytest -q test_conftest.py
+    pytest -q test_conftest.py -k <selected_test>
+"""
+
+from os import remove
+from os.path import join, isfile, abspath
+from pathlib import Path
+
+from datetime import datetime
+
+from pytest import raises, mark
+
+from nipype import Node, Workflow
+from nipype.interfaces.utility import Function
+
+from narps_open.utils.configuration import Configuration
+from narps_open.runner import PipelineRunner
+from narps_open.pipelines import Pipeline
+from narps_open.pipelines.team_2T6S import PipelineTeam2T6S
+
+class MockupPipeline(Pipeline):
+    """ A simple Pipeline class for test purposes """
+
+    def __init__(self):
+        super().__init__()
+        self.test_file = abspath(
+            join(Configuration()['directories']['test_runs'], 'test_conftest.txt'))
+        if isfile(self.test_file):
+            remove(self.test_file)
+
+    def __del__(self):
+        if isfile(self.test_file):
+            remove(self.test_file)
+
+    # @staticmethod
+    def write_to_file(_, text_to_write: str, file_path: str):
+        """ Method used inside a nipype Node, to write a line in a test file """
+        with open(file_path, 'a', encoding = 'utf-8') as file:
+            file.write(text_to_write)
+
+    def create_workflow(self, workflow_name: str):
+        """ Return a nipype workflow with two nodes writing in a file """
+        node_1 = Node(Function(
+            input_names = ['_', 'text_to_write', 'file_path'],
+            output_names = ['_'],
+            function = self.write_to_file),
+            name = 'node_1'
+            )
+        # this input is set to now(), so that it changes at every run, thus preventing
+        # nipype's cache to work
+        node_1.inputs._ = datetime.now()
+        node_1.inputs.text_to_write = 'MockupPipeline : '+workflow_name+' node_1\n'
+        node_1.inputs.file_path = self.test_file
+
+        node_2 = Node(Function(
+            input_names = ['_', 'text_to_write', 'file_path'],
+            output_names = [],
+            function = self.write_to_file),
+            name = 'node_2'
+            )
+        node_2.inputs.text_to_write = 'MockupPipeline : '+workflow_name+' node_2\n'
+        node_2.inputs.file_path = self.test_file
+
+        workflow = Workflow(
+            base_dir = Configuration()['directories']['test_runs'],
+            name = workflow_name
+            )
+        workflow.add_nodes([node_1, node_2])
+        workflow.connect(node_1, '_', node_2, '_')
+
+        return workflow
+
+    def get_preprocessing(self):
+        """ Return a fake preprocessing workflow """
+        return self.create_workflow('TestPipelineRunner_preprocessing_workflow')
+
+    def get_run_level_analysis(self):
+        """ Return a fake run level workflow """
+        return self.create_workflow('TestPipelineRunner_run_level_workflow')
+
+    def get_subject_level_analysis(self):
+        """ Return a fake subject level workflow """
+        return self.create_workflow('TestPipelineRunner_subject_level_workflow')
+
+    def get_group_level_analysis(self):
+        """ Return a fake subject level workflow """
+        return self.create_workflow('TestPipelineRunner_group_level_workflow')
+
+    def get_preprocessing_outputs(self):
+        """ Return a list of templates of the output files generated by the preprocessing """
+        return [join(Configuration()['directories']['test_runs'], 'preprocessing_output.md')]
+
+    def get_run_level_outputs(self):
+        """ Return a list of templates of the output files generated by the run level analysis.
+            Templates are expressed relatively to the self.directories.output_dir.
+        """
+        return [join(Configuration()['directories']['test_runs'], 'run_output.md')]
+
+    def get_subject_level_outputs(self):
+        """ Return a list of templates of the output files generated by the subject level analysis.
+            Templates are expressed relatively to the self.directories.output_dir.
+        """
+        templates = [
+            join(Configuration()['directories']['test_runs'], 'subject_{subject_id}_output_1.md'),
+            join(Configuration()['directories']['test_runs'], 'subject_{subject_id}_output_2.md')
+            ]
+        return_list = []
+        for subject_id in self.subject_list:
+            return_list += [t.format(subject_id = subject_id) for t in templates]
+
+        return return_list
+
+    def get_group_level_outputs(self):
+        """ Return a list of templates of the output files generated by the group level analysis.
+            Templates are expressed relatively to the self.directories.output_dir.
+        """
+        templates = [
+            join(Configuration()['directories']['test_runs'], 'group_{nb_subjects}_output_a.md'),
+            join(Configuration()['directories']['test_runs'], 'group_{nb_subjects}_output_b.md')
+            ]
+        return [t.format(nb_subjects = len(self.subject_list)) for t in  templates]
+
+    def get_hypotheses_outputs(self):
+        """ Return the names of the files used by the team to answer the hypotheses of NARPS.
+        """
+        template = join(Configuration()['directories']['test_runs'], 'hypothesis_{id}.md')
+        return [template.format(id = i) for i in range(1,18)]
+
+class TestPipelineRunner:
+    """ A class that contains all the unit tests for the PipelineRunner class."""