[TEST] test update [skip ci]

bclenet · Jan 9, 2025 · 042f763 · 042f763
1 parent a7deb46
commit 042f763
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Showing 2 changed files with 50 additions and 18 deletions.
diff --git a/narps_open/runner.py b/narps_open/runner.py
@@ -140,31 +140,30 @@ def start(self, level: PipelineRunnerLevel = PipelineRunnerLevel.ALL) -> None:
             f'{self.team_id}, with {len(self.subjects)} subjects: {self.subjects}')
         print(f'\tThe following levels will be run: {level}')
 
-        # Generate workflow list & check for missing outputs
+        # Generate workflow list & level list
         workflows = []
-        output_checks = []
+        levels = []
         if bool(level & PipelineRunnerLevel.PREPROCESSING):
             workflows += self.get_workflows(self._pipeline.get_preprocessing())
-            output_checks += self.get_missing_outputs(PipelineRunnerLevel.PREPROCESSING)
+            levels.append(PipelineRunnerLevel.PREPROCESSING)
         if bool(level & PipelineRunnerLevel.RUN):
             workflows += self.get_workflows(self._pipeline.get_run_level_analysis())
-            output_checks += self.get_missing_outputs(PipelineRunnerLevel.RUN)
+            levels.append(PipelineRunnerLevel.RUN)
         if bool(level & PipelineRunnerLevel.SUBJECT):
             workflows += self.get_workflows(self._pipeline.get_subject_level_analysis())
-            output_checks += self.get_missing_outputs(PipelineRunnerLevel.SUBJECT)
+            levels.append(PipelineRunnerLevel.SUBJECT)
         if bool(level & PipelineRunnerLevel.GROUP):
             workflows += self.get_workflows(self._pipeline.get_group_level_analysis())
-            output_checks += self.get_missing_outputs(PipelineRunnerLevel.GROUP)
+            levels.append(PipelineRunnerLevel.GROUP)
 
         # Launch workflows
-        for workflow, output_check in zip(workflows, output_checks):
+        for workflow, current_level in zip(workflows, levels):
             nb_procs = Configuration()['runner']['nb_procs']
             if nb_procs > 1:
                 workflow.run('MultiProc', plugin_args = {'n_procs': nb_procs})
-                output_check()
             else:
                 workflow.run()
-                output_check()
+            self.get_missing_outputs(current_level)
 
     def get_missing_outputs(self, level: PipelineRunnerLevel = PipelineRunnerLevel.ALL):
         """

diff --git a/tests/test_runner.py b/tests/test_runner.py
@@ -271,20 +271,13 @@ def test_start_nok():
         with raises(AttributeError):
             runner.start()
 
-        # 2b - test starting a pipeline with wrong workflow type
+        # 3 - test starting a pipeline with wrong workflow type
         runner = PipelineRunner('2T6S')
         runner._pipeline = MockupWrongPipeline2() # hack the runner by setting a test Pipeline
 
         with raises(AttributeError):
             runner.start()
 
-        # 2b - test starting a pipeline with wrong options (fist_level_only + group_level_only)
-        runner = PipelineRunner('2T6S')
-        runner._pipeline = MockupPipeline() # hack the runner by setting a test Pipeline
-
-        with raises(AttributeError):
-            runner.start(True, True)
-
     @staticmethod
     @mark.unit_test
     def test_start_ok():
@@ -358,6 +351,37 @@ def test_start_ok():
                 assert file.readline() == 'MockupPipeline : '+workflow+' node_1\n'
                 assert file.readline() == 'MockupPipeline : '+workflow+' node_2\n'
 
+    @staticmethod
+    @mark.unit_test
+    def test_get_workflows():
+        """ Test the get_workflows method """
+        runner = PipelineRunner('2T6S')
+        workflow_1 = Workflow(name = 'workflow_1')
+        workflow_2 = Workflow(name = 'workflow_2')
+
+        # Error when passing something that is not a nipype.Workflow
+        with raises(AttributeError):
+            runner.get_workflows(183)
+
+        # Error when passing something that is not a list of nipype.Workflow
+        with raises(AttributeError):
+            runner.get_workflows([workflow_1, 183])
+
+        # Check output when passing a nipype.Workflow
+        test = runner.get_workflows(workflow_1)
+        assert isinstance(test, list)
+        assert test == [workflow_1]
+
+        # Check output when passing a list of nipype.Workflow
+        test = runner.get_workflows([workflow_1, workflow_2])
+        assert isinstance(test, list)
+        assert test == [workflow_1, workflow_2]
+
+        # Check output when passing None
+        test = runner.get_workflows(None)
+        assert isinstance(test, list)
+        assert test == []
+
     @staticmethod
     @mark.unit_test
     def test_get_missing_outputs():
@@ -393,10 +417,19 @@ def test_get_missing_outputs():
         Path(runner.pipeline.get_subject_level_outputs()[1]).touch()
 
         # 1e - Check again for missing files
-        missing_files = runner.get_missing_first_level_outputs()
+        missing_files = runner.get_missing_outputs(PipelineRunnerLevel.FIRST)
         assert len(missing_files) == 1
         assert 'run_output.md' in missing_files[0]
 
+        missing_files = runner.get_missing_outputs(PipelineRunnerLevel.RUN)
+        assert len(missing_files) == 1
+        assert 'run_output.md' in missing_files[0]
+
+        missing_files = runner.get_missing_outputs(PipelineRunnerLevel.GROUP)
+        assert len(missing_files) == 2
+        assert 'group_1_output_a.md' in missing_files[0]
+        assert 'group_1_output_b.md' in missing_files[1]
+
         # 2a - Instantiate a pipeline
         runner = PipelineRunner('2T6S')
         runner._pipeline = MockupPipeline() # hack the runner by setting a test Pipeline