diff --git a/src/nextflow_file.py b/src/nextflow_file.py index 69302228eb9ba9a08a89c300943f89524e6bc85c..70684e4f2c4f1346bd294de102bdb17258121f0d 100644 --- a/src/nextflow_file.py +++ b/src/nextflow_file.py @@ -91,13 +91,20 @@ class Nextflow_File(Nextflow_Building_Blocks): if(self.first_file): return self.output_dir else: - return self.origin.get_output_dir() + if(self.origin==None): + return self.output_dir + else: + return self.origin.get_output_dir() def get_display_info(self): if (self.first_file): return self.display_info else: - return self.origin.get_display_info() + if(self.origin==None): + return self.display_info + else: + return self.origin.get_display_info() + def set_name(self): diff --git a/tests/test_process.py b/tests/test_process.py index 4c2f6400190fc2127e1b0e6a909ba385ea9c6262..37a242c772430ad29c6905c9fdfe30f744dbeb8d 100644 --- a/tests/test_process.py +++ b/tests/test_process.py @@ -10,20 +10,20 @@ class TestProcess(unittest.TestCase): def test_initialise_name(self): #DSL1 - file = Nextflow_File("tests/ressources/process/process_DSL1.nf", display_info=False) + file = Nextflow_File("tests/ressources/process/process_DSL1.nf", display_info=False, DSL = "DSL1") file.initialise() process_DSL1 = file.processes[0] self.assertEqual(process_DSL1.get_name(), "cleanSpeciesTree") self.assertEqual(process_DSL1.get_alias(), "cleanSpeciesTree") #DSL2 - file = Nextflow_File("tests/ressources/process/process_DSL2.nf", display_info=False) + file = Nextflow_File("tests/ressources/process/process_DSL2.nf", display_info=False, DSL = "DSL2") file.initialise() process_DSL2 = file.processes[0] self.assertEqual(process_DSL2.get_name(), "OPENMS_FALSEDISCOVERYRATE") self.assertEqual(process_DSL2.get_alias(), "OPENMS_FALSEDISCOVERYRATE") def test_set_alias(self): - file = Nextflow_File("tests/ressources/process/process_DSL2.nf", display_info=False) + file = Nextflow_File("tests/ressources/process/process_DSL2.nf", display_info=False, DSL = "DSL2") file.initialise() process_DSL2 = file.processes[0] self.assertEqual(process_DSL2.get_alias(), "OPENMS_FALSEDISCOVERYRATE") @@ -35,24 +35,24 @@ class TestProcess(unittest.TestCase): def test_which_DSL(self): #DSL1 - file = Nextflow_File("tests/ressources/process/process_DSL1.nf", display_info=False) + file = Nextflow_File("tests/ressources/process/process_DSL1.nf", display_info=False, DSL = "DSL1") file.initialise() process_DSL1 = file.processes[0] self.assertEqual(process_DSL1.which_DSL(), "DSL1") #DSL2 - file = Nextflow_File("tests/ressources/process/process_DSL2.nf", display_info=False) + file = Nextflow_File("tests/ressources/process/process_DSL2.nf", display_info=False, DSL = "DSL1") file.initialise() process_DSL2 = file.processes[0] self.assertEqual(process_DSL2.which_DSL(), "DSL2") def test_is_initialised(self): #DSL1 - file = Nextflow_File("tests/ressources/process/process_DSL1.nf", display_info=False) + file = Nextflow_File("tests/ressources/process/process_DSL1.nf", display_info=False, DSL = "DSL1") file.initialise() process_DSL1 = file.processes[0] self.assertTrue(process_DSL1.is_initialised()) #DSL2 - file = Nextflow_File("tests/ressources/process/process_DSL2.nf", display_info=False) + file = Nextflow_File("tests/ressources/process/process_DSL2.nf", display_info=False, DSL = "DSL2") file.initialise() process_DSL2 = file.processes[0] self.assertTrue(process_DSL2.is_initialised()) @@ -60,12 +60,12 @@ class TestProcess(unittest.TestCase): def test_get_type(self): #DSL1 - file = Nextflow_File("tests/ressources/process/process_DSL1.nf", display_info=False) + file = Nextflow_File("tests/ressources/process/process_DSL1.nf", display_info=False, DSL = "DSL1") file.initialise() process_DSL1 = file.processes[0] self.assertEqual(process_DSL1.get_type(), "Process") #DSL2 - file = Nextflow_File("tests/ressources/process/process_DSL2.nf", display_info=False) + file = Nextflow_File("tests/ressources/process/process_DSL2.nf", display_info=False, DSL = "DSL2") file.initialise() process_DSL2 = file.processes[0] self.assertEqual(process_DSL2.get_type(), "Process") @@ -74,7 +74,7 @@ class TestProcess(unittest.TestCase): def test_get_structure(self): #DSL1 - file = Nextflow_File("tests/ressources/process/process_DSL1.nf", display_info=False) + file = Nextflow_File("tests/ressources/process/process_DSL1.nf", display_info=False, DSL = "DSL1") file.initialise() process_DSL1 = file.processes[0] dico = {} @@ -82,10 +82,11 @@ class TestProcess(unittest.TestCase): dico['edges'] = [] dico['subworkflows'] = {} process_DSL1.get_structure(dico) - dico_true = {'nodes': [{'id': str(process_DSL1), 'name': 'cleanSpeciesTree', 'shape': 'ellipse', 'xlabel': ''}], 'edges': [], 'subworkflows': {}} + dico_true = {'nodes': [{'id': str(process_DSL1), 'name': 'cleanSpeciesTree', 'shape': 'ellipse', 'xlabel': '', 'fillcolor': ''}], 'edges': [], 'subworkflows': {}} self.assertEqual(dico, dico_true) + #DSL2 - file = Nextflow_File("tests/ressources/process/process_DSL2.nf", display_info=False) + file = Nextflow_File("tests/ressources/process/process_DSL2.nf", display_info=False, DSL = "DSL2") file.initialise() process_DSL2 = file.processes[0] dico = {} @@ -97,7 +98,7 @@ class TestProcess(unittest.TestCase): self.assertEqual(dico, dico_true) def test_(self): - file = Nextflow_File("tests/ressources/process/process_DSL1.nf", display_info=False) + file = Nextflow_File("tests/ressources/process/process_DSL1.nf", display_info=False, DSL = "DSL1") file.initialise() process_DSL1 = file.processes[0]