fix errors

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):

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]