From 7f174dc521bcd0354b28889459f7004b7cba19b5 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Mon, 11 Mar 2024 16:49:40 +0100
Subject: [PATCH] fix errors
---
src/nextflow_file.py | 11 +++++++++--
tests/test_process.py | 27 ++++++++++++++-------------
2 files changed, 23 insertions(+), 15 deletions(-)
diff --git a/src/nextflow_file.py b/src/nextflow_file.py
index 6930222..70684e4 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 4c2f640..37a242c 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]
--
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