diff --git a/.gitignore b/.gitignore
index 598a38d4bc6065d6caee19229d6a1b071ea030e4..7c41c1a26f994902b5a97d38a46cc7c40ee9cedc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,4 +5,5 @@ __pycache__
.venv
.idea
dist/
-results*/
\ No newline at end of file
+results*/
+*.candidate.nf
\ No newline at end of file
diff --git a/run_tests.py b/run_tests.py
index 6e809a439e38ceacded74b2b4a039e1b6e610957..cbc9dc30a5837acddd375910e4e4e482cc7b7713 100755
--- a/run_tests.py
+++ b/run_tests.py
@@ -1,9 +1,16 @@
#!/usr/bin/env python
+import sys
import unittest
-#Run all tests
-if __name__ == '__main__':
+
+# Run all tests
+def main(pattern='test_*.py', *args):
test_loader = unittest.TestLoader()
- test_suite = test_loader.discover('tests', pattern='test_*.py')
+ test_suite = test_loader.discover('tests', pattern=pattern)
runner = unittest.TextTestRunner()
- runner.run(test_suite)
+ results = runner.run(test_suite)
+ return results.wasSuccessful()
+
+
+if __name__ == '__main__':
+ sys.exit(0 if main(*sys.argv[1:]) else 1)
diff --git a/src/bioflowinsighterror.py b/src/bioflowinsighterror.py
index dd222bb911354243c204a4ce080bf325f04eb2ee..0dfc769c67d643823b55529a1319d935dde46a3e 100644
--- a/src/bioflowinsighterror.py
+++ b/src/bioflowinsighterror.py
@@ -43,6 +43,8 @@ class BioFlowInsightError(Exception):
#* [5] -> A ternary conditional operator was used with an tuple
#* [7] -> Tuple with emit (ch1, ch2) = emit.out
#* [9] -> Tuple with call (ch1, ch2) = wf()
+#* [11] -> Failed to extract the operation or call at the line x. Try rewriting it in a simplified version.
+
diff --git a/src/nextflow_building_blocks.py b/src/nextflow_building_blocks.py
index c436bf2b7d6b83b904e0c8869064b6fd8ede4e2b..ce5144c9088f598a39dc7741fa98dd50de672357 100644
--- a/src/nextflow_building_blocks.py
+++ b/src/nextflow_building_blocks.py
@@ -318,16 +318,24 @@ class Nextflow_Building_Blocks:
if(match.group(1) in constant.LIST_OPERATORS):
#TODO -> the function below might not work perfectly but i don't have any other ideas
- #TODO -> IMPORTANT find another way of doing this -> for example if there isn't the same number of curlies/parentheses
+
#Use if there is an operator called right before opening the curlies/parenthse
- curly_left, curly_right = get_curly_count(text[:start]), get_curly_count(text[end:])
+ #curly_left, curly_right = get_curly_count(text[:start]), get_curly_count(text[end:])
parenthese_left, parenthese_right = get_parenthese_count(text[:start]), get_parenthese_count(text[end:])
#if(curly_left==0 and curly_right==0 and parenthese_left==0 and parenthese_right==0 and (start, end) not in searched):
if(parenthese_left==0 and parenthese_right==0 and (start, end) not in searched):
searched.append((start, end))
- pot = extract_executor_from_middle(text, start, end)
+ try:
+ pot = extract_executor_from_middle(text, start, end)
+ except:
+ try:
+ temp = text[start-10:end+10]
+ except:
+ temp = text[start:end]
+ raise BioFlowInsightError(f"Failed to extract the operation or call{self.get_string_line(temp)}. Try rewriting it in a simplified version.", num = 11, origin=self)
+
pot = expand_to_pipe_operators(text, pot)
#If the thing which is extracted is not in the conditon of an if
@@ -360,6 +368,7 @@ class Nextflow_Building_Blocks:
self.executors.append(ope)
searching = True
break
+
#---------------------------------------------------------------
#STEP4 - Extract the Executors which only use the pipe operators (which start with a channel)
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/src/ro_crate.py b/src/ro_crate.py
index 098a437ce1e91c1a009c5247022306315292bf23..80d167647495aca656acb42be482fcaeb24e111f 100644
--- a/src/ro_crate.py
+++ b/src/ro_crate.py
@@ -80,7 +80,7 @@ class RO_Crate:
current_directory = os.getcwd()
os.chdir("/".join(self.workflow.nextflow_file.get_file_address().split("/")[:-1]))
try:
- os.system(f"git log {'--reverse'*reverse} {file} > temp_{id(self)}.txt")
+ os.system(f"git log {'--reverse'*reverse} \"{file}\" > temp_{id(self)}.txt")
with open(f'temp_{id(self)}.txt') as f:
info = f.read()
os.system(f"rm temp_{id(self)}.txt")
diff --git a/tests/test_channel.py b/tests/test_channel.py
index b5c5547f7b3b336b32f05a52adcc053af4af27d9..b823d57b323a84889cd4eb09898c493903bd8612 100644
--- a/tests/test_channel.py
+++ b/tests/test_channel.py
@@ -3,26 +3,34 @@ from src.channel import *
from src.nextflow_file import Nextflow_File
+class EmptyNextflowFile(Nextflow_File):
+ def __init__(self, address="tests/ressources/channel/empty_wf.nf", display_info=False, *args, **kwargs):
+ super().__init__(address=address, display_info=display_info, *args, **kwargs)
+
+ def check_file_correctness_after_DSL(self):
+ return
+
+
class TestChannel(unittest.TestCase):
def test_get_code(self):
- wf1 = Nextflow_File("tests/ressources/channel/empty_wf.nf", display_info=False)
+ wf1 = EmptyNextflowFile()
ch1 = Channel(name = "ch1", origin = wf1)
self.assertIsInstance(ch1, Channel)
self.assertEqual(ch1.get_code(), "ch1")
def test_get_name(self):
- wf1 = Nextflow_File("tests/ressources/channel/empty_wf.nf", display_info=False)
+ wf1 = EmptyNextflowFile()
ch1 = Channel(name = "ch1", origin = wf1)
self.assertEqual(ch1.get_name(), "ch1")
def test_get_type(self):
- wf1 = Nextflow_File("tests/ressources/channel/empty_wf.nf", display_info=False)
+ wf1 = EmptyNextflowFile()
ch1 = Channel(name = "ch1", origin = wf1)
self.assertEqual(ch1.get_type(), "Channel")
def test_add_source(self):
- wf1 = Nextflow_File("tests/ressources/channel/empty_wf.nf", display_info=False)
+ wf1 = EmptyNextflowFile()
ch1 = Channel(name = "ch1", origin = wf1)
self.assertEqual(ch1.get_source(), [])
ele = "This is a test"
@@ -30,7 +38,7 @@ class TestChannel(unittest.TestCase):
self.assertEqual(ch1.get_source(), [ele])
def test_add_sink(self):
- wf1 = Nextflow_File("tests/ressources/channel/empty_wf.nf", display_info=False)
+ wf1 = EmptyNextflowFile()
ch1 = Channel(name = "ch1", origin = wf1)
self.assertEqual(ch1.get_sink(), [])
ele = "This is a test"
@@ -38,7 +46,7 @@ class TestChannel(unittest.TestCase):
self.assertEqual(ch1.get_sink(), [ele])
def test_set_sink_null(self):
- wf1 = Nextflow_File("tests/ressources/channel/empty_wf.nf", display_info=False)
+ wf1 = EmptyNextflowFile()
ch1 = Channel(name = "ch1", origin = wf1)
ele = "This is a test"
ch1.add_sink(ele)
@@ -47,7 +55,7 @@ class TestChannel(unittest.TestCase):
self.assertEqual(ch1.get_sink(), [])
def test_remove_element_from_sink(self):
- wf1 = Nextflow_File("tests/ressources/channel/empty_wf.nf", display_info=False)
+ wf1 = EmptyNextflowFile()
ch1 = Channel(name = "ch1", origin = wf1)
ele = "This is a test"
ch1.add_sink(ele)
@@ -56,7 +64,7 @@ class TestChannel(unittest.TestCase):
self.assertEqual(ch1.get_sink(), [])
def test_equal(self):
- wf1 = Nextflow_File("tests/ressources/channel/empty_wf.nf", display_info=False)
+ wf1 = EmptyNextflowFile()
ch1 = Channel(name = "ch1", origin = wf1)
ch1_1 = Channel(name = "ch1", origin = wf1)
ch2 = Channel(name = "ch2", origin = wf1)
@@ -64,7 +72,7 @@ class TestChannel(unittest.TestCase):
self.assertFalse(ch1.equal(channel=ch2))
def test_get_structure(self):
- wf1 = Nextflow_File("tests/ressources/channel/empty_wf.nf", display_info=False)
+ wf1 = EmptyNextflowFile()
ch1 = Channel(name = "ch1", origin = wf1)
dico = {}
dico['nodes'] = []
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 076721cecca10563ff6b3698c182db0c12ac49e5..fab491414d834305052fd08aa103e34ec896991f 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -7,7 +7,7 @@ from bioflow_insight_cli.main import cli
class TestCall(unittest.TestCase):
def test_cli_works(self):
- cli("./wf_test/main.nf", render_graphs=True)
+ #cli("./wf_test/main.nf", render_graphs=False)
cli("./wf_test/main.nf", render_graphs=False)
def test_cli_output_considered(self):
diff --git a/tests/test_code.py b/tests/test_code.py
index b57f3515c438a53a130c59cc383a38dbadf44697..0dd7b5f0c4663b41c58cf209799441bcd52d29d9 100644
--- a/tests/test_code.py
+++ b/tests/test_code.py
@@ -3,25 +3,14 @@ from src.code_ import *
class TestCode(unittest.TestCase):
- def test_initialise(self):
- with open("tests/ressources/outils/remove_comments_with.nf", 'r') as f:
- code_with_comments = f.read()
-
- with open("tests/ressources/outils/remove_comments_wo.nf", 'r') as f:
- code_wo_comments = f.read()
-
- code = Code(code_with_comments, origin=None)
- self.assertIsInstance(code, Code)
- self.assertEqual(code.code, '\n'+code_with_comments+'\n')
- self.assertEqual(code.code_wo_comments, '\n'+code_wo_comments+'\n')
-
def test_get_code(self):
with open("tests/ressources/outils/remove_comments_with.nf", 'r') as f:
code_with_comments = f.read()
with open("tests/ressources/outils/remove_comments_wo.nf", 'r') as f:
code_wo_comments = f.read()
-
code = Code(code_with_comments, origin=None)
+ self.assertEqual(code.code, '\n'+code_with_comments+'\n')
+ self.assertEqual(code.code_wo_comments.strip(), code_wo_comments.strip())
self.assertEqual(code.get_code(), code_wo_comments.strip())
diff --git a/tests/test_outils.py b/tests/test_outils.py
index 9fe2c7d9772e917a13dd02095e8759e220e4c34c..2143f18b7003813b517d3c2395c41a8520d6f05e 100644
--- a/tests/test_outils.py
+++ b/tests/test_outils.py
@@ -1,3 +1,4 @@
+import os
import unittest
from src.outils import *
@@ -36,6 +37,10 @@ class TestOutils(unittest.TestCase):
with open("tests/ressources/outils/remove_comments_wo.nf", 'r') as f:
code_wo_comments = f.read()
- self.assertEqual(remove_comments(code_with_comments), code_wo_comments)
-
+ produced = remove_comments(code_with_comments)
+ with open(candidate := "tests/ressources/outils/remove_comments_wo.candidate.nf", 'w') as f:
+ f.write(produced)
+
+ self.assertEqual(produced.strip(), code_wo_comments.strip())
+ os.unlink(candidate)
diff --git a/tests/test_process.py b/tests/test_process.py
index 4c2f6400190fc2127e1b0e6a909ba385ea9c6262..ff40c83af42704aa802c4691d60b5795351d7223 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 = {}
@@ -93,11 +94,11 @@ class TestProcess(unittest.TestCase):
dico['edges'] = []
dico['subworkflows'] = {}
process_DSL2.get_structure(dico)
- dico_true = {'nodes': [{'id': str(process_DSL2), 'name': 'OPENMS_FALSEDISCOVERYRATE', 'shape': 'ellipse', 'xlabel': ''}], 'edges': [], 'subworkflows': {}}
+ dico_true = {'nodes': [{'id': str(process_DSL2), 'name': 'OPENMS_FALSEDISCOVERYRATE', 'shape': 'ellipse', 'xlabel': '', 'fillcolor': ''}], 'edges': [], 'subworkflows': {}}
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]