diff --git a/src/constant.py b/src/constant.py
index c8a56f6f8d6c8c4270ae7c1be9d3ca1dfc2276a8..8b7ab2bc545e12f8aab1805d67b6c9515d46f6bf 100644
--- a/src/constant.py
+++ b/src/constant.py
@@ -124,7 +124,7 @@ END_PIPE_OPERATOR = r"\s*(\s*\|\s*\w+)+"
# PROCESS
#--------------------------
FILE = r'file +(\w+) *\n'
-FROM = r'from([^\n]+)\n'
+FROM = r' from ([^\n]+)\n'
INPUT = r"\n\s*input *:"
INTO = r'into +([\w, ]+)'
INTO_2 = r'into +\(?( *\w+ *(, *\w+)*) *\)?'
diff --git a/src/nextflow_building_blocks.py b/src/nextflow_building_blocks.py
index 82a782269820625db1d8e5db1f37196df6c60c0d..af0bc0b307ee6839376a7c174f554f868e57e84e 100644
--- a/src/nextflow_building_blocks.py
+++ b/src/nextflow_building_blocks.py
@@ -348,8 +348,9 @@ class Nextflow_Building_Blocks:
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))
+ #if(parenthese_left==0 and parenthese_right==0 and (start, end, temp) not in searched):
+ if(parenthese_left==0 and parenthese_right==0):
+
try:
pot = extract_executor_from_middle(text, start, end)
@@ -361,37 +362,39 @@ class Nextflow_Building_Blocks:
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
- if(not checks_in_condition_if(text, pot) and not checks_in_string(text, pot)):
- if(self.get_DSL()=="DSL2"):
- to_call = self.get_list_name_processes()+self.get_list_name_subworkflows()+self.get_list_name_includes()
- if(pot.find("|")!=-1):
- if(not checks_in_condition_if(pot, '|') and not checks_in_string(pot, '|')):#TODO checks_in_string is the first occurance
- first_thing_called = pot.split('|')[-1].strip()
- if(first_thing_called in to_call):
- call = Call(code =pot, origin =self)
- self.executors.append(call)
- elif(first_thing_called in constant.LIST_OPERATORS):
- ope = Operation(code =pot, origin =self)
- self.executors.append(ope)
+ #IF the exact potential hasn't already been searched, then we don't do it
+ if((start, end, pot) not in searched):
+ searched.append((start, end, pot))
+ #If the thing which is extracted is not in the conditon of an if
+ if(not checks_in_condition_if(text, pot) and not checks_in_string(text, pot)):
+ if(self.get_DSL()=="DSL2"):
+ to_call = self.get_list_name_processes()+self.get_list_name_subworkflows()+self.get_list_name_includes()
+ if(pot.find("|")!=-1):
+ if(not checks_in_condition_if(pot, '|') and not checks_in_string(pot, '|')):#TODO checks_in_string is the first occurance
+ first_thing_called = pot.split('|')[-1].strip()
+ if(first_thing_called in to_call):
+ call = Call(code =pot, origin =self)
+ self.executors.append(call)
+ elif(first_thing_called in constant.LIST_OPERATORS):
+ ope = Operation(code =pot, origin =self)
+ self.executors.append(ope)
+ else:
+ raise BioFlowInsightError(f"'{first_thing_called}' is neither a process, subworkflow or an operator. In the executor '{pot}'{self.get_string_line(pot)}.", num=14,origin=self)#TODO -> try rewriting the operation using the standard syntaxe
+
else:
- raise BioFlowInsightError(f"'{first_thing_called}' is neither a process, subworkflow or an operator. In the executor '{pot}'{self.get_string_line(pot)}.", num=14,origin=self)#TODO -> try rewriting the operation using the standard syntaxe
+ from .executor import Executor
+ executor = Executor(pot, self)
+ self.executors.append(executor.return_type())
else:
from .executor import Executor
executor = Executor(pot, self)
self.executors.append(executor.return_type())
-
else:
- from .executor import Executor
- executor = Executor(pot, self)
- self.executors.append(executor.return_type())
- else:
- ope = Operation(pot, self)
- self.executors.append(ope)
- searching = True
- break
+ ope = Operation(pot, self)
+ self.executors.append(ope)
+ searching = True
+ break
#---------------------------------------------------------------
diff --git a/src/process.py b/src/process.py
index 522a02afde4f967080aad36e1546fc9182a5a9ff..33122ac347103d381fa80bfce91e0c038c8190f9 100644
--- a/src/process.py
+++ b/src/process.py
@@ -585,12 +585,12 @@ class Process(Nextflow_Building_Blocks):
lines.append(line)
code = "\n".join(lines)
#Removing the extra emits
- #For it to only have one
+ #For it to only have one,
for line in self.outputs_per_line:
def replacer(match):
- return ""
+ return match.group(1)
for o in line[1:]:
- code = re.sub(fr"\,\s*{re.escape(o.get_code())}", replacer, code)
+ code = re.sub(fr"\,\s*{re.escape(o.get_code())}(\s|\,|\))", replacer, code)
return code