From ba7c4522f6c3ceb65635418b7948c7b873654c5f Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Mon, 2 Dec 2024 15:58:35 +0100
Subject: [PATCH] Just cleaning up a bit
---
src/bioflowinsighterror.py | 1 -
src/condition.py | 2 ++
src/include.py | 2 --
src/main_DSL2.py | 9 ++++++++-
src/nextflow_file.py | 15 +++++++--------
src/outils.py | 2 --
6 files changed, 17 insertions(+), 14 deletions(-)
diff --git a/src/bioflowinsighterror.py b/src/bioflowinsighterror.py
index a948908..f7490de 100644
--- a/src/bioflowinsighterror.py
+++ b/src/bioflowinsighterror.py
@@ -11,7 +11,6 @@ class BioFlowInsightError(Exception):
"""
def __init__(self, error, num, origin = None):
self.origin = origin
- #TODO -> add message at the end
if(origin!=None):
super().__init__(f"[{num}] Error in the file '{self.origin.get_file_address()}': "+error)
else:
diff --git a/src/condition.py b/src/condition.py
index da5da03..34a1fcb 100644
--- a/src/condition.py
+++ b/src/condition.py
@@ -16,6 +16,8 @@ class Condition:
conditions_dico = self.origin.get_file_conditions()
+ #conditions_dico_temp = extract_conditions(code)
+ #print(conditions_dico==conditions_dico_temp)
pos = code.find(thing_defined)
for c in conditions_dico:
condition_extend = conditions_dico[c]
diff --git a/src/include.py b/src/include.py
index 3ff4fff..35ccf9d 100644
--- a/src/include.py
+++ b/src/include.py
@@ -125,8 +125,6 @@ class Include(Nextflow_Building_Blocks):
for match in re.finditer(pattern_as, include):
found = True
if(self.get_duplicate_status()):
- #TODO -> try shallow copy too
- #thing_as = copy.copy(self.file.get_element_from_name(match.group(1)))
thing_as = copy.deepcopy(self.file.get_element_from_name(match.group(1)))
thing_as.set_alias(match.group(3))
self.defines.append(thing_as)
diff --git a/src/main_DSL2.py b/src/main_DSL2.py
index ecde61b..7360194 100644
--- a/src/main_DSL2.py
+++ b/src/main_DSL2.py
@@ -1,23 +1,30 @@
from .nextflow_building_blocks import Nextflow_Building_Blocks
from .bioflowinsighterror import BioFlowInsightError
import re
-from .outils import get_dico_from_tab_from_id
+from .outils import get_dico_from_tab_from_id, extract_conditions
from . import constant
+
class Main_DSL2(Nextflow_Building_Blocks):
def __init__(self, code, origin):
Nextflow_Building_Blocks.__init__(self, code)
self.origin = origin
self.calls = []
self.initialised = False
+ self.conditions=None
def get_channels(self):
return self.channels
def get_workflow_code(self):
return self.get_code()
+
+ def get_file_conditions(self):
+ if(self.conditions==None):
+ self.conditions = extract_conditions(self.get_code())
+ return self.conditions
def get_type(self):
return "Main DSL2"
diff --git a/src/nextflow_file.py b/src/nextflow_file.py
index e199cf5..f4112fd 100644
--- a/src/nextflow_file.py
+++ b/src/nextflow_file.py
@@ -37,9 +37,8 @@ class Nextflow_File(Nextflow_Building_Blocks):
if(self.first_file==True):
self.origin.set_DSL(self.which_DSL())
self.graph = None
- self.conditions = extract_conditions(self.get_code())
-
self.added_2_rocrate = False
+ self.conditions=None
self.check_file_correctness()
self.do_start_stuff()
#self.extract_metadata()
@@ -55,6 +54,8 @@ class Nextflow_File(Nextflow_Building_Blocks):
return self.get_code()
def get_file_conditions(self):
+ if(self.conditions==None):
+ self.conditions = extract_conditions(self.get_code())
return self.conditions
@@ -237,16 +238,14 @@ class Nextflow_File(Nextflow_Building_Blocks):
def which_DSL(self):
DSL = "DSL2"
#If there are include
- self.extract_includes()
- if(len(self.includes)>0):
+ pattern = constant.FULL_INLCUDE_2
+ for match in re.finditer(pattern, self.get_code()):
return DSL
#If there are subworkflows
- self.extract_subworkflows()
- if(len(self.subworkflows)>0):
+ for match in re.finditer(constant.SUBWORKFLOW_HEADER, self.get_code()):
return DSL
#If there is the main
- self.extract_main()
- if(self.main!=None):
+ for match in re.finditer(constant.WORKFLOW_HEADER_2, '\n'+self.get_code()+'\n'):
return DSL
#Analyse the processes
self.extract_processes()
diff --git a/src/outils.py b/src/outils.py
index c4004c6..3b7bc90 100644
--- a/src/outils.py
+++ b/src/outils.py
@@ -975,9 +975,7 @@ def extract_conditions(code):
if(code[start-1]!="\\" or (code[start-1]=="\\" and code[start-2]=="\\")):
quote_double=False
- #TODO add "else if" compatibaliaty
#TODO Right now -> support only for if/else written with curlies -> not on single line
-
def adding_inside(conditions_dico, code, start_inside, end_inside):
temp_dico = extract_conditions(code[start_inside:end_inside])
for c in temp_dico:
--
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