From 19de4648363b6be2044877a530a5b719b0826764 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Tue, 25 Mar 2025 15:25:30 +0100
Subject: [PATCH] Add initialise condition for the code -> so it doesn't
initialises every time (only one when you do the file)
---
src/call.py | 2 +-
src/code_.py | 7 ++++---
src/executor.py | 2 +-
src/function.py | 2 +-
src/include.py | 2 +-
src/main.py | 2 +-
src/nextflow_building_blocks.py | 4 ++--
src/nextflow_file.py | 4 +++-
src/operation.py | 4 ++--
src/process.py | 2 +-
src/root.py | 2 +-
src/subworkflow.py | 28 ++++++++++++++--------------
12 files changed, 32 insertions(+), 29 deletions(-)
diff --git a/src/call.py b/src/call.py
index 6a03975..8873b57 100644
--- a/src/call.py
+++ b/src/call.py
@@ -14,7 +14,7 @@ from . import constant
class Call(Executor):
def __init__(self, code, origin, OG_code = ''):
- self.code = Code(code = code, origin = self)
+ self.code = Code(code = code, origin = self, initialise=False)
self.origin = origin
self.called = []
self.first_element_called = None
diff --git a/src/code_.py b/src/code_.py
index 7f529f7..295f564 100644
--- a/src/code_.py
+++ b/src/code_.py
@@ -4,11 +4,12 @@ import re
from . import constant
class Code:
- def __init__(self, code, origin):
+ def __init__(self, code, origin, initialise):
self.code = code
- self.code_wo_comments = ""
+ self.code_wo_comments = code
self.origin = origin
- self.initialise()
+ if(initialise):
+ self.initialise()
#self.check_its_nextflow()
diff --git a/src/executor.py b/src/executor.py
index 0073716..dca03da 100644
--- a/src/executor.py
+++ b/src/executor.py
@@ -19,7 +19,7 @@ from .bioflowinsighterror import BioFlowInsightError
class Executor(Nextflow_Building_Blocks):
def __init__(self, code, origin):
self.origin = origin
- self.code = Code(code = code, origin = self)
+ self.code = Code(code = code, origin = self, initialise=False)
diff --git a/src/function.py b/src/function.py
index 0d04135..8e1a3a4 100644
--- a/src/function.py
+++ b/src/function.py
@@ -7,7 +7,7 @@ from .nextflow_building_blocks import Nextflow_Building_Blocks
class Function(Nextflow_Building_Blocks):
def __init__(self, code, name, origin):
self.origin = origin
- self.code = Code(code, origin = self)
+ self.code = Code(code, origin = self, initialise=False)
self.name = name
self.alias = name
diff --git a/src/include.py b/src/include.py
index e2ee93f..39627e1 100644
--- a/src/include.py
+++ b/src/include.py
@@ -23,7 +23,7 @@ class Include(Nextflow_Building_Blocks):
def __init__(self, code, file, importing, nextflow_file):
self.nextflow_file_origin = nextflow_file
self.importing = importing
- self.code = Code(code = code, origin = self)
+ self.code = Code(code = code, origin = self, initialise=False)
self.nextflow_file = None
self.define_file(file)
self.defines = {}
diff --git a/src/main.py b/src/main.py
index 477c0b5..7f1f38b 100644
--- a/src/main.py
+++ b/src/main.py
@@ -10,7 +10,7 @@ from . import constant
class Main(Nextflow_Building_Blocks):
def __init__(self, code, nextflow_file):
- Nextflow_Building_Blocks.__init__(self, code)
+ Nextflow_Building_Blocks.__init__(self, code, initialise_code=False)
self.nextflow_file = nextflow_file
self.initialised = False
self.root = None
diff --git a/src/nextflow_building_blocks.py b/src/nextflow_building_blocks.py
index 0dc2e69..aba604f 100644
--- a/src/nextflow_building_blocks.py
+++ b/src/nextflow_building_blocks.py
@@ -11,8 +11,8 @@ from .bioflowinsighterror import BioFlowInsightError
class Nextflow_Building_Blocks:
- def __init__(self, code):
- self.code = Code(code = code, origin = self)
+ def __init__(self, code, initialise_code):
+ self.code = Code(code = code, origin = self, initialise=initialise_code)
#---------------------------------
#AUXILIARY METHODS FOR ALL CLASSES
diff --git a/src/nextflow_file.py b/src/nextflow_file.py
index 824b613..c4dfcd8 100644
--- a/src/nextflow_file.py
+++ b/src/nextflow_file.py
@@ -33,7 +33,7 @@ class Nextflow_File(Nextflow_Building_Blocks):
self.functions = []
self.initialised = False
contents = check_file_exists(self.get_file_address(), self)
- Nextflow_Building_Blocks.__init__(self, contents)
+ Nextflow_Building_Blocks.__init__(self, contents, initialise_code=True)
self.check_file_correctness()
#----------------------
@@ -338,6 +338,8 @@ class Nextflow_File(Nextflow_Building_Blocks):
temp = code
code = code.replace(proecess.get_code(), "")
if(temp==code):
+ print(code)
+ print(proecess.get_code())
raise Exception("This souldn't happen")
diff --git a/src/operation.py b/src/operation.py
index 3b2b9ff..82b697b 100644
--- a/src/operation.py
+++ b/src/operation.py
@@ -18,7 +18,7 @@ from . import constant
class Operation(Executor):
def __init__(self, code, origin, OG_code = ''):
self.origin = origin
- self.code = Code(code, origin = self)
+ self.code = Code(code, origin = self, initialise=False)
self.origins = []
self.gives = []
self.label = ""
@@ -33,7 +33,7 @@ class Operation(Executor):
def change_code(self, code):
self.OG_code = self.get_code()
- self.code = Code(code, origin = self)
+ self.code = Code(code, origin = self, initialise=False)
def set_as_artificial(self):
self.artificial = True
diff --git a/src/process.py b/src/process.py
index c82cac1..f54bbd0 100644
--- a/src/process.py
+++ b/src/process.py
@@ -13,7 +13,7 @@ from . import constant
class Process(Nextflow_Building_Blocks):
def __init__(self, code, nextflow_file):
self.nextflow_file = nextflow_file
- self.code = Code(code, origin = self)
+ self.code = Code(code, origin = self, initialise=False)
#Origin is only used in the case DSL1
self.origin = None
self.name = ""
diff --git a/src/root.py b/src/root.py
index 60c76ee..f5306bb 100644
--- a/src/root.py
+++ b/src/root.py
@@ -11,7 +11,7 @@ import re
class Root(Nextflow_Building_Blocks):
def __init__(self, code, origin, modules_defined,
subworkflow_inputs = []):#These channels are the inputs of the subworkflow
- Nextflow_Building_Blocks.__init__(self, code)
+ Nextflow_Building_Blocks.__init__(self, code, initialise_code=False)
self.origin = origin
self.executors = []
self.blocks = []
diff --git a/src/subworkflow.py b/src/subworkflow.py
index ad6b204..8c4c057 100644
--- a/src/subworkflow.py
+++ b/src/subworkflow.py
@@ -165,13 +165,13 @@ class Subworkflow(Main):
#Case everything is there
if(take_pos!=(0, 0) and main_pos!=(0, 0) and emit_pos!=(0, 0)):
if(take_pos[0]<main_pos[0] and main_pos[0]<emit_pos[0]):
- self.take = Code(code[take_pos[1]:main_pos[0]].strip(), origin = self)
- self.work = Code(code[main_pos[1]:emit_pos[0]].strip(), origin = self)
- self.emit = Code(code[emit_pos[1]:code.rfind('}')].strip(), origin = self)
+ self.take = Code(code[take_pos[1]:main_pos[0]].strip(), origin = self, initialise=False)
+ self.work = Code(code[main_pos[1]:emit_pos[0]].strip(), origin = self, initialise=False)
+ self.emit = Code(code[emit_pos[1]:code.rfind('}')].strip(), origin = self, initialise=False)
elif(take_pos[0]<emit_pos[0] and emit_pos[0]<main_pos[0]):
- self.take = Code(code[take_pos[1]:emit_pos[0]].strip(), origin = self)
- self.emit = Code(code[emit_pos[1]:main_pos[0]].strip(), origin = self)
- self.work = Code(code[main_pos[1]:code.rfind('}')].strip(), origin = self)
+ self.take = Code(code[take_pos[1]:emit_pos[0]].strip(), origin = self, initialise=False)
+ self.emit = Code(code[emit_pos[1]:main_pos[0]].strip(), origin = self, initialise=False)
+ self.work = Code(code[main_pos[1]:code.rfind('}')].strip(), origin = self, initialise=False)
else:
raise Exception('You need to add a case')
#Case nothing is there
@@ -179,33 +179,33 @@ class Subworkflow(Main):
#raise Exception(f"Subworkflow {code} doesn't have anything defined")
firt_curly = code.find("{")
last_curly = code.rfind('}')
- self.work = Code(code[firt_curly+1:last_curly], origin = self)
+ self.work = Code(code[firt_curly+1:last_curly], origin = self, initialise=False)
#Case there is an input but no output
if(take_pos!=(0, 0) and main_pos!=(0, 0) and emit_pos==(0, 0)):
if(take_pos[0]<main_pos[0]):
- self.take = Code(code[take_pos[1]:main_pos[0]].strip(), origin = self)
- self.work = Code(code[main_pos[1]:code.rfind('}')].strip(), origin = self)
+ self.take = Code(code[take_pos[1]:main_pos[0]].strip(), origin = self, initialise=False)
+ self.work = Code(code[main_pos[1]:code.rfind('}')].strip(), origin = self, initialise=False)
else:
raise Exception('You need to add a case')
#Case there is no input but an output
if(take_pos==(0, 0) and main_pos!=(0, 0) and emit_pos!=(0, 0)):
if(main_pos[0]<emit_pos[0]):
- self.work = Code(code[main_pos[1]:emit_pos[0]].strip(), origin = self)
- self.emit = Code(code[emit_pos[1]:code.rfind('}')].strip(), origin = self)
+ self.work = Code(code[main_pos[1]:emit_pos[0]].strip(), origin = self, initialise=False)
+ self.emit = Code(code[emit_pos[1]:code.rfind('}')].strip(), origin = self, initialise=False)
else:
raise Exception('You need to add a case')
#Case there is a main but no input and no output
if(take_pos==(0, 0) and main_pos!=(0, 0) and emit_pos==(0, 0)):
- self.work = Code(code[main_pos[1]:code.rfind('}')].strip(), origin = self)
+ self.work = Code(code[main_pos[1]:code.rfind('}')].strip(), origin = self, initialise=False)
if( main_pos==(0, 0) and (take_pos!=(0, 0) or emit_pos!=(0, 0))):
if(take_pos!=(0, 0) and emit_pos!=(0, 0)):
raise Exception("TODO")
elif(take_pos!=(0, 0) and emit_pos==(0, 0)):
raise Exception("TODO")
elif(take_pos==(0, 0) and emit_pos!=(0, 0)):
- self.emit = Code(code[emit_pos[1]:code.rfind('}')].strip(), origin = self)
+ self.emit = Code(code[emit_pos[1]:code.rfind('}')].strip(), origin = self, initialise=False)
firt_curly = code.find("{")
- self.work = Code(code[firt_curly+1:emit_pos[0]].strip(), origin = self)
+ self.work = Code(code[firt_curly+1:emit_pos[0]].strip(), origin = self, initialise=False)
else:
raise Exception("Not possible!")
--
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