From d259d50a6adacc710addb1abfe8653f7ac8d549e Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Wed, 19 Mar 2025 15:21:44 +0100
Subject: [PATCH] Fixed bug with pipe operators when rewritting (within
operations and calls) -> using the modified code instead of the OG
---
src/main.py | 8 +++++++-
src/operation.py | 49 +++++++++++++++++++++++++++++++++++++++++++-----
2 files changed, 51 insertions(+), 6 deletions(-)
diff --git a/src/main.py b/src/main.py
index 98127ae..0239858 100644
--- a/src/main.py
+++ b/src/main.py
@@ -50,7 +50,13 @@ class Main(Nextflow_Building_Blocks):
for exe in sorted_executor_2_length:
if(exe.get_type()=="Call" or exe.get_type()=="Operation"):
- code = code.replace(exe.get_code(get_OG = True), exe.simplify_code(), 1)
+ old = exe.get_code(get_OG = True)
+ new = exe.simplify_code()
+ if(new!=old):
+ temp = code
+ code = code.replace(exe.get_code(get_OG = True), exe.simplify_code(), 1)
+ if(temp==code):
+ raise Exception("This shouldn't happen the Exeutor was not replaced")
else:
raise Exception("This shouldn't happen")
return code
diff --git a/src/operation.py b/src/operation.py
index fbcb5a9..62a1a97 100644
--- a/src/operation.py
+++ b/src/operation.py
@@ -80,6 +80,39 @@ class Operation(Executor):
tab+=o.get_elements_called()
return tab
+ #def add_origin_channel(self, name):
+ # from .channel import Channel
+ # #Check that the name is not the list of illegal words
+ # #and Check that the thing extarcted is not WorkflowNameFile like 'WorkflowHgtseq' in nf-core/hgtseq
+ # if(name not in constant.ERROR_WORDS_ORIGINS):# and name.lower()!=f"workflow{self.get_name_file().lower()}"):
+ # #channel = Channel(name=name, origin=self.origin)
+ # if(self.origin.get_type()!="Subworkflow"):
+ # #First check that the channel is not defined at the same level
+ # channels = self.origin.get_channels_from_name_same_level(name)
+ # #Then check that the channel is defined in the below level
+ # if(channels==[]):
+ # channels = self.origin.get_channels_from_name_inside_level(name)
+ # #Finally check if the channels is defined above
+ # if(channels==[]):
+ # channels = self.origin.get_channels_from_name_above_level(name)
+ # if(channels==[]):
+ # channels = self.origin.get_channels_from_name_other_blocks_on_same_level(name)
+ # #If it still doesn't exist -> we create it
+ # if(channels==[]):
+ # channel = Channel(name=name, origin=self.origin)
+ # self.origin.add_channel(channel)
+ # channels = [channel]
+ # else:
+ # channel = Channel(name=name, origin=self.origin)
+ # self.origin.takes_channels.append(channel)
+ # channels = [channel]
+ #
+ # for channel in channels:
+ # self.origins.append(channel)
+ # #channel.initialise()
+ # channel.add_sink(self)
+
+
def add_origin_channel(self, name):
from .channel import Channel
@@ -890,7 +923,12 @@ class Operation(Executor):
#Method that rewrites operations to simplify it -> decompose it into multiple line -> to be able to manipulate the calls in a easier way
def simplify_code(self):
- code = self.get_code(get_OG=True)
+ code = self.get_code(replace_calls =False, clean_pipe=True)
+ #Remove "emit:" and "takes:" for the subworkklfow inputs and outputs
+ if(code[:6] in ["emit: ", "take: "]):
+ code = code[6:]
+ code = code.strip()
+ #code = self.get_code(get_OG=True)
index = 1
operation_id = str(self)[-7:-2]
@@ -907,17 +945,18 @@ class Operation(Executor):
to_add = []
dico_origin_2_replace = {}
for o in self.origins:
+ OG_code = o.get_code(get_OG=True)
try:
- tmp = dico_origin_2_replace[o.get_code(get_OG=True)]
+ tmp = dico_origin_2_replace[OG_code]
except:
- dico_origin_2_replace[o.get_code(get_OG=True)] = []
+ dico_origin_2_replace[OG_code] = []
if(o.get_type()=="Call"):
#If it's not a function -> then we rewrite it
if(o.get_first_element_called().get_type()!="Function"):
to_add.append(add_origin_equals(o, index))
- dico_origin_2_replace[o.get_code(get_OG=True)].append(f"operation_{operation_id}_{index}")
+ dico_origin_2_replace[OG_code].append(f"operation_{operation_id}_{index}")
elif(o.get_type()=="Emitted"):
- dico_origin_2_replace[o.get_code(get_OG=True)].append(o)
+ dico_origin_2_replace[OG_code].append(o)
index += 1
temporary_index = 1
--
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