From f0484852d9bb1e074503a3c658b2ba7d65af1eaf Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Fri, 21 Mar 2025 14:20:25 +0100
Subject: [PATCH] Update simplified calls + updated the remove of elents inside
of maps -> it actually removes them and not just puts ''' inside the maps (so
it's cleaner now)
---
src/call.py | 4 ++--
src/code_.py | 21 ++++++++++++++++-----
src/emitted.py | 2 +-
src/nextflow_building_blocks.py | 3 +++
src/nextflow_file.py | 3 +++
src/operation.py | 6 +++---
src/outils_graph.py | 8 +++++++-
src/process.py | 3 +++
src/workflow.py | 19 ++++++++++++-------
9 files changed, 50 insertions(+), 19 deletions(-)
diff --git a/src/call.py b/src/call.py
index 5929123..6a03975 100644
--- a/src/call.py
+++ b/src/call.py
@@ -98,7 +98,7 @@ class Call(Executor):
if(temp==code):
raise Exception("This souldn't happen")
#code = code.replace(param.get_code(get_OG=True), param_new_name)
- new_bit = param.simplify_code(new_name = param_new_name)
+ new_bit = param.simplify_code(new_name = param_new_name, return_tab = False)
temp = code
code = code.replace(tag_to_add, f"{tag_to_add}\n{new_bit}")
if(temp==code):
@@ -148,7 +148,7 @@ class Call(Executor):
if(temp==code):
raise Exception("This souldn't happen")
#code = code.replace(param.get_code(get_OG=True), param_new_name)
- new_bit = f"{param_new_name} = {param.simplify_code()}"
+ new_bit = f"{param_new_name} = {param.simplify_code(return_tab = False)}"
temp = code
code = code.replace(tag_to_add, f"{tag_to_add}\n{new_bit}")
if(temp==code):
diff --git a/src/code_.py b/src/code_.py
index 0ab7136..0a6a0cb 100644
--- a/src/code_.py
+++ b/src/code_.py
@@ -22,7 +22,7 @@ class Code:
self.code_wo_comments = self.code_wo_comments.replace("||", "$OR$")
self.code_wo_comments = self.turn_single_condition_into_multiline(self.code_wo_comments)
self.code_wo_comments = self.rewrite_ternary_operation_to_normal_condition(self.code_wo_comments)
- self.code_wo_comments = self.add_triple_quote_inside_map(self.code_wo_comments )
+ self.code_wo_comments = self.remove_things_inside_map(self.code_wo_comments )
self.code_wo_comments = self.rewrite_jump_dot(self.code_wo_comments)
@@ -123,7 +123,8 @@ class Code:
return code
#This function takes the code and adds '''...''' inside the map operator
- def add_triple_quote_inside_map(self, code):
+ def remove_things_inside_map(self, code):
+ index = 0
searching = True
while(searching):
searching = False
@@ -134,10 +135,17 @@ class Code:
for match in re.finditer(pattern, code):
start_map, end = match.span(0)
end_map = extract_curly(code, end)
- old = code[start_map:end_map]
- new_code = f".{word}_modified {{ ¤'''\n{code[end:end_map-1]}\n'''¤ }}"
- code = code.replace(old, new_code)
+
+ old = code[end:end_map-1]
+ new = f"¤{id(self)}_{index}¤"
+ self.add_map_element(old, new)
+
+ old_code = code[start_map:end_map]
+ new_code = f".{word}_modified {{ {new} }}"
+ code = code.replace(old_code, new_code)
+
searching = True
+ index+=1
break
return code
@@ -145,6 +153,9 @@ class Code:
def add_to_ternary_operation_dico(self, old, new):
self.origin.add_to_ternary_operation_dico(old, new)
+ def add_map_element(self, old, new):
+ self.origin.add_map_element(old, new)
+
#This methods rewrite ternary operation into "normal" conditions
#variable = (condition) ? Expression2 : Expression3;
def rewrite_ternary_operation_to_normal_condition(self, code):
diff --git a/src/emitted.py b/src/emitted.py
index 946ac4a..42e5475 100644
--- a/src/emitted.py
+++ b/src/emitted.py
@@ -19,7 +19,7 @@ class Emitted(Channel):
def get_all_conditions(self):
return self.origin.get_all_conditions()
- def simplify_code(self):
+ def simplify_code(self, return_tab):
code = self.get_code(get_OG=True)
thing_which_emits = self.emitted_by.get_first_element_called()
old_name = thing_which_emits.get_alias()
diff --git a/src/nextflow_building_blocks.py b/src/nextflow_building_blocks.py
index 5f024e5..0dc2e69 100644
--- a/src/nextflow_building_blocks.py
+++ b/src/nextflow_building_blocks.py
@@ -20,6 +20,9 @@ class Nextflow_Building_Blocks:
def add_to_ternary_operation_dico(self, old, new):
self.origin.add_to_ternary_operation_dico(old, new)
+
+ def add_map_element(self, old, new):
+ self.origin.add_map_element(old, new)
def get_code(self, get_OG = False):
return self.code.get_code(get_OG = get_OG)
diff --git a/src/nextflow_file.py b/src/nextflow_file.py
index 829999c..824b613 100644
--- a/src/nextflow_file.py
+++ b/src/nextflow_file.py
@@ -42,6 +42,9 @@ class Nextflow_File(Nextflow_Building_Blocks):
def add_to_ternary_operation_dico(self, old, new):
self.workflow.add_to_ternary_operation_dico(old, new)
+
+ def add_map_element(self, old, new):
+ self.workflow.add_map_element(old, new)
def get_root_directory(self):
return self.workflow.get_root_directory()
diff --git a/src/operation.py b/src/operation.py
index 4de0c43..e682a16 100644
--- a/src/operation.py
+++ b/src/operation.py
@@ -945,7 +945,7 @@ class Operation(Executor):
operation_id = str(self)[-7:-2]
def add_origin_equals(call, index):
- simplified_code = call.simplify_code()
+ simplified_code = call.simplify_code(return_tab = False)
lines = simplified_code.split('\n')
return f"{simplified_code}\noperation_{operation_id}_{index} = {call.get_first_element_called().get_alias_and_id()}.out[0]"
#if(len(lines)==1):
@@ -980,7 +980,7 @@ class Operation(Executor):
if(type(val)==str):
code = code.replace(origin, val)
else:
- code = code.replace(origin, val.simplify_code())
+ code = code.replace(origin, val.simplify_code(return_tab = False))
if(temp==code):
raise Exception("This souldn't happen")
#Case there are mutiple origins then:
@@ -1000,7 +1000,7 @@ class Operation(Executor):
temp = calls[e.emitted_by]
except:
calls[e.emitted_by] = []
- calls[e.emitted_by].append(e.simplify_code())
+ calls[e.emitted_by].append(e.simplify_code(return_tab = False))
for c in calls:
#This is just one value
if(len(c.get_all_conditions())>1):
diff --git a/src/outils_graph.py b/src/outils_graph.py
index 3248fe7..eee7ab3 100644
--- a/src/outils_graph.py
+++ b/src/outils_graph.py
@@ -1170,7 +1170,13 @@ def check_if_equal(dicoA, dicoB):
return translated
#TO do that we rewrite the structure using a commun language (without using the ids) -> then just check if the translated structures are the same
- return translate_dico(dicoA) ==translate_dico(dicoB)
+ equal = translate_dico(dicoA) ==translate_dico(dicoB)
+ if(not equal):
+ #TODO -> make a better affichage des differences
+ print(translate_dico(dicoA))
+ print(translate_dico(dicoB))
+ print()
+ return equal
#This function removes the artificial nodes from the dico
#MAtching the nodes together between the artificial nodes
diff --git a/src/process.py b/src/process.py
index bc1f5ce..40f8f76 100644
--- a/src/process.py
+++ b/src/process.py
@@ -63,6 +63,9 @@ class Process(Nextflow_Building_Blocks):
def add_to_ternary_operation_dico(self, old, new):
self.nextflow_file.add_to_ternary_operation_dico(old, new)
+
+ def add_map_element(self, old, new):
+ self.nextflow_file.add_map_element(old, new)
def add_to_emits(self, emit):
self.later_emits.append(emit)
diff --git a/src/workflow.py b/src/workflow.py
index 96a5aca..4c5c701 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -77,6 +77,7 @@ class Workflow:
self.graph = None
self.conditions_2_ignore = []
self.ternary_operation_dico = {}
+ self.map_element_dico = {}
OG_file = Nextflow_File(file, workflow = self, first_file = True)
@@ -440,20 +441,23 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
def add_to_ternary_operation_dico(self, old, new):
self.ternary_operation_dico[new] = old
+ def add_map_element(self, old, new):
+ self.map_element_dico[new] = old
+
def put_back_old_ternary_operations(self, code, ternary_operation_dico):
for new in ternary_operation_dico:
old = ternary_operation_dico[new]
code = code.replace(new.strip(), old)
return code
- def put_modified_operations_back(self, code):
+ def put_modified_operations_back(self, code, dico_operations):
searching = True
while(searching):
searching = False
- for match in re.finditer(r"\.(\w+)_modified\s*\{\s*¤\'\'\'([^¤]+)¤\s*\}", code):
+ for match in re.finditer(r"\.(\w+)_modified\s*\{\s*(¤[^¤]+¤)\s*\}", code):
operator = match.group(1)
- inside = match.group(2)[:-3]#Cause we want to remove the extras ...'''
- code = code.replace(match.group(0), f".{operator} {{ {inside} }}")
+ inside = match.group(2)#Cause we want to remove the extras ...'''
+ code = code.replace(match.group(0), f".{operator} {{ {dico_operations[inside]} }}")
searching = True
break
return code
@@ -577,9 +581,9 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
self.graph.initialise(processes_2_remove = self.processes_2_remove)
if(def_check_the_same and not self.graph.check_if_process_dependendy_is_equivalent_to_other_without_subworkflows(temp_process_dependency_graph)):
if(render_graphs==True):
- generate_graph(self.get_output_dir()/ "debug" /"spec_graph_OG", temp_spec_graph, render_graphs = True)
+ #generate_graph(self.get_output_dir()/ "debug" /"spec_graph_OG", temp_spec_graph, render_graphs = True)
generate_graph(self.get_output_dir()/ "debug" /"spec_graph", self.graph.full_dico, render_graphs = True)
- generate_graph(self.get_output_dir()/ "debug" /"process_dependency_graph_OG", temp_process_dependency_graph, render_graphs = True)
+ #generate_graph(self.get_output_dir()/ "debug" /"process_dependency_graph_OG", temp_process_dependency_graph, render_graphs = True)
generate_graph(self.get_output_dir()/ "debug" /"process_dependency_graph", self.graph.get_process_dependency_graph() , render_graphs = True)
raise Exception("Something went wrong: The flat dependency graph is not the same!")
@@ -746,6 +750,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
self.iniatilise_tab_processes_2_remove()
self.graph.initialise(processes_2_remove = self.processes_2_remove)
ternary_operation_dico = self.ternary_operation_dico
+ map_element_dico = self.map_element_dico
if(self.get_DSL()=="DSL1"):
code = self.convert_to_DSL2()
@@ -1165,7 +1170,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
#Putting || back
code = self.put_back_old_ternary_operations(code, ternary_operation_dico)
code = code.replace("$OR$", "||")
- code = self.put_modified_operations_back(code)
+ code = self.put_modified_operations_back(code, map_element_dico)
code = remove_extra_jumps(format_with_tabs(code))
f = open(self.get_output_dir()/ "debug" / "rewritten.nf", "w")
f.write(code)
--
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