From e5b0b0777ad14638801378f660c21febb6492046 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Wed, 26 Mar 2025 09:59:11 +0100
Subject: [PATCH] Small updates
---
src/channel.py | 2 +-
src/outils_graph.py | 30 ++++++++++++++++++++-----
src/process.py | 53 ++++++++++++++++++++++++++-------------------
3 files changed, 56 insertions(+), 29 deletions(-)
diff --git a/src/channel.py b/src/channel.py
index bcd76de..7ca4387 100644
--- a/src/channel.py
+++ b/src/channel.py
@@ -22,7 +22,7 @@ class Channel(Nextflow_Building_Blocks):
for m in self.get_modules_defined():
to_call.append(m.get_alias())
if(self.name in to_call):
- raise BioFlowInsightError(f"'{self.name}' is trying to be created as a channel{self.get_string_line(self.origin.get_code())}. It already exists as a process or a subworkflow in the nextflow file.", num = 4, origin=self)
+ raise BioFlowInsightError(f"'{self.name}' is trying to be created as a channel{self.get_string_line(self.origin.get_code())}. It already exists as a process, a function or a subworkflow in the nextflow file.", num = 4, origin=self)
diff --git a/src/outils_graph.py b/src/outils_graph.py
index eee7ab3..54cec76 100644
--- a/src/outils_graph.py
+++ b/src/outils_graph.py
@@ -1168,14 +1168,32 @@ def check_if_equal(dicoA, dicoB):
translated["subworkflows"] = {}
rewrite(dico, translated)
return translated
-
+
+ translated_new, translated_original = translate_dico(dicoA), translate_dico(dicoB)
#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
- equal = translate_dico(dicoA) ==translate_dico(dicoB)
+ equal = translated_new == translated_original
if(not equal):
#TODO -> make a better affichage des differences
- print(translate_dico(dicoA))
- print(translate_dico(dicoB))
- print()
+ if(translated_new['nodes']!=translated_original["nodes"]):
+ diff = list(set(translated_original['nodes']) - set(translated_new['nodes']))
+ if(diff!=[]):
+ print(f"The processes {diff} are missing from the new workflow")
+ diff = list(set(translated_new['nodes']) - set(translated_original['nodes']))
+ if(diff!=[]):
+ print(f"The processes {diff} have been added to the new workflow")
+
+ if(translated_new['edges']!=translated_original["edges"]):
+ edges_new, edges_original = [], []
+ for e in translated_original['edges']:
+ edges_original.append(str(e))
+ for e in translated_new['edges']:
+ edges_new.append(str(e))
+ diff = list(set(edges_original) - set(edges_new))
+ if(diff!=[]):
+ print(f"The edges {diff} are missing from the new workflow")
+ diff = list(set(edges_new) - set(edges_original))
+ if(diff!=[]):
+ print(f"The edges {diff} have been added to the new workflow")
return equal
#This function removes the artificial nodes from the dico
@@ -1212,7 +1230,7 @@ def remove_artificial_nodes(param_dico):
if(e["A"]==node_id):
links["sink"].append({"sink": e["B"], "label": e["label"]})
to_remove.append(e)
- if(e["B"]==node_id):
+ elif(e["B"]==node_id):
links["source"].append({"source": e["A"], "label": e["label"]})
to_remove.append(e)
for e in to_remove:
diff --git a/src/process.py b/src/process.py
index f54bbd0..d4edcb6 100644
--- a/src/process.py
+++ b/src/process.py
@@ -33,6 +33,7 @@ class Process(Nextflow_Building_Blocks):
self.called_by = []#List of calls
self.initialised = False
self.number_times_copied = 0
+ self.initialise_name()
def copy(self):
@@ -208,29 +209,37 @@ class Process(Nextflow_Building_Blocks):
positions = [publishDir_pos, input_pos, output_pos, when_pos, script_pos]
variables_index = ['pusblishDir', 'input', 'output', 'when', 'script']
- positions, variables_index = sort_and_filter(positions, variables_index)
+ if(positions!=[(0, 0), (0, 0), (0, 0), (0, 0), (0, 0)]):
+ positions, variables_index = sort_and_filter(positions, variables_index)
- for i in range(len(positions)):
- temp_code = ""
- if(i==len(positions)-1):
- temp_code = code[positions[i][1]:code.rfind('}')].strip()
- else:
- temp_code = code[positions[i][1]:positions[i+1][0]].strip()
-
- if(variables_index[i]=='input'):
- self.input_code = temp_code
- elif(variables_index[i]=='output'):
- self.output_code = temp_code
- elif(variables_index[i]=='pusblishDir'):
- self.pusblishDir_code = temp_code
- elif(variables_index[i]=='when'):
- self.when_code = temp_code
- elif(variables_index[i]=='script'):
- self.script_code = temp_code
- #self.extract_tools()
- else:
- raise Exception("This shoudn't happen!")
+ for i in range(len(positions)):
+ temp_code = ""
+ if(i==len(positions)-1):
+ temp_code = code[positions[i][1]:code.rfind('}')].strip()
+ else:
+ temp_code = code[positions[i][1]:positions[i+1][0]].strip()
+
+ if(variables_index[i]=='input'):
+ self.input_code = temp_code
+ elif(variables_index[i]=='output'):
+ self.output_code = temp_code
+ elif(variables_index[i]=='pusblishDir'):
+ self.pusblishDir_code = temp_code
+ elif(variables_index[i]=='when'):
+ self.when_code = temp_code
+ elif(variables_index[i]=='script'):
+ self.script_code = temp_code
+ #self.extract_tools()
+ else:
+ raise Exception("This shoudn't happen!")
+ else:
+ self.input_code = ""
+ self.output_code = ""
+ self.pusblishDir_code = ""
+ self.when_code = ""
+ self.script_code = ""
+
#Method that returns the input part of the process code
@@ -449,7 +458,7 @@ class Process(Nextflow_Building_Blocks):
def initialise(self):
if(not self.initialised):
self.initialised = True
- self.initialise_name()
+
self.initialise_parts()
self.initialise_inputs_outputs()
--
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