diff --git a/src/block.py b/src/block.py
index 4c2d7fd49b6a412ffcc07ae970f6793c8b766a1a..4a4b5c4c5b6bd803d426ab8baa9fb0ba4bc50807 100644
--- a/src/block.py
+++ b/src/block.py
@@ -3,12 +3,14 @@ from .root import Root
from .condition import Condition
class Block(Root):
- def __init__(self, code, origin, condition, modules_defined):
- Root.__init__(self = self, code = code, origin = origin, modules_defined = modules_defined)
+ def __init__(self, code, origin, condition, modules_defined, existing_channels):
+ Root.__init__(self = self, code = code, origin = origin, modules_defined = modules_defined, subworkflow_inputs = existing_channels)
self.condition = Condition(origin=self, condition = condition)
def initialise(self):
- return super().initialise()
+ print(self.condition.condition)
+ if(self.condition.condition not in ["params.downloadFastq == true", "params.downloadGenome == true"]):
+ return super().initialise()
def get_type(self):
return "Root"
@@ -18,6 +20,9 @@ class Block(Root):
def get_executors(self):
return self.executors+self.origin.get_executors()
+
+ def get_structure(self, dico):
+ return super().get_structure(dico)
#def check_in_channels(self, channel):
# for c in self.get_channels():
diff --git a/src/call.py b/src/call.py
index 9fee23aaeb35af5c7f54463053517cc60455fabb..77f63f932bc9680c0cc0383a3e8781b8a20c85d1 100644
--- a/src/call.py
+++ b/src/call.py
@@ -80,7 +80,6 @@ class Call(Executor):
elif(param.get_type()=="Emitted"):
None
else:
- print(param.get_code(), param.get_type())
raise Exception("This shouldn't happen")
index+=1
return code.replace(tag_to_add, "").strip()
@@ -224,34 +223,35 @@ class Call(Executor):
add_parameter(p)
#If they are not -> we check that the right number isn't implied
else:
- num_inputs = 0
- for p in self.parameters:
- if(p.get_type()=="Call"):
- num_inputs+= p.get_nb_outputs()
- elif(p.get_type()=="Emitted"):
- emitted = p
- if(emitted.get_emitted_by().get_type()=="Subworkflow"):
- if(emitted.get_emits()==None):
- num_inputs+= emitted.get_emitted_by().get_nb_emit()
- else:
- num_inputs+=1
- elif(emitted.get_emitted_by().get_type()=="Process"):
- if(emitted.get_emits()==None):
- num_inputs+= emitted.get_emitted_by().get_nb_outputs()
- else:
- num_inputs+=1
- else:
- raise Exception("This shoudn't happen")
- else:
- #Cause in case channel, operation or emit, it is only one channel given
- num_inputs+=1
- if(num_inputs==process.get_nb_inputs()):
- for p in self.parameters:
- add_parameter(p)
-
- else:
- print(num_inputs, process.get_nb_inputs())
- raise BioFlowInsightError(f"Not the same number of parameters given as input for the process '{process.get_alias()}'{self.get_string_line(self.get_code(get_OG=True))}.", num=2, origin=self)
+ #TODO this needs to be checked
+ #num_inputs = 0
+ #for p in self.parameters:
+ # if(p.get_type()=="Call"):
+ # num_inputs+= p.get_nb_outputs()
+ # elif(p.get_type()=="Emitted"):
+ # emitted = p
+ # if(emitted.get_emitted_by().get_type()=="Subworkflow"):
+ # if(emitted.get_emits()==None):
+ # num_inputs+= emitted.get_emitted_by().get_nb_emit()
+ # else:
+ # num_inputs+=1
+ # elif(emitted.get_emitted_by().get_type()=="Process"):
+ # if(emitted.get_emits()==None):
+ # num_inputs+= emitted.get_emitted_by().get_nb_outputs()
+ # else:
+ # num_inputs+=1
+ # else:
+ # raise Exception("This shoudn't happen")
+ # else:
+ # #Cause in case channel, operation or emit, it is only one channel given
+ # num_inputs+=1
+ #if(num_inputs==process.get_nb_inputs()):
+ # for p in self.parameters:
+ # add_parameter(p)
+ #
+ #else:
+ # raise BioFlowInsightError(f"Not the same number of parameters given as input for the process '{process.get_alias()}'{self.get_string_line(self.get_code(get_OG=True))}.", num=2, origin=self)
+ raise BioFlowInsightError(f"Not the same number of parameters given as input for the process '{process.get_alias()}'{self.get_string_line(self.get_code(get_OG=True))}.", num=2, origin=self)
elif(self.get_first_element_called().get_type()=="Subworkflow"):
sub = self.get_first_element_called()
@@ -281,7 +281,7 @@ class Call(Executor):
operation = p
if(operation.show_in_structure):
operation.get_structure(dico)
- dico["edges"].append({'A':str(operation), 'B':str(sub_input), "label":""})
+ #dico["edges"].append({'A':str(operation), 'B':str(sub_input), "label":""})
#Case parameter is a Call
elif(p.get_type()=="Call"):
@@ -304,22 +304,24 @@ class Call(Executor):
#If the name number of parameters are given
if(len(self.parameters)==sub.get_nb_takes()):
for p in self.parameters:
- param_index = add_parameter(p, param_index )
- #If they are not -> we check that the right number isn't implied
+ param_index = add_parameter(p, param_index)
+ ##If they are not -> we check that the right number isn't implied
else:
- num_inputs = 0
- for p in self.parameters:
- if(p.get_type()=="Call"):
- num_inputs+= p.get_nb_outputs()
- else:
- #Cause in case channel, operation or emit, it is only one channel given
- num_inputs+=1
- if(num_inputs==sub.get_nb_takes()):
- for p in self.parameters:
- param_index = add_parameter(p, param_index )
-
- else:
- raise BioFlowInsightError(f"Not the same number of parameters given as input for the subworklfow '{sub.get_alias()}' in the call{self.get_string_line(self.get_code())}.", num = 2, origin=self)
+ #TODO check this
+ raise BioFlowInsightError(f"Not the same number of parameters given as input for the subworklfow '{sub.get_alias()}' in the call{self.get_string_line(self.get_code())}.", num = 2, origin=self)
+ # num_inputs = 0
+ # for p in self.parameters:
+ # if(p.get_type()=="Call"):
+ # num_inputs+= p.get_nb_outputs()
+ # else:
+ # #Cause in case channel, operation or emit, it is only one channel given
+ # num_inputs+=1
+ # if(num_inputs==sub.get_nb_takes()):
+ # for p in self.parameters:
+ # param_index = add_parameter(p, param_index )
+ #
+ # else:
+ # raise BioFlowInsightError(f"Not the same number of parameters given as input for the subworklfow '{sub.get_alias()}' in the call{self.get_string_line(self.get_code())}.", num = 2, origin=self)
elif(self.get_first_element_called().get_type()=="Function"):
@@ -328,87 +330,6 @@ class Call(Executor):
else:
raise Exception(f"This shoudn't happen! is type")
- #This function synthaxes the one above -> needs to be rechecked
- def get_structure_2(self, dico):
-
- def add_parameter(p, to_link):
-
- #Case parameter is a channel
- if(p.get_type()=="Channel"):
- channel = p
- channel.get_structure(dico, B=to_link)
-
- #Case parameter is a Emitted
- elif(p.get_type()=="Emitted"):
- emitted = p
- emitted.get_structure(dico, B=to_link)
-
- #Case parameter is a Operation
- elif(p.get_type()=="Operation"):
- operation = p
- operation.get_structure(dico)
- dico["edges"].append({'A':str(operation), 'B':str(to_link), "label":""})
-
- #Case parameter is a Call
- elif(p.get_type()=="Call"):
- call = p
- call.get_structure(dico)
- #Case the first call is a process
- if(call.get_first_element_called().get_type()=="Process"):
- for output in call.get_first_element_called().get_outputs():
- dico["edges"].append({'A':str(call.get_first_element_called()), 'B':str(to_link), "label":""})#TODO check name of channel
- #Case the first call is a subworkflow
- elif(call.get_first_element_called().get_type()=="Subworkflow"):
- for emit in call.get_first_element_called().get_emit():
- dico["edges"].append({'A':str(emit), 'B':str(to_link), "label":""})#TODO check name of channel
-
- else:
- raise Exception(f"Type '{p.get_type()}' was given as a parameter -> I don't know how to handle this!")
-
-
- first_call = self.get_first_element_called()
- param_index = 0
- if(first_call.get_type()=="Process" or first_call.get_type()=="Subworkflow"):
- if(first_call.get_type()=="Process"):
- first_call.get_structure(dico)
- else:
- temp_dico = {}
- temp_dico['nodes'] = []
- temp_dico['edges'] = []
- temp_dico['subworkflows'] = {}
- first_call.get_structure(temp_dico)
- dico['subworkflows'][first_call.get_alias()] = temp_dico
-
- #If the name number of parameters are given
- if(len(self.parameters)==first_call.get_nb_inputs()):
- for p in self.parameters:
- if(first_call.get_type()=="Subworklow"):
- sub_input = first_call.get_takes()[param_index]
- add_parameter(p, sub_input)
- param_index+=1
- else:
- add_parameter(p, first_call)
- #If they are not -> we check that the right number isn't implied
- else:
- num_inputs = 0
- for p in self.parameters:
- if(p.get_type()=="Call"):
- num_inputs+= p.get_nb_outputs()
- else:
- #Cause in case channel, operation or emit, it is only one channel given
- num_inputs+=1
- if(num_inputs==first_call.get_nb_inputs()):
- for p in self.parameters:
- if(first_call.get_type()=="Subworklow"):
- sub_input = first_call.get_takes()[param_index]
- add_parameter(p, sub_input)
- param_index+=1
- else:
- add_parameter(p, first_call)
-
- else:
- raise Exception(f"Not the same number of parameters given as input for the process '{first_call.get_alias()}' in the call ('{self.get_code()}')")
-
def analyse_call(self, call):
@@ -420,7 +341,6 @@ class Call(Executor):
if(params[-1]==')'):
params = params[:-1]
else:
- print(self.get_code())
raise Exception("This shouldn't happens")
self.analye_parameters(params)
diff --git a/src/condition.py b/src/condition.py
index a7de014c1f972527e41319863b9b4a8eaddf1b30..f081c0126b02a6ed0e4a5466b27643e3971a70fb 100644
--- a/src/condition.py
+++ b/src/condition.py
@@ -4,29 +4,6 @@ from .outils import extract_conditions
class Condition:
def __init__(self, origin, condition):
self.origin = origin
- self.conditions = condition
+ self.condition = condition
#self.initialise()
- #def get_conditions(self):
- # return self.conditions
-
-
- #def initialise(self):
- # thing_defined = self.origin.get_code(get_OG=True)
- # code = self.origin.get_workflow_code()
- # #print(f"'{thing_defined}'")
- # #print(f"'{code}'")
- #
- #
- # 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]
- # if(condition_extend[0]<pos and pos<condition_extend[1]):
- # self.conditions.append(c)
- # #print(conditions_dico)
- # #print(thing_defined, self.conditions)
- # #print()
-
diff --git a/src/emitted.py b/src/emitted.py
index 40745c4e634f537fb25f7c9292865e575dfc196d..e5b6f5232cab6c1f462f21bd026cd340f3b79862 100644
--- a/src/emitted.py
+++ b/src/emitted.py
@@ -9,8 +9,6 @@ class Emitted(Channel):
def __init__(self, name, origin, emitted_by):
Channel.__init__(self, name=name, origin=origin)
- print(self, emitted_by)
-
self.emitted_by = emitted_by
emitted_by.add_to_emits(self)
@@ -47,7 +45,6 @@ class Emitted(Channel):
self.emits = o
if(self.emits==None):
- print(self.get_code())
raise Exception(f"No emitted matched with '{name}' (in file '{self.get_file_address()}'). Should match with emittes from '{self.emitted_by.get_name()}' (in file '{self.emitted_by.get_file_address()}'")
def set_emits(self, input):
@@ -71,30 +68,16 @@ class Emitted(Channel):
def get_structure(self, dico, B):
emits = self.get_emitted_by()
- #if(not emits.is_called(self)):
- # end = "in the file"
- # if(self.origin.get_type()=="Subworkflow"):
- # end = f"in the subworkflow '{self.origin.get_name()}'"
- # raise BioFlowInsightError(f"Tried to access the emit '{self.get_code()}' but the {emits.get_type()} '{emits.get_name()}' ({emits}) has not been called {end}.", num = 8, origin=self)
- #
-
- #Case if the emit emits a process
- if(emits.get_type()=="Process"):
- #emits.get_structure(dico)
- if(self.emits==None):
- #for i in range(emits.get_nb_outputs()):
- # print("here")
- # #I don't need to add the process (node) to the structure -> cause it's either there or will be added later on
- dico["edges"].append({'A':str(emits), 'B':str(B), "label":self.get_code()})
- else:
- dico["edges"].append({'A':str(self.emits), 'B':str(B), "label":self.get_code()})
- #Case if the emit emits a subworkflow
- elif(emits.get_type()=="Subworkflow"):
- if(self.emits==None):
- raise Exception("Just a check")
- for ope in emits.get_emit():
- dico["edges"].append({'A':str(ope), 'B':str(B), "label":self.get_code()})
- else:
- dico["edges"].append({'A':str(self.emits), 'B':str(B), "label":self.get_name()})
+ if(emits.get_type()=="Call"):
+ first_element_called = emits.get_first_element_called()
+ if(first_element_called.get_type()=="Process"):
+ dico["edges"].append({'A':str(first_element_called), 'B':str(B), "label":self.get_code()})
+ elif(first_element_called.get_type()=="Subworkflow"):
+ if(self.emits==None):
+ raise Exception("Just a check")
+ else:
+ dico["edges"].append({'A':str(self.emits), 'B':str(B), "label":self.get_name()})
+ else:
+ raise Exception("This shouldn't happen")
diff --git a/src/executor.py b/src/executor.py
index adf9b5541aaf52695e0dd93eee108cf067ae62ec..9c6b57cc99e5857f9b0deb6cfd0eb8a9bf5336b2 100644
--- a/src/executor.py
+++ b/src/executor.py
@@ -148,8 +148,6 @@ class Executor(Nextflow_Building_Blocks):
pipe = pipe + '|'+'|'.join(pipe_split[2:])
if not added:
if(re.fullmatch(constant.OPERATOR_IN_PIPE, thing)):
- print(pipe, self.get_file_address())
- print(f"'{thing}'")
raise Exception('problem')
raise BioFlowInsightError(f"Don't know how to handle '{thing}' in a pipe operator{self.get_string_line(thing)}. Try using the recommended operator composition.", num=3,origin = self)
@@ -216,9 +214,7 @@ class Executor(Nextflow_Building_Blocks):
return None
else:
- print(self.get_code())
return self.origin.get_call_by_name(name)
- #print(self.origin.get_calls())
- #print(self.origin)
+
diff --git a/src/graph.py b/src/graph.py
index bce297469f066ec9506ceb9dc0a4e50804d30d0f..c74c3ec4cb6b944ae86bc5983b4a5b26c76ec5c0 100644
--- a/src/graph.py
+++ b/src/graph.py
@@ -74,8 +74,8 @@ class Graph():
remove_node(self.full_dico, node_id)
- self.get_dependency_graph()
- self.get_process_dependency_graph()
+ #self.get_dependency_graph()
+ #self.get_process_dependency_graph()
#self.networkX_wo_operations = self.get_networkx_graph(self.dico_process_dependency_graph, self.networkX_wo_operations)
@@ -453,7 +453,6 @@ class Graph():
node_B_temp = tmp
exists, _ = exist_path_dico(node_A_temp, node_B_temp, dependency_level)
if(not exists):
- print("False dependency", edge_user)
return True
@@ -485,7 +484,7 @@ class Graph():
dico = {}
for node in G.nodes(data=True):
if(node[1]=={}):
- print(node)
+ None
process_nodes = [node for node, data in G.nodes(data=True) if data['type'] == 'Process']
operation_nodes = [node for node, data in G.nodes(data=True) if data['type'] == 'Operation']
diff --git a/src/main.py b/src/main.py
index ed6fdf98d9384210902797fd6213c09e35ffc97d..522bde77c2048d390b8bcd83a775a9cfea9e606f 100644
--- a/src/main.py
+++ b/src/main.py
@@ -56,8 +56,7 @@ class Main(Nextflow_Building_Blocks):
def initialise(self):
if(not self.initialised):
- #print(self, self.get_all_processes())
-
+
self.initialised=True
#Get the modules (Processes defined for the main/subworkflow)
@@ -74,7 +73,6 @@ class Main(Nextflow_Building_Blocks):
def get_structure(self, dico):
-
self.root.get_structure(dico)
return dico
\ No newline at end of file
diff --git a/src/operation.py b/src/operation.py
index d72bbdc0e946f5ac56db8da0d8775d03bd9b2964..0cbb3a54c0e961ad1ec1f40a9881b99897494b68 100644
--- a/src/operation.py
+++ b/src/operation.py
@@ -86,9 +86,6 @@ class Operation(Executor):
#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)
- #TODO -> problem might be here
-
- #TODO -> this needs to be checked
if(self.origin.get_type()!="Subworkflow"):
if(not self.origin.check_in_channels(channel)):
self.origin.add_channel(channel)
@@ -120,10 +117,8 @@ class Operation(Executor):
if( splited[-1] in constant.LIST_OPERATORS):
full_code = '.'.join(splited[:-1])
if(name_called not in IGNORE_NAMES):
- #print(self.origin.origin.get_name(), self.origin.origin.get_processes())
call = self.get_call_by_name(name_called)
#process = self.get_process_from_name(name_called)
- ##print(process)
#subworkflow = self.get_subworkflow_from_name(name_called)
#
#if(process!=None and subworkflow!=None):
@@ -228,12 +223,10 @@ class Operation(Executor):
#subworkflow = self.origin.get_subworkflow_from_name(name)
#process = self.origin.get_process_from_name(name)
#if(subworkflow!=None):
- # print("George it's a subworkflow")
# #Case suborkflow
# self.origins.append(subworkflow)
##Case process
#elif(process!=None):
- # print("George it's a process")
# #Case process
# self.origins.append(process)
##In this case it's a channel
@@ -533,7 +526,6 @@ class Operation(Executor):
# if(bool(re.fullmatch(r'\w+', name))):
# self.add_origin(name)
- #print(self.origin)
#self.origins = list(set(origin))
@@ -561,7 +553,6 @@ class Operation(Executor):
raise Exception("Something unexpected")
#else:
- # print(self.get_code())
# raise Exception("Something unexpected!")
@@ -589,7 +580,6 @@ class Operation(Executor):
raise Exception(f"I don't know what i'm looking at '{c}' in '{self.get_code()}'")
- #print(operator, s, start, end)
@@ -610,15 +600,7 @@ class Operation(Executor):
tab.append(g)
return tab
- def print_operation(self):
- print(self.get_code())
- #TODO -> put this somewhere
- def check_loop(self):
- for g in self.gives:
- for o in self.origins:
- if(g==o):
- print(f"Loop here:\n- {self.get_code()}\n- For the {o.get_name()} channel")
#This method checks if an operation is just a full emited
#This is in the case of a parameter in a call
@@ -634,17 +616,7 @@ class Operation(Executor):
return False
- #def print_summary(self, tab = 0, print_code=False):
- # print(" "*tab+f"{self}")
- # if(print_code):
- # print(" "*(tab+1)+"* Code :", self.get_code())
- # print(" "*(tab+1)+"* Origins")
- # for o in self.get_origins():
- # print(" "*(tab+1+2)+o.get_code(), f"'{o.get_type()}'")
- # print(" "*(tab+1)+"* Gives")
- # for g in self.get_gives():
- # print(" "*(tab+1+2)+g.get_code(), f"'{g.get_type()}'")
-
+
def write_summary(self, address, tab = 0):
file = open(address, "a")
file.write(" "*tab+f"{self}\n")
@@ -696,7 +668,6 @@ class Operation(Executor):
p = p.strip()
if(p!=""):
name = p
- #print(name)
if(bool(re.fullmatch(constant.WORD, name))):
self.add_origin(name)
elif(self.check_is_emit(name)):
@@ -739,7 +710,6 @@ class Operation(Executor):
# text = text.replace(self.calls[c].get_code(), "")
# for match in re.finditer(pattern_call_pipe, text):
# if(match.group(1) in to_call):
- # print(match.group(1), text)
# start, end = match.span(0)
# from .outils import checks_in_condition_if, checks_in_string, extract_inside_parentheses
# if(not checks_in_condition_if(text, match.group(1)) and not checks_in_string(text, match.group(1))):
@@ -790,7 +760,6 @@ class Operation(Executor):
def initialise_from_call(self):
if(self.get_code()!="" and self.get_code()[0]=="[" and self.get_code()[-1]=="]"):
- #print("in list", self.get_code())
None
#TODO
#basically in this code -> i want to do the same thing for analye_parameters for a call
@@ -815,89 +784,78 @@ class Operation(Executor):
self.write_summary(self.get_output_dir() / "debug/operations_in_call.nf")
def get_structure(self, dico, to_remove = False):
- if(self.show_in_structure):
- code = self.get_code(replace_calls=False)
- #Need to replace /* and */ by /\* and *\/ so graphivz doesn't think it's a comment
- #Same for // -> replace it by /\/\
- code = code.replace("/*", "/\*").replace("*/", "*\/").replace("//", "/\/\\")
- code = code.replace('"', "'")
- if(self.get_operation_type()=="Branch"):
- fillcolor = "white"
- else:
- fillcolor = ""
+ code = self.get_code(replace_calls=False)
+ #Need to replace /* and */ by /\* and *\/ so graphivz doesn't think it's a comment
+ #Same for // -> replace it by /\/\
+ code = code.replace("/*", "/\*").replace("*/", "*\/").replace("//", "/\/\\")
+ code = code.replace('"', "'")
+ if(self.get_operation_type()=="Branch"):
+ fillcolor = "white"
+ else:
+ fillcolor = ""
- #TODO check this -> IMPORTANT
- if(not to_remove):
- dico['nodes'].append({'id':str(self), 'name':"", "shape":"point", 'xlabel': code, 'fillcolor':fillcolor})
- else:
- #The ones which have the 'to_remove' name is because they are used in as takes and emits in subworkflow (they will be removed in post)
- dico['nodes'].append({'id':str(self), 'name':"to_remove", "shape":"point", 'xlabel': code, 'fillcolor':fillcolor})
+ dico['nodes'].append({'id':str(self), 'name':"", "shape":"point", 'xlabel': code, 'fillcolor':fillcolor})
- for o in self.origins:
- #Case origins is a channel
- if(o.get_type()=="Channel"):
- channel = o
- channel.get_structure(dico, B=self)
-
- #Case origins is a call
- elif(o.get_type()=="Call"):
- call = o
- call.get_structure(dico)
- #Case the first call is a process
- if(call.get_first_element_called().get_type()=="Process"):
- dico["edges"].append({'A':str(call.get_first_element_called()), 'B':str(self), "label":""})#TODO check name of channel
- #Case the first call is a subworkflow
- elif(call.get_first_element_called().get_type()=="Subworkflow"):
- sub = call.get_first_element_called()
- if(sub.get_nb_emit()==0):
- raise BioFlowInsightError(f"The subworkflow '{sub.get_name()}' doesn't emit anything. It is given to an operation{self.get_string_line(call.get_code())}.", num=20, origin=self)
- elif(sub.get_nb_emit()>1):
- #In the case test().a.view() and test is a subworkflow
- added = False
- element_after_call = self.get_element_after_call(o)
- emits = sub.get_emit()
- for e in emits:
- if(e.get_gives()==[]):
- for o in e.get_origins():
- if(o.get_code()==element_after_call):
- dico["edges"].append({'A':str(e), 'B':str(self), "label":e.get_code()})
- added =True
- else:
- for g in e.get_gives():
- if(g.get_code()==element_after_call):
- dico["edges"].append({'A':str(e), 'B':str(self), "label":e.get_code()})
- added =True
-
- if(not added):
- raise BioFlowInsightError(f"To much to unpack : The subworkflow '{sub.get_name()}' emits over one channel in a operation{self.get_string_line(call.get_code())}.", num=20, origin=self)
- #TODO recommendation -> try using an emit subworkflow.out
- else:
- emit = sub.get_emit()[0]
- dico["edges"].append({'A':str(emit), 'B':str(self), "label":emit.get_code()})
- #for out in sub.get_emit():
- # print(out, out.get_code())
- # #These are channels
- # #TODO check this -> it was the one line 644 before
- # #out.get_structure(dico, B=self)
- # out.get_structure(dico)
-
- elif(call.get_first_element_called().get_type()=="Function"):
- #TODO check if this is actually the cas
- None
+ for o in self.origins:
+ #Case origins is a channel
+ if(o.get_type()=="Channel"):
+ channel = o
+ channel.get_structure(dico, B=self)
+
+ #Case origins is a call
+ elif(o.get_type()=="Call"):
+ call = o
+ call.get_structure(dico)
+ #Case the first call is a process
+ if(call.get_first_element_called().get_type()=="Process"):
+ dico["edges"].append({'A':str(call.get_first_element_called()), 'B':str(self), "label":""})#TODO check name of channel
+ #Case the first call is a subworkflow
+ elif(call.get_first_element_called().get_type()=="Subworkflow"):
+ sub = call.get_first_element_called()
+ if(sub.get_nb_emit()==0):
+ raise BioFlowInsightError(f"The subworkflow '{sub.get_name()}' doesn't emit anything. It is given to an operation{self.get_string_line(call.get_code())}.", num=20, origin=self)
+ elif(sub.get_nb_emit()>1):
+ #In the case test().a.view() and test is a subworkflow
+ added = False
+ element_after_call = self.get_element_after_call(o)
+ emits = sub.get_emit()
+ for e in emits:
+ if(e.get_gives()==[]):
+ for o in e.get_origins():
+ if(o.get_code()==element_after_call):
+ dico["edges"].append({'A':str(e), 'B':str(self), "label":e.get_code()})
+ added =True
+ else:
+ for g in e.get_gives():
+ if(g.get_code()==element_after_call):
+ dico["edges"].append({'A':str(e), 'B':str(self), "label":e.get_code()})
+ added =True
+
+ if(not added):
+ raise BioFlowInsightError(f"To much to unpack : The subworkflow '{sub.get_name()}' emits over one channel in a operation{self.get_string_line(call.get_code())}.", num=20, origin=self)
+ #TODO recommendation -> try using an emit subworkflow.out
else:
- raise Exception("This souldn't happen!")
-
-
- #Case origins is a Emmited
- elif(o.get_type()=="Emitted"):
- emitted = o
- emitted.get_structure(dico, B=self)
-
+ emit = sub.get_emit()[0]
+ dico["edges"].append({'A':str(emit), 'B':str(self), "label":emit.get_code()})
+ #for out in sub.get_emit():
+ # #These are channels
+ # #TODO check this -> it was the one line 644 before
+ # #out.get_structure(dico, B=self)
+ # out.get_structure(dico)
+ elif(call.get_first_element_called().get_type()=="Function"):
+ #TODO check if this is actually the cas
+ None
else:
- print(self.get_code())
- print(self.get_file_address())
- raise Exception(f"This souldn't happen! The origin of an operation is of type '{o.get_type()}'. It's code is '{o.get_code()}'")
+ raise Exception("This souldn't happen!")
+
+
+ #Case origins is a Emmited
+ elif(o.get_type()=="Emitted"):
+ emitted = o
+ emitted.get_structure(dico, B=self)
+ else:
+ raise Exception(f"This souldn't happen! The origin of an operation is of type '{o.get_type()}'. It's code is '{o.get_code()}'")
def convert_to_DSL2(self):
code = self.get_code(get_OG=True)
diff --git a/src/outils.py b/src/outils.py
index 61906be272f0af809b6ff52afde9fb0e6a79b27a..84da8804f8eb0ece59bb8ab29f83048940ff76fc 100644
--- a/src/outils.py
+++ b/src/outils.py
@@ -369,7 +369,6 @@ def extract_curly(text, start):
while(parenthese_count!=0 or curly_count!=0 or quote_single or quote_double or triple_single or triple_double):
- #print(parenthese_count, curly_count, quote_single, quote_double, triple_single, triple_double)
checked_triple = False
@@ -489,7 +488,7 @@ def remove_comments(input_text):
#input_text = re.sub(r'\/([^($\/)]+)\$\/', r'"\g<1>"', input_text)
#if(temp!=input_text):
- # print("-",start)
+
to_remove = []
quote_single, quote_double = False, False
@@ -1029,7 +1028,7 @@ def extract_conditions(code):
start_inside, end_inside = match.span(0)[1]+end, end_else-1
conditions_dico[' && '.join(["!({})".format(v) for v in conditions])] = (start_inside, end_inside)
#conditions_dico = adding_inside(conditions_dico, code, start_inside, end_inside)
- #print(code[start_else:end_else])
+
break
end = end_else
if(found_if_bloc):
@@ -1233,8 +1232,6 @@ def replace_thing_by_call(tab):
call = ele.get_call()
#This verification is really important
if(len(call)!=1):
- for c in call:
- print(c.get_code(get_OG=True))
raise Exception("This shoudn't happen since duplicate mode is activated")
call = call[0]
to_add.append(call)
@@ -1265,10 +1262,9 @@ def group_together_ifs(code):
big_start, end_1 = match.span(0)
end = extract_curly(code, end_1)
inside_1 = code[end_1:end-1].strip()
- #print(re.escape(code[big_start:end])+r'\s*'+pattern)
+
for motch in re.finditer(re.escape(code[big_start:end])+r'\s*'+pattern, code):
condition_2 = motch.group(1)
- #print('-', motch.group(1))
_, end_2 = motch.span(0)
end = extract_curly(code, end_2)
big_end = end
diff --git a/src/outils_graph.py b/src/outils_graph.py
index 48401ac717f2f7c3189d888c64fbbdf5ad6f0f9b..01eb94fcd343d57a7a977615a235b65084ec3f5e 100644
--- a/src/outils_graph.py
+++ b/src/outils_graph.py
@@ -765,15 +765,14 @@ def relev_user_view_builder(dico_param, relevant_modules):
return True, i
return False, -1
- #print('n', get_name_from_id(dico, n), '-> rPred', get_names_tab(dico, rPred(n, dico, R, ['input'])))
- #print('n', get_name_from_id(dico, n), '-> rSucc', get_names_tab(dico, rSucc(n, dico, R, ['output'])))
+
check, index = condition_line_13(NRC, n, dico, R, ["input"], ['output'])
if(check):
NRC[index].append(n)
else:
M = [n]
NRC.append(M)
- #print(get_names_tab(dico, NRC))
+
#Step 3
changes_in_NRC = True
@@ -918,7 +917,6 @@ def get_graph_level_l(dico, level):
node_2_subworkflows = {}
fill_node_2_subworkflows(dico, node_2_subworkflows)
- #print(node_2_subworkflows)
def add_nodes(dico, level, current_level):
diff --git a/src/process.py b/src/process.py
index 0baa5363d6d68d9cfc7ed7bf1d1e98e79f302bb5..affecbe0c3bd6e48c8a3ffccae61827fe2883323 100644
--- a/src/process.py
+++ b/src/process.py
@@ -245,7 +245,7 @@ class Process(Nextflow_Building_Blocks):
for match in re.finditer(pattern, line+"\n"):
extracted = match.group(1).strip()
self.raw_input_names.append(extracted)
- #print(extracted)
+
if(bool(re.fullmatch(constant.WORD, extracted))):
add_channel(extracted)
else:
diff --git a/src/root.py b/src/root.py
index 3006ead384f22cda73ca4e308e278e7d420c30d1..cddaca9d8e039325fdb8031154ecd99df82520d0 100644
--- a/src/root.py
+++ b/src/root.py
@@ -69,7 +69,7 @@ class Root(Nextflow_Building_Blocks):
for c in conditions:
from .block import Block
body = code[conditions[c][0]:conditions[c][1]]
- block = Block(code=body, origin=self, condition=c, modules_defined=self.modules_defined)
+ block = Block(code=body, origin=self, condition=c, modules_defined=self.modules_defined, existing_channels = self.channels)
block.initialise()
self.blocks.append(block)
@@ -330,8 +330,7 @@ class Root(Nextflow_Building_Blocks):
# tab_to_call = txt_call.split('|')
# start = f"{tab_to_call[0]}({params})"
# txt_call = start + '|' + '|'.join(tab_to_call[1:])
- # print(start)
- #print(params, full_executor)
+
#If the thing which is extracted is not in the conditon of an if
if(not checks_in_condition_if(text, full_executor) and not checks_in_string(text, full_executor)):
@@ -378,10 +377,8 @@ class Root(Nextflow_Building_Blocks):
self.executors.remove(e)
def get_structure(self, dico):
-
for block in self.blocks:
block.get_structure(dico)
-
for e in self.executors:
if(e.get_type()=="Operation"):
e.get_structure(dico)
diff --git a/src/subworkflow.py b/src/subworkflow.py
index 655c65ba1578adc0f9140fa76ee43d1e99ab0562..3402a3c062e727d3e500388452fb0a7dbbfdc285 100644
--- a/src/subworkflow.py
+++ b/src/subworkflow.py
@@ -64,9 +64,6 @@ class Subworkflow(Main):
return re.sub(r"workflow\s*(\w+)\s*\{", replacer, code)
- def print_summary(self, tab = 0):
- print(" "*tab+f"* {self.name} ({self})")
- super().print_summary(tab)
def set_alias(self, alias):
self.alias = alias
@@ -187,6 +184,7 @@ class Subworkflow(Main):
+
def initialise_emit(self):
from .operation import Operation
if(self.emit!=[]):
@@ -215,7 +213,6 @@ class Subworkflow(Main):
# #TODO -> check not add origin too!
# gives.add_sink(operation)
#tab.append(operation)
- #print(operation)
##self.add_operation(operation)
##self.executors.append(operation)
self.emit = tab
@@ -258,10 +255,10 @@ class Subworkflow(Main):
for ope in self.get_takes():
#ope.set_operation_type("Branch")
- ope.get_structure(dico, to_remove = True)
-
+ ope.get_structure(dico)
+
for ope in self.get_emit():
#ope.set_operation_type("Branch")
- ope.get_structure(dico, to_remove = True)
+ ope.get_structure(dico)
\ No newline at end of file
diff --git a/src/workflow.py b/src/workflow.py
index cc4ef304fd33c58f500c18c6a2f6816367cb3449..5e4248f95f292962184cb7d47c947d7daac8da77 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -124,9 +124,8 @@ class Workflow:
if(self.display_info):
- citation = """To cite BioFlow-Insight, please use the following publication:
+ citation = """\nTo cite BioFlow-Insight, please use the following publication:
George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen-Boulakia, BioFlow-Insight: facilitating reuse of Nextflow workflows with structure reconstruction and visualization, NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae092, https://doi.org/10.1093/nargab/lqae092"""
- print()
print(citation)
if(self.graph==None):