diff --git a/src/block.py b/src/block.py
index 4a4b5c4c5b6bd803d426ab8baa9fb0ba4bc50807..8fc620bced3c5c3e86ad6f2d1ba78cf359c44210 100644
--- a/src/block.py
+++ b/src/block.py
@@ -7,10 +7,8 @@ class Block(Root):
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):
- print(self.condition.condition)
- if(self.condition.condition not in ["params.downloadFastq == true", "params.downloadGenome == true"]):
- return super().initialise()
+ #def initialise(self):
+ # return super().initialise()
def get_type(self):
return "Root"
diff --git a/src/call.py b/src/call.py
index 77f63f932bc9680c0cc0383a3e8781b8a20c85d1..ea7f06154c9c6c8f4e82d3edd416a278c5f52123 100644
--- a/src/call.py
+++ b/src/call.py
@@ -22,6 +22,7 @@ class Call(Executor):
self.OG_code = OG_code
self.initialised = False
self.emits = []
+ self.analyse_first_element_called(self.get_code(clean_pipe = True))
#It's important this is last
#self.condition = Condition(self)
@@ -344,26 +345,58 @@ class Call(Executor):
raise Exception("This shouldn't happens")
self.analye_parameters(params)
+ # process = self.get_process_from_name(tab_call[0])
+ # subworkflow = self.get_subworkflow_from_name(tab_call[0])
+ # fun = self.get_function_from_name(tab_call[0])
+ # if(process!=None and subworkflow==None and fun==None):
+ # #If the elements need to duplicated -> then we need to duplicate it
+ # if(self.get_duplicate_status()):
+ # process = process.copy()
+ # process.initialise()
+ # self.first_element_called = process
+ # self.origin.add_element_to_elements_being_called(process)
+ # #temp.incremente_number_times_called()
+ # if(process==None and subworkflow!=None and fun==None):
+ # if(self.get_duplicate_status()):
+ # subworkflow = subworkflow.copy()
+ # subworkflow.initialise()
+ # self.first_element_called = subworkflow
+ # self.origin.add_element_to_elements_being_called(subworkflow)
+ # if(process==None and subworkflow==None and fun!=None):
+ # self.first_element_called = fun
+ # if(process==None and subworkflow==None and fun==None):
+ # raise Exception("No first call found!!")
+ # self.called.append(self.first_element_called)
+ #else:
+ # raise BioFlowInsightError(f"Failed to extract the call{self.get_string_line(self.get_code())}. Try rewriting it in a simplified version.", num = 15, origin=self)
+
+ def analyse_first_element_called(self, call):
+ tab_call = self.get_code_split_space(call)
+ if(re.fullmatch(constant.WORD, tab_call[0]) and tab_call[1]=='('):
+ #params1 = ' '.join(tab_call[2:-1])
+ start = re.findall(tab_call[0]+constant.END_CALL, call)[0]
+ params = call.replace(start, "")
+ if(params[-1]==')'):
+ params = params[:-1]
+ else:
+ raise Exception("This shouldn't happens")
+
+ #self.analye_parameters(params)
process = self.get_process_from_name(tab_call[0])
subworkflow = self.get_subworkflow_from_name(tab_call[0])
fun = self.get_function_from_name(tab_call[0])
if(process!=None and subworkflow==None and fun==None):
#If the elements need to duplicated -> then we need to duplicate it
- #temp = process
- #if(self.get_duplicate_status()):
- # if(process.get_number_times_called()>0):
- # temp = copy.copy(process)
- # temp.set_alias(f"{process.get_name()}_{process.get_number_times_called()}")
if(self.get_duplicate_status()):
process = process.copy()
- process.initialise()
+ process.initialise()
self.first_element_called = process
self.origin.add_element_to_elements_being_called(process)
#temp.incremente_number_times_called()
if(process==None and subworkflow!=None and fun==None):
if(self.get_duplicate_status()):
subworkflow = subworkflow.copy()
- subworkflow.initialise()
+ subworkflow.initialise()
self.first_element_called = subworkflow
self.origin.add_element_to_elements_being_called(subworkflow)
if(process==None and subworkflow==None and fun!=None):
@@ -373,6 +406,7 @@ class Call(Executor):
self.called.append(self.first_element_called)
else:
raise BioFlowInsightError(f"Failed to extract the call{self.get_string_line(self.get_code())}. Try rewriting it in a simplified version.", num = 15, origin=self)
+
def get_called(self):
@@ -421,6 +455,7 @@ class Call(Executor):
self.initialised = True
self.analyse_call(self.get_code(clean_pipe = True))
self.write_summary()
+
diff --git a/src/emitted.py b/src/emitted.py
index e5b6f5232cab6c1f462f21bd026cd340f3b79862..55142b0f2d98df41b35030a26bd7766d3a7f7c44 100644
--- a/src/emitted.py
+++ b/src/emitted.py
@@ -48,23 +48,26 @@ class Emitted(Channel):
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):
- if(input!=""):
- try:
- input = int(input)
- self.set_emits_decimal(decimal=input)
- except:
- self.set_emits_name(name=input)
+ thing_which_emits = self.emitted_by.get_first_element_called()
+ if(thing_which_emits.get_type()=="Process"):
+ #TODO -> i don't konw what to do with this
+ #self.emits = thing_which_emits
+ None
+
else:
- thing_which_emits = self.emitted_by.get_first_element_called()
- if(thing_which_emits.get_type()=='Process'):
- #self.emits = self.emitted_by
- None
- elif(thing_which_emits.get_type()=='Subworkflow'):
- if(len(thing_which_emits.emit)!=1):
- raise BioFlowInsightError(f"One channel was expected in the emit '{self.get_code()}'. Even though multiple emits are defined for the workflow '{self.emitted_by.get_name()}'", num=6, origin=self)
- self.emits = thing_which_emits.emit[0]
+ if(input!=""):
+ try:
+ input = int(input)
+ self.set_emits_decimal(decimal=input)
+ except:
+ self.set_emits_name(name=input)
else:
- raise Exception("This shoudn't happen!")
+ if(thing_which_emits.get_type()=='Subworkflow'):
+ if(len(thing_which_emits.emit)!=1):
+ raise BioFlowInsightError(f"One channel was expected in the emit '{self.get_code()}'. Even though multiple emits are defined for the workflow '{self.emitted_by.get_name()}'", num=6, origin=self)
+ self.emits = thing_which_emits.emit[0]
+ else:
+ raise Exception("This shoudn't happen!")
def get_structure(self, dico, B):
emits = self.get_emitted_by()
@@ -76,6 +79,7 @@ class Emitted(Channel):
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 9c6b57cc99e5857f9b0deb6cfd0eb8a9bf5336b2..6e54eb9c0c3bb2f49e1e42f2d1ef934cb7632e4b 100644
--- a/src/executor.py
+++ b/src/executor.py
@@ -206,11 +206,17 @@ class Executor(Nextflow_Building_Blocks):
#Method which returns the call which calls the element called
def get_call_by_name(self, name):
+ #We get the calls that have already been analysed or which are currently being analysed
+ #for example "p(a.out)" -> the call for 'a' may not have been analysed yet
+ #In that case when calling "get_calls" -> we don't want to reanalyse the "p(a.out)"
+ calls_that_have_been_analysed = self.get_calls_that_have_been_analysed()
if(self.origin.get_type() in ['Root', 'Block']):
for c in self.origin.get_calls():
- c.initialise()
- if(c.first_element_called.get_alias()==name):
- return c
+ if(c not in calls_that_have_been_analysed):
+ calls_that_have_been_analysed[c] = True
+ #c.initialise()
+ if(c.first_element_called.get_alias()==name):
+ return c
return None
else:
diff --git a/src/graph.py b/src/graph.py
index c74c3ec4cb6b944ae86bc5983b4a5b26c76ec5c0..ef0caf11ff6e6592b77abae6af3593e26af3106f 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)
diff --git a/src/include.py b/src/include.py
index 9ac48bebaab00b8b32649f453f063300754dc2ea..4a92090fb58d491d31fcb69535c2e0b13ae82722 100644
--- a/src/include.py
+++ b/src/include.py
@@ -37,14 +37,14 @@ class Include(Nextflow_Building_Blocks):
return self.origin.get_root_directory()
- def get_list_name_includes(self):
- if(self.get_duplicate_status()):
- names = []
- for ele in self.defines:
- names.append(ele.get_alias())
- return names
- else:
- return list(self.aliases.keys())
+ #def get_list_name_includes(self):
+ # if(self.get_duplicate_status()):
+ # names = []
+ # for ele in self.defines:
+ # names.append(ele.get_alias())
+ # return names
+ # else:
+ # return list(self.aliases.keys())
def define_file(self, file):
from .nextflow_file import Nextflow_File
@@ -112,7 +112,6 @@ class Include(Nextflow_Building_Blocks):
for match in re.finditer(pattern_as, include):
found = True
if(self.get_duplicate_status()):
- #thing_as = copy.copy(self.nextflow_file.get_element_from_name(match.group(1)))
thing_as = self.nextflow_file.get_element_from_name(match.group(1)).copy()
thing_as.set_alias(match.group(3))
self.defines[match.group(3)] = thing_as
diff --git a/src/main.py b/src/main.py
index 522bde77c2048d390b8bcd83a775a9cfea9e606f..5b80b7d2f44503b596bf303c340e53c031abc048 100644
--- a/src/main.py
+++ b/src/main.py
@@ -15,6 +15,9 @@ class Main(Nextflow_Building_Blocks):
self.initialised = False
self.root = None
+ def get_calls_that_have_been_analysed(self):
+ return self.nextflow_file.get_calls_that_have_been_analysed()
+
def get_string_line(self, bit_of_code):
return self.nextflow_file.get_string_line(bit_of_code)
diff --git a/src/nextflow_building_blocks.py b/src/nextflow_building_blocks.py
index 1488bf347cd01bf768fad073ae3db8e94aaf64ad..c004e35b967f63712ac356f71ea3a5ab0d7320d8 100644
--- a/src/nextflow_building_blocks.py
+++ b/src/nextflow_building_blocks.py
@@ -21,6 +21,9 @@ class Nextflow_Building_Blocks:
#AUXILIARY METHODS FOR ALL CLASSES
#---------------------------------
+ def get_calls_that_have_been_analysed(self):
+ return self.origin.get_calls_that_have_been_analysed()
+
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 c3724a34aa0b844454e3d2b5cd7afa8ff591c8ed..48e105704d98daf9a2adb5c2421d72265ca491eb 100644
--- a/src/nextflow_file.py
+++ b/src/nextflow_file.py
@@ -50,6 +50,9 @@ class Nextflow_File(Nextflow_Building_Blocks):
def get_DSL(self):
return self.workflow.get_DSL()
+ def get_calls_that_have_been_analysed(self):
+ return self.workflow.get_calls_that_have_been_analysed()
+
#Method which returns the DSL of the workflow -> by default it's DSL2
#I use the presence of include, subworkflows and into/from in processes as a proxy
def find_DSL(self):
diff --git a/src/process.py b/src/process.py
index affecbe0c3bd6e48c8a3ffccae61827fe2883323..6372e462dd25cb8fddb9467aed8ffd286387a6f9 100644
--- a/src/process.py
+++ b/src/process.py
@@ -28,6 +28,7 @@ class Process(Nextflow_Building_Blocks):
self.script_code = ""
self.called_by = []#List of calls
+ self.initialised = False
def copy(self):
@@ -44,6 +45,7 @@ class Process(Nextflow_Building_Blocks):
process.pusblishDir_code = ""
process.script_code = ""
process.called_by = []#List of calls
+ process.initialised = False
return process
def add_to_emits(self, emit):
@@ -386,8 +388,10 @@ class Process(Nextflow_Building_Blocks):
def initialise(self):
- self.initialise_name()
- self.initialise_parts()
- self.initialise_inputs_outputs()
+ if(not self.initialised):
+ self.initialised = True
+ self.initialise_name()
+ self.initialise_parts()
+ self.initialise_inputs_outputs()
diff --git a/src/root.py b/src/root.py
index cddaca9d8e039325fdb8031154ecd99df82520d0..24f7a310d6e3b2b7c64083c0abdd8e77f489fd91 100644
--- a/src/root.py
+++ b/src/root.py
@@ -70,12 +70,14 @@ class Root(Nextflow_Building_Blocks):
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, existing_channels = self.channels)
- block.initialise()
self.blocks.append(block)
self.extract_executors()
+ for block in self.blocks:
+ block.initialise()
+
#Analyse Executors
for e in self.executors:
e.initialise()
diff --git a/src/subworkflow.py b/src/subworkflow.py
index 3402a3c062e727d3e500388452fb0a7dbbfdc285..3ce064e6f45a2bfe98d91846ca039c66457fa6a7 100644
--- a/src/subworkflow.py
+++ b/src/subworkflow.py
@@ -44,10 +44,13 @@ class Subworkflow(Main):
return sub
def get_call_by_name(self, name):
+ calls_that_have_been_analysed = self.get_calls_that_have_been_analysed()
for c in self.root.get_calls():
- c.initialise()
- if(c.first_element_called.get_alias()==name):
- return c
+ if(c not in calls_that_have_been_analysed):
+ calls_that_have_been_analysed[c] = True
+ #c.initialise()
+ if(c.first_element_called.get_alias()==name):
+ return c
return None
diff --git a/src/workflow.py b/src/workflow.py
index 5e4248f95f292962184cb7d47c947d7daac8da77..a0ac31e3d2c2463f3a88ea15222bf23b830e5c34 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -61,6 +61,8 @@ class Workflow:
self.name = name
self.graph = None
+ self.calls_that_have_been_analysed = {}
+
OG_file = Nextflow_File(file, workflow = self, first_file = True)
self.DSL = OG_file.find_DSL()
self.create_empty_results()
@@ -80,6 +82,9 @@ class Workflow:
with open(self.output_dir / "debug" / "operations_in_call.nf",'w') as file:
pass
+ def get_calls_that_have_been_analysed(self):
+ return self.calls_that_have_been_analysed
+
def get_duplicate_status(self):
return self.duplicate