diff --git a/src/block.py b/src/block.py
index 8d03cfc7b2c9d8a28d278b4c33c96c8a5cd513be..375341bcdbb1a8e757721cb45014a094037a3820 100644
--- a/src/block.py
+++ b/src/block.py
@@ -7,6 +7,11 @@ 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 delete(self):
+ super().delete()
+ self.condition.delete()
+ del self.condition
+
def initialise(self):
if(self.condition.value not in self.origin.get_conditions_2_ignore()):
return super().initialise()
diff --git a/src/call.py b/src/call.py
index 7febe835f765d4744ab2d5016d3c8753b654d3d7..1ad4f150602852a84b9de83fc3ed74ac3e3af1db 100644
--- a/src/call.py
+++ b/src/call.py
@@ -25,7 +25,11 @@ class Call(Executor):
self.analyse_first_element_called(self.get_code(clean_pipe = True))
#It's important this is last
#self.condition = Condition(self)
-
+
+ def delete(self):
+ self.condition.delete()
+ del self.condition
+
#This method returns all the calls inside a call eg p1(p2(), p3()) returns [p1(p2(), p3()), p2(), p3()]
def get_all_calls(self):
tab = []
diff --git a/src/code_.py b/src/code_.py
index 6e459133f061940f008f5d4373ed30fd80c41629..c03ff903748d78a9658f6d1324215e56626cf607 100644
--- a/src/code_.py
+++ b/src/code_.py
@@ -11,6 +11,10 @@ class Code:
self.initialise()
#self.check_its_nextflow()
+ def delete(self):
+ del self.code
+ del self.code_wo_comments
+
def initialise(self):
#I do this just to avoid out of file problems later on
diff --git a/src/graph.py b/src/graph.py
index ef0caf11ff6e6592b77abae6af3593e26af3106f..bc0afd123bf2a7a0583ca7f2e6868d264471618f 100644
--- a/src/graph.py
+++ b/src/graph.py
@@ -15,9 +15,10 @@ def get_object(address):
class Graph():
def __init__(self, workflow):
self.workflow = workflow
- self.full_dico = workflow.get_structure()
- with open(f"{self.get_output_dir()}/graphs/specification_graph.json", 'w') as output_file :
- json.dump(self.full_dico, output_file, indent=4)
+ self.full_dico = {}
+ #self.full_dico = workflow.get_structure()
+ #with open(f"{self.get_output_dir()}/graphs/specification_graph.json", 'w') as output_file :
+ # json.dump(self.full_dico, output_file, indent=4)
#This dico give for the nodes its sister nodes
self.link_dico = None
#Dico to graph without operations
@@ -36,6 +37,10 @@ class Graph():
def initialise(self, processes_2_remove = []):
if(not self.is_initialised()):
+ self.initialised = True
+ self.full_dico = self.workflow.get_structure()
+ with open(f"{self.get_output_dir()}/graphs/specification_graph.json", 'w') as output_file :
+ json.dump(self.full_dico, output_file, indent=4)
def get_node_id(dico, process):
for node in dico["nodes"]:
if(node['name']==process):
@@ -83,7 +88,7 @@ class Graph():
self.dico_flattened["edges"] = []
#This will stay empty -> it's just so we can use the same function
self.dico_flattened["subworkflows"] = []
- self.initialised = True
+
def is_initialised(self):
return self.initialised
diff --git a/src/main.py b/src/main.py
index 9b2d0a9b7eb666cc275ae3fc60022a65676c8877..2e2551b03f778392e1fcc6087293ebe868f1aa4f 100644
--- a/src/main.py
+++ b/src/main.py
@@ -73,9 +73,7 @@ class Main(Nextflow_Building_Blocks):
#Check that includes are not defined in the main or subworkflows
self.check_includes()
-
self.root = Root(code=self.get_code(), origin=self, modules_defined=self.modules_defined)
-
self.root.initialise()
diff --git a/src/nextflow_building_blocks.py b/src/nextflow_building_blocks.py
index cf683ff77e19c08e4755d90f3e2a60ba6c445767..993e58505de0404d9c28a03dd1041c6681489a50 100644
--- a/src/nextflow_building_blocks.py
+++ b/src/nextflow_building_blocks.py
@@ -14,6 +14,10 @@ class Nextflow_Building_Blocks:
def __init__(self, code):
self.code = Code(code = code, origin = self)
+ def delete(self):
+ self.code.delete()
+ del self.code
+
diff --git a/src/nextflow_file.py b/src/nextflow_file.py
index d62b04dc1ac6c68003ad09e8172754af06922e1d..719cb961e8bc54a4360cb5e90eeb3fe55fc1477a 100644
--- a/src/nextflow_file.py
+++ b/src/nextflow_file.py
@@ -73,7 +73,9 @@ class Nextflow_File(Nextflow_Building_Blocks):
for p in self.processes:
DSL = p.which_DSL()
if(DSL=="DSL1"):
+ self.processes = []
return DSL
+ self.processes = []
return DSL
def get_workflow(self):
@@ -299,3 +301,19 @@ class Nextflow_File(Nextflow_Building_Blocks):
#for sub in self.subworkflows:
# sub.initialise()
# indice+=1
+ elif(self.get_DSL()=="DSL1"):
+ if(self.workflow.get_display_info_bool()):
+ print(f"Analysing -> '{self.get_file_address()}'")
+ from .main import Main
+ #Extarct Processes
+ self.extract_processes()
+ print(len(self.processes))
+ code = self.get_code()
+ #Replacing the processes defined with their identifiers -> this is to simplifly the analysis with the conditions
+ for process in self.processes:
+ code = code.replace(process.get_code(), f"process: {str(process)}")
+ self.main = Main(code= code, nextflow_file=self)
+ self.main.initialise()
+
+ else:
+ raise Exception("This shouldn't happen")
diff --git a/src/operation.py b/src/operation.py
index 29d383f12fab3ba81fedae2199bf29dd7b12c7f6..77356940cf8dd9cc96de1c19a9d05b1c654ef989 100644
--- a/src/operation.py
+++ b/src/operation.py
@@ -191,7 +191,7 @@ class Operation(Executor):
from .channel import Channel
#Case it's a call and it's been replaced
if(re.fullmatch(constant.CALL_ID, name)):
- self.gives.append(self.calls[name])
+ self.add_element_gives(self.calls[name])
raise Exception("This shoudn't happen! -> a call is taking a value")
else:
@@ -216,7 +216,7 @@ class Operation(Executor):
channels = [channel]
for channel in channels:
- self.gives.append(channel)
+ self.add_element_gives(channel)
#channel.initialise()
channel.add_source(self)
diff --git a/src/process.py b/src/process.py
index 5c0cdf489730afb8c857adb176bff7914ef5dc8a..e717fe84b02b048c9109155602c7ce7d23371132 100644
--- a/src/process.py
+++ b/src/process.py
@@ -14,12 +14,15 @@ class Process(Nextflow_Building_Blocks):
def __init__(self, code, nextflow_file):
self.nextflow_file = nextflow_file
self.code = Code(code, origin = self)
+ #Origin is only used in the case DSL1
+ self.origin = None
self.name = ""
self.alias = ""
self.printed_name = ""
self.inputs = []
self.raw_input_names = []#This is used to convert DSL1 workflows to DSL2
self.outputs = []
+ self.outputs_per_line = []
self.input_code = ""
self.output_code = ""
@@ -51,6 +54,12 @@ class Process(Nextflow_Building_Blocks):
self.number_times_copied += 1
return process, num
+ def set_origin(self, thing):
+ if(self.nextflow_file.get_DSL()=="DSL1"):
+ self.origin = thing
+ else:
+ raise Exception("This shouldn't happen")
+
def add_to_emits(self, emit):
self.later_emits.append(emit)
@@ -226,16 +235,21 @@ class Process(Nextflow_Building_Blocks):
code = re.sub(constant.JUMP_DOT, '.', code)
def add_channel(name):
- from .channel import Channel
- input = Channel(name=name, origin=self.origin)
- if(not self.origin.check_in_channels(input)):
+ channels = self.origin.get_channels_from_name_same_level(name)
+ channels += self.origin.get_channels_from_name_above_level(name)
+ channels += self.origin.get_channels_from_name_inside_level(name)
+ channels += self.origin.get_channels_from_name_other_blocks_on_same_level(name)
+ if(len(channels)==0):
+ from .channel import Channel
+ input = Channel(name=name, origin=self.origin)
self.origin.add_channel(input)
input.add_sink(self)
self.inputs.append(input)
else:
- input = self.origin.get_channel_from_name(name)
- self.inputs.append(input)
- input.add_sink(self)
+ for ch in channels:
+ self.inputs.append(ch)
+ ch.add_sink(self)
+
for line in code.split("\n"):
@@ -333,18 +347,22 @@ class Process(Nextflow_Building_Blocks):
code = self.get_output_code()
code = remove_jumps_inbetween_parentheses(code)
code = remove_jumps_inbetween_curlies(code)
+
def add_channel(name):
- from .channel import Channel
- output = Channel(name=name, origin=self.origin)
- if(not self.origin.check_in_channels(output)):
+ channels = self.origin.get_channels_from_name_same_level(name)
+ channels += self.origin.get_channels_from_name_above_level(name)
+ channels += self.origin.get_channels_from_name_inside_level(name)
+ channels += self.origin.get_channels_from_name_other_blocks_on_same_level(name)
+ if(len(channels)==0):
+ from .channel import Channel
+ output = Channel(name=name, origin=self.origin)
self.origin.add_channel(output)
output.add_source(self)
self.outputs.append(output)
else:
- output = self.origin.get_channel_from_name(outputs[i].strip())
- self.outputs.append(output)
- output.add_source(self)
-
+ for ch in channels:
+ self.outputs.append(ch)
+ ch.add_source(self)
pattern =constant.INTO_2
for match in re.finditer(pattern, code):
diff --git a/src/root.py b/src/root.py
index bd202ced0760582157abd04a3631c1b750e3b0a5..fd4c755b27103cdef355d4d5164b09ff0513c7ad 100644
--- a/src/root.py
+++ b/src/root.py
@@ -18,6 +18,7 @@ class Root(Nextflow_Building_Blocks):
self.modules_defined = modules_defined
self.elements_being_called = []
self.channels = subworkflow_inputs
+ self.defined_processes = []
#############
@@ -219,12 +220,21 @@ class Root(Nextflow_Building_Blocks):
# c.get_first_element_called().root.get_all_calls(calls = calls)
-
-
-
-
-
+ #############
+ # PROCESSES
+ #############
+ def extract_defined_processes(self):
+ code = self.get_code()
+ #For each block -> remove its code
+ for b in self.blocks:
+ code = code.replace(b.get_code(), "")
+ for match in re.finditer(r"\<src\.process\.Process object at \w+\>", code):
+ for process in self.modules_defined:
+ if(str(process)==match.group(0)):
+ process.set_origin(self)
+ self.defined_processes.append(process)
+
def initialise(self):
#Define the blocks
@@ -244,6 +254,9 @@ class Root(Nextflow_Building_Blocks):
self.extract_executors()
+
+ #Case DSL1 -> need to extract the processes which have been defined but rplaced in the code
+ self.extract_defined_processes()
#This is to get the order of execution
code = self.get_code()
@@ -261,6 +274,17 @@ class Root(Nextflow_Building_Blocks):
block_code = block_code[:-1]
if(not found):
raise Exception("This shouldn't happen")
+
+ for process in self.defined_processes:
+ found = False
+ pos = code.find(str(process))
+ if(pos!=-1):
+ position_2_thing_2_analyse[pos] = process
+ found = True
+ if(not found):
+ raise Exception("This shouldn't happen")
+
+
for e in self.executors:
e_code = e.get_code()
found = False
@@ -273,7 +297,8 @@ class Root(Nextflow_Building_Blocks):
else:
e_code = e_code[:-1]
if(not found):
- raise Exception("This shouldn't happen")
+ raise Exception("This shouldn't happen")
+
sorted_position_2_thing_2_analyse = dict(sorted(position_2_thing_2_analyse.items()))
for key in sorted_position_2_thing_2_analyse:
@@ -586,6 +611,17 @@ class Root(Nextflow_Building_Blocks):
self.executors.remove(e)
def get_structure(self, dico):
+ #This only for DSL1 workflows
+ if(self.origin.get_DSL()=="DSL1"):
+ for process in self.defined_processes:
+ process.get_structure(dico)
+ for channel in self.channels:
+ for sink in channel.get_sink():
+ #If the sink an operation then the edge has already been added in the get_structure method for the operation
+ if(sink.get_type()=="Process"):
+ channel.get_structure(dico, sink)
+
+
for block in self.blocks:
block.get_structure(dico)
for e in self.executors:
diff --git a/src/workflow.py b/src/workflow.py
index 280392ce4fc92ac44c2192af31c9542ba48da0ed..21ddda5ecd1cc93f2f5beb1c87067fc63610f406 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -163,11 +163,13 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
dico['subworkflows'] = {}
if(self.get_DSL() == "DSL1"):
- return self.get_structure_DSL1(dico=dico)
+ main = self.get_workflow_main()
+ if(main!=None):
+ return main.get_structure(dico)
elif(self.get_DSL() == "DSL2"):
main = self.get_workflow_main()
if(main!=None):
- return self.get_workflow_main().get_structure(dico)
+ return main.get_structure(dico)
else:
return dico
#return self.get_structure_DSL2(dico=dico, start = True)