diff --git a/src/block.py b/src/block.py index 375341bcdbb1a8e757721cb45014a094037a3820..8d03cfc7b2c9d8a28d278b4c33c96c8a5cd513be 100644 --- a/src/block.py +++ b/src/block.py @@ -7,11 +7,6 @@ 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 1ad4f150602852a84b9de83fc3ed74ac3e3af1db..02d68ebce33b886a9911015dc94cf0cbffd50417 100644 --- a/src/call.py +++ b/src/call.py @@ -26,9 +26,7 @@ class Call(Executor): #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): diff --git a/src/channel.py b/src/channel.py index cf2a68c4013865f8daf121e30e472e823f17bf4a..ca7a9e59c757d5e26e72fc29f9d64167a70be94d 100644 --- a/src/channel.py +++ b/src/channel.py @@ -16,13 +16,14 @@ class Channel(Nextflow_Building_Blocks): def __init__(self, name, origin): self.name = name.strip() self.origin = origin + self.source = [] + self.sink = [] to_call = [] 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) - self.source = [] - self.sink = [] + def get_code(self, get_OG = True): diff --git a/src/code_.py b/src/code_.py index c03ff903748d78a9658f6d1324215e56626cf607..3fd7bd378c367e96cc487d0a74fbbd0f0d940a46 100644 --- a/src/code_.py +++ b/src/code_.py @@ -11,9 +11,6 @@ class Code: self.initialise() #self.check_its_nextflow() - def delete(self): - del self.code - del self.code_wo_comments def initialise(self): diff --git a/src/executor.py b/src/executor.py index cda35319befd895b8bdb6e3afb9bce16e36ece90..f37341a1f73f71bdbe79f5a1bf401f3c93fe8d39 100644 --- a/src/executor.py +++ b/src/executor.py @@ -20,7 +20,7 @@ class Executor(Nextflow_Building_Blocks): def __init__(self, code, origin): self.origin = origin self.code = Code(code = code, origin = self) - self.condition = None + diff --git a/src/main.py b/src/main.py index 2e2551b03f778392e1fcc6087293ebe868f1aa4f..916787520b59cda1e4a5516e8e336fe66a84aa0d 100644 --- a/src/main.py +++ b/src/main.py @@ -73,7 +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 = Root(code=self.get_code(), origin=self, modules_defined=self.modules_defined, subworkflow_inputs = []) self.root.initialise() diff --git a/src/nextflow_building_blocks.py b/src/nextflow_building_blocks.py index 993e58505de0404d9c28a03dd1041c6681489a50..78954c0304ef37d0155c058877f6df70a83e7e6e 100644 --- a/src/nextflow_building_blocks.py +++ b/src/nextflow_building_blocks.py @@ -13,14 +13,7 @@ from .bioflowinsighterror import BioFlowInsightError class Nextflow_Building_Blocks: def __init__(self, code): self.code = Code(code = code, origin = self) - - def delete(self): - self.code.delete() - del self.code - - - - + #--------------------------------- #AUXILIARY METHODS FOR ALL CLASSES #--------------------------------- diff --git a/src/nextflow_file.py b/src/nextflow_file.py index 719cb961e8bc54a4360cb5e90eeb3fe55fc1477a..ba05366767208fb507f337f717cf6c7e6a6b3a26 100644 --- a/src/nextflow_file.py +++ b/src/nextflow_file.py @@ -307,7 +307,6 @@ class Nextflow_File(Nextflow_Building_Blocks): 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: