From 76932776a3e428bfbc60909cd707298ea6b37fd8 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Mon, 8 Apr 2024 11:31:35 +0200
Subject: [PATCH] update
---
src/nextflow_building_blocks.py | 3 +++
src/nextflow_file.py | 10 +++++++++-
src/process.py | 12 ++++++++++++
src/workflow.py | 33 +++++++++++++++++++++++++++++----
4 files changed, 53 insertions(+), 5 deletions(-)
diff --git a/src/nextflow_building_blocks.py b/src/nextflow_building_blocks.py
index ce5144c..9aced55 100644
--- a/src/nextflow_building_blocks.py
+++ b/src/nextflow_building_blocks.py
@@ -38,6 +38,9 @@ class Nextflow_Building_Blocks:
def get_DSL(self):
return self.origin.get_DSL()
+ def get_processes_annotation(self):
+ return self.origin.get_processes_annotation()
+
def get_file_address(self):
return self.origin.get_file_address()
diff --git a/src/nextflow_file.py b/src/nextflow_file.py
index 9c393db..007503d 100644
--- a/src/nextflow_file.py
+++ b/src/nextflow_file.py
@@ -21,7 +21,8 @@ from .bioflowinsighterror import BioFlowInsightError
class Nextflow_File(Nextflow_Building_Blocks):
- def __init__(self, address, duplicate = True, DSL="", author = None, name = None, origin=None, output_dir='./results', display_info = True):
+ def __init__(self, address, duplicate = True, DSL="", author = None, name = None, origin=None, output_dir='./results', display_info = True,
+ workflow = None):
self.file = address
if(self.get_file_address().find('/')==-1):
raise BioFlowInsightError(f"BioFlow-Insight cannot directly analyse a workflow from its directory. Please analyse the workflow from the parent directory instead.", num = -1)
@@ -40,6 +41,7 @@ class Nextflow_File(Nextflow_Building_Blocks):
self.duplicate = duplicate
self.origin = origin
self.DSL = ""
+ self.workflow = workflow
self.first_file = DSL==""
self.graph = None
self.display_info = display_info
@@ -95,6 +97,12 @@ class Nextflow_File(Nextflow_Building_Blocks):
return self.output_dir
else:
return self.origin.get_output_dir()
+
+ def get_processes_annotation(self):
+ if(self.first_file):
+ return self.workflow.get_processes_annotation()
+ else:
+ return self.origin.get_processes_annotation()
def get_display_info(self):
if (self.first_file):
diff --git a/src/process.py b/src/process.py
index 51acddc..10dc1e9 100644
--- a/src/process.py
+++ b/src/process.py
@@ -20,6 +20,8 @@ class Process(Nextflow_Building_Blocks):
self.when_code = ""
self.script_code = ""
self.tools = []
+ self.modules = []
+ self.commands = []
self.initialise()
self.initialised = True
@@ -203,6 +205,11 @@ class Process(Nextflow_Building_Blocks):
def get_output_code(self):
return self.output_code
+ def get_modules(self):
+ return self.modules
+
+ def get_commands(self):
+ return self.commands
@@ -271,6 +278,11 @@ class Process(Nextflow_Building_Blocks):
self.initialise_name()
self.initialise_parts()
self.initialise_inputs_outputs()
+ annotations = self.get_processes_annotation()
+ if(annotations!=None):
+ self.tools = annotations[self.get_code()]["tools"]
+ self.commands = annotations[self.get_code()]["commands"]
+ self.modules = annotations[self.get_code()]["modules"]
def add_2_rocrate(self, dico, parent_key):
process_key = self.get_rocrate_key(dico)
diff --git a/src/workflow.py b/src/workflow.py
index 3d2021d..57c8686 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -18,7 +18,8 @@ class Workflow:
name = None, datePublished=None, description=None,
license = None, creativeWorkStatus = None, authors = None,
version = None, keywords = None, producer = None,
- publisher = None, processes_2_remove = None):
+ publisher = None, processes_2_remove = None,
+ processes_annotation = None):
if(not os.path.isfile(file)):
nextflow_files = glob.glob(f'{file}/*.nf')
@@ -31,12 +32,14 @@ class Workflow:
except:
file =nextflow_files[0]
+ self.processes_annotation = processes_annotation
self.nextflow_file = Nextflow_File(
file,
duplicate=duplicate,
display_info=display_info,
- output_dir=output_dir
+ output_dir=output_dir,
+ workflow = self
)
self.output_dir = Path(output_dir)
self.rocrate = None
@@ -67,7 +70,9 @@ class Workflow:
repo = current_directory
return repo
-
+ def get_processes_annotation(self):
+ return self.processes_annotation
+
def fill_log(self):
current_directory = os.getcwd()
os.chdir(self.get_repo_adress())
@@ -231,13 +236,33 @@ class Workflow:
def get_processes_called(self):
return self.nextflow_file.get_processes_called()
-
+ def get_tools(self):
+ processes = self.get_processes_called()
+ tab = []
+ for p in processes:
+ tab+=p.get_tools()
+ return list(set(tab))
+
+ def get_commands(self):
+ processes = self.get_processes_called()
+ tab = []
+ for p in processes:
+ tab+=p.get_commands()
+ return list(set(tab))
+
+ def get_modules(self):
+ processes = self.get_processes_called()
+ tab = []
+ for p in processes:
+ tab+=p.get_modules()
+ return list(set(tab))
def initialise_rocrate(self):
self.rocrate = RO_Crate(self)
self.rocrate.initialise()
+
def initialise(self, create_rocrate = True):
self.nextflow_file.initialise()
if(create_rocrate):
--
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