From 8ae5e926c7af4338022b084d00c38d15a47925a8 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Thu, 29 Aug 2024 16:44:55 +0200
Subject: [PATCH] added recursive functionnality for the external script call
---
src/process.py | 45 ++++++++++++++++++++++++++++++++++-----------
1 file changed, 34 insertions(+), 11 deletions(-)
diff --git a/src/process.py b/src/process.py
index d7b0287..6390c1a 100644
--- a/src/process.py
+++ b/src/process.py
@@ -24,6 +24,7 @@ class Process(Nextflow_Building_Blocks):
self.tools = []
self.modules = []
self.commands = []
+ self.external_scripts = [-1]
self.initialise()
self.initialised = True
@@ -55,21 +56,24 @@ class Process(Nextflow_Building_Blocks):
return self.tools
- def get_external_scripts_call(self):
- code = self.get_script_code()
+ def get_external_scripts_call(self, code):
tab = []
- for match in re.finditer(r"([^\s\\\*\{\}\[\]]+\.(sh|py|R|r|pl|rg))[^\w]", code):
- tab.append(match.group(1))
+ for match in re.finditer(r"(\s|\/)([\w\_\-\&]+\/)*([\w\_\-\&]+)\.(sh|py|R|r|pl|rg)", code):
+ tab.append(match.group(0).strip())
return list(set(tab))
- def get_external_scripts_code(self):
- calls = self.get_external_scripts_call()
+ def initialise_external_scripts_code(self, code, extension = "", previously_called = {}):
+ calls = self.get_external_scripts_call(code+'\n')
+
#workflow_directory = self.origin.get_address()
#print(workflow_directory)
#import os
#print(os.getcwd(), self.origin.get_address(), self.get_workflow_address())
scripts = []
+ extensions = []
+ bash_scripts = []
+ tab = []
for call in calls:
#Check first if the file is in the bin
file = glob.glob(f'{self.get_workflow_address()}/bin/**/{call}', recursive=True)
@@ -80,14 +84,32 @@ class Process(Nextflow_Building_Blocks):
file = glob.glob(f'{self.get_workflow_address()}/**/{call}', recursive=True)
if(len(file)>1):
raise BioFlowInsightError(f"More than one script named '{call}' in the workflow source code, don't know which one to use when using the process '{self.get_name()}'", num = 13, origin=self)
-
+
+
for f in file:
- with open(f, 'r') as s:
- scripts.append(s.read())
+ if(f not in previously_called):
+ val = ""
+ with open(f, 'r', encoding='latin-1') as s:
+ #with open(f, 'r') as s:
+ val = s.read()
+ scripts.append(val)
+ previously_called[f] = ""
+ #Recursive Call to get the ones which are being called if the current file is a bash script
+ if(extension not in ["py", "R", "pl", "rg", "r"]):
+ tab += self.initialise_external_scripts_code(val, extension=f.split(".")[-1], previously_called= previously_called)
+ scripts+=tab
- return scripts
+ return list(set(scripts))
+ def get_external_scripts_code(self):
+ if(self.external_scripts!=[-1]):
+ None
+ else:
+ self.external_scripts = self.initialise_external_scripts_code(self.get_script_code())
+ return self.external_scripts
+
+
def get_python_packages_imported_internal_script(self):
packages = []
packages+= get_python_packages(self.get_script_code())
@@ -95,7 +117,8 @@ class Process(Nextflow_Building_Blocks):
def get_python_packages_imported_external_scripts(self):
packages = []
- for s in self.get_external_scripts_code():
+ external_scripts = self.get_external_scripts_code()
+ for s in external_scripts:
packages+= get_python_packages(s)
return packages
--
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