From aa312abcb00628b86b03b519dcacfa7564a9fc77 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Wed, 31 Jul 2024 19:12:51 +0200
Subject: [PATCH] Started implementing external script extraction
---
src/nextflow_building_blocks.py | 5 +++++
src/nextflow_file.py | 8 ++++++++
src/process.py | 31 +++++++++++++++++++++++++++++++
src/workflow.py | 10 ++++++++++
4 files changed, 54 insertions(+)
diff --git a/src/nextflow_building_blocks.py b/src/nextflow_building_blocks.py
index 5f8de68..0c60005 100644
--- a/src/nextflow_building_blocks.py
+++ b/src/nextflow_building_blocks.py
@@ -80,6 +80,11 @@ class Nextflow_Building_Blocks:
def get_rocrate_key(self, dico):
return f"{self.get_file_address()[len(dico['temp_directory'])+1:]}#{self.get_name()}"
+ def get_address(self):
+ return self.origin.get_address()
+
+ def get_workflow_address(self):
+ return self.origin.get_workflow_address()
diff --git a/src/nextflow_file.py b/src/nextflow_file.py
index 5eadc6e..4a43c44 100644
--- a/src/nextflow_file.py
+++ b/src/nextflow_file.py
@@ -115,6 +115,13 @@ class Nextflow_File(Nextflow_Building_Blocks):
return self.display_info
else:
return self.origin.get_display_info()
+
+
+ def get_workflow_address(self):
+ if(self.origin==None):
+ return self.workflow.get_workflow_directory()
+ else:
+ return self.origin.get_workflow_address()
@@ -259,6 +266,7 @@ class Nextflow_File(Nextflow_Building_Blocks):
def get_DSL(self):
return self.DSL
+
#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 which_DSL(self):
diff --git a/src/process.py b/src/process.py
index ef3d222..78f39e4 100644
--- a/src/process.py
+++ b/src/process.py
@@ -1,4 +1,5 @@
import re
+import glob
from .code_ import Code
from .nextflow_building_blocks import Nextflow_Building_Blocks
@@ -53,6 +54,36 @@ class Process(Nextflow_Building_Blocks):
return self.tools
+ def get_external_scripts_call(self):
+ code = self.get_script_code()
+ tab = []
+ for match in re.finditer(r"([^\s\\\*]+\.(sh|py|R|r|pl))[^\w]", code):
+ tab.append(match.group(1))
+ return list(set(tab))
+
+ def get_external_scripts_code(self):
+ calls = self.get_external_scripts_call()
+ #workflow_directory = self.origin.get_address()
+ #print(workflow_directory)
+ #import os
+ #print(os.getcwd(), self.origin.get_address(), self.get_workflow_address())
+
+ 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)
+ if(len(file)>1):
+ print(file)
+ print("More than one file found!")
+ #If not we search again
+ if(len(file)==0):
+ file = glob.glob(f'{self.get_workflow_address()}/**/{call}', recursive=True)
+ if(len(file)>1):
+ print(file)
+ print("More than one file found!")
+
+
+
+
#def get_source(self):
# return [self]
diff --git a/src/workflow.py b/src/workflow.py
index c3b6dae..5565d67 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -67,6 +67,7 @@ class Workflow:
output_dir=output_dir,
workflow = self
)
+ self.workflow_directory = '/'.join(file.split('/')[:-1])
self.output_dir = Path(output_dir)
self.rocrate = None
self.name = name
@@ -133,6 +134,15 @@ class Workflow:
"""
return self.address
+
+ def get_workflow_directory(self):
+ """Method that returns the workflow directory
+
+ Keyword arguments:
+
+ """
+ return self.workflow_directory
+
def set_address(self):
"""Method that sets the adress of the workflow main
--
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