From 30ac8ea5bc4802176a51e06dca640875abadbbd1 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Wed, 23 Apr 2025 10:47:26 +0200
Subject: [PATCH] Update the extraction of the tools in processes
---
src/outils.py | 33 +++++++++++++++++++--------------
1 file changed, 19 insertions(+), 14 deletions(-)
diff --git a/src/outils.py b/src/outils.py
index a4da11a..6d23850 100644
--- a/src/outils.py
+++ b/src/outils.py
@@ -1565,20 +1565,25 @@ def extract_tools(script, extract_general_tools = False):
command = command[:-1]
if(command[0]=="&"):
command = command[1:]
- test_apptainer = True
- #In the case the command is "var = ..." we don't run it
- for match in re.finditer(r"\w+\s*=", command):
- if(match.span(0)[0]==0):
- test_apptainer = False
- #Running the command in the empty environment
- if(test_apptainer):
- apptainer_command = f"apptainer exec ../ressources/empty.sif {command} >> output.txt 2>&1"
- f = open("apptainer_script.sh", "w")
- f.write(apptainer_command)
- f.close()
- os.system(f"chmod +x apptainer_script.sh")
- #apptainer pull empty.sif docker://cfgarden/empty
- os.system(f"./apptainer_script.sh >> .out 2>&1 && rm -rf .out")
+ for c in command.split(";"):
+ c = c.strip()
+ test_apptainer = True
+ if(c[:len("do ")]=="do "):
+ c = c[len("do "):]
+ c = c.strip()
+ #In the case the command is "var = ..." we don't run it
+ for match in re.finditer(r"\w+\s*=", c):
+ if(match.span(0)[0]==0):
+ test_apptainer = False
+ #Running the command in the empty environment
+ if(test_apptainer):
+ apptainer_command = f"apptainer exec ../ressources/empty.sif {c} >> output.txt 2>&1"
+ f = open("apptainer_script.sh", "w")
+ f.write(apptainer_command)
+ f.close()
+ os.system(f"chmod +x apptainer_script.sh")
+ #apptainer pull empty.sif docker://cfgarden/empty
+ os.system(f"./apptainer_script.sh >> .out 2>&1 && rm -rf .out")
#Parsing the error to extarct the tool
--
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