From 3a0525106ae3d66714ade916df2305862d75650e Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Mon, 14 Apr 2025 10:18:51 +0200
Subject: [PATCH] Added the extraction of the tools funnction to the process
object
---
ressources/empty.sif | Bin 0 -> 40960 bytes
src/outils.py | 245 +++++++++++++++++++++++++++++++++++++++++++
src/process.py | 5 +-
3 files changed, 249 insertions(+), 1 deletion(-)
create mode 100755 ressources/empty.sif
diff --git a/ressources/empty.sif b/ressources/empty.sif
new file mode 100755
index 0000000000000000000000000000000000000000..4195d8ae42fdba5b066423fdb7d4d6c2f8ee9b9c
GIT binary patch
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diff --git a/src/outils.py b/src/outils.py
index ea78ff6..7116f09 100644
--- a/src/outils.py
+++ b/src/outils.py
@@ -1391,5 +1391,250 @@ def remove_empty_conditions_place_anker(code, workflow):
code = code.replace(OG_anker, new_anker)
code = remove_empty_conditions(code)
return code
+
+
+def extract_single_quote(text, start):
+ end = start
+ code= text
+ quote_single = True
+
+ while(quote_single):
+ if(code[end]=="'" and quote_single):
+ if(code[end-1]!="\\" or (code[end-1]=="\\" and code[end-2]=="\\")):
+ quote_single=False
+ end+=1
+ if(end>=len(code)):
+ raise Exception('Unable to extract')
+ return end
+
+def extract_double_quote(text, start):
+ temp_start = start
+ end = start
+ code= text
+ quote_double = True
+
+ while(quote_double):
+ if(code[end]=='"' and quote_double):
+ if(code[end-1]!="\\" or (code[end-1]=="\\" and code[end-2]=="\\")):
+ quote_double=False
+ end+=1
+ if(end>=len(code)):
+ raise Exception('Unable to extract')
+ return end
+
+#This function extracts the tools used in a script by running each line in the bash script
+#in an empty bash envrionment using a singularity image (by doing this with parse the errors
+#and extract the tools)
+def extract_tools(script, extract_general_tools = False):
+ #If we want to extract the general tools we define a list of the general tools 'to remove' from the tools extracted
+ if(extract_general_tools):
+ general_tools = []
+ else:
+ general_tools = ['cd', 'cat', 'sed', 'echo', 'mv', 'mkdir', 'cp', 'awk', 'touch', 'tabix',
+ 'gzip', 'rm', 'bgzip', 'set', 'grep', 'egrep', 'pigz', 'head', 'tar', 'tail',
+ 'gunzip', 'wc', 'ls', 'find', "sort", "uniq", "printf", "ln", "zcat", "which",
+ "eval", "paste", "tr", "gawk", "date", "tee", "trap","base64", 'parallel', 'time',
+ "pwd", "sleep", "ssh", "cpu", "fgrep", "bc", "chmod", "whereis", "conda", "wait",
+ "split", "git", "join", "unzip", "wget", "print", "rev", 'rmdir']
+
+ OG_script = script
+ script = " "+script+" "
+
+ #Detecting cases of none bash environments
+ python = ["#!/usr/bin/env python"]
+ for p in python:
+ if(p in script):
+ return []
+ rscript = ["#!/usr/bin/env Rscript"]
+ for r in rscript:
+ if(r in script):
+ return []
+ perl_script = ['#!/usr/bin/env perl']
+ for p in perl_script:
+ if(p in script):
+ return []
+
+
+ tools = []
+
+ #----------------------------
+ #"CLEANING" the script
+ #----------------------------
+ #Removing the curlies and the elements inside them -> to avoid the errors not recognising the variables
+ searching = True
+ while(searching):
+ searching = False
+ for match in re.finditer(r'\{.+\}', script):
+ start, _ = match.span(0)
+ end = extract_curly(script+"\n\n\n\n", start+1)
+ if(end!=-1):
+ inside_curly = script[start:end]
+ script = script.replace(inside_curly, "")
+ searching = True
+ break
+ #Removing the triple quotes from the script
+ script = re.sub(r"\"\"\"", "\n", script)
+ script = re.sub(r"\'\'\'", "\n", script)
+
+ #Removing elements inside the single quotes
+ searching = True
+ while(searching):
+ searching = False
+ for match in re.finditer(r'\'', script):
+ start, end = match.span(0)
+ end = extract_single_quote(script+"\n\n\n\n", start+1)
+ inside_single_quote = script[start:end]
+ script = script.replace(inside_single_quote, "")
+ searching = True
+ break
+
+ #Removing elements inside the doucle quotes
+ searching = True
+ while(searching):
+ searching = False
+ for match in re.finditer(r'\"', script):
+ start, end = match.span(0)
+ end = extract_double_quote(script+"\n\n\n\n", start+1)
+ inside_double_quote = script[start:end]
+ script = script.replace(inside_double_quote, "")
+ searching = True
+ break
+ script = re.sub(r"\\\$", "", script)
+ script = re.sub(r"\$", "", script)
+ script = re.sub(r"\(", "", script)
+ script = re.sub(r"\)", "", script)
+ script = re.sub(r'\(', "", script)
+ script = re.sub(r'\)', "", script)
+ script = re.sub(r"\n *\<[^\>.]+\>", " ", script)
+ script = re.sub(r"\<", " ", script)
+ script = re.sub(r"\>", " ", script)
+ script = re.sub(r"\&", " ", script)
+ script = re.sub(r"\n\s*\\", " ", script)
+ script = re.sub(r"\s*\\", " ", script)
+ script = re.sub(r" then ", " ", script)
+ #Repalcing xargs by nothing
+ #"xargs" -> is not really a tool in a traditional sense
+ temp = script
+ def replacer(match):
+ return match.group(0).replace(match.group(1), '')
+ for tool in ["xargs"]:
+ script = re.sub(fr"[^\w]({tool})\s", replacer, script)
+
+ #Removing the pipe operators
+ searching = True
+ while(searching):
+ searching = False
+ to_replace = []
+ for command in script.split('\n'):
+ if('|' in command):
+ left, right = command.split('|')[0], '|'.join(command.split('|')[1:])
+ if(left.count('(')==left.count(')') and right.count('(')==right.count(')')):
+ searching = True
+ to_replace.append([command, f"{left}\n{right}"])
+ for r in to_replace:
+ script = script.replace(r[0], r[1], 1)
+
+ OG_path = os.getcwd()
+ #Change working directory to the one of the file
+ os.chdir("/".join((str(__file__).split("/")[:-1])))
+
+ #Get list of files which already exist in folder
+ OG_files = os.listdir()
+
+ #Create empty output.txt file
+ os.system(f"> output.txt")
+ for command in script.split('\n'):
+ command = command.strip()
+ os.system(f"> output.txt")
+ if(command!=""):
+ if(command[-1]==";"):
+ 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")
+
+
+ #Parsing the error to extarct the tool
+ results = open("output.txt").read()
+ #print("*", f"'{results}'")
+ for pattern in [r'FATAL: +\"([^"]+)"', r'FATAL: +stat +([^:]+):']:
+ for match in re.finditer(pattern, results):
+ extarcted = match.group(1).split("/")[-1].strip()
+ #List of things to ignore -> these can be detected for tools -> obviously they are not tools
+ random_things = ['if', 'elif', "else", "done", "fi", 'do', 'for', 'module','then',
+ "def", "{", "}", "end_versions", ":", "stub:", "stub :", "__pycache__",
+ "cut", "source", "export", "[", "]", "$", ",", "case", "esac", "exit",
+ "cli", "e0f", "gnu", "env", "!", "function", "readme.md", "false", "while"]
+ to_add = True
+ for match2 in re.finditer(r"\w+\s*=", extarcted):
+ if(match2.span(0)[0]==0):
+ to_add = False
+ extarcted = extarcted.lower()
+ if(to_add and extarcted not in random_things):
+ #If it's a parameter
+ if(extarcted[0]=="-"):
+ None
+ #If it's a script -> we get of which kind
+ elif(extarcted[-3:]==".py" or extarcted=="python3" or extarcted=="python2"):
+ tools.append("python")
+ elif(extarcted[-2:]==".R" or extarcted[-2:]==".r"):
+ tools.append("r")
+ elif(extarcted[-3:]==".pl"):
+ tools.append("perl")
+ elif(extarcted[-3:]==".jl"):
+ tools.append("julia")
+ elif(extarcted[-3:]==".sh"):
+ #For now the bash script is not considered
+ #tools.append("bash")
+ None
+ else:
+ ex = extarcted.lower().strip()
+ if(ex=="rscript"):
+ tools.append("r")
+ elif(ex=="bash"):
+ None
+ #If the tool extarcted is "template" -> we search for the script used
+ elif(ex=="template"):
+ for extension_search in re.finditer(r'template *[^\/\s]+(\.\w+)', OG_script):
+ extension = extension_search.group(1)
+ if(extension==".py"):
+ tools.append("python")
+ elif(extension==".R" or extension==".r"):
+ tools.append("r")
+ elif(extension==".pl"):
+ tools.append("perl")
+ elif(extension==".jl"):
+ tools.append("julia")
+ elif (ex!="" and len(ex)>1 and ex not in general_tools and ex[-1]!=":" and re.fullmatch(r"\w", ex[0])):
+ tools.append(ex)
+ #If the tool is java -> we search for the jar file in the command
+ if(ex=="java"):
+ for java_search in re.finditer(r'([^\/\s]+)\.jar', command):
+ tools.append(java_search.group(1).lower())
+ tools.remove('java')
+
+ #We remove the remaining files which have been created in the meantime
+ for file in os.listdir():
+ if(file not in OG_files):
+ os.system(f'rm {file}')
+
+ #Change working directory back to the OG one
+ os.chdir(OG_path)
+
+ #Return the tools extarcted
+ return list(set(tools))
diff --git a/src/process.py b/src/process.py
index d73f94f..8d4c181 100644
--- a/src/process.py
+++ b/src/process.py
@@ -5,7 +5,7 @@ import copy
from .code_ import Code
from .condition import Condition
from .nextflow_building_blocks import Nextflow_Building_Blocks
-from .outils import remove_jumps_inbetween_parentheses, remove_jumps_inbetween_curlies, sort_and_filter, get_dico_from_tab_from_id, check_if_element_in_tab_rocrate, get_python_packages, get_R_libraries, get_perl_modules, process_2_DSL2
+from .outils import remove_jumps_inbetween_parentheses, remove_jumps_inbetween_curlies, sort_and_filter, get_dico_from_tab_from_id, check_if_element_in_tab_rocrate, get_python_packages, get_R_libraries, get_perl_modules, process_2_DSL2, extract_tools
from .bioflowinsighterror import BioFlowInsightError
from . import constant
@@ -578,6 +578,9 @@ class Process(Nextflow_Building_Blocks):
# call.append(f"{o.get_code()} = {self.get_name()}.out.{o.get_code()}")
call = "\n".join(call)
return code, call
+
+ def get_tools(self, extract_general_tools = False):
+ return extract_tools(self.get_script_code(), extract_general_tools = extract_general_tools)
--
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