Fix harmful shell injection vulnerability in mkconcore.py by GREENRAT-K405 · Pull Request #212 · ControlCore-Project/concore

GREENRAT-K405 · 2026-02-05T19:15:32Z

Changes made:

POSIX/docker: Implemented shlex.quote() for all user-controlled inputs in generated shell scripts.
for windows: Applied strict double-quoting ("{var}") to prevents argument splitting and basic injection attacks in generated .bat files. (since shlex doesn't work for windows, this had to be done manually)
Introduced a safe_name() helper function that strictly validates all node and edge labels from the GraphML file at ingestion time.

Impacts:

This should prevent path traversal characters (/, ) and shell metacharacters (&, |, ;, $, etc.).
This prevents malicious GraphML files from writing outside the output directory or executing arbitrary commands during build/run time

This fixes #194

Copilot

Pull request overview

This pull request addresses shell injection vulnerabilities in mkconcore.py by adding input validation and shell escaping mechanisms. The PR introduces a safe_name() validation function to block dangerous characters at GraphML ingestion time, applies shlex.quote() for POSIX shell escaping, and implements double-quoting for Windows batch files.

Changes:

Added input validation via safe_name() function with regex-based character blocking
Implemented shlex.quote() for user-controlled inputs in POSIX/Docker shell scripts
Applied double-quoting for Windows batch file generation to prevent argument splitting

Comments suppressed due to low confidence (14)

mkconcore.py:180

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    funlock = open("unlock", "w") # 12/4/21

mkconcore.py:178

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    fclear = open("clear", "w")

mkconcore.py:168

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    fclear = open("clear.bat", "w")

mkconcore.py:167

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    fstop = open("stop.bat", "w")  #3/27/21

mkconcore.py:176

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    fdebug = open("debug", "w")

mkconcore.py:169

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    fmaxtime = open("maxtime.bat", "w") # 9/12/21

mkconcore.py:179

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    fmaxtime = open("maxtime", "w") # 9/12/21

mkconcore.py:170

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    funlock = open("unlock.bat", "w") # 12/4/21

mkconcore.py:181

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    fparams = open("params", "w") # 9/18/22

mkconcore.py:165

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    frun = open("run.bat", "w")

mkconcore.py:177

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    fstop = open("stop", "w")  #3/27/21

mkconcore.py:166

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    fdebug = open("debug.bat", "w")

mkconcore.py:171

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    fparams = open("params.bat", "w") # 9/18/22

mkconcore.py:175

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    frun = open("run", "w")

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

Copilot · 2026-02-05T19:25:02Z

mkconcore.py

-                    fdebug.write('osascript -e "tell application \\"Terminal\\" to do script \\"cd \\\\\\"$concorewd/' + containername + '\\\\\\"; ./' + sourcecode + ' ' + MCRPATH + '\\"" \n')
+                    fdebug.write('osascript -e "tell application \\"Terminal\\" to do script \\"cd \\\\\\"$concorewd/' + safe_container + '\\\\\\"; ./' + safe_source + ' ' + MCRPATH + '\\"" \n')

            elif langext == "m":    #3/23/21


Potential command injection in eval command construction: The safe_eval_cmd is constructed as shlex.quote(f"run('{sourcecode}')"), which means if sourcecode contains a single quote, the resulting MATLAB/Octave command could be malformed or exploitable. For example, if sourcecode is "test'); system('evil", the eval command becomes "run('test'); system('evil')". While shlex.quote() will escape the outer shell layer, the inner MATLAB/Octave eval still executes the command. Consider validating that sourcecode doesn't contain quotes, or use a safer parameter passing mechanism.

Suggested change

elif langext == "m": #3/23/21

elif langext == "m": #3/23/21

# validate MATLAB/Octave source filename to prevent injection in run('...'):

# allow only common filename characters (no quotes, semicolons, or whitespace)

if not re.match(r'^[A-Za-z0-9_./\\-]+$', sourcecode):

raise ValueError("Invalid MATLAB source file name: {!r}".format(sourcecode))

Copilot · 2026-02-05T19:25:02Z

mkconcore.py

+    #blocks path traversal (/, \\) and shell metacharacters (*, ?, <, >, |, ;, &, $, `)
+    if re.search(r'[\\/:*?"<>|;&`$]', value):


Incomplete validation regex: While newlines are replaced before validation (line 217), the regex pattern doesn't block all potentially dangerous characters. Consider adding:

Null byte (\x00) which could truncate paths in C-based programs

Other control characters (tabs are replaced, but other control chars are not)

Parentheses which could be problematic in some shell contexts
Note that single quotes are missing from the regex (see separate comment), which is the most critical omission.

Suggested change

#blocks path traversal (/, \\) and shell metacharacters (*, ?, <, >, |, ;, &, $, `)

if re.search(r'[\\/:*?"<>|;&`$]', value):

# blocks path traversal (/, \\), control chars, and shell metacharacters

if re.search(r'[\x00-\x1F\x7F\\/:*?"<>|;&`$\'()]', value):

Copilot · 2026-02-05T19:25:03Z

mkconcore.py

                if ubuntu:
                    fdebug.write('concorewd="$(pwd)"\n')
-                    fdebug.write('xterm -e bash -c "cd \\"$concorewd/' + containername + '\\"; ./' + sourcecode + ' ' + MCRPATH + '; bash" &\n')
+                    fdebug.write('xterm -e bash -c "cd \\"$concorewd/' + safe_container + '\\"; ./' + safe_source + ' ' + MCRPATH + '; bash" &\n')


Shell injection vulnerability: MCRPATH is used without escaping in the xterm command. This creates the same injection risk as in the frun.write() call above.

Copilot · 2026-02-05T19:25:03Z

mkconcore.py

                else:
                    fdebug.write('concorewd="$(pwd)"\n')
-                    fdebug.write('osascript -e "tell application \\"Terminal\\" to do script \\"cd \\\\\\"$concorewd/' + containername + '\\\\\\"; ./' + sourcecode + ' ' + MCRPATH + '\\"" \n')
+                    fdebug.write('osascript -e "tell application \\"Terminal\\" to do script \\"cd \\\\\\"$concorewd/' + safe_container + '\\\\\\"; ./' + safe_source + ' ' + MCRPATH + '\\"" \n')


Shell injection vulnerability: MCRPATH is used without escaping in the osascript command for macOS.

Copilot · 2026-02-05T19:25:03Z

mkconcore.py

            writeedges = volswr[i]
            while writeedges.find(":") != -1: 
-                fclear.write(DOCKEREXE+' volume rm ' +writeedges.split(":")[0].split("-v")[1]+"\n")
+                fclear.write(DOCKEREXE+' volume rm ' +writeedges.split(":")[0].split("-v")[1].strip()+"\n") # Added strip()


Incomplete shell escaping: While .strip() was added to clean whitespace, the volume path extracted from volswr (which contains validated edge labels) is not escaped with shlex.quote(). Although edge labels are validated by safe_name(), defense-in-depth suggests these should still be escaped when used in shell commands.

Copilot · 2026-02-05T19:25:06Z

mkconcore.py

+                    safe_name(container_part, f"Node container name '{container_part}'")
+                    safe_name(source_part, f"Node source file '{source_part}'")
+                else:
+                    safe_name(node_label, f"Node label '{node_label}'")


Input validation inconsistency: The validation logic allows node labels without colons (line 225), but all subsequent code expects node labels to follow the "container:source" format and calls split(':') without error handling. This will cause a ValueError crash if a GraphML file contains a node label without a colon. Either require colons in the validation (reject labels without colons), or handle the ValueError in all the places that use split(':').

Suggested change

safe_name(node_label, f"Node label '{node_label}'")

raise ValueError(

f"Invalid node label '{node_label}': expected format 'container:source' with a ':' separator."

)

Copilot · 2026-02-05T19:25:07Z

mkconcore.py

-            fdebug.write(DOCKEREXE+' run -it --name='+containername+volswr[i]+volsro[i]+" docker-"+dockername+"&\n")
+            # safe_container added to debug line (POSIX)
+            safe_container = shlex.quote(containername) 
+            fdebug.write(DOCKEREXE+' run -it --name='+safe_container+volswr[i]+volsro[i]+" docker-"+dockername+"&\n")


Incomplete escaping for Docker debug script: While safe_container is properly defined with shlex.quote(), the dockername variable (derived from sourcecode.split(".")[0]) is used directly without escaping in the docker run command. Although dockername comes from a validated source, it should be escaped with shlex.quote() for consistency and defense-in-depth.

Suggested change

fdebug.write(DOCKEREXE+' run -it --name='+safe_container+volswr[i]+volsro[i]+" docker-"+dockername+"&\n")

# Quote the full Docker image name for shell safety

safe_image = shlex.quote("docker-" + dockername)

fdebug.write(DOCKEREXE+' run -it --name='+safe_container+volswr[i]+volsro[i]+" "+safe_image+"&\n")

Copilot · 2026-02-05T19:25:07Z

mkconcore.py

                node_label = prefixedgenode + node_label_tag.text
-                nodes_dict[node['id']] = re.sub(r'(\s+|\n)', ' ', node_label)
+                node_label = re.sub(r'(\s+|\n)', ' ', node_label)


Command-line argument used in label prefix without validation: The outdir argument from sys.argv[3] is concatenated into node and edge labels via prefixedgenode without validation. While command-line arguments are typically trusted, this creates an additional injection vector if the script is called by another program with untrusted input. Consider validating outdir with safe_name() or a similar function to ensure it doesn't contain shell metacharacters.

Copilot · 2026-02-05T19:25:07Z

mkconcore.py

            while writeedges.find(":") != -1: 
                funlock.write('sudo docker cp ~/concore.apikey concore:/')
-                funlock.write(writeedges.split(":")[0].split("-v ")[1]+"/concore.apikey\n")
+                funlock.write(writeedges.split(":")[0].split("-v ")[1].strip()+"/concore.apikey\n")


Incomplete shell escaping: Volume path is not escaped with shlex.quote() before being used in the docker cp command.

Suggested change

funlock.write(writeedges.split(":")[0].split("-v ")[1].strip()+"/concore.apikey\n")

volume_path = writeedges.split(":")[0].split("-v ")[1].strip()

safe_dest_path = shlex.quote(volume_path + "/concore.apikey")

funlock.write(safe_dest_path + "\n")

Copilot · 2026-02-05T19:25:07Z

mkconcore.py

-                #    print(DOCKEREXE+' run --name='+containername+volswr[i]+volsro[i]+" docker-"+dockername+' octave  -qf --eval "run('+"'"+sourcecode+"'"+')"'+"&\n")
-                #    frun.write(DOCKEREXE+' run --name='+containername+volswr[i]+volsro[i]+" docker-"+dockername+' octave  -qf --eval "run('+"'"+sourcecode+"'"+')"'+"&\n")
+                # Use safe_container
+                frun.write(DOCKEREXE+' run --name='+safe_container+volswr[i]+volsro[i]+" docker-"+shlex.quote(dockername)+"&\n")


Shell injection vulnerability: Same issue as line 695 - volswr[i] and volsro[i] are concatenated without proper escaping.

GREENRAT-K405 · 2026-02-05T20:27:12Z

This should fix it! (I have considered some essential github copilot suggestions and added them)

GREENRAT-K405 · 2026-02-05T20:29:46Z

@pradeeban, I have fixed the most essential shell injection vulnerabilities, I have tried to keep the core functionality unchanged.

Please do let me know if I am missing out on something.

GREENRAT-K405 added 2 commits February 6, 2026 00:29

fix harmful shell injections from graphml

58fc130

fix harmful shell injections from graphml

83193b5

Copilot AI review requested due to automatic review settings February 5, 2026 19:15

Copilot started reviewing on behalf of GREENRAT-K405 February 5, 2026 19:16 View session

Copilot AI reviewed Feb 5, 2026

View reviewed changes

complete shell escaping

991373c

-            elif langext == "m":    #3/23/21
+            elif langext == "m":    #3/23/21
+                # validate MATLAB/Octave source filename to prevent injection in run('...'):
+                # allow only common filename characters (no quotes, semicolons, or whitespace)
+                if not re.match(r'^[A-Za-z0-9_./\\-]+$', sourcecode):
+                    raise ValueError("Invalid MATLAB source file name: {!r}".format(sourcecode))

		#blocks path traversal (/, \\) and shell metacharacters (*, ?, <, >, \|, ;, &, $, `)
		if re.search(r'[\\/:*?"<>\|;&`$]', value):

-            fdebug.write(DOCKEREXE+' run -it --name='+safe_container+volswr[i]+volsro[i]+" docker-"+dockername+"&\n")
+            # Quote the full Docker image name for shell safety
+            safe_image = shlex.quote("docker-" + dockername)
+            fdebug.write(DOCKEREXE+' run -it --name='+safe_container+volswr[i]+volsro[i]+" "+safe_image+"&\n")

-                funlock.write(writeedges.split(":")[0].split("-v ")[1].strip()+"/concore.apikey\n")
+                volume_path = writeedges.split(":")[0].split("-v ")[1].strip()
+                safe_dest_path = shlex.quote(volume_path + "/concore.apikey")
+                funlock.write(safe_dest_path + "\n")

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GREENRAT-K405 commented Feb 5, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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GREENRAT-K405 commented Feb 5, 2026 •

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GREENRAT-K405 commented Feb 5, 2026 •

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