CVE-2025-23410: GMOD Apollo Path Traversal Vulnerability

CVE-2025-23410 Overview

A critical path traversal vulnerability exists in GMOD Apollo, a genome annotation editor. When uploading organism or sequence data via the web interface, GMOD Apollo will unzip and inspect uploaded files without checking for path traversal in supported archive types. This flaw allows an unauthenticated remote attacker to write arbitrary files to arbitrary locations on the server filesystem, potentially leading to full system compromise.

Critical Impact
This path traversal vulnerability allows attackers to write malicious files outside the intended upload directory, enabling remote code execution, system takeover, or data destruction on affected GMOD Apollo installations.

Affected Products

GMOD Apollo (genome annotation editor)
Systems utilizing GMOD Apollo web interface for organism/sequence data uploads

Discovery Timeline

2025-03-05 - CVE CVE-2025-23410 published to NVD
2025-03-05 - Last updated in NVD database

Technical Details for CVE-2025-23410

Vulnerability Analysis

This vulnerability is classified under CWE-23 (Relative Path Traversal). The core issue lies in GMOD Apollo's file upload handling mechanism, which fails to properly validate file paths contained within uploaded archive files (such as ZIP or TAR archives). When a user uploads an archive containing organism or sequence data, the application extracts the contents without sanitizing the file paths within the archive.

An attacker can craft a malicious archive containing files with relative path sequences (such as ../) in their filenames. When the application extracts these files, it writes them to locations outside the intended upload directory. This can be leveraged to overwrite critical system files, inject malicious scripts into web-accessible directories, or place executable files in locations that will be executed by the system.

The vulnerability is particularly severe because it requires no authentication and can be exploited over the network with low attack complexity. Successful exploitation could result in complete compromise of the server's confidentiality, integrity, and availability.

Root Cause

The root cause of this vulnerability is the absence of path validation during archive extraction. The application trusts the file paths embedded within uploaded archives without verifying that extracted files remain within the designated upload directory. This violates the principle of never trusting user-supplied input, especially when that input controls filesystem operations.

Attack Vector

The attack is network-based and requires no user interaction or authentication. An attacker can exploit this vulnerability by:

Crafting a malicious archive file (ZIP, TAR, or other supported format) containing files with path traversal sequences in their names (e.g., ../../var/www/html/shell.php)
Uploading this archive through the GMOD Apollo web interface as organism or sequence data
The application extracts the archive without validating file paths
Malicious files are written to arbitrary locations on the filesystem
The attacker can then access the deployed malicious files to execute code or further compromise the system

This attack technique is commonly known as a "Zip Slip" vulnerability when targeting ZIP archives. The vulnerability allows traversal outside the intended extraction directory, enabling arbitrary file write operations.

Detection Methods for CVE-2025-23410

Indicators of Compromise

Unexpected files appearing outside designated upload directories, particularly in web-accessible paths or system directories
Archive uploads containing suspicious path sequences such as ../, ..\\, or absolute paths
Web shells or unauthorized scripts appearing in web root directories
Unusual file modification timestamps on critical system or application files
Log entries showing file extraction operations writing to unexpected locations

Detection Strategies

Implement web application firewall (WAF) rules to inspect uploaded archives for path traversal sequences before processing
Monitor file system integrity using tools like AIDE or Tripwire to detect unauthorized file modifications
Analyze web server and application logs for unusual upload activity or error messages related to file operations
Deploy endpoint detection solutions to identify suspicious file creation events in sensitive directories

Monitoring Recommendations

Enable verbose logging for file upload and extraction operations in GMOD Apollo
Set up alerts for file creation events in web-accessible directories outside normal upload paths
Monitor network traffic for unusual upload patterns or large archive file transfers
Implement file integrity monitoring on critical system directories and web roots

How to Mitigate CVE-2025-23410

Immediate Actions Required

Restrict access to the GMOD Apollo web interface to trusted networks or users until patching is possible
Implement network-level controls to limit who can upload files to the application
Review file systems for evidence of exploitation, particularly looking for unauthorized files in web-accessible directories
Consider temporarily disabling archive upload functionality if the feature is not critical to operations

Patch Information

Organizations should consult the CISA ICS Advisory ICSA-25-063-07 for official remediation guidance and patch availability. Contact the GMOD Apollo maintainers for the latest security updates and recommended versions.

Workarounds

Deploy a reverse proxy or WAF in front of GMOD Apollo that inspects uploaded archives and rejects any containing path traversal sequences
Implement network segmentation to isolate GMOD Apollo servers from critical infrastructure
Configure the application to run with minimal filesystem permissions, limiting the directories where the application process can write files
Use containerization or sandboxing to restrict the application's filesystem access to a limited scope

bash

# Example: Restrict upload directory permissions
# Ensure the application user cannot write outside designated directories
chmod 755 /var/gmod-apollo/uploads
chown gmod-apollo:gmod-apollo /var/gmod-apollo/uploads

# Example: WAF rule to block archives with path traversal (ModSecurity)
SecRule FILES_TMPNAMES "@rx \.\.(\/|\\)" \
    "id:1001,phase:2,deny,status:403,msg:'Path traversal detected in uploaded archive'"