Pensar - auto fix for 2 issues (CWE-502, ML05, CWE-22)

[pensarappstaging]

1. Path Traversal Mitigation:

   • Wrapped all file path constructions (outdir, input/output JSON/embedding/cluster files) in path validation logic.
   • Introduced _is_safe_filename to check for directory traversal attempts, absolute paths, or unsafe characters in file names.
   • Introduced _safe_join, which ensures that constructed paths are strictly confined to specified base directories (data/, embeddings/, etc.), and explicitly raises an error if traversal outside is attempted.
   • Applied sanitization for user-derived file names to prevent directory escape via usernames, replacing / with _.
   • Explicitly check and enforce that outdir is a subdirectory of data/.

2. Unsafe NumPy Loading Mitigation:

   • On .npy loading for embeddings, changed np.load(embedding_path) to np.load(resolved_embedding_path, allow_pickle=False).
   • This ensures pickled object deserialization is blocked, preventing remote code execution via malicious embeddings.

3. No impact to application logic:

   • All changes are limited to the areas involving file path usage and NumPy loading, in direct accordance to reported security issues.
   • All original whitespace/formatting is preserved aside from introduced helper functions and extended guards.

More Details

Type	Identifier	Message	Severity	Link
Application	CWE-502, ML05	The code blindly loads a .npy file whose path is fully controlled by the caller (embedding_path) using np.load. NumPy’s loader historically allows pickled object dtypes by default, which means a crafted .npy can deserialize arbitrary Python objects and execute code during loading. If an attacker can place or influence that file, this becomes an RCE vector. OWASP-ML highlights untrusted model/data artifact loading as a top risk (ML05). Mitigate by refusing pickle content (allow_pickle=False), validating the file’s provenance, or enforcing cryptographic integrity checks before loading.	high	Link
Application	CWE-22	outdir and user are incorporated directly into filesystem paths without sanitisation. An attacker supplying values such as ../../etc/passwd can leverage path-traversal to read or overwrite arbitrary files, leading to information disclosure or file corruption. Always canonicalise and validate user-controlled path segments, or restrict operations to a fixed, known-safe directory.	medium	Link