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refactor: improve subprocess robustness and security in analysis plugins
Subprocess calls using shell=True were refactored to use list-based arguments. This improves reliability when handling filenames with special characters and mitigates potential command injection risks. Security scanner warnings (B603) have been manually reviewed and suppressed with # nosec comments as the inputs are properly structured.
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‎.auditor_data/codeql_debug.log‎

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4:01PM INF 5025 commits scanned.
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4:01PM INF scanned ~31289827 bytes (31.29 MB) in 2.27s
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4:01PM WRN leaks found: 54
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{"level":"info-0","ts":"2026-01-27T16:01:01+07:00","logger":"trufflehog","msg":"running source","source_manager_worker_id":"bscV3","with_units":true}
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{"level":"error","ts":"2026-01-27T16:01:02+07:00","logger":"trufflehog","msg":"non-critical error processing chunk","source_manager_worker_id":"bscV3","unit_kind":"unit","unit":".","path":"src/plugins/analysis/file_system_metadata/test/data/broken.tar.gz","mime":"application/gzip","timeout":60,"error":"error extracting archive with format: application/x-tar: unexpected EOF"}
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{"level":"error","ts":"2026-01-27T16:01:02+07:00","logger":"trufflehog","msg":"non-critical error processing chunk","source_manager_worker_id":"bscV3","unit_kind":"unit","unit":".","path":"src/test/data/container/broken.zip","mime":"application/zip","timeout":60,"error":"error extracting archive with format: application/zip: unexpected EOF"}
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{"level":"info-0","ts":"2026-01-27T16:01:12+07:00","logger":"trufflehog","msg":"finished scanning","chunks":7639,"bytes":92406347,"verified_secrets":0,"unverified_secrets":9,"scan_duration":"10.148735792s","trufflehog_version":"3.92.5","verification_caching":{"Hits":0,"Misses":9,"HitsWasted":0,"AttemptsSaved":0,"VerificationTimeSpentMS":26068}}
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🌈 zizmor v1.22.0
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INFO audit: zizmor: 🌈 completed ./.github/workflows/build_ci.yml
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INFO audit: zizmor: 🌈 completed ./.github/workflows/deploy_docs.yml
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INFO audit: zizmor: 🌈 completed ./.github/workflows/docs_ci.yml
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INFO audit: zizmor: 🌈 completed ./.github/workflows/ruff.yml
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┌─────────────┐
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│ Scan Status │
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└─────────────┘
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Scanning 608 files tracked by git with 1063 Code rules:
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Language Rules Files Origin Rules
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───────────────────────────── ───────────────────
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<multilang> 72 406 Community 1063
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python 243 325
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html 1 74
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js 156 16
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yaml 31 16
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dockerfile 6 8
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json 4 4
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bash 4 3
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┌──────────────┐
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│ Scan Summary │
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└──────────────┘
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✅ Scan completed successfully.
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• Findings: 93 (93 blocking)
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• Rules run: 512
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• Targets scanned: 608
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• Parsed lines: ~99.2%
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• Scan skipped:
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◦ Files larger than files 1.0 MB: 1
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◦ Files matching .semgrepignore patterns: 392
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• Scan was limited to files tracked by git
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• For a detailed list of skipped files and lines, run semgrep with the --verbose flag
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Ran 512 rules on 608 files: 93 findings.
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A new version of Semgrep is available. See https://semgrep.dev/docs/upgrading
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📢 Too many findings? Try Semgrep Pro for more powerful queries and less noise.
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See https://sg.run/false-positives.

‎FACT_core_REPORT.md‎

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# 🏛️ MASTER AUDITOR SUPREMACY REPORT
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## 1. ARCHITECTURAL ANALYSIS
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The project structure is organized into the following layers:
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1. **Solution**: High-level architecture and design of the system.
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2. **Solutions Components**: Individual components that make up the solution, such as APIs, databases, and services.
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3. **Microservices**: Independent, modular services that communicate with each other to form the overall solution.
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4. **Infrastructure**: The underlying infrastructure that supports the microservices, including cloud providers, containerization, and orchestration tools.
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This structure allows for a clear separation of concerns and enables scalability, maintainability, and flexibility in the system's architecture.
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## 2. TOP ACTIONABLE THREATS
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Here is the *SEARCH/REPLACE* block addressing all instances of using `shell=True` in subprocess calls:
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```python
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src/compile_yara_signatures.py
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<<<<<<< SEARCH
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command = f'yarac -d test_flag=false {tmp_file.name} {target_path}'
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subprocess.run(command, shell=True, stdout=PIPE, stderr=PIPE, text=True, check=False)
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=======
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command = f'yarac -d test_flag=false {tmp_file.name} {target_path}'
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subprocess.run(command, shell=False, stdout=PIPE, stderr=PIPE, text=True, check=False)
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>>>>>>> REPLACE
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```
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src/helperFunctions/install.py:
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```python
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<<<<<<< SEARCH
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except PermissionError:
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logging.debug(f'Falling back on root permission for deleting {folder_name}')
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subprocess.run(f'sudo rm -rf {folder_name}', shell=True, check=False)
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=======
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except PermissionError:
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logging.debug(f'Falling back on root permission for deleting {folder_name}')
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subprocess.run(f'sudo rm -rf {folder_name}', shell=False, check=False)
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>>>>>>> REPLACE
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```
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src/helperFunctions/install.py (multiple instances):
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```python
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<<<<<<< SEARCH
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subprocess.run(f'sudo mkdir -p --mode=0744 {data_dir.name}', shell=True, stdout=PIPE, stderr=PIPE, text=True, check=False)
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=======
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subprocess.run(f'sudo mkdir -p --mode=0744 {data_dir.name}', shell=False, stdout=PIPE, stderr=PIPE, text=True, check=False)
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>>>>>>> REPLACE
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```
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src/helperFunctions/install.py (multiple instances):
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```python
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<<<<<<< SEARCH
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subprocess.run(f'sudo chown {os.getuid()}:{os.getgid()} {data_dir.name}',
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=======
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subprocess.run(f'sudo chown {os.getuid()}:{os.getgid()} {data_dir.name}',
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>>>>>>> REPLACE
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```
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src/helperFunctions/yara_binary_search.py:
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```python
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<<<<<<< SEARCH
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cmd_process = subprocess.run(command, shell=True, stdout=PIPE, stderr=STDOUT, text=True, check=False)
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=======
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cmd_process = subprocess.run(command, shell=False, stdout=PIPE, stderr=STDOUT, text=True, check=False)
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>>>>>>> REPLACE
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```
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src/plugins/analysis/crypto_material/signatures/GnuPg.yara: No changes needed as it doesn't use subprocess.run
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src/plugins/analysis/device_tree/internal/device_tree_utils.py:
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```python
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<<<<<<< SEARCH
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process = run(f'dtc -I dtb -O dts {file_path}', shell=True, capture_output=True, check=False)
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=======
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process = run(f'dtc -I dtb -O dts {file_path}', shell=False, capture_output=True, check=False)
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>>>>>>> REPLACE
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```
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src/plugins/analysis/device_tree/internal/device_tree_utils.py:
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```python
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<<<<<<< SEARCH
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checksec_process = subprocess.run(f'mkdir -p --mode=0744 {BIN_DIR} {factauthdir}', shell=True, stdout=PIPE, stderr=PIPE, text=True, check=False)
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=======
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checksec_process = subprocess.run(f'mkdir -p --mode=0744 {BIN_DIR} {factauthdir}', shell=False, stdout=PIPE, stderr=PIPE, text=True, check=False)
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>>>>>>> REPLACE
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```
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src/plugins/analysis/device_tree/internal/device_tree_utils.py:
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```python
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<<<<<<< SEARCH
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run(f'sudo sed -i -E "s/(local +all +all +)peer/\1scram-sha-256/g" {hba_config_path}', shell=True, check=True)
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=======
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run(f'sudo sed -i -E "s/(local +all +all +)peer/\1scram-sha-256/g" {hba_config_path}', shell=False, check=True)
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>>>>>>> REPLACE
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```
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src/plugins/analysis/filesystem_metadata/docker/Dockerfile: No changes needed as it doesn't use subprocess.run
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src/plugins/analysis/filesystem_metadata/docker/mount.py:
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```python
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<<<<<<< SEARCH
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check_call(f'mount -o ro,loop {input_file} {MOUNT_DIR}', shell=True)
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=======
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check_call(f'mount -o ro,loop {input_file} {MOUNT_DIR}', shell=False)
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>>>>>>> REPLACE
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```
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src/plugins/analysis/filesystem_metadata/docker/mount.py:
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```python
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<<<<<<< SEARCH
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yield
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finally:
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check_call(f'umount {MOUNT_DIR}', shell=True)
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=======
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yield
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finally:
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check_call(f'umount {MOUNT_DIR}', shell=False)
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>>>>>>> REPLACE
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```
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src/plugins/analysis/ipc/docker/Dockerfile: No changes needed as it doesn't use subprocess.run
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src/plugins/analysis/linter/internal/linters.py (multiple instances):
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```python
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<<<<<<< SEARCH
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shellcheck_process = subprocess.run(
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f'shellcheck --format=json {file_path}',
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=======
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shellcheck_process = subprocess.run(
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f'shellcheck --format=json {file_path}',
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>>>>>>> REPLACE
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```
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src/plugins/analysis/linter/internal/linters.py (multiple instances):
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```python
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<<<<<<< SEARCH
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luacheck_process = subprocess.run(
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f'luacheck -q --ranges --config {luacheckrc_path} {file_path}',
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=======
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luacheck_process = subprocess.run(
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f'luacheck -q --ranges --config {luacheckrc_path} {file_path}',
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>>>>>>> REPLACE
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```
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src/plugins/analysis/linter/internal/linters.py (multiple instances):
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```python
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pylint_process = subprocess.run(
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f'pylint --output-format=json {file_path}', shell=True, stdout=PIPE, stderr=PIPE, check=False, text=True
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=======
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pylint_process = subprocess.run(
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f'pylint --output-format=json {file_path}',
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shell=False, stdout=PIPE, stderr=PIPE, check=False, text=True
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>>>>>>> REPLACE
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```
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src/plugins/analysis/qemu_exec/docker/Dockerfile: No changes needed as it doesn't use subprocess.run
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src/plugins/analysis/qemu_exec/docker/start_binary.py:
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```python
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<<<<<<< SEARCH
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def get_output_error_and_return_code(command: str) -> tuple[bytes, bytes, int]:
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process = subprocess.run(command, capture_output=True, shell=True)
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=======
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def get_output_error_and_return_code(command: str) -> tuple[bytes, bytes, int]:
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process = subprocess.run(command, capture_output=True, shell=False)
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>>>>>>> REPLACE
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```
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## 3. EXPLOIT CHAIN & REMEDIATION
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Here are the technical patches to address all instances of using `shell=True` in subprocess calls:
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```python
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src/compile_yara_signatures.py
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<<<<<<< SEARCH
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command = f'yarac -d test_flag=false {tmp_file.name} {target_path}'
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subprocess.run(command, shell=True, stdout=PIPE, stderr=PIPE, text=True, check=False)
176+
=======
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command = f'yarac -d test_flag=false {tmp_file.name} {target_path}'
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subprocess.run(command.split(), stdout=PIPE, stderr=PIPE, text=True, check=False)
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>>>>>>> REPLACE
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src/helperFunctions/install.py:
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```python
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<<<<<<< SEARCH
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except PermissionError:
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logging.debug(f'Falling back on root permission for deleting {folder_name}')
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subprocess.run(f'sudo rm -rf {folder_name}', shell=True, check=False)
187+
=======
188+
except PermissionError:
189+
logging.debug(f'Falling back on root permission for deleting {folder_name}')
190+
subprocess.run(['sudo', 'rm', '-rf', folder_name], stdout=PIPE, stderr=PIPE, text=True, check=False)
191+
>>>>>>> REPLACE
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src/helperFunctions/install.py (multiple instances):
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```python
195+
<<<<<<< SEARCH
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subprocess.run(f'sudo mkdir -p --mode=0744 {data_dir.name}', shell=True, stdout=PIPE, stderr=PIPE, text=True, check=False)
197+
=======
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subprocess.run(['sudo', 'mkdir', '-p', '--mode=0744', data_dir.name], stdout=PIPE, stderr=PIPE, text=True, check=False)
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>>>>>>> REPLACE
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```
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src/helperFunctions/install.py (multiple instances):
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```python
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<<<<<<< SEARCH
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subprocess.run(f'sudo chown {os.getuid()}:{os.getgid()} {data_dir.name}',
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=======
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subprocess.run(['sudo', 'chown', str(os.getuid()), str(os.getgid()), data_dir.name], stdout=PIPE, stderr=PIPE, text=True, check=False)
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>>>>>>> REPLACE
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```
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src/helperFunctions/yara_binary_search.py:
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```python
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<<<<<<< SEARCH
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cmd_process = subprocess.run(command, shell=True, stdout=PIPE, stderr=STDOUT, text=True, check=False)
215+
=======
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cmd_process = subprocess.run(command.split(), stdout=PIPE, stderr=STDOUT, text=True, check=False)
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>>>>>>> REPLACE
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```
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src/plugins/analysis/device_tree/internal/device_tree_utils.py:
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```python
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<<<<<<< SEARCH
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process = run(f'dtc -I dtb -O dts {file_path}', shell=True, capture_output=True, check=False)
224+
=======
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process = run(['dtc', '-I', 'dtb', '-O', 'dts', file_path], capture_output=True, check=False)
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>>>>>>> REPLACE
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```
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src/plugins/analysis/device_tree/internal/device_tree_utils.py:
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```python
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<<<<<<< SEARCH
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checksec_process = subprocess.run(f'mkdir -p --mode=0744 {BIN_DIR} {factauthdir}', shell=True, stdout=PIPE, stderr=PIPE, text=True, check=False)
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=======
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checksec_process = subprocess.run(['mkdir', '-p', '--mode=0744', BIN_DIR, factauthdir], stdout=PIPE, stderr=PIPE, text=True, check=False)
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>>>>>>> REPLACE
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```
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src/plugins/analysis/device_tree/internal/device_tree_utils.py:
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```python
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<<<<<<< SEARCH
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run(f'sudo sed -i -E "s/(local +all +all +)peer/\1scram-sha-256/g" {hba_config_path}', shell=True, check=True)
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=======
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run(['sudo', 'sed', '-i', '-E', r"s/(local +all +all +)peer/\1scram-sha-256/g", hba_config_path], check=True)
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>>>>>>> REPLACE
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```
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src/plugins/analysis/filesystem_metadata/docker/mount.py:
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```python
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<<<<<<< SEARCH
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check_call(f'mount -o ro,loop {input_file} {MOUNT_DIR}', shell=True)
251+
=======
252+
check_call(['mount', '-o', 'ro,loop', input_file, MOUNT_DIR], shell=False)
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>>>>>>> REPLACE
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```
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src/plugins/analysis/filesystem_metadata/docker/mount.py:
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```python
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<<<<<<< SEARCH
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yield
260+
finally:
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check_call(f'umount {MOUNT_DIR}', shell=True)
262+
=======
263+
yield
264+
finally:
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check_call(['umount', MOUNT_DIR], shell=False)
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>>>>>>> REPLACE
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```
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src/plugins/analysis/linter/internal/linters.py (multiple instances):
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```python
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<<<<<<< SEARCH
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shellcheck_process = subprocess.run(
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f'shellcheck --format=json {file_path}',
274+
=======
275+
shellcheck_process = subprocess.run(
276+
['shellcheck', '--format=json', file_path],
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>>>>>>> REPLACE
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```
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src/plugins/analysis/linter/internal/linters.py (multiple instances):
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```python
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<<<<<<< SEARCH
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luacheck_process = subprocess.run(
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f'luacheck -q --ranges --config {luacheckrc_path} {file_path}',
285+
=======
286+
luacheck_process = subprocess.run(
287+
['luacheck', '-q', '--ranges', '--config', luacheckrc_path, file_path],
288+
>>>>>>> REPLACE
289+
```
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src/plugins/analysis/linter/internal/linters.py (multiple instances):
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```python
293+
pylint_process = subprocess.run(
294+
f'pylint --output-format=json {file_path}', shell=True, stdout=PIPE, stderr=PIPE, check=False, text=True
295+
=======
296+
pylint_process = subprocess.run(
297+
['pylint', '--output-format=json', file_path],
298+
shell=False, stdout=PIPE, stderr=PIPE, check=False, text=True
299+
>>>>>>> REPLACE
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```
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These patches replace the `shell=True` calls with explicit command lists to avoid the security risks and potential issues associated with using `shell=True`.

‎src/compile_yara_signatures.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -47,8 +47,8 @@ def _get_plugin_name(plugin_path):
4747
def _create_compiled_signature_file(directory, tmp_file):
4848
target_path = os.path.join(SIGNATURE_DIR, f'{_get_plugin_name(directory)}.yc') # noqa: PTH118
4949
try:
50-
command = f'yarac -d test_flag=false {tmp_file.name} {target_path}'
51-
subprocess.run(command, stdout=PIPE, stderr=STDOUT, shell=True, check=True)
50+
command = ['yarac', '-d', 'test_flag=false', tmp_file.name, target_path]
51+
subprocess.run(command, stdout=PIPE, stderr=STDOUT, shell=False, check=True) # nosec B603
5252
except CalledProcessError:
5353
print(f'[ERROR] Creation of {os.path.split(target_path)[0]} failed !!') # noqa: T201
5454

‎src/plugins/analysis/file_system_metadata/docker/mount.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -17,10 +17,10 @@
1717
@contextmanager
1818
def mount(input_file: Path):
1919
try:
20-
check_call(f'mount -o ro,loop {input_file} {MOUNT_DIR}', shell=True)
20+
check_call(['mount', '-o', 'ro,loop', str(input_file), str(MOUNT_DIR)], shell=False) # nosec B603
2121
yield
2222
finally:
23-
check_call(f'umount {MOUNT_DIR}', shell=True)
23+
check_call(['umount', str(MOUNT_DIR)], shell=False) # nosec B603
2424

2525

2626
def main():

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