Codex, Plugin
Codex Surface Atlas
Identify cell-surface targets in a disease state, compare accessible binding sites, and select targets for screening or binder design.
Compatibility: Not stated.
Grade D
Two or more Medium findings, or a High finding. Only try it in a sandbox.
Not a guarantee. A hygiene check of the source at the commit shown, not a security audit.
Rescanned at commit 300ad38651b5, unchanged since the check below.
PERMISSION_SHELL_UNDECLARED NETWORK_HOST_FROM_INPUT
Why this grade
- PERMISSION_SHELL_UNDECLARED Medium
Runs shell commands that the manifest or description does not mention.
scripts/check_distribution.py, line 510
result = subprocess.run(command, cwd=root, env=environment, text=True, - NETWORK_HOST_FROM_INPUT Medium
A file takes a URL or endpoint as input and has no fixed host list.
src/surface_atlas/assets/report/structure-preview.js, line 206
const response = await fetch(url.href, { signal, credentials: '
Any High, or two or more Medium findings, give D. One Medium gives C. Low findings or a security Note give B. Each code names a finding behind the letter.
If you think this grade is wrong, email [email protected] with the entry link and your evidence. We aim to acknowledge within two working days and decide within seven. If we confirm an error, we aim to correct it within 24 hours of confirming it. These are aims, not guarantees.
Grades are a hygiene check of the source at the commit shown, on the date checked, not a security audit or a guarantee. The free directory grades are automated. Before release, a PlugVet engineer reviews every paid report and any grade we hold back, including all F grades, against the source code and the evidence we quote.
What was checked
Plain notes from the hygiene checks.
Permissions
Concern
requests shell access. No manifest field names shell or command execution. can delete files.
PERMISSION_SHELL_UNDECLARED PERMISSION_DELETE_FILES
scripts/check_distribution.py, line 510
result = subprocess.run(command, cwd=root, env=environment, text=True,
scripts/check_repository.py, line 15
top = subprocess.run(['git', 'rev-parse', '--show-toplevel'], cwd=root,
scripts/check_repository.py, line 21
entries = subprocess.run(['git', 'ls-files', '--stage', '-z'], cwd=root,
Show more
scripts/check_repository.py, line 43
diff = subprocess.run(['git', 'diff', '--quiet', '--no-ext-diff', '--'], cwd=root)
scripts/check_repository.py, line 47
staged = subprocess.run(['git', 'cat-file', 'blob', oid], cwd=root,
src/surface_atlas/evidence_intake.py, line 310
shutil.rmtree(inherited_directory)
src/surface_atlas/evidence_intake.py, line 327
shutil.rmtree(stage)
src/surface_atlas/export.py, line 826
shutil.rmtree(temporary, ignore_errors=True)
Install and update
Pass
No install-time script found, and dependencies are pinned or absent.
Network
Serious
accepts a host from input, with no fixed list in this file.
NETWORK_HOST_FROM_INPUT
src/surface_atlas/assets/report/structure-preview.js, line 206
const response = await fetch(url.href, { signal, credentials: '
Secrets
Concern
reads a credential or environment file.
SECRETS_PATH_DOTENV
.gitignore, line 14
# Credentials and machine-local settings
.gitignore, line 15
.env
.gitignore, line 17
!.env.example
Agent instructions
Pass
No instruction to ignore earlier instructions or to hide a step.
Obfuscation
Note
a file was over the read cap and was not fully read.
OBFUSCATION_FILE_OVER_READ_CAP
examples/research-case/media/coordinates/ceacam5-8bw0.cif, line 1
data_8BW0
examples/research-case/media/coordinates/fap-6y0f.cif, line 1
data_6Y0F
examples/research-case/media/coordinates/fap-prepared-receptor.pdb, line 1
ATOM 1 N ASN A 37 11.522 -98.557 91.525 1.00 61.49 N
Show more
examples/research-case/media/coordinates/itgb6-8tcg.cif, line 1
data_8TCG
examples/research-case/media/coordinates/itgb6-prepared-target.pdb, line 1
ATOM 1 N PHE A 1 196.527 176.093 193.646 1.00 72.25 N
Licence
Pass
A licence file is present (LICENSE).
Maintainer activity
Pass
The latest commit is within the last 365 days.
Note
Hygiene check of commit 300ad38651b5. requests shell access. No manifest field names shell or command execution. can delete files. accepts a host from input, with no fixed list in this file. reads a credential or environment file. a file was over the read cap and was not fully read.
Date and source
Date checked:
github.com
Commit graded: 300ad38651b57d6aeaf762c1fbe1ebc0bd816a07
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