Grades are a hygiene check, not a security guarantee.

MCP, MCP server

cdk_pywrapper

A Python wrapper for the Chemistry Development Kit (CDK), which is written in Java * Primary purpose: * Generate diverse chemical compound identifiers (SMILES, InChI).

Compatibility: Not stated.

Grade B

Minor issues only, no Medium or High. Worth a quick look at the findings below before installing.

Graded by PlugVetRubric v2

Not a guarantee. A hygiene check of the source at the commit shown, not a security audit.

Rescanned at commit b26972e28a1d, unchanged since the check below.

INSTALL_UNPINNED NETWORK_NO_FIXED_HOST SECRETS_PATH_DOTENV PERMISSION_SHELL_DECLARED

Why this grade

  • INSTALL_UNPINNED Low

    Dependencies use a range or git URL with no lockfile.

    requirements.txt, line 1 py4j

  • NETWORK_NO_FIXED_HOST Low

    Makes a network call whose host is not written as a fixed address.

    cdk_pywrapper/chemlib.py, line 827 r = requests.get(url, params=params)

  • SECRETS_PATH_DOTENV Low

    Mentions a .env file.

    .gitignore, line 82 # dotenv

  • PERMISSION_SHELL_DECLARED Note

    Runs shell commands, and the manifest or description says so.

    setup.py, line 64 subprocess.check_call(javac_cmd, shell=True)

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.

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

    Note

    requests shell access. The manifest names this permission.

    PERMISSION_SHELL_DECLARED

    setup.py, line 64

    subprocess.check_call(javac_cmd, shell=True)

    setup.py, line 76

    subprocess.check_call(javac_cmd, shell=True)

    cdk_pywrapper/cdk_pywrapper.py, line 75

    # with subprocess.Popen(['{} aux | {} CDK'.format(ps_path, grep_path)], shell=True, stdout=subprocess.PIPE) as proc:

    Show more

    cdk_pywrapper/cdk_pywrapper.py, line 111

    # subprocess.check_call(["javac -cp '{}:.{}' ../cdk/cdk_bridge.java".format(py4j_path, cdk_path)], shell=True)

    cdk_pywrapper/cdk_pywrapper.py, line 113

    # subprocess.check_call(["javac -cp '{}:{}' ../cdk_pywrapper/cdk/cdk_bridge.java".format(py4j_jar_path,

    cdk_pywrapper/cdk_pywrapper.py, line 117

    # p = subprocess.Popen(['{} -cp {};{};{}\\ CDKBridge'.format(java_path, py4j_jar_path,

    cdk_pywrapper/cdk_pywrapper.py, line 122

    p = subprocess.Popen([java_path +

    cdk_pywrapper/cdk_pywrapper.py, line 131

    p = subprocess.Popen([java_path,

  • Install and update

    Concern

    dependencies are not pinned.

    INSTALL_UNPINNED

    requirements.txt, line 1

    py4j

  • Network

    Concern

    can reach a host that is not written as a fixed address.

    NETWORK_NO_FIXED_HOST

    cdk_pywrapper/chemlib.py, line 827

    r = requests.get(url, params=params)

    cdk_pywrapper/chemlib.py, line 1249

    res = requests.get(url=self.base_url.format(k + '.json'), headers=self.headers).json()

    cdk_pywrapper/chemlib.py, line 1351

    reply = requests.get(url, headers=PubChemMolecule.headers)

    Show more

    cdk_pywrapper/chemlib.py, line 1362

    r = requests.get(cmpnd_url, headers=PubChemMolecule.headers).json()

    cdk_pywrapper/chemlib.py, line 1371

    descr_json = requests.get(url, headers=PubChemMolecule.headers).json()

    cdk_pywrapper/chemlib.py, line 1391

    response = requests.get(url, params=params, headers=PubChemMolecule.headers)

    cdk_pywrapper/chemlib.py, line 1421

    r = requests.get(url, headers=PubChemMolecule.headers).json()

  • Secrets

    Concern

    reads a credential or environment file.

    SECRETS_PATH_DOTENV

    .gitignore, line 82

    # dotenv

  • Agent instructions

    Pass

    No instruction to ignore earlier instructions or to hide a step.

  • Obfuscation

    Pass

    No encoded or minified payload found.

  • Licence

    Pass

    A licence file is present (LICENSE).

  • Maintainer activity

    Note

    the latest commit is more than 365 days old.

    MAINTAINER_STALE

    No file path was stored.

    2025-09-09T23:04:07+02:00

Get the full report on this tool, £49

Note

Hygiene check of commit b26972e28a1d. requests shell access. The manifest names this permission. dependencies are not pinned. can reach a host that is not written as a fixed address. reads a credential or environment file. the latest commit is more than 365 days old.

Date and source

Date checked:

View source

github.com

Commit graded: b26972e28a1df7a1d54041f119eaeb9471b0229b

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Read how this letter is chosen