This sounds like something I have done for work (open-source software dev stuff). In my case, I needed to test an except block raised when an executable file could not be run on a particular OS version. In our testing framework we use pytest and monkeypatch to test things. I've included the relevant bits of code below, along with some explanation about what is happening. I think this is probably what you mean by 'patch the sdk error', and I believe that is probably what you need to do. If anything is unclear, or you have more questions, let me know.
In conftest.py I define pytest fixtures that get used for tests in more than one test file. Here, I mock the scenario I want to test, using monkeypatch to fake the results I want from the parts of the get_version() function I'm not trying to test.
# conftest.py
import subprocess
import shutil
import os
import re
import platform
from pathlib import Path
import pytest
@pytest.fixture
def executable_incompatible_with_os(monkeypatch):
"""
Mocks an executable file that is incompatible with the OS.
(This situation likely only applies to blastall.)
"""
def mock_which(*args, **kwargs):
"""Mock an absolute file path."""
return args[0]
def mock_isfile(*args, **kwargs):
"""Mock a call to `os.path.isfile()`."""
return True
def mock_access(*args, **kwargs):
"""Mock a call to `os.access()`."""
return True
def mock_subprocess(*args, **kwargs):
"""Mock a call to `subprocess.run()` with an incompatible program."""
raise OSError
# Replace calls to existing methods with my mocked versions
monkeypatch.setattr(shutil, "which", mock_which)
monkeypatch.setattr(Path, "is_file", mock_isfile)
monkeypatch.setattr(os.path, "isfile", mock_isfile)
monkeypatch.setattr(os, "access", mock_access)
monkeypatch.setattr(subprocess, "run", mock_subprocess)
In test_aniblastall.py I test parts of aniblastall.py. In this case, I'm testing the behaviour when an OSError is raised; the code that raises the error in the test is in conftest.py. The entire pytest fixture I defined there is passed as a parameter to the test.
# test_aniblastall.py
from pathlib import Path
import unittest
# Test case 4: there is an executable file, but it will not run on the OS
def test_get_version_os_incompatible(executable_incompatible_with_os):
"""Test behaviour when the program can't run on the operating system.
This will happen with newer versions of MacOS."""
test_file_4 = Path("/os/incompatible/blastall")
assert (
aniblastall.get_version(test_file_4)
== f"blastall exists at {test_file_4} but could not be executed"
)
aniblastall.py contains the function the error should be raised from.
# aniblastall.py
import logging
import os
import platform
import re
import shutil
import subprocess
from pathlib import Path
def get_version(blast_exe: Path = pyani_config.BLASTALL_DEFAULT) -> str:
"""
The following circumstances are explicitly reported as strings
- no executable at passed path
- non-executable file at passed path (this includes cases where the user doesn't have execute permissions on the file)
- no version info returned
- executable cannot be run on this OS
"""
logger = logging.getLogger(__name__)
try:
blastall_path = Path(shutil.which(blast_exe)) # type:ignore
except TypeError:
return f"{blast_exe} is not found in $PATH"
if not blastall_path.is_file(): # no executable
return f"No blastall at {blastall_path}"
# This should catch cases when the file can't be executed by the user
if not os.access(blastall_path, os.X_OK): # file exists but not executable
return f"blastall exists at {blastall_path} but not executable"
if platform.system() == "Darwin":
cmdline = [blast_exe, "-version"]
else:
cmdline = [blast_exe]
try:
result = subprocess.run(
cmdline, # type: ignore
shell=False,
stdout=subprocess.PIPE, # type: ignore
stderr=subprocess.PIPE,
check=False, # blastall doesn't return 0
)
except OSError:
logger.warning("blastall executable will not run", exc_info=True)
return f"blastall exists at {blastall_path} but could not be executed"
version = re.search( # type: ignore
r"(?<=blastall\s)[0-9\.]*", str(result.stderr, "utf-8")
).group()
if 0 == len(version.strip()):
return f"blastall exists at {blastall_path} but could not retrieve version"
return f"{platform.system()}_{version} ({blastall_path})"
