Move unit tests to their own sub-dir in tests
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Julian Stirling
parent
62b414af3c
commit
d08d4cd325
35 changed files with 6 additions and 7 deletions
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"""Test that the code that talks to the external stitching process acts as expected.
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This does not actually run stitching. Instead it checks that the expected commands are
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generated, and the subprocess calling works as expected.
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"""
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import logging
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import os
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import re
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import time
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from copy import copy
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import pytest
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import labthings_fastapi as lt
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from openflexure_microscope_server.stitching import (
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STITCHING_RESOLUTION,
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BaseStitcher,
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FinalStitcher,
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PreviewStitcher,
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StitcherValidationError,
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)
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from .utilities.lt_test_utils import LabThingsTestEnv
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# A global logger pretending to the logger from a thing
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LOGGER = logging.getLogger("mock-thing_logger")
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FAKE_DIR: list[str] = os.path.join("a", "dir", "that", "is", "fake")
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THIS_DIR: str = os.path.dirname(os.path.realpath(__file__))
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MOCK_STITCHER: str = os.path.join(THIS_DIR, "mock_stitching", "mock-stitch.py")
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def test_base_stitcher():
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"""Test the logic in BaseStitcher.
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Pretty much the only logic in base stitcher is forming a command, and calculating
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the min_overlap from overlap.
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The BaseStitcher can't start as the start method is explicitly NotImplemented.
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"""
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# Overlaps and expected minimum overlap to be in command line argument.
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overlaps = [(0.1, "0.09"), (0.4, "0.36"), (0.8, "0.72")]
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for overlap, min_overlap in overlaps:
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expected_command = [
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"openflexure-stitch",
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"--stitching_mode",
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"all",
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"--minimum_overlap",
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min_overlap,
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"--resize",
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"0.5",
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FAKE_DIR,
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]
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stitcher = BaseStitcher(FAKE_DIR, overlap=overlap, correlation_resize=0.5)
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assert stitcher.command == expected_command
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def test_preview_stitcher_command():
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"""Check preview stitcher command for a specific example."""
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expected_command = [
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"openflexure-stitch",
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"--stitching_mode",
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"preview_stitch",
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"--minimum_overlap",
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"0.09",
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"--resize",
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"0.5",
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FAKE_DIR,
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]
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stitcher = PreviewStitcher(FAKE_DIR, overlap=0.1, correlation_resize=0.5)
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assert stitcher.command == expected_command
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FINAL_EXPECTED_COMMAND = [
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"openflexure-stitch",
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"--stitching_mode",
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"all",
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"--stitch_dzi",
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"--no-stitch_tiff",
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"--tile_size",
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"8192",
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"--minimum_overlap",
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"0.09",
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"--resize",
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"0.5",
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FAKE_DIR,
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]
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def test_final_stitcher_command_defaults(caplog):
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"""Check the FinalStitcher stitches with expected default values.
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It should warn when default values are used as they are a fallback.
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"""
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n_logs = 0
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# Test with no dictionary data and with irrelevant dictionary data.
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with caplog.at_level(logging.WARNING):
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for data_dict in [None, {"irrelevant": "data"}]:
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stitcher = FinalStitcher(FAKE_DIR, logger=LOGGER, scan_data_dict=data_dict)
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# Should log for overlap being None and correlation_resize being None
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n_logs += 2
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assert len(caplog.records) == n_logs
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assert stitcher.command == FINAL_EXPECTED_COMMAND
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def test_final_stitcher_command_tiff(caplog):
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"""Check that the tiff can be requested."""
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# Modify defaults
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expected_command = copy(FINAL_EXPECTED_COMMAND)
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expected_command[4] = "--stitch_tiff"
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stitcher = FinalStitcher(FAKE_DIR, logger=LOGGER, stitch_tiff=True)
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# Should log for overlap being None and correlation_resize being None
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assert len(caplog.records) == 2
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assert stitcher.command == expected_command
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def test_final_stitcher_command_set_val_directly():
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"""Check that values are set as expected when directly input."""
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# Modify defaults
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expected_command = copy(FINAL_EXPECTED_COMMAND)
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expected_command[8] = "0.36"
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expected_command[10] = "0.25"
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# Test with no data dictionary, irrelevant data, and also the wrong data
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# When wrong data is submitted, it should take the directly input data.
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dict_vals = [
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None,
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{"irrelevant": "data"},
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{"overlap": 0.2, "save_resolution": [5, 5]},
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]
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for data_dict in dict_vals:
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stitcher = FinalStitcher(
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FAKE_DIR,
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logger=LOGGER,
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overlap=0.4,
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correlation_resize=0.25,
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scan_data_dict=data_dict,
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)
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assert stitcher.command == expected_command
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def test_final_stitcher_command_set_with_dict():
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"""Check that values are set as expected when set from a ScanData dictionary."""
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# Modify defaults
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expected_command = copy(FINAL_EXPECTED_COMMAND)
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expected_command[8] = "0.36"
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expected_command[10] = "0.25"
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# Check same thing works with a dictionary, resize is calculated from the saved image
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# resolution. Make 4x bigger than STITCHING_RESOLUTION to get 0.25
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resolution = [dim * 4 for dim in STITCHING_RESOLUTION]
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# Check legacy key as well as current one:
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for resolution_key in ["save_resolution", "capture resolution"]:
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stitcher = FinalStitcher(
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FAKE_DIR,
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logger=LOGGER,
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scan_data_dict={"overlap": 0.4, resolution_key: resolution},
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)
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assert stitcher.command == expected_command
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def _validation_error_tester(scan_path, **kwargs):
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"""Check each type of stitcher throws a validation error for the given init args."""
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# If scan_data_dict is in the kwargs only test the scan_data_dict
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if "scan_data_dict" not in kwargs:
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with pytest.raises(StitcherValidationError):
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BaseStitcher(scan_path, **kwargs).command
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with pytest.raises(StitcherValidationError):
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PreviewStitcher(scan_path, **kwargs).command
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with pytest.raises(StitcherValidationError):
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FinalStitcher(scan_path, logger=LOGGER, **kwargs).command
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def test_validation_error():
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"""Test a number of ways to try to inject malicious arguments into the stitcher.
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The stitcher should throw a validation error each attempt.
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"""
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_validation_error_tester("/dir;rm -rf /;", overlap=".2", correlation_resize=".25")
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_validation_error_tester(FAKE_DIR, overlap=".2", correlation_resize=".25;rm -rf /;")
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_validation_error_tester(FAKE_DIR, overlap=".2;rm -rf /;", correlation_resize=".25")
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_validation_error_tester(FAKE_DIR, scan_data_dict={"overlap": ".2;rm -rf /;"})
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def test_extra_arg_validation():
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"""Test that malicious arguments in extra_args also throw validation error.
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Currently extra args do not come from user input. But this makes checks more
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future-proof.
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"""
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stitcher = FinalStitcher(FAKE_DIR, logger=LOGGER)
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stitcher._extra_args = ["&&rm -rf /&&"]
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with pytest.raises(StitcherValidationError):
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stitcher.command
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def test_preview_stitching_command(caplog, mocker):
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"""Check the preview process runs in a background thread and doesn't log."""
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mock_cmd = "python -m mock_command.py"
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mocker.patch("openflexure_microscope_server.stitching.STITCHING_CMD", mock_cmd)
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with caplog.at_level(logging.INFO):
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stitcher = PreviewStitcher(FAKE_DIR, overlap=0.1, correlation_resize=0.5)
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stitcher.start()
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# Should take a second or so to run so will still be running
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assert stitcher.running
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# Can't start another time, instead get a runtime error
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with pytest.raises(RuntimeError):
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stitcher.start()
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# Wait for it to complete
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stitcher.wait()
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# It is now not running
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assert not stitcher.running
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assert len(caplog.records) == 0
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class StitchingTestThing(lt.Thing):
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"""A Thing for running stitching in invocation threads.
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This is needed to check cancellation behaviour.
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"""
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@lt.action
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def run_preview(self):
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"""Run the preview stitcher."""
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stitcher = PreviewStitcher(FAKE_DIR, overlap=0.1, correlation_resize=0.5)
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# Send in the argument HANG to mock-stitch and it just hang for 10s
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stitcher._extra_args = ["HANG"]
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stitcher.start()
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stitcher.wait()
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@lt.action
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def run_final(self):
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"""Run the final stitcher."""
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stitcher = FinalStitcher(FAKE_DIR, logger=self.logger)
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# Send in the argument HANG to mock-stitch and it just hang for 10s
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stitcher.run()
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@pytest.fixture
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def stitching_test_env():
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"""Return a test environment for a server with just StitchingTestThing."""
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with LabThingsTestEnv(things={"stitcher": StitchingTestThing}) as env:
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yield env
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def test_preview_stitching_cancelled(stitching_test_env, mocker):
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"""Check that preview stitch can be cancelled."""
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mock_cmd = f"python {MOCK_STITCHER}"
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mocker.patch("openflexure_microscope_server.stitching.STITCHING_CMD", mock_cmd)
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t_start = time.time()
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# Start the action
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response = stitching_test_env.start_action("stitcher", "run_preview")
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# Sleep long enough for at least 1 log.
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time.sleep(0.5)
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# Cancel using a DELETE request
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stitching_test_env.cancel_action(response)
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invocation_data = stitching_test_env.poll_action(response)
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# If it wasn't cancelled it would hang for 10 s. Here we check the cancel killed
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# it within 2s.
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assert time.time() - t_start < 2
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assert invocation_data["status"] == "cancelled"
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logs = invocation_data["log"]
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assert len(logs) == 1
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assert re.match(r"^Invocation [0-9a-f-]+ was cancelled", logs[0]["message"])
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def test_final_stitching_command(caplog, mocker):
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"""Check the final stitch runs until completion, and print statements are logged."""
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mock_cmd = f"python {MOCK_STITCHER}"
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mocker.patch("openflexure_microscope_server.stitching.STITCHING_CMD", mock_cmd)
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with caplog.at_level(logging.INFO):
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# Input values to prevent logging
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stitcher = FinalStitcher(
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FAKE_DIR, logger=LOGGER, overlap=0.1, correlation_resize=0.5
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)
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# For the final stitcher it will always complete before returning.
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stitcher.run()
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# The mock command logs the inputs (but not the initial command) and the
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# stitcher logs # "Stitching complete" when it ends.
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assert len(caplog.records) == len(FINAL_EXPECTED_COMMAND)
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for i, record in enumerate(caplog.records):
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msg = record.message.strip()
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if i == len(FINAL_EXPECTED_COMMAND) - 1:
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assert msg == "Stitching complete"
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else:
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assert msg == FINAL_EXPECTED_COMMAND[i + 1]
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def test_final_stitching_command_cancelled(stitching_test_env, mocker):
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"""Check that final stitch can be cancelled."""
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mock_cmd = f"python {MOCK_STITCHER}"
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mocker.patch("openflexure_microscope_server.stitching.STITCHING_CMD", mock_cmd)
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# Start the action
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response = stitching_test_env.start_action("stitcher", "run_final")
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# Sleep long enough for at least 1 log.
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time.sleep(0.5)
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# Cancel using a DELETE request
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stitching_test_env.cancel_action(response)
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invocation_data = stitching_test_env.poll_action(response)
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assert invocation_data["status"] == "cancelled"
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logs = invocation_data["log"]
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assert len(logs) < len(FINAL_EXPECTED_COMMAND) + 1
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assert logs[-2]["message"] == "Stitching cancelled by user"
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assert re.match(r"^Invocation [0-9a-f-]+ was cancelled", logs[-1]["message"])
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def test_final_stitching_command_error(caplog, mocker):
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"""Check that ChildProcessError is raised if the final stitch errors."""
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mock_cmd = f"python {MOCK_STITCHER}"
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mocker.patch("openflexure_microscope_server.stitching.STITCHING_CMD", mock_cmd)
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with caplog.at_level(logging.INFO):
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stitcher = FinalStitcher(FAKE_DIR, logger=LOGGER)
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# Send in the argument ERROR to mock-stitch and it will raise an error rather
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# than echo.
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stitcher._extra_args = ["ERROR"]
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with pytest.raises(ChildProcessError):
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stitcher.run()
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