Skip to content

test(qupath): drop annotation count assertion from GUI e2e test #726

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We鈥檒l occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
olivermeyer merged 1 commit into from
Sep 25, 2026
Merged

test(qupath): drop annotation count assertion from GUI e2e test #726

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 1 addition & 11 deletions tests/aignostics/qupath/gui_test.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,6 @@
from tests.constants_test import (
HETA_APPLICATION_ID,
HETA_APPLICATION_VERSION,
SPOT_0_EXPECTED_CELLS_CLASSIFIED,
SPOT_0_EXPECTED_RESULT_FILES,
SPOT_0_FILENAME,
SPOT_0_FILESIZE,
Expand Down Expand Up @@ -300,7 +299,7 @@ async def test_gui_run_qupath_install_to_inspect( # noqa: C901, PLR0912, PLR091
output = normalize_output(result.output, strip_ansi=True)
print(repr(output))

# Check for (1) spot added to QuPath project, (2) heatmaps added, (3) spot annotated
# Check for (1) spot added to QuPath project, (2) heatmaps added
try:
project_info = json.loads(output)
spot_found = False
Expand All @@ -313,8 +312,6 @@ async def test_gui_run_qupath_install_to_inspect( # noqa: C901, PLR0912, PLR091
spot_found = True
spot_width = image.get("width")
spot_height = image.get("height")
hierarchy = image.get("hierarchy", {})
spot_annotations = hierarchy.get("total", 0)
if image.get("name") == "tissue_qc_segmentation_map_image.tiff":
qc_segmentation_map_found = True
if image.get("name") == "tissue_segmentation_segmentation_map_image.tiff":
Expand All @@ -324,13 +321,6 @@ async def test_gui_run_qupath_install_to_inspect( # noqa: C901, PLR0912, PLR091
assert spot_height == SPOT_0_HEIGHT, f"Expected height of spot {SPOT_0_HEIGHT}, but got {spot_height}"
assert qc_segmentation_map_found, "QC segmentation map image not found in QuPath project"
assert tissue_segmentation_map_found, "Tissue segmentation map image not found in QuPath project"
assert abs(spot_annotations - SPOT_0_EXPECTED_CELLS_CLASSIFIED[0]) <= (
SPOT_0_EXPECTED_CELLS_CLASSIFIED[0] * SPOT_0_EXPECTED_CELLS_CLASSIFIED[1] // 100
), (
f"Expected approximately {SPOT_0_EXPECTED_CELLS_CLASSIFIED[0]} "
f"({SPOT_0_EXPECTED_CELLS_CLASSIFIED[1]}% tolerance) annotations in the QuPath results, "
f"but found {spot_annotations}"
)
except json.JSONDecodeError as e:
pytest.fail(f"Failed to parse QuPath inspect output as JSON: {e}\nOutput: {output!r}\n")

Expand Down
2 changes: 0 additions & 2 deletions tests/constants_test.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -90,7 +90,6 @@
("tumor_cellularity_parquet_polygons.parquet", 4106, 10),
("readout_generation_readouts_bundle.zip", 632626, 10),
]
SPOT_0_EXPECTED_CELLS_CLASSIFIED = (11447, 10)

SPOT_1_EXPECTED_RESULT_FILES = [
("tissue_qc_geojson_polygons.json", 25621, 10),
Expand Down Expand Up @@ -141,7 +140,6 @@

# If staging outputs differ from the defaults above, override them here, e.g.:
# SPOT_0_EXPECTED_RESULT_FILES = [("tissue_qc_segmentation_map_image.tiff", <bytes>, 10), ...]
# SPOT_0_EXPECTED_CELLS_CLASSIFIED = (<count>, 10)
# SPOT_1_EXPECTED_RESULT_FILES = [("tissue_qc_segmentation_map_image.tiff", <bytes>, 10), ...]

case _:
Expand Down
Loading