Skip to content

fix(test): add cell_detection parquet files to HETA e2e expected results #669

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’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
olivermeyer wants to merge 1 commit into from
+61 −33
Closed

fix(test): add cell_detection parquet files to HETA e2e expected results #669

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
94 changes: 61 additions & 33 deletions tests/constants_test.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -72,37 +72,8 @@
# the "staging" case below — only the constants that actually differ need to be reassigned.
# Note: defined here rather than inside each match arm to avoid SonarCloud flagging the
# nearly-identical blocks as duplicated code (the 3% duplication threshold).
SPOT_0_EXPECTED_RESULT_FILES = [
("tissue_qc_segmentation_map_image.tiff", 1645652, 10),
("tissue_qc_geojson_polygons.json", 101150, 10),
("tissue_segmentation_geojson_polygons.json", 327625, 10),
("readout_generation_slide_readouts.csv", 303585, 10),
("readout_generation_cell_readouts.csv", 1660865, 10),
("cell_classification_geojson_polygons.json", 6117357, 10),
("tissue_segmentation_segmentation_map_image.tiff", 2858496, 10),
("tissue_segmentation_csv_class_information.csv", 452, 10),
("tissue_qc_csv_class_information.csv", 285, 10),
("tissue_qc_parquet_polygons.parquet", 39435, 10),
("tissue_segmentation_parquet_polygons.parquet", 117509, 10),
("cell_classification_parquet_polygons.parquet", 1985592, 10),
]
SPOT_0_EXPECTED_CELLS_CLASSIFIED = (39798, 10)

SPOT_1_EXPECTED_RESULT_FILES = [
("tissue_qc_segmentation_map_image.tiff", 1288632, 10),
("tissue_qc_geojson_polygons.json", 75281, 10),
("tissue_segmentation_geojson_polygons.json", 152301, 10),
("readout_generation_slide_readouts.csv", 299361, 10),
("readout_generation_cell_readouts.csv", 464838, 10),
("cell_classification_geojson_polygons.json", 1726813, 10),
("tissue_segmentation_segmentation_map_image.tiff", 1783376, 10),
("tissue_segmentation_csv_class_information.csv", 446, 10),
("tissue_qc_csv_class_information.csv", 290, 10),
("tissue_qc_parquet_polygons.parquet", 29087, 10),
("tissue_segmentation_parquet_polygons.parquet", 56563, 10),
("cell_classification_parquet_polygons.parquet", 562536, 10),
]

match os.getenv("AIGNOSTICS_PLATFORM_ENVIRONMENT", "production"):
case "production":
TEST_APPLICATION_ID = "test-app"
Expand All @@ -119,6 +90,35 @@
PIPELINE_CPU_PROVISIONING_MODE = "SPOT"
PIPELINE_NODE_ACQUISITION_TIMEOUT_MINUTES = 25

SPOT_0_EXPECTED_RESULT_FILES = [
("tissue_qc_segmentation_map_image.tiff", 1645652, 10),
("tissue_qc_geojson_polygons.json", 101150, 10),
("tissue_segmentation_geojson_polygons.json", 327625, 10),
("readout_generation_slide_readouts.csv", 303585, 10),
("readout_generation_cell_readouts.csv", 1660865, 10),
("cell_classification_geojson_polygons.json", 6117357, 10),
("tissue_segmentation_segmentation_map_image.tiff", 2858496, 10),
("tissue_segmentation_csv_class_information.csv", 452, 10),
("tissue_qc_csv_class_information.csv", 285, 10),
("tissue_qc_parquet_polygons.parquet", 39435, 10),
("tissue_segmentation_parquet_polygons.parquet", 117509, 10),
("cell_classification_parquet_polygons.parquet", 1985592, 10),
]
Comment on lines +103 to +106
SPOT_1_EXPECTED_RESULT_FILES = [
("tissue_qc_segmentation_map_image.tiff", 1288632, 10),
("tissue_qc_geojson_polygons.json", 75281, 10),
("tissue_segmentation_geojson_polygons.json", 152301, 10),
("readout_generation_slide_readouts.csv", 299361, 10),
("readout_generation_cell_readouts.csv", 464838, 10),
("cell_classification_geojson_polygons.json", 1726813, 10),
("tissue_segmentation_segmentation_map_image.tiff", 1783376, 10),
("tissue_segmentation_csv_class_information.csv", 446, 10),
("tissue_qc_csv_class_information.csv", 290, 10),
("tissue_qc_parquet_polygons.parquet", 29087, 10),
("tissue_segmentation_parquet_polygons.parquet", 56563, 10),
("cell_classification_parquet_polygons.parquet", 562536, 10),
]
Comment on lines +117 to +120

case "staging":
TEST_APPLICATION_ID = "test-app"
TEST_APPLICATION_VERSION = "1.0.0"
Expand All @@ -134,10 +134,38 @@
PIPELINE_CPU_PROVISIONING_MODE = "SPOT"
PIPELINE_NODE_ACQUISITION_TIMEOUT_MINUTES = 25

# 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), ...]
SPOT_0_EXPECTED_RESULT_FILES = [
("tissue_qc_segmentation_map_image.tiff", 1645652, 10),
("tissue_qc_geojson_polygons.json", 101150, 10),
("tissue_segmentation_geojson_polygons.json", 327625, 10),
("readout_generation_slide_readouts.csv", 303585, 10),
Comment on lines +137 to +141
("readout_generation_cell_readouts.csv", 1660865, 10),
("cell_classification_geojson_polygons.json", 6117357, 10),
("tissue_segmentation_segmentation_map_image.tiff", 2858496, 10),
("tissue_segmentation_csv_class_information.csv", 452, 10),
("tissue_qc_csv_class_information.csv", 285, 10),
("tissue_qc_parquet_polygons.parquet", 39435, 10),
("tissue_segmentation_parquet_polygons.parquet", 117509, 10),
("cell_classification_parquet_polygons.parquet", 1985592, 10),
("cell_detection_parquet_polygons.parquet", 1978790, 10),
("cell_detection_parquet_centers.parquet", 657740, 10),
]
SPOT_1_EXPECTED_RESULT_FILES = [
("tissue_qc_segmentation_map_image.tiff", 1288632, 10),
("tissue_qc_geojson_polygons.json", 75281, 10),
("tissue_segmentation_geojson_polygons.json", 152301, 10),
("readout_generation_slide_readouts.csv", 299361, 10),
("readout_generation_cell_readouts.csv", 464838, 10),
("cell_classification_geojson_polygons.json", 1726813, 10),
("tissue_segmentation_segmentation_map_image.tiff", 1783376, 10),
("tissue_segmentation_csv_class_information.csv", 446, 10),
("tissue_qc_csv_class_information.csv", 290, 10),
("tissue_qc_parquet_polygons.parquet", 29087, 10),
("tissue_segmentation_parquet_polygons.parquet", 56563, 10),
("cell_classification_parquet_polygons.parquet", 562536, 10),
("cell_detection_parquet_polygons.parquet", 1985614, 10),
("cell_detection_parquet_centers.parquet", 657740, 10),
]

case _:
message = f"Unsupported AIGNOSTICS_PLATFORM_ENVIRONMENT value: {os.getenv('AIGNOSTICS_PLATFORM_ENVIRONMENT')}"
Expand Down
Loading