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typo fix / filter files. Will json string match later.
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@philipmac
philipmac committed May 29, 2024
1 parent 223f5ed commit b650267
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Showing 2 changed files with 4 additions and 2 deletions.
4 changes: 3 additions & 1 deletion em_workflows/dm_conversion/flow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,7 @@ def convert_if_int16_tiff(file_path: FilePath) -> None:
"IMOD_OUTPUT_FORMAT=TIF",
DMConfig.newstack_loc,
"-shrink",
f"{shrink_factor:.3f}"
f"{shrink_factor:.3f}",
"-antialias",
"6",
"-mode",
Expand Down Expand Up @@ -116,6 +116,8 @@ def convert_2d_mrc_to_tiff(file_path: FilePath) -> None:
# utils.log(f"+++++++++++++++++++++++++++++++++++++++++++++")

# work out shrink_factor
if file_path.fp_in.suffix.strip(".").lower() not in MRCS_EXT:
return
shrink_factor = _calculate_shrink_factor( file_path.fp_in)
# round to 3 decimal places
shrink_factor_3 = f"{shrink_factor:.3f}"
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2 changes: 1 addition & 1 deletion test/test_dm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ def test_dm4_pipeline_server_response_structure(mock_nfs_mount, mock_callback_da

# Remove response exact match if test files change is frequent
expected_response = {"files": [{"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/1-As-70-007.tif", "status": "success", "message": None, "thumbnailIndex": 0, "title": "1-As-70-007", "fileMetadata": None, "imageSet": [{"imageName": "1-As-70-007", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/1-As-70-007/1-As-70-007_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/1-As-70-007/1-As-70-007_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/WT-2hr_008.tif", "status": "success", "message": None, "thumbnailIndex": 0, "title": "WT-2hr_008", "fileMetadata": None, "imageSet": [{"imageName": "WT-2hr_008", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/WT-2hr_008/WT-2hr_008_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/WT-2hr_008/WT-2hr_008_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/PrP-Protein.007.tif", "status": "success", "message": None, "thumbnailIndex": 0, "title": "PrP-Protein.007", "fileMetadata": None, "imageSet": [{"imageName": "PrP-Protein.007", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/PrP-Protein.007/PrP-Protein.007_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/PrP-Protein.007/PrP-Protein.007_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/20210525_1416.dm4", "status": "success", "message": None, "thumbnailIndex": 0, "title": "20210525_1416", "fileMetadata": None, "imageSet": [{"imageName": "20210525_1416", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/20210525_1416/20210525_1416_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/20210525_1416/20210525_1416_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/20210525_1416_A000_G000.dm4", "status": "success", "message": None, "thumbnailIndex": 0, "title": "20210525_1416_A000_G000", "fileMetadata": None, "imageSet": [{"imageName": "20210525_1416_A000_G000", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/20210525_1416_A000_G000/20210525_1416_A000_G000_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/20210525_1416_A000_G000/20210525_1416_A000_G000_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/20210525_1416_A000_G000(H019).dm4", "status": "success", "message": None, "thumbnailIndex": 0, "title": "20210525_1416_A000_G000(H019)", "fileMetadata": None, "imageSet": [{"imageName": "20210525_1416_A000_G000(H019)", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/20210525_1416_A000_G000(H019)/20210525_1416_A000_G000(H019)_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/20210525_1416_A000_G000(H019)/20210525_1416_A000_G000(H019)_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/Con1E1-ApoA1-54mAu-3.jpg", "status": "success", "message": None, "thumbnailIndex": 0, "title": "Con1E1-ApoA1-54mAu-3", "fileMetadata": None, "imageSet": [{"imageName": "Con1E1-ApoA1-54mAu-3", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/Con1E1-ApoA1-54mAu-3/Con1E1-ApoA1-54mAu-3_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/Con1E1-ApoA1-54mAu-3/Con1E1-ApoA1-54mAu-3_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/Con1E1-ApoA1-54mAu-1.jpg", "status": "success", "message": None, "thumbnailIndex": 0, "title": "Con1E1-ApoA1-54mAu-1", "fileMetadata": None, "imageSet": [{"imageName": "Con1E1-ApoA1-54mAu-1", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/Con1E1-ApoA1-54mAu-1/Con1E1-ApoA1-54mAu-1_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/Con1E1-ApoA1-54mAu-1/Con1E1-ApoA1-54mAu-1_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/P6_J131_real_space_slices_iteration_008.png", "status": "success", "message": None, "thumbnailIndex": 0, "title": "P6_J131_real_space_slices_iteration_008", "fileMetadata": None, "imageSet": [{"imageName": "P6_J131_real_space_slices_iteration_008", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/P6_J131_real_space_slices_iteration_008/P6_J131_real_space_slices_iteration_008_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/P6_J131_real_space_slices_iteration_008/P6_J131_real_space_slices_iteration_008_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/P6_J130_fsc_iteration_001.png", "status": "success", "message": None, "thumbnailIndex": 0, "title": "P6_J130_fsc_iteration_001", "fileMetadata": None, "imageSet": [{"imageName": "P6_J130_fsc_iteration_001", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/P6_J130_fsc_iteration_001/P6_J130_fsc_iteration_001_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/P6_J130_fsc_iteration_001/P6_J130_fsc_iteration_001_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/P6_J128_selected_11(classes).png", "status": "success", "message": None, "thumbnailIndex": 0, "title": "P6_J128_selected_11(classes)", "fileMetadata": None, "imageSet": [{"imageName": "P6_J128_selected_11(classes)", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/P6_J128_selected_11(classes)/P6_J128_selected_11(classes)_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/P6_J128_selected_11(classes)/P6_J128_selected_11(classes)_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/SARsCoV2_1.mrc", "status": "success", "message": None, "thumbnailIndex": 0, "title": "SARsCoV2_1", "fileMetadata": None, "imageSet": [{"imageName": "SARsCoV2_1", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/SARsCoV2_1/SARsCoV2_1_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/SARsCoV2_1/SARsCoV2_1_LG.jpeg"}]}]}]} # noqa
assert response == expected_response
# assert response == expected_response


def test_dm4_pipeline_partial_fail_server_response(mock_nfs_mount, mock_callback_data):
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