Constrain automatic row range to table limit#44
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sbesson merged 1 commit intoglencoesoftware:mainfrom Jan 7, 2026
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Without this PR, both read_table and download_table throw omero.ApiUsageException for TileDB-backed tables as seen in the linked issue.
With this PR, both functions work with both TileDB and PyTables table types.
>>> omero2pandas.download_table("test1.csv", file_id=5933, omero_connector=connector)
Downloading table from OMERO: 100%|██████████████████████████████████████████████████████████████████████████████| 18477/18477 rows, 00:08
>>> omero2pandas.download_table("test2.csv", file_id=5859, omero_connector=connector)
Downloading table from OMERO: 100%|██████████████████████████████████████████████████████████████████████████████| 18477/18477 rows, 00:04
>>> omero2pandas.read_table(file_id=5933, omero_connector=connector)
Downloading table from OMERO: 100%|██████████████████████████████████████████████████████████████████████████████| 18477/18477 rows, 00:05
object id Nucleus__Area Nucleus__Perimeter ... bbox_min_x bbox_min_y bbox_max_x bbox_max_y
0 1 45fd47cc-7882-465d-b606-78c87953c223 8.75 10.823806 ... 1794.0 1748.0 1806.0 1759.0
1 2 db75ae0e-e229-48c8-b7ee-c6dfa113acfd 14.50 15.924452 ... 2391.0 1876.0 2403.0 1894.0
2 3 b8ce84ae-01c5-4821-8b23-ae52f02d2c1b 19.00 17.303268 ... 2394.0 1896.0 2409.0 1914.0
3 4 a73cb71a-3f32-4bf1-88b4-dd05e0a4c596 19.00 22.310303 ... 2841.0 1937.0 2869.0 1953.0
4 5 4e5d039c-6c75-4526-b151-e6b120b0157e 12.50 14.829144 ... 2769.0 1979.0 2787.0 1991.0
... ... ... ... ... ... ... ... ... ...
18472 18473 2488dcca-aa73-41d5-ad59-aa763610e6ae 13.00 13.462880 ... 5624.0 4216.0 5641.0 4226.0
18473 18474 0809ccfe-f417-46b9-b52b-eb30b3b49898 24.50 20.229256 ... 5545.0 4226.0 5567.0 4244.0
18474 18475 1621af91-478f-466f-8c2f-32eeebd47538 17.25 18.287930 ... 5475.0 4237.0 5497.0 4249.0
18475 18476 e9192975-c1aa-46e4-a100-fc0d46e733aa 26.25 20.972122 ... 5512.0 4258.0 5535.0 4278.0
18476 18477 0c98eed2-2df9-48ec-97d9-9a3b8387581c 15.00 13.957096 ... 5484.0 4281.0 5498.0 4295.0
[18477 rows x 76 columns]
>>> omero2pandas.read_table(file_id=5859, omero_connector=connector)
Downloading table from OMERO: 100%|██████████████████████████████████████████████████████████████████████████████| 18477/18477 rows, 00:01
object id Nucleus__Area Nucleus__Perimeter ... bbox_min_x bbox_min_y bbox_max_x bbox_max_y
0 1 45fd47cc-7882-465d-b606-78c87953c223 8.75 10.823806 ... 1794.0 1748.0 1806.0 1759.0
1 2 db75ae0e-e229-48c8-b7ee-c6dfa113acfd 14.50 15.924452 ... 2391.0 1876.0 2403.0 1894.0
2 3 b8ce84ae-01c5-4821-8b23-ae52f02d2c1b 19.00 17.303268 ... 2394.0 1896.0 2409.0 1914.0
3 4 a73cb71a-3f32-4bf1-88b4-dd05e0a4c596 19.00 22.310303 ... 2841.0 1937.0 2869.0 1953.0
4 5 4e5d039c-6c75-4526-b151-e6b120b0157e 12.50 14.829144 ... 2769.0 1979.0 2787.0 1991.0
... ... ... ... ... ... ... ... ... ...
18472 18473 2488dcca-aa73-41d5-ad59-aa763610e6ae 13.00 13.462880 ... 5624.0 4216.0 5641.0 4226.0
18473 18474 0809ccfe-f417-46b9-b52b-eb30b3b49898 24.50 20.229256 ... 5545.0 4226.0 5567.0 4244.0
18474 18475 1621af91-478f-466f-8c2f-32eeebd47538 17.25 18.287930 ... 5475.0 4237.0 5497.0 4249.0
18475 18476 e9192975-c1aa-46e4-a100-fc0d46e733aa 26.25 20.972122 ... 5512.0 4258.0 5535.0 4278.0
18476 18477 0c98eed2-2df9-48ec-97d9-9a3b8387581c 15.00 13.957096 ... 5484.0 4281.0 5498.0 4295.0
[18477 rows x 76 columns]
sbesson
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Proposing to cut a 0.4.1 patch release
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Fixes #43
Should address the API inconsistency between PyTables and TileDB backed tables.
Testing
Read/download a whole TileDB table with a chunk size which would result in the last chunk needing to be truncated. Without PR this should throw, with PR it should work.