Verify CXG conversion works for certain datasets
See original GitHub issueLink to Collection with errored dataset: https://cellxgene.cziscience.com/collections/60358420-6055-411d-ba4f-e8ac80682a2e/private
Stack trace:
File "/usr/local/lib/python3.8/dist-packages/backend/czi_hosted/common/utils/cxg_generation_utils.py", line 75, in convert_dataframe_to_cxg_array
array[:] = value\n File "tiledb/libtiledb.pyx", line 4885, in tiledb.libtiledb.DenseArrayImpl.__setitem__
File "tiledb/libtiledb.pyx", line 415, in tiledb.libtiledb._write_array
File "tiledb/libtiledb.pyx", line 479, in tiledb.libtiledb._raise_ctx_err
File "tiledb/libtiledb.pyx", line 464, in tiledb.libtiledb._raise_tiledb_error
tiledb.libtiledb.TileDBError: [TileDB::IO] Error: Cannot open file \'/local.cxg/obs/__1617759016805_1617759016805_a11917d04be346c2a937ba82cbd16ae8_6/BEST4/OTOP2 Cells.tdb\'; No such file or directory
TEAM COMMENTS:
- Old tileDB version didn’t process slashes correctly.
- tileDB just put out 0.19, which fixes this issue. Other tickets in this epic upgrade the version, this ticket is to verify that it worked for this dataset.
- In scope: add a test with a slash in the observation, make sure it uploads successfully.
Issue Analytics
- State:
- Created 2 years ago
- Comments:10 (3 by maintainers)
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Hi @metakuni, I was able to reproduce your findings. It looks like this was in fact initially supported by this PR in TileDB Embedded 2.2.
Finally managed to reproduce the error using repro test script from https://github.com/TileDB-Inc/TileDB-Py/issues/294.
The test seems to fail only for tiledb versions <0.8.1. tiledb 0.8.1+ appears to work fine, so perhaps the fixed version quoted in the bug comment was incorrect.
Using
tiledb==0.8.0
: