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Better file open/closing in `create`

See original GitHub issue

In testing loompy I’ve had to rerun several times because I made an error in the input, but when I rerun, I get OSError because the hdf5 file was opened and never closed. The file should get closed when errors happen during create

---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
<timed exec> in <module>()

~/miniconda3/envs/loom-env/lib/python3.6/site-packages/loompy/loompy.py in create(filename, matrix, row_attrs, col_attrs, file_attrs, chunks, chunk_cache, dtype, compression_opts)
   1022 
   1023         # Create the file (empty).
-> 1024         f = h5py.File(name=filename, mode='w')
   1025         f.create_group('/layers')
   1026         f.create_group('/row_attrs')

~/miniconda3/envs/loom-env/lib/python3.6/site-packages/h5py/_hl/files.py in __init__(self, name, mode, driver, libver, userblock_size, swmr, **kwds)
    267             with phil:
    268                 fapl = make_fapl(driver, libver, **kwds)
--> 269                 fid = make_fid(name, mode, userblock_size, fapl, swmr=swmr)
    270 
    271                 if swmr_support:

~/miniconda3/envs/loom-env/lib/python3.6/site-packages/h5py/_hl/files.py in make_fid(name, mode, userblock_size, fapl, fcpl, swmr)
    103         fid = h5f.create(name, h5f.ACC_EXCL, fapl=fapl, fcpl=fcpl)
    104     elif mode == 'w':
--> 105         fid = h5f.create(name, h5f.ACC_TRUNC, fapl=fapl, fcpl=fcpl)
    106     elif mode == 'a':
    107         # Open in append mode (read/write).

h5py/_objects.pyx in h5py._objects.with_phil.wrapper()

h5py/_objects.pyx in h5py._objects.with_phil.wrapper()

h5py/h5f.pyx in h5py.h5f.create()

OSError: Unable to create file (unable to truncate a file which is already open)

Issue Analytics

State:
Created 6 years ago
Comments:31 (20 by maintainers)

Top GitHub Comments

1reaction

slinnarssoncommented, Feb 8, 2018

No let’s leave the current behaviour for create, i.e. to overwrite. This is close to how open works in Python, so is expected behaviour. Changing it will break a lot of code, unless you make the option default to True, in which case it will not catch any mistakes anyway.

1reaction

slinnarssoncommented, Feb 8, 2018

Good point (timestamp). I fixed it.

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