Some HDF5 variable length data are missing

[kyang2014]

1. File: ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/HDFCompass/kent-files/hdf5-handler-fake/ntypes.h5

2. Testing version: Windows version of the release candidate from S3

For a 1-D (4 element) variable length array)(vl_type), compass misses values of the index 2 and 3.

For index 2, h5dump shows the values (200),(210,211),(220,221,222)
compass only shows (200),(210,211)

For index 3, h5dump shows the values (300), (310, 311), (320, 321, 322), (330, 331, 332, 333)
compass only shows (300),,(310,311)

It looks like compass correctly picks up all the values in index 1 and then keep using the number of elements in index 1 for the rest indexes. This is wrong for a variable length array.

[jreadey]

I can reproduce.
@kyang2014 - can you create a smaller test file that just contains the vl_type dataset?

[kyang2014]

At:
ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/HDFCompass/kent-files/hdf5-testing-files/vl_vl.h5

Please note that the basetype of this variable length type is a variable length type:
The snippet of h5dump:
DATATYPE H5T_VLEN { H5T_VLEN { H5T_STD_U32LE}}

If you try a simple variable length datatype file, ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/HDFCompass/kent-files/hdf5-testing-files/tvldtypes1.h5
HDF5 compass works fine.

However, I do think this issue needs to be addressed some way since as a user I am OK if the values are not displayed at all. It is bad if I read data that makes feel complete but actually only partial data values present.

Kent

From: John Readey [mailto:[email protected]]
Sent: Tuesday, October 13, 2015 12:41 PM
To: HDFGroup/hdf-compass
Cc: Kent Yang
Subject: Re: [hdf-compass] Some HDF5 variable length data are missing (#96)

I can reproduce.

@kyang2014https://github.com/kyang2014 - can you create a smaller test file that just contains the vl_type dataset?

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Reply to this email directly or view it on GitHubhttps://github.com//issues/96#issuecomment-147788578.