Problems with H5::DataSet::read(H5std_string...) for fixed length H5T_STR_NULLPAD strings

Hdf-forum archives
1

There seem to be a problem reading fixed length strings that are not null-terminated (H5T_STR_NULLPAD) with the H5::DataSet::read(H5std_string...) method. What happens is the following:
1: H5::DataSet::read(H5std_string...) calls DataSet::p_read_fixed_len.
2: A new "strg_C" string buffer of lenght attr_size+1 is allocated in DataSet::p_read_fixed_len. This buffer is neither cleared nor null-terminated in any way.
3: The "strg_C" buffer is filled with data from a H5Dread call. H5Dread will only copy in actual string data, and _not_ zero-termination for H5T_STR_NULLPAD strings. This leaves "strg_C" without any zero-termination.
4: "strg_C" is assigned to the std::string output. This operation is nondeterministic, and will generate output of arbitrary length, depending on memory content.

I believe that the above problem can be resolved by clearing the "strg_C" immediately after allocation. This will ensure that the string is always zero-terminated, independent of actual length. A patch that attempt to fix this issue is attached.

Best regards,
Fredrik Orderud

H5DataSet.cpp.patch (495 Bytes)

2

Hello Fredrik,

Thank you for reporting the problem. It will be addressed in the next release.

Binh-Minh

ยทยทยท

________________________________________
From: Hdf-forum <hdf-forum-bounces@lists.hdfgroup.org> on behalf of Fredrik Orderud <fredrik@orderud.no>
Sent: Tuesday, February 18, 2014 5:50 PM
To: HDF Users Discussion List
Subject: [Hdf-forum] Problems with H5::DataSet::read(H5std_string...) for fixed length H5T_STR_NULLPAD strings

There seem to be a problem reading fixed length strings that are not
null-terminated (H5T_STR_NULLPAD) with the
H5::DataSet::read(H5std_string...) method. What happens is the following:
1: H5::DataSet::read(H5std_string...) calls DataSet::p_read_fixed_len.
2: A new "strg_C" string buffer of lenght attr_size+1 is allocated in
DataSet::p_read_fixed_len. This buffer is neither cleared nor
null-terminated in any way.
3: The "strg_C" buffer is filled with data from a H5Dread call. H5Dread
will only copy in actual string data, and _not_ zero-termination for
H5T_STR_NULLPAD strings. This leaves "strg_C" without any zero-termination.
4: "strg_C" is assigned to the std::string output. This operation is
nondeterministic, and will generate output of arbitrary length,
depending on memory content.

I believe that the above problem can be resolved by clearing the
"strg_C" immediately after allocation. This will ensure that the string
is always zero-terminated, independent of actual length. A patch that
attempt to fix this issue is attached.

Best regards,
Fredrik Orderud