Re: [Pytables-users] bug in pytables/hdf

[Francesc A. <fa...@ca...>]

Yes, you have detected a bug in PyTables. You can solve it by replacing the
function H5TB_find_field in src/H5TB.c by the next one:

int H5TB_find_field( const char *field, const char *field_list )
{
 const char *start =3D field_list;=20
 const char *end;=20

 while ( (end =3D strstr( start, "," )) !=3D 0 ) {=20
    if ( strncmp(start,field,end-start) =3D=3D 0 ) return 1;=20
    start =3D end + 1;=20
 }=20

 if ( strcmp( start, field ) =3D=3D 0 ) return 1;=20

 return -1;  =20

}  =20

I'll commit the necessary changes to the software repository soon.

Cheers,


A Divendres 07 Gener 2005 09:58, russ va escriure:
> Hello, I'm working with pytables 0.9.1 on windows 2000 and seem to have=20
> discovered a bug somewhere in the works.  Essentially I have a table=20
> with two columns, "mmid" and "mmidn", and pytables can't read the=20
> "mmidn" column.  Following is a short program that demonstrates the=20
> problem, and following that is the output of the program.  The problem=20
> seems to be in the naming; changing "mmidn" to "abcd" fixes the=20
> problem.  Similarly, changing the pair to "abc" and "abcd" recreates the=
=20
> problem.  Any help would be appreciated.
> Thanks, -Russ
> ru...@ag...
> -------------------------------------------------------------------------=
=2D------
> import sys,os
> import tables as hdf
>=20
> class Consolidatedtable(hdf.IsDescription):
>     mmid =3D hdf.Int32Col(pos=3D4)
>     mmidn =3D hdf.Int32Col(pos=3D5)
> fname=3D'tmp.h5'
> print 'pytables version:', hdf.__version__
>=20
> print 'writing', fname
> h5 =3D hdf.openFile(fname, mode=3D'w', title=3D'bwdata')
> t=3Dh5.createTable('/','q',Consolidatedtable,'data',expectedrows=3D10000)
> r=3Dt.row
> r['mmid']=3D0
> r['mmidn']=3D0
> r.append()
> h5.close()
>=20
>=20
> print 'reading'
> h5=3Dhdf.openFile(fname)
> print 'this works:', h5.root.q['mmid']
> print 'this does not:', h5.root.q['mmidn']
>=20
>=20
> -------------------------------------------------------------------------=
=2D------
> program output:
>=20
> $ /d/py/test_mmidn.py
> pytables version: 0.9.1
> writing tmp.h5
> reading
> this works: [0]
> this does not:HDF5-DIAG: Error detected in HDF5 library version:=20
> 1.6.3-patch thr
> ead 0.  Back trace follows.
>   #000: D:\hdf5\src\H5Tcompound.c line 327 in H5Tinsert(): unable to=20
> insert memb
> er
>     major(13): Datatype interface
>     minor(45): Unable to insert object
>   #001: D:\hdf5\src\H5Tcompound.c line 418 in H5T_insert(): member=20
> overlaps with
>  another member
>     major(13): Datatype interface
>     minor(45): Unable to insert object
>=20
> Traceback (most recent call last):
>   File "d:/util/mypython.py", line 15, in ?
>     execfile(sys.argv[0])
>   File "d:/py/test_mmidn.py", line 24, in ?
>     print 'this does not:', h5.root.q['mmidn']
>   File "D:\Python23\lib\site-packages\tables\Table.py", line 778, in=20
> __getitem__
>=20
>     return self.read(field=3Dkey)
>   File "D:\Python23\lib\site-packages\tables\Table.py", line 592, in read
>     return self._read(start, stop, step, field, coords)
>   File "D:\Python23\lib\site-packages\tables\Table.py", line 731, in _read
>     self._read_field_name(result, start, stop, step, field)
>   File "hdf5Extension.pyx", line 1831, in=20
> hdf5Extension.Table._read_field_name
> RuntimeError: Problems reading table column.
>=20
>=20
>=20
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>=20

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