[Pytables-users] Problem creating Table

[Pepe B. <elv...@gm...>]

Hello everyone,

I have a script that reads data from plaint text files and writes the
information in a PyTables DB.

I've tested the script with some initial data and it seems to work
fine. I got a different set of data that is longer and it seems to
crash and I can't pinpoint the problem to be originating from my code.
Moreover, if I remove some information from the text data I want to
write it seems to work fine with the new data.

Basically to summarize, the script works with my original data that
has less than 4000 different entries (Each entry is a row in a Table).
The new data has over 6500 entries and it makes my script crash. If I
reduce the data to be less than 5000 the same data just works without
anything additional.

Below you can see the error that Python is returning.

Thanks,
Pepe

PS. Francesc, I am copying you because I've hard problems between
GMail and the SF mailing lists.

  File "gen_phob.py", line 10, in ?
    a.createdb()
  File "/Users/elventear/Projects/workspace/libSVM
Scripts/src/gen_db.py", line 418, in createdb
    dupes += param[5](table)
  File "/Users/elventear/Projects/workspace/libSVM
Scripts/src/gen_db.py", line 135, in __expression2gene_table
    row.append()
  File "TableExtension.pyx", line 1016, in TableExtension.Row.append
  File "/sw/lib/python2.4/site-packages/tables/Table.py", line 1445,
in _saveBufferedRows
    self.flushRowsToIndex(lastrow=0)
  File "/sw/lib/python2.4/site-packages/tables/Table.py", line 1698,
in flushRowsToIndex
    rowsadded = self._addRowsToIndex(
  File "/sw/lib/python2.4/site-packages/tables/Table.py", line 1720,
in _addRowsToIndex
    index.append(self.read(start=i, stop=i+nelemslice, field=colname))
  File "/sw/lib/python2.4/site-packages/tables/Index.py", line 470, in append
    self.sorted.append(arr[s])
  File "/sw/lib/python2.4/site-packages/tables/IndexArray.py", line
237, in append
    self._append(arr)
  File "hdf5Extension.pyx", line 1431, in hdf5Extension.Array._append
AttributeError: 'numpy.ndarray' object has no attribute '_data'
Error in atexit._run_exitfuncs:
Traceback (most recent call last):
  File "/sw/lib/python2.4/atexit.py", line 24, in _run_exitfuncs
    func(*targs, **kargs)
  File "/sw/lib/python2.4/site-packages/tables/File.py", line 2105, in
close_open_files
    fileh.close()
  File "/sw/lib/python2.4/site-packages/tables/File.py", line 1925, in close
    lambda path: aliveNodes[path])
  File "/sw/lib/python2.4/site-packages/tables/File.py", line 1897, in
_closeNodes
    node._f_close()
  File "/sw/lib/python2.4/site-packages/tables/Table.py", line 1944, in _f_close
    self.flush()
  File "/sw/lib/python2.4/site-packages/tables/Table.py", line 1917, in flush
    self._saveBufferedRows(flush=1)
  File "/sw/lib/python2.4/site-packages/tables/Table.py", line 1445,
in _saveBufferedRows
    self.flushRowsToIndex(lastrow=0)
  File "/sw/lib/python2.4/site-packages/tables/Table.py", line 1698,
in flushRowsToIndex
    rowsadded = self._addRowsToIndex(
  File "/sw/lib/python2.4/site-packages/tables/Table.py", line 1720,
in _addRowsToIndex
    index.append(self.read(start=i, stop=i+nelemslice, field=colname))
  File "/sw/lib/python2.4/site-packages/tables/Index.py", line 470, in append
    self.sorted.append(arr[s])
  File "/sw/lib/python2.4/site-packages/tables/IndexArray.py", line
237, in append
    self._append(arr)
  File "hdf5Extension.pyx", line 1431, in hdf5Extension.Array._append
AttributeError: 'numpy.ndarray' object has no attribute '_data'
Error in sys.exitfunc:
Traceback (most recent call last):
  File "/sw/lib/python2.4/atexit.py", line 24, in _run_exitfuncs
    func(*targs, **kargs)
  File "/sw/lib/python2.4/site-packages/tables/File.py", line 2105, in
close_open_files
    fileh.close()
  File "/sw/lib/python2.4/site-packages/tables/File.py", line 1925, in close
    lambda path: aliveNodes[path])
  File "/sw/lib/python2.4/site-packages/tables/File.py", line 1897, in
_closeNodes
    node._f_close()
  File "/sw/lib/python2.4/site-packages/tables/Table.py", line 1944, in _f_close
    self.flush()
  File "/sw/lib/python2.4/site-packages/tables/Table.py", line 1917, in flush
    self._saveBufferedRows(flush=1)
  File "/sw/lib/python2.4/site-packages/tables/Table.py", line 1445,
in _saveBufferedRows
    self.flushRowsToIndex(lastrow=0)
  File "/sw/lib/python2.4/site-packages/tables/Table.py", line 1698,
in flushRowsToIndex
    rowsadded = self._addRowsToIndex(
  File "/sw/lib/python2.4/site-packages/tables/Table.py", line 1720,
in _addRowsToIndex
    index.append(self.read(start=i, stop=i+nelemslice, field=colname))
  File "/sw/lib/python2.4/site-packages/tables/Index.py", line 470, in append
    self.sorted.append(arr[s])
  File "/sw/lib/python2.4/site-packages/tables/IndexArray.py", line
237, in append
    self._append(arr)
  File "hdf5Extension.pyx", line 1431, in hdf5Extension.Array._append
AttributeError: 'numpy.ndarray' object has no attribute '_data'