From: Pepe B. <elv...@gm...> - 2006-06-16 04:34:26
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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' |