/usr/share/vitables/vitables/queries/query.py is in vitables 2.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#!/usr/bin/env python
# Copyright (C) 2005-2007 Carabos Coop. V. All rights reserved
# Copyright (C) 2008-2011 Vicent Mas. All rights reserved
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# Author: Vicent Mas - vmas@vitables.org
"""
This module executes `tables.Table` queries at low level.
It collects information from the `New Query` dialog, processes it and then
executes the query.
"""
__docformat__ = 'restructuredtext'
import tables
import numpy
from PyQt4 import QtCore
from PyQt4 import QtGui
import vitables.utils
translate = QtGui.QApplication.translate
class Query(QtCore.QObject):
"""Class implementing a tables.Table query.
Ideally queries SHOULD be sequentially executed in a secondary thread for
keeping the GUI responsive (i.e. not frozen) while a query (a potentially
long-running operation) is taking place. Unfortunately this goal has
proven difficult to achieve because `PyTables` is not thread-safe. So one
more task to the TO DO list :-)
The query is implemented in a clever way that doesn't interfer with the
lazy population of the tree of databases view: the query results table is
stored under a hidden group of the temporary database until the query
finishes. Then it is moved to the root node and becomes visible to the
world. This way, while the query results table is partially filled it
is not seen by the lazy population algorithm so it is not added to the
tree of databases view and neither the user nor ViTables will try to read
it. So no problems can occur trying to read a partially filled table.
:Parameters:
- `table_uid`: UID of the tables.Table instance being queried
- `table`: the table being queried
- `qdescr`: dictionary description of the query
"""
query_completed = QtCore.pyqtSignal(bool, unicode, name="queryCompleted")
def __init__(self, tmp_h5file, table_uid, table, qdescr):
"""Initialises the query."""
super(Query, self).__init__()
self.completed = False
self.tmp_h5file = tmp_h5file
self.table_uid = table_uid
self.table = table
self.qdescr = qdescr
def run(self):
"""
Query a table and add a the result to the temporary database.
"""
self.queryTable()
self.query_completed.emit(self.completed, self.table_uid)
def flushTable(self, ftable):
"""Flush the filtered table and setup some user attributes.
:Parameters:
- `ftable`: the filtered table being flushed
"""
ftable.flush()
# Set some user attributes that define this filtered table
asi = ftable.attrs
asi.query_path = self.qdescr[u'src_filepath']
asi.query_table = self.qdescr[u'src_path']
asi.query_condition = self.qdescr[u'title']
def queryWithIndex(self, src_dict):
"""Do the query (`PyTables` level).
"""
# The query range is made of numpy scalars with dtype int64
(start, stop, step) = self.qdescr[u'rows_range']
chunk_size = 10000
div = numpy.divide(stop - start, chunk_size)
# Create the destination table: its first column will contain
# the indices of the rows selected in the source table so a new
# description dictionary is needed. Int64 values are necessary
# to keep full 64-bit indices
ft_dict = \
{self.qdescr[u'indices_field_name'].encode('utf_8'): \
tables.Int64Col(pos=-1)}
ft_dict.update(src_dict)
f_table = self.tmp_h5file.createTable(\
u'/_p_query_results',
self.qdescr[u'ft_name'],
ft_dict,
self.qdescr[u'title'])
# Get the array of rows that fulfil the condition
# Selection is done in several steps. It saves a *huge*
# amount of memory when querying large tables
for i in numpy.arange(0, div+1):
QtGui.qApp.processEvents()
lstart = start + chunk_size*i
if lstart > stop:
lstart = stop
lstop = lstart + chunk_size
if lstop > stop:
lstop = stop
coordinates = self.table.getWhereList(\
self.qdescr[u'condition'],
self.qdescr[u'condvars'],
start=lstart, stop=lstop, step=step)
selection = self.table.readCoordinates(coordinates)
if selection.shape == (0, ):
continue
coord_dtype = numpy.dtype(\
[(str(self.qdescr[u'indices_field_name']), '<i8')])
new_dtype = numpy.dtype(\
coord_dtype.descr + selection.dtype.descr)
new_buffer = numpy.empty(selection.shape, dtype=new_dtype)
for field in selection.dtype.fields:
new_buffer[field] = selection[field]
new_buffer[str(self.qdescr[u'indices_field_name'])] = \
coordinates
f_table.append(new_buffer)
self.flushTable(f_table)
# Move the intermediate table to its final destination
self.tmp_h5file.moveNode(\
u'/_p_query_results/' + self.qdescr[u'ft_name'],
u'/', newname=self.qdescr[u'ft_name'],
overwrite=True)
self.completed = True
def queryWithNoIndex(self, src_dict):
"""Do the query (`PyTables` level).
"""
# The query range is made of numpy scalars with dtype int64
(start, stop, step) = self.qdescr[u'rows_range']
chunk_size = 10000
div = numpy.divide(stop - start, chunk_size)
# Create the destination table
f_table = self.tmp_h5file.createTable(\
u'/_p_query_results',
self.qdescr[u'ft_name'],
src_dict,
self.qdescr[u'title'])
# Get the array of rows that fulfil the condition
# Selection is done in several steps. It saves a *huge*
# amount of memory when querying large tables
for i in numpy.arange(0, div+1):
QtGui.qApp.processEvents()
lstart = start + chunk_size*i
if lstart > stop:
lstart = stop
lstop = lstart + chunk_size
if lstop > stop:
lstop = stop
selection = self.table.readWhere(\
self.qdescr[u'condition'],
self.qdescr[u'condvars'],
start=lstart, stop=lstop, step=step)
f_table.append(selection)
self.flushTable(f_table)
# Move the intermediate table to its final destination
self.tmp_h5file.moveNode(\
u'/_p_query_results/' + self.qdescr[u'ft_name'],
u'/', newname=self.qdescr[u'ft_name'],
overwrite=True)
self.completed = True
def queryTable(self):
"""Do the query (`PyTables` level).
"""
try:
src_dict = self.table.description._v_colObjects
# Add an `indexes` column to the result table
if self.qdescr[u'indices_field_name']:
self.queryWithIndex(src_dict)
# Do no add an `indexes` column to the result table
else:
self.queryWithNoIndex(src_dict)
except:
vitables.utils.formatExceptionInfo()
self.tmp_h5file.removeNode(\
u'/_p_query_results/' + self.qdescr[u'ft_name'])
else:
self.tmp_h5file.flush()
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