SimpleTable: simple wrapper around the Table object

"""
SimpleTable: simple wrapper around pytables hdf5
------------------------------------------------------------------------------
Example Usage::
 >>> from simpletable import SimpleTable
 >>> import tables
 # define the table as a subclass of simple table.
 >>> class ATable(SimpleTable):
 ... x = tables.Float32Col()
 ... y = tables.Float32Col()
 ... name = tables.StringCol(16)
 # instantiate with: args: filename, tablename
 >>> tbl = ATable('test_docs.h5', 'atable1')
 # insert as with pytables:
 >>> row = tbl.row
 >>> for i in range(50):
 ... row['x'], row['y'] = i, i * 10
 ... row['name'] = "name_%i" % i
 ... row.append()
 >>> tbl.flush()
 # there is also insert_many() method() with takes an iterable
 # of dicts with keys matching the colunns (x, y, name) in this
 # case.
 # query the data (query() alias of tables' readWhere()
 >>> tbl.query('(x > 4) & (y < 70)') #doctest: +NORMALIZE_WHITESPACE
 array([('name_5', 5.0, 50.0), ('name_6', 6.0, 60.0)],
 dtype=[('name', '|S16'), ('x', '<f4'), ('y', '<f4')])
"""
import tables
_filter = tables.Filters(complib="lzo", complevel=1, shuffle=True)
class SimpleTable(tables.Table):
 def __init__(self, file_name, table_name, description=None,
 group_name='default', mode='a', title="", filters=_filter,
 expectedrows=512000):
 f = tables.openFile(file_name, mode)
 self.uservars = None
 if group_name is None: group_name = 'default'
 parentNode = f._getOrCreatePath('/' + group_name, True)
 if table_name in parentNode: # existing table
 description = None
 elif description is None: # pull the description from the attrs
 description = dict(self._get_description())
 tables.Table.__init__(self, parentNode, table_name,
 description=description, title=title,
 filters=filters,
 expectedrows=expectedrows,
 _log=False)
 self._c_classId = self.__class__.__name__
 def _get_description(self):
 # pull the description from the attrs
 for attr_name in dir(self):
 if attr_name[0] == '_': continue
 try:
 attr = getattr(self, attr_name)
 except:
 continue
 if isinstance(attr, tables.Atom):
 yield attr_name, attr
 def insert_many(self, data_generator, attr=False):
 row = self.row
 cols = self.colnames
 if not attr:
 for d in data_generator:
 for c in cols:
 row[c] = d[c]
 row.append()
 else:
 for d in data_generator:
 for c in cols:
 row[c] = getattr(d, c)
 row.append()
 self.flush()
 query = tables.Table.readWhere
# convience sublcass that i use a lot.
class BlastTable(SimpleTable):
 query = tables.StringCol(5)
 subject = tables.StringCol(5)
 pctid = tables.Float32Col()
 hitlen = tables.UInt16Col()
 nmismatch = tables.UInt16Col()
 ngaps = tables.UInt16Col()
 qstart = tables.UInt32Col()
 qstop = tables.UInt32Col()
 sstart = tables.UInt32Col()
 sstop = tables.UInt32Col()
 evalue = tables.Float64Col()
 score = tables.Float32Col()
if __name__ == '__main__':
 import doctest
 doctest.testmod()
 import os
 os.unlink('test_docs.h5')