tbl | Python Fiddle

"""

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')

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