python-biopython 1.63-1 / usr / lib / python2.7 / dist-packages / Bio / DocSQL.py

#!/usr/bin/env python
#
# Copyright 2002-2003 by Michael Hoffman.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

"""Bio.DocSQL: easy access to DB API databases.

>>> import os
>>> import MySQLdb
>>> from Bio import DocSQL
>>> db=MySQLdb.connect(passwd='', db='test')
>>> class CreatePeople(DocSQL.Create):
...     '''
...     CREATE TEMPORARY TABLE people
...     (id INT UNSIGNED NOT NULL PRIMARY KEY AUTO_INCREMENT,
...     last_name TINYTEXT,
...     first_name TINYTEXT)
...     '''
...
>>> CreatePeople(connection=db)
CreatePeople(message=Success)
"""

from __future__ import print_function

import sys

from Bio import MissingPythonDependencyError

try:
    import MySQLdb
except:
    raise MissingPythonDependencyError("Install MySQLdb if you want to use "
                                       "Bio.DocSQL.")

connection = None


class NoInsertionError(Exception):
    pass


def _check_is_public(name):
    if name[:6] == "_names":
        raise AttributeError


class QueryRow(list):
    def __init__(self, cursor):
        try:
            row = cursor.fetchone()
            super(QueryRow, self).__init__(row)
        except TypeError:
            raise StopIteration

        object.__setattr__(self, "_names", [x[0] for x in cursor.description]) # FIXME: legacy
        object.__setattr__(self, "_names_hash", {})

        for i, name in enumerate(self._names):
            self._names_hash[name] = i

    def __getattr__(self, name):
        _check_is_public(name)
        try:
            return self[self._names_hash[name]]
        except (KeyError, AttributeError):
            raise AttributeError("'%s' object has no attribute '%s'"
                                 % (self.__class__.__name__, name))

    def __setattr__(self, name, value):
        try:
            self._names_hash
        except AttributeError:
            return object.__setattr__(self, name, value)

        _check_is_public(name)
        try:
            index = self._names_hash[name]
            self[index] = value
        except KeyError:
            return object.__setattr__(self, name, value)


class Query(object):
    """
    SHOW TABLES
    """
    MSG_FAILURE = "Failure"
    MSG_SUCCESS = "Success"
    message = "not executed"
    error_message = ""
    prefix = ""
    suffix = ""
    row_class = QueryRow

    def __init__(self, *args, **keywds):
        try:
            self.connection = keywds['connection']
        except KeyError:
            self.connection = connection
        try:
            self.diagnostics = keywds['diagnostics']
        except KeyError:
            self.diagnostics = 0

        self.statement = self.prefix + self.__doc__ + self.suffix
        self.params = args

    def __iter__(self):
        return IterationCursor(self, self.connection)

    def __repr__(self):
        return "%s(message=%s)" % (self.__class__.__name__, self.message)

    def cursor(self):
        return iter(self).cursor

    def dump(self):
        for item in self:
            print(item)


class QueryGeneric(Query):
    def __init__(self, statement, *args, **keywds):
        Query.__init__(self, *args, **keywds)
        self.statement = statement,


class IterationCursor(object):
    def __init__(self, query, connection=connection):
        if connection is None:
            raise TypeError("database connection is None")
        self.cursor = connection.cursor()
        self.row_class = query.row_class
        if query.diagnostics:
            sys.stderr.write("Query statement: %s\n" % query.statement)
            sys.stderr.write("Query params: %s\n" % query.params)
        self.cursor.execute(query.statement, query.params)

    def __next__(self):
        return self.row_class(self.cursor)

    if sys.version_info[0] < 3:
        def next(self):
            """Deprecated Python 2 style alias for Python 3 style __next__ method."""
            import warnings
            from Bio import BiopythonDeprecationWarning
            warnings.warn("Please use next(my_iterator) instead of my_iterator.next(), "
                          "the .next() method is deprecated and will be removed in a "
                          "future release of Biopython.", BiopythonDeprecationWarning)
            return self.__next__()


class QuerySingle(Query, QueryRow):
    ignore_warnings = 0

    def __init__(self, *args, **keywds):
        message = self.MSG_FAILURE
        Query.__init__(self, *args, **keywds)
        try:
            self.single_cursor = Query.cursor(self)
        except MySQLdb.Warning:
            if not self.ignore_warnings:
                raise
        self.row_class.__init__(self, self.cursor())
        object.__setattr__(self, "message", self.MSG_SUCCESS)

    def cursor(self):
        return self.single_cursor


class QueryAll(list, Query):
    def __init__(self, *args, **keywds):
        Query.__init__(self, *args, **keywds)
        list.__init__(self, [self.process_row(r) for r in self.cursor().fetchall()])

    def process_row(self, row):
        return row


class QueryAllFirstItem(QueryAll):
    def process_row(self, row):
        return row[0]


class Create(QuerySingle):
    def __init__(self, *args, **keywds):
        try:
            QuerySingle.__init__(self, *args, **keywds)
        except StopIteration:
            self.message = self.MSG_SUCCESS


class Update(Create):
    pass


class Insert(Create):
    MSG_INTEGRITY_ERROR = "Couldn't insert: %s. "

    def __init__(self, *args, **keywds):
        try:
            Create.__init__(self, *args, **keywds)
        except MySQLdb.IntegrityError as error_data:
            self.error_message += self.MSG_INTEGRITY_ERROR % error_data[1]
            try:
                self.total_count
            except AttributeError:
                self.total_count = 0

            raise MySQLdb.IntegrityError(self.error_message)

        self.id = self.cursor().insert_id()
        try:
            self.total_count += self.cursor().rowcount
        except AttributeError:
            self.total_count = self.cursor().rowcount

        if self.cursor().rowcount == 0:
            raise NoInsertionError


def _test(*args, **keywds):
    import doctest
    doctest.testmod(sys.modules[__name__], *args, **keywds)

if __name__ == "__main__":
    if __debug__:
        _test()