Gadfly (database)
Encyclopedia
Gadfly is a relational database management system
Relational database management system
A relational database management system is a database management system that is based on the relational model as introduced by E. F. Codd. Most popular databases currently in use are based on the relational database model....

 written in Python
Python (programming language)
Python is a general-purpose, high-level programming language whose design philosophy emphasizes code readability. Python claims to "[combine] remarkable power with very clear syntax", and its standard library is large and comprehensive...

. Gadfly is a collection of Python modules that provides relational database functionality entirely implemented in Python. It supports a subset of the standard RDBMS Structured Query Language (SQL)
SQL
SQL is a programming language designed for managing data in relational database management systems ....

.

Gadfly runs wherever Python runs and supports client
Client (computing)
A client is an application or system that accesses a service made available by a server. The server is often on another computer system, in which case the client accesses the service by way of a network....

/server
Server (computing)
In the context of client-server architecture, a server is a computer program running to serve the requests of other programs, the "clients". Thus, the "server" performs some computational task on behalf of "clients"...

 on any platform that supports the standard Python socket
Berkeley sockets
The Berkeley sockets application programming interface comprises a library for developing applications in the C programming language that perform inter-process communication, most commonly for communications across a computer network....

 interface. The file format
File format
A file format is a particular way that information is encoded for storage in a computer file.Since a disk drive, or indeed any computer storage, can store only bits, the computer must have some way of converting information to 0s and 1s and vice-versa. There are different kinds of formats for...

s used by Gadfly for storage are cross-platform—a gadfly database directory can be moved from Win95 to Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...

 using a binary copying mechanism and gadfly will read and run the database.

It supports persistent databases consisting of a collection of structured tables with indices, and a large subset of SQL for accessing and modifying those tables. It supports a log based recovery protocol which allows committed operations of a database
Database
A database is an organized collection of data for one or more purposes, usually in digital form. The data are typically organized to model relevant aspects of reality , in a way that supports processes requiring this information...

 to be recovered even if the database was not shut down in a proper manner (i.e., in the event of a CPU or software crash, [but not in the event of a disk crash]). It also supports a TCP/IP Client/Server mode where remote clients can access a Gadfly database over a TCP/IP network (such as the Internet) subject to configurable security mechanisms.

Since Gadfly depends intimately on the kwParsing
Parsing
In computer science and linguistics, parsing, or, more formally, syntactic analysis, is the process of analyzing a text, made of a sequence of tokens , to determine its grammatical structure with respect to a given formal grammar...

 package it is distributed as part of the kwParsing package, under the same copyright.

Gadfly allows Python programs to store, retrieve and query tabular data without having to rely on any external database engine or package. It provides an in-memory relational database style engine for Python programs, complete with a notion of a "committed, recoverable transaction" and "aborts".

Usage

The main "gadfly" module attempts to faithfully adhere to Greg Stein
Greg Stein
Greg Stein , living in Fairfax, VA, USA, is a programmer, speaker, sometime standards architect, and open-source software advocate, appearing frequently at conferences and in interviews on the topic of open-source software development and use.He is a director of the Apache Software Foundation, and...

's Python Database API
Application programming interface
An application programming interface is a source code based specification intended to be used as an interface by software components to communicate with each other...

, as discussed and certified by the Python DB-SIG.

Concurrent database updates are not supported. The "databases" are currently designed to be written/modified by one process in isolation. Multiple processes can access a Gadfly database when accesses are arbitrated by a tcp/ip Gadfly server process.

Creating a new database

Unlike most Python/database-engine interfaces Gadfly databases must be created using Python. To accomplish this programmers use:

import gadfly
connection = gadfly.gadfly

with no arguments. Then they startup a database using the startup method:

connection.startup("mydatabase", "mydirectory")

Here "mydirectory" must be a directory which exists and which can be written to in order to store the database files. The startup creates some files in "mydirectory". This has the effect of clobbering any existing Gadfly database called "mydatabase" in the directory "mydirectory". Gadfly will not allow a start up the same connection twice, however.

The first "import gadfly" reads in and initializes some rather large data structures used for parsing SQL, and thus may take longer than other module imports.

Within the database the user can create tables, populate them, and commit the result when they are happy:

cursor = connection.cursor
cursor.execute("create table ph (nm varchar, ph varchar)")
cursor.execute("insert into ph(nm, ph) values ('arw', '3367')")
cursor.execute("select * from ph")
for x in cursor.fetchall:
print x
# prints ('arw', '3367')
connection.commit

Reconnecting to an existing database

Once a database exists it can be reconnected to:

import gadfly
connection = gadfly.gadfly("mydatabase", "mydirectory")

This will read in the database tables with the most recently committed values. The initialized database is then queried and updated:

cursor = connection.cursor
cursor.execute("update ph set nm='aaron' where nm='arw'")
cursor.execute("select * from ph")
for x in cursor.fetchall:
print x
# prints ('aaron', '3367')

If the user does not want to commit updates then the do not execute a commit on the connection object (which writes out the tables). To restore the old values from the existing database they use:

connection.abort

Updates are only stored upon a connection.commit. [Actually, if autocheckpoint is disabled, updates are only stored to table files on checkpoint—see the documentation on the recovery mechanism.]

print cursor.pp

to "pretty print" the result of any evaluation (which might be None for a non-select).

Features

In this version all tables are read into memory upon "connecting" to the database and "touched" tables are written out upon checkpoint. Each table is represented as a separate file in the destination directory, and there is a "data definition" file as well (a list of data definition declarations). During active use a log file
Log file
The term log file can refer to:*Text saved by a computer operating system to recored its activities, such as by the Unix syslog facility*Output produced by a data loggerAlso see Wikibooks chapter...

 appears int the active directory as well, and if the process crashes this log file is used to recover committed operations.
The SELECT statement

At this point Gadfly supports quite a lot of the SQL semantics requested in the ODBC 2.0 specification. SQL statements supported include the SELECT:

SELECT [DISTINCT|ALL] expressions or *
FROM tables
[WHERE condition]
[GROUP BY group-expressions]
[HAVING aggregate-condition]
[union-clause]
[ORDER BY columns]

This statement is quite powerful. It reads as follows:

1.Make all combinations of rows from the tables (FROM line)
2. Eliminate those combinations not satisfying condition (WHERE line)
3.(if GROUP present) form aggregate groups that match on group-expressions
4.(if HAVING present) eliminate aggregate groups that don't satisfy the aggregate-condition.
5. compute the columns to keep (SELECT line).
6.(if union-clause present) combine (union, difference, intersect) the result with the result of another select statement.
7. if DISTINCT, throw out redundant entries.
8.(if ORDER present) order the result by the columns (ascending or descending as specified, with precedence as listed).

The actual implementation in gadfly is much better than the intuitive reading, particularly at steps 1 and 2 (which are combined via optimizing transformations and hash join algorithms).

Conditions may include equalities, and inequalities of expressions. Conditions may also be combined using AND, OR, NOT. Expressions include column names, constants, and standard arithmetic operations over them.

Embedded queries supported include subquery expressions, expr IN (subselect), quantified comparisons, and the EXISTS (subselect) predicate.

Aggregate tests and computations can only be applied after the GROUPing and before the columns are selected (steps 3,4,5). Aggregate operations include COUNT(*), COUNT(expression), AVG(expression), SUM(expression), MAX(expression), MIN(expression), and the non-standard MEDIAN(expression). These may be applied to DISTINCT values (throwing out redundancies, as in COUNT(DISTINCT drinker). if no GROUPing is present the aggregate computations apply to the entire result after step 2.

There is much more to know about the SELECT statement. The test suite test/test_gadfly.py gives numerous examples of SELECT statements.

Table creation and "data types"

Create tables using the CREATE TABLE statement:

CREATE TABLE name (colname datatype [, colname datatype...])

Data types currently "supported" are integer
Integer
The integers are formed by the natural numbers together with the negatives of the non-zero natural numbers .They are known as Positive and Negative Integers respectively...

, float
Float
-Float:* Public float, the free float of a public company is an estimate of number of shares of a stock held in public hands* Fishing float, a bite indicator used in angling...

, and varchar
Varchar
A varchar or Variable Character Field is a set of character data of indeterminate length. The term varchar refers to a data type of a field in a database management system...

. They are ignored by the implementation, anything that is hashable and marshallable can currently go in any column (but that is likely to change). For example:

create table frequents
(drinker varchar,
bar varchar,
perweek integer)

At present tuples, complexes, or anything else can be put into a column specified as "varchar".
Other supported statements

Gadfly also supports the searched DELETE and UPDATE; INSERT VALUES and INSERT subselect; CREATE/DROP INDEX, and DROP TABLE. These have the informal syntax:

DELETE FROM table WHERE condition
UPDATE table SET col=expr [, col=expr...] WHERE condition
INSERT INTO table [(column [, column...])] values (value [, value...])
INSERT INTO table [(column [, column...])] subselect
CREATE [UNIQUE] INDEX name ON table (column [, column...])
DROP TABLE table
DROP INDEX name
Multiple statements may be executed in one cursor.execute(S) by separating the statements with semicolons in S, for example S might have the string value:

drop index tdindex;
drop table templikes
SQL is case insensitive.
Dynamic Values

Expressions also include the special expression '?' (the ODBC-style dynamic expression) as in:

insertstat = "insert into ph(nm,ph) values (?, ?)"
cursor.execute(insertstat, ('nan', "0356"))
cursor.execute(insertstat, ('bill', "2356"))
cursor.execute(insertstat, ('tom', "4356"))

Dynamic values allow the cursor to use the same parsed expression many times for a similar operation. Above the insertstat is parsed and bound to the database only once. Using dynamic attributes should speed up accesses. Thus the above should run much faster than the equivalent:

cursor.execute("insert into ph(nm,ph) values ('nan', '0356')");
cursor.execute("insert into ph(nm,ph) values ('bill', '2356')");
cursor.execute("insert into ph(nm,ph) values ('tom', '4356')");

Dynamic attributes can appear in other statements containing expressions (such as SELECTs, UPDATEs and DELETEs too).

For SELECT, UPDATE, and DELETE the dynamic expression substitutions must consist of a single tuple, as in:

stat = "select * from ph where nm=?"
cursor.execute(stat, ("nan",))
...
cursor.execute(stat, ("bob",))
...

Since the dynamic substitution eliminates the need for parsing and binding (expensive operations!) the above should run faster than the equivalent:

cursor.execute("select * from ph where nm='nan'")
...
cursor.execute("select * from ph where nm='bob'")
...

If several similar queries are repeated multiple times, each query "template string" is assiciated with a unique cursor object so that each template must be parsed and bound only once. Some relatively complex queries from the test suite run 2 to 3 times faster after they have been parsed and bound, even without the kjbuckets builtin. With kjbuckets the same ran 5 to 10 times faster.
Multiple Batch Inserts and Dynamic Values

For the special case of INSERT VALUES a list of substitution tuples allows the query engine to perform the inserts in optimized batch mode. Thus the fastest way to perform the three inserts given earlier is:

data = [('nan', "0356")), ('bill', "2356"), ('tom', "4356")]
stat = "insert into ph(nm,ph) values (?, ?)"
cursor.execute(stat, data)

It would be even faster if the cursor had previously executed the stat with different data (since then no parsing or binding would occur).
Introspection

By default a gadfly database automatically includes "introspective" tables which allow a gadfly query to "query the shape of the database" -- for example to view table names and names of rows in tables:

>>> g = gadfly
>>> g.startup("dbtest", "dbtest")
>>> c = g.cursor
>>> c.execute("select * from __table_names__")
>>> print c.pp
IS_VIEW | TABLE_NAME
=

1 | __TABLE_NAMES__
1 | DUAL
1 | __DATADEFS__
1 | __COLUMNS__
1 | __INDICES__
1 | __INDEXCOLS__

Here DUAL is a standard one row/one column test table (from the Oracle tradition) and the other tables provide information about the database schema:

>>> c.execute("create table t1 (a varchar, b varchar)")
>>> c.execute("create table t2 (b varchar, c varchar)")
>>> c.execute("create unique index t1a on t1(a)")
>>> c.execute("create index t1b on t1(b)")
>>> c.execute("select * from __table_names__")
>>> print c.pp
IS_VIEW | TABLE_NAME
=

0 | T1
1 | __DATADEFS__
1 | __INDICES__
0 | T2
1 | __TABLE_NAMES__
1 | __COLUMNS__
1 | DUAL
1 | __INDEXCOLS__
>>> c.execute("select * from __columns__")
>>> print c.pp
COLUMN_NAME | TABLE_NAME

A | T1
B | T1
NAME | __DATADEFS__
DEFN | __DATADEFS__
INDEX_NAME | __INDICES__
TABLE_NAME | __INDICES__
IS_UNIQUE | __INDICES__
TABLE_NAME | __TABLE_NAMES__
IS_VIEW | __TABLE_NAMES__
B | T2
C | T2
COLUMN1 | DUAL
TABLE_NAME | __COLUMNS__
COLUMN_NAME | __COLUMNS__
INDEX_NAME | __INDEXCOLS__
COLUMN_NAME | __INDEXCOLS__
>>> c.execute("select * from __indices__")
>>> print c.pp
IS_UNIQUE | TABLE_NAME | INDEX_NAME

0 | T1 | T1B
1 | T1 | T1A
>>> c.execute("select * from __indexcols__")
>>> print c.pp
COLUMN_NAME | INDEX_NAME

B | T1B
A | T1A
>>> c.execute("select * from dual")
>>> print c.pp
COLUMN1
=

0

Interactive testing

After installation, the created database can be interactively tested from the same directory using the interactive interpreter:

Python 2.1.3 (#1, Apr 30 2002, 19:37:40)
[GCC 2.96 20000731 (Red Hat Linux 7.1 2.96-96)] on linux2
Type "copyright", "credits" or "license" for more information.
>>>
>>> from gadfly import gadfly
>>> connection = gadfly("test", "dbtest")
>>> cursor = connection.cursor
>>> cursor.execute("select * from frequents")
>>> cursor.description
(('DRINKER', None, None, None, None, None, None), ('PERWEEK', None, None,
None, None, None, None), ('BAR', None, None, None, None, None, None))
>>> print cursor.pp
DRINKER | PERWEEK | BAR

adam | 1 | lolas
woody | 5 | cheers
sam | 5 | cheers
norm | 3 | cheers
wilt | 2 | joes
norm | 1 | joes
lola | 6 | lolas
norm | 2 | lolas
woody | 1 | lolas
pierre | 0 | frankies
>>>

Architecture

The SQL grammar is described in grammar.py, the binding of the grammar constructs to semantic objects is performed in bindings.py, the semantic objects and their execution strategies is defined in semantics.py. The semantics use a lot of classical and non-classical logic (cylindric logic) as well as optimization heuristics to define a relatively efficient and correct implementation of SQL.

The most basic data structures of the implementation are given in either kjbuckets0.py or the faster kjbucketsmodule.c, which implement the same data type signatures in Python and in a C extension to Python respectively.

The database.py module is a simple wrapper that provides a standard DBAPI interface to the system.

The test suite test/test_gadfly.py attempts to provide a regression test and a demonstration of the system.

The SQL parser also requires the kwParsing parser generation package, which consists of a number of additional python modules.

Tools

With gfplus a gadfly database can be interactively manipulated with SQL commands.
The tool works similar to Oracle
Oracle Database
The Oracle Database is an object-relational database management system produced and marketed by Oracle Corporation....

's SQL*Plus.

Concurrency

Because it lacks true concurrency control
Concurrency control
In information technology and computer science, especially in the fields of computer programming , operating systems , multiprocessors, and databases, concurrency control ensures that correct results for concurrent operations are generated, while getting those results as quickly as possible.Computer...

 and file-system based indexing it is not appropriate for very large multiprocess transaction
Database transaction
A transaction comprises a unit of work performed within a database management system against a database, and treated in a coherent and reliable way independent of other transactions...

-based systems.

Two applications may access the same database concurrently. However, changes made by one application may not be seen by the other application until after it restarts. This may be because each application loads the database in-memory at startup only.

External links

The source of this article is wikipedia, the free encyclopedia.  The text of this article is licensed under the GFDL.
 
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