SQL
What is a database? a collection of data Usually consists of entities and
relations An entity is an individual “object” that exists and is distinguishable from other individuals. Example: specific person, company, event, plant Entities have attributes Example: people have names and addresses A relationship is an association among several entities
Database Management System (DBMS) A computerized record-keeping system Allows operations such as: Adding new files Inserting data into existing files Retrieving data from existing files Changing data Deleting data Removing existing files from the database
Data Models A data model is a collection of concepts for describing data. A schema is a description of a particular collection of data, using the given data model. The relational model of data is the most widely used model today. Main concept: relation, basically a table with
rows and columns. Every relation has a schema, which describes the columns, or fields.
Levels of Abstraction
Relational Databases Data is logically perceived as a two-
dimensional table Relational databases are sets of tables tables are relations
Example Table
Relational Database Query A relational database query is a question about the data, and the answer consists of a new relation containing the result. Queries are one part of the Data
Manipulation Language of a DBMS (we also need to create, update, insert data) Language: Structured Query Language (SQL)
Example SQL query Select G.Accession, G.Medline From Genebank G Where G.source=`baker’s yeast’;
No explicit links between tables Of course, there may be implicit links
in that two tables share the same attribute (like the accession number) In fact, in a relational DB, this is the only way to connect distinct tables, at the logical level anyway A link between one table and another is called a foreign key
Why use a DBMS Data independence and efficient
access. Reduced application development time. Data integrity and security. Uniform data administration. Concurrent access, recovery from crashes.
Example Suppose you created a file to hold names, ID numbers and faculty/student status This was a flat file that resembled a table in a database What if you wanted to now add new data for some of the faculty with credit card information? How would you connect the two tables?
Example Fred
1234567
Mark
2345678
George
3456789
Quinn
4567890
ID
Credit Card
1234567
44444444
4567890
55555555
How to use MySQL Connect to MySQL Server shell> ~clement/mysqlbin/bin/mysql -h pathogen.cs.byu.edu –u cs360 <Enter> Welcome to the MySQL monitor. Type 'help' for help. mysql>
How to use MySQL ď ą Data Definition 1 mysql> SHOW DATABASES;
Database mysql
test tmp
Creating Tables CREATE TABLE image ( image_id INT, image_type CHAR(3), filename CHAR(40), url CHAR(128), Primary Key(image_id)); creates a table with 4 columns and no rows
Another table ď &#x2021; create table image_decoder
(image_type CHAR(3), decoder_program varchar(20), args varchar(20));
Basic Data Types INT - signed integer value. Implementation-dependent
# bits NUMERIC(total length, number of decimal places)
NUMERIC(8,4) - 3 digits, a decimal point, 4 decimal places
REAL - floating point number BIT - single boolean value DATE - year, month, day TIME TIMESTAMP - date/time VARCHAR(length) - variable length string <= length BLOB - Binary Large Object
How to use MySQL Values must be in the right order and fill all columns
INSERT INTO image ( image_id, image_type, filename, url) VALUES ( 1, ‘jpg’, ‘image1’, ‘http://host/dir/image1’)
Values must be the order specified. But, you don’t need to fill all columns.
More insert into image_decoder
values('jpg','/usr/bin/jpgview’,’’);
Selecting Rows SELECT image_type from image
WHERE filename=‘image1’ SELECT image_decoder.decoder_program FROM image_decoder, image WHERE image.filename=‘image1’ AND image.image_type=image_decoder.image_type The Join operation can be viewed as creating a virtual table
on the fly from rows in two or more tables
SELECT * from image GROUP by image_type
Basic Where Clauses Operators =, <, >, <=, >=, != (or <>) WHERE image_id = 2
LIKE - wildcard comparison WHERE decoder_program LIKE ‘c:%’
ISNULL - checks for null value IN - contained in a set (usually for subqueries) WHERE image_id IN (1,2) WHERE image_id IN
SELECT image_id FROM Image
Updating Rows UPDATE Image SET url=‘http://newhost/image1’ WHERE filename=‘image1’
The where clause may select multiple rows e.g. WHERE image_id < 50 If the WHERE clause is excluded, the SET operation is applied to every row in the table
Deleting Rows DELETE from Image WHERE image_id=2 Entire row is removed from the table
DELETE from Image Every row is removed from the table!!!
How to use MySQL ď &#x2021; Data manipulation 2 mysql> SELECT * FROM seqs; +-------+-----------+----------+ | title | accession | sequence | +-------+-----------+----------+ | Human | u235 | cgatcagt | +-------+-----------+----------+
mysql> insert into seqs -> values('Dog','u222','ccgtacgt'); mysql> SELECT * FROM seqs; +-------+-----------+----------+ | title | accession | sequence | +-------+-----------+----------+ | Human | u235 | cgatcagt | | Dog | u222 | ccgtacgt | +-------+-----------+----------+
Add data from file mysql> load data local infile ’/users/faculty/snell/CS360/sample.txt' into table seqs; Delete it mysql> delete from seqs
Redo load with up arrow select title, accession from seqs; update seqs set accession = 'H0794' where title = 'Human-01'; select * from seqs order by title;
More commands ď &#x2021; mysql> select * from seqs where title
like 'Human%';
More commands use mysql; show tables; describe db;
PERL DBI $dbh = DBI->connect("dbi:mysql: database=sequences; host=paintball:1236;", "phylo","") or die("Couldn't connect"); $SQL= "select * from seqs";
$Select = $dbh->prepare($SQL); $Select->execute(); while($Row=$Select->fetchrow_hashref) print "title $Row->{title}, sequence $Row->{sequence} \n"; $dbh->disconnect();
What Is the Perl DBI? The standard Database Interface for
Perl “A perl module and specification that defines a consistent database interface independent of the actual database being used”
Why the Perl DBI? Once upon a time… One language, many database interfaces
Perl 5 - A new way Modules and Objects. The DBI is born.
The future is now… ODBC, Oracle, Informix, Ingres, mSQL, mysql, DB2, Solid,
Sybase, Postgress,
Quickbase,
Empress, Fulcrum, ...
The same database interface
Making simple things easy and difficult things possible Goals Be simple to use for simple applications Have sufficient flexibility to accommodate unusual
functionality and non-SQL databases Conform to applicable standards (ODBC etc.) Enable the creation of database-independent Perl scripts without being limited to the lowest functionality Be free.
A ‘higher-level’ interface than ODBC/JDBC
Under the Hood DBI defines and implements an interface Driver modules do much of the real work DBI provides default methods, functions, tools etc for
drivers Not limited to the lowest common denominator mechanism provided for driver specific extensions Designed and built for speed Valuable detailed call tracing/debugging built-in
So why use the Perl DBI? Because... It delivers what it promises It’s here, there and everywhere
It’s fast, flexible and well proven It’s free, with source Commercial support is available
It has a large user base and a strong future