MySQL Introduction. Practical Course Integrative Bioinformatics. March 7, 2012

Transcription

1 MySQL Introduction Practical Course Integrative Bioinformatics March 7,

2 What is MySQL? MySQL ist the most popular open source SQL database. Originally developed by MySQL AB it is now owned by Oracle Corporation. From the beginning, MySQL was distributed under a dual license scheme, with a commercial license and an open source license (GPL) in parallel. The business model of MySQL AB was to sell support and services for MySQL users. MySQL is a database management system. A database is a structured collection of data. This can be everything, from a simple shopping list over image galeries to the huge collections of information in a corporate network. In order to add data to a computer database, to retrieve the data, and to process the data, a database management system such as MySQL is necessary. As computers are particularly good for handling large amounts of data, database management plays a central role in computer science. Database management systems can be stand alone programs as well as parts of other applications. MySQL is a relational database management system. A relational database stores data in separate tables instead of storing them in just a single storage area. In this fashion, speed and flexibility are increased. Tables are interconnected by defined relations allowing to combine data of different tables in queries. In oder to formulate such queries, the structured query language SQL, the most widely used standardized query language for databases, is used. Introduction This section contains a quick introduction to MySQL in form of a tutorial. It will be shown, how to use the mysql client program to create and use a database. The program mysql is an interactive program that connects to the MySQL server, sends queries to the database, and displays their results. mysql can also be used in batch mode, i.e. you write your query into a file and then send it to mysql for processing. In this tutorial both modes are described. More detailed information about MySQL can be found in the MySQL Manual available online under the URL You can start mysql with the option --help to get a list of options: shell> mysql --help 2

3 Connecting to and disconnecting from a server To connect to a server you typically have to specify a MySQL user name and a password. If the server runs on a computer different from yours, you also have to specify the host name. If you want to use MySQL that does not run on the default port, you also have to specify the port. shell> mysql -h host -P port -u user -p Enter password: ******** In our group the MySQL server runs on the host pride. Details of your log in information are given in the assignment for day 4. If the connection is established, you can see some introductory information followed by the MySQL prompt: shell> mysql -h host -P port -u user -p Enter password: ******** Welcome to the MySQL monitor. Commands end with ; or \g. Your MySQL connection id is 1272 Server version: log Source distribution Type help; or \h for help. Type \c to clear the buffer. mysql> The prompt shows you that mysql is ready for entering commands. After successful connection, you can disconnect at any time with the command QUIT at the mysql prompt: mysql> QUIT Bye Entering commands At the mysql prompt you can enter commands. These can be MySQLspecific commands or SQL-queries. A command needs not to be entered in a single line; instead, commands that need more lines can also be given. mysql detects the end of your statement not by a linebreak but by a semicolon at the end. In other words: mysql collects the lines but starts executing them not until it sees the semicolon. 3

4 Selecting and creating a database Use the command SHOW to discover which databases are currently available on the server: mysql> SHOW DATABASES; Creation of a database named sip (supplier, items, projects) mysql> create database sip; Query OK, 1 row affected (0.00 sec) and selection of the database sip mysql> USE ltp database changed Creation of tables Tables can be created you guessed it with the CREATE TABLE statement. mysql> CREATE TABLE supplier ( -> snr VARCHAR(5) NOT NULL PRIMARY KEY, -> sname VARCHAR(20) NOT NULL, -> status INTEGER, -> city VARCHAR(20) NOT NULL -> ); Query OK, 0 rows affected (0.01 sec) mysql> CREATE TABLE item ( -> inr VARCHAR(5) NOT NULL PRIMARY KEY, -> iname VARCHAR(20) NOT NULL, -> color VARCHAR(10), -> weight DOUBLE NOT NULL, -> city VARCHAR(20) NOT NULL -> ); Query OK, 0 rows affected (0.00 sec) mysql> CREATE TABLE project ( -> pnr VARCHAR(5) NOT NULL, -> pname VARCHAR(20) NOT NULL, -> city VARCHAR(20) NOT NULL, 4

5 -> PRIMARY KEY (pnr) -> ); Query OK, 0 rows affected (0.00 sec) mysql> CREATE TABLE shipment ( -> snr VARCHAR(5) NOT NULL, -> inr VARCHAR(5) NOT NULL, -> pnr VARCHAR(5) NOT NULL, -> count INTEGER NOT NULL, -> PRIMARY KEY (snr,inr,pnr), -> FOREIGN KEY (snr) REFERENCES supplier, -> FOREIGN KEY (inr) REFERENCES item, -> FOREIGN KEY (pnr) REFERENCES project -> ); Query OK, 0 rows affected (0.01 sec) Meaning of the tables: supplier A supplier has an identifier (snr), a name (sname), a status, and is located in a city. item An item is described by its identifier (inr), name (iname), color, weight, and the city where it is stored. project A project has an identifier (pnr), a name (pname), and is located in a city. shipments A supplier (snr) ships a certain number (count) of items (inr) to a project (pnr). More information about the CREATE TABLE statement, data types, primary keys, and foreign keys can be found in the MySQL Manual. The MySQL command SHOW TABLES lists all tables from the currently selected database. mysql> SHOW TABLES; Tables_in_sip 5

6 supplier shipment project item rows in set (0.00 sec) With the command DESCRIBE you can obtain more detailed information about the structure of a table. mysql> DESCRIBE supplier; Field Type Null Key Default Extra snr varchar(5) PRI sname varchar(20) status int(11) YES NULL city varchar(20) rows in set (0.00 sec) Listed are all attributes (Field) with their respective data types (Type). The field Null informs you whether a tuple can also have an undefined value in a row. Important is also the field Key providing all attributes of the primary key. Deletion of tables Tables can be deleted with the command DROP: mysql>drop TABLE supplier; For the following let us assume, we did not delete the table. Filling the tables with data After the creation of tables they have to be filled with data. For this purpose the LOAD DATA and the INSERT commands are used. The following table shows some data for the supplier table: 6

7 Table 1: Data for the supplier table lname status city S1 Smith 20 London S2 Jones 10 Paris S3 Blake 30 Paris S4 Clark 20 London S5 Adams 30 Athens LOAD DATA statement You can write a text file supplier.txt containing one data record per line using tab-separated values in the order of the rows of the CREATE TABLE command. mysql> LOAD DATA LOCAL INFILE "supplier.txt" -> INTO TABLE supplier; INSERT statement If you wand to add data records individually, use the INSERT command. In its simplest form you can specify values for each row, again in the order of the CREATE TABLE statement. mysql> INSERT INTO supplier -> VALUES ( S1, Smith,20, London ); Note that strings are within hyphens. To indicate a missing value, use NULL in the INSERT command. With LOAD DATA use \N, instead. SELECT statement The SELECT statement is used to retrieve data from a table. The general form of the command is: SELECT rows_to_select FROM table WHERE constraints_to_fulfill rows to select specifies what you want to see. This can either be a list of rows or * to see all rows. table denotes the table from which you want 7

8 to see the rows. The WHERE part is optional. If it is given, it specifies constraints that have to match with the rows in order to see them. Examples Select all data fro the supplier table: mysql> SELECT * FROM supplier; snr sname status city S1 Smith 20 London S2 Jones 10 Paris S3 Blake 30 Paris S4 Clark 20 London S5 Adams 30 Athens 5 rows in set (0.00 sec) Select a defined row: mysql> SELECT * FROM supplier WHERE sname = "Blake"; snr sname status city S3 Blake 30 Paris row in set (0.00 sec) Combine two or more constraints: mysql> SELECT * FROM supplier WHERE city = "London" OR status = 10; snr sname status city S1 Smith 20 London S2 Jones 10 Paris S4 Clark 20 London 3 rows in set (0.00 sec) mysql> SELECT * FROM suplier WHERE city = "Paris" AND status > 20; 8

9 snr sname status city S3 Blake 30 Paris row in set (0.00 sec) mysql> SELECT * FROM supplier WHERE (city = "Paris" AND status = 30) -> OR (city = "Athens" AND status = 30); lnr lname status city S3 Blake 30 Paris S5 Adams 30 Athens 2 rows in set (0.00 sec) Select only some rows: mysql> SELECT sname,city FROM supplier; sname city Smith London Jones Paris Blake Paris Clark London Adams Athens rows in set (0.00 sec) Use of DISTINCT: mysql> SELECT city FROM supplier; city London Paris Paris London 9

10 Athens rows in set (0.00 sec) mysql> SELECT DISTINCT city FROM supplier; city London Paris Athen rows in set (0.00 sec) Sorting of results: mysql> SELECT * FROM supplier ORDER BY sname; snr sname status city S5 Adams 30 Athen S3 Blake 30 Paris S4 Clark 20 London S2 Jones 10 Paris S1 Smith 20 London 5 rows in set (0.00 sec) Working with NULL values: It can happen that the value of an attribute is not set, as long as it is allowed according to the definition of the tabhe in the CREATE TABLE statement. The value of this attribute is then NULL in the respective tuple. mysql> INSERT INTO supplier -> VALUES ( S6, Hofer,NULL, Vienna ); mysql> SELECT * FROM lieferant; snr sname status city S1 Smith 20 London S2 Jones 10 Paris 10

11 S3 Blake 30 Paris S4 Clark 20 London S5 Adams 30 Athens S6 Hofer NULL Vienna 6 rows in set (0.00 sec) mysql> SELECT * FROM supplier WHERE status IS NULL; snr sname status city S6 Hofer NULL Vienna 1 row in set (0.00 sec) mysql> SELECT * FROM supplier WHERE status IS NOT NULL; snr sname status city S1 Smith 20 London S2 Jones 10 Paris S3 Blake 30 Paris S4 Clark 20 London S5 Adams 30 Athens 5 rows in set (0.00 sec) Please note the following important difference: mysql> SELECT * FROM supplier WHERE status = NULL; Empty set (0.00 sec) mysql> SELECT * FROM supplier WHERE status!= NULL; Empty set (0.00 sec) Pattern matching For pattern matching, MySQL offers the standard SQL search pattern commands. It also offers a search pattern option based on regular expressions, similar to those used in the UNIX tools such as vi, grep, or sed. The SQL search patterns allow to use to match to a single character and % to 11

12 match to any number of character. In the MySQL SQL search patterns capitalizion by default does not play a role. Note that = or!= cannot be used when you use SQL search patterns. Use the LIKE or NOT LIKE comparision operators instead. For instance, this is how to find cities starting with the letter L : mysql> SELECT city FROM supplier WHERE city LIKE "L%"; city London London rows in set (0.00 sec) This is how to find names ending with an s : mysql> SELECT sname FROM supplier WHERE sname LIKE "%s"; sname Jones Adams rows in set (0.00 sec) This is how to find names containing the letter a at any position: mysql> SELECT sname FROM supplier WHERE sname LIKE "%a%"; sname Blake Clark Adams rows in set (0.00 sec) In order to find cities with exactly five characters, use the search pattern symbol: mysql> SELECT city FROM supplier WHERE city LIKE " "; 12

13 city Paris Paris rows in set (0.00 sec) The other pattern matching method uses extended regular expressions. If you want to use these search patterns, use the REGEXP and NOT REGEXP operators (or the synonymous RLIKE and NOT RLIKE). UPDATE statement Modifiation of tuples: mysql> UPDATE supplier SET status = 15 WHERE snr = S6 ; mysql> SELECT * FROM supplier; lnr lname status city S1 Smith 20 London S2 Jones 10 Paris S3 Blake 30 Paris S4 Clark 20 London S5 Adams 30 Athens S6 Hofer 15 Vienna 6 rows in set (0.00 sec) DELETE statement Deletion of tuples: mysql> DELETE FROM supplier WHERE snr = S6 ; mysql> SELECT * FROM supplier; lnr lname status city S1 Smith 20 London S2 Jones 10 Paris S3 Blake 30 Paris 13

14 S4 Clark 20 London S5 Adams 30 Athens 5 rows in set (0.00 sec) Delete everything: mysql> DELETE FROM supplier; mysql> SELECT * FROM supplier; Empty set (0.00 sec) For the following examples we need again a filled table: LOAD DATA LOCAL INFILE "supplier.txt" INTO TABLE supplier; COUNT() function To count tuples: mysql> SELECT COUNT(*) FROM lieferant; COUNT(*) row in set (0.00 sec) MAX() function To determine the maximal value in a column: mysql> SELECT * FROM item; inr tname color weight city P1 Nut red 12 London P2 Bolt yellow 17 Paris P3 SCREW blue 17 Rome P4 Screw red 14 London P5 Cam blue 12 Paris P6 Cog red 19 London rows in set (0.00 sec) 14

15 mysql> SELECT MAX(weight) FROM item; MAX(weight) row in set (0.00 sec) You can find many more functions in the MySQL Manual. GROUP BY and HAVING These commands are helpful to arrange the contents of a result table. With the following query the question is answered, how many suppliers are located in each town: mysql> SELECT city, COUNT(*) FROM supplier GROUP BY city; city COUNT(*) Athens 1 London 2 Paris rows in set (0.00 sec) Which cities have more than one supplier? mysql> SELECT city, COUNT(*) -> FROM supplier -> GROUP BY city -> HAVING COUNT(*) >1; city COUNT(*) London 2 Paris rows in set (0.00 sec) 15

16 Using more than one table In the FROM clause more than one table can be specified. Content of the table shipments: mysql> SELECT * FROM shipments; snr inr pnr count S1 P1 J1 200 S1 P1 J4 700 S2 P3 J1 400 S2 P3 J2 200 S2 P3 J3 200 S2 P3 J4 500 S2 P3 J5 600 S2 P3 J6 400 S2 P3 J7 800 S2 P5 J2 100 S3 P3 J1 200 S3 P4 J2 500 S4 P6 J3 300 S4 P6 J7 300 S5 P2 J2 200 S5 P2 J4 100 S5 P5 J5 500 S5 P5 J7 100 S5 P6 J2 200 S5 P1 J4 100 S5 P3 J4 200 S5 P4 J4 800 S5 P5 J4 400 S5 P6 J rows in set (0.00 sec) We now want to expand the output with the city names of the suppliers. mysql> SELECT supplier.city, shipments.* -> FROM shipments, supplier -> WHERE shipment.snr=supplier.snr; 16

17 city snr tnr pnr anzahl London S1 P1 J1 200 London S1 P1 J4 700 Paris S2 P3 J1 400 Paris S2 P3 J2 200 Paris S2 P3 J3 200 Paris S2 P3 J4 500 Paris S2 P3 J5 600 Paris S2 P3 J6 400 Paris S2 P3 J7 800 Paris S2 P5 J2 100 Paris S3 P3 J1 200 Paris S3 P4 J2 500 London S4 P6 J3 300 London S4 P6 J7 300 Athens S5 P1 J4 100 Athens S5 P2 J2 200 Athens S5 P2 J4 100 Athens S5 P3 J4 200 Athens S5 P4 J4 800 Athens S5 P5 J4 400 Athens S5 P5 J5 500 Athens S5 P5 J7 100 Athens S5 P6 J2 200 Athens S5 P6 J rows in set (0.02 sec) What happened here? To obtain the information about the cities of the suppliers, both tables had to be given in the FROM clause. The meaning of this FROM clause is that the Cartesian product of both tables is calculated. This results in 5*24=120 result tuples. However, we are only interested in the cities of each supplier. Thus, the Cartesian product is filtered using the constraints in the WHERE clause. Only tuples were selected that match in the values of their snr attributes. As both tables have the attribute snr in common, it is helpful to use the notation table name.attribute name to avoid name conflicts. 17

18 Batch mode In the previous sections you learned to use mysql interactively to enter queries and inspect the results. You can use mysql also in batch mode. All you have to do is to write the commands you want to use to a file and tell mysql to read its input from this file: shell> mysql -h host -u user -p < batch-file 18