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Preliminary Definitions
•
MySQL: An Open Source, Enterprise-level, multi-threaded, relational
database management system that stores and retrieves data using the
Structured Query Language
o licensed with the GNU General public license http://www.gnu.org/
•
Structured Query Language (SQL): A standardized query language for getting
information from a relational database.
•
Relational Database: A database that stores data in the form of relational tables
as 0pposed to flat files.
•
Database Management System (DBMS): A system that manages relational
databases; A collection of programs that enabling the storage, modification, and
extraction of information from a database.
Main Features
• Fully multi-threaded using kernel threads.
• Works on many different platforms.
• Many column types
• Very fast joins using an optimized one-sweep multi-join
• Full operator and function support in the SELECT and
WHERE parts of queries.
• You can mix tables from different databases in the same
query.
• A privilege and password system that is very flexible and
secure.
• Handles large databases.
• Tested with a broad range of different compilers. (C/C++)
• No memory leaks.
• Full support for several different character sets.
Cells, Rows, Tables and Databases
• Cell -- a single (scalar) value.
12134
Cells, Rows, Tables and Databases
• Row -- a group of scalar values representing
a single instance of an object or event.
12135
1310391314 Letter: July 23,1842
Cells, Rows, Tables and Databases
• Table -- a series of rows describing separate
objects or events.
ID
12134
12135
12136
METSID
LABEL
1090313313 Letter: Nov ember 18, 1838
1310391314 Letter: July 23,1842
1313020414 Waterloo at Sunset
Cells, Rows, Tables and Databases
• Database -- a collection of related tables
describing various facets of a group of objects
or events.
OBJECTS
ID
METSID
LABEL
CLINKS
METSID
COLID
COLS
ID
NAME
URL
ABSTRACT
Relations -- One to One
Table1
Record
Record
Record
Record
Record
Record
Record
Table2
Record
Record
Record
Record
Record
Record
Record
Relations -- One to Many
Table1
Record
Record
Record
Record
Record
Record
Record
Table2
Record
Record
Record
Record
Record
Record
Record
Relations -- Many to Many
Table1
Record
Record
Record
Record
Record
Record
Record
Table2
Record
Record
Record
Record
Record
Record
Record
Relational Databases
• A database is a collection of tables
• Columns define attributes of the data
o
All data in a column must have the same data type
• A record is stored in a row
table name
row
First Name
Nadia
Madhu
Ajuma
Wade
Helen
Employees
Last Name
Li
Charu
Kinsaka
Randal
Clark
Phone
2687
7856
4489
5257
2147
column
Use a Relational Database When…
• You have a very large dataset
• There is redundant data
o Wastes disk space
o Increases errors
• Information must be updated in multiple
locations
• Security is important
o Different users can be granted different
permissions
• Strict enforcement of data types is important
Spreadsheet Example
Title
A House for Mr. Biswas
Midnight's Children
On the Road
Author
VS Naipaul
Salman Rushdie
Jack Kerouac
Borrower
Sarah
Phone
646.555.1234
Spreadsheet Example
Title
A House for Mr. Biswas
Midnight's Children
On the Road
Author
VS Naipaul
Salman Rushdie
Jack Kerouac
Borrower
Sarah
Phone
646.555.1234
One Flew Over the Cuckoo's Nest
Sula
Villette
Ken Kesey
Toni Morrison
Charlotte Bronte
Sarah
646.555.1244
Jim
646.555.4586
Data is inconsistent!
Now imagine you are designing the New York Public
Library database which has tens of million books and
well over a million cardholders.
Database Design
Entity Relationship Design
Entity (“thing”, “object”)
Table
Attributes (describe entity)
Columns
Entity Instance
Row
Relationships between entities preserved in relationships
between tables.
If you are interested in learning more formal design
methods look up “normalization” and/or “third normal
form”.
Our data
Ensembl Gene ID
Symbol /
Name
Chromo
some
Common
Name
Species
ENSG00000186891.3
TNFRSF18
1
1044947
1048147
8784
9606
human
Homo sapiens
ENSG00000078808.4
CAB45
1
1058370
1073469
51150
9606
human
Homo sapiens
ENSG00000176022.1
B3GALT6
1
1073703
1076476
126792
9606
human
Homo sapiens
ENSG00000160087.5
UBE2J2
1
1095352
1115292
118424
9606
human
Homo sapiens
ENSG00000162572.4
SCNN1D
1
1123634
1133467
6339
9606
human
Homo sapiens
ENSG00000162576.4
MGC3047
1
1194130
1199973
84308
9606
human
Homo sapiens
ENSG00000175756.3
AKIP
1
1215168
1216641
54998
9606
human
Homo sapiens
ENSG00000131586.2
MRPL20
1
1288703
1294063
55052
9606
human
Homo sapiens
ENSG00000179403.2
WARP
1
1322311
1327547
64856
9606
human
Homo sapiens
ENSG00000160072.5
ATAD3B
1
1358611
1396091
83858
9606
human
Homo sapiens
ENSG00000008128.5
CDC2L2
1
1582617
1604060
985
9606
human
Homo sapiens
ENSG00000169911.4
SLC35E2
1
1611978
1625728
9906
9606
human
Homo sapiens
ENSG00000008130.3
FLJ13052
1
1630975
1659805
65220
9606
human
Homo sapiens
ENSG00000078369.3
GNB1
1
1665027
1770792
2782
9606
human
Homo sapiens
ENSMUSG00000041954.1
TNFRSF18
4
154139702
154142251
21936
10090
mouse
Mus musculus
mouse
Mus musculus
ENSMUSG00000023286.1
Start
Position
(bp)
End
Position
(bp)
LocusLink
ID
Taxonomy
ID
UBE2J2
154057210
1540722964
140499
10090
What entities or “objects”
are 4defined
here?
Is there any redundant data?
What happens if we want to add another species attribute (e.g. genus)?
Our tables
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How do we know which organism a gene belongs to?
Do we have unique identifiers?
Can the organism have more than one gene?
Can the gene have more than one organism?
Our tables
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Means each gene has “one and only one”
organism, but that each organism can
have more than one gene.
This is an example of an entity relationship diagram.
Our tables
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• A primary key is a unique identifier for a record in a
table.
• A foreign key in one table refers to the primary key of
another.
• The gene table has a foreign key, Organism_ID. Each
record in the gene table will have an organism id to link it
to the correct species record in the organism table.
Database Design Caveat
• Sometimes design is “sacrificed” for
speed.
Data Types
float
integer
tinyint
varchar(size)
o stores strings
o size can be between 0 - 255, inclusive
• datetime
What data types should our attributes (columns) be?
• + more
•
•
•
•
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Complete Design
Database name: ensmartdb
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Column
gene_id
ensembl_gene_id
organism_id
name
locuslink
chromosome
chromo_start
chromo_end
description
Column
organism_id
taxonomy_id
common_name
species
Gene
Data Type
integer
varchar(50)
integer
varchar(35)
varchar(10)
tinyint
integer
integer
varchar(255)
Organism
Data Type
integer
integer
varchar(35)
varchar(35)
Connecting to MySQL from the Command
Line
mysql -uusername -p
Example:
>mysql -uroot
To EXIT MySQL:
EXIT;
Basic SQL Commands
• SQL statements end with a semicolon
• View databases
SHOW DATABASES;
START A MYSQL CLIENT
• Without using passwords
(when the password for the specified user is
empty)
mysql -u <user> -h <Host>
• Using passwords
mysql -u <user> -h <Host> -p
Example:
mysql -u root -h localhost
• Exitting with the command quit or exit.
DATA MANAGEMENT
•
•
•
•
•
•
•
•
•
•
•
•
•
•
SHOW DATABASES;
USE databaseName;
SHOW TABLES;
DESCRIBE table;
SELECT * FROM table;
SELECT * FROM table \G
CREATE DATABASE databaseName;
DROP DATABASE databaseName;
CREATE TABLE tableName(name1 type1, name2 type2, ...);
DROP TABLE tableName;
INSERT INTO TABLE VALUES( value1, value2, ...);
SELECT field1, field2, ... FROM tableName;
SELECT * INTO OUTFILE 'C:/tmp/skr.txt' FROM skr;
LOAD DATA INFILE /path/file.txt INTO TABLE skr;
Importing a Database
• Creating a database
CREATE DATABASE trii;
• From the command line:
mysql -uusername -ppassword databasename <
filename.sql
• Example:
o
mysql -uroot trii < trii.sql
Basic SQL Commands
• Use database databasename
USE databasename;
• Display all tables in a database
SHOW TABLES;
Create Table
database name
CREATE TABLE organism (
organism_id INTEGER NOT NULL AUTO_INCREMENT,
column
taxonomy_id INTEGER NOT NULL,
names
common_name VARCHAR(35) NOT NULL,
species VARCHAR(35) NOT NULL,
PRIMARY KEY (organism_id),
UNIQUE (taxonomy_id)
);
View column details for a table
DESC tablename;
Selecting all data
SELECT * FROM tablename;
Select only the columns you need
be faster)
SELECT common_name, species
FROM organism;
(it will
Limiting your data
• Get the species name for a specific
organism (you have the id)
SELECT species
FROM organism
WHERE organism_id=1;
How do we select all the gene names for chromosome 1?
Insert
• Inserting a gene
INSERT INTO gene
(ensembl_gene_id,
organism_id,
name,
chromosome,
chromo_start,
chromo_end) VALUES (‘MY_NEW_GENE’,
1, ‘MY GENE’, 1, 12345, 67890);
• Get the id of the gene:
SELECT gene_id FROM gene WHERE name='MY GENE';
Delete/Update
• Deleting a gene
DELETE FROM gene WHERE gene_id=19;
• Updating a gene
UPDATE gene SET name=‘NEW NAME’
WHERE name=‘AKIP’;
Documentation
• http://www.mysql.com/documentation/
• http://www.mysql.com/documentation/manual.ph
p
• As text
manual.txt
• As HTML
manual_toc.html
• As GNU Info
mysql.info
• As PostScript
manual.ps
http://www.turbolift.com/mysql
PHPMyAdmin
• Web application
• Makes it easier to use MySQL
• To launch: http://localhost/phpmyadmin/
• Download it here:
http://www.phpmyadmin.net/home_page/
downloads.php
Create Database
You are
logged in
as “root”
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To get back to this
page at any time
select “Databases”
Enter name
of database
here and
click
“Create”
Create Table
SQL query used
to create
“ensmartdb”
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We are
currently
using this
database
Enter table name and
number of fields then
click “Go”
We are defining
the columns for
table “gene”
Define Columns
Select
“auto_increment”
here
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Don’t forget to
click “Save”!
Select “Primary”
here since this is
the primary key
Select
“ensmartdb”
to view
tables in
database
Click “gene”
to view
“gene” table
View Database
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Add another
table here
Insert Data
Click on
“insert” to
add data to
table
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Don’t forget to
save by clicking
“Go”!
Click on “Browse”
to
view/edit/delete
data
View/Delete/Edit Data
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Check rows to
edit or delete
Click here to delete
checked rows
Click here to edit
checked rows
Database Users
• To use MySQL you must have a username and
password
• A user in MySQL has permissions set regarding
o
o
MySQL itself (ex. whether or not the user can
create a database)
Specific databases within MySQL
• For example, user “guest” may have permission to view
database “x” but not database “y”
• Multiple users can access a MySQL database
simultaneously
Granting a User Privileges
• PHPMyAdmin is logged in
as user “root”, and has
permission to do anything
• You should NOT make a
habit of connecting to
your database as root
• Create a user with
restricted permissions to
your database instead
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Click “Add new
User”
Granting a User Privileges (Continued)
Enter “User name”,
“Host”, and
“Password”
This are privileges the
user will have on ALL
databases
Granting a User Privileges (Continued)
After you save the
“global” permissions,
you may add database
specific permissions
QuickTime™ and a
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are needed to see this picture.
Select “ensmartdb” to edit
user permissions for
database “ensmartdb”
On the next screen select ONLY the
permissions the user must have
MySQL Access Privilege System
What the Privilege System Does?
• The primary function of the MySQL
privilege system is to authenticate a user
connecting from a given host, and to
associate that user with privileges on a
database such as SELECT, INSERT,
UPDATE, and DELETE.
• When you connect to a MySQL server, your
identity is determined by the host from
which you connect and the username you
specify. When you issue requests after
connecting, the system grants privileges
according to your identity and what you
want to do.
How the Privilege System Works
• MySQL access control involves two stages:
o Stage 1: The server checks whether it should
allow you to connect.
o Stage 2: Assuming that you can connect, the
server checks each statement you issue to see
whether you have sufficient privileges to
perform it.
• For example, if you try to select rows from a
table in a database or drop a table from the
database, the server verifies that you have
the SELECT privilege for the table or the
DROP privilege for the database.
Grant Tables
• The server stores privilege information in the
grant tables of the mysql database
• Access-control decisions are based on the inmemory copies of the grant tables
o The MySQL server reads the contents of these
tables into memory when it starts and re-reads
them under some circumstances
• Normally, you manipulate the contents of the
grant tables indirectly by using the GRANT and
REVOKE statements to set up accounts and
control the privilegee
• The server uses the user, db, and host tables in
the mysql database at both stages of access
control
Columns of user, db, and host
Possible values in privilege columns are ‘Y’ and ‘N’,
default to ‘N’
Columns of user, db, and host
(Cont.)
Important Columns of table_priv
and columns_priv
The tables_priv and columns_priv tables
provide finer privilege
control at the table and column levels.
Scope Columns
Case insensit
The default value for each is the
empty string
Possible Values in tables_priv, and
columns_priv
How the grant tables are used?
• The user table scope columns determine whether to reject
or allow incoming connections. For allowed connections, any
privileges granted in the user table indicate the user's
global (superuser) privileges. These privileges apply to all
databases on the server
• The db table scope columns determine which users can
access which databases from which hosts. The privilege
columns determine which operations are allowed. A privilege
granted at the database level applies to the database and to
all its tables
• The host table is used in conjunction with the db table when
you want a given db table row to apply to several hosts. For
example, if you want a user to be able to use a database
from several hosts in your network, leave the Host value
empty in the user's db table row, then populate the host
table with a row for each of those hosts.
o
The host table is not affected by the GRANT and REVOKE
statements. Most MySQL installations need not use this table
at all.
How the grant tables are used? (Cont.)
• The tables_priv and columns_priv tables
are similar to the db table, but are more
finegrained: They apply at the table and
column levels rather than at the database
level. A privilege granted at the table level
applies to the table and to all its columns.
A privilege granted at the column level
applies only to a specific column.
• The procs_priv table applies to stored
routines. A privilege granted at the routine
level applies only to a single routine.
How the grant tables are used?
• The user table grants privileges that are assigned to you on
a global basis and that apply no matter what the current
database is.
o
For example, if the user table grants you the DELETE privilege,
you can delete rows from any table in any database on the
server host!
• Wise to grant privileges in the user table only to superusers
such as DBA.
• For other users, you should leave the privileges in the user
table set to 'N' and grant privileges at more specific levels
only. You can grant privileges for particular databases,
tables, or columns.
• Global priv. OR (data priv. AND host priv.) OR table priv. OR
column priv.
MySQL Privileges
Grant and Revoke Syntax
Grant Levels
• Global level
o
Global privileges apply to all databases on a given server. These
privileges are stored in the mysql.user table. GRANT ALL ON
*.* and REVOKE ALL ON *.* grant and revoke only global
privileges
• Database level
o
Database privileges apply to all objects in a given database.
These privileges are stored in the mysql.db and mysql.host
tables. GRANT ALL ON db_name.* and REVOKE ALL ON
db_name.* grant and revoke only database privileges
• Table level
o
Table privileges apply to all columns in a given table. These
privileges are stored in the mysql.tables_priv table. GRANT
ALL ON db_name.tbl_name and REVOKE ALL ON
db_name.tbl_name grant and revoke only table privileges.
Grant Levels (Cont.)
• Column level
o Column privileges apply to single columns in a
given table. These privileges are stored in the
mysql.columns_priv table. When using REVOKE,
you must specify the same columns that were
granted
• Routine level
o The CREATE ROUTINE, ALTER ROUTINE,
EXECUTE, and GRANT privileges apply to
stored routines. They can be granted at the
global and database levels. Also, except for
CREATE ROUTINE, these privileges can be
granted at the routine level for individual
routines and are stored in the mysql.procs_priv
table.
64
Priv_type in Grant and Revoke
Priv_type in Grant and Revoke
(Cont.)
When Privilege Changes Take Effect
• When MySQL starts, all grant table contents are
read into memory and become effective for access
control at that point.
• When the server reloads the grant tables,
privileges for existing client connections are
affected as follows:
o Table and column privilege changes take effect
with the client's next request.
o Database privilege changes take effect at the
next USE db_name statement.
o Changes to global privileges and passwords take
effect the next time the client connects.
When Privilege Changes Take Effect (Cont.)
• If you modify the grant tables using GRANT,
REVOKE, or SET PASSWORD, the server notices
these changes and reloads the grant tables into
memory again immediately.
• If you modify the grant tables directly using
statements such as INSERT, UPDATE, or DELETE,
your changes have no effect on privilege checking
until you either restart the server or tell it to
reload the tables.
• To reload the grant tables manually, issue a
FLUSH PRIVILEGES statement or execute a
mysqladmin flush-privileges or mysqladmin reload
command.
MySQL User Account Management
MySQL Usernames and Passwords
• A MySQL account is defined in terms of a
username and the client host or hosts from which
the user can connect to the server. The account
also has a password.
• Difference from the MySQL username and OS
username
o Usernames, as used by MySQL for
authentication purposes, have nothing to do
with login names as used by Windows or Unix
o MySQL usernames can be up to a maximum of
16 characters long
o MySQL passwords have nothing to do with
passwords for logging in to your OS
o MySQL encrypts passwords using its own
algorithm
Adding New User Accounts to MySQL
• You can create MySQL accounts in three
ways:
o By using GRANT statements
o By using CREATE USER statement
o By manipulating the MySQL grant
tables directly
• Create a user without any privileges
• To specify the password as the hashed
value as returned by the PASSWORD(),
include the keyword PASSWORD
Example 1
Example 2
Example 2 (Cont.)
Removing User Accounts
• DROP USER ‘jeffrey’@’locahost’
Limiting Account Resources
• In MySQL 5.0, you can limit the following server resources
for individual accounts:
o The number of queries that an account can issue per hour
o The number of updates that an account can issue per
hour
o The number of times an account can connect to the
server per hour
o The number of simultaneous connections to the server on
a per-account basis
• To set or change limits for an existing account, use a GRANT
USAGE statement at the global level (ON *.*)
• To reset the current counts to zero for all accounts, issue a
FLUSH USER_RESOURCES statement
Example
Assigning Account Password