BITS training: Introduction to relational databases and MySQL - Module 3: Schema design. See http://www.bits.vib.be/index.php?option=com_content&view=article&id=17204047:green-basics-of-databases&catid=81:training-pages&Itemid=190

1. Introduction to MySQL
● Introduction
● Installation
● SQL
● Schema design
● Perl
BITS/VIB Bioinformatics Training – Jun 29, 2011 – Luc Ducazu <luc@daphnia.com>

2. Database schema
● Although you can execute DDL commands from
the MySQL monitor directly, this is not often
done
● There are tools that allow you to design a schema
graphically and generate the CREATE TABLE ...
statements
● Examples:
– MySQL workbench
– Dia

3. MySQL workbench
● Available as a standard package on some Linux
distros (eg Fedora)
● Available as Windows MSI, Linux DEB or RPM
package or source archive from
http://dev.mysql.com/downloads/workbench/
● To install a DEB package:
# dpkg ­i package.deb
● To install a RPM package:
# rpm ­Uvh package.rpm

4. MySQL workbench ­ demo

5. Database schema
● Once the schema is designed, MySQL workbench
can generate a 'script' containing all SQL
statements to create the tables and other objects:
File ­>
Export ­>
Forward Engineer SQL CREATE Script
● This 'script' can be executed as usual from the
MySQL monitor

6. Inserting rows
● To populate tables, use the INSERT SQL
statement:
mysql> insert into tbl
(col1, col2, ...)
values
(val1, val2, ...) [,
(valx, valy, ...) , ...]
● With:
– tbl the name of the table
– col1, col2, ... a list (subset) of column names
– val1 value for col1
– val2 value for col2

7. Inserting rows ­ examples
● Example (biodb version 1)
insert into modorg
(id, class, genus, species,
nchr, gsize, draft)
values
(1, “Bacteria”, “Escherichia”, “coli”,
1, 4.639, “1997­09­05 00:00:00”)
● Note that strings and dates have to be properly
quoted

8. Inserting rows
● You can leave out the column list if
– a value is given for all columns
– the values are specified in the order dictated by the
schema
mysql> insert into tbl
values
(val1, val2, ...) [,
(valx, valy, ...) , ...]

9. Changing rows
● To change one or more rows, use the UPDATE
SQL statement:
mysql> update tbl
set col1=expr1 [, col2=expr2, ...]
[where cond]
● With:
– tbl the name of the table
– col1 the column to change
– expr1 the new value
– cond the row filter ­ if unspecified, all rows of the
table will be updated

10. Changing rows ­ examples
● To change the C elegans number of
chromosomes to 7:
update modorg
set nchr = 7
where genus = “caenorhabditis”
and species = “elegans”;
● To change the draft date to the current date:
update modorg
set draft = now();

11. Deleting rows
● To remove rows, you use the DELETE SQL
statement:
delete from tbl
[where cond]
● With:
– tbl the name of the table
– cond the row filter ­ if unspecified, all rows of the
table will be deleted
– note: since you can only remove entire rows, there is
no need to specify column names

12. Deleting rows ­ examples
● To remove all in model organisms with a genome
publishing date before 2000:
delete from modorg
where year(draft) < 2000;

13. Introduction to MySQL
● Introduction
● Installation
● SQL
● Schema design
● Perl
BITS/VIB Bioinformatics Training – Jun 29, 2011 – Luc Ducazu <luc@daphnia.com>

14. Perl
● Perl is a scripting language that has excellent text
manipulation capabilities
● Many biological 'databases' are available as flat
text files
● Perl is very handy in the automation of the
population of MySQL databases

15. Automated population
● There are basically two ways Perl can help to
insert data into tables:
– The Perl script generates USE, INSERT, ... SQL
statements. You can than execute these statements
using the MySQL monitor:
$ perl myscript.pl | mysql
– The Perl script connects to the database and executes
SQL statements directly: DBI

16. Perl DBI
● Perl DBI provides a programming interface that
abstracts most of the RDBMS specifics
● In principle it should be possible to port scripts,
written for other RDBMS's (like PostgreSQL), to
MySQL with only minimal effort: all you have to
do is change the connection string
● Packages to install (Ubuntu)
– libdbi­perl: Perl DBI
– libdbd­mysql­perl: MySQL driver for DBI

17. Perl DBI ­ connecting
● Here is a minimal program:
#!/usr/bin/perl ­w
use strict;
use DBI;
my $dbh = DBI­>connect(
“DBI:mysql:host=localhost;database=biodb”,
“user”,
“password”) or die;
...
$dbh­>disconnect();

18. Perl DBI ­ connecting
● Some highlights:
– use DBI;
Load Perl DBI library
– DBI­>connect(connection string);
Connect to a database
● it is a MySQL database server
● the DB server is running on the local machine
● you can provide the name of the database
● you can provide a user name and password
The connect() function returns
● a database handle ($dbh) on success
● false on failure
– $dbh­>disconnect() to clean up resources

19. Perl DBI
● To execute a SQL statement that does not return a
result set, eg INSERT, DELETE, use do():
my $n = $dbh­>do(stmt);
● This function
– requires a valid database handle
– returns the number of rows affected, if no rows are
affected, a special value is returned: 0E0 (evaluates
true)
– false in case of an error
● You can use execute() as well

20. Perl DBI
● To execute a SQL statement that returns a result
set, eg SELECT use the following recipe:
1. Prepare a statement:
my $sth = $dbh­>prepare(stmt);
2. Send the query to the database server:
$sth­>execute();
3. Read the result, row by row:
my @row = $sth­>fetchrow_array();
my $ref = $sth­>fetchrow_hashref();
4. Clean up resources:
$sth­>finish();

21. Perl DBI ­ examples
● To list all classes in modorg:
...
my $qry = “select distinct class ”
. “from modorg ”
. “order by class”;
my $sth = $dbh­>prepare($qry);
$sth­>execute();
while(my @row = $sth­>fetchrow_array())
{
print “$row[0]n”;
};
$sth­>finish();
...

22. Perl DBI ­ examples
● To list all organisms in modorg:
...
my $qry = “select genus, species ”
. “from modorg ”
. “order by genus”;
my $sth = $dbh­>prepare($qry);
$sth­>execute();
while(my $ref = $sth­>fetchrow_hashref())
{
print $ref­>{“genus”} . “ “
. $ref­>{“species”} . “n”;
};
$sth­>finish();
...

23. Perl DBI ­ examples
● To insert a bunch of rows into modorg:
...
my $qry = “insert into modorg ”
. “(id, class, genus, species) ”
. “values (?, ?, ?, ?)”;
my $sth = $dbh­>prepare($qry);
$sth­>execute(11, “Mammels”,
“Sus”, “scrofa”);
...

24. Quoting
● Never allow arbitrary user input in SQL
statements