BioPerl-DB
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docs/HOWTO-MySQL.html view on Meta::CPAN
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Now we can start the MySQL datbase...<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>/etc/rc.d/init.d/mysql
start<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Important!</span></b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'> Protect your database by setting a root MySQL password:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'># mysqladmin -u
root password 'xxxxxxx'<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>After installing, configuring, starting and enabling a root
password it should be possible to logoff as root and re-login as a ‘normal’
system user.<span style="mso-spacerun: yes"> </span><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>To test this I made the switch from root user to my normal 'dag'
user account and confirmed that I can login as root to the mysql instance:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[dag@pe3
scripts]$ mysql -u root -p<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Enter password:
<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Welcome to the
MySQL monitor.<span style="mso-spacerun: yes"> </span>Commands end with ; or
\g.<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Your MySQL
connection id is 8 to server version: 3.23.41-log<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Type 'help;' or
'\h' for help. Type '\c' to clear the buffer.<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql> exit<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Bye</span><span
style='font-family:Arial;mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Success! We now have a working MySQL instance.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Step 2 Install the perl interfaces to MySQL <o:p></o:p></span></b></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></b></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>In future steps we are going to use perl to help us talk to the
MySQL database. In order to do this we need some additional perl modules
installed. We need:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in;text-indent:-.25in;mso-list:l13 level1 lfo7;
tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>·<span
style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>DBI:: - The perl generic database interface<o:p></o:p></span></p>
docs/HOWTO-MySQL.html view on Meta::CPAN
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>The files found in the biosql-schema do not need to be installed
or otherwise processed. We are going to use the scripts and documents found in
this module directly.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-size:11.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial;mso-fareast-font-family:"MS Mincho"'>Step 7 – Putting it all
together: creating a biosql instance within MySQL<o:p></o:p></span></b></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Inside the biosql-schema/scripts folder there is a perl script called
"create_mysqldb.pl". This script is just a helper script that
automates the process of connecting to the datbase and issuing<span
style="mso-spacerun: yes"> </span>the SQL statements that cause the proper
database tables to be created. The script reads the actual SQL commands from
the file found in biosql-schema/sql/biosql-mysqldb.sql<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>After looking at how simple this script is I felt the need to
bypass it completely and just perform the steps manually for curiosity sake.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Here is the output from creating an initial database named ‘biosql’:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[dag@pe3]$
mysql -u root -p<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Enter password:
<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Welcome to the
MySQL monitor.<span style="mso-spacerun: yes"> </span>Commands end with ; or
\g.<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Your MySQL
connection id is 9 to server version: 3.23.41-log<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Type 'help;' or
'\h' for help. Type '\c' to clear the buffer.<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql>
create database biosql;<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
affected (0.00 sec)<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql> exit<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Bye</span><span
style='font-family:Arial;mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Now that the database is created we need to connect to the
database and issue the SQL commands contained in
biosql-scheme/sql/biosqldb-mysql.sql file:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Within the mysql client interface we can use the command
"source" to read in SQL statements from a file.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Here is the output from that process:<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[dag@pe3]$
mysql -u root -p biosql<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Enter password:
<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Welcome to the
MySQL monitor.<span style="mso-spacerun: yes"> </span>Commands end with ; or
\g.<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Your MySQL
connection id is 11 to server version: 3.23.41-log<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Type 'help;' or
'\h' for help. Type '\c' to clear the buffer.<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql>
source sql/biosqldb-mysql.sql<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 0
rows affected (0.00 sec)<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Records: 0<span
style="mso-spacerun: yes"> </span>Duplicates: 0<span style="mso-spacerun:
yes"> </span>Warnings: <o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><i><span style='font-family:
Arial;mso-fareast-font-family:"MS Mincho"'><snip - lots of boring output cut
here...> <o:p></o:p></span></i></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
affected (0.00 sec)<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
affected (0.00 sec)<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
affected (0.00 sec)<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
( run in 1.898 second using v1.01-cache-2.11-cpan-d8267643d1d )