21.3. Installation instructions

21.3. Installation instructions
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Java

Download and install Java SDK 1.6 (aka Java 6), available from http://java.sun.com/.

Tomcat

Download and install Apache Tomcat 6.0.20 or later, available from http://tomcat.apache.org. It is a good idea to specify the maximum allowed memory that Tomcat can use. The default setting is usually not large enough. If you are using Tomcat 6.0.18 or higher you also need to disable strict parsing of JSP files.

Unless you have manually downloaded and installed JAI (Java Advanced Imaging) native acceleration libraries (see https://jai.dev.java.net/) it is also a good idea to disable the native acceleration of JAI.

All of the above is done by setting Java startup options for Tomcat in the CATALINA_OPTS environment variable. Basically add the next line (as a single line) close to the top of the catalina.sh script that comes with Tomcat (directory bin):

CATALINA_OPTS="-Xmx500m 
-Dorg.apache.jasper.compiler.Parser.STRICT_QUOTE_ESCAPING=false
-Dcom.sun.media.jai.disableMediaLib=true"

For more information about Tomcat options see http://tomcat.apache.org/tomcat-6.0-doc/index.html.

Set up SQL database

BASE utilize Hibernate for object persistence to a relational database. Hibernate supports many database engines, but so far we only work with MySQL and PostgreSQL.

MySQL

Download and install MySQL (tested with version 5.0), available from http://www.mysql.com/. You need to be able to connect to the server over TCP, so the skip-networking option must not be used. The InnoDB table engine is also needed, so do not disable them (not that you would) but you may want to tune the InnoDB behaviour before creating BASE databases. BASE comes pre-configured for MySQL so there is no need to change database settings in the BASE configuration files.

PostgreSQL

PostgreSQL 8.2 seems to be working very well with BASE and Hibernate. Download and install PostgreSQL, available from http://www.postgresql.org/. you must edit your <base-dir>/www/WEB-INF/classes/base.config file. Uncomment the settings for PostgreSQL and comment out the settings for MySQL.

	Note
	PostgreSQL versions prior to 8.2 have a non-optimal solution for locking rows in certain situations. This may cause two seemingly independent transactions to lock if they just reference a common database row. This may happen, for example, when importing raw data that have references to the same reporters. The problem has been solved in PostgreSQL 8.2.

BASE (download and unpacking)

Download BASE and unpack the downloaded file, i.e. tar zxpf base-...tar.gz. If you prefer to have the bleeding edge version of BASE, perform a checkout of the source from the subversion repository (subversion checkout instructions at BASE trac site).

If you choose to download the binary package, skip to the next item. The rest of us, read on and compile BASE. If you downloaded a source distribution, unpack the downloaded file tar zxpf base-...src.tar.gz, or you may have performed a subversion checkout. Change to the 'root' base2 directory, and issue ant package.bin. This will create a binary package in the base2 'root' directory. Unpack this new package (outside of the source file hierarchy), and from now on the instructions are the same irrespective where you got the binary package.

This section is intended for advanced users and programmers only. In cases when you want to change the BASE code and try out personalized features it may be advantageous to run the tweaked BASE server against the development tree. Instructions on how to accomplish this is available in the building BASE document. When you return back after compiling in the subversion tree you can follow the instruction here (with obvious changes to paths).

BASE (database engine)

Instructions for MySQL and PostgreSQL are available below. The database names (base2 and base2dynamic is used here), the db_user, and the db_password can be changed during the creation of the databases. It is recommended to change the db_password, the other changes can be made if desired. The database names, the db_user, and the db_password are needed in a later step below when configuring BASE.

	Note
	Note that the db_user name and db_password set here is used internally by BASE in communication with the database and is never used to log on to the BASE application.

	The database must use the UTF-8 character set
	Otherwise there will be a problem with storing values that uses characters outside the normal Latin1 range, for example unit-related such as µ (micro) and Ω (ohm).

MySQL

Create a new database for BASE, and add a db_user with at least SELECT, INSERT, UPDATE, DELETE, CREATE, DROP, INDEX, and ALTER permission for the new database. To do this, connect to your MySQL server and issue the next lines:

CREATE DATABASE base2 DEFAULT CHARACTER SET utf8;
CREATE DATABASE base2dynamic DEFAULT CHARACTER SET utf8;
GRANT ALL ON base2.* TO db_user@localhost IDENTIFIED BY 'db_password';
GRANT ALL ON base2dynamic.* TO db_user@localhost;

The <base-dir>/misc/sql/createdb.mysql.sql file contains the above statements and can be used by the mysql command-line tool (remember to edit the db_user, db_password, and the database names in the script file before executing the command): mysql -uroot -p < ./misc/sql/createdb.mysql.sql. The header in the script file contains further information about the script.

PostgreSQL

Create a new database for BASE, and add a db_user with the proper privileges. To do this, log in as your PostgreSQL user and issue these lines (omit comments):

createuser db_user -P
  # this will prompt for an password for the new user, and issue two
  # more question that should be answered with character 'n' for no.
createdb --owner db_user --encoding UTF8 base2
psql base2
  # this will start the psql command line tool. Issue the next line
  # within the tool and quit with a '\q'.
CREATE SCHEMA "dynamic" AUTHORIZATION "db_user";

The <base-dir>/misc/sql/createdb.postgresql.sql file contains the above statements and can be used by the psql command-line tool: psql -f ./misc/sql/createdb.posgres.sql template1 The header in the script file contains further information about the script.

BASE (file storage setup)

An area for file storage must be setup. Create an empty directory in a proper location in your file system, and set the owner to be the same as the one that the Tomcat server will be running as. Remember this location for later use.

BASE (configuration)

Basic BASE configuration is done in <base-dir>/www/WEB-INF/classes/base.config:

Uncomment the database engine section that match your setup.
Modify the db.url, db.dynamic.catalog, db.username, and db.password settings to match your choice above. (database host and database name (e.g. base2), e.g. base2dynamic, db_user, and db_password, respectively.)
Modify the userfiles setting to match your choice above.

See the Appendix C, base.config reference for more information about the settings in the base.config file.

Optional but recommended. You may want to modify extended properties to fit your needs. Extended properties are defined in <base-dir>/www/WEB-INF/classes/extended-properties.xml. There is an administrator document discussing extended properties available. If you plan to perform a migration of a BASE version 1.2 database you should probably not remove any extended properties columns (this is not tested so the outcome is currently undefined). However, adding columns does not affect migration.

BASE (database initialization)

Change directory to <base-dir>/bin and execute the following commands:

./initdb.sh [base_root_login] base_root_password
./updateindexes.sh

The second command is important for PostgreSQL users since the Hibernate database initialisation utility is not able to create all indexes that are required. BASE will still work without the indexes but performance may suffer.

	Important
	The base_root_login and base_root_password you use here is given to the BASE web application root user account. The base_root_login is optional. If not specified, `root` is used for the login.

If the initialisation script fail, it is most probably a problem related to the underlying database. Make sure that the database accepts network connection and make sure that db_user has proper credentials.

BASE and Tomcat

Either move the <base-dir>/www directory to the Tomcat webapps directory or create a symbolic link from the Tomcat webapps directory to the <base-dir>/www directory

cd /path/to/tomcat/webapps
ln -s /path_to_base/www base2

If you plan to install extensions you should make sure that the <base-dir>/www/extensions directory is writable by the user account Tomcat is running as.

Start/restart Tomcat, and try http://hostname:8080/base2 (change hostname to your hostname) in your favourite browser. The BASE log-in page should appear after a few seconds.

BASE, Apache, and Apache/Tomcat connector

This step is optional.

If you want run the Tomcat server through the Apache web server, you need to install the Apache version 2 web server, available from http://www.apache.org/, and a apache-tomcat connector, available from http://jakarta.apache.org/tomcat/connectors-doc/index.html. So, we got you there;-) To be honest, this step is not really well documented since we previously used SuSE 9.3 on our demo/test server, and apache/tomcat/mod_jk comes pre-installed. The current server does not use the apache/tomcat connector. What you need to do is something like this

Get that Tomcat server running in stand-alone mode.
Get the Apache 2 server running.
Install mod_jk. Note, different version are used for apache 1.3 and 2. In SuSE 9.3 this step is done by installing mod_jk-ap20.
Create a workers.properties file in the Tomcat base directory (commonly copied from a template).
Create a jk.conf file in the apache conf directory (commonly copied from a template), and make sure that jk is added to the modules to be loaded when apache starts.

In jk.conf add the lines below and change paths appropriately.

# The following lines makes apache aware of the location of
# the /base2 context
Alias /base2 "/srv/www/tomcat6/base/webapps/base2"
<Directory "/srv/www/tomcat6/base/webapps/base2">
Options Indexes FollowSymLinks
allow from all
</Directory>
# The following lines mounts all base2 jsp files to Tomcat
JkMount /base2 ajp13
JkMount /base2/* ajp13
# The following lines prohibits users from directly accessing WEB-INF
<Location "/base2/WEB-INF/">
AllowOverride None
deny from all
</Location>

You must restart the Apache and the Tomcat server after above steps.

Setup done!

Happy BASEing. Now you can log on to your BASE server as user root (use the base_root_password from the database initialization step above). You should begin with creating a couple user accounts, for more information on how to create user accounts please refer to Chapter 24, Account administration.

If you are planning to perform a migration of data from BASE version 1.2.x please perform the steps in Section 21.5, “Migration instructions” before doing anything else with your new BASE installation.

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