Proteios 2 Installation

Description

This note describes issues regarding installation of Proteios 2.
Note! This Wiki page is under construction. Its contents may change during development of the software, and instructions on this page should therefore be used with caution before the official Proteios 2 release.

Terms used

DBMS

Database Management System, e.g. MySQL.

SQL

Structured Query Language. Standard protocol for managing a DBMS.

SDK

Software Development Kit

J2SE

Java 2 Standard Edition

JDK

J2SE Development Kit

General Description of Installation Steps

Requirements

Installed Applications

1. A DBMS must be installed (default is MySQL). The following information is needed:
   1. DBMS username and password for a database manager with create privileges on the DBMS.
   2. Name of database for Proteios to use on the DBMS.
   3. DBMS username and password that the Proteios application can use to connect to the DBMS.
2. Java SDK (JDK) version 5 or newer must be installed. Java can be downloaded for free; see information on ​http://java.sun.com/. The version to download is SDK for Java 2 Platform Standard Edition 5.0 or newer (make sure that you download the JDK, and not just the JRE, the J2SE Runtime Environment).
3. Apache Tomcat servlet container needs to be installed in order for Proteios to work. Tomcat can be downloaded for free; see information on ​http://tomcat.apache.org/.

Additional Information Needed

1. Password that should be used for the root account in Proteios. The root account is used to add/delete users, groups, and roles in Proteios.
2. Tomcat installation directory, if the installation program/script cannot determine it from the value of environment variable CATALINA_HOME (Catalina is the name of a Java class in the Tomcat package). If you need to find the directory yourself, first search for a directory with "tomcat" in the name. The "Catalina home" directory is the one with a sub-directory named "webapps".

Proteios 2 Installation - General

Example Notes

On many systems the installation procedure can be performed by running a program or script, and is in that case the recommended way to install the Proteios package. In this section the different steps in the setup are described, and an example of each step is provided. The example is based on the following assumptions:

Operating system	Unix/Linux?
DBMS used	MySQL
Database manager's DBMS username	caesar
Database manager's DBMS password	spqr
Name of database to use	proteios_db
Proteios' DBMS username	cicero
Proteios' DBMS password	palatium
Proteios' root account password	protagoras
Tomcat installation directory	/usr/local/packages/apache-tomcat-5.5.15/
Proteios-2 installation directory	/usr/local/packages/Proteios-2.0/

Example setup.

In order for the examples to be brief, the operations are given as commands on a command line. It should be noted that it is not in general recommended to perform all operations in this way, as user names and passwords may easily become exposed.

Steps in Installation

1. [Optional] Delete ("drop" in SQL parlance) the existing database to use. Example command:
   
   mysql -u caesar -p spqr -e DROP DATABASE IF EXISTS `proteios_db`;
   
   
2. Create the database to use, if it doesn't already exist. Example command:
   
   mysql -u caesar -p spqr -e CREATE DATABASE IF NOT EXISTS `proteios_db` DEFAULT CHARACTER SET utf8;
   
   
3. Set full access rights for the database to the Proteios application. Example command:
   
   mysql -u caesar -p spqr -e GRANT ALL ON `proteios_db`.* TO 'cicero'@'localhost' IDENTIFIED BY 'palatium'; FLUSH PRIVILEGES;
   
   
4. The Java class path variable is created by first adding the directory ./proteomics/WEB-INF/classes. Java archive files (*.jar) in directory ./proteomics/WEB-INF/lib/ is then listed and appended to the class path, separated by a character specific for the operative system (':' on Unix/Linux?, ';' on Microsoft Windows, where in addition directories are separated with '\' instead of '/', although Java does not seem to be sensitive to this). Example command (the command line has been broken into several lines for clarity and shortened in order to save space):
   
   CP=./proteomics/WEB-INF/classes
:./proteomics/WEB-INF/lib/antlr-2.7.6rc1.jar
:./proteomics/WEB-INF/lib/asm-attrs.jar
...
:./proteomics/WEB-INF/lib/xml-apis.jar
   
   
5. The Proteios database installation java program InitDB.class in package org.proteios.install is then run with the previously created class path and with the root account password as argument. Example command (the command line has been broken into several lines for clarity and shortened in order to save space):
   
   java -server -cp ./proteomics/WEB-INF/classes
:./proteomics/WEB-INF/lib/antlr-2.7.6rc1.jar
:./proteomics/WEB-INF/lib/asm-attrs.jar
...
:./proteomics/WEB-INF/lib/xml-apis.jar
org.proteios.install.InitDB protagoras
   
   
6. Proteios is deployed into the Tomcat installation webapps directory by creating a symbolic link named proteios pointing to the proteomics directory of the Proteios package. Example commands:
   
   cd /usr/local/packages/apache-tomcat-5.5.15/webapps
ln -s /usr/local/packages/Proteios-2.0/dist/proteomics proteios
   
   
7. The Proteios configuration file proteios.config is updated with the username and password to use to connect to the DBMS. The configuration file is located in directory webapps/proteios/WEB-INF/classes/ in the Tomcat installation directory. In the example setup used, the configuration file is:
   
   /usr/local/packages/apache-tomcat-5.5.15/webapps/proteios/WEB-INF/classes/proteios.config
   
   The entries that are updated using the example values are:
   
   db.username = cicero
db.password = palatium
   
   
8. The Proteios installation is now completed. Start Tomcat before use. To use Proteios, start a web browser on the system the installation was performed on and access the link:
   
   http://localhost:8080/proteios/
   
   

This concludes the tour of the Proteios installation. Please visit the gift shop on your way out.