Proteios 2 Installation

Description

This note describes how to install Proteios 2 from a binary archive or compiled source code.

Requirements

1. Proteios distribution (binary archive or source code).
2. A database management system (DBMS), e.g. MySQL.
3. JDK (Java SDK) version 5 or higher (see ​http://java.sun.com/).
4. Apache Tomcat servlet container should be installed (see ​http://tomcat.apache.org/).

Quick Install

1. Unpack the binary archive or build Proteios from source code (see Build Proteios from Source Code).
2. Move to directory dist, which contains the installation scripts install-linux.sh for Unix/Linux?, and install-win.bat for Windows.
3. Run the appropriate installation script at a command prompt and input requested information.
4. Start Tomcat if not already running. Proteios can now be accessed from a web browser at ​http://localhost:8080/proteios/.

Detailed Instructions

Notes on Installed Software

1. The DBMS server must be running during the Proteios installation (in case of MySQL, the daemon mysqld), so the DBMS can be accessed. In addition, the path for the DBMS program (mysql for MySQL) must allow it to be run from the directory the installation is performed from.
2. JDK (Java SDK): The version to download is SDK for Java 2 Platform Standard Edition 5.0 or higher (make sure that you download the JDK, and not just the JRE, the J2SE Runtime Environment).
3. Tomcat must have "write" access to the directory for Proteios user files and the directory for Proteios temporary files.

Information Needed

Installed Packages

1. DBMS username and password for a database manager with privileges to create and drop databases, as well as creating accounts on the DBMS. Note that if you are going to install the web application on a a different server than the database server, you will need to make sure that the user has right to connect from the machine where you are putting the Proteios application. Instructions for mySQL remote access can be found here.
2. Tomcat installation directory, if it cannot be determined 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 Configuration (Set at Installation)

1. Name of database for Proteios to use on the DBMS.
2. DBMS username and password that the Proteios application can use to connect to the DBMS.
3. 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.
4. Location of directory for Proteios user files.
5. Location of directory for Proteios temporary files.
6. Control port number for Proteios FTP Server (see section FTP Communication Ports). If in doubt, use default setting 8021.

Example Setup

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
DBMS computer host name or IP number	localhost (same as Proteios is installed on)
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
Directory for Proteios' user files	/usr/local/proteios/files/
Directory for Proteios' temporary files	/usr/local/proteios/temp/
Control port for Proteios FTP Server	8021
Tomcat installation directory	/usr/local/packages/apache-tomcat-5.5.15/
Proteios-2 installation directory	/usr/local/packages/Proteios-2.0/

Example setup.

Summary - What Happens During Proteios Installation

Proteios is a web application. It uses Tomcat to be accessed through a web browser, and it uses a database to store its data. Below is a summary of the installation procedure.

1. The supplied information on the DBMS host name and manager account (username caesar and password spqr in the example) is used to create a database with the specified name (proteios_db in the example).
2. A new DBMS account (username cicero and password palatium in the example) is set up on the newly created database.
3. Information on the new DBMS account is stored in a configuration file, so Proteios can use it to access the database later on.
4. Information on directory for temporary files is stored in configuration file web.xml.
5. Information on control port for Proteios FTP Server is stored in configuration file ftp.properties.
6. Log configuration file log4j.properties is created if not existing.
7. The database is prepared for storing data on Proteios users, groups, experimental data, and other topics. Initially, it only contains the Proteios root account (with password protagoras in the example), that is used to create all other accounts in Proteios, from which proteomics data can be stored. If a database already exists, you have the option to update instead of dropping it, thus keeping/adjusting stored records (however, please see Restrictions for database structure update).
8. The directory for user files is created, if not existing.
9. The directory for temporary files is created, if not existing.
10. When the DBMS setup is finished, Proteios is prepared for use by being deployed into Tomcat, either by copying a number of files to the Tomcat webapps directory, or, preferrably, by creating a link between the latter and a directory with the Proteios files.
11. After the installation is finished, start Tomcat if not already running. Proteios can now be accessed from a web browser through http://localhost:8080/proteios/. If the installation is correct, the browser will be re-directed to the Proteios log-in page. To log in for the first time, use username root and the accompanying password (protagoras in the example).

Some comments regarding the installation

• The DBMS manager account is only used to prepare the DBMS, and information on this account (username caesar and password spqr in the example) is not stored by Proteios in its configuration files. The account is not affected by the installation, and it remains on the DBMS afterwards.
• The DBMS account that the installation prepares for Proteios' internal use (username cicero and password palatium in the example), will not normally be used by human users. It is therefore not necessary that the username and password are easy to remember, so more or less cryptical choices like gh45jsd8765j and k5f89n could be used in principle. As there is no difference between this account and other from the DBMS point of view, you might want to use non-trivial choices for the username and password, to make sure that the account is not used to access data directly via a DBMS client program.

Restrictions for database structure update

Some changes in database structure cannot be performed by updating an existing database and adjusting stored records. One example is addition of columns with property not-null="true".

Alternative 1 - Installation from Script

This section describes the installation using the Linux installation script install-linux.sh. Move to the directory containing the script. If Proteios 2 has been downloaded as source code and compiled on the system, it is the directory created by ant target package. Start the installation by typing install-linux.sh in the command shell. Enter requested information when prompted. A value inside square brackets [] denotes a default value, that will be used if just pressing <Return> (in the case of [Y|n], the value in upper-case denotes the default, in this case 'Y').

For a more detailed description of the steps performed by the script, please see section Alternative 2 - Installation from Command Line.

Installation from Script Step-by-Step

Values entered by the user is shown in monospace font.

1. Enter host name and user name with create privileges on your DBMS.
   Host name [localhost]:
   Username [root]: caesar
   Password: spqr (Not shown on console)
2. Enter a password for the root account in proteios.
   Password: protagoras (Not shown on console)
3. Configure the database name and user that proteios will use to connect to your DBMS.
   Database name [proteios]: proteios_db
   Username: cicero
   Password: palatium (Not shown on console)
4. Select a directory for proteios to use for user files.
   User files directory [/usr/local/proteios/data]: /usr/local/proteios/files
5. Select a directory for proteios to use for temporary files.
   Temporary files directory [/usr/local/proteios/tmp]: /usr/local/proteios/temp
6. Select control port for proteios FTP Server.
   FTP Server Control Port [8021]: 8021
   
   Thank you! Letś continue with the installation.
   
   Do you want to update an existing 'proteios_db' database[y|N]? N
   Do you want to drop an existing 'proteios_db' database[y|N]? Y
   Dropping database...done
   Updating proteios *.config files
   Updating proteios web.xml file
   Updating proteios ftp.properties file
   Creating log config file log4j.properties...
   [0%] Building database....................................
   [30%] Database built successfully.
   [35%] Initializing database...
   [37%] --Creating quota types...
   ...
   [79%] --Creating news...
   [90%] Database initialised successfully.
   Creating user files directory... done
   Creating temporary files directory... done
   
   
7. Let's deploy the webapplication into tomcat.
   
   Deploying proteios into /usr/local/packages/apache-tomcat-5.5.15
   
   proteios is now installed. 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/

Alternative 2 - Installation from Command Line

The operations are here 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.

Installation from Command Line Step-by-Step

1. The installation should be performed from the directory in the Proteios 2 distribution containing the installation scripts, e.g. install-linux.sh, whether these are used or not. If Proteios 2 has been downloaded as source code and compiled on the system, it is the dist directory relative to the Proteios-2 installation directory (/usr/local/packages/Proteios-2.0/dist in the example). This will be assumed to be the working directory if not otherwise stated.
2. [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`;"
   
   
3. 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;"
   
   
4. 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;"
   
   
5. The Proteios configuration file proteios.config is updated with the database name, username and password to use to connect to the DBMS, and location of directory for storing user files. The configuration file is located in directory www/WEB-INF/classes. In the example setup used, the configuration file is:
   
   /usr/local/packages/Proteios-2.0/www/WEB-INF/classes/proteios.config
   
   When Proteios later is deployed into the Tomcat installation webapps directory, this will in the example correspond to the file:
   
   /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.url = jdbc:mysql://localhost/proteios_db
db.username = cicero
db.password = palatium
userfiles = /usr/local/proteios/files
   
   
6. The Proteios configuration file web.xml is updated with the directory location for storing temporary files. The web.xml file is located in directory www/WEB-INF/. In the example setup used, the configuration file is:
   
   /usr/local/packages/Proteios-2.0/www/WEB-INF/web.xml
   
   When Proteios later is deployed into the Tomcat installation webapps directory, this will in the example correspond to the file:
   
   /usr/local/packages/apache-tomcat-5.5.15/webapps/proteios/WEB-INF/web.xml
   
   The entry that is updated using the example value is:
   
   <init-param>
<param-name>temporary.file.repository</param-name>
<param-value>/usr/local/proteios/temp</param-value>
</init-param>
   
   
7. The Proteios FTP Server configuration file ftp.properties is updated with the control port. The ftp.properties file is located in directory www/WEB-INF/classes. In the example setup used, the configuration file is:
   
   /usr/local/packages/Proteios-2.0/www/WEB-INF/classes/ftp.properties
   
   When Proteios later is deployed into the Tomcat installation webapps directory, this will in the example correspond to the file:
   
   /usr/local/packages/apache-tomcat-5.5.15/webapps/proteios/WEB-INF/classes/ftp.properties
   
   The entry that is updated using the example value is:
   
   PORT_NR=8021
   
   
8. The log configuration file log4j.properties is created from template file log4j.properties.in, if the former does not exist. The log4j.properties file is located in directory www/WEB-INF/classes. In the example setup used, the configuration file is:
   
   /usr/local/packages/Proteios-2.0/www/WEB-INF/classes/log4j.properties
   
   When Proteios later is deployed into the Tomcat installation webapps directory, this will in the example correspond to the file:
   
   /usr/local/packages/apache-tomcat-5.5.15/webapps/proteios/WEB-INF/classes/log4j.properties
   
   
9. The Java class path variable is created by first adding the directory ./www/WEB-INF/classes. Java archive files (*.jar) in directory ./www/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=./www/WEB-INF/classes
:./www/WEB-INF/lib/antlr-2.7.6rc1.jar
:./www/WEB-INF/lib/asm-attrs.jar
...
:./www/WEB-INF/lib/xml-apis.jar
   
   
10. 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 ./www/WEB-INF/classes
:./www/WEB-INF/lib/antlr-2.7.6rc1.jar
:./www/WEB-INF/lib/asm-attrs.jar
...
:./www/WEB-INF/lib/xml-apis.jar
org.proteios.install.InitDB protagoras
    
    In the case when an existing database is not dropped before initialization, program InitDB.class is run with extra argument update:
    
    ...
org.proteios.install.InitDB update protagoras
    
    
11. The directory for user files is created if not existing. If it could not be created, the user is instructed to create the directory by hand. Example commands:
    
    mkdir -p /usr/local/proteios/files
    
    
12. The directory for temporary files is created if not existing. If it could not be created, the user is instructed to create the directory by hand. Example commands:
    
    mkdir -p /usr/local/proteios/temp
    
    
13. Proteios is deployed into the Tomcat installation webapps directory by creating a symbolic link named proteios pointing to the www 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/www proteios
    
    
14. 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.