Xper2 - Install FAQ



Before starting

What is Xper²?

Xper² is a knowledge base management tool that allows creating, editing (e.g. addition, modification, suppression) of descriptive knowledge, in order to perform interactive identification key or diagnosis. Xper² is, at the moment, mainly used in life sciences, e.g. botany, entomology, etc. However, Xper² may be used in a wide range of fields.

What are the minimal requirements for running Xper²?

Minimal Recommended
Processor 500 MHz > 1 GHz
Memory (RAM) 256 Mo > 1 Go
Free HD space 20 Mo 100 Mo
Internet connection  56K modem ADSL
JRE 1.5 1.6

Xper² is developed in Java, and thus requires the Java virtual machine to work. (cf.How to check the presence of a Java virtual machine on my computer?)

Where can I download Xper²?

The Xper² software is freely downloadable from our website Laboratory of Informatics and Systematics (LIS) at:
http://www.infosyslab.fr/lis/?q=en/resources/software/cai/xper2/downloads/last

You will find two versions there:
- Xper²: full version
- Xper²-Identification: the interactive identification module only

Xper² is available for the following operating systems: Windows XP/Vista/7, Linux, and MacOS X.

Who develops Xper²?

Xper² is developed by the Laboratory of Informatics and Systematics (LIS). Xper² is a upgraded Java version of XPER, a software developed by Jacques LEBBE and Régine VIGNES in the 1980s.

The Xper² team:
- Florian Causse (florian.causse@upmc.fr): developer
- Régine VIGNES-LEBBE (regine.vignes_lebbe@upmc.fr): coordinator
- Visotheary Rivière-Ung (visotheary.riviere_ung@upmc.fr): communication officer

What are the terms of use of Xper²?

Xper² is a free software developped under the Creative Commons License. You can freely use it, but not modify, reproduce or distribute it without the acknowledgement of the creators. For more information, visit the official Creative Commons web site creativecommons.org.


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Windows

How do I install Xper² on Windows?

Double-clicking on “Xper²_setup.exe”will automatically launch the installation process that will guide you. Xper² program will be installed in the “C:\Program Files\Xper²\” folder by default. If you install the Xper² with Java version, Java installation will automatically be launched after the installation of Xper².

How-to uninstall Xper² on Windows?

Double-clicking on the “Xper²_uninstall.exe” shortcut will automatically uninstall Xper². You will find the shortcut in the menu “Start \ Xper²”, or in“Control panel \ Addition-Suppression of programs” in the Windows Start menu.

How do I launch Xper² on Windows?

Double-click on the“Xper²” shortcut present:
- on the desktop,
- in the quick launch bar,
- in the menu “Start \ Xper²”
- in the folder where Xper2 is installed

How do I open a MS-DOS command window?

- Type “cmd” in the Windows "Start\Run" menu or
- Click on “MS-DOS comand” in the Windows “Start \ Accessoires” menu


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Linux

How do I install Xper² on Linux?

Once the “jar” file is downloaded, copy it in the folder of your choice.

How do I uninstall Xper² on Linux?

There is no automatic uninstall on Linux. Just remove the Xper² repertory, using, for example, the command “rm - RF Xper²”. Please be careful to not remove your knowledge bases!

How do I launch Xper² on Linux?

To launch Xper², just run the jar file with the command “java −jar xper2−Editor−2.x.x.jar”.


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MacOS

How do I install Xper² on MacOS?

Download the “zip” and extract Xper² to the folder of your choice.

How do I uninstall Xper² on MacOS?

Just remove the Xper² repertory:
- Open a terminal and type “rm - RF Xper²” or
- Right click on the file and select “Place in the wastebasket”
Be careful to not remove your knowledge bases!

How do I launch Xper² on MacOS?

Click on the application “Xper²” or type “Xper²” in a terminal


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General troubleshooting

Where do I find JRE?

You can freely download it from the official Java website java.sun.
Go to the J2SE 6.0 section, then choose JRE 6.0. Choose your OS and accept the terms of the license.

For Windows users, you can download the Xper² software with the installation of Java integrated.

Which is the JRE version needed to run Xper²?

Use a Java virtual machine (JRE) of version 1.5 (5.0) or higher.

How to check the presence of a JRE on my computer?

On Windows, open one invites orders MS-DOS (cf.How do I open a MS-DOS command window?)
On Linux and MacOS, open a console or terminal.
Type the command “java”. If a JRE is installed on your computer, you will see a message of the type:

$java 
		Use:java [- options] class [args…]
		(to run a class)
		or java [- options] -jar jarfile [args…]
		(to run a jar file)
		

Else, you will see a message indicating that the command is unknown or not found:

$java 
		bash: java:command not found 

How do I know the version of the JRE installed on my computer?

On Windows, open a command prompt MS-DOS (cf.How to open a command prompt MS-DOS?)
On Linux and MacOS, open a console or terminal.
Type the command “java -version”. If a JRE is installed on your computer, you will see a message indicating the version of the JRE used:

$ java -version
java version “1.6.0_02” Java (TM) 2 Runtime Environment,
Standard Edition (build 1.6.0_02-b09) 
Java HotSpot (TM) Customer VM (build 1.6.0_02-b09, mixed mode, sharing)

If not, you will see a message indicating that the orderis is unknown or not found:

$ java -version 
		bash: java: command not found 

How do I know the value of the JAVA_HOME environment variable?

On Windows, open a MS-DOS command window (cf.How do I open a MS-DOS command window?)
On Linux and MacOS, open a console or terminal
Type the command “echo $JAVA_HOME”:

$echo $JAVA_HOME 
		/home/user_name/dev/jdk1.6.0_02 

How do I consult the value of the CLASSPATH environment variable?

On Windows, open a MS-DOS command window (cf.How do I open a MS-DOS command window?)
on Linux and MacOS, open a console or terminal.
Type the order “echo CLASSPATH”:

$ echo CLASSPATH /home/user_name/dev/jdk1.6.0_02/lib:. 

What should I do if nothing happens when I launch Xper²?

Launching the program may take quite a long time, depending on the performance of your computer (cf.Which are the minimal requirements for running Xper²?) If nothing happens after a reasonnable time, try to launch the program again. Check also if the program (or the process) Xper² is active.

What should I do if an error message “Could not find a JDK…” appearswhen starting Xper²?

This message means that there is no compatible JRE installed on your computer.

To solve the problem, there are four checks to make:

  1. Be sure to have a virtual Java machine properly installed (JRE).
    (cf.How to check the presence of a JRE on my computer?)
  2. In addition be sure that the JRE installed is compatible.
    (cf.How to know the version of the JRE installed on my computer?)
  3. Check the existence of the JAVA_HOME variable environement and that the path to the Java 1.6 repertory is correct.
    (cf.How to consult the value of the JAVA_HOME environment variable?)
  4. Check the existence of the CLASSPATH variable environement and that the path to the Java 1.6 repertory is correct.
    (cf.How to consult the value of the CLASSPATH environment variable?)

What should I do if Xper² still does not start?

Initially be sure to have correctly followed the indications present in this FAQ. If you still do not manage to launch Xper², contact us and report the problem. (cf. What to do in case of bugs?)

What should I do if Xper² crashes when I quit?

Probably the problem is due to the crash of the Java virtual machine , or to the Windows program. In general, after rebooting your computer Xper² will run again without problems. However, write down the error message and verify if the bug has already been reported. (cf.What should I do if I find a bug?)

What to do in case of bugs?

First of all check if the bug has already been identified. Consult the bugs report on our Web site. If there's no report, please send an email to xper@lis.snv.jussieu.fr. Please detail the type and the context of the error, and do not forget to specify your environment(Windows, Linux, Mac). If possible join to your email a screenshot of the error.


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On-line Interactive Identification Key: create your own Applet

In order to use the interactive identification module on-line, you only have to copy/paste the following code in an html file.
<html>
<head>
<title></title>
<head>
<body>
<applet codebase="." 
    code="fr_jussieu_snv_lis.XPIdApplet" 
    archive="http://lis-upmc.snv.jussieu.fr/lis/ressources/xper2/online/Xper2-Applet.jar,
    http://lis-upmc.snv.jussieu.fr/lis/ressources/xper2/online/xercesImpl.jar" 
    width="100%" 
    height="100%">

<param name="nbBase" value="1"/>
<param name="base1" value="http://myServer/myXPDfileName;title;xper2"/>
<param name="viewxperURL" value="http://lis.snv.jussieu.fr/cgi-bin/viewxper.cgi"/>

<param name="makeyURL" value="http://baron.snv.jussieu.fr/cgi-bin/david/HPS"/> 
Your browser is completely ignoring the APPLET tag!
</applet>
</body>
</html>

The file 'Xper2-Applet.jar' is the Xper² identification module in an applet version. The file 'xercesImpl.jar' is the library that can read XML files.
They are both necessary to open Xper² KB.

The parameter 'http://myServer/myXPDfileName' is the path to the xpd file of your KB (there is no need to add the file extension).

The parameter 'nbBase' indicate the number of KB to be integrated in the applet. (minimum is 1)

The parameter 'baseX' (X is the number of the base) precise the information to open the base. The fiel 'value' is divided into three parts separated with comas.
1)Path to the base : the_folder_of_the_base/the_name_of_the_file_of_the_base_without_extension
2)Title of the base : whatever you like
3)Format of the base : xper OU xper2

The following parameters are optional:
'viewxperURL' indicate the path to the 'viewxper.cgi' script.
'paramBase' indicate the name of the BASE parameter when a query is done via 'viewxper.cgi' script.
'paramTaxon' indicate the name of the TAXON parameter when a query is done via 'viewxper.cgi' script.
'makeyURL' indicate the path to the maKey script for the generation of identification keys.

Note : To use those external scripts, the base must be install on the servers where thoses scripts are available.


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Glossary


FAQ:
Frequently Asked Questions

GPL:
General Public License

CAI:
Computer-Aided Identification

JRE:
Java Runtime Environment or Java virtual machine

LGPL:
General Lesser Public License

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