[SOLVED] JEMBOSS Bioinformatic Program Failure

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lcfiorini
Posts: 4
Joined: 06 Oct 2020, 02:07

[SOLVED] JEMBOSS Bioinformatic Program Failure

Post by lcfiorini »

Hello everybody,

I'm an ordinary Windows PC user and I have downloaded a Java version of a bioinformatic program suite called EMBOSS, publicly available at https://www.emboss.sourceforge.net/Jemboss. I've previously installed OpenWebStart in order to locally run the .jar file. Whenever I try to do so, though, a pop up window appears with the text below, I hope you can get a clue at what's going on in my machine.

Thank you,
Leonardo.



Waiting for exception dialog to be closed
Exiting Boot.mainWithReturnCode() with 1
failed to launch
netx: Read Error: Could not read or parse the JNLP file at 'file:/C:/Users/Leonardo/Downloads/jemboss.jar'. (Invalid XML document syntax. (O nome do atributo "zic5k-fktj5" associado a um tipo de elemento "_6j" deve ser seguido do caractere ' = '.))
[Fatal Error] :9:199: O nome do atributo "zic5k-fktj5" associado a um tipo de elemento "_6j" deve ser seguido do caractere ' = '.
Using MalformedXMLParser
Download done. Shutting down executor
Resource is not cacheable: jemboss.jar
Checking download state of jemboss.jar
Download for jemboss.jar has not been started until now
Will check and maybe put into cache: jemboss.jar
Will add resource 'jemboss.jar'
Will add resource at location 'file:/C:/Users/Leonardo/Downloads/jemboss.jar'
JNLP file location: C:\Users\Leonardo\Downloads\jemboss.jar
Proceeding with jnlp
Proxy disabled ( registry value 'ProxyEnable'). Will use direct proxy.
Windows based proxy created
Selected ProxyProvider : OPERATION_SYSTEM
Operating Keystore C:\Users\Leonardo\.config\icedtea-web\security\trusted.clientcerts
Loading Keystore C:\Users\Leonardo\.config\icedtea-web\security\trusted.clientcerts
Keystore file C:\Users\Leonardo\.config\icedtea-web\security\trusted.clientcerts exists.
Operating Keystore Unknown
Loading Keystore Unknown
Keystore file c:\program files\openwebstart\jre\lib\security\trusted.clientcerts does not exists.
Operating Keystore C:\Users\Leonardo\.config\icedtea-web\security\trusted.cacerts
Loading Keystore C:\Users\Leonardo\.config\icedtea-web\security\trusted.cacerts
Keystore file C:\Users\Leonardo\.config\icedtea-web\security\trusted.cacerts exists.
Operating Keystore C:\Users\Leonardo\.config\icedtea-web\security\trusted.jssecacerts
Loading Keystore C:\Users\Leonardo\.config\icedtea-web\security\trusted.jssecacerts
Keystore file C:\Users\Leonardo\.config\icedtea-web\security\trusted.jssecacerts exists.
Operating Keystore c:\program files\openwebstart\jre\lib\security\cacerts
Loading Keystore c:\program files\openwebstart\jre\lib\security\cacerts
Keystore file c:\program files\openwebstart\jre\lib\security\cacerts exists.
Operating Keystore Unknown
Loading Keystore Unknown
Keystore file c:\program files\openwebstart\jre\lib\security\jssecacerts does not exists.
Operating Keystore C:\Users\Leonardo\.config\icedtea-web\security\trusted.certs
Loading Keystore C:\Users\Leonardo\.config\icedtea-web\security\trusted.certs
Keystore file C:\Users\Leonardo\.config\icedtea-web\security\trusted.certs exists.
Operating Keystore C:\Users\Leonardo\.config\icedtea-web\security\trusted.jssecerts
Loading Keystore C:\Users\Leonardo\.config\icedtea-web\security\trusted.jssecerts
Keystore file C:\Users\Leonardo\.config\icedtea-web\security\trusted.jssecerts exists.
Operating Keystore Unknown
Loading Keystore Unknown
Keystore file c:\program files\openwebstart\jre\lib\security\trusted.certs does not exists.
Operating Keystore Unknown
Loading Keystore Unknown
Keystore file c:\program files\openwebstart\jre\lib\security\trusted.jssecerts does not exists.
Operating Keystore Unknown
Operating Keystore C:\Users\Leonardo\.config\icedtea-web\security\trusted.clientcerts
Loading Keystore C:\Users\Leonardo\.config\icedtea-web\security\trusted.clientcerts
Keystore file C:\Users\Leonardo\.config\icedtea-web\security\trusted.clientcerts exists.
Starting security dialog thread
using com.openwebstart.extensionpoint.OwsExtensionPoint extension point
Java Runtime AdoptOpenJDK-1.8.0_252
OS: Windows 10
OpenWebStartLauncher called with args: [-verbose, C:\Users\Leonardo\Downloads\jemboss.jar].
Calling ITW Boot with args [-verbose, C:\Users\Leonardo\Downloads\jemboss.jar].
RelevantJavawsArgs: '[-verbose, C:\Users\Leonardo\Downloads\jemboss.jar]'
Checking if installation time (1601928933548) is after last initial config time (1601929023775)
Setting download indicator to com.openwebstart.download.ApplicationDownloadIndicator@17f6480
Trying to set download indicator
Property 'ows.install4j.propertyUpdate' is unknown.
Loading USER level properties from: file:/C:/Users/Leonardo/.config/icedtea-web/deployment.properties
Property 'ows.install4j.propertyUpdate' is unknown.
Loading USER level properties from: file:/C:/Users/Leonardo/.config/icedtea-web/deployment.properties
Ico provider registered correctly.
Ico provider registered correctly.
Starting OpenWebStart 1.2.1
OWS main args [-verbose, C:\Users\Leonardo\Downloads\jemboss.jar].
init logger factory to net.sourceforge.jnlp.util.logging.OutputControllerLoggerFactory@694f9431

Janak Mulani
Posts: 158
Joined: 24 Mar 2020, 13:37

Re: JEMBOSS Bioinformatic Program Failure

Post by Janak Mulani »

There is an error reading the jnlp file:

Code: Select all

ailed to launch
netx: Read Error: Could not read or parse the JNLP file at 'file:/C:/Users/Leonardo/Downloads/jemboss.jar'. (Invalid XML document syntax. (O nome do atributo "zic5k-fktj5" associado a um tipo de elemento "_6j" deve ser seguido do caractere ' = '.))
[Fatal Error] :9:199: O nome do atributo "zic5k-fktj5" associado a um tipo de elemento "_6j" deve ser seguido do caractere ' = '. 
Can you please attach the jnlp file?

Stephan Classen
Posts: 139
Joined: 27 Mar 2020, 09:55

Re: JEMBOSS Bioinformatic Program Failure

Post by Stephan Classen »

It looks like you are passing a JAR file to OpenWebStart instead of a JNLP file.

Code: Select all

OWS main args [-verbose, C:\Users\Leonardo\Downloads\jemboss.jar]
In order for OWS to work correctly you need a JNLP file. Ask the provider of your application if they support Java Web Start and can provide you with a JNLP file.

lcfiorini
Posts: 4
Joined: 06 Oct 2020, 02:07

Re: JEMBOSS Bioinformatic Program Failure

Post by lcfiorini »

Exactly. After opening with WinRar I realized all of the folders' substructure: all of them contain at least one file, but only with filenames other than .jnlp: some are .html, others are .java, .xml, .gif, .bat, .jar, .sh, .am, .pl, .in or .apache. Two files are .fasta, a filename extension usually saved when you have a DNA sequence. These .fasta files may be easily opened and edited with notepad without problems. The vast majority, though, is comprised of .java files and there wasn't a single .jnlp file to be found. At a last resource I tried to change the filename extension of one of these files called "Jemboss.java" to "Jemboss.jnlp". It didn't work either. Any further guidance is greatly appreciated.

lcfiorini
Posts: 4
Joined: 06 Oct 2020, 02:07

Re: JEMBOSS Bioinformatic Program Failure

Post by lcfiorini »

Just a correction: the vast majority of the files found in the subfolders are EITHER .JAVA OR .HTML files, thank you.

Stephan Classen
Posts: 139
Joined: 27 Mar 2020, 09:55

Re: JEMBOSS Bioinformatic Program Failure

Post by Stephan Classen »

What you are describing sounds a lot like a source code bundle.
This means it is the actual code written by humans and not a program ready to be executed in a Java Virtual Machine.

Did you download the jemboss from this site: http://emboss.sourceforge.net/Jemboss/ ??

If yes please contact the authors of jemboss to provide you with instructions on how to install it.

lcfiorini
Posts: 4
Joined: 06 Oct 2020, 02:07

Re: JEMBOSS Bioinformatic Program Failure

Post by lcfiorini »

Yes, but navigating the folders I found an executable .exe under a "windows" folder. Now I'm trying to execute if to see if it finally installs the software.

ptai
Posts: 10
Joined: 13 Aug 2020, 14:50

Re: JEMBOSS Bioinformatic Program Failure

Post by ptai »

I think the only thing you need to do after either installing OWS is to go to this page:
http://emboss.sourceforge.net/Jemboss/

Scroll to the bottom and click on one of those "red buttons". These are links to jnlp files. Dependent on your browser you either have to save the .jnlp file and double-click it when downloaded, or you can directly say to "open" the file. See what happens when you do that.

There is no further "installation" necessary for an OWS application (no files to download and put into some folder etc.), the jnlp file you start (here by clicking a link) will install the application within OWS.

Once you have done this, you will be able to start the application through a desktop-shortcut or a windows start-menu entry (you can choose during install) or by visiting that link again.

Stephan Classen
Posts: 139
Joined: 27 Mar 2020, 09:55

Re: JEMBOSS Bioinformatic Program Failure

Post by Stephan Classen »

I can confirm that by clicking the red buttons OWS is starting the java applications

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