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Pride inspector program not opening properly. #9

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Download the pride inspector from this site.
2. Double-click on the "pride-inspector-1.3.1.jar"
3. Error occurs immediately.

What is the expected output? What do you see instead?
I would expect for the program to work normally.

I get the following error:
The Java JAR file "pride-inspector-1.3.1.jar" could not be launched. Check the 
Console for possible error messages. No additional error messages were seen.

What version of the product are you using? On what operating system?
1.3.1

Please provide any additional information below.
This is the first time I've tried to use pride inspector.

Original issue reported on code.google.com by GhanM...@gmail.com on 10 Oct 2013 at 10:00

GoogleCodeExporter commented 9 years ago 
Dear Ryan,

Sorry you have experienced problems getting the PRIDE Inspector tool to launch.

Would you be able to find any error messages in the Java console? To view this, 
you may need to enable some further options:
http://www.java.com/en/download/help/javaconsole.xml

May I ask what operating system you are using, I am assuming it's a version of 
Windows?

Also can you confirm which version of Java you're running? This might be useful 
to verify it:
http://www.java.com/en/download/installed.jsp

I have encountered a similar problem before with Inspector not launching, and 
it could be down to user/file permissions. Please could you try extracting and 
running the tool from a different directory, or hard drive?

In the meantime if you want to get going with PRIDE Inspector, you can also try 
the Webstart launcher:
http://code.google.com/p/pride-toolsuite/wiki/PRIDEInspector#Launch_via_Webstart

Best regards,
Tobias Ternent
Bioinformatician
PRIDE Team

Original comment by tob...@ebi.ac.uk on 11 Oct 2013 at 9:03

GoogleCodeExporter commented 9 years ago 
Hi Tobias-

I am running OS X 10.8.5, with Java Standard Edition (Version 7 Update 25, 
build 1.7.0_25-b15).

As you instructed, I enabled the Java Console, according to Java's 
instructions, but I am still not clear how to view the Java console to review 
any error messages that might be displayed. The only way I have been able to 
see the console was when I tried the link to view the Java version you 
provided. This starts a Java Applet, which I believe is the console. However, 
this quickly closes when I attempted to restart the inspector.jar. Googling 
'how to view java console mac" repeats the steps of enabling the console, but 
does not explicitly state how to view the console. Any ideas would be greatly 
appreciated. I am comfortable navigating within the terminal, should that be a 
requirement to view the console. I am just not sure where I should be looking.

I have also adjusted the amount of memory allocated in the "JavaOptions.txt" to 
> 4 GB.

Also, I have also tried running the jar on my personal laptop, and still get 
the same error (I am also running 10.8.5 with the latest version of java), and 
again I am still not sure how to even view the Java Console.

I will give the webstart launcher a look. Mainly, I was just curious what the 
inspector did and wanted to try the tool with some of my data that I am in the 
process of converting, prior to submission on proteomexchange.

Cheers,
Ryan

Original comment by GhanM...@gmail.com on 14 Oct 2013 at 6:48

GoogleCodeExporter commented 9 years ago 
Hi Ryan,

Please could you try running the tool from the command line terminal using:
java -jar pride-inspector.1.3.1.jar

This should then hopefully display any error message about launching the 
Inspector tool. If so, could you copy and paste me what it says?

Best regards,
Tobias Ternent
Bioinformatician
PRIDE Team

Original comment by tob...@ebi.ac.uk on 16 Oct 2013 at 9:26

GoogleCodeExporter commented 9 years ago 
Hello Tobias-

Running the tool as indicated above:

$ java -jar pride-inspector-1.3.1.jar

Produces this error on the command line:

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 0
    at uk.ac.ebi.pride.data.io.db.DBMetadataExtractor.main(DBMetadataExtractor.java:27)

Cheers,
Ryan

Original comment by GhanM...@gmail.com on 16 Oct 2013 at 6:56

GoogleCodeExporter commented 9 years ago 
Hi Ryan,

Thanks for the exception message. Our developer has identified and fixed this 
bug now in the latest version of PRIDE Inspector, 1.3.2. Please could you 
download it:
http://code.google.com/p/pride-toolsuite/downloads/list
and give it another try?

Hopefully this should be working well for you.

Best regards,
Tobias Ternent
Bioinformatician
PRIDE Team

Original comment by tob...@ebi.ac.uk on 17 Oct 2013 at 9:53

GoogleCodeExporter commented 9 years ago 
HI Tobias-

Everything seems to be running fine! Many thanks to you and your developers for 
their assistance.

Cheers,
Ryan

Original comment by GhanM...@gmail.com on 17 Oct 2013 at 4:47