Hi,
I am regular Jalview user. I am not able to use Jalview web services. It gives me the Preferences problem-
“URLs that could not be contacted:
http://www.compbio.dundee.ac.uk/jabaws
It may be that you have invalid JABA URLs in your web service preferences.
Go to the Web services tab of the Tools->Preferences dialog box to change them.”
The URL is default one and I am not able to understand why it is not working.
In Jaview news update they are saying that-“Jalview Web services are up and running again!” but I still cant access the web services and it displays the same preference problem when I start the application.
It would be really helpful and nice if anyone tell me how to fix this OR is there any alternative that I can try to solve the problem and use the webservices again.
Than you fo any help !
Ganesh
Hello Ganesh.
I am regular Jalview user. I am not able to use Jalview web services.
It gives me the Preferences problem-
"URLs that could not be contacted:
http://www.compbio.dundee.ac.uk/jabaws
It may be that you have invalid JABA URLs in your web service preferences.
Go to the Web services tab of the Tools->Preferences dialog box to
change them."
Jalview gives you this dialog box if it cannot reach the given URL. It might be that a firewall on your machine is blocking Jalview from accessing the internet.
1. First check that you can you browse to http://www.compbio.dundee.ac.uk/jabaws on your machine.
2. Check your web settings/firewall settings and/or with your network administrator to verify that Java is allowed access to the internet, and that if you need to set a WWW proxy username and password, they are correctly set in the 'Connections' tab in preferences (if you need to set these, then after pressing 'OK', close Jalview and re-launch it to check if the settings worked).
3. If the proxy settings don't work, then open the Java Console (from the Tools menu on the Jalview Desktop), then go to the Web services tab in preferences, and hit the 'refresh services' button. You should see some output in the console. Send that to me.
Best of luck Ganesh - let me know how you get on..
Jim.
···
On Fri Aug 10 16:55:35 2012, Ganesh Phad wrote:
Hi Ganesh. From the startup log, I notice you are using java 7 - that may have been the recent update that changed Jalview's behaviour.
I've opened a bug about this (http://issues.jalview.org/browse/JAL-1138), since there does seem to be a problem with windows 7 and Java 1.7 update 4 (noticed in the minecraft forums, of course 
).
Could you try to launch Jalview with this link:
http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/latest/webstart/jalview_ip4.jnlp
If this works, then it is definitely the same problem noticed in the forums... a bug in the java 7 networking stack causing it only work in IPv6 internet environments (which may not be the case in your office!).
Jim.
ps. if this is the problem, then you probably can't download anything using the sequence fetcher either. Please check that you can download one of the example sequence IDs using the 'Fetch sequences' dialog box as well as checking that the web services work.
pps. yes - sent twice - forgot to cc the list!
very welcome !
Could you confirm that the normal webstart link works, too ?
http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/latest/webstart/jalview.jnlp
Jim.
···
On Tue Aug 14 14:27:56 2012, Ganesh Phad wrote:
Good news- Jalview is working perfectly now! 
I tried to launch http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/latest/webstart/jalview_ip4.jnlp but it was unable to do that.
Then I installed java 6 (http://java.com/en/download/manual_v6.jsp) after uninstalling Java7 & updates and then tried to launch the jalview_ip4.jnlp again and it works perfectly.
A special thanks to you !