[Jalview-discuss] Web start failing if caching turned off

Jim Procter jprocter at compbio.dundee.ac.uk
Wed Jan 11 15:10:31 GMT 2012


Hi Fred.

On 11/01/2012 13:22, Fred Ludlow wrote:
> Awesome, works here too!
very glad to hear it!
> but (and there's always a but...) I was trying to use the web start 
> version so I could see if a different bug was fixed in the latest 
> jalview before reporting it.
oh oh...
> If I do the following steps:
>
> Fetch Sequences -> Uniprot P00325 (alcohol dehydrogenase)
> Right click on sequence name -> Structure -> View all 9 structures
>
> This gives me a jmol window with an error message at the top saying 
> file not found, the filepath it gives is:
> C:\Documents and 
> Settings\username\Desktop\DOCUME~1usernameLOCALS~1Tempjalview..... etc
>
> so it looks like somewhere the temporary path is getting mangled
>
> If I try and load the structures sequentially, the first one loads, 
> but subsequent ones give a similar error in the console log:
>
> FileManager opening C:\Documents and 
> Settings\fludlow\Desktop\DOCUME~1fludlowLOCALS~1Tempjalview1776115461567806960.xml
> file ERROR: java.io.FileNotFoundException: C:\Documents and 
> Settings\fludlow\Desktop\DOCUME~1fludlowLOCALS~1Tempjalview1776115461567806960.xml 
> (The system cannot find the file specified)
> openFiles(2) 16 ms
> eval ERROR: java.io.FileNotFoundException: C:\Documents and 
> Settings\fludlow\Desktop\DOCUME~1fludlowLOCALS~1Tempjalview1776115461567806960.xml 
> (The system cannot find the file specified)
> ----
>          load append 
> "C:\DOCUME~1\fludlow\LOCALS~1\Temp\jalview3072553079554317356.xml" >> 
> "C:DOCUME~1fludlowLOCALS~1Tempjalview1776115461567806960.xml" <<
>
>
> (This is running the web-start version from the link you just sent 
> with 1.6.0_29 on XP).
>
>
> Thanks again for the very quick fix to the previous issue, and sorry 
> to report another one (this is the last one I know about!)
It's always good to get bug reports - I'd much rather that I was told 
when things were failing!

Luckily enough, I had already hit this bug myself - 
http://issues.jalview.org/browse/JAL-1023
We encountered it during the last two Jalview courses of 2011. The root 
of the problem is that Jmol was upgraded, and it now behaves differently 
when working with file paths on windows. The problem also causes the 
linked structure highlighting to fail (since Jalview uses the filename 
as a unique ID when broadcasting mouseover events).

If you register, you can subscribe to the issue which will mean you'll 
get an email when I get around to fixing it!
Jim.



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