WWW - Emma is not able to create SOME temporary files

[David Starks-Browning]

On Monday 7 Oct 02, Tõnu Margus writes:
> Hi,
> 
> I am using EMBOSS via Luke McCarthy's web interface. All other programs are working, 
> but emma didn not work correctly.
> 
> It gives an error:
> 
> Error: failed to open filename 8808B Problem writing out EMBOSS alignment fileError: failed to open filename 8808B Problem writing out EMBOSS alignment file
> 
> It seems that by some reasón it can not create a file under runs/temp directory.
> Why not -  is for me unclea.  All other files are there. 
> 
> Files under catalog     runs/fileVxWbES$/) 
> 
> root at kobra:fileVxWbES$ ls -l
> total 16
> -rw-r--r--   1 www      java          915 Oct  7 20:51 8825A
> -rw-r--r--   1 www      java            0 Oct  7 20:51 dendoutfile
> -rw-r--r--   1 www      java          384 Oct  7 20:51 error
> -rw-r--r--   1 www      java         2145 Oct  7 20:51 index.html
> drwxr-xr-x   2 www      java         4096 Oct  7 20:51 input
> -rw-r--r--   1 www      java            0 Oct  7 20:51 outseq
> 
> Command line clustalw works  ok

You don't show the permissions of the directory itself (use 'ls -la').
It's the directory permissions that determine whether files can be
created.

However, this may not be the problem.  We have seen problems with emma
on Linux, because the underlying application, clustalw, cannot deal
with filenames that are 5 characters long on Linux.  String buffer
management bugs in emma cause it to emit garbage characters after the
filename to the open() system call.  With emma, you will see this when
emma's PID is 4 digits long.  (You won't see the garbage characters in
error messages.  You only see them under strace.)

Clustalw should be fixed.  If that won't happen, emma.c could be
modified to pad the temporary file name with enough extra characters
so that, regardless of Linux PID, emma will use temp filenames longer
than 5 characters.

I don't have a patch for the latest version of emma, because I applied
the workaround to an old (1.9.1) version of EMBOSS.  Emma.c has changed a bit
since then, although the change is still straightforward to apply.

If you think this is your problem, I can provide details on how to
modify emma.c.

Hope this helps.

Kind regards,
David

 -------------------------------------------------------------------
  David Starks-Browning                  | starksb at ebi.ac.uk
  EMBL Outstation --                     |
  The European Bioinformatics Institute  |
  Wellcome Trust Genome Campus           | tel: +44 (1223) 494 616
  Hinxton, Cambridge, CB10 1SD, UK       | fax: +44 (1223) 494 468
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