[ome-devel] thumbnail generation + original files

[kris]

Hello all,

  I've recently tried upgrading from OME 2.4 to OME 2.6+ (cvs version
dated 11/30).   I've noticed two annoyances and was wondering if
anybody could shed some light on the situation.  

I first removed OME completely from the development machine.
    (rm -rf /OME ; dropdb ome) 
and did a fresh install 
  sudo perl install.pl

All went well as far I can tell. 

I then imported some images several hundred images, using the command
line importer.  

1.  Thumbnails are not generated automatically by OMEIS

    under /OME/OMEIS/Pixels/ 
    I see numbered (1-578) and .info files.
      This appears to have changed since the last version where
      it stored .bz2 and .thumb and .info files.

    Permission on the /OME/OMEIS
     $ ll -d /OME/OMEIS/Pixels/
   drwx--S--- 2 www-data ome 28288 2006-12-05 17:20 /OME/OMEIS/Pixels//

   Nothing else to speak of in the logs (apache) except the missing file

   Here is the generated thumbnail link:

    http://arno.ece.ucsb.edu/cgi-bin/omeis?Method=GetThumb&PixelsID=165;

  and the response:

Error calling GetThumb with PixelsID=165: Could not get information for thumbnail at Pixels/165.thumb
System Error: No such file or directory


2.  Original files are missing.

     We use a temporary directory on symbolic links to our real data
     during import.  In previous versions, the original file was also 
     stored on the OMEIS, is this not the case anymore?


I should not that we are using our own image reader based on 
OME::ImportEngine::AbstractFormat.  I believe we have ported 
all the changes needed since the previous version (mostly cosmetic
changes of renaming subroutine names i.e. __storeFileInfo ->
storeFileInfo) and a few other dealing with the groups (filename -> file
id), but do not believe this is related.  The images themselves 
are there, just not the thumbnails and original files).
Code is here just in case:

http://biodev.ece.ucsb.edu/projects/bisque/browser/perl/BISQUE/ImportEngine/UCSBreader.pm


Thanks for any help,
kris




-- 
Kristian Kvilekval
kris at cs.ucsb.edu  http://www.cs.ucsb.edu/~kris w:805-893-2526 h:504-9756