Open Microscopy Environment

Hi,


I migrated my server from 4.3.4 to 4.4.0, but I have two problems...

When I try to import a file through DropBox (or through the command line) I get :

Code: Select all

Exception in thread "main" java.lang.NoClassDefFoundError: ome/formats/importer/cli/CommandLineImporter
Caused by: java.lang.ClassNotFoundException: ome.formats.importer.cli.CommandLineImporter
        at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
Could not find the main class: ome.formats.importer.cli.CommandLineImporter.  Program will exit.

Regarding the webserver, I use lighttpd. I modified the config file, but I'm not sure of what has changed for the links. Basically, I just removed the "appmedia" alias and replaced it with a "static" alias, but I wonder if there is more to it...
For example, I can't get webstart to work... But besides that, everything seems to display fine...

Other than that, from what I've seen, OMERO 4.4 looks great !

But if I could just get the DropBox to work again, it would be fantastic...

PS : I use the Ice 3.3 version, since my server runs Debian Squeeze...

Hi Pierre,

I'm looking into the DropBox issue. It will likely require a new server-download. In the meantime, can you post your lighttpd configurations (old and new) and we'll see if we can help? Thanks!

Cheers,
~Josh

My configuration for OMERO 4.3.4 was :

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# OMERO Web Server (Client / Admin)
$HTTP["url"] =~ "^/web(client|admin)" {
  server.document-root = "/srv/omero/var/omero.fcgi/"
  fastcgi.server = ( "/" =>
    (( "docroot"   => "/",
       "min-procs" => 8,
       "max-procs" => 16,
       "max-load-per-proc" => 4,
       "socket"    => "/srv/omero/var/django_fcgi.sock",
       "check-local" => "disable",
       # Fix for prefix "/". Lighttpd >= 1.4.23 needed
       "fix-root-scriptname" => "enable",
    ))
  )
}

alias.url += ( "/appmedia" => "/srv/omero/lib/python/omeroweb/media/" )
$HTTP["url"] =~ "^/appmedia" {
  dir-listing.activate = "disable"
}

alias.url += ( "/api" => "/srv/omero/docs/api/" )
$HTTP["url"] =~ "^/api" {
  dir-listing.activate = "disable"
}


In my new config file, I have :

Code: Select all

# OMERO Web Server (Client / Admin)
$HTTP["url"] =~ "^/web(client|admin)" {
  server.document-root = "/srv/omero/var/omero.fcgi/"
  fastcgi.server = ( "/" =>
    (( "docroot"   => "/",
       "min-procs" => 8,
       "max-procs" => 16,
       "max-load-per-proc" => 4,
       "socket"    => "/srv/omero/var/django_fcgi.sock",
       "check-local" => "disable",
       # Fix for prefix "/". Lighttpd >= 1.4.23 needed
       "fix-root-scriptname" => "enable",
    ))
  )
}

alias.url += ( "/static" => "/srv/omero/lib/python/omeroweb/static" )
$HTTP["url"] =~ "^/static" {
  dir-listing.activate = "disable"
}


I tried to use "/omero" instead of "/web(client|admin)", but it didn't work.
This config seems to be ok, except for webstart...

Can you add "start" to the list of excepted suffixes? I.e.:

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$HTTP["url"] =~ "^/web(client|admin|start)" {


There may be other changes the rest of the team will want to suggest on Monday.

Cheers,
~Josh

Thanks !

Why didn't I think of that...

Could I find a working "OmeroImporter.jar" file to put on my server somewhere ?
I suppose, it wouldn't solve my problem though...
(But I still need DropBox to be running...)

I just uploaded a new OMERO.server-4.4.0-ice33-b3033.zip. The new MD5 is: 5ea0f87041e0d8e31c250d071613ce70. If you could give that a try, that'd be great.

I'm checking the ice34 zip for the same corruption now. Update: the ice34 zip is fine.

Cheers,
~Josh

Thank you very much, it works !

Glad to hear it! Thanks for debugging for us.

~Josh