[ome-devel] Error importing files to OME
Graham Klyne
Graham.Klyne at zoo.ox.ac.uk
Fri Jan 7 14:39:51 GMT 2005
Now I have OME installed and running. So far, by way of exploring and
testing the system, using just the web client interface, I am trying to
import a random collection of images I happen to have (these have been
converted to TIFF from JPEG and copied onto the OME server host).
First I create a new project and dataset.
Then, in the import files page, I selected the images from the displayed
directory contents, added them to the import queue, and clicked the 'import
files' link.
A new page is displayed indicating the import is in progress:
[[
Tasks Update | Clear Selected | Clear All
Select Task Status Message Error Last step N
steps PID
Importing images IN PROGRESS Starting
import 1 23 12799
]]
I clicked the "Importing images" link and obtain a new page that indicates
there has been an error, containing the following diagnostic text:
[[
Task: Importing images id 1
error Error calling UploadFile: UploadFile failed. System Error: Invalid
argument
OME::Image::Server::__callOMEIS('OME::Image::Server','Method','UploadFile','File','/home/grahamome/20041226-1308-002.tiff')
called at /usr/kits/OME/OME/src/perl2/OME/Image/Server.pm line 1050
OME::Image::Server::uploadFile('OME::Image::Server','/home/grahamome/20041226-1308-002.tiff')
called at /usr/kits/OME/OME/src/perl2/OME/Image/Server/File.pm line 112
OME::Image::Server::File::upload('OME::Image::Server::File','/home/grahamome/20041226-1308-002.tiff')
called at /usr/kits/OME/OME/src/perl2/OME/Tasks/ImageTasks.pm line 140 eval
{...} called at /usr/kits/OME/OME/src/perl2/OME/Tasks/ImageTasks.pm line
135
OME::Tasks::ImageTasks::importFiles('OME::Dataset=HASH(0xb1aea88)','ARRAY(0xad8fc0c)','undef','OME::Task=HASH(0xa57d1a0)')
called at /usr/kits/OME/OME/src/perl2/OME/Tasks/ImageTasks.pm line 228
OME::Tasks::ImageTasks::__ANON__ called at
/usr/kits/OME/OME/src/perl2/OME/Fork.pm line 210 OME::Fork::__ANON__()
called at -e line 0 eval {...} called at -e line 0
last_step 11
message Uploaded /home/grahamome/20041226-1313-007.tiff
n_steps 23
name Importing images
process_id 12799
session 1
state DIED
t_last 2005-01-07 17:20:33
t_start 2005-01-07 17:20:04
t_stop 2005-01-07 17:20:35
]]
I then clicked the "1" link (by "session"), and another error is displayed,
indicating an internal server error.
[[
Error serving OME::Web::DBObjDetail: Could not remove file: Is a directory
at /usr/lib/perl5/5.8.3/CGI/Carp.pm line 314.
(in cleanup) Could not remove file: Is a directory at
/usr/lib/perl5/5.8.3/CGI/Carp.pm line 314.
Internal Error
The server encountered an internal error or misconfiguration and was unable
to complete your request.
Please contact the server administrator, root at localhost and inform them of
the time the error occurred, and anything you might have done that may have
caused the error.
More information about this error may be available in the server error log.
Apache/2.0.51 (Fedora) Server at delos.zoo.ox.ac.uk Port 80
]]
I'm also getting similar errors if I click any of the menu items on the
left hand side of the page ... even if I try to logout.
Also if I restart my browser and try to reconnect to the OME server home
page.
The problem persists of I stop and restart httpd.
Next I stop httpd again, and try to stop and restart postgresql, which fails:
[[
[root at delos bin]# /etc/init.d/httpd stop
Stopping httpd: [ OK ]
[root at delos bin]# /etc/init.d/postgresql stop
Stopping postgresql service: [ OK ]
[root at delos bin]# /etc/init.d/postgresql start
Starting postgresql service: [FAILED]
[root at delos bin]#
]]
...
Is this all indicative of me doing something wrong, or is there a bug here?
I'm not really sure where to look for further information... is there a
printable manual somewhere, or are the online web pages the entire OME
documentation?
#g
--
I include below a copy of the httpd error_log file -- the messages don't
really help me to understand what is failing here:
[[
[root at delos bin]# cd /var/log
[root at delos log]# ls
acpid cron.2 mail messages.2 rpmpkgs.2 spooler
vbox Xorg.1.log.old
boot.log cups maillog pgsql samba spooler.1
wtmp yum.log
boot.log.1 dmesg maillog.1 ppp scrollkeeper.log spooler.2
wtmp.1
boot.log.2 gdm maillog.2 prelink.log secure squid
Xorg.0.log
cron httpd messages rpmpkgs secure.1 up2date
Xorg.0.log.old
cron.1 lastlog messages.1 rpmpkgs.1 secure.2 up2date.1
Xorg.1.log
[root at delos log]# cd httpd
[root at delos httpd]# ls
access_log error_log ssl_access_log ssl_error_log ssl_request_log
[root at delos httpd]# less error_log
[Thu Jan 06 19:33:34 2005] [notice] LDAP: Built with OpenLDAP LDAP SDK
[Thu Jan 06 19:33:34 2005] [notice] LDAP: SSL support unavailable
[Thu Jan 06 19:33:34 2005] [notice] suEXEC mechanism enabled (wrapper:
/usr/sbin/suexec)
[Thu Jan 06 19:33:36 2005] [notice] Digest: generating secret for digest
authentication ...
[Thu Jan 06 19:33:36 2005] [notice] Digest: done
[Thu Jan 06 19:33:36 2005] [notice] LDAP: Built with OpenLDAP LDAP SDK
[Thu Jan 06 19:33:36 2005] [notice] LDAP: SSL support unavailable
[Thu Jan 06 19:33:36 2005] [notice] mod_python: Creating 32 session mutexes
based on 150 max processes and 0
max threads.
[Thu Jan 06 19:33:37 2005] [notice] Apache/2.0.51 (Fedora) configured --
resuming normal operations
[Thu Jan 06 19:33:37 2005] [error] [client 127.0.0.1] Error calling OMEIS:
[Thu Jan 06 19:33:37 2005] [error] [client 127.0.0.1] Method parameter missing
[Thu Jan 06 19:33:37 2005] [error] [client 127.0.0.1]
[Fri Jan 07 11:30:37 2005] [warn] child process 15605 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:37 2005] [warn] child process 15606 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:37 2005] [warn] child process 15607 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:37 2005] [warn] child process 15608 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:37 2005] [warn] child process 15609 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:37 2005] [warn] child process 15610 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:37 2005] [warn] child process 15611 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:37 2005] [warn] child process 15612 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:37 2005] [warn] child process 15605 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:37 2005] [warn] child process 15606 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:37 2005] [warn] child process 15607 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:37 2005] [warn] child process 15608 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:37 2005] [warn] child process 15609 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:37 2005] [warn] child process 15610 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:37 2005] [warn] child process 15611 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:37 2005] [warn] child process 15612 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:39 2005] [warn] child process 15605 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:39 2005] [warn] child process 15606 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:39 2005] [warn] child process 15607 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:39 2005] [warn] child process 15608 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:39 2005] [warn] child process 15609 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:39 2005] [warn] child process 15610 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:39 2005] [warn] child process 15611 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:39 2005] [warn] child process 15612 still did not exit,
sending a SIGTERM
[Fri Jan 07 11:30:43 2005] [notice] caught SIGTERM, shutting down
[Fri Jan 07 15:55:42 2005] [notice] LDAP: Built with OpenLDAP LDAP SDK
[Fri Jan 07 15:55:42 2005] [notice] LDAP: SSL support unavailable
[Fri Jan 07 15:55:42 2005] [notice] suEXEC mechanism enabled (wrapper:
/usr/sbin/suexec)
[Fri Jan 07 15:55:44 2005] [notice] Digest: generating secret for digest
authentication ...
[Fri Jan 07 15:55:44 2005] [notice] Digest: done
[Fri Jan 07 15:55:44 2005] [notice] LDAP: Built with OpenLDAP LDAP SDK
[Fri Jan 07 15:55:44 2005] [notice] LDAP: SSL support unavailable
[Fri Jan 07 15:55:44 2005] [notice] mod_python: Creating 32 session mutexes
based on 150 max processes and 0
max threads.
[Fri Jan 07 15:55:45 2005] [notice] Apache/2.0.51 (Fedora) configured --
resuming normal operations
[Fri Jan 07 15:55:45 2005] [error] [client 127.0.0.1] Error calling OMEIS:
[Fri Jan 07 15:55:45 2005] [error] [client 127.0.0.1] Method parameter missing
[Fri Jan 07 15:55:45 2005] [error] [client 127.0.0.1]
[Fri Jan 07 16:02:27 2005] [notice] SIGHUP received. Attempting to restart
[Fri Jan 07 16:02:28 2005] [warn] The ScriptAlias directive in
/usr/OME/conf/httpd2.omeis-dev.conf at line 2
will probably never match because it overlaps an earlier ScriptAlias.
[Fri Jan 07 16:02:28 2005] [notice] Digest: generating secret for digest
authentication ...
[Fri Jan 07 16:02:28 2005] [notice] Digest: done
[Fri Jan 07 16:02:28 2005] [notice] LDAP: Built with OpenLDAP LDAP SDK
[Fri Jan 07 16:02:28 2005] [notice] LDAP: SSL support unavailable
[Fri Jan 07 16:02:28 2005] [notice] mod_python: Creating 32 session mutexes
based on 150 max processes and 0
max threads.
[Fri Jan 07 16:02:29 2005] [error] [client 127.0.0.1] Error calling OMEIS:
[Fri Jan 07 16:02:29 2005] [error] [client 127.0.0.1] Method parameter missing
[Fri Jan 07 16:02:29 2005] [error] [client 127.0.0.1]
[Fri Jan 07 16:02:30 2005] [notice] Apache/2.0.51 (Fedora) configured --
resuming normal operations
[Fri Jan 07 16:04:27 2005] [notice] SIGHUP received. Attempting to restart
[Fri Jan 07 16:04:28 2005] [warn] The ScriptAlias directive in
/usr/OME/conf/httpd2.omeis-dev.conf at line 2
will probably never match because it overlaps an earlier ScriptAlias.
[Fri Jan 07 16:04:28 2005] [notice] Digest: generating secret for digest
authentication ...
[Fri Jan 07 16:04:28 2005] [notice] Digest: done
[Fri Jan 07 16:04:28 2005] [notice] LDAP: Built with OpenLDAP LDAP SDK
[Fri Jan 07 16:04:28 2005] [notice] LDAP: SSL support unavailable
[Fri Jan 07 16:04:28 2005] [notice] mod_python: Creating 32 session mutexes
based on 150 max processes and 0
max threads.
[Fri Jan 07 16:04:28 2005] [notice] Apache/2.0.51 (Fedora) configured --
resuming normal operations
[Fri Jan 07 16:08:01 2005] [notice] SIGHUP received. Attempting to restart
[Fri Jan 07 16:08:02 2005] [warn] The ScriptAlias directive in
/usr/OME/conf/httpd2.omeis-dev.conf at line 2
will probably never match because it overlaps an earlier ScriptAlias.
[Fri Jan 07 16:08:02 2005] [notice] Digest: generating secret for digest
authentication ...
[Fri Jan 07 16:08:02 2005] [notice] Digest: done
[Fri Jan 07 16:08:02 2005] [notice] LDAP: Built with OpenLDAP LDAP SDK
[Fri Jan 07 16:08:02 2005] [notice] LDAP: SSL support unavailable
[Fri Jan 07 16:08:02 2005] [notice] mod_python: Creating 32 session mutexes
based on 150 max processes and 0
max threads.
[Fri Jan 07 16:08:03 2005] [notice] Apache/2.0.51 (Fedora) configured --
resuming normal operations
[Fri Jan 07 16:08:03 2005] [error] [client 127.0.0.1] Error calling OMEIS:
[Fri Jan 07 16:08:03 2005] [error] [client 127.0.0.1] Method parameter missing
[Fri Jan 07 16:08:03 2005] [error] [client 127.0.0.1]
[Fri Jan 07 16:10:32 2005] [error] [client 129.67.24.54] Error calling OMEIS:
[Fri Jan 07 16:10:32 2005] [error] [client 129.67.24.54] Method parameter
missing
[Fri Jan 07 16:10:32 2005] [error] [client 129.67.24.54]
05/01/07 16:16:14 serve.pl[12803]: Serving package - OME::Web::Home.
05/01/07 16:16:16 serve.pl[12802]: Serving package - OME::Web::Login.
[Fri Jan 07 16:16:17 2005] [error] [client 129.67.24.47] File does not
exist: /var/www/html/favicon.ico
...skipping...
[Fri Jan 07 17:39:35 2005] [warn] child process 12802 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:39:35 2005] [warn] child process 12803 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:39:35 2005] [warn] child process 12804 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:39:37 2005] [warn] child process 12797 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:39:37 2005] [warn] child process 12798 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:39:37 2005] [warn] child process 12803 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:39:37 2005] [warn] child process 12804 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:39:42 2005] [notice] LDAP: Built with OpenLDAP LDAP SDK
[Fri Jan 07 17:39:42 2005] [notice] LDAP: SSL support unavailable
[Fri Jan 07 17:39:42 2005] [notice] suEXEC mechanism enabled (wrapper:
/usr/sbin/suexec)
[Fri Jan 07 17:39:43 2005] [notice] Digest: generating secret for digest
authentication ...
[Fri Jan 07 17:39:43 2005] [notice] Digest: done
[Fri Jan 07 17:39:43 2005] [notice] LDAP: Built with OpenLDAP LDAP SDK
[Fri Jan 07 17:39:43 2005] [notice] LDAP: SSL support unavailable
[Fri Jan 07 17:39:43 2005] [notice] mod_python: Creating 32 session mutexes
based on 150 max processes and 0
max threads.
[Fri Jan 07 17:39:44 2005] [notice] Apache/2.0.51 (Fedora) configured --
resuming normal operations
05/01/07 17:39:50 serve.pl[13827]: Serving package - OME::Web::Home.
05/01/07 17:39:51 serve.pl[13827]: getApacheSession:
sessionKey=2e165a56aa9399cca13d0eb49634a19e
05/01/07 17:39:51 serve.pl[13827]: getApacheSession: timestamp = . Session
is 18418659 minutes old
05/01/07 17:39:51 serve.pl[13827]: Deleting session
[Fri Jan 7 17:39:52 2005] File.pm: Error serving OME::Web::Home: Could not
remove file: Is a directory at /u
sr/lib/perl5/5.8.3/CGI/Carp.pm line 314.
[Fri Jan 7 17:39:52 2005] File.pm: (in cleanup) Could not remove file:
Is a directory at /usr/lib/perl5/
5.8.3/CGI/Carp.pm line 314.
[Fri Jan 7 17:39:52 2005] File.pm: at
/usr/kits/OME/OME/src/perl2/serve.pl line 105
[Fri Jan 07 17:39:52 2005] [error] 13827: ModPerl::Registry: Can't locate
object method "list" via package "O
ME::Tasks::NotificationManager" (perhaps you forgot to load
"OME::Tasks::NotificationManager"?) at /usr/kits/
OME/OME/src/perl2/serve.pl line 108.\n
[Fri Jan 07 17:39:52 2005] [error] [client 129.67.24.47] File does not
exist: /var/www/html/favicon.ico
[Fri Jan 07 17:39:52 2005] [error] [client 129.67.24.47] File does not
exist: /var/www/html/favicon.ico
05/01/07 17:39:57 serve.pl[13830]: Serving package - OME::Web::Home.
05/01/07 17:39:58 serve.pl[13830]: getApacheSession:
sessionKey=2e165a56aa9399cca13d0eb49634a19e
05/01/07 17:39:58 serve.pl[13830]: getApacheSession: timestamp = . Session
is 18418659 minutes old
05/01/07 17:39:58 serve.pl[13830]: Deleting session
[Fri Jan 7 17:39:58 2005] File.pm: Error serving OME::Web:[Fri Jan 07
17:41:10 2005] [warn] child process 13
827 still did not exit, sending a SIGTERM
[Fri Jan 07 17:41:10 2005] [warn] child process 13828 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:41:10 2005] [warn] child process 13829 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:41:10 2005] [warn] child process 13830 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:41:10 2005] [warn] child process 13831 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:41:10 2005] [warn] child process 13832 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:41:10 2005] [warn] child process 13833 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:41:10 2005] [warn] child process 13834 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:41:10 2005] [warn] child process 13827 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:41:10 2005] [warn] child process 13828 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:41:10 2005] [warn] child process 13829 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:41:10 2005] [warn] child process 13830 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:41:10 2005] [warn] child process 13831 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:41:10 2005] [warn] child process 13832 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:41:10 2005] [warn] child process 13833 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:41:10 2005] [warn] child process 13834 still did not exit,
sending a SIGTERM
[Fri Jan 07 17:41:11 2005] [notice] caught SIGTERM, shutting down
(END)
]]
---
Graham Klyne
Image Bioinformatics Laboratory
Department of Zoology, University of Oxford
South Parks Road, Oxford OX1 3PS, UK
E-mail: <Graham.Klyne at zoo.ox.ac.uk>
Direct phone: +44-(0)1865-281991
Departmental fax: +44-(0)1865-310447
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