Columbus creates and utilizes 2 databases, the omero4_4 db and also the columbus_webapp db.
Both are backed up by a script which runs under /etc/cron.daily and are, by default, stored in /OMERO/OMERO4_4/db_backup
To view details of how to backup the omero4_4 db, click here
To manually backup the columbus_webapp you must first switch to the 'columbus' user account and issue the following command:
$ su columbus -
$ pg_dump -v -Fc -f /OMERO/OMERO4_4/db_backup/columbus_webapp-TEST.pg_dump columbus_webapp
pg_dump -v -Fc -f - the arguments used as part of the pg_dump process to create the backup
/OMERO/OMERO4_4/db_backup/ - the location where you want the backup to be stored
columbus_webapp-TEST.pg_dump - the name of the backup file
columbus_webapp - the name of the db being backed up
RAH
How do I backup the columbus_webapp db?
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How do I delete the Columbus software packages and user data?
The workflow below details the process of removing the main components of a Columbus installation. Note that this will not revert the system to a vanilla installation. Those package dependencies which were provided by the operating system will remain, as will the user accounts which were generated by the Columbus installation scripts.
WARNING: This will erase ALL user data. After these steps have been performed it will only be possible to recover the data if you have an appropriate backup available.
Removing the Columbus packages
1) Connect to the Columbus server via PuTTY/Terminal
2) Stop the Columbus service
$ sudo /etc/init.d/columbus stop
3) Delete the Columbus file repository
$ sudo rm -rf /OMERO/OMERO4_4
4) Access the postgres user account
$ sudo su postgres -
5) Delete the omero and webapp databases
$ dropdb omero4_4
$ dropdb columbus_webapp
6) Exit the postgres user account
$ exit
7) List all installed Columbus and Acapella packages
$ rpm -qa | grep -E 'Acapella|Columbus'
8) Delete any Columbus/Acapella packages listed in the output of the command in step 7)
$ sudo rpm -e --nodeps
9) Check for any remaining packages:
$ sudo rpm -qa | grep -E 'Acapella|Columbus'
The output should be empty.
10) Remove the Columbus software repository from the /etc/yum.repos.d directory (RedHat Enterprise Linux), or the /etc/zypp/repos.d directory (SuSE Linux Enterprise Server).
The PDF copy of this technote is available for download, here:
https://perkinelmer.box.com/s/fe4yve96zaw5gdltzjsbzk27ks8tr13y
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What are the columbus_webapp db dump files used for?
These are backups of the second psql database instance, columbus_webapp. It stores all data that Columbus needs in addition to what Omero holds.
For example the tables stored under the columbus_webapp include login and authentication attempts for users connecting to Columbus from a 3rd party app via the webapp, celery queue information and also contains things like the publishing status, cluster job status and the remote references for the measurements that have been forwarded to Amazon S3 during import for the cluster functionality.
It’s use/relevance depends on the whether or not you are using features like publishing or cluster computing.
RAH
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What is the Celery service used for?
Celery is a task queuing service. It's primary use is for managing image rendering and export jobs being submitted to the Columbus server via 3rd party applications e.g. Spotfire.
The Celery system picks these jobs from the queue runs them asynchronously and when complete prepares a response which is then picked up by the webapp to return to a client or webpage.
Celery runs as another service component, it is started and stopped via /etc/init.d/columbus which actually uses /etc/init.d/columbus-celeryd. If the celery service doesn't respond to the standard /etc/init.d/columbus script then you can call the columbus-celeryd script directly using:
$ /etc/init.d/columbus-celeryd stop/start/restart/status
The Celery service starts multiple worker nodes for accepting image rendering requests, the workers log information regarding those jobs to /var/log/columbus/web/columbus-images-service.log.
RAH
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What can I do if the Celery service is not responsive?
Initially you should try starting/stopping the celery service using:
$ /etc/init.d/columbus-celeryd (stop/start/restart/status)
If the celery service is 'hung' and does not respond to either /etc/init.d/columbus stop, or $ /etc/init.d/columbus-celeryd stop then it might be necessary to kill the Celery related processes. Typically you will see more than 1 process. There's a master but depending on the activity there will be several worker processes. They all run under the columbus account e.g:
$ ps f -fU columbus
UID PID PPID C STIME TTY STAT TIME CMD
columbus 12688 12687 0 08:01 ? S 0:01 nginx: worker process
columbus 12782 1 0 08:01 ? Sl 3:11 /usr/local/PerkinElmerCTG/Columbus2.8/webapp/virtualenv/bin/python -m celery.__main__ worker --app=columbus -n c
columbus 9627 12782 2 13:25 ? Sl 0:01 \_ /usr/local/PerkinElmerCTG/Columbus2.8/webapp/virtualenv/bin/python -m celery.__main__ worker --app=columbus
columbus 9731 12782 0 13:25 ? Sl 0:00 \_ /usr/local/PerkinElmerCTG/Columbus2.8/webapp/virtualenv/bin/python -m celery.__main__ worker --app=columbus
columbus 9751 12782 3 13:25 ? Sl 0:01 \_ /usr/local/PerkinElmerCTG/Columbus2.8/webapp/virtualenv/bin/python -m celery.__main__ worker --app=columbus
You'd need to kill the master with PID 12782 but before that the slave processes must be killed, you can use pkill -P with the parent id to do so:
$ sudo kill -9 -P 12782
# Now kill the master
$ sudo kill -9 12782
Now if you start Celery again it should bring it back to life. If this doesn't help then there is potential for something to be broken meaning that the image rendering jobs will fail, if that is the case then check the /var/log/columbus/web/columbus-images-service.log file for errors and forward on to the PKI informatics support team for further troubleshooting advice.
RAH
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Can I prevent users from submitting local batch analysis jobs on a Columbus+ server?
On a default Columbus+ server users have the option to submit batch analysis jobs locally or within the cluster environment.
Its not possible to restrict users to one method or the other via the Columbus UI, but by modifying the source code its possible to remove the local analysis option, meaning users are forced to submit batch analysis jobs to the cluster.
The following information is valid for Columbus version 2.8.2 and may differ in future versions.
The following change must be made:
/usr/local/PerkinElmerCTG/Acapella-4.1.3/AcapellaResources/AcapellaColumbusWebapp/ProcLib/columbus/nav_batch.proc
line 429
analysisServerOptions = vec(COMPUTE_ON_LOCAL_SERVER);
change to
analysisServerOptions = vec();
Note, it is recommended to make a backup of the nav_batch.proc file before modifying. Any modifications will be reverted during the next Columbus update.
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'Insert Image Column' Dialog Layout Appears Cropped and is Unusable
If the 'Insert Image Column' Dialog appears cropped and messed up like this:
- Exit Spotfire
- Right click Desktop ... Display Settings
- Set Scale and layout to 100%
- Sign out of Windows
- Sign in and it should appear as normal.
The inspiration for this Technical Note comes from:
https://support.tibco.com/s/article/Spotfire-analyst-client-has-display-or-weird-boarder-issues-when-custom-text-size-scale-is-changed-on-a-Windows-7-desktop-machine
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Activation ID/Host owner mismatch error - No Respose from Support Email
Hi,
I have a user who is getting Activation ID/Host owner mismatch error, he has emailed support (perkinelmer@flexnetoperations.com) a number of times with no response. Which is concerning.
Can someone help?
Thanks,
Fraser
University of St Andrews
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Will my user session in Columbus expire?
After a user logs in to Columbus the session is kept alive as long as the browser is running with a Columbus application in any of the tabs. More precisely this is for all the pages like navigation, image analysis, import, export etc, not for the admin pages or job status page.
The session is killed if a user logs out (as long as there are no background jobs running under this session). The session is also killed 10 minutes after the user closes the browser (or the tabs) that displayed the Columbus app.
When background jobs are running the session will not be terminated, the 10 minute timeout would be applied at the point the background job finishes.
RAH
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Can I disable SSLv3 encryption on the Columbus server?
For servers where HTTPS support has been enabled for the Columbus login and webadmin pages, its possible to disable SSLv3 encryption and leave only TLSv1 support enabled. To do that users must add a line to the server section of the /usr/local/PerkinElmerCTG/Columbus/webapp/server/config/nginx.tmpl file to specifiy ONLY the supported protocols. See the last line in the excerpt below as an example.
~~~~~~~~~~~~~~~~~~~~~
# https server for /login and /webadmin requests
server {
listen ${https_port} ssl;
ssl_certificate ${https_certificate};
ssl_certificate_key ${https_key};
# turn off SSL encryption
ssl_protocols TLSv1;
...
}
~~~~~~~~~~~~~~~~~~~~~
The Columbus service must be restarted after making the modifications.
$ sudo /etc/init.d/columbus restart
Note: Any modification will be overwritten during the next Columbus update.
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Maximum image file size for Columbus import
Is there an upper limit to the size of image files imported to Columbus?
I have been unable to successfully import TIF files > 30 MB. I am using the Import Type method 'Columbus CSV' and have had no issues importing TIF files
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Columbus could not handle the request:
Assertion failed: status
status: 0
Assertion failed: status
status: 0
Hide details
/usr/local/PerkinElmerCTG/Acapella-4.1.2/AcapellaResources/AcapellaColumbusWebapp/ProcLib/columbus/navigator.proc(260) [Columbus::nav_DisplayImage]: /usr/local/PerkinElmerCTG/Acapella-4.1.2/AcapellaResources/AcapellaColumbusWebapp/ProcLib/columbus/util_imageview.proc(262) [::Assert]: Assertion failed: status status: 0
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A possible solution to my problem may require tiling/segmenting these large image files into smaller image files?
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ChemDraw drawing not appearing on word 16
Hello all,
I am having a problem while copy pasting the ChemDraw (V16) structures to MS Powerpoint or MS Word 2016. I can only see the frame after I copy, no image appears. Earlier I didn't have that issue, I am also using high DPI laptop this time. Not sure why this is happening, please help if you have any solution.
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ChemDraw drawing not appearing on word 16
Hello all,
I am having a problem while copy pasting the ChemDraw (V16) structures to MS Powerpoint or MS Word 2016. I can only see the frame after I copy, no image appears. Earlier I didn't have that issue, I am also using high DPI laptop this time. Not sure why this is happening, please help if you have any solution.
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How To Solve Chrome Crashing Windows 10?
When I open a few tabs like two to three tabs my Google chrome keeps crashing windows 10 repeatedly. I want to fix this problem please help. This happens only in windows 10. I tired with edge and Firefox browser, they are working flawlessly.
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Failed to start Nginx server ERROR
Issue with columbus webapp start after installing 2.8.2 on Oracle Linux (RedHat)
Starting Columbus
Database: [ OK ]
Acc: [ OK ]
Web: ERROR : Failed to start Nginx server ERROR : Sub-process call error message: nginx: [emerg] bind() to 0.0.0.0:80 failed (98: Address already in use) nginx: [emerg] bind() to 0.0.0.0:80 failed (98: Address already in use) nginx: [emerg] bind() to 0.0.0.0:80 failed (98: Address already in use) nginx: [emerg] bind() to 0.0.0.0:80 failed (98: Address already in use) nginx: [emerg] bind() to 0.0.0.0:80 failed (98: Address already in use) nginx: [emerg] still could not bind() ERROR : Failed to start Nginx server INFO : Fast-CGI se[FAILED][up]
Celery: [ OK ]
Resolution:
If you get following error, when you try to start nginx…
[emerg]: bind() to 0.0.0.0:80 failed (98: Address already in use)
Then it means nginx or some other process is already using port 80.
You can kill it using:
sudo fuser -k 80/tcp
Then restart columbus service ![]()
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Need suggestion to solve google drive server error
I am using Google drive for store files and it is really the best platform for free files storage service but from few days I am getting Google drive server error, after searching on the internet I got to know that it happens due to server issue as well as cookies and caches but yet not get the appropriate solution regarding this issue. If anyone has an idea about this error then kindly inform me.
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Gmail issue
I am using Gmail for the official purpose and it is really the best platform for free email service but from few days I am getting Gmail error 007 but cannot able to understand why such an error is occurring. Can anyone tell me the valid reason and also any suggestion to solve this issue?
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How to solve windows7 installation problem
In today's date we all know that most of the people use windows operating system but when I want to install windows7 in my system then I faced an error. But if you have any type of solution then just reply with this thread. But I have Fix Windows update error code 8007000e.
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How to Publish and Download Results in Columbus Interface
When you publish in Columbus a Measurement's results are made available on the Columbus server as a tab delimited text file. This result file can then be downloaded through the Columbus interface or via the Columbus Connector in Spotfire. Downloading via publishing yields a single file per result and involves fewer steps than using the Columbus Export view, thus can be more convenient.
To try this approach please take the following steps:
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How to automatically clean up stale python processes
Under certain circumstances we observe that the number of python processes (manage.py) serving the Columbus webapp will accumulate. Most of these processes end up in an unused state (only the 6 most recent processes should remain active) and can ultimately have a negative impact on the Columbus application.
The following command will provide a count of the manage.py processes on the Columbus server.
$ ps -fU columbus | grep [m]anage.py | wc -l
If the output is greater than 10, the unused processes can be safely killed using the following command:
$ kill `ps kstart_time -fU columbus | awk '$3 != 1 && /[m]anage.py/ {print $2}' | head -n -10`
This command lists the PID of all but the 10 most recently spawned manage.py processes owned by the columbus user, then passes those PIDs to the kill command for removal.
As it is safe to remove these processes whilst the Columbus application is running, the cleanup can be automated using cron. Create a file named 'columbus_python_cleanup' within the /etc/cron.daily directory on the Columbus server and give the file the following content:
~~~~~~~~~~~~~~~
#!/bin/bash -e
## script to clean up stale python processes
proc_limit=10
cmd="ps kstart_time -fU columbus | awk '\$3 != 1 && /[m]anage.py/ {print \$2}' | head -n -$proc_limit"
orphans=$(eval $cmd)
if [[ ! -z "$orphans" ]]
then
kill $orphans
fi
~~~~~~~~~~~~~~~
Now make the script executable.
$ chmod a+x /etc/cron.daily/columbus_python_cleanup
The script will be executed daily, but the cleanup command will only be executed if the number of python processes exceeds 10.
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