Old Users - UCSC Genome Browser

[McCully, Dwayne (NIH/NIAMS) [C]]

Hello Support,

 

How do I remove users from UCSC Genome Browser and their generated data (files/sessions, etc)?

 

I have reviewed the namedSessionDb table in Mysql and found old users who should be removed.

 

Dwayne

 

Dwayne McCully

NIAMS, NIH

Contractor

[McCully, Dwayne (NIH/NIAMS) [C]]

[Gerardo Perez]

Hello, Dwayne.

Thank you for your interest in the Genome Browser and for sending your inquiry.

Removing users from the namedSessionDb table can be done using a simple SQL command; however, the hard part would be figuring out what data files and custom track tables are used by the old users' sessions and only by old users' sessions, since multiple sessions can share the same data.

We have never wanted to remove user's saved session data, so we don't have any tools to do this. It will be up to you if you want to examine the session settings to trace custom tracks back to users. The ctfile_* settings (ctfile_hg38, ctfile_hg19, and so on) would be the place to start since those settings point to files that in turn point to custom track tables and possibly some saved files.

I hope this is helpful. If you have any further questions, please reply to genome...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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[McCully, Dwayne (NIH/NIAMS) [C]]

Hi Gerardo,

 

Where can I find the ctfile_hg38, ctfile_hg19, and so on as I did a find  command and did not get any hits.

I scanned with the find command directories /usr/local/apache, /gbdb, and /var/lib/mysql.  

 

Want to review these files and determine the level of effort before proceeding.

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[Gerardo Perez]

Hello, Dwayne.

Thank you for your follow-up question.

ctfile_ is part of the setting name and not the file name. Here is an example SQL command to get the paths to those files for userName="oldUser" (You would need to substitute in the correct username and password for your local hgcentral):

mysql -u... -p... hgcentral -NBe 'select contents from namedSessionDb where userName="oldUser";' | tr '&' $'\n' | grep ^ctfile_ | sed -re 's@%2F@/@g;'

Then each line of each of those files contains a large amount of settings. Some settings to check for would be: dbTableName, vcfFile, htmlFile, bigDataUrl.

The bigDataUrl might be a URL or a local file, for example, BLAT custom tracks are saved in a local bigBed file.

The database table pointed to by dbTableName might contain a path to a file (if it is a wiggle, maf, or vcf custom track table).

But when tracing all those paths, keep in mind that tables and files might be shared with some current users' saved sessions, so they shouldn't be removed unless you can also ensure they are not reachable from current users' sessions.

I hope this is helpful. If you have any further questions, please reply to genome...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute