Re: Clarifications Required for Session Migration in UCSC Genome Browser Setup

[Vasundhara Anbalagan]

Dear Team,

Good day!

Just a follow up mail. As communicated earlier, we are in the process of migrating the UCSC Genome Browser (RUGB) from an on-premises RHEL7 environment to AWS running RHEL9. The migration of all components, including the cgi-bin, /gbdb/<genome assembly> data, and the corresponding databases (including the hgcentral database), has been completed.

We require clarification on the following points related to session management:

Case 1: Replicating Saved Sessions in the New Setup

In the current setup, there are saved sessions shared with users. We need guidance on replicating these sessions in the new environment.

For example, after modifying the DNS, using the same URL does not yield the expected output, despite having identical cgi-bin, gbdb data, and database configurations in both environments.

Example URLs:

1. https://<on-premDNS>/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=<username>&hgS_otherUserSessionName=sesmGeneTargeting
2. https://<EC2DNS>/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=<username>&hgS_otherUserSessionName=sesmGeneTargeting

The output of these URLs is not consistent. Could you provide insights into why this discrepancy occurs and the steps required to ensure saved sessions function as expected in the new setup?

Case 2: "My Sessions" Feature

We noticed that under the "My Sessions" tab, users can create accounts to create and save their sessions. We need clarification on the following:

1. Where are the user account details (username, password, and session data) stored on the server?
2. Are these details stored entirely in the hgcentral database? If so, how can we ensure that all relevant data has been fully migrated to the new setup?

Additional Considerations

Are there any other tools or features within the UCSC Genome Browser that store user data or work, which require special attention during the migration process?

Please let us know if you need further details or clarification.

Best regards,
Vasundhara A

---

From: Vasundhara Anbalagan <vasundhara...@regeneron.com>
Sent: Monday, December 1, 2025 11:51 PM
To: Hiram Clawson <hi...@soe.ucsc.edu>; Maximilian Haeussler <mhae...@ucsc.edu>; Clay Fischer <clayf...@ucsc.edu>
Cc: DL HPCOps <HPC-Ope...@regeneron.com>
Subject: Re: Clarifications Required for Session Migration in UCSC Genome Browser Setup

Dear Team,

Good day!

Just a follow up mail. As communicated earlier, we are in the process of migrating the UCSC Genome Browser (RUGB) from an on-premises RHEL7 environment to AWS running RHEL9. The migration of all components, including the cgi-bin, /gbdb/<genome assembly> data, and the corresponding databases (including the hgcentral database), has been completed.

We require clarification on the following points related to session management:

Case 1: Replicating Saved Sessions in the New Setup

In the current setup, there are saved sessions shared with users. We need guidance on replicating these sessions in the new environment.

For example, after modifying the DNS, using the same URL does not yield the expected output, despite having identical cgi-bin, gbdb data, and database configurations in both environments.

Example URLs:

1. https://<on-premDNS>/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=<username>&hgS_otherUserSessionName=sesmGeneTargeting
2. https://<EC2DNS>/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=<username>&hgS_otherUserSessionName=sesmGeneTargeting

The output of these URLs is not consistent. Could you provide insights into why this discrepancy occurs and the steps required to ensure saved sessions function as expected in the new setup?

Case 2: "My Sessions" Feature

We noticed that under the "My Sessions" tab, users can create accounts to create and save their sessions. We need clarification on the following:

1. Where are the user account details (username, password, and session data) stored on the server?
2. Are these details stored entirely in the hgcentral database? If so, how can we ensure that all relevant data has been fully migrated to the new setup?

Additional Considerations

Are there any other tools or features within the UCSC Genome Browser that store user data or work, which require special attention during the migration process?

Please let us know if you need further details or clarification.

Best regards,
Vasundhara A

---

From: Vasundhara Anbalagan <vasundhara...@regeneron.com>
Sent: Friday, November 28, 2025 7:20 PM
To: Hiram Clawson <hi...@soe.ucsc.edu>; Maximilian Haeussler <mhae...@ucsc.edu>; Clay Fischer <clayf...@ucsc.edu>
Cc: DL HPCOps <HPC-Ope...@regeneron.com>
Subject: Clarifications Required for Session Migration in UCSC Genome Browser Setup

Dear Team,

Good day!

As communicated earlier, we are in the process of migrating the UCSC Genome Browser (RUGB) from an on-premises RHEL7 environment to AWS running RHEL9. The migration of all components, including the cgi-bin, /gbdb/<genome assembly> data, and the corresponding databases (including the hgcentral database), has been completed.

We require clarification on the following points related to session management:

Case 1: Replicating Saved Sessions in the New Setup

In the current setup, there are saved sessions shared with users. We need guidance on replicating these sessions in the new environment.

For example, after modifying the DNS, using the same URL does not yield the expected output, despite having identical cgi-bin, gbdb data, and database configurations in both environments.

Example URLs:

1. https://<on-premDNS>/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=<username>&hgS_otherUserSessionName=sesmGeneTargeting
2. https://<EC2DNS>/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=<username>&hgS_otherUserSessionName=sesmGeneTargeting

The output of these URLs is not consistent. Could you provide insights into why this discrepancy occurs and the steps required to ensure saved sessions function as expected in the new setup?

Case 2: "My Sessions" Feature

We noticed that under the "My Sessions" tab, users can create accounts to create and save their sessions. We need clarification on the following:

1. Where are the user account details (username, password, and session data) stored on the server?
2. Are these details stored entirely in the hgcentral database? If so, how can we ensure that all relevant data has been fully migrated to the new setup?

Additional Considerations

Are there any other tools or features within the UCSC Genome Browser that store user data or work, which require special attention during the migration process?

Please let us know if you need further details or clarification.

Best regards,
Vasundhara A

Regeneron - Internal

Regeneron - Internal

Regeneron - Internal

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[Matthew Speir]

Hello, Vasundhara.

Thank you for your questions about migrating sessions between mirrors.

Here's an answer to a previous mailing list question that may be of use: https://groups.google.com/a/soe.ucsc.edu/g/genome-mirror/c/JqfDd7DLxp0.

In short, our advice was to run these following commands:

• First, dump and gzip the necessary databases:

mysqldump customTrash | gzip -c > customTrash.sql.gz
mysqldump hgcentral | gzip -c > hgcentral.sql.gz

• Next, gzip the necessary custom track files that are referenced by the customTrash database. You can remove userdata/ part if that directory doesn't exist on your machine.

tar cvfz files.tar.gz /usr/local/apache/trash/ct/* /usr/local/apache/userdata/*

• Finally, copy over the three files to the new machine, then run on the new machine:

zcat customTrash.sql.gz | mysql customTrash
zcat hgcentral.sql.gz | mysql hgcentral
tar xvfz files.tar.gz -C /

• I should add we now store custom track tables in "customDataNN" databases, so if your mirror is configured in the same way, you will need to copy over these databases as well. The database prefix is determined by "sessionDataDbPrefix" setting in your hg.conf. These can be dumped/loaded via similar commands to the hgcentral database as described above.

Here's a bit of context one of our engineers shared in case it's helpful to understand how the hgcentral databases and files are organized:

There is a namedSessionDb table in hgcentral that is the key to all saved sessions. There is a 'gbMembers' table that contains all the login information for registered users. The userName from gbMembers corresponds to the userName in namedSessionDb.

 

Beyond an entry in the namedSessionDb table, there are various files in a filesystem that belong to a saved session. Our system here is configured to keep such files out of trash in a userdata/ directory, although this is controlled by configuration settings and if they are not set, the files remain in trash/, which be a little more difficult to move around.

 

There are also 'customTrash' tables in MySQL that can belong to a saved session. Examination of the 'namedSessionDb' table contents can lead to where all the files and tables are that belong to a saved session

If you have any further questions, please reply to gen...@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.

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Matthew Speir

UCSC Genome Browser, User Support

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