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Problem with Regulatory Overview with Web Ptools 23.5 on Centos 7

asked 2020-02-11 15:58:02 -0600

gpharhay gravatar image

updated 2020-02-11 22:15:41 -0600

Suzanne Paley gravatar image


I've run into a strange problem with the Regulatory Overview in Web Ptools (v 23.5) on Centos 7 that is not present in desktop ptools. This problem is also not present when running Web Ptools (23.5) on Ubuntu 18 LTS.

Briefly, when one mouses over a regulatory gene in the regulatory overview, the system generates a box with data for a gene other than the gene that was moused over. Screen shot is CrpWebProolsProblem.png C:\fakepath\CrpWebPtoolsProblem.png. However, when using desktop ptools to access the same PGDB, the system yields CrpDesktopPtoolsCorrect C:\fakepath\CrpDesktopPtoolsCorrect.png. Any of the non-K12 PGDBs at (link text) show this effect, with most, but not all, regulatory genes showing this effect. I've loaded the same PGDBs on my workstation running UBUNTU 18 LTS and Web Ptools (23.5) works just fine. Also, the K12 regulatory overview on Centos 7 looks great.

My question: Is there something about Centos 7 ( September 20, 2019 update) that is causing this problem with Web Ptools? Javascript weirdness? Should I ditch Centos 7 altogether and stick with Ubuntu 18 LTS?

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answered 2020-02-12 12:20:15 -0600

Suzanne Paley gravatar image

Hi Greg,

This sounds similar to a bug we'd already noticed (for some organisms on our biocyc website) but hadn't yet gotten around to looking into. I don't know of any reason why it should be OS-dependent, but since I don't know the source of the problem, it's hard to say. We'll have someone look into it and get back to you.

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Hi Greg, If this is the problem I think it is, it is probably dependent on the zoom level in your diagram - at the default zoom the genes and roll-over boxes should align, but things get disconnected if you zoom in or out. If there is something that you can reproduce where disconnect occurs at the default zoom level, please let us know.

pmidford gravatar imagepmidford ( 2020-02-12 12:32:15 -0600 )edit

Hi Peter, I ran into this problem as you described before too. I think this is different. I poked around with different zoom levels, but the problem persisted, even after clearing the browser cache, although I was not clearing at all zoom levels. I can't log into the AWS instance at the moment to bounce ptools on the EC2 instance, but I should be able to tomorrow. I'll run a more systematic check as you recommended and will get back to you. I'll probably just reboot the whole EC2 instance.

gpharhay gravatar imagegpharhay ( 2020-02-12 13:44:17 -0600 )edit

I was able to reboot the EC2 machine and ran the experiment for looking at what the system reported when I hovered over rpoD with the M. haemolytica PGDB in the Regulatory Overview. After clearing my Chrome cache, clicked on the regulatory overview and hovered on rpoD in the overview at default zoom level with the system reporting the gene as D650_10200, hypothetical protein (wrong). Zooming all of the way in, the system hover shows rpoD to be D650_25930, 30S ribosomal protein S13 (wrong again). However, for the malT regulatory gene, the system reports the correct gene at all zoom levels.

gpharhay gravatar imagegpharhay ( 2020-02-12 15:30:55 -0600 )edit

Hi BRG, I've decided to move our ptools instance to UBUNTU 18 LTS on AWS EC2. Seems like the most direct way to get fully functional. From my perspective, there is not much of an imperative to get the Centos 7 instance fully functional. Thanks.

gpharhay gravatar imagegpharhay ( 2020-02-14 09:43:35 -0600 )edit

Hi Greg, Moving over to Ubuntu is probably the best plan. We develop on Ubuntu and though I have tested the installer on a Centos VM, I don't think I exercised the reg overview. Peter is reluctant to spend much time on the zoom problem since we a planning to rewrite the reg overview to use our new webgraphics system (like we did with the cell overview) in the near future. Hopefully that will resolve both problems.

pmidford gravatar imagepmidford ( 2020-02-14 14:18:57 -0600 )edit

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Asked: 2020-02-11 15:58:02 -0600

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Last updated: Feb 12