When comparing histology types there's a time out issue in portal

[Kathryn Kananen]

Hello,

We’ve been trying to compare histology types across mutations specifically I was trying to see if a more complex survival plot could be generated with these groups but every time I try to compare histologies I keep getting a 

“””

Sorry - please don’t close the Study summary window until the comparison page has finished loading.

Back to Study Summary

“””

dialog box on the page despite closing nothing. 

How can I bypass this? Is there an internal timer checking for updates / queries that is refreshing that is causing this I can deactivate somewhere? Moreover is this even how I do this? If not then how does one go about selecting these groups based on the other tabs in the query for two or more genes? 

Best,

Kat

[Tali Mazor]

Hi Kat,

To help us troubleshoot, can you please share additional details about what you are doing: Which study are you looking at, and how are you defining the groups for the group comparison? Can you share the URL?

Thanks!

-Tali

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[Tali Mazor]

Hi Kat,

Thanks for the additional information - if this is happening on your own locally hosted instance, it may be related to your local setup. I can't help with that, but others on our dev team may have some ideas. Any additional information you or Kurt can provide would be helpful - for example, are you able to enter group comparison with other group definitions?

-Tali

PS Please keep the google group cc'ed so others can contribute to the conversation and benefit from the answer.

On Fri, Jul 23, 2021 at 9:49 AM Kathryn Kananen <keka...@gmail.com> wrote:

Hey Tali,

Likely not directly to our cbioportal at this moment without checking on a few permissions things, but it’s our own personal project.

Here is an unrelated sudy though that achieves the same result:

Home page (I added histologies and made compaisons) - https://www.cbioportal.org/study/summary?id=brca_tcga_pub2015

Survival curves is what we are after that look like this - https://www.cbioportal.org/comparison/survival?comparisonId=60fac77ce4b015b63e9f6d14

I’ve CC’d in our senior dev, Kurt, since he may know more as we go along.

Best,

Kat

[Benjamin Gross]

Hi Kat, Tali,

This may be a local setup issue as I’m not able to generate an error following the links provided.  Is there an error message you can provide either via the browser console or backend log?

Best,

Benjamin

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[Kathryn Kananen]

Sorry I checked the place I would have thought a source stack would have been thrown but none was produced. If you want me to snoop in the inspect element I can as well though that is well out of my knowledge range. The error message is is produced as follows:

1. Slecet out study

2. Select two histologies on study and click the generate comparison

3. Error thrown as shown, more or less just on a jframe, below here as it opens a different page after a long time of waiting:

“”"

Sorry - please don’t close the Study summary window until the comparison page has finished loading.

Back to Study Summary

“”"

Sorry I can’t give a trace! I’m just not quite sure on where to go to get to it at this point.

Best,

Kat

[Benjamin Gross]

Hi Kurt, Kat,

Sorry for the delay.  Looking at what you’ve provided (the post URL), there could be an issue communicating with the cBioPortal session service.  Many times this is resolved by making sure you have the latest version of the session service.  Assuming you’ve deployed with docker-compose, you could update the reference to the version here:

https://github.com/cBioPortal/cbioportal-docker-compose/blob/master/docker-compose.yml#L38

To answer your question about logging, backend logging can be viewed by running the following docker log command:

docker logs -f cbioportal_container

In the event that the session service version is not the issue, I’ve added Karthik Kalletla to this thread. He’s familiar with the session service codebase and may be able to help.

Regards,

Benjamin

On Jul 26, 2021, at 3:08 PM, Mueller, Kurt <Kurt.M...@osumc.edu> wrote:

Hey Ben and Tali,

 

First, thank you for your help, time, and patience. I appreciate the effort you and your coworkers are spending to help us debug this problem.

 

Second, I get the same error that Kat gets when looking at our cBioPortal instance. However, when I look at “Breast Invasive Carcinoma” from cbioportal.org, the “Compare Groups” functionality works. Can you tell me where the backend log is located? Would frontend errors from the application be logged there?

 

Additionally, when Kat and I were recreating the bug together, I made sure to have the browser’s javascript console window open.

When we clicked “Compare Groups”, several javascript exceptions occurred. I’ve attached a screenshot so you can see two errors, including part of a stack trace from an uncaught error within a javascript promise.

 

Let me know if you need any additional information from me. Thank you again for your time.

 

Sincerely,

 

Kurt Mueller

Senior Web Development Analyst

A-STOR/O-STOR

The Ohio State University Comprehensive Cancer Center

Biomedical Research Tower

460 W. 12th Ave

Columbus, OH 43210

 

From: Benjamin Gross <benjami...@gmail.com>
Date: Friday, July 23, 2021 at 11:49 AM
To: Tali Mazor <tma...@ds.dfci.harvard.edu>
Cc: Kathryn Kananen <keka...@gmail.com>, cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>, Mueller, Kurt <Kurt.M...@osumc.edu>
Subject: Re: [cbioportal] When comparing histology types there's a time out issue in portal

CAUTION: External Email

[Aaron Lisman]

Hi guys, 

I'm happy to do a live debugging session on this.  Should be able to tell pretty quick what's going wrong.

--Aaron

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