Cbioportal: White screen after refreshing results of query from study view

[fedde-s]

When I deploy v2.0.1 according to the documented deployment steps, open an Oncoprint for a few dozen patients selected in the study summary view, and refresh the results view page, I see a blank page, and several exceptions in the browser console.

I believe it might be related to the ?session_id=pending parameter in the URL.

[fedde-s]

@jjgao or @zhx828, do you know whether this bug is caused by the study view or some other page along the way? If I click the ‘back’ button (trying to get away from the blank page), I see a URL ending in /results/legacy_submission.

[fedde-s]

Did some recent release introduce an undocumented requirement to deploy a session service?

[jjgao]

@fedde-s could you reproduce it on https://cbioportal.herokuapp.com?

[fedde-s]

I'm not sure how, I've never done that. Do you know any docs on where to start?

[zhx828]

@fedde-s I'm not aware of the issue. And could not reproduce the issue in the public portal. @adamabeshouse do you know anything about this? ?session_id=pending

[adamabeshouse]

I know that session_id=pending is something @alisman set up as a temporary thing in the URL while the actual session gets saved and an id exists to put into the URL. I'm not aware of what happens when theres no session service. I don't believe any page would directly link to session_id=pending - the page replaces the URL with session_id=pending after its been navigated to

[fedde-s]

@zhx828:

[I] could not reproduce the issue in the public portal

I think that's probably because the public portal is integrated with a session service, which is optional (barely even mentioned) according to the documented way to set up a custom installation.

[pieterlukasse]

@jjgao I think we probably need to make a decision regarding session service, i.e. whether it is a required dependency or not.

• If it is to remain optional, then we would need some regression tests in place to make sure this scenario keeps working at each new release.
• If it is to be made mandatory, then we need some documentation updates, and perhaps add it to the release notes of the last release. Better exception handling will also be needed to avoid blank pages like Fedde described.

Please let me know which solution you think is better to pursue.

[jjgao]

@pieterlukasse I was thinking about that too. I think it's probably time to make session service mandatory.

[Sjoerd-van-Hagen]

@jjgao Will you(r team) take care of the updates of the documentations, release notes and exception handling? We will need to install this for all our clients when they next update.

[jjgao]

Create a ticket for the discussion: https://github.com/cBioPortal/cbioportal/issues/5773.

Our team can take a lead on this, but I think we should get some feedback from the community first. @Sjoerd-van-Hagen

[alisman]

Hi all, the app should be capable of functioning without session service (with limitation on url length). So, the failure @fedde-s describes is either a bug or misconfiguration (perhaps stemming from lack of documentation or inappropriate example config). I will investigate this today. @fedde-s could you post here the portal.properties file you are using?

[fedde-s]

Only a few lines different from the common example file: https://github.com/thehyve/cbioportal-docker/blob/v2.0.1-iss5758/portal.properties#L184

[fedde-s]

Side-note: I'm hoping to get that difference down even further at some point in the process of integrating our dockerisation solutions, and limit the config file to options for which the defaults don't apply as demonstrated in the end-to-end tests.

[alisman]

yeah, the empty assignment might be the problem. i see that is what is in the EXAMPLE file. i will confirm that frontend interprets that inappropriately as ON. you could also try commenting out at that line, which may fix the problem.

[fedde-s]

For anyone reading along: @alisman made PR https://github.com/cBioPortal/cbioportal/pull/5796 to address this.

[alisman]

@fedde-s when you get a blank screen (b/c server fails with too long URL) do you see what http response code is?

[fedde-s]

Without your changes in #5796, the portal doesn't put too much data into the URL. Instead, it sends a POST request to the (non-functional) session service proxy endpoint, and renders the Oncoprint normally as long as I don't try to refresh.

[inodb]

we decided to make session service a requirement

[fedde-s]

Yep, that resolved this, several releases ago already :+1: