Cbioportal: Problem loading patient view if a sample has no _sequenced sample list

[jjgao]

http://www.cbioportal.org/case.do#/patient?studyId=prad_mskcc_2014&caseId=PCA0300

Why do we need to load the sample list?

[jjgao]

BTW, displaying the message below for any kind of js error is confusing -- it's nothing to do with "not finding the sample"

I logged it separately #3128

[onursumer]

Seems like we need the sequenced sample ids for Genomic Overview rendering...

[fedde-s]

Possibly related to this discussion on how to structure the information expressed by sample list data files.

[jjgao]

Thanks, @onursumer.

Let's switch to the new fields Ersin added in #3070 for deciding whether there are mutations or seg data for Genome Overview so that we don't have to load the whole case list.

[fedde-s]

@jjgao: from this line it looks like those fields are only an alternative way to retrieve that sample list information in the back-end. @ersinciftci, can you comment?

[ersinciftci]

@fedde-s sorry I just saw this now. I didn't get what you meant by only an alternative way to retrieve that sample list. I think @jjgao suggested to switch to the new fields only for convenience, i.e. 1 less API call.

[fedde-s]

Ah, okay. I just meant that that by itself would not fix the issue that something in the frontend breaks when a study does not have a sample list with the _sequenced suffix, as it's a ‘view’ on the data (not) loaded from the same case list file.

[ersinciftci]

Right, I don't think @jjgao suggested it as a fix to this problem.

[jjgao]

https://github.com/cBioPortal/cbioportal-frontend/pull/639 solve the problem of the pop up window. Let's keep it open until Ersin's API #3070 is used.