unable to hide by default clinical data for study view

[timchu90]

As described here (https://github.com/cBioPortal/cbioportal/blob/master/docs/File-Formats.md#data-files), attribute charts should be able to be hidden in the study view when given a priority value of 0.

This currently isn't working in a local build of cbioportal release 2.2.0

[AndyBlake]

Also the order of fields is being completely ignored on my version of 2.2.0 but 2.1.0 works fine with the same data.

[jjgao]

@zhx828 @kalletlak thoughts?

[zhx828]

@timchu90 @AndyBlake I do need some more information about the issue. Could you tell me the following

• which db schema version you are using?
• In the endpoint api/clinical-attributes/fetch, does it return proper priority?
• Do you have a testing instance anywhere that I can take a look?

[timchu90]

• 2.8.2
• yes it is the proper priority.
• sorry unfortunately no.

A little more information, I encountered this when building a new combo type chart for the study view in cbioportal-frontend. My input had multiple new values for a patient that were combined to make a new chart similar to the survival chart. So the idea was to hide the default bar/pie charts that show up as a result of adding custom attributes.

This bug however also occurs in standard attributes like 'PATIENT_SEX'.

Neither setting the input clinical priority in the text file to 0, or editing the serverConfigDefaults values to 0 for a chart will hide the chart properly, but will instead just move them to the bottom of study view.

[zhx828]

@timchu90 sounds like you are trying to debug in the frontend? Did you modify both serverConfigDefaults and StudyViewConfig?

[AndyBlake]

Hiya

2.8.2 Yes and response is the same between versions sorry behind basic auth and keycloak auth

Can send api response data via email if that is of any help?

[AndyBlake]

2.20 Version missing and ignoring ordering clin_api_reteurn_edited.txt working in 2.1.0 same data

json response with study id changed but which data is the same between instances and screenshots of the different outputs

[AndyBlake]

Shall I open an new issue as it looks like we have different problems? I'll await your input @zhx828 @kalletlak

[zhx828]

@AndyBlake @timchu90 I do want to let you know we updated the sorting method in this pr(https://github.com/cBioPortal/cbioportal-frontend/pull/2101), so the charts layout will be different comparing to 2.1.0 but priority should be respected though. I do want to get the bottom of this issue, so @AndyBlake I'm going to setup a seed database and mock your data to see whether I can reproduce the expected layout or the layout I think it should be.

@timchu90 I do need to get some more data to be helpful. If you could give me the same data AndyBlack gave to me, I can try to do something. And side note, if you are making a combination chart, if any of the priority is 0, the combination chart will be hidden.

[timchu90]

@zhx828 Sorry for the delay in response. While I am debugging cbioportal-frontend, this is something that i observe in a fresh install of cbioportal-frontend 2.2.0.

[AndyBlake]

@zhx828 Thanks - It looks as if it's ignoring the priorities and just doing the default load as if they were all 1 hence the reduced number of plots displayed and default ordering. Just a guess but perhaps there is something in the "has custom priorities or not" logic that is getting tripped incorrectly? If there is anything else I can do to help just let me know.

[zhx828]

@AndyBlake thanks for the info. If it's true like you said, the priorities are ignored, that explains the different layout. But like you mentioned before, the clinical attributes list does have the updated priority though. If you already have the frontend setup, that would be supper help for since you have all the data. I just haven't gotten a chance to take a look at yet.