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Studyview clinical data tab lists Overall Survival column twice, but not OS_MONTHS column #10696

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alisman opened this issue Mar 8, 2024 · 5 comments · Fixed by cBioPortal/cbioportal-frontend#4883
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@alisman
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alisman commented Mar 8, 2024

This would seem to suggest that OS_MONTHS could NEVER have made it to table:

            // filter out survival attributes (only keep 'OS_STATUS' attribute)
            // create a dict which contains all survival attribute Ids that will be excluded from study view
            // get all survival attribute Ids into a dict
            let survivalAttributeIdsDict = createSurvivalAttributeIdsDict(
                this.survivalClinicalAttributesPrefix.result
            );
            // omit 'OS_STATUS' from dict
            survivalAttributeIdsDict = _.omit(survivalAttributeIdsDict, [
                'OS_STATUS',
            ]);

            return Promise.resolve(
                _.filter(
                    this.clinicalAttributes.result,
                    attribute =>
                        !(
                            attribute.clinicalAttributeId in
                            survivalAttributeIdsDict
                        )
                )
            );
@alisman alisman added the bug label Mar 8, 2024
@alisman alisman assigned gblaih and alisman and unassigned gblaih Mar 8, 2024
@alisman
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alisman commented Mar 8, 2024

@inodb the curation team has reported an issue with study view clinical data tab. 1) Survival status appears twice. 2) OS_MONTHS doesn't appear--where they say it once did appear. The code above leads me to believe that it never did appear. Do you have any memory about this?

image

@alisman
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alisman commented Mar 11, 2024

We have decided to allow OS_* for the columns on the clincialda data table. But continue to disallow them for the charts.

_.omit(survivalAttributeIdsDict, [
                'OS_STATUS',
            ]);

@alisman
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alisman commented May 13, 2024

@gblaih can you see why Overall Survival Status disapears from this https://www.cbioportal.org/study/clinicalData?id=laml_tcga?

Results in e2e error

@inodb
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inodb commented May 16, 2024

@sbabyanusha does this fix the issue you found?

@sbabyanusha
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sbabyanusha commented May 16, 2024

It is fixed now in the public portal. Thanks @alisman @inodb

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