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cBioPortal / cbioportal

cBioPortal for Cancer Genomics
https://cbioportal.org
GNU Affero General Public License v3.0
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Study view page can't hide the clinical chart by default even priority is set to 0 #10351

Closed dippindots closed 10 months ago

dippindots commented 1 year ago

See this example https://beta.cbioportal.mskcc.org/study/summary?id=um_tcga And other_patient_id other_sample_id can't be hidden by default even if the priority is set to 0

Related pr: https://github.com/cBioPortal/cbioportal-frontend/pull/4598 Related document: https://docs.cbioportal.org/deployment/customization/studyview/#priorities

alisman commented 10 months ago

@dippindots I cannot reproduce this. I think you meant "uvm_tcga" right? From my experiments, if I set prioirity to

-1: hidden from add chart list 0: the chart is hidden by default but appears in the add chart list. 1: chart is on be default

Note that this is NOT true for these standard clinical attributes, which have hard coded priorities which cannot be overridden from data (whether that is desirable is separate question)

CANCER_TYPE: 3000, CANCER_TYPE_DETAILED: 2000, GENOMIC_PROFILES_SAMPLE_COUNT: 1000, CASE_LISTS_SAMPLE_COUNT: 1000, OS_SURVIVAL: 400, DFS_SURVIVAL: 300, DSS_SURVIVAL: 250, PFS_SURVIVAL: 250, MUTATED_GENES_TABLE: 90, STRUCTURAL_VARIANT_GENES_TABLE: 85, STRUCTURAL_VARIANTS_TABLE: 85, CNA_GENES_TABLE: 80, PATIENT_TREATMENTS_TABLE: 75, PATIENT_TREATMENT_GROUPS_TABLE: 75, PATIENT_TREATMENT_TARGET_TABLE: 75, SAMPLE_TREATMENTS_TABLE: 75, SAMPLE_TREATMENT_GROUPS_TABLE: 75, SAMPLE_TREATMENT_TARGET_TABLE: 75, CLINICAL_EVENT_TYPE_COUNTS_TABLE: 75, CANCER_STUDIES: 70, SEQUENCED: 60, HAS_CNA_DATA: 50, SAMPLE_COUNT: 40, MUTATION_COUNT: 30, FRACTION_GENOME_ALTERED: 20, GENDER: 9, SEX: 9, AGE: 9, RACE: 8, ETHNICITY: 8, SAMPLE_TYPE: 8, HISTOLOGY: 8, TUMOR_TYPE: 8, SUBTYPE: 8, TUMOR_SITE: 8, 'X-VS-Y-FRACTION_GENOME_ALTERED-MUTATION_COUNT': 200,

dippindots commented 10 months ago

@alisman I can still reproduce this issue I believe: If you go to study: https://beta.cbioportal.mskcc.org/study/summary?id=msk_met_2021 And you also need to remove a line from the frontend code (the portal will initially display 20 clinical charts by default. These charts are prioritized from high to low. Additional clinical charts are initially hidden but can be easily selected by users through the 'Add charts' dropdown menu.) Comment out this line: https://github.com/cBioPortal/cbioportal-frontend/blob/master/src/pages/studyView/StudyViewPageStore.ts#L7534

After you local dev mode is up, click Reset Chartsand you will see the e.g. Met Count and Met Site Count still show up although they have priority=0