generic assay data download on download tab #3284
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Thanks @kalletlak , all comments addressed! |
| this.genericAssayProfilesGroupByProfileIdSuffix.result, | ||
| profiles => { | ||
| const stableIds: string[] = []; | ||
| _.forEach(profiles, profile => { |
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not important but i believe this is a mapping operation, so better to use map
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It's not very clear to just use a map function, I will try to use the _.chain() function instead.
| const sampleKeys = samples.map(sample => sample.uniqueSampleKey); | ||
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| // generate row data (keyed by uniqueSampleKey) | ||
| const rows = generateGenericAssayDownloadFileRows( |
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lets call this rowsByUniqueSampleKey
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@alisman Do you think generateGenericAssayRowsByUniqueSampleKey is good? There are some parameters in this function are specific to generic assay data
| stableIds.forEach(stableId => { | ||
| // format: space delimited join | ||
| const formattedValue = | ||
| rowData.alterationData[stableId].join(' ') || 'NA'; |
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i think you mean to catch the condition where stableId doesn't exist in alterationData, and instead return NA. but this will error because of call to join on undefefined.
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@alisman The alterationData[stableId] will never be undefined since we will put an empty list there, please see logic at here: https://github.com/cBioPortal/cbioportal-frontend/pull/3284/files#diff-fc7a2c223844f7cba7399ed39f7813adR482. I can put a comment here if that will make this more clear.
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Fix cBioPortal/cbioportal#7363
implement generic assay data download on download tab.
Example for study (Cancer Cell Line Encyclopedia (Broad, 2019)):
https://deploy-preview-3284--cbioportalfrontend.netlify.app/results/download?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=ccle_broad_2019&case_set_id=ccle_broad_2019_cnaseq&data_priority=0&gene_list=TP53&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=ccle_broad_2019_cna&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=ccle_broad_2019_mutations&profileFilter=0&tab_index=tab_visualize