cBioPortal / cbioportal

cBioPortal for Cancer Genomics
https://cbioportal.org
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Genomic data bin counts discrepancy #11102

Closed alisman closed 1 month ago

alisman commented 1 month ago
curl 'http://localhost:8082/api/column-store/genomic-data-bin-counts/fetch?dataBinMethod=STATIC'           -H 'accept: application/json, text/plain, */*'           -H 'accept-language: en-US,en;q=0.9'           -H 'cache-control: no-cache'           -H 'content-type: application/json'           -H 'cookie: _ga_ET18FDC3P1=GS1.1.1727902893.87.0.1727902893.0.0.0; _gid=GA1.2.1570078648.1728481898; _ga_CKJ2CEEFD8=GS1.1.1728589307.172.1.1728589613.0.0.0; _ga_5260NDGD6Z=GS1.1.1728612388.318.1.1728612389.0.0.0; _gat_gtag_UA_17134933_2=1; _ga=GA1.1.1260093286.1710808634; _ga_334HHWHCPJ=GS1.1.1728647421.32.1.1728647514.0.0.0'           -H 'pragma: no-cache'           -H 'priority: u=1, i'            -H 'sec-ch-ua: "Google Chrome";v="129", "Not=A?Brand";v="8", "Chromium";v="129"'           -H 'sec-ch-ua-mobile: ?0'           -H 'sec-ch-ua-platform: "macOS"'           -H 'sec-fetch-dest: empty'           -H 'user-agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/129.0.0.0 Safari/537.36'           --data-raw '{"studyViewFilter":{"studyIds":["brca_tcga"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"includeDriver":true,"includeSomatic":true,"includeUnknownTier":true,"includeGermline":true,"includeUnknownStatus":true,"includeUnknownOncogenicity":true,"includeVUS":true},"clinicalDataFilters":[{"attributeId":"CANCER_TYPE","values":[{"value":"Breast Cancer"}]},{"attributeId":"CANCER_TYPE_DETAILED","values":[{"value":"Breast Invasive Ductal Carcinoma"},{"value":"Breast Invasive Lobular Carcinoma"}]},{"attributeId":"PR_STATUS_BY_IHC","values":[{"value":"Positive"},{"value":"Negative"},{"value":"NA"},{"value":"Indeterminate"}]}],"genomicProfiles":[["mrna_median_Zscores"],["mrna"],["mrna_median_all_sample_Zscores"],["rna_seq_v2_mrna_median_Zscores"],["rna_seq_v2_mrna_median_all_sample_Zscores"],["rna_seq_v2_mrna"]]},"genomicDataBinFilters":[{"hugoGeneSymbol":"MIR-760/760","profileType":"linear_CNA","disableLogScale":false}]}';
fuzhaoyuan commented 1 month ago

I think this problem lives in the clinical-data endpoints. I tested the version before NA is added for clinical-data and it works. So @haynescd if you have time to take a look? The SQL error is about can't find patient_id so I'd assume it's some new query related to patients.