cBioPortal / cbioportal

cBioPortal for Cancer Genomics
https://cbioportal.org
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Clinical data discepancy in public portal #11179

Closed alisman closed 1 week ago

alisman commented 2 weeks ago

http://localhost:8082/study/summary?id=liad_inserm_fr_2014

onursumer commented 2 weeks ago

Looks like one attribute is missing in the clickhouse response (see below). All other counts are the same. There are uppercase/lowercase and sort order differences but I assume those are handled properly by the validator.

{
    "attributeId": "ASSOCIATED_GENETIC_METABOLIC_DISEASE",
    "counts": [
        {
            "value": "NA",
            "count": 30
        }
    ]
}
onursumer commented 2 weeks ago

11163 seems to fix this issue.

alisman commented 1 week ago
curl 'http://localhost:8082/api/column-store/clinical-data-counts/fetch' \
  -H 'Accept: application/json' \
  -H 'Accept-Language: en-US,en;q=0.9' \
  -H 'Cache-Control: no-cache' \
  -H 'Connection: keep-alive' \
  -H 'Content-Type: application/json' \
  -H 'Cookie: _ga=GA1.1.1887007066.1710956751; _ga_5260NDGD6Z=GS1.1.1721930557.11.1.1721930574.0.0.0' \
  -H 'Origin: http://localhost:8082' \
  -H 'Pragma: no-cache' \
  -H 'Referer: http://localhost:8082/study/summary?id=liad_inserm_fr_2014' \
  -H 'Sec-Fetch-Dest: empty' \
  -H 'Sec-Fetch-Mode: cors' \
  -H 'Sec-Fetch-Site: same-origin' \
  -H 'User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/130.0.0.0 Safari/537.36' \
  -H 'sec-ch-ua: "Chromium";v="130", "Google Chrome";v="130", "Not?A_Brand";v="99"' \
  -H 'sec-ch-ua-mobile: ?0' \
  -H 'sec-ch-ua-platform: "macOS"' \
  --data-raw '{"attributes":[{"attributeId":"CANCER_TYPE"},{"attributeId":"CANCER_TYPE_DETAILED"},{"attributeId":"SAMPLE_COUNT"},{"attributeId":"SEX"},{"attributeId":"ASSOCIATED_GENETIC_METABOLIC_DISEASE"},{"attributeId":"BMI"},{"attributeId":"KNOWN_MOLECULAR_CLASSIFIER"},{"attributeId":"ISHAK_FIBROSIS_SCORE"},{"attributeId":"NODULE_NUMBER"},{"attributeId":"ONCOTREE_CODE"},{"attributeId":"ORAL_CONTRACEPTION"},{"attributeId":"PATHOLOGICAL_DIAGNOSIS"}],"studyViewFilter":{"studyIds":["liad_inserm_fr_2014"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}}'