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Clin-data filtering discrepancy in Clickhouse #11020

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alisman opened this issue Sep 25, 2024 · 0 comments
Open

Clin-data filtering discrepancy in Clickhouse #11020

alisman opened this issue Sep 25, 2024 · 0 comments
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alisman commented Sep 25, 2024

With this filter the bin counts for age 70-75 are slightly different between clickhouse and legacy (defference of 1)

http://localhost:8082/study/summary?id=cesc_tcga_pan_can_atlas_2018#filterJson={"clinicalDataFilters":[{"attributeId":"FRACTION_GENOME_ALTERED","values":[{"start":0.3,"end":0.35}]}],"studyIds":["cesc_tcga_pan_can_atlas_2018"],"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":{}}}

You can see it in this CURL: (remove "column-store" from url for legacy)

curl --location 'http://localhost:8082/api/column-store/clinical-data-bin-counts/fetch?dataBinMethod=STATIC&=null' \
--header 'Accept: */*' \
--header 'Accept-Language: en-US,en;q=0.9' \
--header 'Cache-Control: no-cache' \
--header 'Connection: keep-alive' \
--header 'Content-Type: application/json' \
--header 'Cookie: _ga=GA1.1.1887007066.1710956751; _ga_5260NDGD6Z=GS1.1.1721930557.11.1.1721930574.0.0.0' \
--header 'Origin: http://localhost:8082' \
--header 'Pragma: no-cache' \
--header 'Referer: http://localhost:8082/study/summary?id=cesc_tcga_pan_can_atlas_2018' \
--header 'Sec-Fetch-Dest: empty' \
--header 'Sec-Fetch-Mode: cors' \
--header 'Sec-Fetch-Site: same-origin' \
--header 'User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/127.0.0.0 Safari/537.36' \
--header 'X-Requested-With: XMLHttpRequest' \
--header 'sec-ch-ua: "Not)A;Brand";v="99", "Google Chrome";v="127", "Chromium";v="127"' \
--header 'sec-ch-ua-mobile: ?0' \
--header 'sec-ch-ua-platform: "macOS"' \
--data '{"attributes":[{"attributeId":"MUTATION_COUNT","disableLogScale":false,"showNA":false},{"attributeId":"AGE","disableLogScale":false,"showNA":false},{"attributeId":"MSI_SCORE_MANTIS","disableLogScale":false,"showNA":false,"customBins":[0.4,0.6]},{"attributeId":"MSI_SENSOR_SCORE","disableLogScale":false,"showNA":false,"customBins":[4,10]},{"attributeId":"ANEUPLOIDY_SCORE","disableLogScale":false,"showNA":false},{"attributeId":"DAYS_TO_BIRTH","disableLogScale":false,"showNA":false}],"studyViewFilter":{"clinicalDataFilters":[{"attributeId":"FRACTION_GENOME_ALTERED","values":[{"start":0.05,"end":0.1},{"start":0.1,"end":0.15},{"start":0.15,"end":0.2},{"start":0.2,"end":0.25},{"start":0.25,"end":0.3}]}],"studyIds":["cesc_tcga_pan_can_atlas_2018"],"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":{}}}}'

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