alisman

Not serializable error

1

Run this against the TCGA genie database, you'll see some kind of "not serializable" error in java logs. Note that the server DOES respond, so this error may have to...

Violin plot discrepancy

3

@onursumer i'm seeing a discrepancy in the sample ids in the response. Looks like counts are matching. Clickhouse:  Legacy 

Filtered samples discrepancy on public portal

1

``` curl 'http://localhost:8082/api/column-store/filtered-samples/fetch' -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...

[escapeing_discreps.txt](https://github.com/user-attachments/files/17509094/escapeing_discreps.txt)

Seems like legacy doesn't filter on NA properly. When we filter be sex=NA, there is only a single patient, butwe get a ton of mutations which don't seem to relate...

Mutual exclusivity tab of results view is failing

2

 For some reason the mutex tab reports these as unprofiled genes when cleary they are not because query was created from the study view. Lets figure out why it...

Legacy uses gene panel data. When there is NO gene panel (WES?), we get a row per sample because of the join even though both sampleid and panelid will be...

Missing one sample in filtered samples (CH is 1 less)

5

``` curl 'http://localhost:8082/api/column-store/filtered-samples/fetch' -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...

ClinicalDataBinCounts discrepancy

1

 ``` curl 'http://localhost:8082/api/column-store/clinical-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'...