pamag
commented
2 years ago REST end point samples/search queryparam id pass ALL the samples in the cohort => FAILS! if large number of samples
curl 'https://ws.opencb.org/opencga-prod/webservices/rest/v2/samples/search?study=demo%40population%3A1000g&limit=10&skip=0&count=true&exclude=qualityControl&id=NA19209%2CNA19210%2CHG00158%2CNA19206%2CNA19207%2CHG00096%2CNA19159%2CHG00097%2CNA19160%2CHG00099%2CHG00100%2CNA19225%2CHG00101%2CHG00102%2CHG00103%2CNA19222%2CHG00104%2CNA19223%2CHG00105%2CNA19116%2CHG00106%2CNA19119%2CHG00107%2CHG00108%2CNA19121%2CHG00109%2CHG00110%2CHG00111%2CHG00112%2CHG00113%2CNA19141%2CHG00114%2CHG00115%2CNA19152%2CHG00116%2CNA19153%2CHG00117%2CHG00118%2CNA19149%2CHG00119%2CHG00120%2CHG00121%2CHG00122%2CNA19143%2CHG00123%2CNA19144%2CHG00125%2CNA19146%2CHG00126%2CNA19147%2CHG00127%2CHG00128%2CHG00129%2CHG00130%2CNA19129%2CHG00131%2CNA19113%2CHG00132%2CNA19114%2CHG00133%2CHG00134%2CNA19256%2CHG00135%2CNA19257%2CHG00136%2CHG00137%2CHG00138%2CNA19117%2CHG00139%2CNA19118%2CHG00140%2CHG00141%2CNA19130%2CHG00142%2CNA19131%2CHG00143%2CHG00145%2CNA19098%2CHG00148%2CNA19099%2CHG00149%2CHG00150%2CHG00151%2CNA19213%2CHG00152%2CNA19214%2CHG00154%2CHG00156%2CNA19189%2CHG00157%2CNA19190%2CHG00159%2CHG00160%2CNA19235%2CHG00231%2CNA19236%2CHG00232%2CHG00233%2CNA19238%2CHG00234%2CNA19239%2CHG00235%2CHG00236%2CHG00237%2CNA19247%2CHG00238%2CNA19248%2CHG00239%2CHG00240%2CHG00242%2CHG00243%2CHG00244%2CHG00245%2CHG00246%2CHG00249%2CHG00250%2CHG00251%2CHG00252%2CHG00253%2CHG00254%2CHG00255%2CHG00256%2CHG00257%2CHG00258%2CHG00259%2CHG00260%2CHG00261%2CHG00262%2CHG00263%2CHG00264%2CHG00265%2CHG01334%2CHG01789%2CHG01790%2CHG01791%2CHG02215%2CHG04301%2CHG04302%2CHG04303%2CNA20868%2CNA20886%2CNA20910%2CNA20845%2CNA20846%2CNA20847%2CNA20849%2CNA20850%2CNA20851%2CNA20852%2CNA20853%2CNA20854%2CNA20856%2CNA20858%2CNA20859%2CNA20861%2CNA20862%2CNA20863%2CNA20864%2CNA20866%2CNA20867%2CNA20869%2CNA20870%2CNA20872%2CNA20873%2CNA20874%2CNA20875%2CNA20876%2CNA20877%2CNA20878%2CNA20881%2CNA20882%2CNA20883%2CNA20884%2CNA20885%2CNA20887%2CNA20888%2CNA20889%2CNA20890%2CNA20891%2CNA20892%2CNA20894%2CNA20895%2CNA20896%2CNA20897%2CNA20899%2CNA20900%2CNA20901%2CNA20902%2CNA20903%2CNA20904%2CNA20905%2CNA20906%2CNA20908%2CNA20911%2CNA21086%2CNA21087%2CNA21088%2CNA21089%2CNA21090%2CNA21091%2CNA21092%2CNA21093%2CNA21094%2CNA21095%2CNA21097%2CNA21098%2CNA21099%2CNA21100%2CNA21101%2CNA21102%2CNA21103%2CNA21104%2CNA21105%2CNA21106%2CNA21107%2CNA21108%2CNA21109%2CNA21110%2CNA21111%2CNA21112%2CNA21113%2CNA21114%2CNA21115%2CNA21116%2CNA21117%2CNA21118%2CNA21119%2CNA21120%2CNA21121%2CNA21122%2CNA21123%2CNA21124%2CNA21125%2CNA21126%2CNA21127%2CNA21128%2CNA21129%2CNA21130%2CNA21133%2CNA21135%2CNA21137%2CNA21141%2CNA21142%2CNA21143%2CNA21144%2CHG03024%2CHG03025%2CHG03027%2CHG03028%2CHG03039%2CHG03040%2CHG03045%2CHG03046%2CHG03048%2CHG03049%2CHG03240%2CHG03241%2CHG03246%2CHG03247%2CHG03258%2CHG03259%2CHG03538%2CHG03539%2CHG02461%2CHG02462%2CHG02464%2CHG02465%2CHG02561%2CHG02562%2CHG02568%2CHG02570%2CHG02571%2CHG02573%2CHG02574%2CHG02582%2CHG02583%2CHG02585%2CHG02586%2CHG02588%2CHG02589%2CHG02594%2CHG02595%2CHG02610%2CHG02611%2CHG02613%2CHG02614%2CHG02620%2CHG02621%2CHG02623%2CHG02624%2CHG02628%2CHG02629%2CHG02634%2CHG02635%2CHG02642%2CHG02643%2CHG02645%2CHG02646%2CHG02666%2CHG02667%2CHG02675%2CHG02676%2CHG02678%2CHG02679%2CHG02702%2CHG02703%2CHG02715%2CHG02716%2CHG02721%2CHG02722%2CHG02756%2CHG02757%2CHG02759%2CHG02760%2CHG02763%2CHG02768%2CHG02769%2CHG02771%2CHG02772%2CHG02798%2CHG02799%2CHG02804%2CHG02805%2CHG02807%2CHG02808%2CHG02810%2CHG02811%2CHG02813%2CHG02814%2CHG02816%2CHG02817%2CHG02819%2CHG02820%2CHG02836%2CHG02837%2CHG02839%2CHG02840%2CHG02851%2CHG02852%2CHG02854%2CHG02855%2CHG02860%2CHG02861%2CHG02870%2CHG02878%2CHG02879%2CHG02881%2CHG02882%2CHG02884%2CHG02885%2CHG02887%2CHG02888%2CHG02890%2CHG02891%2CHG02895%2CHG02896%2CHG02982%2CHG02983%2CHG01500%2CHG01501%2CHG01503%2CHG01504%2CHG01506%2CHG01507%2CHG01509%2CHG01510%2CHG01512%2CHG01513%2CHG01515%2CHG01516%2CHG01518%2CHG01519%2CHG01521%2CHG01522%2CHG01524%2CHG01525%2CHG01527%2CHG01528%2CHG01530%2CHG01531%2CHG01536%2CHG01537%2CHG01631%2CHG01632%2CHG01628%2CHG01630%2CHG01625%2CHG01626%2CHG01623%2CHG01624%2CHG01619%2CHG01620%2CHG01617%2CHG01618%2CHG01613%2CHG01615%2CHG01610%2CHG01612%2CHG01607%2CHG01608%2CHG01605%2CHG01606%2CHG01602%2CHG01603%2CHG01668%2CHG01669%2CHG01670%2CHG01672%2CHG01673%2CHG01675%2CHG01676%2CHG01678%2CHG01679%2CHG01680%2CHG01682%2CHG01684%2CHG01685%2CHG01686%2CHG01694%2CHG01695%2CHG01697%2CHG01699%2CHG01700%2CHG01702%2CHG01704%2CHG01705%2CHG01707%2CHG01708%2CHG01709%2CHG01710%2CHG01746%2CHG01747%2CHG01756%2CHG01757%2CHG01761%2CHG01762%2CHG01765%2CHG01766%2CHG01767%2CHG01768%2CHG01770%2CHG01771%2CHG01773%2CHG01775%2CHG01776%2CHG01777%2CHG01779%2CHG01781%2CHG01783%2CHG01784%2CHG01785%2CHG01786%2CHG02219%2CHG02220%2CHG02221%2CHG02223%2CHG02224%2CHG02230%2CHG02231%2CHG02232%2CHG02233%2CHG02235%2CHG02236%2CHG02238%2CHG02239%2CHG03871%2CHG04206%2CHG04239%2CHG03713%2CHG03722%2CHG03727%2CHG03772%2CHG03773%2CHG03874%2CHG04018%2CHG03714%2CHG03716%2CHG03717%2CHG03718%2CHG03730%2CHG03729%2CHG03731%2CHG03742%2CHG03770%2CHG03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915%2CHG00339%2CNA18916%2CHG00341%2CNA18917%2CHG00342%2CHG00343%2CNA18923%2CHG00344%2CNA18924%2CHG00345%2CHG00346%2CHG00349%2CNA19197%2CHG00350%2CNA19198%2CHG00351%2CNA18933%2CHG00353%2CNA18934%2CHG00355%2CHG00356%2CHG00357%2CNA19184%2CHG00358%2CNA19185%2CHG00359%2CHG00360%2CNA19092%2CHG00361%2CNA19093%2CHG00362%2CHG00364%2CNA19095%2CHG00365%2CNA19096%2CHG00366%2CHG00367%2CHG00368%2CNA19102%2CHG00369%2CHG00371%2CNA19137%2CHG00372%2CNA19138%2CHG00373%2CHG00375%2CNA19175%2CHG00376%2CHG00377%2CHG00378%2CNA19200%2CHG00379%2CNA19201%2CHG00380%2CHG00381%2CNA19171%2CHG00382%2CNA19172%2CHG00383%2CHG00384%2CNA19204%2CHG00155%2CHG00146' \ -X 'OPTIONS' \ -H 'Connection: keep-alive' \ -H 'Accept: /' \ -H 'Access-Control-Request-Method: GET' \ -H 'Access-Control-Request-Headers: authorization' \ -H 'Origin: http://bioinfo.hpc.cam.ac.uk' \ -H 'User-Agent: Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/90.0.4430.212 Safari/537.36' \ -H 'Sec-Fetch-Mode: cors' \ -H 'Sec-Fetch-Site: cross-site' \ -H 'Sec-Fetch-Dest: empty' \ -H 'Referer: http://bioinfo.hpc.cam.ac.uk/' \ -H 'Accept-Language: en-US,en;q=0.9' \ --compressed
Describe the bug
The Samples tab in the Cohort Browser is returning a meaningless (to me) string rather than interpretable content
To Reproduce
Go to http://bioinfo.hpc.cam.ac.uk/web-apps/iva-prod/#cohort, user:demouser Cohort Browser for 1k Genomes phase3 study, and click the Samples tab under the main grid.
Expected behavior
I expect to see information on the Samples in the cohort.
ERROR
For big cohorts the sample tab shows and error.
Screenshots
[detected by user in ucam prod installation ]
Replicated in another installation: here it says that the error is in CELLBASE
[NOTE_01]: if any error occur, it is not captured by IVA and no proper error message is shown.
[NOTE_02]: this error happens ONLY in one of the test projct/study: 1000 genomes phase3
Error explained
REST end point samples/search query param id pass ALL the samples in the cohort => FAILS! if large number of samples
https://ws.opencb.org/opencga-prod/webservices/rest/v2/samples/search?study=demo%40population%3A1000g&limit=10&skip=0&count=true&exclude=qualityControl&id=NA19209%2CNA19210%2C [....]