context("Tests for raw and intermediate data")
rm(list=ls())
verbose <- FALSE
#setup to work with environment
instance <<- "test_environments/beer2.json"
test_that(paste("test get expt., expt. sample, raw and intermediate data", instance),
{
verbose <- TRUE
api <- CoreAPIV2::coreAPI(instance)
con<- CoreAPIV2::authBasic(api,useVerbose=verbose)
expect_match(api$coreUrl,con$coreApi$coreUrl,all=verbose)
expect_that(is.null(con$coreApi$jsessionId),equals(FALSE))
#get the experiment
expt <- CoreAPIV2::getEntityByBarcode(con$coreApi,"BITTERNESS EXPERIMENT",barcode = "BTXP2",useVerbose = verbose)
expect_match(expt$entity$Barcode,"BTXP2",all=verbose)
exptSamples <- CoreAPIV2::getExperimentSamples(con$coreApi,"BITTERNESS EXPERIMENT",barcode = "BTXP2",
useVerbose = verbose)
exptSampleBarcode = exptSamples$entity[1]
# get expt. container
exptContainer <- CoreAPIV2::getExperimentContainers(con$coreApi,"BITTERNESS EXPERIMENT",barcode = "BTXP2",
useVerbose = verbose)
#get raw data
rawData <- getExperimentSamplesRawData(con$coreApi, exptContainer$entity[1],useVerbose = FALSE)
expect_equal(nrow(rawData$entity),2,all=verbose)
#update raw data
rdUpdate <-
updateExperimentSampleRawData(
con$coreApi,
exptContainer$entity[1],
1,
values = list(DATA_VALUE = 100 ,CI_ACCEPT = FALSE),
useVerbose = FALSE
)
expect_equal(rdUpdate$entity$DATA_VALUE,100,all=verbose)
expect_equal(rdUpdate$entity$CI_ACCEPT,FALSE,all=verbose)
#change it back to original value
rdUpdate2 <-
updateExperimentSampleRawData(
con$coreApi,
exptContainer$entity[1],
1,
values = list(DATA_VALUE = as.numeric(rawData$entity[rawData$entity$CI_CELL ==1,]$DATA_VALUE),
CI_ACCEPT =as.logical(rawData$entity[rawData$entity$CI_CELL ==1,]$CI_ACCEPT)),
useVerbose = FALSE
)
expect_equal(rdUpdate2$entity$DATA_VALUE,
as.numeric(rawData$entity[rawData$entity$CI_CELL ==1,]$DATA_VALUE) ,all=verbose)
expect_equal(rdUpdate2$entity$CI_ACCEPT,
as.logical(rawData$entity[rawData$entity$CI_CELL ==1,]$CI_ACCEPT),all=verbose)
#get intermediate data
intermediateData <- CoreAPIV2::getExperimentSamplesIntermediateData(con$coreApi,experimentType = "BITTERNESS EXPERIMENT",
assayType = "BITTERNESS_ASSAY",
experimentSamplebarcode = exptSampleBarcode,
dataName = "%i", useVerbose = verbose)
#This line may need to be changed since we changed the tennent and exp type
expect_equal(nrow(rawData$entity),2,all=verbose)
#assay data is in assay data
ad<-CoreAPIV2::getExperimentSamplesAssayData(coreApi = con$coreApi,assayType = "BITTERNESS_ASSAY",
experimentSamplebarcode = exptSamples$entity[1])
expect_match(ad$entity[[1]]$Barcode,exptSamples$entity[1],all=verbose)
logout<-CoreAPIV2::logOut(con$coreApi,useVerbose = verbose)
expect_match(logout$success,"Success")
})
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