context("Tests for container operations")
rm(list=ls())
verbose <- FALSE
#setup to work with environment
instance <- "test_environments/5-2-2.json"
test_that(paste("test log in and get an single well container", instance),
{
verbose <- FALSE
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$jsessionId),equals(FALSE))
b<-CoreAPIV2::getEntityByBarcode(con$coreApi,"VIAL","VIA1",fullMetadata=FALSE,useVerbose=verbose)$entity
expect_match(b$Barcode,"VIA1",all=verbose)
cc<-CoreAPIV2::getContainerContents(con$coreApi,"VIAL","VIA1")
expect_match(cc$entity$CELLS[[1]]$CELL_CONTENTS[[1]]$SAMPLE_LOT$Name,
"PS2-1",all=verbose)
logout<-CoreAPIV2::logOut(api,useVerbose = verbose)
expect_match(logout$success,"Success")
})
test_that(paste("test login and get container and cell contents for multi well plate", instance),
{
verbose <- FALSE
api <- CoreAPIV2::coreAPI(instance)
con<- CoreAPIV2::authBasic(api,useVerbose=verbose)
expect_match(api$coreUrl,con$coreApi$coreUrl,all=verbose)
expect_that(is.null(con$coreApi$jsessionId),equals(FALSE))
lheader <- c(Accept = "application/json;odata.metadata=full")
container<-CoreAPIV2::getEntityByBarcode(con$coreApi,entityType = "384 WELL PLATE",
barcode='TE1',fullMetadata = TRUE,useVerbose = TRUE)
expect_match(container$entity$CONTAINER_FORMAT,"384 Well",all=verbose)
p<- CoreAPIV2::getWellContents(con$coreApi,"384 WELL PLATE","TE1","1",useVerbose = FALSE)
expect_match(p$entity$CELL_CONTENTS[[1]]$SAMPLE_LOT$Barcode,"PS1-1",all=verbose)
cc<-CoreAPIV2::getContainerContents(con$coreApi,"384 WELL PLATE","TE1")
expect_match(cc$entity$CELLS[[1]]$CELL_CONTENTS[[1]]$SAMPLE_LOT$Name,
"PS1-1",all=verbose)
logout<-CoreAPIV2::logOut(api,useVerbose = verbose)
expect_match(logout$success,"Success")
})
test_that(paste("test get container IDs for multi well plate and Vial", instance),
{
verbose <- FALSE
api <- CoreAPIV2::coreAPI(instance)
con<- CoreAPIV2::authBasic(api,useVerbose=verbose)
expect_match(api$coreUrl,con$coreApi$coreUrl,all=verbose)
expect_that(is.null(con$coreApi$jsessionId),equals(FALSE))
cells<-CoreAPIV2::getContainerCellIds(con$coreApi,containerType = "384 WELL PLATE",
containerBarcode = 'TE1',useVerbose = FALSE)
expect_equal(cells$entity[1],18535078,all=verbose)
I
cells<-CoreAPIV2::getContainerCellIds(con$coreApi,containerType = "VIAL",
containerBarcode='VIA1',useVerbose = TRUE)
expect_equal(cells$entity[1],18161996,all=verbose)
c<-CoreAPIV2::getCellContents(con$coreApi,cells$entity[1],useVerbose = TRUE)
expect_equal(c$entity$Id,18161996,all=verbose)
logout<-CoreAPIV2::logOut(api,useVerbose = verbose)
expect_match(logout$success,"Success")
})
test_that(paste("test create container, setContents, and update contents", instance),
{
verbose <- FALSE
api <- CoreAPIV2::coreAPI(instance)
con<- CoreAPIV2::authBasic(api,useVerbose=verbose)
expect_match(api$coreUrl,con$coreApi$coreUrl,all=verbose)
expect_that(is.null(con$coreApi$jsessionId),equals(FALSE))
vial<-CoreAPIV2::createEntity(con$coreApi,"VIAL",body=jsonlite::fromJSON("{}"))$entity
barcode<-vial$Barcode
setCont<-CoreAPIV2::setWellContents(coreApi = con$coreApi,containerType = 'VIAL',
containerBarcode = barcode,
containerWellNum = "1",sampleLotType = "PATIENT SAMPLE LOT",
sampleLotBarcode = "PS1-1",amount = 1,
amountUnit = "ml",concentration =1,concentrationUnit = "nM",useVerbose=TRUE)
wc1<- CoreAPIV2::getWellContents(con$coreApi, "VIAL", barcode, 1, useVerbose = FALSE)
expect_equal(wc1$entity$CI_AMOUNT,1,all=verbose)
expect_equal(wc1$entity$CELL_CONTENTS[[1]]$CI_CONC,1,all=verbose)
wc1<-CoreAPIV2::updateCellContents(coreApi = con$coreApi,containerType = 'VIAL',
containerBarcode = barcode,
containerCellNum = 0,
sampleLotBarcode = "PS1-1",amount = 2,
amountUnit = "ml",concentration =2,concentrationUnit = "nM",useVerbose=TRUE)
expect_equal( wc1$entity$cells[[1]]$amount,2,all=verbose)
expect_equal(wc1$entity$cells[[1]]$cellContents[[1]]$concentration,"0.002",all=verbose)
logout<-CoreAPIV2::logOut(api,useVerbose = verbose)
expect_match(logout$success,"Success")
})
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