## ----eval = FALSE--------------------------------------------------------
# api<-CoreAPI("PATH TO JSON FILE")
# login<- CoreAPI::authBasic(api)
# response <-CoreAPI::apiCall(login$coreApi,body,"json",,special=NULL,useVerbose=FALSE)
# logOut(login$coreApi )
## ----eval = FALSE--------------------------------------------------------
#
# #get login information
#
# loginInfo<-CoreAPI::coreAPI(CoreAccountInfo="path/account.json")
#
# # authenticate
# response<- CoreAPI::authBasic(loginInfo)
#
# #print the session ID
# print(response$coreApi$jsessionId)
#
# #log out
# CoreAPI::logOut(response$coreApi)$success
#
## ----eval = FALSE--------------------------------------------------------
#
# CoreAPI::createEntity(response$coreApi,entityType)
#
## ----eval = FALSE--------------------------------------------------------
#
# attributeValues<-list(SOURCE_LAB = "New York Medical Center",Number = 5,REQUESTOR="CEP")
#
## ----eval= FALSE---------------------------------------------------------
# associations<-list(SAMPLE_ENZYME=data.frame(name="",entitiyId="",barcode="ENZ1"))
## ----eval = FALSE--------------------------------------------------------
#
# entityType <- "Patient Sample"
#
# attributeValues<-list(SOURCE_LAB = "New York Medical Center",Number = 5,REQUESTOR="CEP")
#
# associations<-list(SAMPLE_ENZYME=data.frame(name="",entitiyId="",barcode="ENZ1"))
#
# CoreAPI::createEntity(response$coreApi,entityType,attributeValues,associations)
#
## ----eval = FALSE--------------------------------------------------------
# entityBarcode <-"PS100"
#
# CoreAPI::updateEntity(response$coreApi,entityType,entitybarcode,
# attributevalues=attributeValues,associations = associations)
#
## ----eval = FALSE--------------------------------------------------------
#
# get<-getEntityByBarcode(response$coreApi, entityType, barcode)
#
# item <- get$entity
## ----eval = FALSE--------------------------------------------------------
#
# get<-getEntityById(response$coreApi, entityType, entityId = "ID")
#
# item <- get$entity
## ----eval = FALSE--------------------------------------------------------
#
# # attach to the attribute named File
#
# items2<-CoreAPI::attachFile(response$coreApi,barcode,"SAgraph.png",filepath,targetAttributeName="File")
#
# #attach to the entity
#
# attachFile(response$coreApi,barcode,filename="SAgraph.png",filepath=filepath,targetAttributeName="")
#
#
## ----eval =FALSE---------------------------------------------------------
# item$entity$values$FILE
# $stringData
# [1] "{'file':'SAgraph.png.16','url':'https://experience.platformforscience.com/corelims?cmd=view-file&entityType=FILE ATTRIBUTE&entityId=9532882'}"
#
## ----eval = FALSE--------------------------------------------------------
#
#
# #Create Sample
#
# sample<-createEntity(response$coreApi, "WHOLE BLOOD", attributeValues = attributes)
#
# #get barcode of the sample
#
# sampleBC <-sample$entity$barcode
#
# #Create Lot
#
# item<-createSampleLot(login$coreApi,"WHOLE BLOOD LOT", sampleBarcode=sampleBC,
# attributes = lotAttributes )
#
## ----eval = FALSE--------------------------------------------------------
#
#
# api<-CoreAPI::coreAPI(CoreAccountInfo = "testfiles/account.json")
#
# #login
#
# login<-CoreAPI::authBasic(tapi)
#
# #create sample
#
# sample<- CoreAPI::createEntity(r$coreApi,"Patient Sample")
#
# sampleBarcode<-sample$entity$barcode
#
# #create lot
#
# lot<-CoreAPI::createSampleLot(r$coreApi,"PATIENT SAMPLE LOT",sampleBarcode)
#
# #create container
#
# cont <- CoreAPI::createEntity(r$coreApi,containerType)
#
# cont_barcode <- cont$entity$barcode
#
# #fill container
#
# filledContainer<-CoreAPI::updateCellContents(r$coreApi,containerType,
# cont_barcode,"1", lot_barcode,2, "ml", 3, "uM")
#
# #log out
#
# out<-CoreAPI::logOut(r$coreApi)
#
#
## ----eval = FALSE--------------------------------------------------------
#
# cell<-getCellContents(login$coreApi,"VIA9","1")
#
## ----eval = FALSE--------------------------------------------------------
#
# contCell <- CoreAPI::getCellContents(r$coreApi,cont$entity$barcode,"1")
#
# sourceCellID <-contCell$entity$cells[[1]]$cellId
#
# cont2Cell<- CoreAPI::getCellContents(r$coreApi,cont2$entity$barcode,"1")
#
# destCellID <- cont2Cell$entity$cells[[1]]$cellId
#
#
# move<-transferCellContents(r$coreApi,sourceCellID,destCellID,amount,concentration,
# amountUnit, concentrationUnit,useVerbose = FALSE)
#
#
## ----eval = FALSE--------------------------------------------------------
#
# lineage<-CoreAPI::getContainerLineage(r$coreApi,cont$entity$barcode)
#
## ----eval=FALSE----------------------------------------------------------
#
# item <- CoreAPI::createEntity(r$coreApi,entityType = experimentType,
# attributeValues = list(TEST_ATTRIBUTE = "a value"),
# associations = list(EXPERIMENT_ASSAY=
# data.frame(name="",entityId ="",barcode=assayBarcode),
# EXPERIMENT_PROTOCOL=
# data.frame(name="",entityId ="",barcode=protocolBarcode))
# )
#
# newExptbarcode <-item$entity$barcode
#
# #add a container which creates an experiment sample
#
# update<-CoreAPI::updateExperimentContainers(r$coreApi,containerBarcode, experimentType, newExptbarcode,useVerbose = FALSE)
#
#
## ----eval = FALSE--------------------------------------------------------
#
# secondSample<-CoreAPI::createExperimentSample(r$coreApi,experimentSampleType,sampleLot,newExptbarcode,useVerbose=FALSE)
#
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