#
#
.setUp <-
function()
{
myQD <-
function(contribution)
{
if(contribution$qry==2){
return(NULL)
}
qryResult <- list(study.id="12345", study.lastUpdate="2004-02-11")
return(qryResult)
}
myGD <-
function(x)
{
load(file.path(.path.package("rSCR"), "extdata/testData/egStudy.Rda"))
return(dataset)
}
myCE <-
function(x)
{
return(x)
}
unloadNamespace("rSCR")
assignInNamespace(".queryDatasetExistence", myQD, "rSCR")
unloadNamespace("synapseClient")
assignInNamespace("getEntity", myGD , "synapseClient")
assignInNamespace("createEntity", myCE , "synapseClient")
assignInNamespace("updateEntity", myCE , "synapseClient")
attachNamespace("synapseClient")
attachNamespace("rSCR")
}
.tearDown <-
function()
{
unloadNamespace("rSCR")
unloadNamespace("synapseClient")
attachNamespace("synapseClient")
attachNamespace("rSCR")
}
unitTestcreateStudy <-
function()
{
contribution <- list(study.name = "GSE7765_eg",
species = "Homo sapiens",
description = "MCF7 cells were treated with DMSO or 100 nM Dioxin for 16 hr. Gene expression changes were quantified by microarray ...",
numSamples = 12,
platform = "hgu133a;hgu133b",
cellLine = "MCF7",
parentId = "syn299343",
data.url = "ftp://anonymous:anonymous@ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE7765/GSE7765_RAW.tar",
data.status = "raw",
data.type = "E",
data.lastUpdate = "2007/05/12",
data.name = "GSE7765 Raw Data Layer from NCBI GEO",
data.compound = "DMSO,Dixoin")
contribution$qry = 2
res <- createStudy(contribution,"eg.txt")
checkEquals(class(res)[1], "Study")
contribution$qry = 3
res <- createStudy(contribution, "eg.txt")
checkEquals(class(res)[1], "Study")
contribution$study.lastUpdate <- "2004-02-12"
res <- createStudy(contribution, "eg.txt")
checkEquals(class(res)[1], "Study")
}
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