inst/integrationTests/test_loadEntity.R

In Sage-Bionetworks/rSynapseClientRewrite: Synapse R Client from Sage Bionetworks

### Test loadEntity methods
### 
### Author: Matthew D. Furia <matt.furia@sagebase.org
#################################################################################

.setUp <- 
  function()
{
  ## create a project
  project <- Project()
  propertyValues(project) <- list(
    name = paste("myProject", gsub(':', '_', date()))
  )
  project <- createEntity(project)
  synapseClient:::.setCache("testProject", project)
  
}

.tearDown <-
  function()
{
  deleteEntity(synapseClient:::.getCache("testProject"))
  synapseClient:::.deleteCache("testProject")
  synapseClient:::.deleteCache("testDataset")
}

integrationTestLoadRbinData <- 
  function()
{
  project <- synapseClient:::.getCache("testProject")
  
  ## create a data entity
  data <- Data(list(parentId=propertyValue(project,"id"), type="C", name="myData"))
  ##annotValue(data, "format") <- "rbin"
  
  phenotypes <- diag(nrow=10, ncol=10)
  tmpFile <- tempfile()
  save(phenotypes, file=tmpFile)
  addFile(data, tmpFile, "/my_test_packet/phenotypes.rbin")
  
  
  checksum <- as.character(tools::md5sum(file.path(data$cacheDir, data$files)))
  
  storedData <- storeEntity(data)
  checkEquals(propertyValue(storedData, "name"), propertyValue(data, "name"))
  checkEquals(propertyValue(storedData, "type"), propertyValue(data, "type"))
  checkEquals(propertyValue(storedData, "parentId"), propertyValue(data, "parentId"))
  
  checkEquals(as.character(tools::md5sum(file.path(storedData$cacheDir, storedData$files))), checksum)
  loadedData <- loadEntity(storedData)
  checkEquals(propertyValue(loadedData, "name"), propertyValue(storedData, "name"))
  checkEquals(propertyValue(loadedData, "id"), propertyValue(storedData, "id"))
  checkEquals(propertyValue(loadedData, "parentId"), propertyValue(storedData, "parentId"))
  checkEquals(propertyValue(loadedData, "type"), propertyValue(storedData, "type"))
  checkEquals(loadedData$cacheDir, storedData$cacheDir)
  checkTrue(all(loadedData$files %in% storedData$files))
  checkTrue(all(storedData$files %in% loadedData$files))
  checkEquals(names(loadedData$objects), "phenotypes")
  
  checkTrue(all(file.exists(file.path(storedData$cacheDir, storedData$files))))
  
  
  ## load entity using entity id
  loadedData <- loadEntity(propertyValue(storedData, "id"))
  checkEquals(propertyValue(loadedData, "name"), propertyValue(storedData, "name"))
  checkEquals(propertyValue(loadedData, "id"), propertyValue(storedData, "id"))
  checkEquals(propertyValue(loadedData, "parentId"), propertyValue(storedData, "parentId"))
  checkEquals(propertyValue(loadedData, "type"), propertyValue(storedData, "type"))
  checkEquals(loadedData$cacheDir, storedData$cacheDir)
  checkTrue(all(loadedData$files %in% storedData$files))
  checkTrue(all(storedData$files %in% loadedData$files))
  checkEquals(names(loadedData$objects), "phenotypes")
  
}