tests/testthat/test-mgr_fetch.R

In epivizrData: Data Management API for epiviz interactive visualization app

context("manager fetch")

test_that("disconnected mgr fetch works", {
  skip_if_not_installed("hgu133plus2.db")
  gr1 <- GRanges(seqnames="chr6", 
                 ranges=IRanges::IRanges(start=30000000+(1:10), width=100),
                 seqinfo=Seqinfo(seqnames=c("chr6","chr7"),genome="hcb"))
  gr2 <- GRanges(seqnames="chr7", 
                 ranges=IRanges::IRanges(start=30000000+(2:20), width=100),
                 seqinfo=Seqinfo(seqnames=c("chr6","chr7"),genome="hcb"))
  gr3 <- GRanges(seqnames="chr6", 
                 ranges=IRanges::IRanges(start=30000000+seq(1,100,by=5), width=1), score1=seq(1,100,by=5), score2=-seq(1,100,by=5),
                 seqinfo=Seqinfo(seqnames=c("chr6","chr7"),genome="hcb"))
  eset <- make_test_eset()
  

  server <- epivizrServer::createServer()
  mgr <- createMgr(server)
  
  dev1 <- mgr$add_measurements(gr1, "dev1", send_request=FALSE); devId1=dev1$get_id()
  dev2 <- mgr$add_measurements(gr2, "dev2", send_request=FALSE); devId2=dev2$get_id()
  dev3 <- mgr$add_measurements(gr3, "dev3", send_request=FALSE, type="bp"); devId3=dev3$get_id()
  dev4 <- mgr$add_measurements(eset, "dev4", send_request=FALSE, columns=c("SAMP_1", "SAMP_2")); devId4=dev4$get_id()
    
  m <- match(rowRanges(dev4$.object)$PROBEID, featureNames(eset))
  mat <- exprs(eset)[m,c("SAMP_1","SAMP_2")]
  lims <- unname(apply(mat, 2, function(x) range(pretty(range(x)))))
    
  query <- GRanges(seqnames="chr6", ranges=IRanges::IRanges(start=30000000,end=40000000))
    
  hits <- unique(subjectHits(findOverlaps(query, dev4$.object)))
  hits <- seq(min(hits), max(hits))
  tmp <- dev4$.object[hits,]
    
  m <- match(rowRanges(tmp)$PROBEID, featureNames(eset))
  mat <- exprs(eset)[m,c("SAMP_1","SAMP_2")]
    
  # dev 1
  res <- mgr$get_rows(seqnames(query), start(query), end(query), NULL, devId1)
  out <- list(globalStartIndex=1,
              useOffset=FALSE,
              values=list(
                id=1:10,
                chr=rep("chr6", 10),
                start=30000000+(1:10),
                end=30000000+(100:109),
                metadata=NULL))
  expect_equal(res,out)

  # dev 2
  res <- mgr$get_rows(seqnames(query), start(query), end(query), NULL, devId2)
  out <- list(globalStartIndex=NULL,
              useOffset=FALSE,
              values=list(
                id=list(),
                chr=list(),
                start=list(),
                end=list(),
                metadata=NULL))
  expect_equal(res,out)

  # dev 3
  res <- mgr$get_rows(seqnames(query), start(query), end(query), NULL, devId3)
  out <- list(globalStartIndex=1,
              useOffset=FALSE,
              values=list(
                id=seq(len=length(seq(1,100,by=5))),
                chr=rep("chr6", 20),
                start=30000000+seq(1,100,by=5),
                end=30000000+seq(1,100,by=5),
                metadata=NULL))
  expect_equal(res,out)

  res <- mgr$get_values(seqnames(query), start(query), end(query), devId3, "score1")
  out <- list(globalStartIndex=1,
              values=seq(1,100,by=5))
  expect_equal(res,out)

  res <- mgr$get_values(seqnames(query), start(query), end(query), devId3, "score2")
  out <- list(globalStartIndex=1,
              values=-seq(1,100,by=5))
  expect_equal(res,out)

  # dev 4
  res <- mgr$get_rows(seqnames(query), start(query), end(query), c("PROBEID","SYMBOL"), devId4)
  out <- list(globalStartIndex=hits[1],
              useOffset=FALSE,
              values=list(id=hits,
                          chr=as.vector(seqnames(tmp)),
                          start=start(tmp),
                          end=end(tmp),
                          metadata=list(PROBEID=rowRanges(tmp)$PROBEID,
                                        SYMBOL=rowRanges(tmp)$SYMBOL)))
  expect_equal(res,out)

  res <- mgr$get_values(seqnames(query), start(query), end(query), devId4, "SAMP_1")
  out <- list(globalStartIndex=hits[1],
              values=unname(mat[,"SAMP_1"]))
  expect_equal(res,out)

  res <- mgr$get_values(seqnames(query), start(query), end(query), devId4, "SAMP_2")
  out <- list(globalStartIndex=hits[1],
              values=unname(mat[,"SAMP_2"]))
  expect_equal(res,out)
})