if (!"BiocManager" %in% rownames(installed.packages()))
     install.packages("BiocManager")
BiocManager::install("BiocFileCache", dependencies=TRUE)

library(BiocFileCache)

path <- tempfile()
bfc <- BiocFileCache(path, ask = FALSE)

## paste to avoid long line in vignette
url <- paste(
    "ftp://ftp.ensembl.org/pub/release-71/gtf",
    "homo_sapiens/Homo_sapiens.GRCh37.71.gtf.gz",
    sep="/")

library(BiocFileCache)
bfc <- BiocFileCache()
path <- bfcrpath(bfc, url)

gtf <- rtracklayer::import.gff(path)

gtf <- rtracklayer::import.gff(bfcrpath(BiocFileCache(), url))

library(BiocFileCache)
bfc <- BiocFileCache("~/my-experiment/results")

suppressPackageStartupMessages({
    library(DESeq2)
    library(airway)
})
data(airway)
dds <- DESeqDataData(airway, design = ~ cell + dex)
result <- DESeq(dds)

saveRDS(result, bfcnew(bfc, "airway / DESeq standard analysis"))

result <- readRDS(bfcrpath(bfc, "airway / DESeq standard analysis"))

suppressPackageStartupMessages({
    library(BiocFileCache)
    library(rtracklayer)
})

# load the cache
path <- file.path(tempdir(), "tempCacheDir")
bfc <- BiocFileCache(path)

# the web resource of interest
url <- "ftp://ftp.ensembl.org/pub/release-71/gtf/homo_sapiens/Homo_sapiens.GRCh37.71.gtf.gz"

# check if url is being tracked
res <- bfcquery(bfc, url, exact=TRUE)

if (bfccount(res) == 0L) {

    # if it is not in cache, add
    ans <- bfcadd(bfc, rname="ensembl, homo sapien", fpath=url)

} else {

  # if it is in cache, get path to load
  rid = res$rid
  ans <- bfcrpath(bfc, rid)

  # check to see if the resource needs to be updated
  check <- bfcneedsupdate(bfc, rid)
  # check can be NA if it cannot be determined, choose how to handle
  if (is.na(check)) check <- TRUE
  if (check){
    ans < - bfcdownload(bfc, rid)
  }
}

# ans is the path of the file to load
ans

# we know because we search for the url that the file is a .gtf.gz,
# if we searched on other terms we can use 'bfcpath' to see the
# original fpath to know the appropriate load/read/import method
bfcpath(bfc, names(ans))

temp = GTFFile(ans)
info = import(temp)

#
# A simpler test to see if something is in the cache
# and if not start tracking it is using `bfcrpath`
#

suppressPackageStartupMessages({
    library(BiocFileCache)
    library(rtracklayer)
})
## Warning: multiple methods tables found for 'union'
## Warning: multiple methods tables found for 'intersect'
## Warning: multiple methods tables found for 'setdiff'

# load the cache
path <- file.path(tempdir(), "tempCacheDir")
bfc <- BiocFileCache(path, ask=FALSE)

# the web resources of interest
url <- "ftp://ftp.ensembl.org/pub/release-71/gtf/homo_sapiens/Homo_sapiens.GRCh37.71.gtf.gz"

url2 <- "ftp://ftp.ensembl.org/pub/release-71/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_5.0.71.gtf.gz"

# if not in cache will download and create new entry
pathsToLoad <- bfcrpath(bfc, c(url, url2))
## adding rname 'ftp://ftp.ensembl.org/pub/release-71/gtf/homo_sapiens/Homo_sapiens.GRCh37.71.gtf.gz'
## adding rname 'ftp://ftp.ensembl.org/pub/release-71/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_5.0.71.gtf.gz'

pathsToLoad
##                                                                             BFC1 
##        "/tmp/RtmpZM11G5/tempCacheDir/16a83306c595_Homo_sapiens.GRCh37.71.gtf.gz" 
##                                                                             BFC2 
## "/tmp/RtmpZM11G5/tempCacheDir/16a8451646fd_Rattus_norvegicus.Rnor_5.0.71.gtf.gz"

# now load files as see fit
info = import(GTFFile(pathsToLoad[1]))
class(info)
## [1] "GRanges"
## attr(,"package")
## [1] "GenomicRanges"
summary(info)
## [1] "GRanges object with 2253155 ranges and 12 metadata columns"

#
# One could also imagine the following:
#

library(BiocFileCache)

# load the cache
bfc <- BiocFileCache()

#
# Do some work!
#

# add a location in the cache
filepath <- bfcnew(bfc, "R workspace")

save(list = ls(), file=filepath)

# now the R workspace is being tracked in the cache

.get_cache <-
    function()
{
    cache <- tools::R_user_dir("MyNewPackage", which="cache")
    BiocFileCache::BiocFileCache(cache)
}

download_data_file <-
    function( verbose = FALSE )
{
    fileURL <- "http://a_path_to/someremotefile.tsv.gz"

    bfc <- .get_cache()
    rid <- bfcquery(bfc, "geneFileV2", "rname")$rid
    if (!length(rid)) {
     if( verbose )
         message( "Downloading GENE file" )
     rid <- names(bfcadd(bfc, "geneFileV2", fileURL ))
    }
    if (!isFALSE(bfcneedsupdate(bfc, rid)))
    bfcdownload(bfc, rid)

    bfcrpath(bfc, rids = rid)
}

url <- "http://bioconductor.org/packages/stats/bioc/BiocFileCache/BiocFileCache_stats.tab"

headFile <-                         # how to process file before caching
    function(from, to)
{
    dat <- readLines(from)
    writeLines(head(dat), to)
    TRUE
}

rid <- bfcquery(bfc, url, "fpath")$rid
if (!length(rid))                   # not in cache, add but do not download
    rid <- names(bfcadd(bfc, url, download = FALSE))

update <- bfcneedsupdate(bfc, rid)  # TRUE if newly added or stale
if (!isFALSE(update))               # download & process
    bfcdownload(bfc, rid, ask = FALSE, FUN = headFile)
## Warning in readLines(from): incomplete final line found on
## '/tmp/RtmpZM11G5/tempCacheDir/file16a82fc46133'
##                                                                BFC3 
## "/tmp/RtmpZM11G5/tempCacheDir/16a87a1c3332_BiocFileCache_stats.tab"

rpath <- bfcrpath(bfc, rids=rid)    # path to processed result
readLines(rpath)                    # read processed result
## [1] "Year\tMonth\tNb_of_distinct_IPs\tNb_of_downloads"
## [2] "2024\tJan\t25214\t52681"                         
## [3] "2024\tFeb\t23028\t49660"                         
## [4] "2024\tMar\t28213\t78340"                         
## [5] "2024\tApr\t35612\t80526"                         
## [6] "2024\tMay\t28584\t48808"