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.create_cache <-
function(.class, url, cache, proxy, localHub=FALSE, ask=TRUE)
{
hub_bfc <- BiocFileCache(cache=cache, ask=ask)
db_path <- .updateHubDB(hub_bfc, .class, url, proxy, localHub)
.db_is_valid(db_path)
db_path
}
removeCache <- function(x, ask=TRUE){
bfc <- .get_cache(x)
removebfc(bfc, ask=ask)
}
.get_cache <-
function(hub)
{
BiocFileCache(cache=hubCache(hub))
}
.named_cache_path <- function(x)
{
stopifnot(is(x, "Hub"))
path <- .datapathIds(x)
path
}
.cache_internal <- function(x, proxy, max.downloads,
force, verbose)
{
cachepath <- .named_cache_path(x)
localHub <- isLocalHub(x)
rnames <- paste(names(cachepath), cachepath, sep=" : ")
bfc <- .get_cache(x)
if(!localHub){
need <- .cache_download_ok(x, cachepath, max.downloads, force, verbose)
ok <- .hub_resource(x, as.character(cachepath)[need],
cachepath[need], proxy=proxy, verbose=verbose
)
if (!all(ok))
stop(sum(!ok), " resources failed to download", call. = FALSE)
}else{
incache <- bfcinfo(bfc)$rname
if(!all(rnames %in% incache))
stop("Cannot retrieve resource",
"\n Rerun constructor with 'localHub=FALSE' or exclude ID",
"\n Requested resource not found in local cache:",
"\n ", paste0(rnames[!(rnames %in% incache)],
collapse="\n "),
call.=FALSE)
}
tryCatch({
localFiles <- bfcinfo(bfc)$rpath[match(rnames, bfcinfo(bfc)$rname)]
}, error=function(err){
stop("Corrupt Cache: resource id",
"\n See AnnotationHub's TroubleshootingTheHubs vignette section on corrupt cache",
"\n cache: ", bfccache(bfc),
"\n reason: ", conditionMessage(err),
call.=FALSE)
})
names(localFiles) <- names(cachepath)
if (verbose){
message("loading from cache")
}
localFiles
}
.cache_download_ok <- function(x, cachepath, max.downloads, force, verbose)
{
if (force){
need <- rep(TRUE, length(cachepath))
} else {
bfc <- .get_cache(x)
need <- .updateEntry(bfc, cachepath)
}
n <- sum(need)
if (n > max.downloads) {
ans <- "n"
if (interactive())
ans <- .ask(sprintf("download %d resources?", n), c("y", "n"))
if (ans == "n") {
txt <- sprintf(
"resources needed (%d) exceeds max.downloads (%d)",
n, max.downloads
)
stop(txt, call. = FALSE)
}
} else {
if (verbose && (n > 0)) message("downloading ", n, " resources")
}
need
}
.updateEntry <- function(bfc, cachepath)
{
locFiles <- dir(bfccache(bfc))
locFiles <- locFiles[!(endsWith(locFiles, ".sqlite") |
endsWith(locFiles, ".sqlite3")|
endsWith(locFiles, "_index.rds"))]
baseFileName <- suppressWarnings(as.numeric(vapply(locFiles,
FUN=function(x){
vl <- strsplit(x,split="_")
vl[[1]][length(vl[[1]])]
}, FUN.VALUE=character(1), USE.NAMES=FALSE)))
if(any(is.na(baseFileName))){
dx <- is.na(baseFileName)
baseFileName <- baseFileName[!dx]
locFiles <- locFiles[!dx]
}
locFiles = setNames(locFiles, baseFileName)
if (any(duplicated(baseFileName))){
files <- locFiles[names(locFiles) %in%
baseFileName[duplicated(baseFileName)]]
if(any(unname(cachepath) %in% names(files)))
warning("Corrupt Cache: resource path",
"\n See AnnotationHub's TroubleshootingTheHubs vignette section on corrupt cache",
"\n cache: ", bfccache(bfc),
"\n potential duplicate files: ",
"\n ", paste0(files[order(names(files))],
collapse="\n "),
"\nContinuing with first found cached file",
call.=FALSE)
}
allUpdate <- rep(TRUE, length(cachepath))
names(allUpdate) <- as.character(cachepath)
fndFiles <- which(cachepath %in% baseFileName)
Update <- function(rpath, bfc){
res <- bfcquery(bfc, rpath, fields="rpath", exact=TRUE)
cnt <- bfccount(res)
rid <- res %>% collect(Inf) %>% `[[`("rid")
if (cnt > 1){
stop("Corrupt Cache: resource path",
"\n See AnnotationHub's TroubleshootingTheHubs vignette section on corrupt cache",
"\n cache: ", bfccache(bfc),
rpath, call.=FALSE
)
} else if (cnt == 0){
TRUE
} else {
tryCatch({
bfcneedsupdate(bfc, rids=rid)
}, error=function(e){
ahidnf <- res %>% collect(Inf) %>% `[[`("rname") %>%
strsplit(split=" : ") %>% `[[`(1) %>% `[`(1)
message("Could not check id: ",ahidnf," for updates.",
"\n Using previously cached version.")
setNames(FALSE, rid)
})
}
}
if (length(fndFiles) > 0){
cachepath[fndFiles]
update <- vapply(locFiles[match(cachepath[fndFiles], names(locFiles))],
FUN=Update, FUN.VALUE=logical(1), USE.NAMES=TRUE,
bfc=bfc)
if (anyNA(update))
# if no caching information use local file
update[is.na(update)] = FALSE
allUpdate[match(names(update), names(allUpdate))] <- update
}
allUpdate
}
|
