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### =========================================================================
### db helpers for Hub objects
### -------------------------------------------------------------------------
###
.db_open <- function(path) {
tryCatch({
conn <- dbFileConnect(path)
}, error=function(err) {
stop("failed to connect to local data base",
"\n database: ", sQuote(path),
"\n reason: ", conditionMessage(err),
call.=FALSE)
})
conn
}
.db_close <- function(conn) {
if (!is.null(conn))
if (RSQLite::dbIsValid(conn))
dbDisconnect(conn)
invisible(conn)
}
.db_query <- function(path, query) {
if (is.character(path)) {
path <- .db_open(path)
on.exit(.db_close(path))
}
dbGetQuery(path, query)
}
.db_uid0 <- function(path, .date, localHub){
tryCatch({
uid <- .uid0(path, .date, localHub)
sort(uid)
}, error=function(err) {
stop("failed to connect to local data base",
"\n database: ", sQuote(path),
"\n reason: ", conditionMessage(err),
call.=FALSE)
})
}
setMethod("dbconn", "Hub",
function(x) .db_open(dbfile(x))
)
setMethod("dbfile", "Hub",
function(x) x@.db_path
)
.db_uid <- function(x) slot(x, ".db_uid")
`.db_uid<-` <- function(x, ..., value)
{
bad <- value[!value %in% .db_uid(x)]
if (any(bad))
stop("invalid subscripts: ",
paste(sQuote(S4Vectors:::selectSome(bad)), collapse=", "))
slot(x, ".db_uid") <- value
x
}
.db_clean_index <- function(x) {
bfc <- .get_cache(x)
index_name <- paste0(tolower(as.character(class(x))),
".index.rds")
bfcremove(bfc, rids=as.data.frame(bfcquery(bfc, index_name))$rid)
}
.db_create_index <- function(x) {
bfc <- .get_cache(x)
index_name <- paste0(tolower(as.character(class(x))),
".index.rds")
res <- bfcquery(bfc, index_name,
field="rname", exact=TRUE)
cnt <- bfccount(res)
rid <- res %>% collect(Inf) %>% `[[`("rid")
if (cnt > 1){
msg <- paste0("Corrupt Cache: index file",
"\n cache: ", bfccache(bfc),
"\n multiple entries for filename: ", index_name,
"\n Attempting to clean cache and regenerate"
)
warning(msg, call.=FALSE)
.db_clean_index(x)
res <- bfcquery(bfc, index_name,
field="rname", exact=TRUE)
cnt <- bfccount(res)
rid <- res %>% collect(Inf) %>% `[[`("rid")
}
if (cnt > 1){
stop("Corrupt Cache: index file",
"\n See AnnotationHub's TroubleshootingTheHubs vignette section on corrupt cache",
"\n cache: ", bfccache(bfc),
"\n filename: ", index_name,
call.=FALSE)
} else {
if (cnt == 1){
index_path <- bfcpath(bfc, rids=rid)
if (file.exists(index_path)) {
if (file.mtime(index_path) > file.mtime(dbfile(x)) &&
length(x) == length(readRDS(index_path)))
return(index_path)
}
}
}
tryCatch({
tbl <- .resource_table(x)
tbl <- setNames(do.call("paste", c(tbl, sep="\r")), rownames(tbl))
index_path <- ifelse(cnt == 0,
bfcnew(bfc, rname=index_name, ext="_hub_index.rds"),
bfcpath(bfc, rids=rid))
saveRDS(tbl, unname(index_path))
}, error=function(err) {
stop("failed to create index",
"\n hubCache(): ", hubCache(x),
"\n reason: ", conditionMessage(err))
})
unname(index_path)
}
.db_index_file <- function(x){
bfc <- .get_cache(x)
index_name <- paste0(tolower(as.character(class(x))),
".index.rds")
res <- bfcquery(bfc, index_name,
field="rname", exact=TRUE)
cnt <- bfccount(res)
rid <- res %>% collect(Inf) %>% `[[`("rid")
if (cnt != 1){
.db_create_index(x)
} else {
unname(bfcpath(bfc, rids=rid))
}
}
.db_index_load <- function(x)
readRDS(.db_index_file(x))[names(x)]
.db_index <- function(x) slot(x, ".db_index")
`.db_index<-` <- function(x, ..., value)
{
if (length(value) > 1L)
stop("'value' must be length 1")
if (!is(value, "character"))
stop("'value' must be a character")
slot(x, ".db_index") <- value
x
}
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