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#' @description Check EnsDb sqlite files found in the specified folder.
#'
#' @param x \code{character(1)} with the folder in which we're looking for EnsDb
#' objects.
#'
#' @author Johannes Rainer
#'
#' @noRd
#'
#' @examples
#' dir <- "/Users/jo/tmp/ensdb_20"
checkEnsDbs <- function(x) {
edbs <- dir(x, pattern = ".sqlite$", full.names = TRUE)
for (i in 1:length(edbs)) {
message("\nChecking EnsDb: ", basename(edbs[i]))
edb <- EnsDb(edbs[i])
ensembldb:::validateEnsDb(edb)
ensembldb:::checkValidEnsDb(edb)
## Now check also some query calls:
gns <- genes(edb)
message(" version: ", ensembldb:::dbSchemaVersion(edb))
message(" OK")
}
}
#' @param x `character(1)` with the directory containing EnsDb SQLite files.
#'
#' @return the species/organism name of the databases that have to be re-created
check_gc_content <- function(x) {
edbs <- dir(x, pattern = ".sqlite$", full.names = TRUE)
failed <- lapply(edbs, function(edb) {
edb <- EnsDb(edb)
if (!any(colnames(mcols(transcripts(edb))) == "gc_content"))
paste0(tolower(organism(edb)), collapse = "_")
else NULL
})
failed[lengths(failed)]
}
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