R/AnnotationHub-class.R

In AnnotationHub: Client to access AnnotationHub resources

### =========================================================================
### AnnotationHub objects
### -------------------------------------------------------------------------
###

setClass("AnnotationHub", contains="Hub")

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### Constructor
###

## Add code to check : https://annotationhub.bioconductor.org/metadata/highest_id
## And if not, delete the DB so it will be re-downloaded...
AnnotationHub <-
    function(..., hub=getAnnotationHubOption("URL"),
             cache=getAnnotationHubOption("CACHE"),
             proxy=getAnnotationHubOption("PROXY"),
             localHub=getAnnotationHubOption("LOCAL"),
             ask=getAnnotationHubOption("ASK"))
{
    if (is.null(proxy)){
        connect <- suppressWarnings(tryCatch({
            readBin(hub, n=1L, what="raw")
            TRUE
        }, error = function(...){
            FALSE
        }))
    } else {
        connect <- TRUE
        message("Assuming valid proxy connection through '",
                ifelse(is(proxy,"request"),
                       paste(unlist(proxy), collapse=":"),
                       proxy),
                "'",
                "\n If you experience connection issues consider ",
                "using 'localHub=TRUE'")
    }
    if (!connect && !localHub){
        message("Cannot connect to AnnotationHub server, using 'localHub=TRUE' instead")
        localHub <- !connect
    }
    .Hub("AnnotationHub", hub, cache, proxy, localHub, ask, ...)
}


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### cache method
###

setMethod("cache", "AnnotationHub",
    function(x, ..., force=FALSE, verbose=FALSE)
{
    callNextMethod(
        x,
        cache.root="AnnotationHub",
        cache.fun=setAnnotationHubOption,
        proxy=getAnnotationHubOption("PROXY"),
        max.downloads=getAnnotationHubOption("MAX_DOWNLOADS"),
        force=force,
        verbose=verbose
    )
})