Hi Arne,
So this time when I look at the bioc-devel email list, I don't see a
record for this last name (or this email). In fact the only way I could
be sure it was you was that your post was the same... ;) If you want to
post from gmail, then you will need to subscribe the gmail address to
the list here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Marc
On 06/30/2015 02:26 AM, Arne Müller wrote:
Hello,
I think there’s a problem in UCSCSession initializer in rtracklayer:
setMethod("initialize", "UCSCSession",
function(.Object, url =http://genome.ucsc.edu/cgi-bin/";,
user =ULL, session = NULL, force = FALSE, ...)
{
.Object@url <- url
.Object@views <- new.env()
gwURL <- ucscURL(.Object, "gateway")
if (force) {
gwURL <- paste0(gwURL, '?redirect=anual"')
}
gw <- httpGet(gwURL, cookiefile =empfile(), header = TRUE,
.parseúLSE)
if (grepl("redirectTd", gw)) {
url <- sub(".*?a href=h([^[:space:]]+cgi-bin/).*",
"h\\1", gw)
return(initialize(.Object, url, user=er, session=session,
force=UE, ...))
}
cookie <- grep("Set-[Cc]ookie: hguid[^==", gw)
if (!length(cookie))
stop("Failed to obtain 'hguid' cookie")
hguid <- sub(".*Set-Cookie: (hguid[^==[^;]*);.*", "\\1", gw)
.Object@hguid <- hguid
if (!is.null(user) && !is.null(session)) { ## bring in other
session
ucscGet(.Object, "tracks",
list(hgS_doOtherUser =submit", hgS_otherUserName user,
hgS_otherUserSessionName =ession))
}
.Object
})
Shouldn’t ‘…’ be passed to httpGet that in turn is passed to RCURL, I.e.
gw <- httpGet(gwURL, cookiefile =empfile(), header = TRUE,
.parseúLSE, …) ?
We run an internal instance of the UCSC genome browser and need to pass a
cookie to all http-requests. The problem is that
session =ew ('UCSCSession', url=myInternalURL, cookie=myAuthCookie)
Does not pass the ‘cookie’ argument to httpGet.
Regards,
Arne
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