[Bioc-devel] rtracklayer bug?

[Michael Lawrence]

I will add "..." to the httpGet call.

On Tue, Jun 30, 2015 at 10:10 AM, Marc Carlson <mcarlson at fredhutch.org> wrote:
> 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 at url <- url
>>
>>              .Object at 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 at 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
>>
>>         [[alternative HTML version deleted]]
>>
>
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