[DAS] Re: Hello Jim
Brian Gilman
gilmanb@genome.wi.mit.edu
Fri, 15 Mar 2002 14:24:41 -0500 (EST)
Wonderful!!
I'm happy we could talk the same protocol ;)
-b
-----------------------
Brian Gilman <gilmanb@genome.wi.mit.edu>
Sr. Software Engineer MIT/Whitehead Inst. Center for Genome Research
One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
phone +1 617 252 1069 / fax +1 617 252 1902
On Fri, 15 Mar 2002, Jim Kent wrote:
> Ah, I get it at last! Sorry to be dense.
>
> Try it on hgwdev-beta.cse.ucsc.edu. We're
> about to do a new release (for the mouse) and
> this all will be moved to genome.ucsc.edu shortly.
>
>
>
> Jim Kent
> Genome Bioinformatics Group
> University of California at Santa Cruz
> http://www.soe.ucsc.edu/~kent/
>
> ----- Original Message -----
> From: "Brian Gilman" <gilmanb@harpo.wi.mit.edu>
> To: "Jim Kent" <jim_kent@pacbell.net>
> Cc: <das@biodas.org>
> Sent: Friday, March 15, 2002 10:43 AM
> Subject: Re: Hello Jim
>
>
> > I know that this is in there when we hit your DAS server with a a das
> > request: dsn, entry_points etc.
> >
> > The problem is when I hit your server with:
> >
> > telnet> open genome.cse.ucsc.edu 80
> > Trying 128.114.50.181...
> > Connected to genome.cse.ucsc.edu.
> > Escape character is '^]'.
> > GET /cgi-bin/das HTTP/1.0
> >
> > HTTP/1.1 200 OK
> > Date: Fri, 15 Mar 2002 18:41:33 GMT
> > Server: Apache/1.3.20 (Unix)
> > Connection: close
> > Content-Type: text/plain; charset=iso-8859-1
> >
> > UCSC Human Genome DAS Server.
> >
> > See http://www.biodas.org for more info on DAS.
> > Connection closed by foreign host.
> >
> > There isn't any DAS information in there. Do you think you could
> > add some DAS-Version and DAS-Status info in there??
> >
> > best,
> >
> > -B
> >
> >
> > -----------------------
> > Brian Gilman <gilmanb@genome.wi.mit.edu>
> > Sr. Software Engineer MIT/Whitehead Inst. Center for Genome Research
> > One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
> > phone +1 617 252 1069 / fax +1 617 252 1902
> >
> >
> > On Fri, 15 Mar 2002, Jim Kent wrote:
> >
> > > I finally remembered how to check this with telnet. It looks like
> > > we are and always have been putting in the X-DAS-Version
> > > stuff:
> > >
> > > hgwdev% telnet genome.cse.ucsc.edu 80
> > > Trying 128.114.50.188...
> > > Connected to genome.cse.ucsc.edu.
> > > Escape character is '^]'.
> > > GET /cgi-bin/das/dsn HTTP/1.0
> > >
> > > HTTP/1.1 200 OK
> > > Date: Fri, 15 Mar 2002 18:24:38 GMT
> > > Server: Apache/1.3.20 (Unix)
> > > X-DAS-Status: 200
> > > X-DAS-Version: DAS/0.95
> > > Connection: close
> > > Content-Type: text/plain; charset=iso-8859-1
> > >
> > > <?xml version="1.0" standalone="no"?>
> > > <DASDSN>
> > > <DSN>
> > > <SOURCE id="hg6" version="1.00">Dec. 12, 2000 Human Genome at UCSC</SOURCE>
> > > <MAPMASTER>http://genome.cse.ucsc.edu:80/cgi-bin/das/hg6</MAPMASTER>
> > > <DESCRIPTION>Dec. 12, 2000 Human Genome at UCSC</DESCRIPTION>
> > > </DSN>
> > > <DSN>
> > > <SOURCE id="hg7" version="1.00">April 1, 2001 Human Genome at UCSC</SOURCE>
> > > <MAPMASTER>http://genome.cse.ucsc.edu:80/cgi-bin/das/hg7</MAPMASTER>
> > > <DESCRIPTION>April 1, 2001 Human Genome at UCSC</DESCRIPTION>
> > > </DSN>
> > > <DSN>
> > > <SOURCE id="hg8" version="1.00">Aug. 6, 2001 Human Genome at UCSC</SOURCE>
> > > <MAPMASTER>http://genome.cse.ucsc.edu:80/cgi-bin/das/hg8</MAPMASTER>
> > > <DESCRIPTION>Aug. 6, 2001 Human Genome at UCSC</DESCRIPTION>
> > > </DSN>
> > > <DSN>
> > > <SOURCE id="hg10" version="1.00">Dec. 22, 2001 (NCBI) Human Genome at UCSC</SOURCE>
> > > <MAPMASTER>http://genome.cse.ucsc.edu:80/cgi-bin/das/hg10</MAPMASTER>
> > > <DESCRIPTION>Dec. 22, 2001 (NCBI) Human Genome at UCSC</DESCRIPTION>
> > > </DSN>
> > > </DASDSN>
> > > Connection closed by foreign host.
> > >
> > >
> > >
> > >
> > > Jim Kent
> > > Genome Bioinformatics Group
> > > University of California at Santa Cruz
> > > http://www.soe.ucsc.edu/~kent/
> > >
> > > ----- Original Message -----
> > > From: "Brian Gilman" <gilmanb@harpo.wi.mit.edu>
> > > To: "Jim Kent" <jim_kent@pacbell.net>
> > > Cc: <das@biodas.org>
> > > Sent: Tuesday, March 12, 2002 2:07 PM
> > > Subject: Re: Hello Jim
> > >
> > >
> > > > Code looks great!
> > > >
> > > > My app doesn't care where the header appears. I just need to see
> > > > it when I hit the server at http://genome.ucsc.edu/cgi-bin/das. If I hit
> > > > the server at http://genome.ucsc.edu/cgi-bin/das/dsn I don't see this
> > > > header either. Looks like an HTTP GET is not outputting these
> > > > headers...Thanks Jim!! I really appreciate this!
> > > >
> > > > -B
> > > >
> > > > -----------------------
> > > > Brian Gilman <gilmanb@genome.wi.mit.edu>
> > > > Sr. Software Engineer MIT/Whitehead Inst. Center for Genome Research
> > > > One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
> > > > phone +1 617 252 1069 / fax +1 617 252 1902
> > > >
> > > >
> > > > On Tue, 12 Mar 2002, Jim Kent wrote:
> > > >
> > > > > Here's the code I have now. It looks like it has the X-DAS-Status
> > > > > and so forth in it, but not in the order you're expecting. Isn't the
> > > > > order supposed to be flexible on your side though?
> > > > >
> > > > > void dasHeader(int err)
> > > > > /* Write out very start of DAS header */
> > > > > {
> > > > > printf("Content-Type:text/plain\n");
> > > > > printf("X-DAS-Version: DAS/0.95\n");
> > > > > printf("X-DAS-Status: %d\n", err);
> > > > > printf("\n");
> > > > > if (err != 200)
> > > > > exit(-1);
> > > > > printf("<?xml version=\"1.0\" standalone=\"no\"?>\n");
> > > > > }
> > > > >
> > > > > +++++++++++++++++++++++++++++++++++++++++++++++
> > > > > Jim Kent. Zahler Lab. University of California at Santa Cruz
> > > > > http://www.cse.ucsc.edu/~kent/
> > > > >
> > > > > ----- Original Message -----
> > > > > From: "Brian Gilman" <gilmanb@harpo.wi.mit.edu>
> > > > > To: "Jim Kent" <jim_kent@pacbell.net>
> > > > > Cc: <das@biodas.org>
> > > > > Sent: Wednesday, March 06, 2002 11:20 AM
> > > > > Subject: Re: Hello Jim
> > > > >
> > > > >
> > > > > > Hello Jim,
> > > > > >
> > > > > > Here is the current output from your server:
> > > > > > HTTP/1.1 200 OK
> > > > > > Date Wed, 06 Mar 2002 19:19:09 GMT
> > > > > > Server Apache/1.3.20 (Unix)
> > > > > > Keep-Alive timeout=15, max=100
> > > > > > Connection Keep-Alive
> > > > > > Transfer-Encoding chunked
> > > > > > Content-Type text/plain; charset=iso-8859-1
> > > > > > content-length 79
> > > > > >
> > > > > >
> > > > > >
> > > > > > Here is what we are looking for:
> > > > > >
> > > > > > HTTP/1.1 200 OK
> > > > > > Date Wed, 06 Mar 2002 19:17:44 GMT
> > > > > > Server Apache/1.3.20 (Unix)
> > > > > > X-DAS-Status 200
> > > > > > X-DAS-Version DAS/0.95
> > > > > > Keep-Alive timeout=15, max=100
> > > > > > Connection Keep-Alive
> > > > > > Transfer-Encoding chunked
> > > > > > Content-Type text/plain; charset=iso-8859-1
> > > > > > content-length 1037
> > > > > >
> > > > > >
> > > > > > This will allow clients to know what version of the spec you are
> > > > > > supporting at an early stage and reduce the # of round trips we need to
> > > > > > make to figure this out.
> > > > > >
> > > > > >
> > > > > > Thanks Jim!!
> > > > > >
> > > > > > -Brian
> > > > > >
> > > > > >
> > > > > > -----------------------
> > > > > > Brian Gilman <gilmanb@genome.wi.mit.edu>
> > > > > > Sr. Software Engineer MIT/Whitehead Inst. Center for Genome Research
> > > > > > One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
> > > > > > phone +1 617 252 1069 / fax +1 617 252 1902
> > > > > >
> > > > > >
> > > > > > On Wed, 6 Mar 2002, Jim Kent wrote:
> > > > > >
> > > > > > > Could you grab the current response from
> > > > > > > http://genome.ucsc.edu/cgi-bin/das
> > > > > > > put the change you want in, and send it to
> > > > > > > me via email? I'm not sure where to put it.
> > > > > > >
> > > > > > >
> > > > > > > Then, could you please stop changing DAS
> > > > > > > so often? Double digit version numbers in
> > > > > > > a *standard* are really a sign something is
> > > > > > > broken in the process....
> > > > > > >
> > > > > > > +++++++++++++++++++++++++++++++++++++++++++++++
> > > > > > > Jim Kent. Zahler Lab. University of California at Santa Cruz
> > > > > > > http://www.cse.ucsc.edu/~kent/
> > > > > > >
> > > > > > > ----- Original Message -----
> > > > > > > From: "Brian Gilman" <gilmanb@harpo.wi.mit.edu>
> > > > > > > To: <jim_kent@pacbell.net>
> > > > > > > Cc: <das@biodas.org>
> > > > > > > Sent: Wednesday, March 06, 2002 7:57 AM
> > > > > > > Subject: Hello Jim
> > > > > > >
> > > > > > >
> > > > > > > > Hello Jim,
> > > > > > > >
> > > > > > > > Long time no talk. As you may know a few of my developers have
> > > > > > > > been pinging you about your DAS server. The spec has changed quite a bit
> > > > > > > > but and there are certain portions that remain ambiguous. One of these
> > > > > > > > ambiguities have caused havok with our DAS API. The specification defines
> > > > > > > > a header called "X-DAS-Version" this header should be available to the
> > > > > > > > requester upon each and every request to the server. However, we have
> > > > > > > > found that if you ping a DAS server without a specific das request ie.
> > > > > > > >
> > > > > > > > http://genome.ucsc.edu/cgi-bin/das
> > > > > > > >
> > > > > > > > We do not see an "X-DAS-Status" header which causes our API to
> > > > > > > > break. I know this is being very nit picky but, with all the versions of
> > > > > > > > DAS laying around, we find that having this header present at the most top
> > > > > > > > level request allows us to handle all these versions seemlessly.
> > > > > > > >
> > > > > > > > To that end, could you please add the "X-DAS-Version" header to
> > > > > > > > your DAS server when querying the top most URL
> > > > > > > > (genome.ucsc.edu/cgi-bin/das)?
> > > > > > > >
> > > > > > > >
> > > > > > > > Thank You!!
> > > > > > > >
> > > > > > > > -Brian Gilman
> > > > > > > >
> > > > > > > >
> > > > > > > > -----------------------
> > > > > > > > Brian Gilman <gilmanb@genome.wi.mit.edu>
> > > > > > > > Sr. Software Engineer MIT/Whitehead Inst. Center for Genome Research
> > > > > > > > One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
> > > > > > > > phone +1 617 252 1069 / fax +1 617 252 1902
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