Re: Thanks for the answer

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Re: Thanks for the answer

Prachi Shah-2
Hi Anton and the galaxy group,

Tests of the ENCODEdb connection on the galaxy test site as Anton suggested
generates this new set of errors:

--------
URL: http://test.g2.bx.psu.edu:9001/async/encode_db1
Module paste.exceptions.errormiddleware:138 in __call__ Module paste.lint:65
in lint_app Module flup.middleware.session:743 in __call__ Module
paste.recursive:54 in __call__ Module paste.httpexceptions:619 in __call__
Module paste.wsgilib:112 in catch_errors_app Module galaxy.web.framework:104
in __call__
<<          kwargs = trans.request.params.copy()
            kwargs.update( map )
            body = method( trans, **kwargs )
            # Now figure out what we got back and try to get it to the
browser in
            # a smart way
    >>  body = method( trans, **kwargs ) Module galaxy.interfaces.async:85
in index
<<              GALAXY_BUILD = params.GALAXY_BUILD or
params.galaxyFreeze or 'hg17'

                data = datatypes.factory(ext=GALAXY_TYPE)()
                data.ext   = GALAXY_TYPE
                data.name  = GALAXY_NAME>>  data =
datatypes.factory(ext=GALAXY_TYPE)()
exceptions.AttributeError: 'module' object has no attribute 'factory'
--------

Thanks
Prachi

> -----Original Message-----
> From: Elnitski, Laura (NIH/NHGRI) [E] [mailto:[hidden email]]
> Sent: Wednesday, June 28, 2006 3:16 PM
> To: [hidden email]; Umayam, Lowell (NIH/NHGRI) [C]
> Cc: Wolfsberg, Tyra (NIH/NHGRI) [E]; Baxevanis, Andy (NIH/NHGRI) [E]
> Subject: Thanks for the answer
>
>
> FYI- here's the response from Anton
>
> -----Original Message-----
> From: Anton Nekrutenko [mailto:[hidden email]]
> Sent: Wed 6/28/2006 5:38 PM
> To: Elnitski, Laura (NIH/NHGRI) [E]
> Cc: [hidden email]
> Subject: Re: [Galaxy-user] FW: Fwd: Fw:  FW: Is Galaxy down?
>
> The Encode db datasource was not loaded into running galaxy. It is
> corrected now and running at http://test.g2.bx.psu.edu
>
> Use this URL for testing and let us know.
>
> anton
>
>
> Anton Nekrutenko
> Assistant Professor
> Department of Biochemistry and Molecular Biology
> Center for Comparative Genomics and Bioinformatics
> 505 Wartik Building
> PennState University
> University Park, PA 16802
> 814 865-4752
> 814 863-6699 FAX
> [hidden email]
> http://www.bx.psu.edu/~anton
> http://g2.bx.psu.edu
>
>
> On Jun 28, 2006, at 5:07 PM, Elnitski, Laura ((NIH/NHGRI)) [E] wrote:
>
> >
> > Hi-
> >
> > thanks for your help. the message below shows another error we're
> > getting. Normally, we'd take more time to investigate the problem
> > before asking you, but our manuscript is out for review right now
> > and we need resolution of this ASAP. If you think it can only be
> > handled on our end, let me know, but if you have suggestions for
> > the fix- we would greatly appreciate hearing them.
> >
> > Thanks again,
> > Laura
> >
> > -----Original Message-----
> > From: Umayam, Lowell (NIH/NHGRI) [C]
> > Sent: Wed 6/28/2006 5:02 PM
> > To: Elnitski, Laura (NIH/NHGRI) [E]; [hidden email]
> > Cc: Wolfsberg, Tyra (NIH/NHGRI) [E]; Baxevanis, Andy (NIH/NHGRI) [E]
> > Subject: Re: Fwd: Fw: [Galaxy-user] FW: Is Galaxy down?
> >
> > Hi Laura,
> > Switched the URL so it's pointing to the correct public port. So now
> > it's getting access to the galaxy server but now another error has
> > developed. It looks like they must have changed the script on their
> > end
> > and that it's now taking different arguments. This error is out of my
> > scope since I really don't have any expertise with the scripts on
> > Galaxy. I think Prachi should look into this.
> >
> > -Lowell
> >
> >
> >   Server Error
> >
> > URL: http://g2.bx.psu.edu:8085/async/encode_db1
> > Module paste.exceptions.errormiddleware:*138* in |__call__|
> > Module paste.lint:*65* in |lint_app|
> > Module flup.middleware.session:*743* in |__call__|
> > Module paste.recursive:*54* in |__call__|
> > Module paste.httpexceptions:*619* in |__call__|
> > Module paste.wsgilib:*112* in |catch_errors_app|
> > Module galaxy.web.framework:*104* in |__call__|
> > |<< <http://g2.bx.psu.edu:8085/async/encode_db1#> kwargs *=*
> > trans*.*request*.*params*.*copy*(**)*
> > kwargs*.*update*(* map *)*
> > body *=* method*(* trans*,* ****kwargs *)*
> > # Now figure out what we got back and try to get it to the browser in
> > # a smart way
> > ||>> <http://g2.bx.psu.edu:8085/async/encode_db1#>body *=* method*(*
> > trans*,* ****kwargs *)*|
> > *exceptions.TypeError: default() takes at least 3 non-keyword
> > arguments
> > (2 given)
> >
> > *
> >
> > Tyra Wolfsberg wrote:
> >
> >>
> >>
> >>
> >>> Subject: Fw: [Galaxy-user] FW: Is Galaxy down?
> >>> Date: Wed, 28 Jun 2006 16:04:56 -0400
> >>> Thread-Topic: [Galaxy-user] FW: Is Galaxy down?
> >>> Thread-Index: Acaau6b4nybF168GSgeMfrMVI4hHmAAMnsjC
> >>> From: "Elnitski, Laura \(NIH/NHGRI\) [E]" <[hidden email]>
> >>> To: "Wolfsberg, Tyra \(NIH/NHGRI\) [E]" <[hidden email]>
> >>>
> >>> Hi can you forward this to Lowell? I'm in italy :-)
> >>> Laura
> >>> --------------------------
> >>> Sent from my BlackBerry Wireless Device
> >>>
> >>>
> >>> ----- Original Message -----
> >>> From: Nate Coraor <[hidden email]>
> >>> To: Elnitski, Laura (NIH/NHGRI) [E]
> >>> Cc: [hidden email] <[hidden email]>
> >>> Sent: Wed Jun 28 10:04:35 2006
> >>> Subject: Re: [Galaxy-user] FW: Is Galaxy down?
> >>>
> >>> On Jun 28, 2006, at 7:49 AM, Elnitski, Laura ((NIH/NHGRI)) [E]
> >>> wrote:
> >>>
> >>>> Can you give us any guidance on our ENCODEdb connection problem?
> >>>
> >>>
> >>> Laura,
> >>>
> >>> It's on port 8885, although the "public" interface is now just:
> >>>
> >>> <http://main.g2.bx.psu.edu/>http://main.g2.bx.psu.edu/
> >>>
> >>> --nate
> >>
> >>
> >
> >
> > _______________________________________________
> > Galaxy-user mailing list
> > [hidden email]
> > http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
>
>
>
>