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:elnitski@mail.nih.gov]
Sent: Wednesday, June 28, 2006 3:16 PM
To: prachi@stanford.edu; 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:anton@bx.psu.edu]
Sent: Wed 6/28/2006 5:38 PM
To: Elnitski, Laura (NIH/NHGRI) [E]
Cc: galaxy-user@bx.psu.edu
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
anton@bx.psu.edu
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]; prachi@stanford.edu
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]" <elnitski@mail.nih.gov>
To: "Wolfsberg, Tyra \(NIH/NHGRI\) [E]" <tyra@nhgri.nih.gov>
Hi can you forward this to Lowell? I'm in italy :-)
Laura
--------------------------
Sent from my BlackBerry Wireless Device
----- Original Message -----
From: Nate Coraor <nate@bx.psu.edu>
To: Elnitski, Laura (NIH/NHGRI) [E]
Cc: galaxy-user@bx.psu.edu <galaxy-user@bx.psu.edu>
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
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Prachi Shah