[Galaxy-user] error at Galaxy

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[Galaxy-user] error at Galaxy

Ross Hardison
This occurred while getting phastOdds scores:

exceptions.ValueError at /history
I/O operation on closed file
Python
/usr/lib/python2.4/cgi.py in __getattr__, line 541
Web
Traceback (innermost first)
/usr/lib/python2.4/cgi.py in __getattr__
  1.             self.file.seek(0) 
  2. ...
/usr/lib/python2.4/cgi.py in __repr__
  1.         return "FieldStorage(%r, %r, %r)" % ( 
  2. ...
/var/opt/universe/trunk-test/modules/Cheetah/Filters.py in filter
  1.             filtered = str(val) 
  2. ...
in respond
/var/opt/universe/trunk-test/galaxy/interfaces/common.py in fill_template
  1.         return str(template) 
  2. ...
/var/opt/universe/trunk-test/galaxy/interfaces/root.py in history
  1.         return self.fill_template(template, history=history, mode=mode ) 
  2. ...
build/bdist.cygwin-1.5.12-i686/egg/cherrypy/_cphttptools.py in main
build/bdist.cygwin-1.5.12-i686/egg/cherrypy/_cphttptools.py in run
Response so far
HEADERS
Date: Sat, 25 Feb 2006 18:52:04 GMT
Set-Cookie: []
Content-Length:
Content-Type: text/html
Server: CherryPy/2.1.1
BODY

Request information
INPUT
No input data.
COOKIES
Variable
Value
universe
Set-Cookie: universe=6488ab1b7e827b13fd5e85de2ef78ab7;
session
Set-Cookie: session=2e41ce0777a1fcf0a6a2f9019dbec55f95e37934;
universe_prefs
Set-Cookie: universe_prefs=three;
universe_ui
Set-Cookie: universe_ui=info66;

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Re: error at Galaxy

Istvan Albert
On 2/25/06, Ross Hardison <[hidden email]> wrote:

> This occurred while getting phastOdds scores:

Do you happen to have the file (or recall the steps) that caused this error?

(It is a very strange error for both the location of where it happens
and the reason it gives back)

Istvan.

--
Istvan Albert,
Research Associate,
Bioinformatics Consulting Center,
Huck Institute for Life Sciences,
Pennsylvania State University
http://www.personal.psu.edu/iua1

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Re: error at Galaxy

Istvan Albert
On 2/25/06, Istvan Albert <[hidden email]> wrote:

> > This occurred while getting phastOdds scores:

I did not find the ultimate cause but I found the symptom for the
history not rendering properly. For one the results the dbkey got
overwritten from being a string to the actual universe instance
(ouch!).

I'll be able to fix the the reason the history fails to render, for
now with a simple fix but we need to make it so that eventually the
history renders no matter what errors it might contain.

--
Istvan Albert,
Research Associate,
Bioinformatics Consulting Center,
Huck Institute for Life Sciences,
Pennsylvania State University
http://www.personal.psu.edu/iua1