Thanks Jeremy, that changeset fixed the issue :)

Cheers,
Liisa




From:
Jeremy Goecks <jeremy.goe...@emory.edu>
To:
Liisa Koski <liisa.ko...@dnalandmarks.ca>
Cc:
<galaxy-dev@lists.bx.psu.edu>
Date:
2011-11-30 18:07
Subject:
Re: [galaxy-dev] Can't view data files from published histories, only 
imported histories



Liisa,

Updating FastQC won't solve this issue. You'll need to manually update 
galaxy-dist with this changeset to see the graphs:

https://bitbucket.org/galaxy/galaxy-central/changeset/c8493a61bbea

Otherwise, you can wait until the next galaxy-dist to get this changeset.

Best,
J.



On Nov 30, 2011, at 2:39 PM, Liisa Koski wrote:

Hi Jeremy, 
I updated to the latest galaxy-dist release and can now see the boxplots 
(png) files from published histories. I can see the FASTQC (html) reports 
too but the individual graphs within the report are missing. I will update 
fastqc itself and see if that makes a difference. 

Thanks, 
Liisa 

Liisa Koski 
Bioinformatics Programmer
Phone: 518-309-3079, E-Mail: liisa.ko...@dnalandmarks.ca
Postal Address: DNA LandMarks Inc, St-jean-sur-Richelieu, J3B 6X3 Québec 
CANADA 
DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant Science 
company 
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From: 
Jeremy Goecks <jeremy.goe...@emory.edu> 
To: 
Liisa Koski <liisa.ko...@dnalandmarks.ca> 
Cc: 
<galaxy-dev@lists.bx.psu.edu> 
Date: 
2011-11-28 14:46 
Subject: 
Re: [galaxy-dev] Can't view data files from published histories, only 
imported histories




Liisa, 

I'm not able to reproduce your issue on our public server. For instance, 
here's a history that includes both FastQC output and a boxplot; both 
display correctly: 

http://main.g2.bx.psu.edu/u/jeremy/h/unnamed-history-2 

(Note that I just committed a fix to galaxy-central so that the images in 
the FastQC output show up correctly.) 

Some questions that might help us figure out the problem: 
*can you reproduce your problem on a public Galaxy instance, such as main 
or test? 
*is your Galaxy instance up to date? 
*is there something unusual about the datasets that you're using, e.g. are 
they imported on non-standard in some way? 

J. 

On Nov 28, 2011, at 1:35 PM, Liisa Koski wrote: 

Hi Jeremy, 
I'm trying to view boxplots (png) and FastQC (html) output. I  can view 
other output types like tabular in the published histories, but not png or 
html. 

Thanks, 
Liisa 

Liisa Koski 
Bioinformatics Programmer
Phone: 518-309-3079, E-Mail: liisa.ko...@dnalandmarks.ca
Postal Address: DNA LandMarks Inc, St-jean-sur-Richelieu, J3B 6X3 Québec 
CANADA 
DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant Science 
company 
Confidentiality notice: The information contained in this e-mail is 
confidential and may be the subject of legal professional privilege. It is 
intended for the authorized use of the individual or entity addressed. If 
the receiver or reader of this message is not the intended recipient, you 
are hereby notified that any disclosure, copying, distribution or use of 
the contents of this message is prohibited. If this email is received in 
error, please accept our apologies, delete all copies from your system, 
and notify us at supp...@dnalandmarks.ca.----Confidentialité: 
L'information contenue dans ce courriel est confidentielle et peut être 
assujettie aux règles concernant le secret professionel. L'information 
contenue dans ce courriel est autorisée uniquement pour l'individu ou 
l'entité légale adressée. Si le récipiendaire ou le lecteur de ce message 
n'est pas celui ou celle prévue, vous êtes tenu de ne pas présenter, 
copier, distribuer ou utiliser le contenu de ce message. Si ce courriel 
est reçu par erreur, veuillez nous en excuser, veuillez détruire toutes 
copies de votre système nous informer à supp...@dnalandmarks.ca. 

From: 
Jeremy Goecks <jeremy.goe...@emory.edu> 
To: 
Liisa Koski <liisa.ko...@dnalandmarks.ca> 
Cc: 
<galaxy-dev@lists.bx.psu.edu> 
Date: 
2011-11-28 13:23 
Subject: 
Re: [galaxy-dev] Can't view data files from published histories, only 
imported histories





Liisa, 

This functionality works fine in some instances, e.g. for this history: 

http://main.g2.bx.psu.edu/u/cartman/h/repeats 

I'd guess that it's related to the particular dataset type. What type of 
dataset are you trying to view when you see this error? Can you view any 
datasets from the history? 

Thanks, 
J. 

On Nov 28, 2011, at 1:11 PM, Liisa Koski wrote: 

Hi, 
I found a weird bug. I am trying to view data files by clicking on the 
'eye' icon from a published history on my local galaxy installation. When 
I click on the eye I get a 'Server Error' and in the log file I get the 
following. 

Error - <type 'exceptions.NameError'>: global name 'data' is not defined 
URL: http://domain:8080/u/user/d/8bdb720fee635874 
File 
'galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', 
line 143 in __call__ 
app_iter = self.application(environ, start_response) 
File 'galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in 
__call__ 
return self.application(environ, start_response) 
File 'galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 
632 in __call__ 
return self.application(environ, start_response) 
File 'galaxy_dist/lib/galaxy/web/framework/base.py', line 160 in __call__ 
body = method( trans, **kwargs ) 
File 'galaxy_dist/lib/galaxy/web/controllers/dataset.py', line 693 in 
display_by_username_and_slug 
trans.response.set_content_type( data.get_mime() ) 
NameError: global name 'data' is not defined 

If I import the history into my own history pane I can click on the eye 
and see the data with no errors. 

Any ideas how I can see the data from the published histories? 

Thanks, 
Liisa 

Liisa Koski 
Bioinformatics Programmer
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