1) The dist is most recent:
[galaxy@galaxy galaxy-dist]$ hg tip
changeset: 7982:12fcd068b12e
tag: tip
user: Daniel Blankenberg <d...@bx.psu.edu>
date: Thu Oct 18 11:22:12 2012 -0400
summary: Do not hide failed datasets with HideDatasetAction post job
action.
2) executed [galaxy_home]/static/scripts/pack_scripts.py
This solved the problem for all, but one visualisation!
One dataset I want to view in Trackster has an error
ConverterDependencyException: 'A dependency (bgzip) was in an error state.
URL: http://localhost/visualization/trackster?id=968205d9ed31733d
File
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py',
line 98 in __call__
environ, self.app)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py',
line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
line 80 in __call__
return self.application(environ, start_response)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
160 in __call__
body = method( trans, **kwargs )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 94 in decorator
return func( self, trans, *args, **kwargs )
File
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/visualization.py',
line 710 in trackster
viz_config = self.get_visualization_config( trans, vis )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/base/controller.py', line
516 in get_visualization_config
tracks.append( pack_track( drawable_dict ) )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/base/controller.py', line
467 in pack_track
source='data' )
File
'/home/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py',
line 94 in get_data_provider
data_provider = self.get_data_provider( trans,
name=data_provider_name, original_dataset=original_dataset )
File
'/home/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py',
line 74 in get_data_provider
converted_dataset = original_dataset.get_converted_dataset( trans, name )
File '/home/galaxy/galaxy-dist/lib/galaxy/model/__init__.py', line 1152
in get_converted_dataset
raise ConverterDependencyException("A dependency (%s) was in an error
state." % dependency)
ConverterDependencyException: 'A dependency (bgzip) was in an error state.'
Thanks,
Joachim
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 11/09/2012 08:34 PM, Jeremy Goecks wrote:
Can you please verify that you're running the most recent dist?
In the most recent dist, requireJS modules are used, so Dataset is
prefixed with its module, e.g.
https://bitbucket.org/galaxy/galaxy-dist/src/12fcd068b12eb844d7eded11bd70826c4275021c/static/scripts/viz/visualization.js?at=default#cl-726
However, the errors you're reporting indicate no module is used.
Another thing to try: repacking/reminifying the JavaScript files:
% cd <galaxy_home>/static/scripts
% python pack_scripts.py
If that still doesn't work, you could try commenting out the apache
rewrite rule for packed scripts and see if that solves the problem. If
so, then the problem is narrowed down to the packed scripts, one way
or another.
J.
On Nov 9, 2012, at 12:37 AM, Joachim Jacob wrote:
Thanks for your suggestion, Hans-Rudolf. Unfortunately, no success.
Looking into it bit deeper. Keep suggestions coming ;-)
Joachim
On 11/08/2012 05:00 PM, Hans-Rudolf Hotz wrote:
Hi Joachim
This might be completely unrelated, but your situation reminds me of
our case when we did the last update (to "Oct 5th release"):
All previously stored visualizations didn't work any more a first. I
had to modify the datatypes_conf.xml file by adding
the following line:
<datatype extension="fli"
type="galaxy.datatypes.tabular:FeatureLocationIndex"
display_in_upload="false"/>
and add
<converter file="bed_to_fli_converter.xml" target_datatype="fli"/>
and <converter file="gff_to_fli_converter.xml" target_datatype="fli"/>
to the bed and gff definitions, respectively.
(the differences are easy to spot when you compare your
'datatypes_conf.xml' file with the new 'datatypes_conf.xml.sample'
file.)
After making the changes and restarting the server, the saved
visualization were re-indexed as soon as I tried to open them, but
finally, the were visible again.
Regards, Hans-Rudolf
On 11/08/2012 04:21 PM, Joachim Jacob wrote:
Clearing cache did not solve it.
The Js console reports (when trying to visualize an short-read
alignment):
Uncaught ReferenceError: Dataset is not defined visualization.js:1
Uncaught ReferenceError: Dataset is not defined tracks.js:1
Uncaught ReferenceError: Dataset is not defined tracks.js:1
Thanks,
Joachim
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 11/08/2012 04:14 PM, Jeremy Goecks wrote:
Try clearing your browser cache and see if that does the trick.
If not, please open your JavaScript console and report the errors that
you're seeing.
Thanks,
J.
On Nov 8, 2012, at 4:56 AM, Joachim Jacob wrote:
Hi all,
After upgrading to the latest galaxy-dist, Trackster does not behave.
Nearly all saved viz's just show a blank main window, while just
displaying the Galaxy header and the trackster header bar.
In contrast, one visualisation gives this error:
ConverterDependencyException: 'A dependency (bgzip) was in an error
state.'
Any help appreciated, thanks.
Joachim
--
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
