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

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