Question: Phyloviz Error after Galaxy Update
1
gravatar for danielfortin86
3.6 years ago by
United States
danielfortin86110 wrote:

I'm currently using a local version of Galaxy (latest stable). After the update Phyloviz no longer opens correctly. When I click on the PhyloViz icon it says:

 

Internal Server Error

Galaxy was unable to successfully complete your request

An error occurred.

This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.
The error has been logged to our team.

 

 

error update phylovz galaxy • 945 views
ADD COMMENTlink modified 3.6 years ago by Dannon Baker3.7k • written 3.6 years ago by danielfortin86110
2
gravatar for Dannon Baker
3.6 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:

It looks at first glance that this is an error that has been fixed in the current development branch, I'll see what we need to do to get the fix into stable.

Edit:  It's fixed in the github release branch too, we just need to propagate some changes to bitbucket.  I'll let you know when it's ready to go.

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Dannon Baker3.7k
1
gravatar for danielfortin86
3.6 years ago by
United States
danielfortin86110 wrote:

Hi Jen,

Unfortunately, I'm the one administering the local instance :)

I found this reference to phyloviz in the paster.log file:

xx.xx.xx.xxx - - [17/Apr/2015:09:23:45 -0700] "GET /galaxy/visualization/phyloviz?dataset_id=0774ab36df5b8f8b HTTP/1.1" 500 - "http://xxxxx/galaxy/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.115 Safari/537.36"
Error - <type 'exceptions.TypeError'>: error_if_uploading() takes exactly 3 arguments (2 given)
URL: http://xxxxx/galaxy/visualization/phyloviz?dataset_id=0774ab36df5b8f8b
File '/opt/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__
  app_iter = self.application(environ, sr_checker)
File '/opt/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__
  return self.application(environ, start_response)
File '/opt/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__
  return self.application(environ, start_response)
File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 133 in __call__
  return self.handle_request( environ, start_response )
File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 191 in handle_request
  body = method( trans, **kwargs )
File '/opt/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/visualization.py', line 1020 in phyloviz
  hda = self.hda_manager.error_if_uploading( hda )
TypeError: error_if_uploading() takes exactly 3 arguments (2 given)

 

ADD COMMENTlink written 3.6 years ago by danielfortin86110
0
gravatar for Jennifer Hillman Jackson
3.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This type of error can show up during many functions when the server is very busy at the exact time the action was taken. It usually goes away immediately or after a few minutes at http://usegalaxy.org. Since you are working on another server (local), contact their admin/support to report the issue - this can sometimes indicate other problems and I am sure they would be glad to know about it.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Jennifer Hillman Jackson25k
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