Phyloviz Error after Galaxy Update

Question: Phyloviz Error after Galaxy Update

3.6 years ago by

United States

danielfortin86 • 110 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

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modified 3.6 years ago by Dannon Baker ♦ 3.7k • written 3.6 years ago by danielfortin86 • 110

3.6 years ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k 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 COMMENT • link modified 3.6 years ago • written 3.6 years ago by Dannon Baker ♦ 3.7k

3.6 years ago by

danielfortin86 • 110

United States

danielfortin86 • 110 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 COMMENT • link written 3.6 years ago by danielfortin86 • 110

3.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link modified 3.6 years ago • written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

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