"Review tool migration stages" Time-out ?

Question: "Review tool migration stages" Time-out ?

3.1 years ago by

France

Hi everyone

I dowloaded Galaxy from Git to install a new local instance of galaxy. Everything from the admin panel works fine but the page "Review tool migration stages". I have a "Time-out" page. The log file shows this error :

----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 37060)
Traceback (most recent call last):
  File "/home/galaxy/Formation/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
    self.finish_request(request, client_address)
  File "/usr/lib/python2.7/SocketServer.py", line 334, in finish_request
    self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib/python2.7/SocketServer.py", line 657, in __init__
    self.finish()
  File "/usr/lib/python2.7/SocketServer.py", line 716, in finish
    self.wfile.close()
  File "/usr/lib/python2.7/socket.py", line 279, in close
    self.flush()
  File "/usr/lib/python2.7/socket.py", line 303, in flush
    self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
----------------------------------------

Does something change in the "Review tool migration stages" recently? I downloaded galaxy like 1 or 2 weeks ago, and I didn't have this error..

Thanks for your help.

Christ

admin time-out review tool migration stages • 735 views

ADD COMMENT • link •

modified 3.1 years ago by Dannon Baker ♦ 3.7k • written 3.1 years ago by christophe.habib • 340

I tried to compare the scripts from my old, and my new instance :

./database/compiled_templates/admin/review_tool_migration_stages.mako.py

There is no difference between them.

ADD REPLY • link written 3.1 years ago by christophe.habib • 340

3.1 years ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k wrote:

It looks like what happens on this page is that Galaxy fetches information from the toolshed about every migrated tool. This results in a whole lot of web requests from the Galaxy server to the toolshed, all during the span of your single request to your local Galaxy. In the case of a brand new instance, there are potentially a *lot* of these tools to fetch information about. My guess is that occasionally one of these threads will hang, blocking up the whole process.

Other than running the migration scripts manually (after which the number of tools displayed on this page will be reduced, and it'll render much faster), I don't have a great fix. On my local instance I simply kept trying it repeatedly and eventually the page succeeded. Maybe someone else can chime in, but short of rearchitecting how this page works I can't think of a great way to make this work better.

ADD COMMENT • link modified 3.1 years ago • written 3.1 years ago by Dannon Baker ♦ 3.7k

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