Startup error after restoring Galaxy DB from backup

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

Startup error after restoring Galaxy DB from backup

Graeme Grimes
I have tried to restart Galaxy after restoring my database from a backup.

Here is the error message I get in the log file. Any idea what is wrong
and how to fix this problem?

------------------------------
galaxy.jobs DEBUG 2014-09-03 08:33:46,367 Loading job configuration from
/export/users/galaxy/galaxy-test/universe_wsgi.ini
galaxy.jobs DEBUG 2014-09-03 08:33:46,367 Done loading job configuration
Traceback (most recent call last):
   File
"/export/users/galaxy/galaxy-test/lib/galaxy/webapps/galaxy/buildapp.py", line
35, in app_factory
     app = UniverseApplication( global_conf = global_conf, **kwargs )
   File "/export/users/galaxy/galaxy-test/lib/galaxy/app.py", line 102,
in __init__
     self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path,
self )
   File "/export/users/galaxy/galaxy-test/lib/galaxy/tools/__init__.py",
line 118, in __init__
     self.load_integrated_tool_panel_keys()
   File "/export/users/galaxy/galaxy-test/lib/galaxy/tools/__init__.py",
line 283, in load_integrated_tool_panel_keys
     tree = parse_xml( self.integrated_tool_panel_config )
   File "/export/users/galaxy/galaxy-test/lib/galaxy/util/__init__.py",
line 132, in parse_xml
     tree = ElementTree.parse(fname)
   File
"/export/users/galaxy/galaxy-test/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
line 859, in parse
     tree.parse(source, parser)
   File
"/export/users/galaxy/galaxy-test/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
line 583, in parse
     parser.feed(data)
   File
"/export/users/galaxy/galaxy-test/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
line 1242, in feed
     self._parser.Parse(data, 0)
ExpatError: not well-formed (invalid token): line 117, column 1
Removing PID file /var/run/paster.pid
-----------------


Thanks,

Graeme


--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Startup error after restoring Galaxy DB from backup

Daniel Blankenberg
Hi Graeme,

It looks like your integrated_tool_panel.xml file has been corrupted. You can move/remove this file and it will be recreated the next time Galaxy is started up.


Thanks for using Galaxy,

Dan


On Sep 3, 2014, at 3:54 AM, Graeme Grimes <[hidden email]> wrote:

> I have tried to restart Galaxy after restoring my database from a backup.
>
> Here is the error message I get in the log file. Any idea what is wrong and how to fix this problem?
>
> ------------------------------
> galaxy.jobs DEBUG 2014-09-03 08:33:46,367 Loading job configuration from /export/users/galaxy/galaxy-test/universe_wsgi.ini
> galaxy.jobs DEBUG 2014-09-03 08:33:46,367 Done loading job configuration
> Traceback (most recent call last):
>  File "/export/users/galaxy/galaxy-test/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory
>    app = UniverseApplication( global_conf = global_conf, **kwargs )
>  File "/export/users/galaxy/galaxy-test/lib/galaxy/app.py", line 102, in __init__
>    self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self )
>  File "/export/users/galaxy/galaxy-test/lib/galaxy/tools/__init__.py", line 118, in __init__
>    self.load_integrated_tool_panel_keys()
>  File "/export/users/galaxy/galaxy-test/lib/galaxy/tools/__init__.py", line 283, in load_integrated_tool_panel_keys
>    tree = parse_xml( self.integrated_tool_panel_config )
>  File "/export/users/galaxy/galaxy-test/lib/galaxy/util/__init__.py", line 132, in parse_xml
>    tree = ElementTree.parse(fname)
>  File "/export/users/galaxy/galaxy-test/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 859, in parse
>    tree.parse(source, parser)
>  File "/export/users/galaxy/galaxy-test/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 583, in parse
>    parser.feed(data)
>  File "/export/users/galaxy/galaxy-test/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 1242, in feed
>    self._parser.Parse(data, 0)
> ExpatError: not well-formed (invalid token): line 117, column 1
> Removing PID file /var/run/paster.pid
> -----------------
>
>
> Thanks,
>
> Graeme
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/


___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Startup error after restoring Galaxy DB from backup

Graeme Grimes
Thanks this fixed the problem.

Graeme

On 03/09/2014 18:30, Daniel Blankenberg wrote:

> Hi Graeme,
>
> It looks like your integrated_tool_panel.xml file has been corrupted. You can move/remove this file and it will be recreated the next time Galaxy is started up.
>
>
> Thanks for using Galaxy,
>
> Dan
>
>
> On Sep 3, 2014, at 3:54 AM, Graeme Grimes <[hidden email]> wrote:
>
>> I have tried to restart Galaxy after restoring my database from a backup.
>>
>> Here is the error message I get in the log file. Any idea what is wrong and how to fix this problem?
>>
>> ------------------------------
>> galaxy.jobs DEBUG 2014-09-03 08:33:46,367 Loading job configuration from /export/users/galaxy/galaxy-test/universe_wsgi.ini
>> galaxy.jobs DEBUG 2014-09-03 08:33:46,367 Done loading job configuration
>> Traceback (most recent call last):
>>   File "/export/users/galaxy/galaxy-test/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory
>>     app = UniverseApplication( global_conf = global_conf, **kwargs )
>>   File "/export/users/galaxy/galaxy-test/lib/galaxy/app.py", line 102, in __init__
>>     self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self )
>>   File "/export/users/galaxy/galaxy-test/lib/galaxy/tools/__init__.py", line 118, in __init__
>>     self.load_integrated_tool_panel_keys()
>>   File "/export/users/galaxy/galaxy-test/lib/galaxy/tools/__init__.py", line 283, in load_integrated_tool_panel_keys
>>     tree = parse_xml( self.integrated_tool_panel_config )
>>   File "/export/users/galaxy/galaxy-test/lib/galaxy/util/__init__.py", line 132, in parse_xml
>>     tree = ElementTree.parse(fname)
>>   File "/export/users/galaxy/galaxy-test/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 859, in parse
>>     tree.parse(source, parser)
>>   File "/export/users/galaxy/galaxy-test/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 583, in parse
>>     parser.feed(data)
>>   File "/export/users/galaxy/galaxy-test/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 1242, in feed
>>     self._parser.Parse(data, 0)
>> ExpatError: not well-formed (invalid token): line 117, column 1
>> Removing PID file /var/run/paster.pid
>> -----------------
>>
>>
>> Thanks,
>>
>> Graeme
>>
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>> ___________________________________________________________
>> 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/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
>
>


--
Bioinformatician
MRC Human Genetics Unit
MRC IGMM
University of Edinburgh
Western General Hospital
Crewe Road, Edinburgh EH4 2XU
United Kingdom
Edinburgh EH4 2XU, UK

Tel: +44 (0)131 332 2471 Ext. 4032

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/