Hello Dannon,

This is the log when a job is executed:

galaxy.jobs DEBUG 2015-04-24 17:25:27,266 (9568) Working directory for job
is:
/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568
galaxy.jobs.handler DEBUG 2015-04-24 17:25:27,313 (9568) Dispatching to
local runner
galaxy.jobs DEBUG 2015-04-24 17:25:27,600 (9568) Persisting job destination
(destination id: local)
galaxy.jobs.handler INFO 2015-04-24 17:25:27,686 (9568) Job dispatched
galaxy.jobs.runners DEBUG 2015-04-24 17:25:28,465 (9568) command is: python
/steno-internal/projects/galaxy/galaxy-dist/tools/table_gen/generator.py
"/steno-internal/projects/galaxy/galaxy-dist/database/files/021/dataset_21041.dat"
"1"; return_code=$?; python
/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/set_metadata_MH6prK.py
/steno-internal/projects/galaxy/galaxy-dist/database/tmp/tmpw80FFi
/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/galaxy.json
/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/metadata_in_HistoryDatasetAssociation_14967_7w0ALE,/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/metadata_kwds_HistoryDatasetAssociation_14967_uH3ZBP,/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/metadata_out_HistoryDatasetAssociation_14967_5iEavP,/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/metadata_results_HistoryDatasetAssociation_14967_6FT2qV,/steno-internal/projects/galaxy/galaxy-dist/database/files/021/dataset_21041.dat,/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/metadata_override_HistoryDatasetAssociation_14967_iOPJoQ;
sh -c "exit $return_code"
galaxy.jobs.runners.local DEBUG 2015-04-24 17:25:28,475 (9568) executing
job script:
/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/galaxy_9568.sh
galaxy.jobs DEBUG 2015-04-24 17:25:28,617 (9568) Persisting job destination
(destination id: local)
galaxy.jobs.runners.local DEBUG 2015-04-24 17:25:31,960 execution finished:
/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/009/9568/galaxy_9568.sh
galaxy.datatypes.metadata DEBUG 2015-04-24 17:25:32,207 loading metadata
from file for: HistoryDatasetAssociation 14967
galaxy.jobs INFO 2015-04-24 17:25:34,775 Collecting job metrics for
<galaxy.model.Job object at 0x7f3154cacad0>
galaxy.jobs DEBUG 2015-04-24 17:25:34,799 job 9568 ended
galaxy.datatypes.metadata DEBUG 2015-04-24 17:25:34,800 Cleaning up
external metadata files






I am not sure at all but I think this is the internal error that I got with
the history panel problem:

130.225.125.174 - - [24/Apr/2015:15:22:19 +0200] "GET
/api/histories/32c70b5011288952/contents HTTP/1.1" 500 - "
http://galaxy.bric.dk/history/view_multiple"; "Mozilla/5.0 (X11; Linux
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/37.0.2062.120
Safari/537.36"
galaxy.web.framework.decorators ERROR 2015-04-24 15:22:20,033 Uncaught
exception in exposed API method:
Traceback (most recent call last):
  File
"/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py",
line 251, in decorator
    rval = func( self, trans, *args, **kwargs)
  File
"/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/history_contents.py",
line 105, in index
    hda_dict = self.hda_serializer.serialize_to_view( trans, content,
view=view )
  File
"/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/managers/base.py",
line 621, in serialize_to_view
    return self.serialize( trans, item, all_keys )
  File
"/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/managers/hdas.py",
line 453, in serialize
    serialized = super( HDASerializer, self ).serialize( trans, hda, keys )
  File
"/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/managers/base.py",
line 566, in serialize
    returned[ key ] = self.serializers[ key ]( trans, item, key )
  File
"/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/managers/hdas.py",
line 403, in <lambda>
    'resubmitted'   : lambda t, i, k: i._state ==
t.app.model.Dataset.states.RESUBMITTED,
AttributeError: 'Bunch' object has no attribute 'RESUBMITTED'


Thanks a lot for your help!

Regards,

Jose


2015-04-24 17:16 GMT+02:00 Dannon Baker <dannon.ba...@gmail.com>:

> Hi Jose,
>
> Can you review (and share, maybe) the relevant part of the logs from when
> you attempt to execute a job?  It'd be worth it, if you still have the
> logs, to know what the "Internal Server Error" indicated in your first
> message was, as well.
>
> -Dannon
>
> On Fri, Apr 24, 2015 at 11:00 AM Jose Juan Almagro Armenteros <
> jjalma...@gmail.com> wrote:
>
>> Hi again,
>>
>> Now it is working, I just went back to the previous version and updated
>> it again. All is okay except that the job table in the postgresql database
>> is empty and is not being updated with new jobs (the problem is only with
>> this table). I run manage_db.sh upgrade but nothing happened.
>>
>> Do you know what could be causing this?
>>
>> Thank you again!
>>
>> Best regards,
>>
>> Jose
>>
>> 2015-04-24 14:22 GMT+02:00 Jose Juan Almagro Armenteros <
>> jjalma...@gmail.com>:
>>
>>> Hello all,
>>>
>>> I have updated my Galaxy distribution today to the latest version 15.03
>>> and the history panel is not being shown. The history seems to be there but
>>> Galaxy can't display the datasets.  Even if I create a new history and I
>>> run a tool the dataset is not shown. It is just displayed an error which
>>> says: "An error occurred while getting updates from the server..." and the
>>> details shows this:
>>>
>>> {
>>>   "agent": "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like 
>>> Gecko) Chrome/37.0.2062.120 Safari/537.36",
>>>   "url": 
>>> "http://galaxy.bric.ku.dk/history/view_multipl/api/histories/782c6cc7ec4cfd9f/contents";,
>>>   "data": "",
>>>   "options": {
>>>     "data": {},
>>>     "silent": true,
>>>     "parse": true,
>>>     "emulateHTTP": false,
>>>     "emulateJSON": false
>>>   },
>>>   "xhr": {
>>>     "readyState": 4,
>>>     "responseText": "{\"err_msg\": \"Uncaught exception in exposed API 
>>> method:\", \"err_code\": 0}",
>>>     "responseJSON": {
>>>       "err_msg": "Uncaught exception in exposed API method:",
>>>       "err_code": 0
>>>     },
>>>     "status": 500,
>>>     "statusText": "Internal Server Error",
>>>     "responseHeaders": {
>>>       "Date": "Fri, 24 Apr 2015 12:09:40 GMT\r",
>>>       "cache-control": "max-age=0,no-cache,no-store\r",
>>>       "Transfer-Encoding": "chunked\r",
>>>       "Server": "PasteWSGIServer/0.5 Python/2.7.3\r",
>>>       "Connection": "close\r",
>>>       "x-frame-options": "SAMEORIGIN\r",
>>>       "content-type": "application/json\r"
>>>     }
>>>   },
>>>   "source": [],
>>>   "user": {
>>>     "username": "jose",
>>>     "quota_percent": 0,
>>>     "total_disk_usage": 101352147,
>>>     "nice_total_disk_usage": "96.7 MB",
>>>     "email": "jjalma...@gmail.com",
>>>     "is_admin": true,
>>>     "tags_used": [],
>>>     "model_class": "User",
>>>     "id": "72ad249754f05d26"
>>>   }
>>> }
>>>
>>> Do you have any idea what could go wrong?
>>>
>>> Thank you and best regards,
>>>
>>> Jose
>>>
>>
>> ___________________________________________________________
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