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.baker@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 < jjalmagro@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 < jjalmagro@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...", "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": "jjalmagro@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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