History panel error

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

History panel error

Jose Juan Almagro Armenteros
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": "[hidden email]",
    "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

___________________________________________________________
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:
  https://lists.galaxyproject.org/

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

Re: History panel error

Jose Juan Almagro Armenteros
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 <[hidden email]>:
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": "[hidden email]",
    "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


___________________________________________________________
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:
  https://lists.galaxyproject.org/

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

Re: History panel error

Dannon Baker-2
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 <[hidden email]> 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 <[hidden email]>:
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": "[hidden email]",
    "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

___________________________________________________________
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:
  https://lists.galaxyproject.org/

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:
  https://lists.galaxyproject.org/

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

Fwd: History panel error

Jose Juan Almagro Armenteros
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 <[hidden email]>:
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 <[hidden email]> 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 <[hidden email]>:
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": "[hidden email]",
    "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

___________________________________________________________
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:
  https://lists.galaxyproject.org/

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:
  https://lists.galaxyproject.org/

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

Re: Fwd: History panel error

Carl Eberhard
Hi, Jose

Our next cycle includes some updates to the resubmission/hda-serialization code that's mentioned in your stack trace.

You can try two things:
1) You can wait for us to officially publish our next stable release (15.05) at the beginning of next month and then update your instance.
2) You can update *now* to the github version that *will be* our 15.05 release: https://github.com/galaxyproject/galaxy/tree/release_15.05

We are still stabilizing 15.05 and not all bug fixes have been committed, but it may be the best option if you need to get past this problem quickly.

If you're unable to do one of the above or are still having issues after doing one of them, let me know and we can work on it further.

Carl


On Mon, Apr 27, 2015 at 4:28 AM, Jose Juan Almagro Armenteros <[hidden email]> wrote:
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 <[hidden email]>:
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 <[hidden email]> 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 <[hidden email]>:
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": "[hidden email]",
    "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

___________________________________________________________
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:
  https://lists.galaxyproject.org/

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:
  https://lists.galaxyproject.org/

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:
  https://lists.galaxyproject.org/

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

Re: Fwd: History panel error

Jose Juan Almagro Armenteros
Hello Carl,

I can wait until the next stable release, my Galaxy distribution is working correctly even though the job table in the database is always empty. This table was used to detect job errors by running a cron job that sends an email. Do you know if there is another way of doing this?

Thank you!

Regards,

Jose

2015-04-27 20:46 GMT+02:00 Carl Eberhard <[hidden email]>:
Hi, Jose

Our next cycle includes some updates to the resubmission/hda-serialization code that's mentioned in your stack trace.

You can try two things:
1) You can wait for us to officially publish our next stable release (15.05) at the beginning of next month and then update your instance.
2) You can update *now* to the github version that *will be* our 15.05 release: https://github.com/galaxyproject/galaxy/tree/release_15.05

We are still stabilizing 15.05 and not all bug fixes have been committed, but it may be the best option if you need to get past this problem quickly.

If you're unable to do one of the above or are still having issues after doing one of them, let me know and we can work on it further.

Carl


On Mon, Apr 27, 2015 at 4:28 AM, Jose Juan Almagro Armenteros <[hidden email]> wrote:
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 <[hidden email]>:
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 <[hidden email]> 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 <[hidden email]>:
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": "[hidden email]",
    "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

___________________________________________________________
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:
  https://lists.galaxyproject.org/

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:
  https://lists.galaxyproject.org/

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:
  https://lists.galaxyproject.org/

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

Re: Fwd: History panel error

Dannon Baker-2
Jose,

Regarding the job table being empty -- how exactly are you checking this?  This table should never be empty (except in the case of a *brand new* galaxy instance) and I cannot think of anything that would cause it to be so.  The log detailing the execution of a job looks totally fine to me.

-Dannon

On Mon, Apr 27, 2015 at 7:02 PM Jose Juan Almagro Armenteros <[hidden email]> wrote:
Hello Carl,

I can wait until the next stable release, my Galaxy distribution is working correctly even though the job table in the database is always empty. This table was used to detect job errors by running a cron job that sends an email. Do you know if there is another way of doing this?

Thank you!

Regards,

Jose

2015-04-27 20:46 GMT+02:00 Carl Eberhard <[hidden email]>:
Hi, Jose

Our next cycle includes some updates to the resubmission/hda-serialization code that's mentioned in your stack trace.

You can try two things:
1) You can wait for us to officially publish our next stable release (15.05) at the beginning of next month and then update your instance.
2) You can update *now* to the github version that *will be* our 15.05 release: https://github.com/galaxyproject/galaxy/tree/release_15.05

We are still stabilizing 15.05 and not all bug fixes have been committed, but it may be the best option if you need to get past this problem quickly.

If you're unable to do one of the above or are still having issues after doing one of them, let me know and we can work on it further.

Carl


On Mon, Apr 27, 2015 at 4:28 AM, Jose Juan Almagro Armenteros <[hidden email]> wrote:
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 <[hidden email]>:
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 <[hidden email]> 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 <[hidden email]>:
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": "[hidden email]",
    "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

___________________________________________________________
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:
  https://lists.galaxyproject.org/

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:
  https://lists.galaxyproject.org/

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:
  https://lists.galaxyproject.org/

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

Re: Fwd: History panel error

Jose Juan Almagro Armenteros
Hi again,

Okay, it is not empty. I was checking the content of the table wrongly, so everything is okay. Sorry for inconvenience and thanks a lot for your help.

Regards,

Jose

2015-04-28 1:12 GMT+02:00 Dannon Baker <[hidden email]>:
Jose,

Regarding the job table being empty -- how exactly are you checking this?  This table should never be empty (except in the case of a *brand new* galaxy instance) and I cannot think of anything that would cause it to be so.  The log detailing the execution of a job looks totally fine to me.

-Dannon

On Mon, Apr 27, 2015 at 7:02 PM Jose Juan Almagro Armenteros <[hidden email]> wrote:
Hello Carl,

I can wait until the next stable release, my Galaxy distribution is working correctly even though the job table in the database is always empty. This table was used to detect job errors by running a cron job that sends an email. Do you know if there is another way of doing this?

Thank you!

Regards,

Jose

2015-04-27 20:46 GMT+02:00 Carl Eberhard <[hidden email]>:
Hi, Jose

Our next cycle includes some updates to the resubmission/hda-serialization code that's mentioned in your stack trace.

You can try two things:
1) You can wait for us to officially publish our next stable release (15.05) at the beginning of next month and then update your instance.
2) You can update *now* to the github version that *will be* our 15.05 release: https://github.com/galaxyproject/galaxy/tree/release_15.05

We are still stabilizing 15.05 and not all bug fixes have been committed, but it may be the best option if you need to get past this problem quickly.

If you're unable to do one of the above or are still having issues after doing one of them, let me know and we can work on it further.

Carl


On Mon, Apr 27, 2015 at 4:28 AM, Jose Juan Almagro Armenteros <[hidden email]> wrote:
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 <[hidden email]>:
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 <[hidden email]> 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 <[hidden email]>:
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": "[hidden email]",
    "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

___________________________________________________________
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:
  https://lists.galaxyproject.org/

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:
  https://lists.galaxyproject.org/

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:
  https://lists.galaxyproject.org/

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

Re: Fwd: History panel error

Dannon Baker-2
Ok, whew, that's a relief!  I'm glad you figured it out, and that the rest of your issues should be resolved with the next release.

-Dannon

On Mon, Apr 27, 2015 at 7:26 PM Jose Juan Almagro Armenteros <[hidden email]> wrote:
Hi again,

Okay, it is not empty. I was checking the content of the table wrongly, so everything is okay. Sorry for inconvenience and thanks a lot for your help.

Regards,

Jose

2015-04-28 1:12 GMT+02:00 Dannon Baker <[hidden email]>:
Jose,

Regarding the job table being empty -- how exactly are you checking this?  This table should never be empty (except in the case of a *brand new* galaxy instance) and I cannot think of anything that would cause it to be so.  The log detailing the execution of a job looks totally fine to me.

-Dannon

On Mon, Apr 27, 2015 at 7:02 PM Jose Juan Almagro Armenteros <[hidden email]> wrote:
Hello Carl,

I can wait until the next stable release, my Galaxy distribution is working correctly even though the job table in the database is always empty. This table was used to detect job errors by running a cron job that sends an email. Do you know if there is another way of doing this?

Thank you!

Regards,

Jose

2015-04-27 20:46 GMT+02:00 Carl Eberhard <[hidden email]>:
Hi, Jose

Our next cycle includes some updates to the resubmission/hda-serialization code that's mentioned in your stack trace.

You can try two things:
1) You can wait for us to officially publish our next stable release (15.05) at the beginning of next month and then update your instance.
2) You can update *now* to the github version that *will be* our 15.05 release: https://github.com/galaxyproject/galaxy/tree/release_15.05

We are still stabilizing 15.05 and not all bug fixes have been committed, but it may be the best option if you need to get past this problem quickly.

If you're unable to do one of the above or are still having issues after doing one of them, let me know and we can work on it further.

Carl


On Mon, Apr 27, 2015 at 4:28 AM, Jose Juan Almagro Armenteros <[hidden email]> wrote:
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 <[hidden email]>:
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 <[hidden email]> 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 <[hidden email]>:
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": "[hidden email]",
    "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

___________________________________________________________
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:
  https://lists.galaxyproject.org/

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:
  https://lists.galaxyproject.org/

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:
  https://lists.galaxyproject.org/

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