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
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
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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participants (2)
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Jose Juan Almagro Armenteros