Local Galaxy - An error occurred while updating with the server

Hello!

I have local installed Galaxy 19.05 on t3.2xlarge instance (8 CPU and 32Gb RAM) and sometimes when I try update page or follow to another job I get next error:

An error occurred while updating with the server. Please contact a Galaxy administrator if the problem persist.

For me only helps close and open new tab on browser, but this very uncomfortable.

Details of error:

{
“userAgent”: “Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/77.0.3865.120 Safari/537.36”,
“onLine”: true,
“version”: “19.05”,
“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”
},
“options”: {
“parse”: true,
“silent”: true,
“limit”: 500,
“offset”: 0,
“details”: “92b83968e0b52980”,
“traditional”: true,
“data”: {
“limit”: 500,
“offset”: 0,
“details”: “92b83968e0b52980”,
“order”: “hid”,
“v”: “dev”,
“q”: [
“deleted”,
“purged”,
“visible”
],
“qv”: [
“False”,
“False”,
“True”
]
},
“emulateHTTP”: false,
“emulateJSON”: false,
“textStatus”: “error”,
“errorThrown”: “Internal Server Error”
},
“url”: “http://18.130.115.156/api/histories/f597429621d6eb2b/contents?limit=500&offset=0&details=92b83968e0b52980&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True”,
“model”: [],
“user”: {
“id”: “f2db41e1fa331b3e”,
“username”: “administrator”,
“total_disk_usage”: 881918595,
“nice_total_disk_usage”: “841.1 MB”,
“quota_percent”: null,
“is_admin”: true,
“preferences”: {},
“tags_used”: [
“name:tissueA”,
“name:tissueB”
],
“deleted”: false,
“purged”: false,
“quota”: null
}
}

I use Nginx as frontend HTTP server and use SQL lite by default.

Thanks!

Log from journalctl:

Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: galaxy.web.framework.decorators ERROR 2019-10-22 10:16:26,345 [p:14873,w:1,m:0] [uWSGIWorker1Core3] Uncaught exception in exposed API method:
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: Traceback (most recent call last):
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: File “lib/galaxy/web/framework/decorators.py”, line 282, in decorator
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: rval = func(self, trans, *args, **kwargs)
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: File “lib/galaxy/webapps/galaxy/api/history_contents.py”, line 82, in index
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: return self.__index_v2(trans, history_id, **kwd)
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: File “lib/galaxy/webapps/galaxy/api/history_contents.py”, line 891, in __index_v2
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: user=trans.user, trans=trans, view=‘detailed’, **serialization_params))
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: File “lib/galaxy/managers/base.py”, line 692, in serialize_to_view
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: return self.serialize(item, all_keys, **context)
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: File “lib/galaxy/managers/hdas.py”, line 367, in serialize
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: return super(HDASerializer, self).serialize(hda, keys, user=user, **context)
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: File “lib/galaxy/managers/datasets.py”, line 604, in serialize
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: serialized = super(DatasetAssociationSerializer, self).serialize(dataset_assoc, keys, **context)
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: File “lib/galaxy/managers/base.py”, line 605, in serialize
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: returned[key] = self.serializers[key](item, key, **context)
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: File “lib/galaxy/managers/hdas.py”, line 374, in serialize_display_apps
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: for display_app in hda.get_display_applications(trans).values():
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: File “lib/galaxy/model/init.py”, line 2757, in get_display_applications
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: return self.datatype.get_display_applications_by_dataset(self, trans)
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: File “lib/galaxy/datatypes/data.py”, line 551, in get_display_applications_by_dataset
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: value = value.filter_by_dataset(dataset, trans)
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: File “lib/galaxy/datatypes/display_applications/application.py”, line 309, in filter_by_dataset
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: if link_value.filter_by_dataset(data, trans):
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: File “lib/galaxy/datatypes/display_applications/application.py”, line 95, in filter_by_dataset
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: if fill_template(filter_elem.text, context=context) != filter_elem.get(‘value’, ‘True’):
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: File “lib/galaxy/util/template.py”, line 91, in fill_template
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: raise first_exception or e
Oct 22 10:16:26 ip-172-31-13-19 run.sh[14713]: NotFound: cannot find ‘site_id’

I found this commit:

https://github.com/galaxyproject/galaxy/pull/8104

But this was merged to 19.09, I tried use it for my 19.05, but have the same error.

Maybe it helps to check the galaxy.log file, it can have more informative errors. It will be created if you start galaxy as a daemon (sh run.sh --daemon).

Thanks you for answer!

I noticed in log next line:

/srv/galaxy/.venv/local/lib/python2.7/site-packages/Cheetah/Compiler.py:1630: UserWarning:
You don’t have the C version of NameMapper installed! I’m disabling Cheetah’s useStackFrames option as it is painfully slow with the Python version of NameMapper. You should get a copy of Cheetah with compiled C version of NameMapper.
"\nYou don’t have the C version of NameMapper installed! "

So I installed cheetah3:

pip install cheetah3

And now it works well!

Thanks!