Problem after updating to v0.11 kolibri

Good day,

I ran an update today, and kolibri stopped working throwing out a bunch of issues: (I will attach the kolibri.log and server.log file in the morning.

Please see a copy and paste from the terminal window:

After running an upgrade on Ubuntu, kolibri updated to v0.11.0:
Commands run: kolibri status && kolibri

kolibri@tsp:~$ kolibri start
INFO Running Kolibri with the following settings: kolibri.deployment.default.settings.base
INFO Sqlite database Vacuum finished.
INFO Running update routines for new version…

0 static files copied to ‘/var/kolibri/.kolibri/static’, 770 unmodified.
Operations to perform:
Apply all migrations: admin, auth, content, contenttypes, device, discovery, exams, kolibriauth, lessons, logger, morango, sessions
Running migrations:
No migrations to apply.
Installed 2 object(s) from 1 fixture(s)
INFO Importing ContentTag data
INFO Importing ContentNode_tags data
INFO Importing ContentNode_related data
INFO Importing ContentNode_has_prerequisite data
INFO Importing ContentNode data
INFO Importing Language data
INFO Importing File data
INFO Importing LocalFile data
INFO Importing AssessmentMetaData data
Traceback (most recent call last):
File “/usr/lib/python3/dist-packages/kolibri/dist/sqlalchemy/engine/base.py”, line 1193, in _execute_context
context)
File “/usr/lib/python3/dist-packages/kolibri/dist/sqlalchemy/engine/default.py”, line 509, in do_execute
cursor.execute(statement, parameters)
sqlite3.DatabaseError: database disk image is malformed

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File “/usr/bin/kolibri”, line 9, in
load_entry_point(‘kolibri==0.11.0’, ‘console_scripts’, ‘kolibri’)()
File “/usr/lib/python3/dist-packages/kolibri/utils/cli.py”, line 664, in main
start(port, daemon=daemon)
File “/usr/lib/python3/dist-packages/kolibri/utils/cli.py”, line 273, in start
update()
File “/usr/lib/python3/dist-packages/kolibri/utils/cli.py”, line 253, in update
update_channel_metadata()
File “/usr/lib/python3/dist-packages/kolibri/core/content/utils/annotation.py”, line 46, in update_channel_metadata
import_channel_from_local_db(channel_id)
File “/usr/lib/python3/dist-packages/kolibri/core/content/utils/channel_import.py”, line 675, in import_channel_from_local_db
import_manager.import_channel_data()
File “/usr/lib/python3/dist-packages/kolibri/core/content/utils/channel_import.py”, line 522, in import_channel_data
raise e
File “/usr/lib/python3/dist-packages/kolibri/core/content/utils/channel_import.py”, line 513, in import_channel_data
unflushed_rows = self.table_import(model, row_mapper, table_mapper, unflushed_rows)
File “/usr/lib/python3/dist-packages/kolibri/core/content/utils/channel_import.py”, line 371, in table_import
result = self.raw_attached_sqlite_table_import(model, row_mapper, table_mapper, unflushed_rows)
File “/usr/lib/python3/dist-packages/kolibri/core/content/utils/channel_import.py”, line 292, in raw_attached_sqlite_table_import
self.destination.session.execute(text(query))
File “/usr/lib/python3/dist-packages/kolibri/dist/sqlalchemy/orm/session.py”, line 1176, in execute
bind, close_with_result=True).execute(clause, params or {})
File “/usr/lib/python3/dist-packages/kolibri/dist/sqlalchemy/engine/base.py”, line 948, in execute
return meth(self, multiparams, params)
File “/usr/lib/python3/dist-packages/kolibri/dist/sqlalchemy/sql/elements.py”, line 269, in _execute_on_connection
return connection._execute_clauseelement(self, multiparams, params)
File “/usr/lib/python3/dist-packages/kolibri/dist/sqlalchemy/engine/base.py”, line 1060, in _execute_clauseelement
compiled_sql, distilled_params
File “/usr/lib/python3/dist-packages/kolibri/dist/sqlalchemy/engine/base.py”, line 1200, in _execute_context
context)
File “/usr/lib/python3/dist-packages/kolibri/dist/sqlalchemy/engine/base.py”, line 1413, in _handle_dbapi_exception
exc_info
File “/usr/lib/python3/dist-packages/kolibri/dist/sqlalchemy/util/compat.py”, line 265, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File “/usr/lib/python3/dist-packages/kolibri/dist/sqlalchemy/util/compat.py”, line 248, in reraise
raise value.with_traceback(tb)
File “/usr/lib/python3/dist-packages/kolibri/dist/sqlalchemy/engine/base.py”, line 1193, in _execute_context
context)
File “/usr/lib/python3/dist-packages/kolibri/dist/sqlalchemy/engine/default.py”, line 509, in do_execute
cursor.execute(statement, parameters)
sqlalchemy.exc.DatabaseError: (sqlite3.DatabaseError) database disk image is malformed [SQL: ‘REPLACE INTO content_assessmentmetadata (id, assessment_item_ids, number_of_assessments, mastery_model, randomize, is_manipulable, contentnode_id) SELECT source.id, source.assessment_item_ids, source.number_of_assessments, source.mastery_model, source.randomize, source.is_manipulable, source.contentnode_id FROM sourcedb.content_assessmentmetadata AS source’] (Background on this error at: http://sqlalche.me/e/4xp6)
kolibri@tsp:~$ kolibri status
INFO Running Kolibri with the following settings: kolibri.deployment.default.settings.base
Stopped (1)
kolibri@tsp:~$ kolibri@tsp:~$
kolibri@tsp:~$: command not found
kolibri@tsp:~$ pwd
/var/kolibri
kolibri@tsp:~$ cd .kolibri/
kolibri@tsp:~/.kolibri$ ls
backups debug.log job_storage.sqlite3-wal server.log
content job_storage.sqlite3 kolibri.log sessions
db.sqlite3 job_storage.sqlite3-shm kolibri_settings.json static
strong text

Hi @Bryan_Fisher -

Are you still having an issue here? It looks like this might be related to your other post? Manually verify import content on database file

thanks

Hi @devon,

Thank you for following up. Yes this “http://community.learningequality.org/t/manually-verify-import-content-on-database-file/89” does seem to be related. I think it was a long night that night :slight_smile:

The issue is resolved yes, after re-imaging our server. and running updates again.

Thanks so much for your support.