Question: local galaxy instance sqlite3.OperationError
0
gravatar for yychangsd
17 months ago by
yychangsd30
yychangsd30 wrote:

Hi,

I'd like to install a local galaxy.

After git clone the release_17.0,

I use sh run.sh to start the galaxy.

But I got an error like this:

migrate.versioning.repository DEBUG 2017-05-19 09:41:03,875 Repository lib/galaxy/model/migrate loaded successfully
migrate.versioning.repository DEBUG 2017-05-19 09:41:03,875 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))])
/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:298: SAWarning: Exception attempting to detect unicode returns: OperationalError('(sqlite3.OperationalError) near "\xf1\x90\x81\x93\xf1\x90\x81\x8c\xf5\x80\x81\x83\xf0\xb0\x80\xa0\xf4\xb0\x81\x81\xfa\x80\x81\x94\xfd\x80\x80\xa7\xfc\xb0\x81\xa5\xf8\x80\x81\xb4\xfb\x80\x81\xb0\xfa\x90\x81\xa1\xf8\x80\x81\xae\xf9\x90\x81\xb2\xfd\x90\x81\xb4\xfb\xa0\x81\xb2\xf9\xb0\x81\xb3\xf0\x90\x80\xa0\xf8\x80\x81\x93\xf0\x90\x81\x96\xf0\xb0\x81\x92\xf0\x90\x81\x88\xfa\x80\x81\x92\xfc\x80\x80\xb6\xfa\x90\x80\xa9\xf0\x90\x80\xa0\xf8\x80\x81\x93\xfb\xa0\x81\xa1\xfb\xa0\x81\xaf\xfc\x90\x81\x9f": syntax error',)
  "detect unicode returns: %r" % de)
/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:298: SAWarning: Exception attempting to detect unicode returns: OperationalError('(sqlite3.OperationalError) near "\xf1\x90\x81\x93\xf1\x90\x81\x8c\xf5\x80\x81\x83\xf0\xb0\x80\xa0\xf4\xb0\x81\x81\xfa\x80\x81\x94\xfd\x80\x80\xa7\xfc\xb0\x81\xa5\xf8\x80\x81\xb4\xfb\xa0\x81\xb5\xf8\xb0\x81\xa9\xf9\x80\x81\xaf\xf8\x80\x81\xa5\xf9\x90\x81\xb2\xfd\x90\x81\xb4\xfb\xa0\x81\xb2\xf9\xb0\x81\xb3\xf0\x90\x80\xa0\xf8\x80\x81\x93\xf0\x90\x81\x96\xf0\xb0\x81\x92\xf0\x90\x81\x88\xfa\x80\x81\x92\xfc\x80\x80\xb6\xfa\x90\x80\xa9\xf0\x90\x80\xa0\xf8\x80\x81\x93\xfb\xa0\x81\xa1\xfb\xa0\x81\xaf\xfc\x90\x81\x9f": syntax error',)
  "detect unicode returns: %r" % de)
Traceback (most recent call last):
  File "/home/oasis/gordon-data/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 55, in paste_app_factory
    app = galaxy.app.UniverseApplication( global_conf=global_conf, **kwargs )
  File "/home/oasis/gordon-data/galaxy/lib/galaxy/app.py", line 65, in __init__
    self._configure_models( check_migrate_databases=True, check_migrate_tools=check_migrate_tools, config_file=config_file )
  File "/home/oasis/gordon-data/galaxy/lib/galaxy/config.py", line 1021, in _configure_models
    create_or_verify_database( db_url, config_file, self.config.database_engine_options, app=self )
  File "/home/oasis/gordon-data/galaxy/lib/galaxy/model/migrate/check.py", line 50, in create_or_verify_database
    Table( "dataset", meta, autoload=True )
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/schema.py", line 440, in __new__
    metadata._remove_table(name, schema)
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
    compat.reraise(exc_type, exc_value, exc_tb)
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/schema.py", line 435, in __new__
    table._init(name, metadata, *args, **kw)
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/schema.py", line 510, in _init
    self._autoload(metadata, autoload_with, include_columns)
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/schema.py", line 534, in _autoload
    self, include_columns, exclude_columns
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1971, in run_callable
    with self.contextual_connect() as conn:
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
    self._wrap_pool_connect(self.pool.connect, None),
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
    e, dialect, self)
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
    exc_info
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
    reraise(type(exception), exception, tb=exc_tb, cause=cause)
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
    return fn()
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
    return _ConnectionFairy._checkout(self)
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
    fairy = _ConnectionRecord.checkout(pool)
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/pool.py", line 480, in checkout
    rec = pool._do_get()
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/pool.py", line 1151, in _do_get
    return self._create_connection()
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/pool.py", line 323, in _create_connection
    return _ConnectionRecord(self)
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/pool.py", line 454, in __init__
    exec_once(self.connection, self)
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/event/attr.py", line 246, in exec_once
    self(*args, **kw)
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/event/attr.py", line 256, in __call__
    fn(*args, **kw)
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 1319, in go
    return once_fn(*arg, **kw)
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 165, in first_connect
    dialect.initialize(c)
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 256, in initialize
    self._check_unicode_description(connection):
  File "/home/oasis/gordon-data/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 343, in _check_unicode_description
    ]).compile(dialect=self)
OperationalError: (sqlite3.OperationalError) near "񐁓񐁌????????????𐀠????????????????????????": syntax error

Any help would be greatly appreciated~~

Thanks.

galaxy • 450 views
ADD COMMENTlink written 17 months ago by yychangsd30

This seems like your system has trouble creating the sqlite database. Can you try using PostgreSQL instead? See this on how to do this.

ADD REPLYlink written 17 months ago by Martin Čech ♦♦ 4.9k
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