Some additional info;
Actually the errors already started at migrate version 93->94.
I just restored the version to prior upgrade to check any other errors. There
were some create errors. I am not sure if these come from the \n\t statements
in the sysntax or whether that is just an error log output thing only.
Bottom line is that some tables are not created. Some seem to already exist due
to the partial pass of the upgrade the previous time.
See log below;
Would it be possible to just create a fresh latest version database with no
data and then transfer the data of the backup I have into that?
Alex
=============================================
sudo sh manage_db.sh -c universe_wsgi.ini upgrade
93 -> 94...
Migration script to create "handler" column in job table.
(OperationalError) (1060, "Duplicate column name 'handler'") u'\nALTER TABLE
job ADD handler VARCHAR(255)' ()
done
94 -> 95...
Migration script to create table for tracking history_dataset_association
subsets.
(OperationalError) (1005, "Can't create table
'galaxy_dist.history_dataset_association_subset' (errno: 150)") u'\nCREATE
TABLE history_dataset_association_subset (\n\tid INTEGER NOT NULL
AUTO_INCREMENT, \n\thistory_dataset_association_id INTEGER,
\n\thistory_dataset_association_subset_id INTEGER, \n\tlocation VARCHAR(255),
\n\tPRIMARY KEY (id), \n\t FOREIGN KEY(history_dataset_association_id)
REFERENCES history_dataset_association (id), \n\t FOREIGN
KEY(history_dataset_association_subset_id) REFERENCES
history_dataset_association (id)\n)\n\n' ()
(ProgrammingError) (1146, "Table
'galaxy_dist.history_dataset_association_subset' doesn't exist") 'CREATE INDEX
ix_hda_id ON history_dataset_association_subset
(history_dataset_association_id)' ()
done
95 -> 96...
Migration script to add column to openid table for provider.
Remove any OpenID entries with nonunique GenomeSpace Identifier
Adding provider column to galaxy_user_openid table failed: (OperationalError)
(1060, "Duplicate column name 'provider'") u'\nALTER TABLE galaxy_user_openid
ADD provider VARCHAR(255)' ()
done
96 -> 97...
Migration script to add the ctx_rev column to the tool_shed_repository table.
Adding ctx_rev column to the tool_shed_repository table failed:
(OperationalError) (1060, "Duplicate column name 'ctx_rev'") u'\nALTER TABLE
tool_shed_repository ADD ctx_rev VARCHAR(10)' ()
done
97 -> 98...
Migration script to create the genome_index_tool_data table.
0098_genome_index_tool_data_table DEBUG 2012-10-12 11:27:46,128 Creating
genome_index_tool_data table failed: (OperationalError) (1005, "Can't create
table 'galaxy_dist.genome_index_tool_data' (errno: 150)") u'\nCREATE TABLE
genome_index_tool_data (\n\tid INTEGER NOT NULL AUTO_INCREMENT, \n\tjob_id
INTEGER, \n\tdataset_id INTEGER, \n\tdeferred_job_id INTEGER,
\n\ttransfer_job_id INTEGER, \n\tfasta_path VARCHAR(255), \n\tcreated_time
DATETIME, \n\tmodified_time DATETIME, \n\tindexer VARCHAR(64), \n\tuser_id
INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(dataset_id) REFERENCES dataset
(id), \n\t FOREIGN KEY(transfer_job_id) REFERENCES transfer_job (id), \n\t
FOREIGN KEY(user_id) REFERENCES galaxy_user (id), \n\t FOREIGN
KEY(deferred_job_id) REFERENCES deferred_job (id), \n\t FOREIGN KEY(job_id)
REFERENCES job (id)\n)\n\n' ()
0098_genome_index_tool_data_table DEBUG 2012-10-12 11:27:46,128 Creating
genome_index_tool_data table failed: (OperationalError) (1005, "Can't create
table 'galaxy_dist.genome_index_tool_data' (errno: 150)") u'\nCREATE TABLE
genome_index_tool_data (\n\tid INTEGER NOT NULL AUTO_INCREMENT, \n\tjob_id
INTEGER, \n\tdataset_id INTEGER, \n\tdeferred_job_id INTEGER,
\n\ttransfer_job_id INTEGER, \n\tfasta_path VARCHAR(255), \n\tcreated_time
DATETIME, \n\tmodified_time DATETIME, \n\tindexer VARCHAR(64), \n\tuser_id
INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(dataset_id) REFERENCES dataset
(id), \n\t FOREIGN KEY(transfer_job_id) REFERENCES transfer_job (id), \n\t
FOREIGN KEY(user_id) REFERENCES galaxy_user (id), \n\t FOREIGN
KEY(deferred_job_id) REFERENCES deferred_job (id), \n\t FOREIGN KEY(job_id)
REFERENCES job (id)\n)\n\n' ()
done
98 -> 99...
Migration script to add the tool_dependency table.
0099_add_tool_dependency_table DEBUG 2012-10-12 11:27:46,268 Creating
tool_dependency table failed: (OperationalError) (1005, "Can't create table
'galaxy_dist.tool_dependency' (errno: 150)") u'\nCREATE TABLE tool_dependency
(\n\tid INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME,
\n\tupdate_time DATETIME, \n\ttool_shed_repository_id INTEGER NOT NULL,
\n\tinstalled_changeset_revision VARCHAR(255), \n\tname VARCHAR(255),
\n\tversion VARCHAR(40), \n\ttype VARCHAR(40), \n\tuninstalled BOOL,
\n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_shed_repository_id) REFERENCES
tool_shed_repository (id)\n)\n\n' ()
0099_add_tool_dependency_table DEBUG 2012-10-12 11:27:46,268 Creating
tool_dependency table failed: (OperationalError) (1005, "Can't create table
'galaxy_dist.tool_dependency' (errno: 150)") u'\nCREATE TABLE tool_dependency
(\n\tid INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME,
\n\tupdate_time DATETIME, \n\ttool_shed_repository_id INTEGER NOT NULL,
\n\tinstalled_changeset_revision VARCHAR(255), \n\tname VARCHAR(255),
\n\tversion VARCHAR(40), \n\ttype VARCHAR(40), \n\tuninstalled BOOL,
\n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_shed_repository_id) REFERENCES
tool_shed_repository (id)\n)\n\n' ()
done
99 -> 100...
Migration script to alter the type of the tool_dependency.version column from
TrimmedString(40) to Text.
Traceback (most recent call last):
File "./scripts/manage_db.py", line 63, in <module>
main( repository=repo, url=db_url )
File
"/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/shell.py",
line 150, in main
ret = command_func(**kwargs)
File
"/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/api.py",
line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
File
"/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/api.py",
line 349, in _migrate
schema.runchange(ver, change, changeset.step)
File
"/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/schema.py",
line 184, in runchange
change.run(self.engine, step)
File
"/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/script/py.py",
line 101, in run
func()
File
"lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py",
line 30, in upgrade
ToolDependency_table = Table( "tool_dependency", metadata, autoload=True )
File
"/opt/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/schema.py",
line 108, in __call__
return type.__call__(self, name, metadata, *args, **kwargs)
File
"/opt/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/schema.py",
line 236, in __init__
_bind_or_error(metadata).reflecttable(self, include_columns=include_columns)
File
"/opt/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py",
line 1265, in reflecttable
self.dialect.reflecttable(conn, table, include_columns)
File
"/opt/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/databases/mysql.py",
line 1664, in reflecttable
sql = self._show_create_table(connection, table, charset)
File
"/opt/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/databases/mysql.py",
line 1835, in _show_create_table
raise exc.NoSuchTableError(full_name)
sqlalchemy.exc.NoSuchTableError: tool_dependency
Error in sys.excepthook:
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/apport_python_hook.py", line 66, in
apport_excepthook
from apport.fileutils import likely_packaged, get_recent_crashes
ImportError: No module named apport.fileutils
Original exception was:
Traceback (most recent call last):
File "./scripts/manage_db.py", line 63, in <module>
main( repository=repo, url=db_url )
File
"/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/shell.py",
line 150, in main
ret = command_func(**kwargs)
File
"/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/api.py",
line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
File
"/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/api.py",
line 349, in _migrate
schema.runchange(ver, change, changeset.step)
File
"/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/schema.py",
line 184, in runchange
change.run(self.engine, step)
File
"/opt/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/script/py.py",
line 101, in run
func()
File
"lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py",
line 30, in upgrade
ToolDependency_table = Table( "tool_dependency", metadata, autoload=True )
File
"/opt/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/schema.py",
line 108, in __call__
return type.__call__(self, name, metadata, *args, **kwargs)
File
"/opt/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/schema.py",
line 236, in __init__
_bind_or_error(metadata).reflecttable(self, include_columns=include_columns)
File
"/opt/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py",
line 1265, in reflecttable
self.dialect.reflecttable(conn, table, include_columns)
File
"/opt/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/databases/mysql.py",
line 1664, in reflecttable
sql = self._show_create_table(connection, table, charset)
File
"/opt/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/databases/mysql.py",
line 1835, in _show_create_table
raise exc.NoSuchTableError(full_name)
sqlalchemy.exc.NoSuchTableError: tool_dependency
======================================================
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