Actually I didn't notice that I had an error in 114->115 in addition to 115->116 (below).
So actually I just deleted the whole database, checked out a fresh version with hg, upgraded, upgraded the database with manage_db, and then ran the add_defaults script for nglims. Everything works and is fine, except I lost all my data. The entire nglims directory is backed up, but I don't have any way of retrieving the data easily in the working version. Do I need to remake all my groups, workflows, roles, and users? Actual analyses were all just test cases.
112 -> 113...
Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate.
done
113 -> 114...
Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate.
done
114 -> 115...
Altering password column failed
Traceback (most recent call last):
File "lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py", line 15, in upgrade
user.c.password.alter(type=String(255))
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/schema.py", line 491, in alter
return alter_column(self, *p, **k)
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/schema.py", line 136, in alter_column
engine._run_visitor(visitorcallable, delta)
File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 2302, in _run_visitor
conn._run_visitor(visitorcallable, element, **kwargs)
File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1972, in _run_visitor
**kwargs).traverse_single(element)
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/ansisql.py", line 53, in traverse_sing le
ret = super(AlterTableVisitor, self).traverse_single(elem)
File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/visitors.py", line 106, in traverse_single
return meth(obj, **kw)
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/databases/sqlite.py", line 53, in visi t_column
self.recreate_table(table,column,delta)
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/databases/sqlite.py", line 36, in recr eate_table
self.execute()
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/ansisql.py", line 42, in execute
return self.connection.execute(self.buffer.getvalue())
File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1449, in execute
params)
File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1628, in _execute_text
statement, parameters
File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1698, in _execute_context
context)
File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1691, in _execute_context
context)
File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line 331, in do_execute
cursor.execute(statement, parameters)
OperationalError: (OperationalError) there is already another table or index with this name: migration_tmp u'ALTER TABLE galaxy_user R ENAME TO migration_tmp' ()
done
115 -> 116...
Tables for a next generation sequencing lims tied to requests.
Traceback (most recent call last):
File "./scripts/manage_db.py", line 65, in <module>
main( repository=repo, url=db_url )
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/shell.py", line 207, in main
ret = command_func(**kwargs)
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py", line 186, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
File "<string>", line 2, in _migrate
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/util/__init__.py", line 159, in with_ engine
return f(*a, **kw)
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py", line 366, in _migrate
schema.runchange(ver, change, changeset.step)
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/schema.py", line 91, in runchange
change.run(self.engine, step)
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/script/py.py", line 145, in run
script_func(engine)
File "lib/galaxy/model/migrate/versions/0116_seq_lims.py", line 52, in upgrade
for table in _get_tables(metadata):
File "lib/galaxy/model/migrate/versions/0116_seq_lims.py", line 34, in _get_tables
primary_key = True),
File "build/bdist.linux-x86_64/egg/sqlalchemy/schema.py", line 305, in __new__
sqlalchemy.exc.InvalidRequestError: Table 'sample_request_map' is already defined for this MetaData instance. Specify 'extend_existin g=True' to redefine options and columns on an existing Table object.
Error in sys.excepthook:
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/apport_python_hook.py", line 64, 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 65, in <module>
main( repository=repo, url=db_url )
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/shell.py", line 207, in main
ret = command_func(**kwargs)
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py", line 186, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
File "<string>", line 2, in _migrate
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/util/__init__.py", line 159, in with_ engine
return f(*a, **kw)
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py", line 366, in _migrate
schema.runchange(ver, change, changeset.step)
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/schema.py", line 91, in runchange
change.run(self.engine, step)
File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/script/py.py", line 145, in run
script_func(engine)
File "lib/galaxy/model/migrate/versions/0116_seq_lims.py", line 52, in upgrade
for table in _get_tables(metadata):
File "lib/galaxy/model/migrate/versions/0116_seq_lims.py", line 34, in _get_tables
primary_key = True),
File "build/bdist.linux-x86_64/egg/sqlalchemy/schema.py", line 305, in __new__
sqlalchemy.exc.InvalidRequestError: Table 'sample_request_map' is already defined for this MetaData instance. Specify 'extend_existin g=True' to redefine options and columns on an existing Table object.