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. original error when upgrading from 108 with the now broken version: 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. On Tue, Jul 2, 2013 at 12:28 PM, Lee Katz <lskatz@gmail.com> wrote:
Thanks! I did hg pull -u. For the database, I downgraded to 108 and then upgraded again but got this error when upgrading. Is it due to the Ubuntu bug? Or something else? Should I be sticking with a particular Hg version instead of the latest?
$ sh manage_db.sh upgrade 115 -> 116...
Tables for a next generation sequencing lims tied to requests.
/home/galaxy/bin/chapman-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/dialects/sqlite/base.py:723: SAWarning: Did not recognize type 'BIGINT' of column 'bytes' 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_existing=True' to redefine options and columns on an existing Table object.
On Tue, Jul 2, 2013 at 10:59 AM, Dannon Baker <dannon.baker@gmail.com>wrote:
On Mon, Jul 1, 2013 at 8:34 PM, Brad Chapman <chapmanb@50mail.com> wrote:
This was a typo in the downgrade function for one of the patches. I pushed a fix so if you update from bitbucket things should work smoothly again (once we get to problem 2 below).
For anyone with galaxy-dist commit privileges, here's the one liner:
https://bitbucket.org/chapmanb/galaxy-central/commits/463852762a6eeadcf17731...
Thanks Brad, added to stable branch in https://bitbucket.org/galaxy/galaxy-central/commits/0a06df7da177a204c7f3800e...
-- Lee Katz, Ph.D.
-- Lee Katz, Ph.D.