Thank you.  I feel like this next error might be my fault (I don't know
python very well).  I think it is saying that I don't have a module, but it
is installed via Ubuntu aptitude, so now I don't really know what to do
next.  I reinstalled the module like so: aptitude reinstall python-apport

$ sh manage_db.sh downgrade --version=108
112 -> 111...
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 202, in downgrade
    return _migrate(url, repository, version, upgrade=False, 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 142, in run
    raise TypeError("upgrade/downgrade functions must accept engine"
TypeError: upgrade/downgrade functions must accept engine parameter (since
version 0.5.4)
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 202, in downgrade
    return _migrate(url, repository, version, upgrade=False, 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 142, in run
    raise TypeError("upgrade/downgrade functions must accept engine"
TypeError: upgrade/downgrade functions must accept engine parameter (since
version 0.5.4)



On Mon, Jul 1, 2013 at 4:14 PM, Dannon Baker <siryopl...@gmail.com> wrote:

> It's that previous versions of sqlalchemy-migrate didn't clean up these
> tables under sqlite and didn't mind overwriting them if they existed, but
> the new version both does clean up after itself, and expects the table to
> not exist, failing miserably if it does.
>
> I think there's a Trello card for fixing this somewhere, but yes, the
> temporary workaround is to just drop the migration_tmp table if this
> happens and migrate again.
>
>
> On Jul 1, 2013, at 3:16 PM, Brad Chapman <chapm...@50mail.com> wrote:
>
> >
> > Lee;
> >
> >> Thanks Brad!  I updated with hg pull -u and then ran "sh manage_db.sh
> >> upgrade" but I have an error.  Could you help?  I backed up my database
> >> before I ran the upgrade script, so I can go back in time.
> >
> > I think there is something funky going on with the version of
> > SQLAlchemy-migrate currently in use in Galaxy, at least on SQLite
> > databases. It creates temporary tables but then they are not getting
> > cleaned up.
> >
> > The best fix is to reset yourself back to the original version (minus
> > 1 to take into account the LIMS tables):
> >
> > sh manage_db.sh downgrade --version=108
> >
> > Then redo the upgrade:
> >
> > sh manage_db.sh uprade
> >
> > Anytime you run into the intermittent error, you can manually fix with:
> >
> > $ sqlite3 database/universe.sqlite
> > sqlite> drop table migration_tmp;
> >
> > Keep your backup around and you can do this with the new version. Sorry
> > for the ugly hack but that was a reasonable workaround. There is some
> > discussion on the mailing list about this previously but I don't think
> > there was a good conclusion:
> >
> > http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014570.html
> >
> > Hope this cleans it up for you,
> > Brad
> >
> >>
> >> (sorry about the wall of text)
> >>
> >> 109 -> 110...
> >>
> /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'
> >>
> >> Add UUID column to dataset table
> >>
> >> done
> >> 110 -> 111...
> >>
> >> Add support for job destinations to the job table
> >>
> >> done
> >> 111 -> 112...
> >>
> >> Migration script to add the data_manager_history_association table and
> >> data_manager_job_association.
> >>
> >>
> 0112_add_data_manager_history_association_and_data_manager_job_association_tables
> >> DEBUG 2013-07-01 14:46:25,549 Created data_manager_history_association
> table
> >>
> 0112_add_data_manager_history_association_and_data_manager_job_association_tables
> >> DEBUG 2013-07-01 14:46:25,549 Created data_manager_history_association
> table
> >> Created data_manager_history_association table
> >>
> 0112_add_data_manager_history_association_and_data_manager_job_association_tables
> >> DEBUG 2013-07-01 14:46:25,890 Created data_manager_job_association table
> >>
> 0112_add_data_manager_history_association_and_data_manager_job_association_tables
> >> DEBUG 2013-07-01 14:46:25,890 Created data_manager_job_association table
> >> Created data_manager_job_association table
> >> done
> >> 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_single
> >>    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 visit_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 recreate_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 RENAME 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_existing=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_existing=True' to
> >> redefine options and columns on an existing Table object.
> >>
> >>
> >> On Mon, Jul 1, 2013 at 12:46 PM, Brad Chapman <chapm...@50mail.com>
> wrote:
> >>
> >>>
> >>> Lee;
> >>>
> >>>> Hi, I would like to remove the "multiplexed" menu from the nglims
> sample
> >>>> information form.  How would I do that?  In our lab, we don't want
> >>>> submitters making their own libraries since they might accidentally
> use
> >>> the
> >>>> same barcodes or somehow mess up others' libraries.  We want to remove
> >>> that
> >>>> option altogether.
> >>>
> >>> Good idea. I added a flag to the nglims.yaml file so you can specify
> >>> whether barcode multiplexing is available or not:
> >>>
> >>>
> >>>
> https://bitbucket.org/chapmanb/galaxy-central/src/62f7dc3864535e68af7aa2a7ef0c37e45eb9707a/tool-data/nglims.yaml?at=default#cl-97
> >>>
> >>> setting `available: false` will turn off the option for the user to
> >>> select and add this.
> >>>
> >>> If you update from the latest in bitbucket it will have this change. I
> >>> also synchronized with the most recent galaxy-dist, so an update will
> >>> pull in those changes as well.
> >>>
> >>>> Actually along the same lines, we would like to remove all "services
> >>>> needed" check boxes too and simply have all of the data entry on one
> >>> page.
> >>>
> >>> Moving to a single page entry would be a big change from the current
> >>> wizard approach. You can control what services are available by default
> >>> using the `default` flag in the nglims.yaml:
> >>>
> >>>
> >>>
> https://bitbucket.org/chapmanb/galaxy-central/src/62f7dc3864535e68af7aa2a7ef0c37e45eb9707a/tool-data/nglims.yaml?at=default#cl-133
> >>>
> >>> Currently sequencing is the only one selected by default but you can
> add
> >>> others if they're commonly used to make the submission process easier
> >>> for users.
> >>>
> >>> Hope this helps,
> >>> Brad
> >>>
> >>
> >>
> >>
> >> --
> >> Lee Katz, Ph.D.
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >  http://lists.bx.psu.edu/
> >
> > To search Galaxy mailing lists use the unified search at:
> >  http://galaxyproject.org/search/mailinglists/
>
>


-- 
Lee Katz, Ph.D.
___________________________________________________________
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