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.

(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.
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