So,

I decided to completely drop the old galaxy psql database (I have a dump of
it) -
hogart# drop database galaxy;

and recreate it again -
[galaxy@cluster ~]$ creatdb

After the launching of the Galaxy it is terminated with the message with
requesting of upgrade the database, from 13 to 115. But the upgrading of
database scheme is also failed:
[galaxy@cluster galaxy-dist]$ sh manage_db.sh upgrade
/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/url.py:105:
SADeprecationWarning: The SQLAlchemy PostgreSQL dialect has been renamed
from 'postgres' to 'postgresql'. The new URL format is
postgresql[+driver]://<user>:<pass>@<host>/<dbname>
13 -> 14...

Migration script to add support for "Pages".
  1) Creates Page and PageRevision tables
  2) Adds username column to User table

Traceback (most recent call last):
  File "./scripts/manage_db.py", line 64, in <module>
    main( repository=repo, url=db_url )
  File
"/export/apps/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/shell.py",
line 207, in main
    ret = command_func(**kwargs)
  File
"/export/apps/galaxy/galaxy-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
"/export/apps/galaxy/galaxy-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
"/export/apps/galaxy/galaxy-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
"/export/apps/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/schema.py",
line 91, in runchange
    change.run(self.engine, step)
  File
"/export/apps/galaxy/galaxy-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/0014_pages.py", line 55, in
upgrade
    col.create( User_table, index_name='ix_user_username',
unique_name='username' )
  File
"/export/apps/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/schema.py",
line 528, in create
    engine._run_visitor(visitorcallable, self, connection, **kwargs)
  File
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
line 2302, in _run_visitor
  File
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
line 1972, in _run_visitor
  File
"/export/apps/galaxy/galaxy-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
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/sql/visitors.py",
line 106, in traverse_single
  File
"/export/apps/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/ansisql.py",
line 101, in visit_column
    self.execute()
  File
"/export/apps/galaxy/galaxy-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
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
line 1449, in execute
  File
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
line 1628, in _execute_text
  File
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
line 1698, in _execute_context
  File
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
line 1691, in _execute_context
  File
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/default.py",
line 331, in do_execute
sqlalchemy.exc.ProgrammingError: (ProgrammingError) column "username" of
relation "galaxy_user" already exists
 '\nALTER TABLE galaxy_user ADD username VARCHAR(255)' {}

Since, it was past release of Galaxy (release_2013.06.03), I pulled the
latest one and repeated the procedure, but the result was the same:

[galaxy@cluster galaxy-dist]$ sh run.sh
...
Exception: Your database has version '13' but this code expects version
'115'.  Please backup your database and then migrate the schema by running
'sh manage_db.sh upgrade'.
[galaxy@cluster galaxy-dist]$ sh manage_db.sh upgrade
/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/url.py:105:
SADeprecationWarning: The SQLAlchemy PostgreSQL dialect has been renamed
from 'postgres' to 'postgresql'. The new URL format is
postgresql[+driver]://<user>:<pass>@<host>/<dbname>
13 -> 14...

Migration script to add support for "Pages".
  1) Creates Page and PageRevision tables
  2) Adds username column to User table

Traceback (most recent call last):
  File "./scripts/manage_db.py", line 62, in <module>
    main( repository=repo, url=db_url )
  File
"/export/apps/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/shell.py",
line 207, in main
    ret = command_func(**kwargs)
  File
"/export/apps/galaxy/galaxy-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
"/export/apps/galaxy/galaxy-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
"/export/apps/galaxy/galaxy-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
"/export/apps/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/schema.py",
line 91, in runchange
    change.run(self.engine, step)
  File
"/export/apps/galaxy/galaxy-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/0014_pages.py", line 67, in
upgrade
    col.create( User_table, index_name='ix_user_username',
unique_name='username' )
  File
"/export/apps/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/schema.py",
line 528, in create
    engine._run_visitor(visitorcallable, self, connection, **kwargs)
  File
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
line 2302, in _run_visitor
  File
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
line 1972, in _run_visitor
  File
"/export/apps/galaxy/galaxy-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
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/sql/visitors.py",
line 106, in traverse_single
  File
"/export/apps/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/ansisql.py",
line 101, in visit_column
    self.execute()
  File
"/export/apps/galaxy/galaxy-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
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
line 1449, in execute
  File
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
line 1628, in _execute_text
  File
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
line 1698, in _execute_context
  File
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py",
line 1691, in _execute_context
  File
"/export/apps/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/default.py",
line 331, in do_execute
sqlalchemy.exc.ProgrammingError: (ProgrammingError) column "username" of
relation "galaxy_user" already exists
 '\nALTER TABLE galaxy_user ADD username VARCHAR(255)' {}

I will be gratefull for any help with this.


2013/9/11 hogart <dr.hog...@gmail.com>

> Dear all,
>
> I have succeffully installed the local instance of Galaxy, that uses the
> postgeSQL database, and it worked fine. After several monthes of uses, it
> appeared the neccessety to reinstall the whole Galaxy. For this, I have
> completely removed the old instance, and hg clone the new one to the same
> location. The psql database remains the same. After upgrading the database
> schema with the corresponding script, I have faced with inability of
> upgrading the counter of history in database. For example, after creating
> the new history, the addition of new dataset (by uploading via ftp, from
> local comp, from UCSC) result in the error:
>
> NotSupportedError: (NotSupportedError) DECLARE CURSOR ... FOR UPDATE/SHARE
> is not supported DETAIL:  Cursors must be READ ONLY.
>  'SELECT history.hid_counter \nFROM history \nWHERE history.id = %(id_1)s
> FOR UPDATE' {'id_1': 5}
>
> I will be very grateful with any help with this issue.
>
> galaxy=> \du
>                                List of roles
>  Role name | Superuser | Create role | Create DB | Connections | Member of
> -----------+-----------+-------------+-----------+-------------+-----------
>  galaxy    | no        | no          | yes       | no limit    |
>  hogart    | yes       | yes         | yes       | no limit    |
>  postgres  | yes       | yes         | yes       | no limit    |
> (3 rows)
>
>
> galaxy=> \l
>         List of databases
>    Name    |  Owner   | Encoding
> -----------+----------+----------
>  galaxy    | galaxy   | LATIN9
>  hogart    | hogart   | LATIN9
>  postgres  | postgres | LATIN9
>  template0 | postgres | LATIN9
>  template1 | postgres | LATIN9
> (5 rows)
>
> galaxy=> select * from history where history.id=5;
>  id |        create_time         |        update_time         | user_id |
>      n
> ame       | hid_counter | deleted | purged | genome_build | importable |
> slug |
> published | importing
>
> ----+----------------------------+----------------------------+---------+-------
>
> ----------+-------------+---------+--------+--------------+------------+------+-
> ----------+-----------
>   5 | 2013-09-10 21:38:31.888226 | 2013-09-10 21:38:31.888237 |       1 |
> Unname
> d history |           1 | f       | f      | ?            | f          |
>    |
> f         | f
> (1 row)
>
> psql -v 8.1.22
>
> - sincerely,
> Sergei
>
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