Hi Sergei,
Your current Galaxy database migration revision (13) is extremely old. How old
was your previous Galaxy installation, and are you certain that the dump you
created was complete, and fully restored?
To solve the original 'DECLARE CURSOR ... FOR UPDATE' problem, you'd need to
update your version of PostgreSQL. 8.1.x is also very old, 9.1 or 9.2 are
recommended.
--nate
On Sep 11, 2013, at 7:58 AM, hogart wrote:
> 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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