[galaxy@cluster galaxy-dist]$ hg heads
changeset:   10416:97d020901403
branch:      stable
tag:         tip
user:        Carl Eberhard <carlfeberh...@gmail.com>
date:        Mon Sep 09 11:20:40 2013 -0400
summary:     Fix to dbkey select in library upload when 'unspecified' is
not in dbkey list

changeset:   10411:c42567f43aa7
user:        greg
date:        Mon Aug 19 13:19:56 2013 -0400
summary:     Filter invalid objects when generating the list of
repository_dependencies objects that are associated with a tool shed
repository installed into Galaxy.



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

> 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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