Dear Hans,

>> "/****/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py",
>> line 42, in _load
>> data = list(result)[0]
>> IndexError: list index out of range

This error is because SQLAlchemy cannot load the controlled schema
version info from the DB, the result is empty, so I think its trying
to load the migrate_version and migrate_tools tables.  Make sure the
tables look like this hopefully they have each one row of data like
this:

mysql> select * from migrate_version;
+---------------+--------------------------+---------+
| repository_id | repository_path          | version |
+---------------+--------------------------+---------+
| Galaxy        | lib/galaxy/model/migrate |      93 |
+---------------+--------------------------+---------+
1 row in set (0.01 sec)

mysql> select * from migrate_tools;
+---------------+------------------------------+---------+
| repository_id | repository_path              | version |
+---------------+------------------------------+---------+
| GalaxyTools   | lib/galaxy/tool_shed/migrate |       1 |
+---------------+------------------------------+---------+
1 row in set (0.01 sec)

hth,
Leandro

On Tue, Apr 24, 2012 at 4:09 PM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:
> Hi everybody
>
> I usually don't like people sending the same e-mail several times, so I
> apologize for just doing this, since nobody has replied to last week's email
> so far.
>
> Although, we do not encounter any problems at the moment, I fear we will run
> into problems at a later stage (ie at the next code update). This is our
> production server.
>
> Thank you very much for any help
>
> Regards, Hans
>
>
>
>
> On 04/16/2012 03:43 PM, Hans-Rudolf Hotz wrote:
>>
>> Hi
>>
>> We are in the process of migrating our Galaxy servers to the current
>> "March 12, 2012" release ('6799:40f1816d6857').
>>
>> We have encountered two issues, which I guess are related:
>>
>>
>> If I restart the server, I get:
>>
>>
>> galaxy.model.migrate.check INFO 2012-04-16 09:24:50,391 At database
>> version 93
>> galaxy.tool_shed.migrate.check DEBUG 2012-04-16 09:24:50,407
>> MySQL_python egg successfully loaded for mysql dialect
>> Traceback (most recent call last):
>> File "/****/galaxy_dist/lib/galaxy/web/buildapp.py", line 82, in
>> app_factory
>> app = UniverseApplication( global_conf = global_conf, **kwargs )
>> File "/****/galaxy_dist/lib/galaxy/app.py", line 37, in __init__
>> verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
>> '__file__', None ), self.config.database_engine_options )
>> File "/****/galaxy_dist/lib/galaxy/tool_shed/migrate/check.py", line 42,
>> in verify_tools
>> db_schema = schema.ControlledSchema( engine, migrate_repository )
>> File
>>
>> "/****/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py",
>> line 24, in __init__
>> self._load()
>> File
>>
>> "/****/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py",
>> line 42, in _load
>> data = list(result)[0]
>> IndexError: list index out of range
>>
>>
>>
>> I can 'temporary' fix this by commenting-out line 36 and 37 in
>> ~/lib/galaxy/app.py
>>
>> 36# from galaxy.tool_shed.migrate.check import verify_tools
>> 37# verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
>> '__file__', None ), self.config.database_engine_options )
>>
>>
>> ...well, I don't like this fix, and I wonder if there is a better one?
>>
>>
>>
>> I have a suspicion, that this is related to problems I encountered
>> during the database schema upgrade to version 93 for our MySQL database:
>>
>> at step "90to91" and "91to92" I get the following:
>>
>>
>> 90 -> 91...
>>
>> Migration script to create the tool_version and tool_version_association
>> tables and drop the tool_id_guid_map table.
>>
>> 0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,719 Creating
>> tool_version table failed: (OperationalError) (1050, "Table
>> 'tool_version' already exists") u'\nCREATE TABLE tool_version (\n\tid
>> INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME,
>> \n\tupdate_time DATETIME, \n\ttool_id VARCHAR(255),
>> \n\ttool_shed_repository_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN
>> KEY(tool_shed_repository_id) REFERENCES tool_shed_repository
>> (id)\n)\n\n' ()
>> 0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,719 Creating
>> tool_version table failed: (OperationalError) (1050, "Table
>> 'tool_version' already exists") u'\nCREATE TABLE tool_version (\n\tid
>> INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME,
>> \n\tupdate_time DATETIME, \n\ttool_id VARCHAR(255),
>> \n\ttool_shed_repository_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN
>> KEY(tool_shed_repository_id) REFERENCES tool_shed_repository
>> (id)\n)\n\n' ()
>> 0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,720 Creating
>> tool_version_association table failed: (OperationalError) (1050, "Table
>> 'tool_version_association' already exists") u'\nCREATE TABLE
>> tool_version_association (\n\tid INTEGER NOT NULL AUTO_INCREMENT,
>> \n\ttool_id INTEGER NOT NULL, \n\tparent_id INTEGER NOT NULL,
>> \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_id) REFERENCES tool_version
>> (id), \n\t FOREIGN KEY(parent_id) REFERENCES tool_version (id)\n)\n\n' ()
>> 0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,720 Creating
>> tool_version_association table failed: (OperationalError) (1050, "Table
>> 'tool_version_association' already exists") u'\nCREATE TABLE
>> tool_version_association (\n\tid INTEGER NOT NULL AUTO_INCREMENT,
>> \n\ttool_id INTEGER NOT NULL, \n\tparent_id INTEGER NOT NULL,
>> \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_id) REFERENCES tool_version
>> (id), \n\t FOREIGN KEY(parent_id) REFERENCES tool_version (id)\n)\n\n' ()
>> Added 0 rows to the new tool_version table.
>> done
>> 91 -> 92...
>>
>> Migration script to create the migrate_tools table.
>>
>> 0092_add_migrate_tools_table DEBUG 2012-04-16 08:55:49,920 Creating
>> migrate_tools table failed: (OperationalError) (1050, "Table
>> 'migrate_tools' already exists") u'\nCREATE TABLE migrate_tools
>> (\n\trepository_id VARCHAR(255), \n\trepository_path TEXT, \n\tversion
>> INTEGER\n)\n\n' ()
>> 0092_add_migrate_tools_table DEBUG 2012-04-16 08:55:49,920 Creating
>> migrate_tools table failed: (OperationalError) (1050, "Table
>> 'migrate_tools' already exists") u'\nCREATE TABLE migrate_tools
>> (\n\trepository_id VARCHAR(255), \n\trepository_path TEXT, \n\tversion
>> INTEGER\n)\n\n' ()
>> done
>>
>>
>> the bizarre thing is, all three tables: 'migrate_tools',
>> 'tool_version_association','tool_version' are present.....well, this
>> explains the error: 'OperationalError 1050, "Table 'migrate_tools'
>> already exists" '....but why were the commands executed a second and
>> third time? - what happened during the first execution?
>>
>>
>> I can execute the three create statements without problems in a dummy
>> database on the same MySQl server (Server version: 5.1.41-3ubuntu12.10)
>>
>> and if I compare the "describe migrate_tools" outcome for the real
>> database (galaxy_xenon1) and the dummy database (galaxy_xenon1_old), I
>> don't see a difference and it corresponds to the 'create statement'
>>
>>
>>
>> mysql> describe galaxy_xenon1.migrate_tools;
>> +-----------------+--------------+------+-----+---------+-------+
>> | Field | Type | Null | Key | Default | Extra |
>> +-----------------+--------------+------+-----+---------+-------+
>> | repository_id | varchar(255) | YES | | NULL | |
>> | repository_path | text | YES | | NULL | |
>> | version | int(11) | YES | | NULL | |
>> +-----------------+--------------+------+-----+---------+-------+
>> 3 rows in set (0.00 sec)
>>
>> mysql> describe galaxy_xenon1_old.migrate_tools;
>> +-----------------+--------------+------+-----+---------+-------+
>> | Field | Type | Null | Key | Default | Extra |
>> +-----------------+--------------+------+-----+---------+-------+
>> | repository_id | varchar(255) | YES | | NULL | |
>> | repository_path | text | YES | | NULL | |
>> | version | int(11) | YES | | NULL | |
>> +-----------------+--------------+------+-----+---------+-------+
>> 3 rows in set (0.00 sec)
>>
>> mysql>
>>
>>
>> Has anybody seen similar issues or can shed some light on our problems?
>>
>>
>>
>> Thank you very much for your help
>>
>> Hans
>>
>>
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