Hi Rob

Yes, this looks like an SQLAlchemy issue, producing an 'create index' statement which is not compatible with MySQL.



I guess line 146 in "~/lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py" is the culprit:

        Column( "annotation", TEXT, index=True) )



I don't know whether this works, but I would suggest you change that line to:
        
        Column( "annotation", TEXT) )

run it again. And then manually add the index by executing

CREATE INDEX ix_tool_annotation_association_annotation ON tool_annotation_association (annotation(100))

        

The problem is: MySQL can only index the first x characters of a BLOB or TEXT. Using the above suggested statement will create an index using the first 100 characters of the name column. See also:

http://dev.mysql.com/doc/refman/5.0/en/create-index.html



Regards, Hans-Rudolf




On 04/12/2013 08:24 AM, Rob Hooft wrote:
To ease the maintenance of our Dutch National galaxy, we're trying to
set up our own toolshed on a system that happens to have a nicely large
MySQL database running. We'd like to make it use that database. The
setup has been ok, until we started running the toolshed on the MySQL
server for the first time, which resulted in the message in the
community_webapp.log I copied below. Is this an incompatibility?

Regards,

Rob Hooft

   File
"lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py",
line 150, in upgrade
     metadata.create_all()
...
     self._handle_dbapi_exception(e, statement, parameters, cursor, context)
   File
"/opt/toolshed/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
line 931, in _handle_dbapi_exception
     raise exc.DBAPIError.instance(statement, parameters, e,
connection_invalidated=is_disconnect)
OperationalError: (OperationalError) (1170, "BLOB/TEXT column
'annotation' used in key specification without a key length") u'CREATE
INDEX ix_tool_annotation_association_annotation ON
tool_annotation_association (annotation)' ()
Removing PID file community_webapp.pid


--
Rob W.W. Hooft
Chief Technology Officer BioAssist, Netherlands Bioinformatics Centre
http://www.nbic.nl/    Skype: robhooft    GSM: +31 6 27034319


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