Can you replace lines 75 - 86 of the file 
~/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py with the 
following for loop and send me your paster log?

Thanks!

    for row in result:
        tool_shed_repository_id = row[0]
        try:
            repository_metadata = from_json_string( str( row[1] ) )
            # Create a new row in the tool table for each tool included in 
repository.  We will NOT
            # handle tool_version_associaions because we do not have the 
information we need to do so.
            tools = repository_metadata.get( 'tools', [] )
            for tool_dict in tools:
                cmd = "INSERT INTO tool_version VALUES (%s, %s, %s, '%s', %s)" 
% \
                    ( nextval( 'tool_version' ), localtimestamp(), 
localtimestamp(), tool_dict[ 'guid' ], tool_shed_repository_id )
                db_session.execute( cmd )
                count += 1
        except Exception, e:
            print "Repository metadata: ", str( row[1] )
            print "Exception setting tool versions for tools in 
tool_shed_repository with id: ", str( tool_shed_repository_id )
            print str( e )

The lines of code you are replacing look like this:

    for row in result:
        if row[1]:
            tool_shed_repository_id = row[0]
            repository_metadata = from_json_string( str( row[1] ) )
            # Create a new row in the tool table for each tool included in 
repository.  We will NOT
            # handle tool_version_associaions because we do not have the 
information we need to do so.
            tools = repository_metadata.get( 'tools', [] )
            for tool_dict in tools:
                cmd = "INSERT INTO tool_version VALUES (%s, %s, %s, '%s', %s)" 
% \
                    ( nextval( 'tool_version' ), localtimestamp(), 
localtimestamp(), tool_dict[ 'guid' ], tool_shed_repository_id )
                db_session.execute( cmd )
                count += 1


On Feb 6, 2012, at 5:23 PM, Anthonius deBoer wrote:

> I manually dropped the tool_version and tool_association table in the 
> database and I am left with the JSON error as shown below:
> 
> 90 -> 91...
> 
> Migration script to create the tool_version and tool_version_association 
> tables and drop the tool_id_guid_map table.
> 
> Traceback (most recent call last):
>   File "./scripts/manage_db.py", line 63, in <module>
>     main( repository=repo, url=db_url )
>   File 
> "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py",
>  line 150, in main
>     ret = command_func(**kwargs)
>   File 
> "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py",
>  line 221, in upgrade
>     return _migrate(url, repository, version, upgrade=True, err=err, **opts)
>   File 
> "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py",
>  line 349, in _migrate
>     schema.runchange(ver, change, changeset.step)
>   File 
> "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py",
>  line 184, in runchange
>     change.run(self.engine, step)
>   File 
> "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py",
>  line 101, in run
>     func()
>   File "lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py", 
> line 78, in upgrade
>     repository_metadata = from_json_string( str( row[1] ) )
>   File 
> "/home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/__init__.py",
>  line 384, in loads
>   File 
> "/home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py",
>  line 402, in decode
>   File 
> "/home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py",
>  line 420, in raw_decode
> simplejson.decoder.JSONDecodeError: No JSON object could be decoded: line 1 
> column 0 (char 0)
> 
> 
> On Feb 06, 2012, at 02:08 PM, Anthonius deBoer <thondeb...@me.com> wrote:
> 
>> Hi Greg,
>> 
>> I tried the downgrade/upgrade path and got the exact same message I sent 
>> before.
>> I am using a postgres database that is running on local host.
>> I did indeed install some toolshed repositories before I tried to upgrade.
>> I also tried to downgrade to 89 and then upgrade, with the exact same 
>> message.
>> 
>> Thon
>> 
>> On Feb 06, 2012, at 10:51 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>> 
>>> Hello Thon,
>>> 
>>> Attempting to run the migration script twice to the same version always 
>>> poses problems.  Can you downgrade successfully as follows?
>>> 
>>> sh manage_db.sh downgrade 90
>>> 
>>> If so, downgrade, then upgrade again and send the paster log from the clean 
>>> upgrade if you see a problem.  Also:
>>> What database are you using?  
>>> Have you installed any tool shed repositories into your local Galaxy 
>>> instance?
>>> 
>>> Thanks,
>>> 
>>> Greg
>>> 
>>> 
>>> On Feb 6, 2012, at 1:32 PM, Thon Deboer wrote:
>>> 
>>>> Hi,
>>>> 
>>>> I updated to the latest galaxy-central version but got this error when 
>>>> trying to upgrade...
>>>> 
>>>> Any ideas? It seems the table had already been created (this was the 
>>>> second time I run upgrade) but the JSON error was one that showed up the 
>>>> first time...)
>>>> 
>>>> Thanks
>>>> 
>>>> Thon
>>>> 
>>>>  sh manage_db.sh upgrade
>>>> 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 2012-02-06 10:23:39,847 Creating 
>>>> tool_version table failed: (ProgrammingError) relation "tool_version" 
>>>> already exists
>>>>  '\nCREATE TABLE tool_version (\n\tid SERIAL NOT NULL, \n\tcreate_time 
>>>> TIMESTAMP WITHOUT TIME ZONE, \n\tupdate_time TIMESTAMP WITHOUT TIME ZONE, 
>>>> \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 2012-02-06 10:23:39,847 Creating 
>>>> tool_version table failed: (ProgrammingError) relation "tool_version" 
>>>> already exists
>>>>  '\nCREATE TABLE tool_version (\n\tid SERIAL NOT NULL, \n\tcreate_time 
>>>> TIMESTAMP WITHOUT TIME ZONE, \n\tupdate_time TIMESTAMP WITHOUT TIME ZONE, 
>>>> \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 2012-02-06 10:23:39,863 Creating 
>>>> tool_version_association table failed: (ProgrammingError) relation 
>>>> "tool_version_association" already exists
>>>>  '\nCREATE TABLE tool_version_association (\n\tid SERIAL NOT NULL, 
>>>> \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 2012-02-06 10:23:39,863 Creating 
>>>> tool_version_association table failed: (ProgrammingError) relation 
>>>> "tool_version_association" already exists
>>>>  '\nCREATE TABLE tool_version_association (\n\tid SERIAL NOT NULL, 
>>>> \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' {}
>>>> Traceback (most recent call last):
>>>>   File "./scripts/manage_db.py", line 63, in <module>
>>>>     main( repository=repo, url=db_url )
>>>>   File 
>>>> "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py",
>>>>  line 150, in main
>>>>     ret = command_func(**kwargs)
>>>>   File 
>>>> "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py",
>>>>  line 221, in upgrade
>>>>     return _migrate(url, repository, version, upgrade=True, err=err, 
>>>> **opts)
>>>>   File 
>>>> "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py",
>>>>  line 349, in _migrate
>>>>     schema.runchange(ver, change, changeset.step)
>>>>   File 
>>>> "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py",
>>>>  line 184, in runchange
>>>>     change.run(self.engine, step)
>>>>   File 
>>>> "/home/tdeboer/code/galaxy-central/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py",
>>>>  line 101, in run
>>>>     func()
>>>>   File 
>>>> "lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py", line 
>>>> 78, in upgrade
>>>>     repository_metadata = from_json_string( str( row[1] ) )
>>>>   File 
>>>> "/home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/__init__.py",
>>>>  line 384, in loads
>>>>   File 
>>>> "/home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py",
>>>>  line 402, in decode
>>>>   File 
>>>> "/home/tdeboer/code/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py",
>>>>  line 420, in raw_decode
>>>> simplejson.decoder.JSONDecodeError: No JSON object could be decoded: line 
>>>> 1 column 0 (char 0)
>>>> 
>>>> 
>>>> 
>>>> Regards,
>>>> 
>>>> Thon de Boer, Ph.D.
>>>> Bioinformatics Guru
>>>> +1-650-799-6839
>>>> thondeb...@me.com
>>>>  
>>>> LinkedIn Profile
>>>>  
>>>> 
>>>> 
>>>> 
>>>> 
>>>> ___________________________________________________________
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>>>> 
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>>>>  
>>> 
>> 
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