On Aug 24, 2010, at 5:06 PM, Nate Coraor wrote:

$ sh manage_db.sh upgrade

51 -> 52... 

Migration script to add the sample_dataset table and remove the 'dataset_files' column 

from the 'sample' table

Traceback (most recent call last):

  File "./scripts/manage_db.py", line 55, in <module>

    main( repository=repo, url=db_url )

  File "/data/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py", line 150, in main

    ret = command_func(**kwargs)

  File "/data/galaxy_dist/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 "/data/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 349, in _migrate

    schema.runchange(ver, change, changeset.step)

  File "/data/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py", line 184, in runchange

    change.run(self.engine, step)

  File "/data/galaxy_dist/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/0052_sample_dataset_table.py", line 65, in upgrade

    dataset_files = from_json_string(r[1])

  File "/data/galaxy_dist/eggs/simplejson-2.1.1-py2.6-solaris-2.10-i86pc_64-ucs2.egg/simplejson/__init__.py", line 384, in loads

  File "/data/galaxy_dist/eggs/simplejson-2.1.1-py2.6-solaris-2.10-i86pc_64-ucs2.egg/simplejson/decoder.py", line 402, in decode

  File "/data/galaxy_dist/eggs/simplejson-2.1.1-py2.6-solaris-2.10-i86pc_64-ucs2.egg/simplejson/decoder.py", line 418, in raw_decode

TypeError: first argument must be a string, not buffer