On Aug 24, 2010, at 5:06 PM, Nate Coraor wrote:
Hi Leandro,
You can do so with:
hg pull -u -r 60448575467f
http://bitbucket.org/galaxy/galaxy-central
Mmm... after the upgrade and restart of the instance I get:
$ 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
/*
Davide Cittaro
Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy
tel.: +39(02)574303007
e-mail: davide.cittaro(a)ifom-ieo-campus.it
*/