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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