New subject: Errors during database migration after updating galaxy

30 Sep 2012


      My cloud galaxy cluster can't boot up after attempting a bitbucket update due to a 502 HTTP error when trying to update the DB. Here's the log:
/mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility
  from csamtools import *
python path is: /mnt/galaxyTools/galaxy-central/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/boto-2.5.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/Fabric-1.4.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/ssh-1.7.14-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Whoosh-0.3.18-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/amqplib-0.6.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/pexpect-2.4-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Babel-0.9.4-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/Mako-0.4.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/WebHelpers-0.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/wchartype-0.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/docutils-0.7-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/WebOb-0.8.5-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Routes-1.12.3-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Paste-1.6-py2.6.egg, /mnt/galaxyTools/galaxy-central/lib, /usr/lib/python2.6/, /usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk, /usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload
galaxy.tool_shed.tool_shed_registry DEBUG 2012-09-30 21:13:18,317 Loading references to tool sheds from tool_sheds_conf.xml
galaxy.tool_shed.tool_shed_registry DEBUG 2012-09-30 21:13:18,317 Loaded reference to tool shed: Galaxy main tool shed
galaxy.tool_shed.tool_shed_registry DEBUG 2012-09-30 21:13:18,318 Loaded reference to tool shed: Galaxy test tool shed
galaxy.model.migrate.check DEBUG 2012-09-30 21:13:18,344 psycopg2 egg successfully loaded for postgres dialect
galaxy.model.migrate.check INFO 2012-09-30 21:13:18,610 At database version 107
galaxy.tool_shed.migrate.check DEBUG 2012-09-30 21:13:18,620 psycopg2 egg successfully loaded for postgres dialect
Traceback (most recent call last):
  File "/mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py", line 36, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/mnt/galaxyTools/galaxy-central/lib/galaxy/app.py", line 47, in __init__
    verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options )
  File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tool_shed/migrate/check.py", line 54, in verify_tools
    missing_tool_configs_dict = check_for_missing_tools( app, tool_panel_configs, latest_tool_migration_script_number )
  File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tool_shed/migrate/common.py", line 33, in check_for_missing_tools
    response = urllib2.urlopen( url )
  File "/usr/lib/python2.6/urllib2.py", line 126, in urlopen
    return _opener.open(url, data, timeout)
  File "/usr/lib/python2.6/urllib2.py", line 397, in open
    response = meth(req, response)
  File "/usr/lib/python2.6/urllib2.py", line 510, in http_response
    'http', request, response, code, msg, hdrs)
  File "/usr/lib/python2.6/urllib2.py", line 435, in error
    return self._call_chain(*args)
  File "/usr/lib/python2.6/urllib2.py", line 369, in _call_chain
    result = func(*args)
  File "/usr/lib/python2.6/urllib2.py", line 518, in http_error_default
    raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
HTTPError: HTTP Error 502: Bad Gateway
Removing PID file paster.pid