Thanks, Hans. I found that the problem lies somewhere else... I was trying to mount a systems temporary directory (/tmp) on an NFS share. The socket to the postgres database however (although sync'ed to the NFS share) was apparently not valid anymore on the NFS share.
I unmounted /tmp again (to reveal the underlying files again) and everything worked again. I have to disable all services using temp, and though I checked it with fuser, postgres was not listed. Perhaps check a little deeper :-)
Oh yes, I am trying to do this to avoid my /tmp being filled when ftp'ing files to it. (/tmp is only 1.5 Gigs now).
Thanks, Joachim
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
On 08/30/2012 10:00 AM, Hans-Rudolf Hotz wrote:
Hi Joachim
I suggest you double check the settings in "reports_wsgi.ini"
One of your error messages: "sqlalchemy.exc.OperationalError: (OperationalError) could not connect to server: Connection refused" indicates that there is something wrong with the value for "database_connection".
And you might also want to read the folowing recent thread from the mailing list:
http://dev.list.galaxyproject.org/Issue-configuring-reports-wsgi-ini-td46560...
Regards, Hans
On 08/30/2012 09:43 AM, Joachim Jacob wrote:
Hi all,
When running galaxy-dist/run_reports.sh I get errors. It has been awhile since I run it, and it worked perfect then however.
python path is: /home/galaxy/galaxy-dist/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
/home/galaxy/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
/home/galaxy/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, /home/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, /home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /home/galaxy/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, /home/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg, /home/galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, /home/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
/home/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, /home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg, /home/galaxy/galaxy-dist/eggs/docutils-0.7-py2.6.egg, /home/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, /home/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, /home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg, /home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg, /home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg, /home/galaxy/galaxy-dist/lib, /usr/local/lib64/python2.6/site-packages, /opt/MACS/1.4.2/lib/python2.6/site-packages, /opt/MACS/1.3.7/lib/python2.6/site-packages, /usr/lib64/python26.zip, /usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2, /usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old, /usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages/PIL, /usr/lib64/python2.6/site-packages/gtk-2.0, /usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg-info, /usr/lib/python2.6/site-packages, /usr/lib64/python2.6/site-packages galaxy.model.custom_types DEBUG 2012-08-30 09:06:58,051 psycopg2 egg successfully loaded for postgres dialect Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 84, in run invoke(command, command_name, options, args[1:]) File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 123, in invoke exit_code = runner.run(args) File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 218, in run result = self.command() File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py",
line 276, in command relative_to=base, global_conf=vars) File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py",
line 313, in loadapp **kw) File "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 225, in loadobj return context.create() File "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 625, in create return self.object_type.invoke(self) File "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 110, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/util/fixtypeerror.py",
line 57, in fix_call val = callable(*args, **kw) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/reports/buildapp.py", line 52, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/reports/app.py", line 22, in __init__ create_tables = True ) File "/home/galaxy/galaxy-dist/lib/galaxy/model/mapping.py", line 1892, in init metadata.create_all() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py",
line 1796, in create_all bind.create(self, checkfirst=checkfirst, tables=tables) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
line 1129, in create self._run_visitor(self.dialect.schemagenerator, entity, connection=connection, **kwargs) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
line 1154, in _run_visitor conn = self.contextual_connect(close_with_result=False) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
line 1229, in contextual_connect return self.Connection(self, self.pool.connect(), close_with_result=close_with_result, **kwargs) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py",
line 142, in connect return _ConnectionFairy(self).checkout() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py",
line 304, in __init__ rec = self._connection_record = pool.get() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py",
line 161, in get return self.do_get() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py",
line 639, in do_get con = self.create_connection() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py",
line 122, in create_connection return _ConnectionRecord(self) File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py",
line 198, in __init__ self.connection = self.__connect() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py",
line 261, in __connect connection = self.__pool._creator() File "/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/strategies.py",
line 80, in connect raise exc.DBAPIError.instance(None, None, e) sqlalchemy.exc.OperationalError: (OperationalError) could not connect to server: Connection refused Is the server running locally and accepting connections on Unix domain socket "/tmp/.s.PGSQL.5432"? None None Removing PID file reports_webapp.pid
The postgres database is running, user credentials are correct. I tried also running as root, as opposed to user galaxy, but no avail.
Thanks for your consideration, Joachim