Re: [galaxy-dev] run_reports.sh not starting

Thu, 30 Aug 2012 01:25:52 -0700

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-td4656027.html 





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



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