Hi Iry

The last but one line: "socket.error: [Errno 98] Address already in use" holds probably the clue.


Looks like something else is running on the same port or you didn't stop the reports server before restarting it (after the upgrade)


Regards, Hans


On 08/17/2012 11:08 PM, Iry Witham wrote:
Hi Team,

Since I upgraded to the latest galaxy-dist I can no longer get the
reports interface to function.  When I go to galaxy:9001 I get the
following server error: An error occurred. See the error logs for more
information. (Turn debug on to display exception reports here).
  The reports_webapp.log is as follows:

python path is:
/hpcdata/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg,
/hpcdata/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg,
/hpcdata/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,
/hpcdata/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg,
/hpcdata/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg,
/hpcdata/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg,
/hpcdata/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.egg,
/hpcdata/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg,
/hpcdata/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg,
/hpcdata/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg,
/hpcdata/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg,
/hpcdata/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg,
/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg,
/hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg,
/hpcdata/galaxy-setup/galaxy-dist/lib, /usr/lib/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,
/usr/lib64/python2.6/site-packages/Numeric,
/usr/lib64/python2.6/site-packages/gtk-2.0,
/usr/local/lib64/python2.6/site-packages
galaxy.model.custom_types DEBUG 2012-08-07 17:13:53,219 psycopg2 egg
successfully loaded for postgres dialect
galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,792 Enabling 'users'
controller, class: Users
galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,815 Enabling
'system' controller, class: System
galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,909 Enabling
'sample_tracking' controller, class: SampleTracking
galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,922 Enabling 'jobs'
controller, class: Jobs
galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,942 Enabling
'workflows' controller, class: Workflows
galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,947 Enabling 'root'
controller, class: Report
galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:13:59,950 Enabling
'httpexceptions' middleware
galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:13:59,971 Enabling
'recursive' middleware
/hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/serial_number_generator.py:11:
DeprecationWarning: the md5 module is deprecated; use hashlib instead
   import md5
galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,708 Enabling
'error' middleware
galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,749 Enabling
'trans logger' middleware
galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,750 Enabling
'config' middleware
galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,888 Enabling
'x-forwarded-host' middleware
Starting server in PID 6345.
Traceback (most recent call last):
   File "./scripts/paster.py", line 34, in <module>
     command.run()
   File
"/hpcdata/galaxy-setup/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
"/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 123, in invoke
     exit_code = runner.run(args)
   File
"/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 218, in run
     result = self.command()
   File
"/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py",
line 303, in command
     serve()
   File
"/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py",
line 287, in serve
     server(app)
   File
"/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 151, in server_wrapper
     **context.local_conf)
   File
"/hpcdata/galaxy-setup/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
"/hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
line 1314, in server_runner
     serve(wsgi_app, **kwargs)
   File
"/hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
line 1264, in serve
     threadpool_options=threadpool_options)
   File
"/hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
line 1114, in __init__
     RequestHandlerClass, ssl_context)
   File
"/hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
line 1094, in __init__
     RequestHandlerClass, ssl_context)
   File
"/hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
line 328, in __init__
     HTTPServer.__init__(self, server_address, RequestHandlerClass)
   File "/usr/lib64/python2.6/SocketServer.py", line 400, in __init__
     self.server_bind()
   File "/usr/lib64/python2.6/BaseHTTPServer.py", line 108, in server_bind
     SocketServer.TCPServer.server_bind(self)
   File "/usr/lib64/python2.6/SocketServer.py", line 411, in server_bind
     self.socket.bind(self.server_address)
   File "<string>", line 1, in bind
socket.error: [Errno 98] Address already in use
Removing PID file reports_webapp.pid

The following is the report_wsgi.ini:

# ---- HTTP Server
----------------------------------------------------------

[server:main]

use = egg:Paste#http
port = 9001
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

# ---- Galaxy Webapps Report Interface
-------------------------------------------------

[app:main]

# Specifies the factory for the universe WSGI application
paste.app_factory = galaxy.webapps.reports.buildapp:app_factory
log_level = DEBUG

# Database connection
#database_file = database/universe.sqlite
# You may use a SQLAlchemy connection string to specify an external
database instead
# database_connection =
postgres:///galaxy_test?user=postgres&password=postgres
database_connection = postgres:///galaxy_1?user=galaxy&password=galaxy


# Where dataset files are saved
file_path = database/files
# Temporary storage for additional datasets, this should be shared
through the cluster
new_file_path = database/tmp

# Session support (beaker)
use_beaker_session = True
session_type = memory
session_data_dir = %(here)s/database/beaker_sessions
session_key = galaxysessions
session_secret = changethisinproduction

# Configuration for debugging middleware
# debug = true
use_lint = false

# NEVER enable this on a public site (even test or QA)
# use_interactive = true

# path to sendmail
#sendmail_path = /usr/sbin/sendmail

# Address to join mailing list
#mailing_join_addr = galaxy-user-j...@bx.psu.edu

# Write thread status periodically to 'heartbeat.log' (careful, uses
disk space rapidly!)
## use_heartbeat = True

# Profiling middleware (cProfile based)
## use_profile = True

# Mail
smtp_server = smtp.jax.org
error_email_to = cbr-h...@jax.org

# Use the new iframe / javascript based layout
use_new_layout = true

# Serving static files (needed if running standalone)
static_enabled = True
static_cache_time = 360
static_dir = %(here)s/static/
static_images_dir = %(here)s/static/images
static_favicon_dir = %(here)s/static/favicon.ico
static_scripts_dir = %(here)s/static/scripts/
static_style_dir = %(here)s/static/june_2007_style/blue

I am sure I have something misconfigured, but can't seem to figure it out.

Thanks for the assistance.

Iry

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