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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