Re: [galaxy-dev] Issue configuring reports_wsgi.ini

[Iry Witham]

Hans,

I set the actual IP address and it works.

Thanks,
Iry

On 8/24/12 8:07 AM, "Hans-Rudolf Hotz"  wrote:

>Hi Iry
>
>  - try different port
>  - try the actual IP address of your host
>
>
>Regards, Hans
>
>
>On 08/24/2012 01:52 PM, Iry Witham wrote:
>> Hi Team,
>>
>> I am attempting to get the reports interface for my galaxy server to
>> function.  I have my reports.wsgi.ini configured so:
>>
>> #  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
>> # Galaxy reports are intended for production Galaxy instances, so sqlite
>> is not supported.
>> # You may use a SQLAlchemy connection string to specify an external
>> database.
>> database_connection = postgres:///galaxy_1
>>
>> # 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
>>
>> The reports_webapp.log shows no errors but the process never completes
>> loading.  I stop the process manually after 20 minutes or more and no
>> reports interface:
>>
>> python path is:
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pycrypto-2.5-py2.6-lin
>>ux-x86_64-ucs4.egg,
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_s
>>tatic-py2.6-linux-x86_64-ucs4.egg,
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff
>>194725-py2.6-linux-x86_64-ucs4.egg,
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.eg
>>g,
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg,
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r
>>6498-py2.6.egg,
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg,
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-
>>linux-x86_64-ucs4.egg,
>> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg,
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.e
>>gg,
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6
>>-linux-x86_64-ucs4.egg,
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.eg
>>g,
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_2005
>>0316-py2.6.egg,
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg
>>,
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg,
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.eg
>>g,
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-li
>>nux-x86_64-ucs4.egg,
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.
>>6.egg,
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.
>>6.egg,
>> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg,
>> /hpcdata/galaxy-test/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

Re: [galaxy-dev] Issue configuring reports_wsgi.ini

[Hans-Rudolf Hotz]

Hi Iry

 - try different port
 - try the actual IP address of your host


Regards, Hans


On 08/24/2012 01:52 PM, Iry Witham wrote:

Hi Team,

I am attempting to get the reports interface for my galaxy server to
function.  I have my reports.wsgi.ini configured so:

#  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
# Galaxy reports are intended for production Galaxy instances, so sqlite
is not supported.
# You may use a SQLAlchemy connection string to specify an external
database.
database_connection = postgres:///galaxy_1

# 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

The reports_webapp.log shows no errors but the process never completes
loading.  I stop the process manually after 20 minutes or more and no
reports interface:

python path is:
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg,
/hpcdata/galaxy-test/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 2012-08-20 13:03:04,572 psycopg2 egg
successfully loaded for postgres dialect
galaxy.web.framework.base DEBUG 2012-08-20 13:03:09,297 Enabling 'users'
controller, class: Users
galaxy.web.framework.base DEBUG 2012-08-20 13:03:09,310 Enabling
'system' controller, class: System
galaxy.web.framework.base DEBUG 2012-08-20 13:03:09,354 Enabling
'sample_tracking' controller, class: SampleTracking
galaxy.web.fram