Hi all,
I've got a relatively fresh installed Galaxy instance running within a
locked network, where internet access is allowed only via a proxy. So
far, so simple; indeed I get internet access via a terminal (e.g.
calling Google with lynx), also wget and mercurial have the chance to
access target URL's. The variables $http_proxy, $https_proxy and
$ftp_proxy are set.
My problem occurs when I try to execute the automatic tests (using
'run_functional_tests.sh') for the FASTX toolbox, described here right
at the end:
http://hannonlab.cshl.edu/fastx_toolkit/download.html
The calls of the scripts generally end up in an error block of the
following scheme:
#####
functional_tests.py DEBUG 2013-06-25 14:15:40,406 Attempting to serve
app on randomly chosen port: 8720
functional_tests.py INFO 2013-06-25 14:15:40,468 Embedded web server started
base.asserts DEBUG 2013-06-25 14:15:40,506 base.asserts.text
base.asserts DEBUG 2013-06-25 14:15:40,506 base.asserts.tabular
base.asserts DEBUG 2013-06-25 14:15:40,506 base.asserts.xml
functional_tests.py INFO 2013-06-25 14:15:40,506 Functional tests will
be run against localhost:8720
nose.plugins.manager DEBUG 2013-06-25 14:15:40,518 DefaultPluginManager
load plugin nosetestdiff = nosetestdiff.plugin:NoseTes
tDiff
nose.plugins.manager DEBUG 2013-06-25 14:15:40,520 DefaultPluginManager
load plugin nosehtml = nosehtml.plugin:NoseHTML
Uncollapse ( cshl_fastx_uncollapser ) > Test-1 ... ERROR
======================================================================
ERROR: Uncollapse ( cshl_fastx_uncollapser ) > Test-1
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/test/base/twilltestcase.py", line 53,
in setUp
self.home()
File "/home/galaxy/galaxy-dist/test/base/twilltestcase.py", line
1141, in home
self.visit_url( self.url )
File "/home/galaxy/galaxy-dist/test/base/twilltestcase.py", line
1324, in visit_url
tc.code( 200 )
File
"/home/galaxy/galaxy-dist/eggs/twill-0.9-py2.6.egg/twill/commands.py",
line 133, in code
should_be))
TwillAssertionError: code is 403 != 200
----------------------------------------------------------------------
Ran 1 test in 0.011s
FAILED (errors=1)
#####
For me it reads like there is problem while testing to call the URL in
self.url, which resolves to 'localhost:9441'. URL and port are drawn
from the environment in the script
".../galaxy-dist/test/base/twilltestcase.py":
#####
class TwillTestCase( unittest.TestCase ):
def setUp( self ):
[...]
self.host = os.environ.get( 'GALAXY_TEST_HOST' )
self.port = os.environ.get( 'GALAXY_TEST_PORT )
self.url = "http://%s:%s"; % ( self.host, self.port )
[...]
#####
I could neither observe any process listening to port 9441 during the
test script execution, nor any of the text files within the galaxy root
dir contained '9441' as part of a configuration option.
Finally I'm a bit confused what that means to me, beyond just not to be
able to use the test suite. Anyone an idea what could and/or should be
fixed or checked?
Thanks in advance,
Sebastian
--
Sebastian Schaaf, M.Sc. Bioinformatics
Department of Medical Informatics,
Biometry and Epidemiology (IBE)
University of Munich
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