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