11:11 a.m.
Hi all,
I'm having trouble with the Galaxy functional tests. On our Linux server
things seem to work, but I'm having trouble on my Mac. This affects
multiple tests.
For example, using a test for my own tool wrapper, on Linux my test
passes. On my Mac, the tool is missing the required binary so I
expect the test to fail with error level 127 and a message to stderr.
However, I get the following cryptic error:
$ ./run_functional_tests.sh -id tmhmm2
...
functional_tests.py INFO 2010-10-28 11:57:01,129 Embedded web server started
functional_tests.py INFO 2010-10-28 11:57:01,185 Functional tests will
be run against localhost:8980
nose.plugins.manager DEBUG 2010-10-28 11:57:01,210
DefaultPluginManager load plugin sqlalchemy =
sqlalchemy.test.noseplugin:NoseSQLAlchemy
nose.plugins.manager DEBUG 2010-10-28 11:57:01,215
DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML
TMHMM 2.0 ( tmhmm2 ) > Test-1 ... Error - <type
'exceptions.TypeError'>: 'NoneType' object is not callable
URL: http://localhost:8980/history
File
'/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Paste-1.7.2-py2.5.egg/paste/exceptions/errormiddleware.py',
line 144 in __call__
app_iter = self.application(environ, sr_checker)
File
'/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Paste-1.7.2-py2.5.egg/paste/recursive.py',
line 80 in __call__
return self.application(environ, start_response)
File
'/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Paste-1.7.2-py2.5.egg/paste/httpexceptions.py',
line 636 in __call__
return self.application(environ, start_response)
File '/Users/xxx/repositories/galaxy-central/lib/galaxy/web/framework/base.py',
line 154 in __call__
return body( environ, start_response )
File
'/Users/xxx/repositories/galaxy-central/lib/galaxy/web/framework/__init__.py',
line 668 in render
template.render_context( context )
File
'/Users/xxx/repositories/galaxy-central/eggs/Mako-0.2.5-py2.5.egg/mako/template.py',
line 146 in render_context
runtime._render_context(self, self.callable_, context, *args, **kwargs)
File
'/Users/xxx/repositories/galaxy-central/eggs/Mako-0.2.5-py2.5.egg/mako/runtime.py',
line 381 in _render_context
_exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
File
'/Users/xxx/repositories/galaxy-central/eggs/Mako-0.2.5-py2.5.egg/mako/runtime.py',
line 414 in _exec_template
callable_(context, *args, **kwargs)
File
'/Users/xxx/repositories/galaxy-central/database/compiled_templates/root/history.mako.py',
line 55 in render_body
__M_writer(u'\n<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01
Transitional//EN"
"http://www.w3.org/TR/html4/loose.dtd">\n\n<html>\n\n<head>\n<title>')
File
'/Users/xxx/repositories/galaxy-central/lib/galaxy/web/framework/__init__.py',
line 665 in write
response_write( d.encode( 'utf-8' ) )
TypeError: 'NoneType' object is not callable
CGI Variables
-------------
CONTENT_LENGTH: '0'
HTTP_ACCEPT: 'text/html; */*'
HTTP_ACCEPT_ENCODING: 'identity'
HTTP_CONNECTION: 'close'
HTTP_COOKIE: '$Version=1;
galaxysession=eb142648ac45b770a711a07bbd8189c4a80d9868f9ceff96f0635391728a47dfe5161bca180a2aae;
$Path="/"'
HTTP_HOST: 'localhost:8980'
PATH_INFO: '/history'
REMOTE_ADDR: '127.0.0.1'
REQUEST_METHOD: 'GET'
SERVER_NAME: '127.0.0.1'
SERVER_PORT: '8980'
SERVER_PROTOCOL: 'HTTP/1.1'
Configuration
-------------
static_enabled: False
use_translogger: False
WSGI Variables
--------------
application: <paste.recursive.RecursiveMiddleware object at 0xbfd2e10>
paste.cookies: (<SimpleCookie:
galaxysession='eb142648ac45b770a711a07bbd8189c4a80d9868f9ceff96f0635391728a47dfe5161bca180a2aae'>,
'$Version=1;
galaxysession=eb142648ac45b770a711a07bbd8189c4a80d9868f9ceff96f0635391728a47dfe5161bca180a2aae;
$Path="/"')
paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
object at 0xbfd3110>
paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
0xccf1f10>
paste.recursive.forward: <paste.recursive.Forwarder from />
paste.recursive.include: <paste.recursive.Includer from />
paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
paste.recursive.script_name: ''
paste.throw_errors: True
webob._parsed_query_vars: (MultiDict([]), '')
wsgi process: 'Multithreaded'
------------------------------------------------------------
ERROR
======================================================================
ERROR: TMHMM 2.0 ( tmhmm2 ) > Test-1
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/Users/xxx/repositories/galaxy-central/test/functional/test_toolbox.py",
line 160, in test_tool
self.do_it( td )
File
"/Users/xxx/repositories/galaxy-central/test/functional/test_toolbox.py",
line 24, in do_it
self.new_history()
File "/Users/xxx/repositories/galaxy-central/test/base/twilltestcase.py",
line 291, in new_history
self.check_history_for_string('Your history is empty')
File "/Users/xxx/repositories/galaxy-central/test/base/twilltestcase.py",
line 215, in check_history_for_string
self.visit_page( "history" )
File "/Users/xxx/repositories/galaxy-central/test/base/twilltestcase.py",
line 1040, in visit_page
tc.code( 200 )
File
"/Users/xxx/repositories/galaxy-central/eggs/twill-0.9-py2.5.egg/twill/commands.py",
line 133, in code
should_be))
TwillAssertionError: code is 500 != 200
----------------------------------------------------------------------
Ran 1 test in 0.824s
FAILED (errors=1)
functional_tests.py INFO 2010-10-28 11:57:02,079 Shutting down
functional_tests.py INFO 2010-10-28 11:57:02,079 Shutting down
embedded web server
...
###############################################################################
Here is my suggested fix:
diff -r 82743fcbf23c lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py Thu Oct 28 11:41:18 2010 +0100
+++ b/lib/galaxy/web/framework/__init__.py Thu Oct 28 11:56:16 2010 +0100
@@ -660,6 +660,9 @@
## return template.render( **data )
def render( environ, start_response ):
response_write = start_response(
self.response.wsgi_status(), self.response.wsgi_headeritems() )
+ if response_write is None:
+ log.error( "Error: this request returned None from
start_response: %s" % self.request.browser_url )
+ return []
class StreamBuffer( object ):
def write( self, d ):
response_write( d.encode( 'utf-8' ) )
###############################################################################
With the patch, I get:
$ ./run_functional_tests.sh -id tmhmm2
...
functional_tests.py INFO 2010-10-28 11:52:37,742 Embedded web server started
functional_tests.py INFO 2010-10-28 11:52:37,800 Functional tests will
be run against localhost:9383
nose.plugins.manager DEBUG 2010-10-28 11:52:37,825
DefaultPluginManager load plugin sqlalchemy =
sqlalchemy.test.noseplugin:NoseSQLAlchemy
nose.plugins.manager DEBUG 2010-10-28 11:52:37,829
DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML
TMHMM 2.0 ( tmhmm2 ) > Test-1 ... galaxy.web.framework ERROR
2010-10-28 11:52:38,685 Error: this request returned None from
start_response: http://localhost:9383/history
ERROR
======================================================================
ERROR: TMHMM 2.0 ( tmhmm2 ) > Test-1
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/Users/xxx/repositories/galaxy-central/test/functional/test_toolbox.py",
line 160, in test_tool
self.do_it( td )
File
"/Users/xxx/repositories/galaxy-central/test/functional/test_toolbox.py",
line 24, in do_it
self.new_history()
File "/Users/xxx/repositories/galaxy-central/test/base/twilltestcase.py",
line 291, in new_history
self.check_history_for_string('Your history is empty')
File "/Users/xxx/repositories/galaxy-central/test/base/twilltestcase.py",
line 217, in check_history_for_string
tc.find(subpatt)
File
"/Users/xxx/repositories/galaxy-central/eggs/twill-0.9-py2.5.egg/twill/commands.py",
line 239, in find
raise TwillAssertionError("no match to '%s'" % (what,))
TwillAssertionError: no match to 'Your'
-------------------- >> begin captured logging << --------------------
galaxy.web.framework: ERROR: Error: this request returned None from
start_response: http://localhost:9383/history
--------------------- >> end captured logging << ---------------------
----------------------------------------------------------------------
Ran 1 test in 0.821s
FAILED (errors=1)
functional_tests.py INFO 2010-10-28 11:52:38,691 Shutting down
functional_tests.py INFO 2010-10-28 11:52:38,691 Shutting down
embedded web server
...
###############################################################################
I'm still puzzled about what is going wrong - this affects other Galaxy tests
as well - not just mine. Is there something obvious wrong with the setup on
this machine? Actually using Galaxy running on this Mac seems to work.
Thanks,
Peter
1:45 p.m.
Hi Peter,
Could you set "debug = 'True'," in the kwargs dict in
./scripts/functional_tests.py and see if you get any more useful output?
Thanks,
--nate
Peter wrote:
Hi all,
I'm having trouble with the Galaxy functional tests. On our Linux server
things seem to work, but I'm having trouble on my Mac. This affects
multiple tests.
For example, using a test for my own tool wrapper, on Linux my test
passes. On my Mac, the tool is missing the required binary so I
expect the test to fail with error level 127 and a message to stderr.
However, I get the following cryptic error:
$ ./run_functional_tests.sh -id tmhmm2
...
functional_tests.py INFO 2010-10-28 11:57:01,129 Embedded web server started
functional_tests.py INFO 2010-10-28 11:57:01,185 Functional tests will
be run against localhost:8980
nose.plugins.manager DEBUG 2010-10-28 11:57:01,210
DefaultPluginManager load plugin sqlalchemy =
sqlalchemy.test.noseplugin:NoseSQLAlchemy
nose.plugins.manager DEBUG 2010-10-28 11:57:01,215
DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML
TMHMM 2.0 ( tmhmm2 ) > Test-1 ... Error - <type
'exceptions.TypeError'>: 'NoneType' object is not callable
URL: http://localhost:8980/history
File
'/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Paste-1.7.2-py2.5.egg/paste/exceptions/errormiddleware.py',
line 144 in __call__
app_iter = self.application(environ, sr_checker)
File
'/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Paste-1.7.2-py2.5.egg/paste/recursive.py',
line 80 in __call__
return self.application(environ, start_response)
File
'/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Paste-1.7.2-py2.5.egg/paste/httpexceptions.py',
line 636 in __call__
return self.application(environ, start_response)
File '/Users/xxx/repositories/galaxy-central/lib/galaxy/web/framework/base.py',
line 154 in __call__
return body( environ, start_response )
File
'/Users/xxx/repositories/galaxy-central/lib/galaxy/web/framework/__init__.py',
line 668 in render
template.render_context( context )
File
'/Users/xxx/repositories/galaxy-central/eggs/Mako-0.2.5-py2.5.egg/mako/template.py',
line 146 in render_context
runtime._render_context(self, self.callable_, context, *args, **kwargs)
File
'/Users/xxx/repositories/galaxy-central/eggs/Mako-0.2.5-py2.5.egg/mako/runtime.py',
line 381 in _render_context
_exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
File
'/Users/xxx/repositories/galaxy-central/eggs/Mako-0.2.5-py2.5.egg/mako/runtime.py',
line 414 in _exec_template
callable_(context, *args, **kwargs)
File
'/Users/xxx/repositories/galaxy-central/database/compiled_templates/root/history.mako.py',
line 55 in render_body
__M_writer(u'\n<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01
Transitional//EN"
"http://www.w3.org/TR/html4/loose.dtd">\n\n<html>\n\n<head>\n<title>')
File
'/Users/xxx/repositories/galaxy-central/lib/galaxy/web/framework/__init__.py',
line 665 in write
response_write( d.encode( 'utf-8' ) )
TypeError: 'NoneType' object is not callable
CGI Variables
-------------
CONTENT_LENGTH: '0'
HTTP_ACCEPT: 'text/html; */*'
HTTP_ACCEPT_ENCODING: 'identity'
HTTP_CONNECTION: 'close'
HTTP_COOKIE: '$Version=1;
galaxysession=eb142648ac45b770a711a07bbd8189c4a80d9868f9ceff96f0635391728a47dfe5161bca180a2aae;
$Path="/"'
HTTP_HOST: 'localhost:8980'
PATH_INFO: '/history'
REMOTE_ADDR: '127.0.0.1'
REQUEST_METHOD: 'GET'
SERVER_NAME: '127.0.0.1'
SERVER_PORT: '8980'
SERVER_PROTOCOL: 'HTTP/1.1'
Configuration
-------------
static_enabled: False
use_translogger: False
WSGI Variables
--------------
application: <paste.recursive.RecursiveMiddleware object at 0xbfd2e10>
paste.cookies: (<SimpleCookie:
galaxysession='eb142648ac45b770a711a07bbd8189c4a80d9868f9ceff96f0635391728a47dfe5161bca180a2aae'>,
'$Version=1;
galaxysession=eb142648ac45b770a711a07bbd8189c4a80d9868f9ceff96f0635391728a47dfe5161bca180a2aae;
$Path="/"')
paste.expected_exceptions: [<class
'paste.httpexceptions.HTTPException'>]
paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
object at 0xbfd3110>
paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
0xccf1f10>
paste.recursive.forward: <paste.recursive.Forwarder from />
paste.recursive.include: <paste.recursive.Includer from />
paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
paste.recursive.script_name: ''
paste.throw_errors: True
webob._parsed_query_vars: (MultiDict([]), '')
wsgi process: 'Multithreaded'
------------------------------------------------------------
ERROR
======================================================================
ERROR: TMHMM 2.0 ( tmhmm2 ) > Test-1
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/Users/xxx/repositories/galaxy-central/test/functional/test_toolbox.py",
line 160, in test_tool
self.do_it( td )
File
"/Users/xxx/repositories/galaxy-central/test/functional/test_toolbox.py",
line 24, in do_it
self.new_history()
File "/Users/xxx/repositories/galaxy-central/test/base/twilltestcase.py",
line 291, in new_history
self.check_history_for_string('Your history is empty')
File "/Users/xxx/repositories/galaxy-central/test/base/twilltestcase.py",
line 215, in check_history_for_string
self.visit_page( "history" )
File "/Users/xxx/repositories/galaxy-central/test/base/twilltestcase.py",
line 1040, in visit_page
tc.code( 200 )
File
"/Users/xxx/repositories/galaxy-central/eggs/twill-0.9-py2.5.egg/twill/commands.py",
line 133, in code
should_be))
TwillAssertionError: code is 500 != 200
----------------------------------------------------------------------
Ran 1 test in 0.824s
FAILED (errors=1)
functional_tests.py INFO 2010-10-28 11:57:02,079 Shutting down
functional_tests.py INFO 2010-10-28 11:57:02,079 Shutting down
embedded web server
...
###############################################################################
Here is my suggested fix:
diff -r 82743fcbf23c lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py Thu Oct 28 11:41:18 2010 +0100
+++ b/lib/galaxy/web/framework/__init__.py Thu Oct 28 11:56:16 2010 +0100
@@ -660,6 +660,9 @@
## return template.render( **data )
def render( environ, start_response ):
response_write = start_response(
self.response.wsgi_status(), self.response.wsgi_headeritems() )
+ if response_write is None:
+ log.error( "Error: this request returned None from
start_response: %s" % self.request.browser_url )
+ return []
class StreamBuffer( object ):
def write( self, d ):
response_write( d.encode( 'utf-8' ) )
###############################################################################
With the patch, I get:
$ ./run_functional_tests.sh -id tmhmm2
...
functional_tests.py INFO 2010-10-28 11:52:37,742 Embedded web server started
functional_tests.py INFO 2010-10-28 11:52:37,800 Functional tests will
be run against localhost:9383
nose.plugins.manager DEBUG 2010-10-28 11:52:37,825
DefaultPluginManager load plugin sqlalchemy =
sqlalchemy.test.noseplugin:NoseSQLAlchemy
nose.plugins.manager DEBUG 2010-10-28 11:52:37,829
DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML
TMHMM 2.0 ( tmhmm2 ) > Test-1 ... galaxy.web.framework ERROR
2010-10-28 11:52:38,685 Error: this request returned None from
start_response: http://localhost:9383/history
ERROR
======================================================================
ERROR: TMHMM 2.0 ( tmhmm2 ) > Test-1
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/Users/xxx/repositories/galaxy-central/test/functional/test_toolbox.py",
line 160, in test_tool
self.do_it( td )
File
"/Users/xxx/repositories/galaxy-central/test/functional/test_toolbox.py",
line 24, in do_it
self.new_history()
File "/Users/xxx/repositories/galaxy-central/test/base/twilltestcase.py",
line 291, in new_history
self.check_history_for_string('Your history is empty')
File "/Users/xxx/repositories/galaxy-central/test/base/twilltestcase.py",
line 217, in check_history_for_string
tc.find(subpatt)
File
"/Users/xxx/repositories/galaxy-central/eggs/twill-0.9-py2.5.egg/twill/commands.py",
line 239, in find
raise TwillAssertionError("no match to '%s'" % (what,))
TwillAssertionError: no match to 'Your'
-------------------- >> begin captured logging << --------------------
galaxy.web.framework: ERROR: Error: this request returned None from
start_response: http://localhost:9383/history
--------------------- >> end captured logging << ---------------------
----------------------------------------------------------------------
Ran 1 test in 0.821s
FAILED (errors=1)
functional_tests.py INFO 2010-10-28 11:52:38,691 Shutting down
functional_tests.py INFO 2010-10-28 11:52:38,691 Shutting down
embedded web server
...
###############################################################################
I'm still puzzled about what is going wrong - this affects other Galaxy tests
as well - not just mine. Is there something obvious wrong with the setup on
this machine? Actually using Galaxy running on this Mac seems to work.
Thanks,
Peter
_______________________________________________
galaxy-dev mailing list
galaxy-dev(a)lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
11:13 a.m.
On Tue, Nov 2, 2010 at 1:45 PM, Nate Coraor <nate(a)bx.psu.edu> wrote:
Hi Peter,
Could you set "debug = 'True'," in the kwargs dict in
./scripts/functional_tests.py and see if you get any more useful output?
Thanks,
--nate
Hi Nate,
Thanks for the suggestions - I tried that,
diff -r 82743fcbf23c scripts/functional_tests.py
--- a/scripts/functional_tests.py Thu Oct 28 11:41:18 2010 +0100
+++ b/scripts/functional_tests.py Wed Nov 03 11:10:42 2010 +0000
@@ -92,7 +92,7 @@
outputs_to_working_directory = 'True',
set_metadata_externally = 'True',
static_enabled = 'False',
- debug = 'False',
+ debug = 'True',
track_jobs_in_database = 'True',
job_scheduler_policy = 'FIFO',
start_job_runners = 'pbs',
However the output appears unchanged with respect to the failing test.
Are there any history/cookie/cache related files I can manually delete which
may be causing this problem?
Regards,
Peter
4:43 p.m.
Hi all,
I've since restarted with a clean clone of the repository, and see the
same problems. See:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-October/003625.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003645.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003665.html
Maybe I should be asking a different question: Has anyone ever used
run_functional_tests.sh successfully on Mac OS X 10.6 Snow Leopard?
Thanks,
Peter
2:43 p.m.
Revival! (This thread was sitting "flagged" in my mailbox since
November)
Peter wrote:
Hi all,
I've since restarted with a clean clone of the repository, and see the
same problems. See:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-October/003625.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003645.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003665.html
Maybe I should be asking a different question: Has anyone ever used
run_functional_tests.sh successfully on Mac OS X 10.6 Snow Leopard?
I was just creating a Bitbucket for this issue and realized that you've
got a locally installed version of Paste (1.7.2) that is overriding the
egg provided with Galaxy (1.6). The egg handling code was recently
updated to prevent this from happening, could you pull the latest and
see if you're still unable to run tests?
Thanks,
--nate
Thanks,
Peter
4:19 p.m.
On Mon, Feb 21, 2011 at 2:43 PM, Nate Coraor <nate(a)bx.psu.edu> wrote:
Revival! (This thread was sitting "flagged" in my mailbox
since
November)
I guess I should try and file issues for things which don't get a prompt
resolution on the mailing list, but its good to know it hadn't been
forgotten.
> Hi all,
>
> I've since restarted with a clean clone of the repository, and see the
> same problems. See:
>
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-October/003625.html
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003645.html
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003665.html
>
> Maybe I should be asking a different question: Has anyone ever used
> run_functional_tests.sh successfully on Mac OS X 10.6 Snow Leopard?
I was just creating a Bitbucket for this issue and realized that you've
got a locally installed version of Paste (1.7.2) that is overriding the
egg provided with Galaxy (1.6). The egg handling code was recently
updated to prevent this from happening, could you pull the latest and
see if you're still unable to run tests?
I'm running with a fresh hg clone of galaxy-central on Mac OS X 10.6,
large changeset 5096:2c9ce797953d, and I still see the same kind of
assertion failures, e.g.
$ ./run_functional_tests.sh -id ncbi_blastp_wrapper
...
TwillAssertionError: code is 500 != 200
...
However, from the stack trace it is still using the locally installed
Paste 1.7.2 rather than the local file eggs/Paste-1.6-py2.5.egg which
was fetched.
Peter
4:24 p.m.
Peter wrote:
On Mon, Feb 21, 2011 at 2:43 PM, Nate Coraor <nate(a)bx.psu.edu>
wrote:
> Revival! (This thread was sitting "flagged" in my mailbox since
> November)
I guess I should try and file issues for things which don't get a prompt
resolution on the mailing list, but its good to know it hadn't been
forgotten.
I usually try to do this if I'm not going to be able to address an issue
quickly, but don't always get to it. Feel free to do so yourself.
>> Hi all,
>>
>> I've since restarted with a clean clone of the repository, and see the
>> same problems. See:
>>
>> http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-October/003625.html
>> http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003645.html
>> http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003665.html
>>
>> Maybe I should be asking a different question: Has anyone ever used
>> run_functional_tests.sh successfully on Mac OS X 10.6 Snow Leopard?
>
> I was just creating a Bitbucket for this issue and realized that you've
> got a locally installed version of Paste (1.7.2) that is overriding the
> egg provided with Galaxy (1.6). The egg handling code was recently
> updated to prevent this from happening, could you pull the latest and
> see if you're still unable to run tests?
I'm running with a fresh hg clone of galaxy-central on Mac OS X 10.6,
large changeset 5096:2c9ce797953d, and I still see the same kind of
assertion failures, e.g.
$ ./run_functional_tests.sh -id ncbi_blastp_wrapper
...
TwillAssertionError: code is 500 != 200
...
However, from the stack trace it is still using the locally installed
Paste 1.7.2 rather than the local file eggs/Paste-1.6-py2.5.egg which
was fetched.
Okay, still a bug here with eggs and functional tests, it would appear.
I'll have a look as soon as possible.
--nate
Peter
3943
days inactive
4059
days old
galaxy-dev@lists.galaxyproject.org
6 comments
2 participants
participants (2)
-
Nate Coraor -
Peter